From eee11fe3976cc8b41067b1adbd6cb0159a5a4d17 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 10 Oct 2024 13:11:09 -0500
Subject: [PATCH 001/180] OLS search for filtered ontologies

---
 src/Contexts/SearchContext.jsx                |  3 ++
 .../MappingsFunctions/DefaultSearch.jsx       | 52 +++++++++++++++++++
 .../MappingsFunctions/GetMappingsModal.jsx    | 17 +++++-
 .../Projects/Tables/TableDetails.jsx          |  6 +--
 4 files changed, 74 insertions(+), 4 deletions(-)
 create mode 100644 src/components/Manager/MappingsFunctions/DefaultSearch.jsx

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index 909846e..e90d907 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -12,6 +12,7 @@ export function SearchContextRoot() {
   const [apiResultsCount, setApiResultsCount] = useState();
   const [apiPage, setApiPage] = useState(0);
   const [apiTotalCount, setApiTotalCount] = useState();
+  const [apiPreferences, setApiPreferences] = useState({});
 
   const context = {
     prefTerminologies,
@@ -30,6 +31,8 @@ export function SearchContextRoot() {
     setApiPage,
     apiTotalCount,
     setApiTotalCount,
+    apiPreferences,
+    setApiPreferences,
   };
 
   return (
diff --git a/src/components/Manager/MappingsFunctions/DefaultSearch.jsx b/src/components/Manager/MappingsFunctions/DefaultSearch.jsx
new file mode 100644
index 0000000..ef91ae6
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/DefaultSearch.jsx
@@ -0,0 +1,52 @@
+import { ontologyReducer } from '../Utilitiy';
+
+export const fetchResults = (
+  page,
+  query,
+  entriesPerPage,
+  //   setLoading,
+  setTotalCount,
+  setResults,
+  setFilteredResultsCount,
+  setResultsCount,
+  searchUrl,
+  selectedBoxes
+) => {
+  if (!query) {
+    return undefined;
+  }
+  //   setLoading(true);
+  const pageStart = page * entriesPerPage;
+
+  return fetch(
+    `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
+    {
+      method: 'GET',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+    }
+  )
+    .then(res => res.json())
+    .then(data => {
+      let res = ontologyReducer(data?.response?.docs);
+
+      // Filter based on selectedBoxes
+      if (selectedBoxes) {
+        res.results = res.results.filter(
+          d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
+        );
+      }
+
+      if (page > 0 && res.results.length > 0) {
+        res.results = results.concat(res.results);
+      } else {
+        setTotalCount(data.response.numFound);
+      }
+
+      setResults(res.results);
+      setFilteredResultsCount(res?.filteredResults?.length);
+      setResultsCount(res.results.length);
+    });
+  // .finally(() => setLoading(false));
+};
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 3c56feb..f8219b3 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -4,6 +4,7 @@ import { myContext } from '../../../App';
 import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const GetMappingsModal = ({
   componentString,
@@ -17,6 +18,7 @@ export const GetMappingsModal = ({
   const { Search } = Input;
 
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
+  const { apiPreferences } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -155,8 +157,21 @@ export const GetMappingsModal = ({
     number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
     on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
     const pageStart = page * entriesPerPage;
+    const apiPreferenceOntologies = () => {
+      if (apiPreferences?.self?.api_preference?.ols) {
+        // Get the ontologies from the 'ols' array and join them with commas
+        const filteredOntologies =
+          apiPreferences.self.api_preference.ols.join(',');
+        console.log(filteredOntologies);
+        // Construct the final URL with the filteredOntologies
+        return filteredOntologies;
+      } else {
+        const defaultOntologies = 'mondo,hp,maxo,ncit';
+        return defaultOntologies;
+      }
+    };
     return fetch(
-      `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
+      `${searchUrl}q=${query}&ontology=${apiPreferenceOntologies()}&rows=${entriesPerPage}&start=${pageStart}`,
       {
         method: 'GET',
         headers: {
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 46b3597..9bd6e05 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -20,12 +20,14 @@ import { Submenu } from '../../Manager/Submenu';
 import { SettingsDropdownTable } from '../../Manager/Dropdown/SettingsDropdownTable';
 import { RequiredLogin } from '../../Auth/RequiredLogin';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const TableDetails = () => {
   const [form] = Form.useForm();
 
   const { vocabUrl, edit, setEdit, table, setTable, user } =
     useContext(myContext);
+  const { apiPreferences, setApiPreferences } = useContext(SearchContext);
   const {
     getMappings,
     setGetMappings,
@@ -37,7 +39,6 @@ export const TableDetails = () => {
   const { studyId, DDId, tableId } = useParams();
   const [loading, setLoading] = useState(true);
   const [load, setLoad] = useState(false);
-  const [apiPreferences, setApiPreferences] = useState({});
 
   const navigate = useNavigate();
 
@@ -66,8 +67,7 @@ export const TableDetails = () => {
                 if (error) {
                   notification.error({
                     message: 'Error',
-                    description:
-                      'An error occurred loading mappings. Please try again.',
+                    description: 'An error occurred loading mappings.',
                   });
                 }
                 return error;

From 903d94e919db1abb8b9e950bc8629d0d26cd5c60 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 10 Oct 2024 15:29:45 -0500
Subject: [PATCH 002/180] added fetch function for ols search

---
 .../MappingsFunctions/GetMappingsModal.jsx    | 100 +++++++++++++-----
 1 file changed, 75 insertions(+), 25 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index f8219b3..010728f 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -146,32 +146,9 @@ export const GetMappingsModal = ({
       });
   };
 
-  // The function that makes the API call to search for the passed code.
-
-  const fetchResults = (page, query) => {
-    if (!!!query) {
-      return undefined;
-    }
-    setLoading(true);
-    /* The OLS API returns 10 results by default unless specified otherwise. The fetch call includes a specified
-    number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
-    on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
-    const pageStart = page * entriesPerPage;
-    const apiPreferenceOntologies = () => {
-      if (apiPreferences?.self?.api_preference?.ols) {
-        // Get the ontologies from the 'ols' array and join them with commas
-        const filteredOntologies =
-          apiPreferences.self.api_preference.ols.join(',');
-        console.log(filteredOntologies);
-        // Construct the final URL with the filteredOntologies
-        return filteredOntologies;
-      } else {
-        const defaultOntologies = 'mondo,hp,maxo,ncit';
-        return defaultOntologies;
-      }
-    };
+  const fetchFunction = (query, ontologiesToSearch, page, pageStart) => {
     return fetch(
-      `${searchUrl}q=${query}&ontology=${apiPreferenceOntologies()}&rows=${entriesPerPage}&start=${pageStart}`,
+      `${searchUrl}q=${query}&ontology=${ontologiesToSearch}&rows=${entriesPerPage}&start=${pageStart}`,
       {
         method: 'GET',
         headers: {
@@ -211,6 +188,79 @@ export const GetMappingsModal = ({
       .then(() => setLoading(false));
   };
 
+  // The function that makes the API call to search for the passed code.
+
+  const fetchResults = (page, query) => {
+    if (!!!query) {
+      return undefined;
+    }
+    setLoading(true);
+    /* The OLS API returns 10 results by default unless specified otherwise. The fetch call includes a specified
+    number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
+    on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
+    const pageStart = page * entriesPerPage;
+
+    if (
+      apiPreferences?.self?.api_preference &&
+      'ols' in apiPreferences?.self?.api_preference
+    ) {
+      const apiPreferenceOntologies = () => {
+        if (apiPreferences?.self?.api_preference?.ols) {
+          // Get the ontologies from the 'ols' array and join them with commas
+          const filteredOntologies =
+            apiPreferences.self.api_preference.ols.join(',');
+          console.log(filteredOntologies);
+          // Construct the final URL with the filteredOntologies
+          return filteredOntologies;
+        } else {
+          const defaultOntologies = 'mondo,hp,maxo,ncit';
+          return defaultOntologies;
+        }
+      };
+      return fetchFunction(query, apiPreferenceOntologies(), page, pageStart);
+    } else {
+      return fetch(
+        `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
+        {
+          method: 'GET',
+          headers: {
+            'Content-Type': 'application/json',
+          },
+        }
+      )
+        .then(res => res.json())
+        .then(data => {
+          // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
+
+          let res = ontologyReducer(data?.response?.docs);
+          // if the page > 0 (i.e. if this is not the first batch of results), the new results
+          // are concatenated to the old
+          if (selectedBoxes) {
+            res.results = res.results.filter(
+              d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
+            );
+          }
+
+          if (page > 0 && results.length > 0) {
+            res.results = results.concat(res.results);
+
+            // Apply filtering to remove results with obo_id in selectedBoxes
+          } else {
+            // Set the total number of search results for pagination
+            setTotalCount(data.response.numFound);
+          }
+
+          //the results are set to res (the filtered, concatenated results)
+
+          setResults(res.results);
+          setFilteredResultsCount(res?.filteredResults?.length);
+          // resultsCount is set to the length of the filtered, concatenated results for pagination
+          setResultsCount(res.results.length);
+        })
+        .then(() => setLoading(false));
+    }
+  };
+
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
   const handleViewMore = e => {
     e.preventDefault();

From 156100e097f9bb4c5d346c2673bd998ae91e6f8c Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 14 Oct 2024 20:42:00 -0500
Subject: [PATCH 003/180] OLS ontology filters for mapping search

---
 src/App.jsx                                   |   2 +
 src/components/Manager/FetchManager.jsx       |  58 ++++++++
 .../MappingsFunctions/GetMappingsModal.jsx    | 132 +++++-------------
 .../Projects/Terminologies/Terminology.scss   |   1 +
 4 files changed, 99 insertions(+), 94 deletions(-)

diff --git a/src/App.jsx b/src/App.jsx
index e036201..f581e8d 100644
--- a/src/App.jsx
+++ b/src/App.jsx
@@ -7,6 +7,7 @@ export const myContext = createContext();
 
 function App() {
   const searchUrl = import.meta.env.VITE_SEARCH_ENDPOINT;
+  const monarchUrl = import.meta.env.VITE_MONARCH_SEARCH;
   const vocabUrl = import.meta.env.VITE_VOCAB_ENDPOINT;
   const clientId = import.meta.env.VITE_CLIENT_ID;
 
@@ -47,6 +48,7 @@ function App() {
           results,
           setResults,
           searchUrl,
+          monarchUrl,
           vocabUrl,
           tablesDD,
           setTablesDD,
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 1b5e44e..fc5f4a6 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -1,3 +1,5 @@
+import { ontologyReducer } from './Utilitiy';
+
 // Fetches all elements at an endpoint
 export const getAll = (vocabUrl, name, navigate) => {
   return fetch(`${vocabUrl}/${name}`, {
@@ -165,3 +167,59 @@ export const getOntologies = vocabUrl => {
     }
   });
 };
+
+export const olsFilterOntologiesSearch = (
+  searchUrl,
+  query,
+  ontologiesToSearch,
+  page,
+  entriesPerPage,
+  pageStart,
+  selectedBoxes,
+  setTotalCount,
+  setResults,
+  setFilteredResultsCount,
+  setResultsCount,
+  setLoading
+) => {
+  setLoading(true);
+  return fetch(
+    `${searchUrl}q=${query}&ontology=${ontologiesToSearch}&rows=${entriesPerPage}&start=${pageStart}`,
+    {
+      method: 'GET',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+    }
+  )
+    .then(res => res.json())
+    .then(data => {
+      // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
+
+      let res = ontologyReducer(data?.response?.docs);
+      // if the page > 0 (i.e. if this is not the first batch of results), the new results
+      // are concatenated to the old
+      if (selectedBoxes) {
+        res.results = res.results.filter(
+          d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
+        );
+      }
+
+      if (page > 0 && results.length > 0) {
+        res.results = results.concat(res.results);
+
+        // Apply filtering to remove results with obo_id in selectedBoxes
+      } else {
+        // Set the total number of search results for pagination
+        setTotalCount(data.response.numFound);
+      }
+
+      //the results are set to res (the filtered, concatenated results)
+
+      setResults(res.results);
+      setFilteredResultsCount(res?.filteredResults?.length);
+      // resultsCount is set to the length of the filtered, concatenated results for pagination
+      setResultsCount(res.results.length);
+    })
+    .then(() => setLoading(false));
+};
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 010728f..e54b6f5 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -5,6 +5,8 @@ import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import { olsFilterOntologiesSearch } from '../FetchManager';
+import { defaultIconPrefixCls } from 'antd/es/config-provider';
 
 export const GetMappingsModal = ({
   componentString,
@@ -21,8 +23,9 @@ export const GetMappingsModal = ({
   const { apiPreferences } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
-  const [loading, setLoading] = useState(true);
+  const [loading, setLoading] = useState(false);
   const [results, setResults] = useState([]);
+  const [monarchResults, setMonarchResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
   const [resultsCount, setResultsCount] = useState();
   const [lastCount, setLastCount] = useState(0); //save last count as count of the results before you fetch data again
@@ -38,6 +41,7 @@ export const GetMappingsModal = ({
     setSelectedBoxes,
   } = useContext(MappingContext);
   let ref = useRef();
+  const defaultOntologies = 'mondo,hp,maxo,ncit';
 
   // since the code is passed through searchProp, the '!!' forces it to be evaluated as a boolean.
   // if there is a searchProp being passed, it evaluates to true and runs the search function.
@@ -146,121 +150,61 @@ export const GetMappingsModal = ({
       });
   };
 
-  const fetchFunction = (query, ontologiesToSearch, page, pageStart) => {
-    return fetch(
-      `${searchUrl}q=${query}&ontology=${ontologiesToSearch}&rows=${entriesPerPage}&start=${pageStart}`,
-      {
-        method: 'GET',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-      }
-    )
-      .then(res => res.json())
-      .then(data => {
-        // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
-
-        let res = ontologyReducer(data?.response?.docs);
-        // if the page > 0 (i.e. if this is not the first batch of results), the new results
-        // are concatenated to the old
-        if (selectedBoxes) {
-          res.results = res.results.filter(
-            d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
-          );
-        }
-
-        if (page > 0 && results.length > 0) {
-          res.results = results.concat(res.results);
-
-          // Apply filtering to remove results with obo_id in selectedBoxes
-        } else {
-          // Set the total number of search results for pagination
-          setTotalCount(data.response.numFound);
-        }
-
-        //the results are set to res (the filtered, concatenated results)
-
-        setResults(res.results);
-        setFilteredResultsCount(res?.filteredResults?.length);
-        // resultsCount is set to the length of the filtered, concatenated results for pagination
-        setResultsCount(res.results.length);
-      })
-      .then(() => setLoading(false));
-  };
-
   // The function that makes the API call to search for the passed code.
 
   const fetchResults = (page, query) => {
     if (!!!query) {
       return undefined;
     }
-    setLoading(true);
     /* The OLS API returns 10 results by default unless specified otherwise. The fetch call includes a specified
     number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
     on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
     const pageStart = page * entriesPerPage;
 
     if (
+      //If there are api preferences and one of them is OLS, it gets the preferred ontologies
       apiPreferences?.self?.api_preference &&
       'ols' in apiPreferences?.self?.api_preference
     ) {
       const apiPreferenceOntologies = () => {
         if (apiPreferences?.self?.api_preference?.ols) {
-          // Get the ontologies from the 'ols' array and join them with commas
-          const filteredOntologies =
-            apiPreferences.self.api_preference.ols.join(',');
-          console.log(filteredOntologies);
-          // Construct the final URL with the filteredOntologies
-          return filteredOntologies;
+          return apiPreferences.self.api_preference.ols.join(',');
         } else {
-          const defaultOntologies = 'mondo,hp,maxo,ncit';
+          // else if there are no preferred ontologies, it uses the default ontologies
           return defaultOntologies;
         }
       };
-      return fetchFunction(query, apiPreferenceOntologies(), page, pageStart);
-    } else {
-      return fetch(
-        `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
-        {
-          method: 'GET',
-          headers: {
-            'Content-Type': 'application/json',
-          },
-        }
-      )
-        .then(res => res.json())
-        .then(data => {
-          // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
-
-          let res = ontologyReducer(data?.response?.docs);
-          // if the page > 0 (i.e. if this is not the first batch of results), the new results
-          // are concatenated to the old
-          if (selectedBoxes) {
-            res.results = res.results.filter(
-              d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
-            );
-          }
-
-          if (page > 0 && results.length > 0) {
-            res.results = results.concat(res.results);
-
-            // Apply filtering to remove results with obo_id in selectedBoxes
-          } else {
-            // Set the total number of search results for pagination
-            setTotalCount(data.response.numFound);
-          }
-
-          //the results are set to res (the filtered, concatenated results)
-
-          setResults(res.results);
-          setFilteredResultsCount(res?.filteredResults?.length);
-          // resultsCount is set to the length of the filtered, concatenated results for pagination
-          setResultsCount(res.results.length);
-        })
-        .then(() => setLoading(false));
-    }
+      //fetch call to search OLS with either preferred or default ontologies
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        apiPreferenceOntologies(),
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
+    } else
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        defaultOntologies,
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
   };
-
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
   const handleViewMore = e => {
     e.preventDefault();
diff --git a/src/components/Projects/Terminologies/Terminology.scss b/src/components/Projects/Terminologies/Terminology.scss
index b640fcb..09485e7 100644
--- a/src/components/Projects/Terminologies/Terminology.scss
+++ b/src/components/Projects/Terminologies/Terminology.scss
@@ -108,6 +108,7 @@
 
 .modal_search_result {
   display: flex;
+  flex-direction: column;
   align-items: center;
   justify-content: space-between;
   margin: 0 10px 10px 6px;

From 27ff5feb41c36b090c9e22987d7c9bf105556aec Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 15 Oct 2024 13:21:42 -0500
Subject: [PATCH 004/180] first pass at editing ontology filters

---
 .../Manager/MappingsFunctions/FilterAPI.jsx   |   2 +
 .../MappingsFunctions/FilterOntology.jsx      | 108 +++++++++++++++---
 .../MappingsFunctions/FilterSelect.jsx        |  40 +++++--
 3 files changed, 123 insertions(+), 27 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index b3a0941..70e5d4a 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -22,6 +22,7 @@ export const FilterAPI = ({
   pageSize,
   setPageSize,
   paginatedOntologies,
+  apiPreferences,
 }) => {
   const { Search } = Input;
 
@@ -126,6 +127,7 @@ export const FilterAPI = ({
                 pageSize={pageSize}
                 setPageSize={setPageSize}
                 paginatedOntologies={paginatedOntologies}
+                apiPreferences={apiPreferences}
               />
             )}
           </div>
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 327f1cd..27cb521 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -12,6 +12,7 @@ export const FilterOntology = ({
   setDisplaySelectedOntologies,
   searchText,
   paginatedOntologies,
+  apiPreferences,
 }) => {
   const [allCheckboxes, setAllCheckboxes] = useState([]);
   const { ontologyForPagination, setOntologyForPagination } =
@@ -110,28 +111,100 @@ export const FilterOntology = ({
       </>
     );
   };
+  const existingDisplay = (ont, i) => {
+    return (
+      <>
+        <div key={i} className="modal_search_result">
+          <div>
+            <div className="modal_term_ontology">
+              <div>{ont.ontology.toUpperCase()}</div>
+            </div>
+          </div>
+        </div>
+      </>
+    );
+  };
+
+  const existingFilters = Object.values(apiPreferences?.self || {}).flat();
+
+  const flattenedFilters = existingFilters
+    .flatMap(item =>
+      Object.keys(item).map(key =>
+        item[key].map(value => ({
+          api: key,
+          ontology: value,
+        }))
+      )
+    )
+    .flat();
+
+  const initialChecked = flattenedFilters?.map(ef =>
+    JSON.stringify({
+      ontology: ef,
+    })
+  );
 
   return (
     <>
       <div className="modal_checkbox_wrapper">
+        {Object.keys(apiPreferences?.self?.api_preference || {}).some(
+          key => apiPreferences?.self?.api_preference[key]?.length > 0
+        ) && (
+          <>
+            <h4>Ontology Filters</h4>
+            <Form.Item
+              initialValue={initialChecked}
+              name={['existing_filters']}
+              valuePropName="value"
+              rules={[
+                {
+                  required: false,
+                },
+              ]}
+            >
+              {flattenedFilters?.length > 0 ? (
+                <Checkbox.Group
+                  className="mappings_checkbox"
+                  options={flattenedFilters?.map((po, index) => {
+                    return {
+                      value: JSON.stringify({
+                        ontology: po,
+                      }),
+                      label: existingDisplay(po, index),
+                    };
+                  })}
+                />
+              ) : (
+                ''
+              )}
+            </Form.Item>
+          </>
+        )}
         {displaySelectedOntologies.length > 0 && (
-          <Form.Item name={'selected_ontologies'} valuePropName="value">
-            <div className="modal_selected">
-              {displaySelectedOntologies?.map((selected, i) => (
-                <Checkbox
-                  key={i}
-                  checked={selectedBoxes.some(
-                    box => box?.ontology_code === selected?.ontology_code
-                  )}
-                  value={selected}
-                  onChange={e => onCheckboxChange(e, selected)}
-                >
-                  {selectedOntDisplay(selected, i)}
-                </Checkbox>
-              ))}
-            </div>
-          </Form.Item>
+          <>
+            <h4>Selected</h4>
+            <Form.Item name={'selected_ontologies'} valuePropName="value">
+              <div className="modal_selected">
+                {displaySelectedOntologies?.map((selected, i) => (
+                  <Checkbox
+                    key={i}
+                    checked={selectedBoxes.some(
+                      box => box?.ontology_code === selected?.ontology_code
+                    )}
+                    value={selected}
+                    onChange={e => onCheckboxChange(e, selected)}
+                  >
+                    {selectedOntDisplay(selected, i)}
+                  </Checkbox>
+                ))}
+              </div>
+            </Form.Item>
+          </>
         )}
+        {(Object.keys(apiPreferences?.self?.api_preference || {}).some(
+          key => apiPreferences?.self?.api_preference[key]?.length > 0
+        ) ||
+          displaySelectedOntologies.length > 0) && <h4>Ontologies</h4>}
         <Form.Item name={'ontologies'} valuePropName="value">
           <Checkbox.Group
             className="mappings_checkbox"
@@ -140,6 +213,9 @@ export const FilterOntology = ({
                 checkbox =>
                   !displaySelectedOntologies.some(
                     dsm => checkbox.ontology_code === dsm.ontology_code
+                  ) &&
+                  !flattenedFilters.some(
+                    ef => checkbox.ontology_code === ef.ontology
                   )
               )
               .map((ont, i) => ({
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index 7063a65..f7364e9 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -63,7 +63,6 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
   // If the api doesn't exist in api_preference, creates an empty array for it
   // If the api_preference array for the api does not include an ontology_code, pushes the code to the array for the api
   // If there is an api in api_preferences that is not included with the ontology_code, it's added to apiPreference with an empty array
-
   const handleSubmit = values => {
     // setLoading(true);
     const apiPreference = {
@@ -71,7 +70,8 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
     };
 
     if (values?.ontologies?.length > 0) {
-      values?.ontologies.forEach(({ ontology_code, api }) => {
+      // If there are ontologies, populate apiPreference with them
+      values.ontologies.forEach(({ ontology_code, api }) => {
         if (!apiPreference.api_preference[api]) {
           apiPreference.api_preference[api] = [];
         }
@@ -80,28 +80,45 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
         }
       });
     } else {
-      values?.selected_apis.forEach(item => {
+      // If no ontologies are provided, initialize api preferences from selected_apis
+      values?.selected_apis?.forEach(item => {
         const apiObj = JSON.parse(item);
         const apiName = apiObj.api_preference;
         apiPreference.api_preference[apiName] = []; // Create an empty array for each api_preference
       });
     }
 
-    values?.selected_apis?.forEach(item => {
-      const apiObj = JSON.parse(item);
-      const apiName = apiObj.api_preference;
-      if (!apiPreference.api_preference[apiName]) {
-        apiPreference.api_preference[apiName] = [];
-      }
-    });
+    // Now handle the existing_filters
+    if (values?.existing_filters?.length > 0) {
+      values.existing_filters.forEach(item => {
+        const apiObj = JSON.parse(item); // Parse the JSON string
+        const apiName = apiObj.ontology.api; // Extract the API
+        const ontologyCode = apiObj.ontology.ontology; // Extract the ontology code
+
+        // Ensure the apiName exists in apiPreference.api_preference
+        if (!apiPreference.api_preference[apiName]) {
+          apiPreference.api_preference[apiName] = []; // Initialize if not already present
+        }
+
+        // Add the ontologyCode to the corresponding api, if it's not already included
+        if (!apiPreference.api_preference[apiName].includes(ontologyCode)) {
+          apiPreference.api_preference[apiName].push(ontologyCode);
+        }
+      });
+    }
 
     const apiPreferenceDTO = {
       api_preference: apiPreference?.api_preference,
       editor: user.email,
     };
 
+    const method =
+      Object.keys(apiPreferences?.self?.api_preference || {}).length === 0
+        ? 'POST'
+        : 'PUT';
+
     fetch(`${vocabUrl}/${table?.terminology?.reference}/filter`, {
-      method: 'POST',
+      method: method,
       headers: {
         'Content-Type': 'application/json',
       },
@@ -259,6 +276,7 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
           pageSize={pageSize}
           setPageSize={setPageSize}
           paginatedOntologies={paginatedOntologies}
+          apiPreferences={apiPreferences}
         />
       </Modal>
     </>

From 970dee2b88d34eb80c576b9791e7a57c2a655554 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 15 Oct 2024 14:31:06 -0500
Subject: [PATCH 005/180] Delete preferred ontologies

---
 .../Manager/MappingsFunctions/FilterAPI.jsx   |  2 +
 .../MappingsFunctions/FilterOntology.jsx      |  6 +-
 .../Manager/MappingsFunctions/FilterReset.jsx | 62 +++++++++++++
 .../MappingsFunctions/FilterSelect.jsx        |  1 +
 .../MappingsFunctions/GetMappingsModal.jsx    |  3 +-
 .../MappingsFunctions/MappingReset.jsx        | 88 +++++++++----------
 .../MappingsFunctions/MappingSearch.jsx       | 88 ++++++++++---------
 .../MappingsFunctions/MappingsFunctions.scss  |  7 ++
 8 files changed, 167 insertions(+), 90 deletions(-)
 create mode 100644 src/components/Manager/MappingsFunctions/FilterReset.jsx

diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 70e5d4a..92c3f24 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -23,6 +23,7 @@ export const FilterAPI = ({
   setPageSize,
   paginatedOntologies,
   apiPreferences,
+  table,
 }) => {
   const { Search } = Input;
 
@@ -128,6 +129,7 @@ export const FilterAPI = ({
                 setPageSize={setPageSize}
                 paginatedOntologies={paginatedOntologies}
                 apiPreferences={apiPreferences}
+                table={table}
               />
             )}
           </div>
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 27cb521..9ed6e40 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -1,6 +1,7 @@
 import { Checkbox, Form, Pagination } from 'antd';
 import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
+import { FilterReset } from './FilterReset';
 
 export const FilterOntology = ({
   ontology,
@@ -13,6 +14,7 @@ export const FilterOntology = ({
   searchText,
   paginatedOntologies,
   apiPreferences,
+  table,
 }) => {
   const [allCheckboxes, setAllCheckboxes] = useState([]);
   const { ontologyForPagination, setOntologyForPagination } =
@@ -151,7 +153,9 @@ export const FilterOntology = ({
           key => apiPreferences?.self?.api_preference[key]?.length > 0
         ) && (
           <>
-            <h4>Ontology Filters</h4>
+            <div className="onto_reset">
+              <h4>Ontology Filters</h4> <FilterReset table={table} />
+            </div>
             <Form.Item
               initialValue={initialChecked}
               name={['existing_filters']}
diff --git a/src/components/Manager/MappingsFunctions/FilterReset.jsx b/src/components/Manager/MappingsFunctions/FilterReset.jsx
new file mode 100644
index 0000000..f5349a8
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/FilterReset.jsx
@@ -0,0 +1,62 @@
+import { Button, message, Modal, notification } from 'antd';
+import { ExclamationCircleFilled } from '@ant-design/icons';
+import { useContext, useState } from 'react';
+import { myContext } from '../../../App';
+import { SearchContext } from '../../../Contexts/SearchContext';
+
+export const FilterReset = ({ table }) => {
+  const { confirm } = Modal;
+
+  const { user, vocabUrl } = useContext(myContext);
+  const { setApiPreferences } = useContext(SearchContext);
+  const [remove, setRemove] = useState(false);
+
+  const deleteOntologies = evt => {
+    return fetch(`${vocabUrl}/${table?.terminology?.reference}/filter`, {
+      method: 'DELETE',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify({ editor: user.email }),
+    })
+      .then(res => {
+        if (res.ok) {
+          return res.json().then(data => {
+            message.success('Ontology filters deleted successfully.');
+          });
+        } else {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred deleting the table.',
+          });
+        }
+      })
+      .then(data => setApiPreferences(data));
+  };
+
+  const showConfirm = () => {
+    confirm({
+      className: 'delete_table_confirm',
+      title: 'Alert',
+      icon: <ExclamationCircleFilled />,
+      content:
+        '          Are you sure you want to remove the ontology filters?',
+      onOk() {
+        deleteOntologies();
+        setRemove(false);
+      },
+      onCancel() {
+        setRemove(false);
+      },
+    });
+  };
+
+  return (
+    <>
+      <Button danger onClick={() => (user ? setRemove(true) : login())}>
+        Reset{' '}
+      </Button>
+      {remove && showConfirm()}
+    </>
+  );
+};
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index f7364e9..ace5cc0 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -277,6 +277,7 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
           setPageSize={setPageSize}
           paginatedOntologies={paginatedOntologies}
           apiPreferences={apiPreferences}
+          table={table}
         />
       </Modal>
     </>
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index e54b6f5..05087a3 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -1,12 +1,11 @@
 import { Checkbox, Input, message, Modal, Form, Tooltip } from 'antd';
 import { useContext, useEffect, useRef, useState } from 'react';
 import { myContext } from '../../../App';
-import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
+import { ellipsisString, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { olsFilterOntologiesSearch } from '../FetchManager';
-import { defaultIconPrefixCls } from 'antd/es/config-provider';
 
 export const GetMappingsModal = ({
   componentString,
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index dc9c75b..68901e7 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -4,6 +4,8 @@ import { myContext } from '../../../App';
 import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
+import { olsFilterOntologiesSearch } from '../FetchManager';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const MappingReset = ({
   searchProp,
@@ -12,6 +14,7 @@ export const MappingReset = ({
   onClose,
 }) => {
   const { searchUrl } = useContext(myContext);
+  const { apiPreferences } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -103,52 +106,49 @@ export const MappingReset = ({
     number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
     on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
     const pageStart = page * entriesPerPage;
-    return fetch(
-      `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
-      {
-        method: 'GET',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-      }
-    )
-      .then(res => res.json())
-      .then(data => {
-        // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
-        let res = ontologyReducer(data?.response?.docs);
-
-        // Filters out results that have already been selected in previous search if there is a change to the search term
-        if (selectedBoxes) {
-          res.results = res.results.filter(
-            d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
-          );
-        }
-
-        // if the page > 0 (i.e. if this is not the first batch of results), the new results
-        // are concatenated to the old
-        if (page > 0 && results.length > 0) {
-          res.results = results.concat(res.results);
+    if (
+      //If there are api preferences and one of them is OLS, it gets the preferred ontologies
+      apiPreferences?.self?.api_preference &&
+      'ols' in apiPreferences?.self?.api_preference
+    ) {
+      const apiPreferenceOntologies = () => {
+        if (apiPreferences?.self?.api_preference?.ols) {
+          return apiPreferences.self.api_preference.ols.join(',');
         } else {
-          // the total number of search results are set to totalCount for pagination
-          setTotalCount(data.response.numFound);
-        }
-        //the results are set to res (the filtered, concatenated results)
-        setResults(res.results);
-        setFilteredResultsCount(res?.filteredResults?.length);
-
-        // resultsCount is set to the length of the filtered, concatenated results for pagination
-        setResultsCount(res.results.length);
-      })
-      .catch(error => {
-        if (error) {
-          notification.error({
-            message: 'Error',
-            description: 'An error occurred. Please try again.',
-          });
+          // else if there are no preferred ontologies, it uses the default ontologies
+          return defaultOntologies;
         }
-        return error;
-      })
-      .finally(() => setLoading(false));
+      };
+      //fetch call to search OLS with either preferred or default ontologies
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        apiPreferenceOntologies(),
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
+    } else
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        defaultOntologies,
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
   };
 
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 80585e8..332083c 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -4,6 +4,8 @@ import { myContext } from '../../../App';
 import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
+import { SearchContext } from '../../../Contexts/SearchContext';
+import { olsFilterOntologiesSearch } from '../FetchManager';
 
 export const MappingSearch = ({
   setEditMappings,
@@ -13,6 +15,8 @@ export const MappingSearch = ({
   searchProp,
 }) => {
   const { searchUrl } = useContext(myContext);
+  const { apiPreferences } = useContext(SearchContext);
+
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -105,51 +109,49 @@ export const MappingSearch = ({
     number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
     on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
     const pageStart = page * entriesPerPage;
-    return fetch(
-      `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
-      {
-        method: 'GET',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-      }
-    )
-      .then(res => res.json())
-      .then(data => {
-        // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
-        let res = ontologyReducer(data?.response?.docs);
-
-        // Filters out results that have already been selected in previous search if there is a change to the search term
-        if (selectedBoxes) {
-          res.results = res.results.filter(
-            d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
-          );
-        }
-        // if the page > 0 (i.e. if this is not the first batch of results), the new results
-        // are concatenated to the old
-        if (page > 0 && results.length > 0) {
-          res.results = results.concat(res.results);
+    if (
+      //If there are api preferences and one of them is OLS, it gets the preferred ontologies
+      apiPreferences?.self?.api_preference &&
+      'ols' in apiPreferences?.self?.api_preference
+    ) {
+      const apiPreferenceOntologies = () => {
+        if (apiPreferences?.self?.api_preference?.ols) {
+          return apiPreferences.self.api_preference.ols.join(',');
         } else {
-          // the total number of search results are set to totalCount for pagination
-          setTotalCount(data.response.numFound);
-        }
-        //the results are set to res (the filtered, concatenated results)
-        setResults(res.results);
-        setFilteredResultsCount(res?.filteredResults?.length);
-
-        // resultsCount is set to the length of the filtered, concatenated results for pagination
-        setResultsCount(res.results.length);
-      })
-      .catch(error => {
-        if (error) {
-          notification.error({
-            message: 'Error',
-            description: 'An error occurred. Please try again.',
-          });
+          // else if there are no preferred ontologies, it uses the default ontologies
+          return defaultOntologies;
         }
-        return error;
-      })
-      .finally(() => setLoading(false));
+      };
+      //fetch call to search OLS with either preferred or default ontologies
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        apiPreferenceOntologies(),
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
+    } else
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        defaultOntologies,
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
   };
 
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index fa074f2..a4a8d45 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -78,3 +78,10 @@
   width: 50vw;
   justify-content: center;
 }
+
+.onto_reset {
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+  gap: 8px;
+}

From b0519ecadfe6adbef85b3f9307471fd20c81c0dc Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 15 Oct 2024 16:06:35 -0500
Subject: [PATCH 006/180] committing to switch branches

---
 src/components/Manager/MappingsFunctions/FilterReset.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterReset.jsx b/src/components/Manager/MappingsFunctions/FilterReset.jsx
index f5349a8..ac37e40 100644
--- a/src/components/Manager/MappingsFunctions/FilterReset.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterReset.jsx
@@ -54,7 +54,7 @@ export const FilterReset = ({ table }) => {
   return (
     <>
       <Button danger onClick={() => (user ? setRemove(true) : login())}>
-        Reset{' '}
+        Reset
       </Button>
       {remove && showConfirm()}
     </>

From 36970255b6560efcdf25d64b5e0fe75bddb44802 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 16 Oct 2024 11:23:45 -0500
Subject: [PATCH 007/180] Newly added ontologies checking by default on load

---
 .../Manager/MappingsFunctions/FilterAPI.jsx   |   2 +-
 .../MappingsFunctions/FilterSelect.jsx        | 128 +++++++++---------
 2 files changed, 66 insertions(+), 64 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 92c3f24..1a63182 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -91,7 +91,7 @@ export const FilterAPI = ({
   ) : (
     <div>
       <div className="api_list">
-        <Form form={form}>
+        <Form form={form} preserve={false}>
           <div>
             <div className="api_label">APIs</div>
 
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index ace5cc0..c194961 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -214,72 +214,74 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
       >
         API Filters {apiPrefObject ? `(${apiPrefLength})` : ''}
       </Button>
-      <Modal
-        open={addFilter}
-        width={'70%'}
-        styles={{
-          body: {
-            minHeight: '60vh',
-            maxHeight: '60vh',
-          },
-        }}
-        onOk={() => {
-          form.validateFields().then(values => {
-            handleSubmit(values);
+      {addFilter && (
+        <Modal
+          open={addFilter}
+          width={'70%'}
+          styles={{
+            body: {
+              minHeight: '60vh',
+              maxHeight: '60vh',
+            },
+          }}
+          onOk={() => {
+            form.validateFields().then(values => {
+              handleSubmit(values);
+              onClose();
+            });
+          }}
+          onCancel={() => {
+            form.resetFields();
+            setAddFilter(false);
             onClose();
-          });
-        }}
-        onCancel={() => {
-          form.resetFields();
-          setAddFilter(false);
-          onClose();
-        }}
-        maskClosable={false}
-        closeIcon={false}
-        footer={(_, { OkBtn, CancelBtn }) => (
-          <>
-            <div className="modal_footer">
+          }}
+          maskClosable={false}
+          closeIcon={false}
+          footer={(_, { OkBtn, CancelBtn }) => (
+            <>
               <div className="modal_footer">
-                <Pagination
-                  current={currentPage}
-                  pageSize={pageSize}
-                  total={filteredOntologiesArray?.length}
-                  onChange={handlePageChange}
-                  showSizeChanger
-                  onShowSizeChange={handlePageSizeChange}
-                  pageSizeOptions={['10', '20', '50']} // Set page size options
-                />
-              </div>
-              <div className="cancel_ok_buttons">
-                <CancelBtn />
-                <OkBtn />
+                <div className="modal_footer">
+                  <Pagination
+                    current={currentPage}
+                    pageSize={pageSize}
+                    total={filteredOntologiesArray?.length}
+                    onChange={handlePageChange}
+                    showSizeChanger
+                    onShowSizeChange={handlePageSizeChange}
+                    pageSizeOptions={['10', '20', '50']} // Set page size options
+                  />
+                </div>
+                <div className="cancel_ok_buttons">
+                  <CancelBtn />
+                  <OkBtn />
+                </div>
               </div>
-            </div>
-          </>
-        )}
-      >
-        <FilterAPI
-          form={form}
-          selectedOntologies={selectedOntologies}
-          setSelectedOntologies={setSelectedOntologies}
-          selectedBoxes={selectedBoxes}
-          setSelectedBoxes={setSelectedBoxes}
-          displaySelectedOntologies={displaySelectedOntologies}
-          setDisplaySelectedOntologies={setDisplaySelectedOntologies}
-          ontologyApis={ontologyApis}
-          active={active}
-          setActive={setActive}
-          searchText={searchText}
-          setSearchText={setSearchText}
-          currentPage={currentPage}
-          setCurrentPage={setCurrentPage}
-          pageSize={pageSize}
-          setPageSize={setPageSize}
-          paginatedOntologies={paginatedOntologies}
-          apiPreferences={apiPreferences}
-          table={table}
-        />
-      </Modal>
+            </>
+          )}
+        >
+          <FilterAPI
+            form={form}
+            selectedOntologies={selectedOntologies}
+            setSelectedOntologies={setSelectedOntologies}
+            selectedBoxes={selectedBoxes}
+            setSelectedBoxes={setSelectedBoxes}
+            displaySelectedOntologies={displaySelectedOntologies}
+            setDisplaySelectedOntologies={setDisplaySelectedOntologies}
+            ontologyApis={ontologyApis}
+            active={active}
+            setActive={setActive}
+            searchText={searchText}
+            setSearchText={setSearchText}
+            currentPage={currentPage}
+            setCurrentPage={setCurrentPage}
+            pageSize={pageSize}
+            setPageSize={setPageSize}
+            paginatedOntologies={paginatedOntologies}
+            apiPreferences={apiPreferences}
+            table={table}
+          />
+        </Modal>
+      )}
     </>
   );
 };

From a3bdbe2a240355cc3e7de61a21339bcf5da59b87 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 16 Oct 2024 15:56:56 -0500
Subject: [PATCH 008/180] ontology filter for mappings search

---
 src/Contexts/SearchContext.jsx                |  2 +
 src/components/Manager/FetchManager.jsx       |  3 +-
 .../Manager/MappingsFunctions/FilterAPI.jsx   | 42 +++++++++++++---
 .../MappingsFunctions/FilterSelect.jsx        | 49 ++++++++++---------
 .../MappingsFunctions/GetMappingsModal.jsx    | 12 +++--
 .../MappingsFunctions/MappingReset.jsx        |  8 +--
 .../MappingsFunctions/MappingSearch.jsx       |  8 +--
 src/components/Nav/NavBar.jsx                 |  4 +-
 .../Projects/Tables/TableDetails.jsx          | 13 +++++
 9 files changed, 100 insertions(+), 41 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index e90d907..a8d1d27 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -13,6 +13,7 @@ export function SearchContextRoot() {
   const [apiPage, setApiPage] = useState(0);
   const [apiTotalCount, setApiTotalCount] = useState();
   const [apiPreferences, setApiPreferences] = useState({});
+  const defaultOntologies = 'mondo,hp,maxo,ncit';
 
   const context = {
     prefTerminologies,
@@ -33,6 +34,7 @@ export function SearchContextRoot() {
     setApiTotalCount,
     apiPreferences,
     setApiPreferences,
+    defaultOntologies,
   };
 
   return (
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index fc5f4a6..6b436c9 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -180,7 +180,8 @@ export const olsFilterOntologiesSearch = (
   setResults,
   setFilteredResultsCount,
   setResultsCount,
-  setLoading
+  setLoading,
+  results
 ) => {
   setLoading(true);
   return fetch(
diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 1a63182..946f435 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -1,5 +1,5 @@
 import { useContext, useEffect, useState } from 'react';
-import { Checkbox, Form, Input } from 'antd';
+import { Checkbox, Form } from 'antd';
 import { ModalSpinner, OntologySpinner } from '../Spinner';
 import { myContext } from '../../../App';
 import { FilterOntology } from './FilterOntology';
@@ -16,7 +16,6 @@ export const FilterAPI = ({
   active,
   setActive,
   searchText,
-  setSearchText,
   currentPage,
   setCurrentPage,
   pageSize,
@@ -25,13 +24,32 @@ export const FilterAPI = ({
   apiPreferences,
   table,
 }) => {
-  const { Search } = Input;
-
   const { vocabUrl } = useContext(myContext);
   const [ontology, setOntology] = useState([]);
   const [loading, setLoading] = useState(false);
   const [tableLoading, setTableLoading] = useState(false);
 
+  // The selected ontology filters that have already been selected
+  const existingFilters = Object.values(apiPreferences?.self || {}).flat();
+
+  // Flattens the existingFilters into a single array
+  const flattenedFilters = existingFilters
+    .flatMap(item =>
+      Object.keys(item).map(key =>
+        item[key].map(value => ({
+          api: key,
+        }))
+      )
+    )
+    .flat();
+
+  // The initial value for the form. The checkboxes for the filters that have already been selected will be checked by default
+  const initialChecked = flattenedFilters?.map(ef =>
+    JSON.stringify({
+      ontology: ef,
+    })
+  );
+
   // Fetches the active ontologyAPI each time the active API changes
   useEffect(() => {
     active && getOntologyApiById();
@@ -56,7 +74,20 @@ export const FilterAPI = ({
           }
         })
         .then(data => {
-          setOntology(data);
+          //Alphabetizes the data
+          const sortedData = data.map(api => {
+            const sortedOntologies = Object.fromEntries(
+              Object.entries(api.ontologies).sort((a, b) =>
+                a[1].ontology_code > b[1].ontology_code ? 1 : -1
+              )
+            );
+
+            return {
+              ...api,
+              ontologies: sortedOntologies,
+            };
+          });
+          setOntology(sortedData);
         })
         .finally(() => setTableLoading(false))
     );
@@ -85,7 +116,6 @@ export const FilterAPI = ({
       </>
     );
   };
-
   return loading ? (
     <ModalSpinner />
   ) : (
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index c194961..538f380 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -4,6 +4,7 @@ import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
 import { FilterAPI } from './FilterAPI';
 import { getOntologies } from '../FetchManager';
+import { ModalSpinner } from '../Spinner';
 
 export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
   const [form] = Form.useForm();
@@ -64,7 +65,7 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
   // If the api_preference array for the api does not include an ontology_code, pushes the code to the array for the api
   // If there is an api in api_preferences that is not included with the ontology_code, it's added to apiPreference with an empty array
   const handleSubmit = values => {
-    // setLoading(true);
+    setLoading(true);
     const apiPreference = {
       api_preference: {},
     };
@@ -259,27 +260,31 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
             </>
           )}
         >
-          <FilterAPI
-            form={form}
-            selectedOntologies={selectedOntologies}
-            setSelectedOntologies={setSelectedOntologies}
-            selectedBoxes={selectedBoxes}
-            setSelectedBoxes={setSelectedBoxes}
-            displaySelectedOntologies={displaySelectedOntologies}
-            setDisplaySelectedOntologies={setDisplaySelectedOntologies}
-            ontologyApis={ontologyApis}
-            active={active}
-            setActive={setActive}
-            searchText={searchText}
-            setSearchText={setSearchText}
-            currentPage={currentPage}
-            setCurrentPage={setCurrentPage}
-            pageSize={pageSize}
-            setPageSize={setPageSize}
-            paginatedOntologies={paginatedOntologies}
-            apiPreferences={apiPreferences}
-            table={table}
-          />
+          {loading ? (
+            <ModalSpinner />
+          ) : (
+            <FilterAPI
+              form={form}
+              selectedOntologies={selectedOntologies}
+              setSelectedOntologies={setSelectedOntologies}
+              selectedBoxes={selectedBoxes}
+              setSelectedBoxes={setSelectedBoxes}
+              displaySelectedOntologies={displaySelectedOntologies}
+              setDisplaySelectedOntologies={setDisplaySelectedOntologies}
+              ontologyApis={ontologyApis}
+              active={active}
+              setActive={setActive}
+              searchText={searchText}
+              setSearchText={setSearchText}
+              currentPage={currentPage}
+              setCurrentPage={setCurrentPage}
+              pageSize={pageSize}
+              setPageSize={setPageSize}
+              paginatedOntologies={paginatedOntologies}
+              apiPreferences={apiPreferences}
+              table={table}
+            />
+          )}
         </Modal>
       )}
     </>
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 05087a3..d079feb 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -19,7 +19,7 @@ export const GetMappingsModal = ({
   const { Search } = Input;
 
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
-  const { apiPreferences } = useContext(SearchContext);
+  const { apiPreferences, defaultOntologies } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(false);
@@ -40,7 +40,6 @@ export const GetMappingsModal = ({
     setSelectedBoxes,
   } = useContext(MappingContext);
   let ref = useRef();
-  const defaultOntologies = 'mondo,hp,maxo,ncit';
 
   // since the code is passed through searchProp, the '!!' forces it to be evaluated as a boolean.
   // if there is a searchProp being passed, it evaluates to true and runs the search function.
@@ -186,7 +185,8 @@ export const GetMappingsModal = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
     } else
       return olsFilterOntologiesSearch(
@@ -201,7 +201,8 @@ export const GetMappingsModal = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
   };
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
@@ -423,6 +424,9 @@ export const GetMappingsModal = ({
                           Displaying {resultsCount}
                           &nbsp;of&nbsp;{totalCount}
                         </Tooltip>
+                        {console.log('total', totalCount)}
+                        {console.log('filtered', filteredResultsCount)}
+                        {console.log('results', filteredResultsCount)}
                         {totalCount - filteredResultsCount !== resultsCount && (
                           <span
                             className="view_more_link"
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 68901e7..a026c91 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -14,7 +14,7 @@ export const MappingReset = ({
   onClose,
 }) => {
   const { searchUrl } = useContext(myContext);
-  const { apiPreferences } = useContext(SearchContext);
+  const { apiPreferences, defaultOntologies } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -132,7 +132,8 @@ export const MappingReset = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
     } else
       return olsFilterOntologiesSearch(
@@ -147,7 +148,8 @@ export const MappingReset = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
   };
 
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 332083c..14724f1 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -15,7 +15,7 @@ export const MappingSearch = ({
   searchProp,
 }) => {
   const { searchUrl } = useContext(myContext);
-  const { apiPreferences } = useContext(SearchContext);
+  const { apiPreferences, defaultOntologies } = useContext(SearchContext);
 
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
@@ -135,7 +135,8 @@ export const MappingSearch = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
     } else
       return olsFilterOntologiesSearch(
@@ -150,7 +151,8 @@ export const MappingSearch = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
   };
 
diff --git a/src/components/Nav/NavBar.jsx b/src/components/Nav/NavBar.jsx
index 13a0c11..80e39ff 100644
--- a/src/components/Nav/NavBar.jsx
+++ b/src/components/Nav/NavBar.jsx
@@ -27,11 +27,11 @@ export const NavBar = () => {
             </NavLink>
             {/* Placeholder elements below. No functionality at this time.*/}
             <NavLink to="/help">
-              <li className="nav_link">Help</li>
+              <li className="nav_link">About</li>
             </NavLink>
 
             <NavLink to="/about">
-              <li className="nav_link">About</li>
+              <li className="nav_link">Ontologies</li>
             </NavLink>
           </div>
           <div className="login">
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 9bd6e05..863cb79 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -51,6 +51,19 @@ export const TableDetails = () => {
     setDataSource(tableData(table));
   }, [table, mapping]);
 
+  const alphabetizeOntologies = ontologies => {
+    // Sort the keys alphabetically
+    const sortedKeys = Object.keys(ontologies).sort();
+
+    // Rebuild object using the sorted keys
+    const sortedOntologies = {};
+    sortedKeys.forEach(key => {
+      sortedOntologies[key] = ontologies[key];
+    });
+
+    return sortedOntologies;
+  };
+
   // fetches the table and sets 'table' to the response
   useEffect(() => {
     setLoading(true);

From 642e2b1534282658db89b7dcc0149ffffaf734ee Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 16 Oct 2024 15:57:35 -0500
Subject: [PATCH 009/180] Removed unnecesary console logs

---
 src/components/Manager/MappingsFunctions/GetMappingsModal.jsx | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index d079feb..1451c01 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -424,9 +424,6 @@ export const GetMappingsModal = ({
                           Displaying {resultsCount}
                           &nbsp;of&nbsp;{totalCount}
                         </Tooltip>
-                        {console.log('total', totalCount)}
-                        {console.log('filtered', filteredResultsCount)}
-                        {console.log('results', filteredResultsCount)}
                         {totalCount - filteredResultsCount !== resultsCount && (
                           <span
                             className="view_more_link"

From fd8452f38b6ee40611e4bbb51eaaab5ec9e2318c Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 10 Oct 2024 13:11:09 -0500
Subject: [PATCH 010/180] OLS search for filtered ontologies

---
 src/Contexts/SearchContext.jsx                |  3 ++
 .../MappingsFunctions/DefaultSearch.jsx       | 52 +++++++++++++++++++
 .../MappingsFunctions/GetMappingsModal.jsx    | 17 +++++-
 .../Projects/Tables/TableDetails.jsx          |  6 +--
 4 files changed, 74 insertions(+), 4 deletions(-)
 create mode 100644 src/components/Manager/MappingsFunctions/DefaultSearch.jsx

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index 909846e..e90d907 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -12,6 +12,7 @@ export function SearchContextRoot() {
   const [apiResultsCount, setApiResultsCount] = useState();
   const [apiPage, setApiPage] = useState(0);
   const [apiTotalCount, setApiTotalCount] = useState();
+  const [apiPreferences, setApiPreferences] = useState({});
 
   const context = {
     prefTerminologies,
@@ -30,6 +31,8 @@ export function SearchContextRoot() {
     setApiPage,
     apiTotalCount,
     setApiTotalCount,
+    apiPreferences,
+    setApiPreferences,
   };
 
   return (
diff --git a/src/components/Manager/MappingsFunctions/DefaultSearch.jsx b/src/components/Manager/MappingsFunctions/DefaultSearch.jsx
new file mode 100644
index 0000000..ef91ae6
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/DefaultSearch.jsx
@@ -0,0 +1,52 @@
+import { ontologyReducer } from '../Utilitiy';
+
+export const fetchResults = (
+  page,
+  query,
+  entriesPerPage,
+  //   setLoading,
+  setTotalCount,
+  setResults,
+  setFilteredResultsCount,
+  setResultsCount,
+  searchUrl,
+  selectedBoxes
+) => {
+  if (!query) {
+    return undefined;
+  }
+  //   setLoading(true);
+  const pageStart = page * entriesPerPage;
+
+  return fetch(
+    `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
+    {
+      method: 'GET',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+    }
+  )
+    .then(res => res.json())
+    .then(data => {
+      let res = ontologyReducer(data?.response?.docs);
+
+      // Filter based on selectedBoxes
+      if (selectedBoxes) {
+        res.results = res.results.filter(
+          d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
+        );
+      }
+
+      if (page > 0 && res.results.length > 0) {
+        res.results = results.concat(res.results);
+      } else {
+        setTotalCount(data.response.numFound);
+      }
+
+      setResults(res.results);
+      setFilteredResultsCount(res?.filteredResults?.length);
+      setResultsCount(res.results.length);
+    });
+  // .finally(() => setLoading(false));
+};
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 3c56feb..f8219b3 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -4,6 +4,7 @@ import { myContext } from '../../../App';
 import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const GetMappingsModal = ({
   componentString,
@@ -17,6 +18,7 @@ export const GetMappingsModal = ({
   const { Search } = Input;
 
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
+  const { apiPreferences } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -155,8 +157,21 @@ export const GetMappingsModal = ({
     number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
     on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
     const pageStart = page * entriesPerPage;
+    const apiPreferenceOntologies = () => {
+      if (apiPreferences?.self?.api_preference?.ols) {
+        // Get the ontologies from the 'ols' array and join them with commas
+        const filteredOntologies =
+          apiPreferences.self.api_preference.ols.join(',');
+        console.log(filteredOntologies);
+        // Construct the final URL with the filteredOntologies
+        return filteredOntologies;
+      } else {
+        const defaultOntologies = 'mondo,hp,maxo,ncit';
+        return defaultOntologies;
+      }
+    };
     return fetch(
-      `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
+      `${searchUrl}q=${query}&ontology=${apiPreferenceOntologies()}&rows=${entriesPerPage}&start=${pageStart}`,
       {
         method: 'GET',
         headers: {
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 46b3597..9bd6e05 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -20,12 +20,14 @@ import { Submenu } from '../../Manager/Submenu';
 import { SettingsDropdownTable } from '../../Manager/Dropdown/SettingsDropdownTable';
 import { RequiredLogin } from '../../Auth/RequiredLogin';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const TableDetails = () => {
   const [form] = Form.useForm();
 
   const { vocabUrl, edit, setEdit, table, setTable, user } =
     useContext(myContext);
+  const { apiPreferences, setApiPreferences } = useContext(SearchContext);
   const {
     getMappings,
     setGetMappings,
@@ -37,7 +39,6 @@ export const TableDetails = () => {
   const { studyId, DDId, tableId } = useParams();
   const [loading, setLoading] = useState(true);
   const [load, setLoad] = useState(false);
-  const [apiPreferences, setApiPreferences] = useState({});
 
   const navigate = useNavigate();
 
@@ -66,8 +67,7 @@ export const TableDetails = () => {
                 if (error) {
                   notification.error({
                     message: 'Error',
-                    description:
-                      'An error occurred loading mappings. Please try again.',
+                    description: 'An error occurred loading mappings.',
                   });
                 }
                 return error;

From ada5d61ec4febf40440b2d5844f8b2ba3767579a Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 10 Oct 2024 15:29:45 -0500
Subject: [PATCH 011/180] added fetch function for ols search

---
 .../MappingsFunctions/GetMappingsModal.jsx    | 100 +++++++++++++-----
 1 file changed, 75 insertions(+), 25 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index f8219b3..010728f 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -146,32 +146,9 @@ export const GetMappingsModal = ({
       });
   };
 
-  // The function that makes the API call to search for the passed code.
-
-  const fetchResults = (page, query) => {
-    if (!!!query) {
-      return undefined;
-    }
-    setLoading(true);
-    /* The OLS API returns 10 results by default unless specified otherwise. The fetch call includes a specified
-    number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
-    on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
-    const pageStart = page * entriesPerPage;
-    const apiPreferenceOntologies = () => {
-      if (apiPreferences?.self?.api_preference?.ols) {
-        // Get the ontologies from the 'ols' array and join them with commas
-        const filteredOntologies =
-          apiPreferences.self.api_preference.ols.join(',');
-        console.log(filteredOntologies);
-        // Construct the final URL with the filteredOntologies
-        return filteredOntologies;
-      } else {
-        const defaultOntologies = 'mondo,hp,maxo,ncit';
-        return defaultOntologies;
-      }
-    };
+  const fetchFunction = (query, ontologiesToSearch, page, pageStart) => {
     return fetch(
-      `${searchUrl}q=${query}&ontology=${apiPreferenceOntologies()}&rows=${entriesPerPage}&start=${pageStart}`,
+      `${searchUrl}q=${query}&ontology=${ontologiesToSearch}&rows=${entriesPerPage}&start=${pageStart}`,
       {
         method: 'GET',
         headers: {
@@ -211,6 +188,79 @@ export const GetMappingsModal = ({
       .then(() => setLoading(false));
   };
 
+  // The function that makes the API call to search for the passed code.
+
+  const fetchResults = (page, query) => {
+    if (!!!query) {
+      return undefined;
+    }
+    setLoading(true);
+    /* The OLS API returns 10 results by default unless specified otherwise. The fetch call includes a specified
+    number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
+    on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
+    const pageStart = page * entriesPerPage;
+
+    if (
+      apiPreferences?.self?.api_preference &&
+      'ols' in apiPreferences?.self?.api_preference
+    ) {
+      const apiPreferenceOntologies = () => {
+        if (apiPreferences?.self?.api_preference?.ols) {
+          // Get the ontologies from the 'ols' array and join them with commas
+          const filteredOntologies =
+            apiPreferences.self.api_preference.ols.join(',');
+          console.log(filteredOntologies);
+          // Construct the final URL with the filteredOntologies
+          return filteredOntologies;
+        } else {
+          const defaultOntologies = 'mondo,hp,maxo,ncit';
+          return defaultOntologies;
+        }
+      };
+      return fetchFunction(query, apiPreferenceOntologies(), page, pageStart);
+    } else {
+      return fetch(
+        `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
+        {
+          method: 'GET',
+          headers: {
+            'Content-Type': 'application/json',
+          },
+        }
+      )
+        .then(res => res.json())
+        .then(data => {
+          // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
+
+          let res = ontologyReducer(data?.response?.docs);
+          // if the page > 0 (i.e. if this is not the first batch of results), the new results
+          // are concatenated to the old
+          if (selectedBoxes) {
+            res.results = res.results.filter(
+              d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
+            );
+          }
+
+          if (page > 0 && results.length > 0) {
+            res.results = results.concat(res.results);
+
+            // Apply filtering to remove results with obo_id in selectedBoxes
+          } else {
+            // Set the total number of search results for pagination
+            setTotalCount(data.response.numFound);
+          }
+
+          //the results are set to res (the filtered, concatenated results)
+
+          setResults(res.results);
+          setFilteredResultsCount(res?.filteredResults?.length);
+          // resultsCount is set to the length of the filtered, concatenated results for pagination
+          setResultsCount(res.results.length);
+        })
+        .then(() => setLoading(false));
+    }
+  };
+
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
   const handleViewMore = e => {
     e.preventDefault();

From ede8b8c121581cf55e3368c191945c7a656ff56f Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 14 Oct 2024 20:42:00 -0500
Subject: [PATCH 012/180] OLS ontology filters for mapping search

---
 src/App.jsx                                   |   2 +
 src/components/Manager/FetchManager.jsx       |  58 ++++++++
 .../MappingsFunctions/GetMappingsModal.jsx    | 132 +++++-------------
 .../Projects/Terminologies/Terminology.scss   |   1 +
 4 files changed, 99 insertions(+), 94 deletions(-)

diff --git a/src/App.jsx b/src/App.jsx
index 64d3e56..2096b18 100644
--- a/src/App.jsx
+++ b/src/App.jsx
@@ -7,6 +7,7 @@ export const myContext = createContext();
 
 function App() {
   const searchUrl = import.meta.env.VITE_SEARCH_ENDPOINT;
+  const monarchUrl = import.meta.env.VITE_MONARCH_SEARCH;
   const vocabUrl = import.meta.env.VITE_VOCAB_ENDPOINT;
   const clientId = import.meta.env.VITE_CLIENT_ID;
 
@@ -47,6 +48,7 @@ function App() {
           results,
           setResults,
           searchUrl,
+          monarchUrl,
           vocabUrl,
           tablesDD,
           setTablesDD,
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 1b5e44e..fc5f4a6 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -1,3 +1,5 @@
+import { ontologyReducer } from './Utilitiy';
+
 // Fetches all elements at an endpoint
 export const getAll = (vocabUrl, name, navigate) => {
   return fetch(`${vocabUrl}/${name}`, {
@@ -165,3 +167,59 @@ export const getOntologies = vocabUrl => {
     }
   });
 };
+
+export const olsFilterOntologiesSearch = (
+  searchUrl,
+  query,
+  ontologiesToSearch,
+  page,
+  entriesPerPage,
+  pageStart,
+  selectedBoxes,
+  setTotalCount,
+  setResults,
+  setFilteredResultsCount,
+  setResultsCount,
+  setLoading
+) => {
+  setLoading(true);
+  return fetch(
+    `${searchUrl}q=${query}&ontology=${ontologiesToSearch}&rows=${entriesPerPage}&start=${pageStart}`,
+    {
+      method: 'GET',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+    }
+  )
+    .then(res => res.json())
+    .then(data => {
+      // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
+
+      let res = ontologyReducer(data?.response?.docs);
+      // if the page > 0 (i.e. if this is not the first batch of results), the new results
+      // are concatenated to the old
+      if (selectedBoxes) {
+        res.results = res.results.filter(
+          d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
+        );
+      }
+
+      if (page > 0 && results.length > 0) {
+        res.results = results.concat(res.results);
+
+        // Apply filtering to remove results with obo_id in selectedBoxes
+      } else {
+        // Set the total number of search results for pagination
+        setTotalCount(data.response.numFound);
+      }
+
+      //the results are set to res (the filtered, concatenated results)
+
+      setResults(res.results);
+      setFilteredResultsCount(res?.filteredResults?.length);
+      // resultsCount is set to the length of the filtered, concatenated results for pagination
+      setResultsCount(res.results.length);
+    })
+    .then(() => setLoading(false));
+};
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 010728f..e54b6f5 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -5,6 +5,8 @@ import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import { olsFilterOntologiesSearch } from '../FetchManager';
+import { defaultIconPrefixCls } from 'antd/es/config-provider';
 
 export const GetMappingsModal = ({
   componentString,
@@ -21,8 +23,9 @@ export const GetMappingsModal = ({
   const { apiPreferences } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
-  const [loading, setLoading] = useState(true);
+  const [loading, setLoading] = useState(false);
   const [results, setResults] = useState([]);
+  const [monarchResults, setMonarchResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
   const [resultsCount, setResultsCount] = useState();
   const [lastCount, setLastCount] = useState(0); //save last count as count of the results before you fetch data again
@@ -38,6 +41,7 @@ export const GetMappingsModal = ({
     setSelectedBoxes,
   } = useContext(MappingContext);
   let ref = useRef();
+  const defaultOntologies = 'mondo,hp,maxo,ncit';
 
   // since the code is passed through searchProp, the '!!' forces it to be evaluated as a boolean.
   // if there is a searchProp being passed, it evaluates to true and runs the search function.
@@ -146,121 +150,61 @@ export const GetMappingsModal = ({
       });
   };
 
-  const fetchFunction = (query, ontologiesToSearch, page, pageStart) => {
-    return fetch(
-      `${searchUrl}q=${query}&ontology=${ontologiesToSearch}&rows=${entriesPerPage}&start=${pageStart}`,
-      {
-        method: 'GET',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-      }
-    )
-      .then(res => res.json())
-      .then(data => {
-        // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
-
-        let res = ontologyReducer(data?.response?.docs);
-        // if the page > 0 (i.e. if this is not the first batch of results), the new results
-        // are concatenated to the old
-        if (selectedBoxes) {
-          res.results = res.results.filter(
-            d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
-          );
-        }
-
-        if (page > 0 && results.length > 0) {
-          res.results = results.concat(res.results);
-
-          // Apply filtering to remove results with obo_id in selectedBoxes
-        } else {
-          // Set the total number of search results for pagination
-          setTotalCount(data.response.numFound);
-        }
-
-        //the results are set to res (the filtered, concatenated results)
-
-        setResults(res.results);
-        setFilteredResultsCount(res?.filteredResults?.length);
-        // resultsCount is set to the length of the filtered, concatenated results for pagination
-        setResultsCount(res.results.length);
-      })
-      .then(() => setLoading(false));
-  };
-
   // The function that makes the API call to search for the passed code.
 
   const fetchResults = (page, query) => {
     if (!!!query) {
       return undefined;
     }
-    setLoading(true);
     /* The OLS API returns 10 results by default unless specified otherwise. The fetch call includes a specified
     number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
     on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
     const pageStart = page * entriesPerPage;
 
     if (
+      //If there are api preferences and one of them is OLS, it gets the preferred ontologies
       apiPreferences?.self?.api_preference &&
       'ols' in apiPreferences?.self?.api_preference
     ) {
       const apiPreferenceOntologies = () => {
         if (apiPreferences?.self?.api_preference?.ols) {
-          // Get the ontologies from the 'ols' array and join them with commas
-          const filteredOntologies =
-            apiPreferences.self.api_preference.ols.join(',');
-          console.log(filteredOntologies);
-          // Construct the final URL with the filteredOntologies
-          return filteredOntologies;
+          return apiPreferences.self.api_preference.ols.join(',');
         } else {
-          const defaultOntologies = 'mondo,hp,maxo,ncit';
+          // else if there are no preferred ontologies, it uses the default ontologies
           return defaultOntologies;
         }
       };
-      return fetchFunction(query, apiPreferenceOntologies(), page, pageStart);
-    } else {
-      return fetch(
-        `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
-        {
-          method: 'GET',
-          headers: {
-            'Content-Type': 'application/json',
-          },
-        }
-      )
-        .then(res => res.json())
-        .then(data => {
-          // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
-
-          let res = ontologyReducer(data?.response?.docs);
-          // if the page > 0 (i.e. if this is not the first batch of results), the new results
-          // are concatenated to the old
-          if (selectedBoxes) {
-            res.results = res.results.filter(
-              d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
-            );
-          }
-
-          if (page > 0 && results.length > 0) {
-            res.results = results.concat(res.results);
-
-            // Apply filtering to remove results with obo_id in selectedBoxes
-          } else {
-            // Set the total number of search results for pagination
-            setTotalCount(data.response.numFound);
-          }
-
-          //the results are set to res (the filtered, concatenated results)
-
-          setResults(res.results);
-          setFilteredResultsCount(res?.filteredResults?.length);
-          // resultsCount is set to the length of the filtered, concatenated results for pagination
-          setResultsCount(res.results.length);
-        })
-        .then(() => setLoading(false));
-    }
+      //fetch call to search OLS with either preferred or default ontologies
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        apiPreferenceOntologies(),
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
+    } else
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        defaultOntologies,
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
   };
-
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
   const handleViewMore = e => {
     e.preventDefault();
diff --git a/src/components/Projects/Terminologies/Terminology.scss b/src/components/Projects/Terminologies/Terminology.scss
index b640fcb..09485e7 100644
--- a/src/components/Projects/Terminologies/Terminology.scss
+++ b/src/components/Projects/Terminologies/Terminology.scss
@@ -108,6 +108,7 @@
 
 .modal_search_result {
   display: flex;
+  flex-direction: column;
   align-items: center;
   justify-content: space-between;
   margin: 0 10px 10px 6px;

From 02fa958d6a5cf213c29eb78b23d1bd6bde24d108 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 15 Oct 2024 13:21:42 -0500
Subject: [PATCH 013/180] first pass at editing ontology filters

---
 .../Manager/MappingsFunctions/FilterAPI.jsx   |   2 +
 .../MappingsFunctions/FilterOntology.jsx      | 108 +++++++++++++++---
 .../MappingsFunctions/FilterSelect.jsx        |  40 +++++--
 3 files changed, 123 insertions(+), 27 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index b3a0941..70e5d4a 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -22,6 +22,7 @@ export const FilterAPI = ({
   pageSize,
   setPageSize,
   paginatedOntologies,
+  apiPreferences,
 }) => {
   const { Search } = Input;
 
@@ -126,6 +127,7 @@ export const FilterAPI = ({
                 pageSize={pageSize}
                 setPageSize={setPageSize}
                 paginatedOntologies={paginatedOntologies}
+                apiPreferences={apiPreferences}
               />
             )}
           </div>
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 327f1cd..27cb521 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -12,6 +12,7 @@ export const FilterOntology = ({
   setDisplaySelectedOntologies,
   searchText,
   paginatedOntologies,
+  apiPreferences,
 }) => {
   const [allCheckboxes, setAllCheckboxes] = useState([]);
   const { ontologyForPagination, setOntologyForPagination } =
@@ -110,28 +111,100 @@ export const FilterOntology = ({
       </>
     );
   };
+  const existingDisplay = (ont, i) => {
+    return (
+      <>
+        <div key={i} className="modal_search_result">
+          <div>
+            <div className="modal_term_ontology">
+              <div>{ont.ontology.toUpperCase()}</div>
+            </div>
+          </div>
+        </div>
+      </>
+    );
+  };
+
+  const existingFilters = Object.values(apiPreferences?.self || {}).flat();
+
+  const flattenedFilters = existingFilters
+    .flatMap(item =>
+      Object.keys(item).map(key =>
+        item[key].map(value => ({
+          api: key,
+          ontology: value,
+        }))
+      )
+    )
+    .flat();
+
+  const initialChecked = flattenedFilters?.map(ef =>
+    JSON.stringify({
+      ontology: ef,
+    })
+  );
 
   return (
     <>
       <div className="modal_checkbox_wrapper">
+        {Object.keys(apiPreferences?.self?.api_preference || {}).some(
+          key => apiPreferences?.self?.api_preference[key]?.length > 0
+        ) && (
+          <>
+            <h4>Ontology Filters</h4>
+            <Form.Item
+              initialValue={initialChecked}
+              name={['existing_filters']}
+              valuePropName="value"
+              rules={[
+                {
+                  required: false,
+                },
+              ]}
+            >
+              {flattenedFilters?.length > 0 ? (
+                <Checkbox.Group
+                  className="mappings_checkbox"
+                  options={flattenedFilters?.map((po, index) => {
+                    return {
+                      value: JSON.stringify({
+                        ontology: po,
+                      }),
+                      label: existingDisplay(po, index),
+                    };
+                  })}
+                />
+              ) : (
+                ''
+              )}
+            </Form.Item>
+          </>
+        )}
         {displaySelectedOntologies.length > 0 && (
-          <Form.Item name={'selected_ontologies'} valuePropName="value">
-            <div className="modal_selected">
-              {displaySelectedOntologies?.map((selected, i) => (
-                <Checkbox
-                  key={i}
-                  checked={selectedBoxes.some(
-                    box => box?.ontology_code === selected?.ontology_code
-                  )}
-                  value={selected}
-                  onChange={e => onCheckboxChange(e, selected)}
-                >
-                  {selectedOntDisplay(selected, i)}
-                </Checkbox>
-              ))}
-            </div>
-          </Form.Item>
+          <>
+            <h4>Selected</h4>
+            <Form.Item name={'selected_ontologies'} valuePropName="value">
+              <div className="modal_selected">
+                {displaySelectedOntologies?.map((selected, i) => (
+                  <Checkbox
+                    key={i}
+                    checked={selectedBoxes.some(
+                      box => box?.ontology_code === selected?.ontology_code
+                    )}
+                    value={selected}
+                    onChange={e => onCheckboxChange(e, selected)}
+                  >
+                    {selectedOntDisplay(selected, i)}
+                  </Checkbox>
+                ))}
+              </div>
+            </Form.Item>
+          </>
         )}
+        {(Object.keys(apiPreferences?.self?.api_preference || {}).some(
+          key => apiPreferences?.self?.api_preference[key]?.length > 0
+        ) ||
+          displaySelectedOntologies.length > 0) && <h4>Ontologies</h4>}
         <Form.Item name={'ontologies'} valuePropName="value">
           <Checkbox.Group
             className="mappings_checkbox"
@@ -140,6 +213,9 @@ export const FilterOntology = ({
                 checkbox =>
                   !displaySelectedOntologies.some(
                     dsm => checkbox.ontology_code === dsm.ontology_code
+                  ) &&
+                  !flattenedFilters.some(
+                    ef => checkbox.ontology_code === ef.ontology
                   )
               )
               .map((ont, i) => ({
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index 7063a65..f7364e9 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -63,7 +63,6 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
   // If the api doesn't exist in api_preference, creates an empty array for it
   // If the api_preference array for the api does not include an ontology_code, pushes the code to the array for the api
   // If there is an api in api_preferences that is not included with the ontology_code, it's added to apiPreference with an empty array
-
   const handleSubmit = values => {
     // setLoading(true);
     const apiPreference = {
@@ -71,7 +70,8 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
     };
 
     if (values?.ontologies?.length > 0) {
-      values?.ontologies.forEach(({ ontology_code, api }) => {
+      // If there are ontologies, populate apiPreference with them
+      values.ontologies.forEach(({ ontology_code, api }) => {
         if (!apiPreference.api_preference[api]) {
           apiPreference.api_preference[api] = [];
         }
@@ -80,28 +80,45 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
         }
       });
     } else {
-      values?.selected_apis.forEach(item => {
+      // If no ontologies are provided, initialize api preferences from selected_apis
+      values?.selected_apis?.forEach(item => {
         const apiObj = JSON.parse(item);
         const apiName = apiObj.api_preference;
         apiPreference.api_preference[apiName] = []; // Create an empty array for each api_preference
       });
     }
 
-    values?.selected_apis?.forEach(item => {
-      const apiObj = JSON.parse(item);
-      const apiName = apiObj.api_preference;
-      if (!apiPreference.api_preference[apiName]) {
-        apiPreference.api_preference[apiName] = [];
-      }
-    });
+    // Now handle the existing_filters
+    if (values?.existing_filters?.length > 0) {
+      values.existing_filters.forEach(item => {
+        const apiObj = JSON.parse(item); // Parse the JSON string
+        const apiName = apiObj.ontology.api; // Extract the API
+        const ontologyCode = apiObj.ontology.ontology; // Extract the ontology code
+
+        // Ensure the apiName exists in apiPreference.api_preference
+        if (!apiPreference.api_preference[apiName]) {
+          apiPreference.api_preference[apiName] = []; // Initialize if not already present
+        }
+
+        // Add the ontologyCode to the corresponding api, if it's not already included
+        if (!apiPreference.api_preference[apiName].includes(ontologyCode)) {
+          apiPreference.api_preference[apiName].push(ontologyCode);
+        }
+      });
+    }
 
     const apiPreferenceDTO = {
       api_preference: apiPreference?.api_preference,
       editor: user.email,
     };
 
+    const method =
+      Object.keys(apiPreferences?.self?.api_preference || {}).length === 0
+        ? 'POST'
+        : 'PUT';
+
     fetch(`${vocabUrl}/${table?.terminology?.reference}/filter`, {
-      method: 'POST',
+      method: method,
       headers: {
         'Content-Type': 'application/json',
       },
@@ -259,6 +276,7 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
           pageSize={pageSize}
           setPageSize={setPageSize}
           paginatedOntologies={paginatedOntologies}
+          apiPreferences={apiPreferences}
         />
       </Modal>
     </>

From 77dbfe353282cdfa6a11fad56b50bb506b194b6b Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 15 Oct 2024 14:31:06 -0500
Subject: [PATCH 014/180] Delete preferred ontologies

---
 .../Manager/MappingsFunctions/FilterAPI.jsx   |  2 +
 .../MappingsFunctions/FilterOntology.jsx      |  6 +-
 .../Manager/MappingsFunctions/FilterReset.jsx | 62 +++++++++++++
 .../MappingsFunctions/FilterSelect.jsx        |  1 +
 .../MappingsFunctions/GetMappingsModal.jsx    |  3 +-
 .../MappingsFunctions/MappingReset.jsx        | 88 +++++++++----------
 .../MappingsFunctions/MappingSearch.jsx       | 88 ++++++++++---------
 .../MappingsFunctions/MappingsFunctions.scss  |  7 ++
 8 files changed, 167 insertions(+), 90 deletions(-)
 create mode 100644 src/components/Manager/MappingsFunctions/FilterReset.jsx

diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 70e5d4a..92c3f24 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -23,6 +23,7 @@ export const FilterAPI = ({
   setPageSize,
   paginatedOntologies,
   apiPreferences,
+  table,
 }) => {
   const { Search } = Input;
 
@@ -128,6 +129,7 @@ export const FilterAPI = ({
                 setPageSize={setPageSize}
                 paginatedOntologies={paginatedOntologies}
                 apiPreferences={apiPreferences}
+                table={table}
               />
             )}
           </div>
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 27cb521..9ed6e40 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -1,6 +1,7 @@
 import { Checkbox, Form, Pagination } from 'antd';
 import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
+import { FilterReset } from './FilterReset';
 
 export const FilterOntology = ({
   ontology,
@@ -13,6 +14,7 @@ export const FilterOntology = ({
   searchText,
   paginatedOntologies,
   apiPreferences,
+  table,
 }) => {
   const [allCheckboxes, setAllCheckboxes] = useState([]);
   const { ontologyForPagination, setOntologyForPagination } =
@@ -151,7 +153,9 @@ export const FilterOntology = ({
           key => apiPreferences?.self?.api_preference[key]?.length > 0
         ) && (
           <>
-            <h4>Ontology Filters</h4>
+            <div className="onto_reset">
+              <h4>Ontology Filters</h4> <FilterReset table={table} />
+            </div>
             <Form.Item
               initialValue={initialChecked}
               name={['existing_filters']}
diff --git a/src/components/Manager/MappingsFunctions/FilterReset.jsx b/src/components/Manager/MappingsFunctions/FilterReset.jsx
new file mode 100644
index 0000000..f5349a8
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/FilterReset.jsx
@@ -0,0 +1,62 @@
+import { Button, message, Modal, notification } from 'antd';
+import { ExclamationCircleFilled } from '@ant-design/icons';
+import { useContext, useState } from 'react';
+import { myContext } from '../../../App';
+import { SearchContext } from '../../../Contexts/SearchContext';
+
+export const FilterReset = ({ table }) => {
+  const { confirm } = Modal;
+
+  const { user, vocabUrl } = useContext(myContext);
+  const { setApiPreferences } = useContext(SearchContext);
+  const [remove, setRemove] = useState(false);
+
+  const deleteOntologies = evt => {
+    return fetch(`${vocabUrl}/${table?.terminology?.reference}/filter`, {
+      method: 'DELETE',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify({ editor: user.email }),
+    })
+      .then(res => {
+        if (res.ok) {
+          return res.json().then(data => {
+            message.success('Ontology filters deleted successfully.');
+          });
+        } else {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred deleting the table.',
+          });
+        }
+      })
+      .then(data => setApiPreferences(data));
+  };
+
+  const showConfirm = () => {
+    confirm({
+      className: 'delete_table_confirm',
+      title: 'Alert',
+      icon: <ExclamationCircleFilled />,
+      content:
+        '          Are you sure you want to remove the ontology filters?',
+      onOk() {
+        deleteOntologies();
+        setRemove(false);
+      },
+      onCancel() {
+        setRemove(false);
+      },
+    });
+  };
+
+  return (
+    <>
+      <Button danger onClick={() => (user ? setRemove(true) : login())}>
+        Reset{' '}
+      </Button>
+      {remove && showConfirm()}
+    </>
+  );
+};
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index f7364e9..ace5cc0 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -277,6 +277,7 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
           setPageSize={setPageSize}
           paginatedOntologies={paginatedOntologies}
           apiPreferences={apiPreferences}
+          table={table}
         />
       </Modal>
     </>
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index e54b6f5..05087a3 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -1,12 +1,11 @@
 import { Checkbox, Input, message, Modal, Form, Tooltip } from 'antd';
 import { useContext, useEffect, useRef, useState } from 'react';
 import { myContext } from '../../../App';
-import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
+import { ellipsisString, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { olsFilterOntologiesSearch } from '../FetchManager';
-import { defaultIconPrefixCls } from 'antd/es/config-provider';
 
 export const GetMappingsModal = ({
   componentString,
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index dc9c75b..68901e7 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -4,6 +4,8 @@ import { myContext } from '../../../App';
 import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
+import { olsFilterOntologiesSearch } from '../FetchManager';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const MappingReset = ({
   searchProp,
@@ -12,6 +14,7 @@ export const MappingReset = ({
   onClose,
 }) => {
   const { searchUrl } = useContext(myContext);
+  const { apiPreferences } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -103,52 +106,49 @@ export const MappingReset = ({
     number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
     on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
     const pageStart = page * entriesPerPage;
-    return fetch(
-      `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
-      {
-        method: 'GET',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-      }
-    )
-      .then(res => res.json())
-      .then(data => {
-        // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
-        let res = ontologyReducer(data?.response?.docs);
-
-        // Filters out results that have already been selected in previous search if there is a change to the search term
-        if (selectedBoxes) {
-          res.results = res.results.filter(
-            d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
-          );
-        }
-
-        // if the page > 0 (i.e. if this is not the first batch of results), the new results
-        // are concatenated to the old
-        if (page > 0 && results.length > 0) {
-          res.results = results.concat(res.results);
+    if (
+      //If there are api preferences and one of them is OLS, it gets the preferred ontologies
+      apiPreferences?.self?.api_preference &&
+      'ols' in apiPreferences?.self?.api_preference
+    ) {
+      const apiPreferenceOntologies = () => {
+        if (apiPreferences?.self?.api_preference?.ols) {
+          return apiPreferences.self.api_preference.ols.join(',');
         } else {
-          // the total number of search results are set to totalCount for pagination
-          setTotalCount(data.response.numFound);
-        }
-        //the results are set to res (the filtered, concatenated results)
-        setResults(res.results);
-        setFilteredResultsCount(res?.filteredResults?.length);
-
-        // resultsCount is set to the length of the filtered, concatenated results for pagination
-        setResultsCount(res.results.length);
-      })
-      .catch(error => {
-        if (error) {
-          notification.error({
-            message: 'Error',
-            description: 'An error occurred. Please try again.',
-          });
+          // else if there are no preferred ontologies, it uses the default ontologies
+          return defaultOntologies;
         }
-        return error;
-      })
-      .finally(() => setLoading(false));
+      };
+      //fetch call to search OLS with either preferred or default ontologies
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        apiPreferenceOntologies(),
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
+    } else
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        defaultOntologies,
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
   };
 
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 80585e8..332083c 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -4,6 +4,8 @@ import { myContext } from '../../../App';
 import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
+import { SearchContext } from '../../../Contexts/SearchContext';
+import { olsFilterOntologiesSearch } from '../FetchManager';
 
 export const MappingSearch = ({
   setEditMappings,
@@ -13,6 +15,8 @@ export const MappingSearch = ({
   searchProp,
 }) => {
   const { searchUrl } = useContext(myContext);
+  const { apiPreferences } = useContext(SearchContext);
+
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -105,51 +109,49 @@ export const MappingSearch = ({
     number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
     on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
     const pageStart = page * entriesPerPage;
-    return fetch(
-      `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
-      {
-        method: 'GET',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-      }
-    )
-      .then(res => res.json())
-      .then(data => {
-        // filters results through the ontologyReducer function (defined in Manager/Utility.jsx)
-        let res = ontologyReducer(data?.response?.docs);
-
-        // Filters out results that have already been selected in previous search if there is a change to the search term
-        if (selectedBoxes) {
-          res.results = res.results.filter(
-            d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
-          );
-        }
-        // if the page > 0 (i.e. if this is not the first batch of results), the new results
-        // are concatenated to the old
-        if (page > 0 && results.length > 0) {
-          res.results = results.concat(res.results);
+    if (
+      //If there are api preferences and one of them is OLS, it gets the preferred ontologies
+      apiPreferences?.self?.api_preference &&
+      'ols' in apiPreferences?.self?.api_preference
+    ) {
+      const apiPreferenceOntologies = () => {
+        if (apiPreferences?.self?.api_preference?.ols) {
+          return apiPreferences.self.api_preference.ols.join(',');
         } else {
-          // the total number of search results are set to totalCount for pagination
-          setTotalCount(data.response.numFound);
-        }
-        //the results are set to res (the filtered, concatenated results)
-        setResults(res.results);
-        setFilteredResultsCount(res?.filteredResults?.length);
-
-        // resultsCount is set to the length of the filtered, concatenated results for pagination
-        setResultsCount(res.results.length);
-      })
-      .catch(error => {
-        if (error) {
-          notification.error({
-            message: 'Error',
-            description: 'An error occurred. Please try again.',
-          });
+          // else if there are no preferred ontologies, it uses the default ontologies
+          return defaultOntologies;
         }
-        return error;
-      })
-      .finally(() => setLoading(false));
+      };
+      //fetch call to search OLS with either preferred or default ontologies
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        apiPreferenceOntologies(),
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
+    } else
+      return olsFilterOntologiesSearch(
+        searchUrl,
+        query,
+        defaultOntologies,
+        page,
+        entriesPerPage,
+        pageStart,
+        selectedBoxes,
+        setTotalCount,
+        setResults,
+        setFilteredResultsCount,
+        setResultsCount,
+        setLoading
+      );
   };
 
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index fa074f2..a4a8d45 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -78,3 +78,10 @@
   width: 50vw;
   justify-content: center;
 }
+
+.onto_reset {
+  display: flex;
+  flex-direction: row;
+  align-items: center;
+  gap: 8px;
+}

From 9b128e52ef9df8b0bd869241faba53ba7c29cf66 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 15 Oct 2024 16:06:35 -0500
Subject: [PATCH 015/180] committing to switch branches

---
 src/components/Manager/MappingsFunctions/FilterReset.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterReset.jsx b/src/components/Manager/MappingsFunctions/FilterReset.jsx
index f5349a8..ac37e40 100644
--- a/src/components/Manager/MappingsFunctions/FilterReset.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterReset.jsx
@@ -54,7 +54,7 @@ export const FilterReset = ({ table }) => {
   return (
     <>
       <Button danger onClick={() => (user ? setRemove(true) : login())}>
-        Reset{' '}
+        Reset
       </Button>
       {remove && showConfirm()}
     </>

From 79255a5ce0c3e598be273183eccb11d9d9a96d47 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 16 Oct 2024 11:23:45 -0500
Subject: [PATCH 016/180] Newly added ontologies checking by default on load

---
 .../Manager/MappingsFunctions/FilterAPI.jsx   |   2 +-
 .../MappingsFunctions/FilterSelect.jsx        | 128 +++++++++---------
 2 files changed, 66 insertions(+), 64 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 92c3f24..1a63182 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -91,7 +91,7 @@ export const FilterAPI = ({
   ) : (
     <div>
       <div className="api_list">
-        <Form form={form}>
+        <Form form={form} preserve={false}>
           <div>
             <div className="api_label">APIs</div>
 
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index ace5cc0..c194961 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -214,72 +214,74 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
       >
         API Filters {apiPrefObject ? `(${apiPrefLength})` : ''}
       </Button>
-      <Modal
-        open={addFilter}
-        width={'70%'}
-        styles={{
-          body: {
-            minHeight: '60vh',
-            maxHeight: '60vh',
-          },
-        }}
-        onOk={() => {
-          form.validateFields().then(values => {
-            handleSubmit(values);
+      {addFilter && (
+        <Modal
+          open={addFilter}
+          width={'70%'}
+          styles={{
+            body: {
+              minHeight: '60vh',
+              maxHeight: '60vh',
+            },
+          }}
+          onOk={() => {
+            form.validateFields().then(values => {
+              handleSubmit(values);
+              onClose();
+            });
+          }}
+          onCancel={() => {
+            form.resetFields();
+            setAddFilter(false);
             onClose();
-          });
-        }}
-        onCancel={() => {
-          form.resetFields();
-          setAddFilter(false);
-          onClose();
-        }}
-        maskClosable={false}
-        closeIcon={false}
-        footer={(_, { OkBtn, CancelBtn }) => (
-          <>
-            <div className="modal_footer">
+          }}
+          maskClosable={false}
+          closeIcon={false}
+          footer={(_, { OkBtn, CancelBtn }) => (
+            <>
               <div className="modal_footer">
-                <Pagination
-                  current={currentPage}
-                  pageSize={pageSize}
-                  total={filteredOntologiesArray?.length}
-                  onChange={handlePageChange}
-                  showSizeChanger
-                  onShowSizeChange={handlePageSizeChange}
-                  pageSizeOptions={['10', '20', '50']} // Set page size options
-                />
-              </div>
-              <div className="cancel_ok_buttons">
-                <CancelBtn />
-                <OkBtn />
+                <div className="modal_footer">
+                  <Pagination
+                    current={currentPage}
+                    pageSize={pageSize}
+                    total={filteredOntologiesArray?.length}
+                    onChange={handlePageChange}
+                    showSizeChanger
+                    onShowSizeChange={handlePageSizeChange}
+                    pageSizeOptions={['10', '20', '50']} // Set page size options
+                  />
+                </div>
+                <div className="cancel_ok_buttons">
+                  <CancelBtn />
+                  <OkBtn />
+                </div>
               </div>
-            </div>
-          </>
-        )}
-      >
-        <FilterAPI
-          form={form}
-          selectedOntologies={selectedOntologies}
-          setSelectedOntologies={setSelectedOntologies}
-          selectedBoxes={selectedBoxes}
-          setSelectedBoxes={setSelectedBoxes}
-          displaySelectedOntologies={displaySelectedOntologies}
-          setDisplaySelectedOntologies={setDisplaySelectedOntologies}
-          ontologyApis={ontologyApis}
-          active={active}
-          setActive={setActive}
-          searchText={searchText}
-          setSearchText={setSearchText}
-          currentPage={currentPage}
-          setCurrentPage={setCurrentPage}
-          pageSize={pageSize}
-          setPageSize={setPageSize}
-          paginatedOntologies={paginatedOntologies}
-          apiPreferences={apiPreferences}
-          table={table}
-        />
-      </Modal>
+            </>
+          )}
+        >
+          <FilterAPI
+            form={form}
+            selectedOntologies={selectedOntologies}
+            setSelectedOntologies={setSelectedOntologies}
+            selectedBoxes={selectedBoxes}
+            setSelectedBoxes={setSelectedBoxes}
+            displaySelectedOntologies={displaySelectedOntologies}
+            setDisplaySelectedOntologies={setDisplaySelectedOntologies}
+            ontologyApis={ontologyApis}
+            active={active}
+            setActive={setActive}
+            searchText={searchText}
+            setSearchText={setSearchText}
+            currentPage={currentPage}
+            setCurrentPage={setCurrentPage}
+            pageSize={pageSize}
+            setPageSize={setPageSize}
+            paginatedOntologies={paginatedOntologies}
+            apiPreferences={apiPreferences}
+            table={table}
+          />
+        </Modal>
+      )}
     </>
   );
 };

From bd0e506efd69b5b60dc4e72ad759dd54af5b82a4 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 16 Oct 2024 15:56:56 -0500
Subject: [PATCH 017/180] ontology filter for mappings search

---
 src/Contexts/SearchContext.jsx                |  2 +
 src/components/Manager/FetchManager.jsx       |  3 +-
 .../Manager/MappingsFunctions/FilterAPI.jsx   | 42 +++++++++++++---
 .../MappingsFunctions/FilterSelect.jsx        | 49 ++++++++++---------
 .../MappingsFunctions/GetMappingsModal.jsx    | 12 +++--
 .../MappingsFunctions/MappingReset.jsx        |  8 +--
 .../MappingsFunctions/MappingSearch.jsx       |  8 +--
 src/components/Nav/NavBar.jsx                 |  4 +-
 .../Projects/Tables/TableDetails.jsx          | 13 +++++
 9 files changed, 100 insertions(+), 41 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index e90d907..a8d1d27 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -13,6 +13,7 @@ export function SearchContextRoot() {
   const [apiPage, setApiPage] = useState(0);
   const [apiTotalCount, setApiTotalCount] = useState();
   const [apiPreferences, setApiPreferences] = useState({});
+  const defaultOntologies = 'mondo,hp,maxo,ncit';
 
   const context = {
     prefTerminologies,
@@ -33,6 +34,7 @@ export function SearchContextRoot() {
     setApiTotalCount,
     apiPreferences,
     setApiPreferences,
+    defaultOntologies,
   };
 
   return (
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index fc5f4a6..6b436c9 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -180,7 +180,8 @@ export const olsFilterOntologiesSearch = (
   setResults,
   setFilteredResultsCount,
   setResultsCount,
-  setLoading
+  setLoading,
+  results
 ) => {
   setLoading(true);
   return fetch(
diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 1a63182..946f435 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -1,5 +1,5 @@
 import { useContext, useEffect, useState } from 'react';
-import { Checkbox, Form, Input } from 'antd';
+import { Checkbox, Form } from 'antd';
 import { ModalSpinner, OntologySpinner } from '../Spinner';
 import { myContext } from '../../../App';
 import { FilterOntology } from './FilterOntology';
@@ -16,7 +16,6 @@ export const FilterAPI = ({
   active,
   setActive,
   searchText,
-  setSearchText,
   currentPage,
   setCurrentPage,
   pageSize,
@@ -25,13 +24,32 @@ export const FilterAPI = ({
   apiPreferences,
   table,
 }) => {
-  const { Search } = Input;
-
   const { vocabUrl } = useContext(myContext);
   const [ontology, setOntology] = useState([]);
   const [loading, setLoading] = useState(false);
   const [tableLoading, setTableLoading] = useState(false);
 
+  // The selected ontology filters that have already been selected
+  const existingFilters = Object.values(apiPreferences?.self || {}).flat();
+
+  // Flattens the existingFilters into a single array
+  const flattenedFilters = existingFilters
+    .flatMap(item =>
+      Object.keys(item).map(key =>
+        item[key].map(value => ({
+          api: key,
+        }))
+      )
+    )
+    .flat();
+
+  // The initial value for the form. The checkboxes for the filters that have already been selected will be checked by default
+  const initialChecked = flattenedFilters?.map(ef =>
+    JSON.stringify({
+      ontology: ef,
+    })
+  );
+
   // Fetches the active ontologyAPI each time the active API changes
   useEffect(() => {
     active && getOntologyApiById();
@@ -56,7 +74,20 @@ export const FilterAPI = ({
           }
         })
         .then(data => {
-          setOntology(data);
+          //Alphabetizes the data
+          const sortedData = data.map(api => {
+            const sortedOntologies = Object.fromEntries(
+              Object.entries(api.ontologies).sort((a, b) =>
+                a[1].ontology_code > b[1].ontology_code ? 1 : -1
+              )
+            );
+
+            return {
+              ...api,
+              ontologies: sortedOntologies,
+            };
+          });
+          setOntology(sortedData);
         })
         .finally(() => setTableLoading(false))
     );
@@ -85,7 +116,6 @@ export const FilterAPI = ({
       </>
     );
   };
-
   return loading ? (
     <ModalSpinner />
   ) : (
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index c194961..538f380 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -4,6 +4,7 @@ import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
 import { FilterAPI } from './FilterAPI';
 import { getOntologies } from '../FetchManager';
+import { ModalSpinner } from '../Spinner';
 
 export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
   const [form] = Form.useForm();
@@ -64,7 +65,7 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
   // If the api_preference array for the api does not include an ontology_code, pushes the code to the array for the api
   // If there is an api in api_preferences that is not included with the ontology_code, it's added to apiPreference with an empty array
   const handleSubmit = values => {
-    // setLoading(true);
+    setLoading(true);
     const apiPreference = {
       api_preference: {},
     };
@@ -259,27 +260,31 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
             </>
           )}
         >
-          <FilterAPI
-            form={form}
-            selectedOntologies={selectedOntologies}
-            setSelectedOntologies={setSelectedOntologies}
-            selectedBoxes={selectedBoxes}
-            setSelectedBoxes={setSelectedBoxes}
-            displaySelectedOntologies={displaySelectedOntologies}
-            setDisplaySelectedOntologies={setDisplaySelectedOntologies}
-            ontologyApis={ontologyApis}
-            active={active}
-            setActive={setActive}
-            searchText={searchText}
-            setSearchText={setSearchText}
-            currentPage={currentPage}
-            setCurrentPage={setCurrentPage}
-            pageSize={pageSize}
-            setPageSize={setPageSize}
-            paginatedOntologies={paginatedOntologies}
-            apiPreferences={apiPreferences}
-            table={table}
-          />
+          {loading ? (
+            <ModalSpinner />
+          ) : (
+            <FilterAPI
+              form={form}
+              selectedOntologies={selectedOntologies}
+              setSelectedOntologies={setSelectedOntologies}
+              selectedBoxes={selectedBoxes}
+              setSelectedBoxes={setSelectedBoxes}
+              displaySelectedOntologies={displaySelectedOntologies}
+              setDisplaySelectedOntologies={setDisplaySelectedOntologies}
+              ontologyApis={ontologyApis}
+              active={active}
+              setActive={setActive}
+              searchText={searchText}
+              setSearchText={setSearchText}
+              currentPage={currentPage}
+              setCurrentPage={setCurrentPage}
+              pageSize={pageSize}
+              setPageSize={setPageSize}
+              paginatedOntologies={paginatedOntologies}
+              apiPreferences={apiPreferences}
+              table={table}
+            />
+          )}
         </Modal>
       )}
     </>
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 05087a3..d079feb 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -19,7 +19,7 @@ export const GetMappingsModal = ({
   const { Search } = Input;
 
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
-  const { apiPreferences } = useContext(SearchContext);
+  const { apiPreferences, defaultOntologies } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(false);
@@ -40,7 +40,6 @@ export const GetMappingsModal = ({
     setSelectedBoxes,
   } = useContext(MappingContext);
   let ref = useRef();
-  const defaultOntologies = 'mondo,hp,maxo,ncit';
 
   // since the code is passed through searchProp, the '!!' forces it to be evaluated as a boolean.
   // if there is a searchProp being passed, it evaluates to true and runs the search function.
@@ -186,7 +185,8 @@ export const GetMappingsModal = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
     } else
       return olsFilterOntologiesSearch(
@@ -201,7 +201,8 @@ export const GetMappingsModal = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
   };
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
@@ -423,6 +424,9 @@ export const GetMappingsModal = ({
                           Displaying {resultsCount}
                           &nbsp;of&nbsp;{totalCount}
                         </Tooltip>
+                        {console.log('total', totalCount)}
+                        {console.log('filtered', filteredResultsCount)}
+                        {console.log('results', filteredResultsCount)}
                         {totalCount - filteredResultsCount !== resultsCount && (
                           <span
                             className="view_more_link"
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 68901e7..a026c91 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -14,7 +14,7 @@ export const MappingReset = ({
   onClose,
 }) => {
   const { searchUrl } = useContext(myContext);
-  const { apiPreferences } = useContext(SearchContext);
+  const { apiPreferences, defaultOntologies } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -132,7 +132,8 @@ export const MappingReset = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
     } else
       return olsFilterOntologiesSearch(
@@ -147,7 +148,8 @@ export const MappingReset = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
   };
 
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 332083c..14724f1 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -15,7 +15,7 @@ export const MappingSearch = ({
   searchProp,
 }) => {
   const { searchUrl } = useContext(myContext);
-  const { apiPreferences } = useContext(SearchContext);
+  const { apiPreferences, defaultOntologies } = useContext(SearchContext);
 
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
@@ -135,7 +135,8 @@ export const MappingSearch = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
     } else
       return olsFilterOntologiesSearch(
@@ -150,7 +151,8 @@ export const MappingSearch = ({
         setResults,
         setFilteredResultsCount,
         setResultsCount,
-        setLoading
+        setLoading,
+        results
       );
   };
 
diff --git a/src/components/Nav/NavBar.jsx b/src/components/Nav/NavBar.jsx
index 13a0c11..80e39ff 100644
--- a/src/components/Nav/NavBar.jsx
+++ b/src/components/Nav/NavBar.jsx
@@ -27,11 +27,11 @@ export const NavBar = () => {
             </NavLink>
             {/* Placeholder elements below. No functionality at this time.*/}
             <NavLink to="/help">
-              <li className="nav_link">Help</li>
+              <li className="nav_link">About</li>
             </NavLink>
 
             <NavLink to="/about">
-              <li className="nav_link">About</li>
+              <li className="nav_link">Ontologies</li>
             </NavLink>
           </div>
           <div className="login">
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 9bd6e05..863cb79 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -51,6 +51,19 @@ export const TableDetails = () => {
     setDataSource(tableData(table));
   }, [table, mapping]);
 
+  const alphabetizeOntologies = ontologies => {
+    // Sort the keys alphabetically
+    const sortedKeys = Object.keys(ontologies).sort();
+
+    // Rebuild object using the sorted keys
+    const sortedOntologies = {};
+    sortedKeys.forEach(key => {
+      sortedOntologies[key] = ontologies[key];
+    });
+
+    return sortedOntologies;
+  };
+
   // fetches the table and sets 'table' to the response
   useEffect(() => {
     setLoading(true);

From 48cefbb7c40409e60bc45d44321e477850c1322d Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 16 Oct 2024 15:57:35 -0500
Subject: [PATCH 018/180] Removed unnecesary console logs

---
 src/components/Manager/MappingsFunctions/GetMappingsModal.jsx | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index d079feb..1451c01 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -424,9 +424,6 @@ export const GetMappingsModal = ({
                           Displaying {resultsCount}
                           &nbsp;of&nbsp;{totalCount}
                         </Tooltip>
-                        {console.log('total', totalCount)}
-                        {console.log('filtered', filteredResultsCount)}
-                        {console.log('results', filteredResultsCount)}
                         {totalCount - filteredResultsCount !== resultsCount && (
                           <span
                             className="view_more_link"

From 895a02c404686c888edbe2f5548a567b4594dad2 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 16 Oct 2024 16:01:49 -0500
Subject: [PATCH 019/180] Rebased branch

---
 .env | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 .env

diff --git a/.env b/.env
new file mode 100644
index 0000000..7471b56
--- /dev/null
+++ b/.env
@@ -0,0 +1,7 @@
+VITE_SEARCH_ENDPOINT = https://www.ebi.ac.uk/ols4/api/search?
+VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
+# VITE_VOCAB_ENDPOINT = http://127.0.0.1:5000/api # local
+VITE_VOCAB_ENDPOINT = https://locutus-110109177269.us-central1.run.app/api # dev
+# VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
+VITE_CLIENT_ID = 907694787484-36jr4oaf04mmniik6482batc87ejemm8.apps.googleusercontent.com
+VITE_CLIENT_SECRET = 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
\ No newline at end of file

From a902065d49c63188b8e750febd24d679efca760f Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 17 Oct 2024 09:50:59 -0500
Subject: [PATCH 020/180] Updated .gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index dd5161b..13a3147 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,3 +27,4 @@ dist-ssr
 .env.local
 .env.qa
 .env.dev
+.env

From 3e80ca641762259d8255e3e0a220d3f5680c8558 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 17 Oct 2024 10:26:52 -0500
Subject: [PATCH 021/180] cleaned up .env

---
 .env | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.env b/.env
index 7471b56..774b5d7 100644
--- a/.env
+++ b/.env
@@ -3,5 +3,4 @@ VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
 # VITE_VOCAB_ENDPOINT = http://127.0.0.1:5000/api # local
 VITE_VOCAB_ENDPOINT = https://locutus-110109177269.us-central1.run.app/api # dev
 # VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
-VITE_CLIENT_ID = 907694787484-36jr4oaf04mmniik6482batc87ejemm8.apps.googleusercontent.com
-VITE_CLIENT_SECRET = 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
\ No newline at end of file
+VITE_CLIENT_ID = 907694787484-36jr4oaf04mmniik6482batc87ejemm8.apps.googleusercontent.com
\ No newline at end of file

From 91bf1c52df2c4a9ac7444f4eac087ce1037fe742 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 17 Oct 2024 13:26:04 -0500
Subject: [PATCH 022/180] Committing to switch branch

---
 src/Contexts/SearchContext.jsx                |   3 +
 src/components/Manager/FetchManager.jsx       |   4 +-
 .../MappingsFunctions/GetMappingsModal.jsx    | 129 ++++++++++--------
 .../MappingsFunctions/MappingReset.jsx        |   9 +-
 .../MappingsFunctions/MappingSearch.jsx       |   9 +-
 .../MappingsFunctions/MappingsFunctions.scss  |  23 +++-
 src/components/Manager/Utilitiy.jsx           |  20 +++
 7 files changed, 131 insertions(+), 66 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index a8d1d27..dc0724c 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -13,6 +13,7 @@ export function SearchContextRoot() {
   const [apiPage, setApiPage] = useState(0);
   const [apiTotalCount, setApiTotalCount] = useState();
   const [apiPreferences, setApiPreferences] = useState({});
+  const [facetCounts, setFacetCounts] = useState([]);
   const defaultOntologies = 'mondo,hp,maxo,ncit';
 
   const context = {
@@ -35,6 +36,8 @@ export function SearchContextRoot() {
     apiPreferences,
     setApiPreferences,
     defaultOntologies,
+    facetCounts,
+    setFacetCounts,
   };
 
   return (
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 6b436c9..ac6f712 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -181,7 +181,8 @@ export const olsFilterOntologiesSearch = (
   setFilteredResultsCount,
   setResultsCount,
   setLoading,
-  results
+  results,
+  setFacetCounts
 ) => {
   setLoading(true);
   return fetch(
@@ -221,6 +222,7 @@ export const olsFilterOntologiesSearch = (
       setFilteredResultsCount(res?.filteredResults?.length);
       // resultsCount is set to the length of the filtered, concatenated results for pagination
       setResultsCount(res.results.length);
+      setFacetCounts(data?.facet_counts?.facet_fields?.ontologyPreferredPrefix);
     })
     .then(() => setLoading(false));
 };
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 1451c01..9856587 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -1,7 +1,7 @@
 import { Checkbox, Input, message, Modal, Form, Tooltip } from 'antd';
 import { useContext, useEffect, useRef, useState } from 'react';
 import { myContext } from '../../../App';
-import { ellipsisString, systemsMatch } from '../Utilitiy';
+import { ellipsisString, ontologyCounts, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
@@ -19,7 +19,8 @@ export const GetMappingsModal = ({
   const { Search } = Input;
 
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
-  const { apiPreferences, defaultOntologies } = useContext(SearchContext);
+  const { apiPreferences, defaultOntologies, setFacetCounts, facetCounts } =
+    useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(false);
@@ -186,7 +187,8 @@ export const GetMappingsModal = ({
         setFilteredResultsCount,
         setResultsCount,
         setLoading,
-        results
+        results,
+        setFacetCounts
       );
     } else
       return olsFilterOntologiesSearch(
@@ -202,9 +204,13 @@ export const GetMappingsModal = ({
         setFilteredResultsCount,
         setResultsCount,
         setLoading,
-        results
+        results,
+        setFacetCounts
       );
   };
+
+  console.log('formattedData:', ontologyCounts(facetCounts));
+
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
   const handleViewMore = e => {
     e.preventDefault();
@@ -320,7 +326,7 @@ export const GetMappingsModal = ({
       <Modal
         open={!!searchProp}
         closeIcon={false}
-        width={'60%'}
+        width={'70%'}
         styles={{ body: { height: '60vh', overflowY: 'auto' } }}
         okText="Save"
         onOk={() => {
@@ -358,61 +364,68 @@ export const GetMappingsModal = ({
                   {results?.length > 0 ? (
                     <div className="result_container">
                       <Form form={form} layout="vertical">
-                        {displaySelectedMappings?.length > 0 && (
-                          <Form.Item
-                            name="selected_mappings"
-                            valuePropName="value"
-                            rules={[{ required: false }]}
-                          >
-                            <div className="modal_display_results">
-                              {displaySelectedMappings?.map((sm, i) => (
-                                <Checkbox
-                                  key={i}
-                                  checked={selectedBoxes.some(
-                                    box => box.obo_id === sm.obo_id
+                        <div className="all_checkboxes_container">
+                          <div className="ontology_form">poop</div>
+                          <div className="result_form">
+                            {displaySelectedMappings?.length > 0 && (
+                              <Form.Item
+                                name="selected_mappings"
+                                valuePropName="value"
+                                rules={[{ required: false }]}
+                              >
+                                <div className="modal_display_results">
+                                  {displaySelectedMappings?.map((sm, i) => (
+                                    <Checkbox
+                                      key={i}
+                                      checked={selectedBoxes.some(
+                                        box => box.obo_id === sm.obo_id
+                                      )}
+                                      value={sm}
+                                      onChange={e => onCheckboxChange(e, sm, i)}
+                                    >
+                                      {selectedTermsDisplay(sm, i)}
+                                    </Checkbox>
+                                  ))}
+                                </div>
+                              </Form.Item>
+                            )}
+                            <Form.Item
+                              name={['filtered_mappings']}
+                              valuePropName="value"
+                              rules={[
+                                {
+                                  required: false,
+                                },
+                              ]}
+                            >
+                              {filteredResultsArray?.length > 0 ? (
+                                <Checkbox.Group
+                                  className="mappings_checkbox"
+                                  options={filteredResultsArray?.map(
+                                    (d, index) => {
+                                      return {
+                                        value: JSON.stringify({
+                                          code: d.obo_id,
+                                          display: d.label,
+                                          description: d.description[0],
+                                          system: systemsMatch(
+                                            d?.obo_id.split(':')[0]
+                                          ),
+                                        }),
+                                        label: checkBoxDisplay(d, index),
+                                      };
+                                    }
                                   )}
-                                  value={sm}
-                                  onChange={e => onCheckboxChange(e, sm, i)}
-                                >
-                                  {selectedTermsDisplay(sm, i)}
-                                </Checkbox>
-                              ))}
-                            </div>
-                          </Form.Item>
-                        )}
-                        <Form.Item
-                          name={['filtered_mappings']}
-                          valuePropName="value"
-                          rules={[
-                            {
-                              required: false,
-                            },
-                          ]}
-                        >
-                          {filteredResultsArray?.length > 0 ? (
-                            <Checkbox.Group
-                              className="mappings_checkbox"
-                              options={filteredResultsArray?.map((d, index) => {
-                                return {
-                                  value: JSON.stringify({
-                                    code: d.obo_id,
-                                    display: d.label,
-                                    description: d.description[0],
-                                    system: systemsMatch(
-                                      d?.obo_id.split(':')[0]
-                                    ),
-                                  }),
-                                  label: checkBoxDisplay(d, index),
-                                };
-                              })}
-                              onChange={onSelectedChange}
-                            />
-                          ) : (
-                            ''
-                          )}
-                        </Form.Item>
+                                  onChange={onSelectedChange}
+                                />
+                              ) : (
+                                ''
+                              )}
+                            </Form.Item>
+                          </div>
+                        </div>
                       </Form>
-                      <div>
+                      <div className="view_more_link">
                         {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index a026c91..2da7ae0 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -14,7 +14,8 @@ export const MappingReset = ({
   onClose,
 }) => {
   const { searchUrl } = useContext(myContext);
-  const { apiPreferences, defaultOntologies } = useContext(SearchContext);
+  const { apiPreferences, defaultOntologies, facetCounts, setFacetCounts } =
+    useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -133,7 +134,8 @@ export const MappingReset = ({
         setFilteredResultsCount,
         setResultsCount,
         setLoading,
-        results
+        results,
+        setFacetCounts
       );
     } else
       return olsFilterOntologiesSearch(
@@ -149,7 +151,8 @@ export const MappingReset = ({
         setFilteredResultsCount,
         setResultsCount,
         setLoading,
-        results
+        results,
+        setFacetCounts
       );
   };
 
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 14724f1..a98cd90 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -15,7 +15,8 @@ export const MappingSearch = ({
   searchProp,
 }) => {
   const { searchUrl } = useContext(myContext);
-  const { apiPreferences, defaultOntologies } = useContext(SearchContext);
+  const { apiPreferences, defaultOntologies, facetCounts, setFacetCounts } =
+    useContext(SearchContext);
 
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
@@ -136,7 +137,8 @@ export const MappingSearch = ({
         setFilteredResultsCount,
         setResultsCount,
         setLoading,
-        results
+        results,
+        setFacetCounts
       );
     } else
       return olsFilterOntologiesSearch(
@@ -152,7 +154,8 @@ export const MappingSearch = ({
         setFilteredResultsCount,
         setResultsCount,
         setLoading,
-        results
+        results,
+        setFacetCounts
       );
   };
 
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index db00c2f..c6d781c 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -5,9 +5,23 @@
   top: 25vh;
 }
 
+.all_checkboxes_container {
+  display: flex;
+  flex-direction: row;
+}
+.ontology_form {
+  width: 10vw;
+  height: 50vh;
+  overflow: auto;
+  position: fixed;
+}
+.result_form {
+  margin-left: 10vw;
+}
+
 .modal_search_results_header {
   background-color: white;
-  top:0;
+  top: 0;
   position: sticky;
   margin: 0 0 15px 0;
   display: flex;
@@ -89,3 +103,10 @@
   align-items: center;
   gap: 8px;
 }
+
+.view_more_link {
+  display: flex;
+  flex-direction: column;
+  margin-left: 10vw;
+  gap: 10px;
+}
diff --git a/src/components/Manager/Utilitiy.jsx b/src/components/Manager/Utilitiy.jsx
index 4052b6d..1515f19 100644
--- a/src/components/Manager/Utilitiy.jsx
+++ b/src/components/Manager/Utilitiy.jsx
@@ -40,3 +40,23 @@ export const ontologySystems = {
 export const systemsMatch = ont => {
   return ontologySystems[ont];
 };
+
+// Iterates over the facet counts in the result to make an object of search results per ontology
+export const ontologyCounts = arr => {
+  let result = [];
+  let i = 0;
+
+  while (i < arr.length) {
+    if (isNaN(arr[i])) {
+      // If element in array, it not a number (i.e. it's a string), it sets it as the key
+      const key = arr[i];
+      const value = arr[i + 1]; // Gets the first number after the string
+      result.push({ [key]: value }); // Pushes the key (string) and value (number) pair to the result array
+      i += 2; // Moves to the next letter-number pair
+    } else {
+      i += 1; // If the element is a number, it keeps going until it starts over and finds a string
+    }
+  }
+
+  return result;
+};

From b71723ee03d1809b0a9a077fc9239bad8fe487e3 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 17 Oct 2024 13:35:46 -0500
Subject: [PATCH 023/180] Ran git rm -r --cached .

---
 .env       | 7 -------
 .gitignore | 1 +
 2 files changed, 1 insertion(+), 7 deletions(-)
 delete mode 100644 .env

diff --git a/.env b/.env
deleted file mode 100644
index 7471b56..0000000
--- a/.env
+++ /dev/null
@@ -1,7 +0,0 @@
-VITE_SEARCH_ENDPOINT = https://www.ebi.ac.uk/ols4/api/search?
-VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
-# VITE_VOCAB_ENDPOINT = http://127.0.0.1:5000/api # local
-VITE_VOCAB_ENDPOINT = https://locutus-110109177269.us-central1.run.app/api # dev
-# VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
-VITE_CLIENT_ID = 907694787484-36jr4oaf04mmniik6482batc87ejemm8.apps.googleusercontent.com
-VITE_CLIENT_SECRET = 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
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index dd5161b..13a3147 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,3 +27,4 @@ dist-ssr
 .env.local
 .env.qa
 .env.dev
+.env

From 3771f7d9abedd9b6cac4046004c84f3cd695d8b4 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 17 Oct 2024 17:54:08 -0500
Subject: [PATCH 024/180] Ontologies with number of results on search page

---
 .../Manager/MappingsFunctions/FilterAPI.jsx   |  9 +++-
 .../MappingsFunctions/GetMappingsModal.jsx    | 10 ++--
 .../MappingsFunctions/MappingsFunctions.scss  |  9 ++--
 .../MappingsFunctions/OntologyCheckboxes.jsx  | 49 +++++++++++++++++++
 4 files changed, 66 insertions(+), 11 deletions(-)
 create mode 100644 src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx

diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 946f435..8998711 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -1,5 +1,5 @@
 import { useContext, useEffect, useState } from 'react';
-import { Checkbox, Form } from 'antd';
+import { Checkbox, Form, Tooltip } from 'antd';
 import { ModalSpinner, OntologySpinner } from '../Spinner';
 import { myContext } from '../../../App';
 import { FilterOntology } from './FilterOntology';
@@ -123,7 +123,12 @@ export const FilterAPI = ({
       <div className="api_list">
         <Form form={form} preserve={false}>
           <div>
-            <div className="api_label">APIs</div>
+            <Tooltip
+              placement="top"
+              title="Default search through OLS using HPO, MAXO, MONDO, NCIT"
+            >
+              <div className="api_label">APIs</div>
+            </Tooltip>
 
             <Form.Item name={'selected_apis'} valuePropName="value">
               <Checkbox.Group
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 9856587..a8add34 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -6,6 +6,7 @@ import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { olsFilterOntologiesSearch } from '../FetchManager';
+import { OntologyCheckboxes } from './OntologyCheckboxes';
 
 export const GetMappingsModal = ({
   componentString,
@@ -22,7 +23,7 @@ export const GetMappingsModal = ({
   const { apiPreferences, defaultOntologies, setFacetCounts, facetCounts } =
     useContext(SearchContext);
   const [page, setPage] = useState(0);
-  const entriesPerPage = 15;
+  const entriesPerPage = 5000;
   const [loading, setLoading] = useState(false);
   const [results, setResults] = useState([]);
   const [monarchResults, setMonarchResults] = useState([]);
@@ -365,7 +366,10 @@ export const GetMappingsModal = ({
                     <div className="result_container">
                       <Form form={form} layout="vertical">
                         <div className="all_checkboxes_container">
-                          <div className="ontology_form">poop</div>
+                          <OntologyCheckboxes
+                            facetCounts={facetCounts}
+                            apiPreferences={apiPreferences}
+                          />
                           <div className="result_form">
                             {displaySelectedMappings?.length > 0 && (
                               <Form.Item
@@ -425,7 +429,7 @@ export const GetMappingsModal = ({
                           </div>
                         </div>
                       </Form>
-                      <div className="view_more_link">
+                      <div className="view_more_wrapper">
                         {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index c6d781c..001d127 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -16,7 +16,7 @@
   position: fixed;
 }
 .result_form {
-  margin-left: 10vw;
+  margin-left: 11vw;
 }
 
 .modal_search_results_header {
@@ -104,9 +104,6 @@
   gap: 8px;
 }
 
-.view_more_link {
-  display: flex;
-  flex-direction: column;
-  margin-left: 10vw;
-  gap: 10px;
+.view_more_wrapper {
+  margin-left: 11vw;
 }
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
new file mode 100644
index 0000000..bc7e044
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -0,0 +1,49 @@
+import { Checkbox, Form } from 'antd';
+
+export const OntologyCheckboxes = ({ facetCounts, apiPreferences }) => {
+  const ontologyCheckboxDisplay = fc => {
+    // Extract the key (assuming it's only one key in the object)
+    const key = Object.keys(fc);
+    console.log(fc);
+    const value = fc[key]; // Get the value for that key
+
+    return `${key} (${value})`; // Format it to "KEY (value)"
+  };
+
+  console.log(apiPreferences);
+
+  return (
+    <div className="ontology_form">
+      <Form.Item
+        name="selected_ontologies"
+        valuePropName="value"
+        rules={[{ required: false }]}
+      >
+        <div className="modal_display_results">
+          {facetCounts?.map((fc, i) => {
+            // Check if the index is even (assuming even index = key and odd index = value)
+            if (i % 2 === 0) {
+              const key = fc.toUpperCase(); // Use the current string as the key (uppercase)
+              const value = facetCounts[i + 1]; // The next element as the value
+
+              return (
+                <Checkbox
+                  key={i}
+                  //   disabled={value === '0'}
+                  // checked={selectedBoxes.some(box => box.obo_id === fc.obo_id)} // Uncomment if needed
+                  value={fc} // You can keep this if you need the whole object
+                  // onChange={(e) => onCheckboxChange(e, sm, i)} // Uncomment if needed
+                >
+                  {`${key} ${value !== '0' ? `(${value})` : ''}`}
+
+                  {/* Display formatted key-value pair */}
+                </Checkbox>
+              );
+            }
+            return null; // Skip odd indexed elements
+          })}
+        </div>
+      </Form.Item>
+    </div>
+  );
+};

From ba803a82df40346bf310380ae8ae58b2169f7c36 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 17 Oct 2024 18:20:17 -0500
Subject: [PATCH 025/180] changed formatting for ontology counts for checkbox
 display

---
 .../MappingsFunctions/GetMappingsModal.jsx    |  2 -
 .../MappingsFunctions/OntologyCheckboxes.jsx  | 40 +++++--------------
 2 files changed, 10 insertions(+), 32 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index a8add34..c4d9d68 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -210,8 +210,6 @@ export const GetMappingsModal = ({
       );
   };
 
-  console.log('formattedData:', ontologyCounts(facetCounts));
-
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
   const handleViewMore = e => {
     e.preventDefault();
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index bc7e044..4fb6d06 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -1,16 +1,8 @@
 import { Checkbox, Form } from 'antd';
+import { ontologyCounts } from '../Utilitiy';
 
 export const OntologyCheckboxes = ({ facetCounts, apiPreferences }) => {
-  const ontologyCheckboxDisplay = fc => {
-    // Extract the key (assuming it's only one key in the object)
-    const key = Object.keys(fc);
-    console.log(fc);
-    const value = fc[key]; // Get the value for that key
-
-    return `${key} (${value})`; // Format it to "KEY (value)"
-  };
-
-  console.log(apiPreferences);
+  const formattedFacetCounts = ontologyCounts(facetCounts);
 
   return (
     <div className="ontology_form">
@@ -20,27 +12,15 @@ export const OntologyCheckboxes = ({ facetCounts, apiPreferences }) => {
         rules={[{ required: false }]}
       >
         <div className="modal_display_results">
-          {facetCounts?.map((fc, i) => {
-            // Check if the index is even (assuming even index = key and odd index = value)
-            if (i % 2 === 0) {
-              const key = fc.toUpperCase(); // Use the current string as the key (uppercase)
-              const value = facetCounts[i + 1]; // The next element as the value
-
-              return (
-                <Checkbox
-                  key={i}
-                  //   disabled={value === '0'}
-                  // checked={selectedBoxes.some(box => box.obo_id === fc.obo_id)} // Uncomment if needed
-                  value={fc} // You can keep this if you need the whole object
-                  // onChange={(e) => onCheckboxChange(e, sm, i)} // Uncomment if needed
-                >
-                  {`${key} ${value !== '0' ? `(${value})` : ''}`}
+          {formattedFacetCounts?.map((fc, i) => {
+            const key = Object.keys(fc)[0];
+            const value = fc[key];
 
-                  {/* Display formatted key-value pair */}
-                </Checkbox>
-              );
-            }
-            return null; // Skip odd indexed elements
+            return (
+              <Checkbox key={i} value={key}>
+                {`${key.toUpperCase()} ${value !== '0' ? `(${value})` : ''}`}
+              </Checkbox>
+            );
           })}
         </div>
       </Form.Item>

From 0c470b2c6b9e324aca8f9f024bc7d67db95a09fc Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Fri, 18 Oct 2024 14:21:43 -0500
Subject: [PATCH 026/180] [FD-1727]showing description in GetMappingsModal
 MappingRest and MappingSearch

---
 .../MappingsFunctions/GetMappingsModal.jsx    |   2 +
 .../MappingsFunctions/MappingReset.jsx        | 185 +++++++++---------
 .../MappingsFunctions/MappingSearch.jsx       |   2 +
 .../MappingsFunctions/MappingsFunctions.scss  |  23 ++-
 .../Tables/EditMappingsTableModal.jsx         |   2 +
 .../Projects/Tables/TableDetails.jsx          |   1 +
 6 files changed, 119 insertions(+), 96 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 1451c01..202f2ca 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -14,6 +14,7 @@ export const GetMappingsModal = ({
   searchProp,
   component,
   mappingProp,
+  mappingDesc
 }) => {
   const [form] = Form.useForm();
   const { Search } = Input;
@@ -353,6 +354,7 @@ export const GetMappingsModal = ({
                         onChange={handleChange}
                       />
                     </div>
+                  <span className="search-desc">{mappingDesc}</span>
                   </div>
                   {/* ant.design form displaying the checkboxes with the search results.  */}
                   {results?.length > 0 ? (
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index a026c91..be0dc58 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -9,6 +9,7 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const MappingReset = ({
   searchProp,
+  mappingDesc,
   setEditMappings,
   form,
   onClose,
@@ -280,109 +281,111 @@ export const MappingReset = ({
               <div className="modal_search_results">
                 <div className="modal_search_results_header">
                   <h4>{searchProp}</h4>
-                  <div className="mappings_search_bar">
-                    <Search
-                      onSearch={handleSearch}
-                      value={inputValue}
-                      onChange={handleChange}
-                    />
-                  </div>
+                <div className="mappings_search_bar">
+                  <Search
+                    onSearch={handleSearch}
+                    value={inputValue}
+                    onChange={handleChange}
+                  />
                 </div>
-                {/* ant.design form displaying the checkboxes with the search results.  */}
-                {results?.length > 0 ? (
-                  <div className="result_container">
-                    <Form form={form} layout="vertical">
-                      {displaySelectedMappings?.length > 0 && (
-                        <Form.Item
-                          name="selected_mappings"
-                          valuePropName="value"
-                          rules={[{ required: false }]}
-                        >
-                          {' '}
-                          <div className="modal_display_results">
-                            {displaySelectedMappings?.map((sm, i) => (
-                              <Checkbox
-                                key={i}
-                                onChange={e => onCheckboxChange(e, sm)}
-                                checked={selectedBoxes.some(
-                                  box => box.obo_id === sm.obo_id
-                                )}
-                                value={sm}
-                              >
-                                {selectedTermsDisplay(sm, i)}
-                              </Checkbox>
-                            ))}
-                          </div>
-                        </Form.Item>
-                      )}
+                <span className="search-desc">{mappingDesc}</span>
+              </div>
+              <span></span>
+              {/* ant.design form displaying the checkboxes with the search results.  */}
+              {results?.length > 0 ? (
+                <div className="result_container">
+                  <Form form={form} layout="vertical">
+                    {displaySelectedMappings?.length > 0 && (
                       <Form.Item
-                        name={['filtered_mappings']}
+                        name="selected_mappings"
                         valuePropName="value"
-                        rules={[
-                          {
-                            required: true,
-                            message: 'Please make a selection.',
-                          },
-                        ]}
+                        rules={[{ required: false }]}
                       >
-                        {filteredResultsArray?.length > 0 ? (
-                          <Checkbox.Group
-                            className="mappings_checkbox"
-                            options={filteredResultsArray?.map((d, index) => {
-                              return {
-                                value: JSON.stringify({
-                                  code: d.obo_id,
-                                  display: d.label,
-                                  // description: d.description[0],
-                                  system: systemsMatch(d?.obo_id.split(':')[0]),
-                                }),
-                                label: checkBoxDisplay(d, index),
-                              };
-                            })}
-                            onChange={onSelectedChange}
-                          />
-                        ) : (
-                          ''
-                        )}
+                        {' '}
+                        <div className="modal_display_results">
+                          {displaySelectedMappings?.map((sm, i) => (
+                            <Checkbox
+                              key={i}
+                              onChange={e => onCheckboxChange(e, sm)}
+                              checked={selectedBoxes.some(
+                                box => box.obo_id === sm.obo_id
+                              )}
+                              value={sm}
+                            >
+                              {selectedTermsDisplay(sm, i)}
+                            </Checkbox>
+                          ))}
+                        </div>
                       </Form.Item>
-                    </Form>
-                    <div>
-                      {/* 'View More' pagination displaying the number of results being displayed
+                    )}
+                    <Form.Item
+                      name={['filtered_mappings']}
+                      valuePropName="value"
+                      rules={[
+                        {
+                          required: true,
+                          message: 'Please make a selection.',
+                        },
+                      ]}
+                    >
+                      {filteredResultsArray?.length > 0 ? (
+                        <Checkbox.Group
+                          className="mappings_checkbox"
+                          options={filteredResultsArray?.map((d, index) => {
+                            return {
+                              value: JSON.stringify({
+                                code: d.obo_id,
+                                display: d.label,
+                                // description: d.description[0],
+                                system: systemsMatch(d?.obo_id.split(':')[0]),
+                              }),
+                              label: checkBoxDisplay(d, index),
+                            };
+                          })}
+                          onChange={onSelectedChange}
+                        />
+                      ) : (
+                        ''
+                      )}
+                    </Form.Item>
+                  </Form>
+                  <div>
+                    {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
                       inconsistencies in results numbers per page. */}
-                      <Tooltip
-                        placement="bottom"
-                        title="Redundant entries have been removed"
+                    <Tooltip
+                      placement="bottom"
+                      title="Redundant entries have been removed"
+                    >
+                      Displaying {resultsCount}
+                      &nbsp;of&nbsp;{totalCount}
+                    </Tooltip>
+                    {totalCount - filteredResultsCount !== resultsCount && (
+                      <span
+                        className="view_more_link"
+                        onClick={e => {
+                          handleViewMore(e);
+                          setLastCount(resultsCount);
+                        }}
                       >
-                        Displaying {resultsCount}
-                        &nbsp;of&nbsp;{totalCount}
-                      </Tooltip>
-                      {totalCount - filteredResultsCount !== resultsCount && (
-                        <span
-                          className="view_more_link"
-                          onClick={e => {
-                            handleViewMore(e);
-                            setLastCount(resultsCount);
-                          }}
-                        >
-                          View More
-                        </span>
-                      )}
-                    </div>
+                        View More
+                      </span>
+                    )}
                   </div>
-                ) : (
-                  <h3>No results found.</h3>
-                )}
-              </div>
-            </>
-          ) : (
-            <div className="loading_spinner">
-              <ModalSpinner />
+                </div>
+              ) : (
+                <h3>No results found.</h3>
+              )}
             </div>
-          )}
         </>
-      </div>
+        ) : (
+        <div className="loading_spinner">
+          <ModalSpinner />
+        </div>
+          )}
+      </>
+    </div >
     </>
   );
 };
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 14724f1..1d21085 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -13,6 +13,7 @@ export const MappingSearch = ({
   mappingsForSearch,
   onClose,
   searchProp,
+  mappingDesc
 }) => {
   const { searchUrl } = useContext(myContext);
   const { apiPreferences, defaultOntologies } = useContext(SearchContext);
@@ -351,6 +352,7 @@ export const MappingSearch = ({
                       onChange={handleChange}
                     />
                   </div>
+                  <span className="search-desc">{mappingDesc}</span>
                 </div>
                 {/* ant.design form displaying the checkboxes with the search results.  */}
                 {results?.length > 0 ? (
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index db00c2f..d74c69a 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -11,15 +11,28 @@
   position: sticky;
   margin: 0 0 15px 0;
   display: flex;
+  flex-wrap: wrap;
   flex-direction: row;
-  align-items: center;
-  gap: 20px;
+  justify-content: flex-start;
+  align-items: end;
   z-index: 10;
+  flex: 1;
+  border-bottom: solid 1px #eeee;
+  h4 {
+    margin:0;
+    padding-right:1rem;
+  }
+  .mappings_search_bar {
+    width: 60%;
+  }
+  .search-desc {
+    flex: 0 0 100%;
+    margin-bottom:1rem;
+  }
 }
 
-.mappings_search_bar {
-  width: 50%;
-}
+
+
 
 .inactive_term,
 .active_term {
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index 3408f96..06c9a84 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -337,11 +337,13 @@ export const EditMappingsTableModal = ({
           reset={reset}
           onClose={form.resetFields}
           searchProp={editMappings.name}
+          mappingDesc={editMappings.description ? editMappings.description : 'No Description'}
         />
       ) : (
         reset && (
           <MappingReset
             searchProp={editMappings.name}
+            mappingDesc={editMappings.description ? editMappings.description : 'No Description'}
             setEditMappings={setEditMappings}
             mappingsForSearch={mappingsForSearch}
             form={form}
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 863cb79..1a759db 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -365,6 +365,7 @@ There is then a tooltip that displays the variables on hover.*/
         setMapping={setMapping}
         tableId={tableId}
         mappingProp={getMappings?.code}
+        mappingDesc={getMappings.description ? getMappings.description : 'No Description'}
       />
       <ClearMappings propId={tableId} component={'Table'} />
     </>

From d1d073027522e500543c6868f6ded458838d1ac0 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 18 Oct 2024 16:04:01 -0500
Subject: [PATCH 027/180] Working on updating ontologies for search by checkbox
 check

---
 src/Contexts/SearchContext.jsx                |  6 ++
 src/components/Manager/FetchManager.jsx       | 58 +++++++++++++++
 .../MappingsFunctions/GetMappingsModal.jsx    | 66 ++++++++++++++---
 .../MappingsFunctions/OntologyCheckboxes.jsx  | 72 +++++++++++++++++--
 4 files changed, 189 insertions(+), 13 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index dc0724c..b6b211a 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -13,6 +13,8 @@ export function SearchContextRoot() {
   const [apiPage, setApiPage] = useState(0);
   const [apiTotalCount, setApiTotalCount] = useState();
   const [apiPreferences, setApiPreferences] = useState({});
+  const [apiPreferencesCode, setApiPreferencesCode] = useState({});
+  const [unformattedPref, setUnformattedPref] = useState([]);
   const [facetCounts, setFacetCounts] = useState([]);
   const defaultOntologies = 'mondo,hp,maxo,ncit';
 
@@ -35,9 +37,13 @@ export function SearchContextRoot() {
     setApiTotalCount,
     apiPreferences,
     setApiPreferences,
+    apiPreferencesCode,
+    setApiPreferencesCode,
     defaultOntologies,
     facetCounts,
     setFacetCounts,
+    unformattedPref,
+    setUnformattedPref,
   };
 
   return (
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index ac6f712..467fddd 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -226,3 +226,61 @@ export const olsFilterOntologiesSearch = (
     })
     .then(() => setLoading(false));
 };
+
+export const getFiltersByCode = (
+  vocabUrl,
+  component,
+  mappingProp,
+  setApiPreferencesCode,
+  notification,
+  apiPreferencesCode,
+  setUnformattedPref
+) => {
+  return fetch(
+    `${vocabUrl}/${component?.terminology?.reference}/filter/${mappingProp}`,
+    {
+      method: 'GET',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+    }
+  )
+    .then(res => {
+      if (res.ok) {
+        return res.json();
+      } else {
+        throw new Error('An unknown error occurred.');
+      }
+    })
+    .then(data => {
+      setUnformattedPref(data);
+
+      // Dynamically derive the mappingProp based on a condition or the structure of the data
+      const codeToSearch = Object.keys(data)[0]; // Example: get the first key in the object
+      if (data?.[codeToSearch]?.api_preference?.ols) {
+        const joinedOntologies =
+          data[codeToSearch].api_preference.ols.join(',');
+        setApiPreferencesCode(joinedOntologies); // Set state to the comma-separated string
+      } else {
+        setApiPreferencesCode(''); // Fallback if no ols found
+      }
+    })
+    .catch(error => {
+      if (error) {
+        notification.error({
+          message: 'Error',
+          description: 'An error occurred loading the ontology preferences.',
+        });
+      }
+      return error;
+    });
+};
+
+//   const preferredCodeOntologies = () => {
+//     if (apiPreferences?.mappingProp?.api_preference?.ols) {
+//       return apiPreferences.self.api_preference.ols.join(',');
+//     } else {
+//       // else if there are no preferred ontologies, it uses the default ontologies
+//       return defaultOntologies;
+//     }
+//   };
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index c4d9d68..c3f6dae 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -1,11 +1,19 @@
-import { Checkbox, Input, message, Modal, Form, Tooltip } from 'antd';
+import {
+  Checkbox,
+  Form,
+  Input,
+  message,
+  Modal,
+  notification,
+  Tooltip,
+} from 'antd';
 import { useContext, useEffect, useRef, useState } from 'react';
 import { myContext } from '../../../App';
 import { ellipsisString, ontologyCounts, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
-import { olsFilterOntologiesSearch } from '../FetchManager';
+import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
 
 export const GetMappingsModal = ({
@@ -20,10 +28,18 @@ export const GetMappingsModal = ({
   const { Search } = Input;
 
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
-  const { apiPreferences, defaultOntologies, setFacetCounts, facetCounts } =
-    useContext(SearchContext);
+  const {
+    apiPreferences,
+    defaultOntologies,
+    setFacetCounts,
+    facetCounts,
+    setApiPreferencesCode,
+    apiPreferencesCode,
+    setUnformattedPref,
+    unformattedPref,
+  } = useContext(SearchContext);
   const [page, setPage] = useState(0);
-  const entriesPerPage = 5000;
+  const entriesPerPage = 2500;
   const [loading, setLoading] = useState(false);
   const [results, setResults] = useState([]);
   const [monarchResults, setMonarchResults] = useState([]);
@@ -33,7 +49,7 @@ export const GetMappingsModal = ({
   const [filteredResultsCount, setFilteredResultsCount] = useState(0);
   const [inputValue, setInputValue] = useState(searchProp); //Sets the value of the search bar
   const [currentSearchProp, setCurrentSearchProp] = useState(searchProp);
-
+  console.log(unformattedPref);
   const {
     setSelectedMappings,
     displaySelectedMappings,
@@ -52,10 +68,24 @@ export const GetMappingsModal = ({
     setCurrentSearchProp(searchProp);
     setPage(0);
     if (!!searchProp) {
-      fetchResults(0, searchProp);
+      getFiltersByCode(
+        vocabUrl,
+        component,
+        mappingProp,
+        setApiPreferencesCode,
+        notification,
+        apiPreferencesCode,
+        setUnformattedPref
+      );
     }
   }, [searchProp]);
 
+  useEffect(() => {
+    if (apiPreferencesCode) {
+      fetchResults(0, searchProp);
+    }
+  }, [apiPreferencesCode, searchProp]);
+
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the code and when the page changes.
@@ -110,6 +140,7 @@ export const GetMappingsModal = ({
     setCurrentSearchProp(query);
     setPage(0);
   };
+
   // Function to send a PUT call to update the mappings.
   // Each mapping in the mappings array being edited is JSON.parsed and pushed to the blank mappings array.
   // The mappings are turned into objects in the mappings array.
@@ -178,7 +209,7 @@ export const GetMappingsModal = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferenceOntologies(),
+        apiPreferencesCode ? apiPreferencesCode : apiPreferenceOntologies(),
         page,
         entriesPerPage,
         pageStart,
@@ -195,7 +226,9 @@ export const GetMappingsModal = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        defaultOntologies,
+        apiPreferencesCode && Object.keys(apiPreferencesCode).length > 0
+          ? apiPreferencesCode
+          : defaultOntologies,
         page,
         entriesPerPage,
         pageStart,
@@ -367,6 +400,21 @@ export const GetMappingsModal = ({
                           <OntologyCheckboxes
                             facetCounts={facetCounts}
                             apiPreferences={apiPreferences}
+                            mappingProp={mappingProp}
+                            component={component}
+                            setCurrentSearchProp={setCurrentSearchProp}
+                            setPage={setPage}
+                            page={page}
+                            entriesPerPage={entriesPerPage}
+                            selectedBoxes={selectedBoxes}
+                            setTotalCount={setTotalCount}
+                            setResults={setResults}
+                            setFilteredResultsCount={setFilteredResultsCount}
+                            setResultsCount={setResultsCount}
+                            setLoading={setLoading}
+                            results={results}
+                            setFacetCounts={setFacetCounts}
+                            setApiPreferencesCode={setApiPreferencesCode}
                           />
                           <div className="result_form">
                             {displaySelectedMappings?.length > 0 && (
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 4fb6d06..a7e2a8d 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -1,9 +1,63 @@
-import { Checkbox, Form } from 'antd';
+import { Checkbox, Form, notification } from 'antd';
 import { ontologyCounts } from '../Utilitiy';
+import { useContext, useEffect, useState } from 'react';
+import { myContext } from '../../../App';
+import { SearchContext } from '../../../Contexts/SearchContext';
+import { olsFilterOntologiesSearch } from '../FetchManager';
+import { MappingContext } from '../../../Contexts/MappingContext';
 
-export const OntologyCheckboxes = ({ facetCounts, apiPreferences }) => {
+export const OntologyCheckboxes = ({ apiPreferences }) => {
+  const { vocabUrl, searchUrl } = useContext(myContext);
+  const { apiPreferencesCode, setApiPreferencesCode, facetCounts } =
+    useContext(SearchContext);
+  const [checkedOntologies, setCheckedOntologies] = useState([]);
+
+  const existingOntologies = apiPreferencesCode
+    ? apiPreferencesCode
+    : Object.values(apiPreferences?.self?.api_preference).flat(); // Flatten arrays into a single array
+  useEffect(() => {
+    setCheckedOntologies(existingOntologies); // Set the initial checked keys
+  }, [apiPreferences]);
+  ``;
+
+  const onCheckboxChange = e => {
+    const { value, checked } = e.target;
+
+    setCheckedOntologies(existingOntologies => {
+      const newCheckedOntologies = checked
+        ? [...existingOntologies, value] // Add key if checked
+        : existingOntologies.filter(key => key !== value); // Remove key if unchecked
+
+      // Update apiPreferencesCode
+      setApiPreferencesCode(existingCode => {
+        if (checked) {
+          // Add value if checked, and avoid duplications
+          return existingCode ? `${existingCode},${value}` : value;
+        } else {
+          // Remove the value if unchecked
+          const updatedCode = existingCode
+            .split(',')
+            .filter(code => code !== value)
+            .join(',');
+
+          return updatedCode;
+        }
+      });
+
+      return newCheckedOntologies;
+    });
+  };
   const formattedFacetCounts = ontologyCounts(facetCounts);
 
+  console.log(apiPreferencesCode);
+
+  // Sort the `formattedFacetCounts` before rendering, not inside the `map()`
+  const sortedFacetCounts = formattedFacetCounts?.sort(
+    (a, b) =>
+      (existingOntologies.includes(Object.keys(a)[0]) ? -1 : 1) -
+      (existingOntologies.includes(Object.keys(b)[0]) ? -1 : 1)
+  );
+
   return (
     <div className="ontology_form">
       <Form.Item
@@ -12,12 +66,22 @@ export const OntologyCheckboxes = ({ facetCounts, apiPreferences }) => {
         rules={[{ required: false }]}
       >
         <div className="modal_display_results">
-          {formattedFacetCounts?.map((fc, i) => {
+          {sortedFacetCounts?.map((fc, i) => {
             const key = Object.keys(fc)[0];
             const value = fc[key];
+            formattedFacetCounts.sort(
+              (a, b) =>
+                (existingOntologies.includes(Object.keys(a)[0]) ? -1 : 1) -
+                (existingOntologies.includes(Object.keys(b)[0]) ? -1 : 1)
+            );
 
             return (
-              <Checkbox key={i} value={key}>
+              <Checkbox
+                key={i}
+                value={key}
+                checked={checkedOntologies.includes(key)} // Check if key is in checkedOntologies array
+                onChange={onCheckboxChange} // Handle the change
+              >
                 {`${key.toUpperCase()} ${value !== '0' ? `(${value})` : ''}`}
               </Checkbox>
             );

From afc0d9e829b00e4072a91565a5d4b9e0f54664ab Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 21 Oct 2024 09:01:48 -0500
Subject: [PATCH 028/180] added pagesize select + remembering pagesize to 
 TerminologyList

---
 .../Projects/Terminologies/TerminologyList.jsx   | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/components/Projects/Terminologies/TerminologyList.jsx b/src/components/Projects/Terminologies/TerminologyList.jsx
index 5b3ca6f..99d0cbf 100644
--- a/src/components/Projects/Terminologies/TerminologyList.jsx
+++ b/src/components/Projects/Terminologies/TerminologyList.jsx
@@ -14,7 +14,8 @@ export const TerminologyList = () => {
   const [terms, setTerms] = useState([]);
   const [filter, setFilter] = useState(null);
   const [deleteId, setDeleteId] = useState(null);
-
+  const [pageSize, setPageSize] = useState(
+    parseInt(localStorage.getItem('pageSize'), 10) || 10);
   const { vocabUrl } = useContext(myContext);
 
   const navigate = useNavigate();
@@ -28,7 +29,8 @@ export const TerminologyList = () => {
         setTerms(data);
       })
       .finally(() => setLoading(false));
-  }, []);
+      localStorage.setItem('pageSize', pageSize);
+  }, [pageSize]);
 
   const terminologyTitle = () => {
     return (
@@ -44,6 +46,9 @@ export const TerminologyList = () => {
       {item.name ? item.name : item.id}
     </Link>
   );
+  const handleTableChange = (current, size) => { 
+    setPageSize(size);     
+  };
 
   const columns = [
     {
@@ -140,9 +145,16 @@ export const TerminologyList = () => {
         <h2>Terminology Index</h2>
         <AddTerminology />
         <Table
+          showSizeChanger={true}
           columns={columns}
           dataSource={dataSource}
           getPopupContainer={trigger => trigger.parentNode}
+          pagination={{ 
+            showSizeChanger: true,
+            pageSizeOptions: ['10', '20', '30'],
+            pageSize: pageSize, // Use the stored pageSize
+            onChange: handleTableChange, // Capture pagination changes
+          }} 
         />
       </div>
       <DeleteTerminology

From 2c9a1ef67617937a29ddc6a98098c88f18564050 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 21 Oct 2024 10:12:38 -0500
Subject: [PATCH 029/180] unchecked checkboxes remove ontology from api call

---
 .../MappingsFunctions/GetMappingsModal.jsx    |  1 -
 .../MappingsFunctions/OntologyCheckboxes.jsx  | 21 ++++++++++++-------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index c3f6dae..09a90b6 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -49,7 +49,6 @@ export const GetMappingsModal = ({
   const [filteredResultsCount, setFilteredResultsCount] = useState(0);
   const [inputValue, setInputValue] = useState(searchProp); //Sets the value of the search bar
   const [currentSearchProp, setCurrentSearchProp] = useState(searchProp);
-  console.log(unformattedPref);
   const {
     setSelectedMappings,
     displaySelectedMappings,
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index a7e2a8d..afd383d 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -20,13 +20,18 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
   }, [apiPreferences]);
   ``;
 
+  console.log(existingOntologies);
+
   const onCheckboxChange = e => {
     const { value, checked } = e.target;
 
     setCheckedOntologies(existingOntologies => {
-      const newCheckedOntologies = checked
-        ? [...existingOntologies, value] // Add key if checked
-        : existingOntologies.filter(key => key !== value); // Remove key if unchecked
+      // Ensure existingOntologies is always an array
+      const newCheckedOntologies = Array.isArray(existingOntologies)
+        ? checked
+          ? [...existingOntologies, value] // Add value if checked
+          : existingOntologies.filter(key => key !== value) // Remove value if unchecked
+        : []; // Fallback to an empty array if it's not an array
 
       // Update apiPreferencesCode
       setApiPreferencesCode(existingCode => {
@@ -34,22 +39,22 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
           // Add value if checked, and avoid duplications
           return existingCode ? `${existingCode},${value}` : value;
         } else {
-          // Remove the value if unchecked
+          // Remove value if unchecked, handling cases where the string might be empty
           const updatedCode = existingCode
             .split(',')
-            .filter(code => code !== value)
+            .filter(code => code !== value) // Remove the unchecked value
             .join(',');
 
-          return updatedCode;
+          // Ensure there's no trailing comma
+          return updatedCode.replace(/,$/, '');
         }
       });
 
       return newCheckedOntologies;
     });
   };
-  const formattedFacetCounts = ontologyCounts(facetCounts);
 
-  console.log(apiPreferencesCode);
+  const formattedFacetCounts = ontologyCounts(facetCounts);
 
   // Sort the `formattedFacetCounts` before rendering, not inside the `map()`
   const sortedFacetCounts = formattedFacetCounts?.sort(

From e798b24de94022b3c60d6a8528b38a3dfcf8b1b2 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 21 Oct 2024 10:39:03 -0500
Subject: [PATCH 030/180] null check

---
 src/components/Projects/Tables/TableDetails.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 1a759db..80a00a4 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -365,7 +365,7 @@ There is then a tooltip that displays the variables on hover.*/
         setMapping={setMapping}
         tableId={tableId}
         mappingProp={getMappings?.code}
-        mappingDesc={getMappings.description ? getMappings.description : 'No Description'}
+        mappingDesc={getMappings?.description ? getMappings?.description : 'No Description'}
       />
       <ClearMappings propId={tableId} component={'Table'} />
     </>

From a2e5e5f574348140bd53615e65991dff263b954c Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 21 Oct 2024 11:04:20 -0500
Subject: [PATCH 031/180] fixes

---
 src/components/Manager/MappingsFunctions/MappingReset.jsx  | 2 +-
 src/components/Projects/Terminologies/EditMappingModal.jsx | 4 ++++
 src/components/Projects/Terminologies/Terminology.jsx      | 2 ++
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index be0dc58..332961e 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -12,7 +12,7 @@ export const MappingReset = ({
   mappingDesc,
   setEditMappings,
   form,
-  onClose,
+  onClose
 }) => {
   const { searchUrl } = useContext(myContext);
   const { apiPreferences, defaultOntologies } = useContext(SearchContext);
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index ecc352c..0288f12 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -21,6 +21,7 @@ export const EditMappingsModal = ({
   setEditMappings,
   terminologyId,
   setMapping,
+  mappingDesc
 }) => {
   const [form] = Form.useForm();
   const [termMappings, setTermMappings] = useState([]);
@@ -320,6 +321,7 @@ export const EditMappingsModal = ({
                 ? editMappings.display
                 : editMappings?.code}
             </h3>
+          <span className="search-desc">{mappingDesc}</span>
           </div>
           <Form form={form} layout="vertical" preserve={false}>
             <Form.Item
@@ -344,6 +346,7 @@ export const EditMappingsModal = ({
           searchProp={
             editMappings?.display ? editMappings.display : editMappings?.code
           }
+          mappingDesc={editMappings?.description}
         />
       ) : (
         reset && (
@@ -356,6 +359,7 @@ export const EditMappingsModal = ({
             form={form}
             reset={reset}
             onClose={form.resetFields}
+            mappingDesc={editMappings?.description}
           />
         )
       )}
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index a7c49b3..65970cf 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -259,6 +259,7 @@ There is then a tooltip that displays the codes on hover.*/
             mapping={mapping}
             terminologyId={terminologyId}
             setMapping={setMapping}
+            mappingDesc={editMappings?.description ? editMappings?.description : 'No Description'}
           />
           <GetMappingsModal
             componentString={'Terminology'}
@@ -271,6 +272,7 @@ There is then a tooltip that displays the codes on hover.*/
             setMapping={setMapping}
             terminologyId={terminologyId}
             mappingProp={getMappings?.code}
+            mappingDesc={getMappings?.description ? getMappings?.description : 'No Description'}
           />
 
           {/* Displays the edit form */}

From 19110298fc0bd1b6dc202a3b9eb9e568c445e038 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 21 Oct 2024 14:12:17 -0500
Subject: [PATCH 032/180] code searching by terminology's filter ontologies

---
 src/Contexts/SearchContext.jsx                |   2 +-
 src/components/Manager/FetchManager.jsx       |   9 -
 .../MappingsFunctions/GetMappingsModal.jsx    | 249 ++++++++----------
 .../MappingsFunctions/OntologyCheckboxes.jsx  |  10 +-
 4 files changed, 112 insertions(+), 158 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index b6b211a..ecfebde 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -13,7 +13,7 @@ export function SearchContextRoot() {
   const [apiPage, setApiPage] = useState(0);
   const [apiTotalCount, setApiTotalCount] = useState();
   const [apiPreferences, setApiPreferences] = useState({});
-  const [apiPreferencesCode, setApiPreferencesCode] = useState({});
+  const [apiPreferencesCode, setApiPreferencesCode] = useState('');
   const [unformattedPref, setUnformattedPref] = useState([]);
   const [facetCounts, setFacetCounts] = useState([]);
   const defaultOntologies = 'mondo,hp,maxo,ncit';
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 467fddd..756ccf0 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -275,12 +275,3 @@ export const getFiltersByCode = (
       return error;
     });
 };
-
-//   const preferredCodeOntologies = () => {
-//     if (apiPreferences?.mappingProp?.api_preference?.ols) {
-//       return apiPreferences.self.api_preference.ols.join(',');
-//     } else {
-//       // else if there are no preferred ontologies, it uses the default ontologies
-//       return defaultOntologies;
-//     }
-//   };
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 09a90b6..1e94ac1 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -32,17 +32,14 @@ export const GetMappingsModal = ({
     apiPreferences,
     defaultOntologies,
     setFacetCounts,
-    facetCounts,
     setApiPreferencesCode,
     apiPreferencesCode,
     setUnformattedPref,
-    unformattedPref,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 2500;
   const [loading, setLoading] = useState(false);
   const [results, setResults] = useState([]);
-  const [monarchResults, setMonarchResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
   const [resultsCount, setResultsCount] = useState();
   const [lastCount, setLastCount] = useState(0); //save last count as count of the results before you fetch data again
@@ -81,19 +78,12 @@ export const GetMappingsModal = ({
 
   useEffect(() => {
     if (apiPreferencesCode) {
+      fetchResults(0, searchProp); // Pass apiPreferencesCode correctly
+    } else {
       fetchResults(0, searchProp);
     }
   }, [apiPreferencesCode, searchProp]);
 
-  // The '!!' forces currentSearchProp to be evaluated as a boolean.
-  // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
-  // The function is run when the code and when the page changes.
-  useEffect(() => {
-    if (!!currentSearchProp) {
-      fetchResults(page, currentSearchProp);
-    }
-  }, [page, currentSearchProp]);
-
   /* Pagination is handled via a "View More" link at the bottom of the page. 
   Each click on the "View More" link makes an API call to fetch the next 15 results.
   This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
@@ -127,7 +117,6 @@ export const GetMappingsModal = ({
   const onClose = () => {
     setPage(0);
     setResults([]);
-    setLoading(true);
     setSelectedMappings([]);
     setDisplaySelectedMappings([]);
     setSelectedBoxes([]);
@@ -180,8 +169,6 @@ export const GetMappingsModal = ({
       });
   };
 
-  // The function that makes the API call to search for the passed code.
-
   const fetchResults = (page, query) => {
     if (!!!query) {
       return undefined;
@@ -208,7 +195,9 @@ export const GetMappingsModal = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferencesCode ? apiPreferencesCode : apiPreferenceOntologies(),
+        apiPreferencesCode !== ''
+          ? apiPreferencesCode
+          : apiPreferenceOntologies(),
         page,
         entriesPerPage,
         pageStart,
@@ -225,9 +214,9 @@ export const GetMappingsModal = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferencesCode && Object.keys(apiPreferencesCode).length > 0
+        apiPreferencesCode !== ''
           ? apiPreferencesCode
-          : defaultOntologies,
+          : apiPreferenceOntologies(),
         page,
         entriesPerPage,
         pageStart,
@@ -376,141 +365,119 @@ export const GetMappingsModal = ({
         cancelButtonProps={{ disabled: loading }}
         okButtonProps={{ disabled: loading }}
       >
-        <div className="results_modal_container">
-          <>
-            {loading === false ? (
-              <>
-                <div className="modal_search_results">
-                  <div className="modal_search_results_header">
-                    <h4>{searchProp}</h4>
-                    <div className="mappings_search_bar">
-                      <Search
-                        onSearch={handleSearch}
-                        value={inputValue}
-                        onChange={handleChange}
-                      />
-                    </div>
+        {loading ? (
+          <ModalSpinner />
+        ) : (
+          <div className="results_modal_container">
+            <>
+              <div className="modal_search_results">
+                <div className="modal_search_results_header">
+                  <h4>{searchProp}</h4>
+                  <div className="mappings_search_bar">
+                    <Search
+                      onSearch={handleSearch}
+                      value={inputValue}
+                      onChange={handleChange}
+                    />
                   </div>
-                  {/* ant.design form displaying the checkboxes with the search results.  */}
-                  {results?.length > 0 ? (
-                    <div className="result_container">
-                      <Form form={form} layout="vertical">
-                        <div className="all_checkboxes_container">
-                          <OntologyCheckboxes
-                            facetCounts={facetCounts}
-                            apiPreferences={apiPreferences}
-                            mappingProp={mappingProp}
-                            component={component}
-                            setCurrentSearchProp={setCurrentSearchProp}
-                            setPage={setPage}
-                            page={page}
-                            entriesPerPage={entriesPerPage}
-                            selectedBoxes={selectedBoxes}
-                            setTotalCount={setTotalCount}
-                            setResults={setResults}
-                            setFilteredResultsCount={setFilteredResultsCount}
-                            setResultsCount={setResultsCount}
-                            setLoading={setLoading}
-                            results={results}
-                            setFacetCounts={setFacetCounts}
-                            setApiPreferencesCode={setApiPreferencesCode}
-                          />
-                          <div className="result_form">
-                            {displaySelectedMappings?.length > 0 && (
-                              <Form.Item
-                                name="selected_mappings"
-                                valuePropName="value"
-                                rules={[{ required: false }]}
-                              >
-                                <div className="modal_display_results">
-                                  {displaySelectedMappings?.map((sm, i) => (
-                                    <Checkbox
-                                      key={i}
-                                      checked={selectedBoxes.some(
-                                        box => box.obo_id === sm.obo_id
-                                      )}
-                                      value={sm}
-                                      onChange={e => onCheckboxChange(e, sm, i)}
-                                    >
-                                      {selectedTermsDisplay(sm, i)}
-                                    </Checkbox>
-                                  ))}
-                                </div>
-                              </Form.Item>
-                            )}
+                </div>
+                {/* ant.design form displaying the checkboxes with the search results.  */}
+                {results?.length > 0 ? (
+                  <div className="result_container">
+                    <Form form={form} layout="vertical">
+                      <div className="all_checkboxes_container">
+                        <OntologyCheckboxes apiPreferences={apiPreferences} />
+                        <div className="result_form">
+                          {displaySelectedMappings?.length > 0 && (
                             <Form.Item
-                              name={['filtered_mappings']}
+                              name="selected_mappings"
                               valuePropName="value"
-                              rules={[
-                                {
-                                  required: false,
-                                },
-                              ]}
+                              rules={[{ required: false }]}
                             >
-                              {filteredResultsArray?.length > 0 ? (
-                                <Checkbox.Group
-                                  className="mappings_checkbox"
-                                  options={filteredResultsArray?.map(
-                                    (d, index) => {
-                                      return {
-                                        value: JSON.stringify({
-                                          code: d.obo_id,
-                                          display: d.label,
-                                          description: d.description[0],
-                                          system: systemsMatch(
-                                            d?.obo_id.split(':')[0]
-                                          ),
-                                        }),
-                                        label: checkBoxDisplay(d, index),
-                                      };
-                                    }
-                                  )}
-                                  onChange={onSelectedChange}
-                                />
-                              ) : (
-                                ''
-                              )}
+                              <div className="modal_display_results">
+                                {displaySelectedMappings?.map((sm, i) => (
+                                  <Checkbox
+                                    key={i}
+                                    checked={selectedBoxes.some(
+                                      box => box.obo_id === sm.obo_id
+                                    )}
+                                    value={sm}
+                                    onChange={e => onCheckboxChange(e, sm, i)}
+                                  >
+                                    {selectedTermsDisplay(sm, i)}
+                                  </Checkbox>
+                                ))}
+                              </div>
                             </Form.Item>
-                          </div>
+                          )}
+                          <Form.Item
+                            name={['filtered_mappings']}
+                            valuePropName="value"
+                            rules={[
+                              {
+                                required: false,
+                              },
+                            ]}
+                          >
+                            {filteredResultsArray?.length > 0 ? (
+                              <Checkbox.Group
+                                className="mappings_checkbox"
+                                options={filteredResultsArray?.map(
+                                  (d, index) => {
+                                    return {
+                                      value: JSON.stringify({
+                                        code: d.obo_id,
+                                        display: d.label,
+                                        description: d.description[0],
+                                        system: systemsMatch(
+                                          d?.obo_id.split(':')[0]
+                                        ),
+                                      }),
+                                      label: checkBoxDisplay(d, index),
+                                    };
+                                  }
+                                )}
+                                onChange={onSelectedChange}
+                              />
+                            ) : (
+                              ''
+                            )}
+                          </Form.Item>
                         </div>
-                      </Form>
-                      <div className="view_more_wrapper">
-                        {/* 'View More' pagination displaying the number of results being displayed
+                      </div>
+                    </Form>
+                    <div className="view_more_wrapper">
+                      {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
                       inconsistencies in results numbers per page. */}
-                        <Tooltip
-                          placement="bottom"
-                          title="Redundant entries have been removed"
+                      <Tooltip
+                        placement="bottom"
+                        title="Redundant entries have been removed"
+                      >
+                        Displaying {resultsCount}
+                        &nbsp;of&nbsp;{totalCount}
+                      </Tooltip>
+                      {totalCount - filteredResultsCount !== resultsCount && (
+                        <span
+                          className="view_more_link"
+                          onClick={e => {
+                            handleViewMore(e);
+                            setLastCount(resultsCount);
+                          }}
                         >
-                          Displaying {resultsCount}
-                          &nbsp;of&nbsp;{totalCount}
-                        </Tooltip>
-                        {totalCount - filteredResultsCount !== resultsCount && (
-                          <span
-                            className="view_more_link"
-                            onClick={e => {
-                              handleViewMore(e);
-                              setLastCount(resultsCount);
-                            }}
-                          >
-                            View More
-                          </span>
-                        )}
-                      </div>
+                          View More
+                        </span>
+                      )}
                     </div>
-                  ) : (
-                    <h3>No results found.</h3>
-                  )}
-                </div>
-              </>
-            ) : (
-              <div className="loading_spinner">
-                <ModalSpinner />
+                  </div>
+                ) : (
+                  <h3>No results found.</h3>
+                )}
               </div>
-            )}
-          </>
-        </div>
+            </>
+          </div>
+        )}
       </Modal>
     </>
   );
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index afd383d..7b62408 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -1,13 +1,9 @@
-import { Checkbox, Form, notification } from 'antd';
+import { Checkbox, Form } from 'antd';
 import { ontologyCounts } from '../Utilitiy';
 import { useContext, useEffect, useState } from 'react';
-import { myContext } from '../../../App';
 import { SearchContext } from '../../../Contexts/SearchContext';
-import { olsFilterOntologiesSearch } from '../FetchManager';
-import { MappingContext } from '../../../Contexts/MappingContext';
 
 export const OntologyCheckboxes = ({ apiPreferences }) => {
-  const { vocabUrl, searchUrl } = useContext(myContext);
   const { apiPreferencesCode, setApiPreferencesCode, facetCounts } =
     useContext(SearchContext);
   const [checkedOntologies, setCheckedOntologies] = useState([]);
@@ -15,13 +11,13 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
   const existingOntologies = apiPreferencesCode
     ? apiPreferencesCode
     : Object.values(apiPreferences?.self?.api_preference).flat(); // Flatten arrays into a single array
+
   useEffect(() => {
     setCheckedOntologies(existingOntologies); // Set the initial checked keys
   }, [apiPreferences]);
   ``;
 
-  console.log(existingOntologies);
-
+  console.log('existing', existingOntologies);
   const onCheckboxChange = e => {
     const { value, checked } = e.target;
 

From 8824917a13efbd90ce41b1be2511a41141593162 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 21 Oct 2024 14:26:56 -0500
Subject: [PATCH 033/180] =?UTF-8?q?OntologyTable=20=E2=88=9A?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/components/About/OntologyTable.jsx | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/src/components/About/OntologyTable.jsx b/src/components/About/OntologyTable.jsx
index 905d099..a326572 100644
--- a/src/components/About/OntologyTable.jsx
+++ b/src/components/About/OntologyTable.jsx
@@ -1,10 +1,19 @@
 import { Button, Input, Space, Table } from 'antd';
 import { SearchOutlined } from '@ant-design/icons';
-import { useState } from 'react';
+import { useState, useEffect } from 'react';
 
 export const OntologyTable = ({ ontology }) => {
   const [filter, setFilter] = useState(null);
 
+  const [pageSize, setPageSize] = useState(
+    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+  const handleTableChange = (current, size) => {
+    setPageSize(size);
+  };
+  useEffect(() => {
+    localStorage.setItem('pageSize', pageSize);
+  }, [pageSize]);
+
   const ontologyTitle = () => {
     return (
       <div className="ontology_filter">
@@ -85,6 +94,8 @@ export const OntologyTable = ({ ontology }) => {
     }))
   );
 
+
+
   return (
     <Table
       columns={columns}
@@ -92,6 +103,12 @@ export const OntologyTable = ({ ontology }) => {
       scroll={{
         y: 470,
       }}
+      pagination={{
+        showSizeChanger: true,
+        pageSizeOptions: ['10', '20', '30'],
+        pageSize: pageSize, // Use the stored pageSize
+        onChange: handleTableChange, // Capture pagination changes
+      }}
     />
   );
 };

From 3beb65b2f0c6fa3bbbff6f1ed8d297fa58c6d9ff Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 21 Oct 2024 14:27:11 -0500
Subject: [PATCH 034/180] =?UTF-8?q?tableDetails=20=E2=88=9A?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/components/Projects/Tables/TableDetails.jsx | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 80a00a4..69eddd6 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -40,6 +40,11 @@ export const TableDetails = () => {
   const [loading, setLoading] = useState(true);
   const [load, setLoad] = useState(false);
 
+  const [pageSize, setPageSize] = useState(
+    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+  const handleTableChange = (current, size) => {
+    setPageSize(size);
+  };
   const navigate = useNavigate();
 
   const handleSuccess = () => {
@@ -49,7 +54,8 @@ export const TableDetails = () => {
 
   useEffect(() => {
     setDataSource(tableData(table));
-  }, [table, mapping]);
+    localStorage.setItem('pageSize', pageSize);
+  }, [table, mapping, pageSize]);
 
   const alphabetizeOntologies = ontologies => {
     // Sort the keys alphabetically
@@ -309,6 +315,12 @@ There is then a tooltip that displays the variables on hover.*/
                         record.data_type === 'INTEGER' ||
                         record.data_type === 'QUANTITY',
                     }}
+                    pagination={{
+                      showSizeChanger: true,
+                      pageSizeOptions: ['10', '20', '30'],
+                      pageSize: pageSize, // Use the stored pageSize
+                      onChange: handleTableChange, // Capture pagination changes
+                    }}
                   />
                 </Form>
                 <ExportFile table={table} />

From 945a8008078bf89b3a8682ad924adc378b8ec6d0 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 21 Oct 2024 14:27:21 -0500
Subject: [PATCH 035/180] =?UTF-8?q?Terminology=20=E2=88=9A?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../Projects/Terminologies/Terminology.jsx    | 20 ++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 65970cf..70d1f3a 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -33,6 +33,16 @@ export const Terminology = () => {
     setMapping,
   } = useContext(MappingContext);
 
+  const [pageSize, setPageSize] = useState(
+    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+  const handleTableChange = (current, size) => {
+    setPageSize(size);
+  };
+  useEffect(() => {
+    localStorage.setItem('pageSize', pageSize);
+  }, [pageSize]);
+
+
   const [loading, setLoading] = useState(true);
   const initialTerminology = { url: '', description: '', name: '', codes: [] }; //initial state of terminology
   const [terminology, setTerminology] = useState(initialTerminology);
@@ -248,7 +258,15 @@ There is then a tooltip that displays the codes on hover.*/
               <Spinner />
             ) : (
               <Form form={form}>
-                <Table columns={columns} dataSource={dataSource} />
+                <Table 
+                columns={columns} 
+                dataSource={dataSource}
+                pagination={{ 
+                  showSizeChanger: true,
+                  pageSizeOptions: ['10', '20', '30'],
+                  pageSize: pageSize, // Use the stored pageSize
+                  onChange: handleTableChange, // Capture pagination changes
+                }}  />
               </Form>
             )}
           </div>

From 234fe1e6039247cadc556ce734e6e339d4b7848e Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 21 Oct 2024 23:06:52 -0500
Subject: [PATCH 036/180] default ontologies checking by default

---
 src/App.jsx                                   |   1 -
 src/Contexts/SearchContext.jsx                |   2 +-
 src/components/Manager/FetchManager.jsx       |   9 +-
 .../MappingsFunctions/GetMappingsModal.jsx    | 193 +++++++++---------
 .../MappingsFunctions/OntologyCheckboxes.jsx  |  36 +++-
 .../Projects/Tables/TableDetails.jsx          |   1 +
 6 files changed, 133 insertions(+), 109 deletions(-)

diff --git a/src/App.jsx b/src/App.jsx
index 2096b18..4769f37 100644
--- a/src/App.jsx
+++ b/src/App.jsx
@@ -41,7 +41,6 @@ function App() {
     top: '25vh',
   });
   return (
-    
     <GoogleOAuthProvider clientId={clientId}>
       <myContext.Provider
         value={{
diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index ecfebde..d7098af 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -13,7 +13,7 @@ export function SearchContextRoot() {
   const [apiPage, setApiPage] = useState(0);
   const [apiTotalCount, setApiTotalCount] = useState();
   const [apiPreferences, setApiPreferences] = useState({});
-  const [apiPreferencesCode, setApiPreferencesCode] = useState('');
+  const [apiPreferencesCode, setApiPreferencesCode] = useState(undefined);
   const [unformattedPref, setUnformattedPref] = useState([]);
   const [facetCounts, setFacetCounts] = useState([]);
   const defaultOntologies = 'mondo,hp,maxo,ncit';
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 756ccf0..013c11c 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -234,10 +234,15 @@ export const getFiltersByCode = (
   setApiPreferencesCode,
   notification,
   apiPreferencesCode,
-  setUnformattedPref
+  setUnformattedPref,
+  table
 ) => {
   return fetch(
-    `${vocabUrl}/${component?.terminology?.reference}/filter/${mappingProp}`,
+    `${vocabUrl}/${
+      component === table
+        ? component?.terminology?.reference
+        : `Terminology/${component.id}`
+    }/filter/${mappingProp}`,
     {
       method: 'GET',
       headers: {
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 1e94ac1..902328d 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -9,7 +9,7 @@ import {
 } from 'antd';
 import { useContext, useEffect, useRef, useState } from 'react';
 import { myContext } from '../../../App';
-import { ellipsisString, ontologyCounts, systemsMatch } from '../Utilitiy';
+import { ellipsisString, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
@@ -23,6 +23,7 @@ export const GetMappingsModal = ({
   searchProp,
   component,
   mappingProp,
+  table,
 }) => {
   const [form] = Form.useForm();
   const { Search } = Input;
@@ -30,6 +31,7 @@ export const GetMappingsModal = ({
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
   const {
     apiPreferences,
+    setApiPreferences,
     defaultOntologies,
     setFacetCounts,
     setApiPreferencesCode,
@@ -71,17 +73,14 @@ export const GetMappingsModal = ({
         setApiPreferencesCode,
         notification,
         apiPreferencesCode,
-        setUnformattedPref
+        setUnformattedPref,
+        table
       );
     }
   }, [searchProp]);
 
   useEffect(() => {
-    if (apiPreferencesCode) {
-      fetchResults(0, searchProp); // Pass apiPreferencesCode correctly
-    } else {
-      fetchResults(0, searchProp);
-    }
+    if (apiPreferencesCode !== undefined) fetchResults(0, searchProp);
   }, [apiPreferencesCode, searchProp]);
 
   /* Pagination is handled via a "View More" link at the bottom of the page. 
@@ -89,7 +88,7 @@ export const GetMappingsModal = ({
   This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
   Because the content is in a modal and not the window, the closest class name to the modal is used for the location of the ref. */
   useEffect(() => {
-    if (results && page > 0) {
+    if (results?.length > 0 && page > 0) {
       const container = ref.current.closest('.ant-modal-body');
       const scrollTop = ref.current.offsetTop - container.offsetTop;
       container.scrollTop = scrollTop;
@@ -119,6 +118,8 @@ export const GetMappingsModal = ({
     setResults([]);
     setSelectedMappings([]);
     setDisplaySelectedMappings([]);
+    setApiPreferencesCode(undefined);
+    setApiPreferences([]);
     setSelectedBoxes([]);
     setSelectedKey(null);
   };
@@ -214,9 +215,7 @@ export const GetMappingsModal = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferencesCode !== ''
-          ? apiPreferencesCode
-          : apiPreferenceOntologies(),
+        apiPreferencesCode !== '' ? apiPreferencesCode : defaultOntologies,
         page,
         entriesPerPage,
         pageStart,
@@ -341,6 +340,7 @@ export const GetMappingsModal = ({
   };
 
   const filteredResultsArray = getFilteredResults();
+
   return (
     <>
       <Modal
@@ -351,7 +351,8 @@ export const GetMappingsModal = ({
         okText="Save"
         onOk={() => {
           form.validateFields().then(values => {
-            handleSubmit(values);
+            // handleSubmit(values);
+            console.log(values);
             onClose();
           });
         }}
@@ -382,98 +383,100 @@ export const GetMappingsModal = ({
                   </div>
                 </div>
                 {/* ant.design form displaying the checkboxes with the search results.  */}
-                {results?.length > 0 ? (
-                  <div className="result_container">
-                    <Form form={form} layout="vertical">
-                      <div className="all_checkboxes_container">
-                        <OntologyCheckboxes apiPreferences={apiPreferences} />
-                        <div className="result_form">
-                          {displaySelectedMappings?.length > 0 && (
+                <div className="result_container">
+                  <Form form={form} layout="vertical" preserve={false}>
+                    <div className="all_checkboxes_container">
+                      <OntologyCheckboxes apiPreferences={apiPreferences} />
+                      <div className="result_form">
+                        {results?.length > 0 ? (
+                          <>
+                            {displaySelectedMappings?.length > 0 && (
+                              <Form.Item
+                                name="selected_mappings"
+                                valuePropName="value"
+                                rules={[{ required: false }]}
+                              >
+                                <div className="modal_display_results">
+                                  {displaySelectedMappings?.map((sm, i) => (
+                                    <Checkbox
+                                      key={i}
+                                      checked={selectedBoxes.some(
+                                        box => box.obo_id === sm.obo_id
+                                      )}
+                                      value={sm}
+                                      onChange={e => onCheckboxChange(e, sm, i)}
+                                    >
+                                      {selectedTermsDisplay(sm, i)}
+                                    </Checkbox>
+                                  ))}
+                                </div>
+                              </Form.Item>
+                            )}
                             <Form.Item
-                              name="selected_mappings"
+                              name={['filtered_mappings']}
                               valuePropName="value"
-                              rules={[{ required: false }]}
+                              rules={[
+                                {
+                                  required: false,
+                                },
+                              ]}
                             >
-                              <div className="modal_display_results">
-                                {displaySelectedMappings?.map((sm, i) => (
-                                  <Checkbox
-                                    key={i}
-                                    checked={selectedBoxes.some(
-                                      box => box.obo_id === sm.obo_id
-                                    )}
-                                    value={sm}
-                                    onChange={e => onCheckboxChange(e, sm, i)}
-                                  >
-                                    {selectedTermsDisplay(sm, i)}
-                                  </Checkbox>
-                                ))}
-                              </div>
-                            </Form.Item>
-                          )}
-                          <Form.Item
-                            name={['filtered_mappings']}
-                            valuePropName="value"
-                            rules={[
-                              {
-                                required: false,
-                              },
-                            ]}
-                          >
-                            {filteredResultsArray?.length > 0 ? (
-                              <Checkbox.Group
-                                className="mappings_checkbox"
-                                options={filteredResultsArray?.map(
-                                  (d, index) => {
-                                    return {
-                                      value: JSON.stringify({
-                                        code: d.obo_id,
-                                        display: d.label,
-                                        description: d.description[0],
-                                        system: systemsMatch(
-                                          d?.obo_id.split(':')[0]
-                                        ),
-                                      }),
-                                      label: checkBoxDisplay(d, index),
-                                    };
-                                  }
-                                )}
-                                onChange={onSelectedChange}
-                              />
-                            ) : (
-                              ''
-                            )}
-                          </Form.Item>
-                        </div>
+                              {filteredResultsArray?.length > 0 ? (
+                                <Checkbox.Group
+                                  className="mappings_checkbox"
+                                  options={filteredResultsArray?.map(
+                                    (d, index) => {
+                                      return {
+                                        value: JSON.stringify({
+                                          code: d.obo_id,
+                                          display: d.label,
+                                          description: d.description[0],
+                                          system: systemsMatch(
+                                            d?.obo_id.split(':')[0]
+                                          ),
+                                        }),
+                                        label: checkBoxDisplay(d, index),
+                                      };
+                                    }
+                                  )}
+                                  onChange={onSelectedChange}
+                                />
+                              ) : (
+                                ''
+                              )}
+                            </Form.Item>{' '}
+                          </>
+                        ) : (
+                          <h3>No results found</h3>
+                        )}
                       </div>
-                    </Form>
-                    <div className="view_more_wrapper">
-                      {/* 'View More' pagination displaying the number of results being displayed
+                    </div>
+                  </Form>
+                  <div className="view_more_wrapper">
+                    {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
                       inconsistencies in results numbers per page. */}
-                      <Tooltip
-                        placement="bottom"
-                        title="Redundant entries have been removed"
+                    <Tooltip
+                      placement="bottom"
+                      title="Redundant entries have been removed"
+                    >
+                      Displaying {resultsCount}
+                      &nbsp;of&nbsp;{totalCount}
+                    </Tooltip>
+                    {totalCount - filteredResultsCount !== resultsCount && (
+                      <span
+                        className="view_more_link"
+                        onClick={e => {
+                          handleViewMore(e);
+                          setLastCount(resultsCount);
+                        }}
                       >
-                        Displaying {resultsCount}
-                        &nbsp;of&nbsp;{totalCount}
-                      </Tooltip>
-                      {totalCount - filteredResultsCount !== resultsCount && (
-                        <span
-                          className="view_more_link"
-                          onClick={e => {
-                            handleViewMore(e);
-                            setLastCount(resultsCount);
-                          }}
-                        >
-                          View More
-                        </span>
-                      )}
-                    </div>
+                        View More
+                      </span>
+                    )}
                   </div>
-                ) : (
-                  <h3>No results found.</h3>
-                )}
+                </div>
               </div>
             </>
           </div>
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 7b62408..e6085d9 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -8,16 +8,23 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
     useContext(SearchContext);
   const [checkedOntologies, setCheckedOntologies] = useState([]);
 
+  const defaultOntologies = ['mondo', 'hp', 'maxo', 'ncit'];
   const existingOntologies = apiPreferencesCode
     ? apiPreferencesCode
-    : Object.values(apiPreferences?.self?.api_preference).flat(); // Flatten arrays into a single array
+    : apiPreferences &&
+      apiPreferences?.self &&
+      apiPreferences?.self?.api_preference
+    ? Object?.values(apiPreferences?.self?.api_preference).flat()
+    : defaultOntologies;
 
   useEffect(() => {
-    setCheckedOntologies(existingOntologies); // Set the initial checked keys
+    setCheckedOntologies(existingOntologies);
   }, [apiPreferences]);
-  ``;
 
-  console.log('existing', existingOntologies);
+  console.log('default', defaultOntologies);
+  console.log('exsiting', existingOntologies);
+  console.log('checked', checkedOntologies);
+
   const onCheckboxChange = e => {
     const { value, checked } = e.target;
 
@@ -52,11 +59,18 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
 
   const formattedFacetCounts = ontologyCounts(facetCounts);
 
+  const existingOntologiesArray = Array.isArray(existingOntologies)
+    ? existingOntologies
+    : [];
+
+  const checkedOntologiesArray = Array.isArray(checkedOntologies)
+    ? checkedOntologies
+    : [];
   // Sort the `formattedFacetCounts` before rendering, not inside the `map()`
   const sortedFacetCounts = formattedFacetCounts?.sort(
     (a, b) =>
-      (existingOntologies.includes(Object.keys(a)[0]) ? -1 : 1) -
-      (existingOntologies.includes(Object.keys(b)[0]) ? -1 : 1)
+      (existingOntologiesArray?.includes(Object.keys(a)[0]) ? -1 : 1) -
+      (existingOntologiesArray?.includes(Object.keys(b)[0]) ? -1 : 1)
   );
 
   return (
@@ -72,16 +86,18 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
             const value = fc[key];
             formattedFacetCounts.sort(
               (a, b) =>
-                (existingOntologies.includes(Object.keys(a)[0]) ? -1 : 1) -
-                (existingOntologies.includes(Object.keys(b)[0]) ? -1 : 1)
+                (existingOntologiesArray?.includes(Object.keys(a)[0])
+                  ? -1
+                  : 1) -
+                (existingOntologiesArray?.includes(Object.keys(b)[0]) ? -1 : 1)
             );
 
             return (
               <Checkbox
                 key={i}
                 value={key}
-                checked={checkedOntologies.includes(key)} // Check if key is in checkedOntologies array
-                onChange={onCheckboxChange} // Handle the change
+                checked={checkedOntologiesArray?.includes(key)} // Check if key is in checkedOntologies array
+                onChange={onCheckboxChange}
               >
                 {`${key.toUpperCase()} ${value !== '0' ? `(${value})` : ''}`}
               </Checkbox>
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 863cb79..f1edf07 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -365,6 +365,7 @@ There is then a tooltip that displays the variables on hover.*/
         setMapping={setMapping}
         tableId={tableId}
         mappingProp={getMappings?.code}
+        table={table}
       />
       <ClearMappings propId={tableId} component={'Table'} />
     </>

From fe5ff4cd9180ba30ab45bdb4d11e9c7ab7400ef1 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Tue, 22 Oct 2024 14:38:28 -0500
Subject: [PATCH 037/180] c2c

---
 .../Projects/Tables/TableDetails.jsx          | 36 ++++++++++---------
 1 file changed, 19 insertions(+), 17 deletions(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 80a00a4..744e922 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -48,6 +48,7 @@ export const TableDetails = () => {
   const login = RequiredLogin({ handleSuccess: handleSuccess });
 
   useEffect(() => {
+
     setDataSource(tableData(table));
   }, [table, mapping]);
 
@@ -177,22 +178,24 @@ The function maps through the mapping array. For each variable, if the mapping v
 variable in the table, AND the mappings array length for the variable is > 0, the mappings array is mapped through
 and returns the length of the mapping array (i.e. returns the number of variables mapped to the table variable). 
 There is then a tooltip that displays the variables on hover.*/
-  const matchCode = variable =>
-    mapping?.length > 0 &&
-    mapping?.map(
-      (item, index) =>
-        item?.code === variable?.code &&
-        item?.mappings?.length > 0 && (
-          <Tooltip
-            title={item.mappings.map(code => {
-              return <div key={index}>{code.code}</div>;
-            })}
-            key={index}
-          >
-            {item?.mappings?.length}
-          </Tooltip>
-        )
-    );
+const noMapping = "noMapping"
+const matchCode = variable => {
+  if (!mapping?.length) { 
+    return noMapping; // Return "noMapping" if there are no mappings
+  }
+
+  const mappedTerms = mapping.map((item, index) => { 
+    if (item?.code === variable?.code && item?.mappings?.length) {
+      return item.mappings.map(code => <div key={index}>{code.display}</div>);
+    } 
+    return null; // Return null if no match is found for this variable
+  });
+
+  // Check if any mappings were found for this variable
+  return mappedTerms.some(term => term !== null) ? mappedTerms : noMapping; 
+};
+
+
 
   // data for the table columns. Each table has an array of variables. Each variable has a name, description, and data type.
   // The integer and quantity data types include additional details.
@@ -365,7 +368,6 @@ There is then a tooltip that displays the variables on hover.*/
         setMapping={setMapping}
         tableId={tableId}
         mappingProp={getMappings?.code}
-        mappingDesc={getMappings?.description ? getMappings?.description : 'No Description'}
       />
       <ClearMappings propId={tableId} component={'Table'} />
     </>

From 11bb27a5ff7c3398ed299fbcc453e0e56dfd8d84 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Tue, 22 Oct 2024 15:06:34 -0500
Subject: [PATCH 038/180] user and access the setmapping window from table

---
 .../Projects/Tables/TableDetails.jsx          | 31 ++++++++++---------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 744e922..375d3fc 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -178,22 +178,25 @@ The function maps through the mapping array. For each variable, if the mapping v
 variable in the table, AND the mappings array length for the variable is > 0, the mappings array is mapped through
 and returns the length of the mapping array (i.e. returns the number of variables mapped to the table variable). 
 There is then a tooltip that displays the variables on hover.*/
-const noMapping = "noMapping"
-const matchCode = variable => {
-  if (!mapping?.length) { 
-    return noMapping; // Return "noMapping" if there are no mappings
+const noMapping = variable => {
+return <button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
+    noMapping
+  </button>
   }
 
-  const mappedTerms = mapping.map((item, index) => { 
-    if (item?.code === variable?.code && item?.mappings?.length) {
-      return item.mappings.map(code => <div key={index}>{code.display}</div>);
-    } 
-    return null; // Return null if no match is found for this variable
-  });
-
-  // Check if any mappings were found for this variable
-  return mappedTerms.some(term => term !== null) ? mappedTerms : noMapping; 
-};
+  const matchCode = variable => {
+    if (!mapping?.length) {
+      return noMapping(variable);
+    }
+  
+    const variableMappings = mapping.find(item => item?.code === variable?.code); 
+  
+    if (variableMappings && variableMappings.mappings?.length) {
+      return variableMappings.mappings.map(code => <div key={code.id}>{code.display}</div>);
+    } else {
+      return noMapping(variable);
+    }
+  };
 
 
 

From d4096f53a0d1e8537a6f5497968cc6c18f970374 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Tue, 22 Oct 2024 15:08:11 -0500
Subject: [PATCH 039/180] user and access the setmapping window from table

---
 src/components/Projects/Tables/TableDetails.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 375d3fc..71de573 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -180,7 +180,7 @@ and returns the length of the mapping array (i.e. returns the number of variable
 There is then a tooltip that displays the variables on hover.*/
 const noMapping = variable => {
 return <button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
-    noMapping
+    Set Mapping
   </button>
   }
 

From eec9f38c5c14c68ccfe1684c5bcfcbe47709716a Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 22 Oct 2024 15:24:52 -0500
Subject: [PATCH 040/180] all ontologies listed with checkboxes

---
 src/Contexts/SearchContext.jsx                |   4 +
 .../Manager/MappingsFunctions/FilterReset.jsx |   2 +-
 .../MappingsFunctions/FilterSelect.jsx        |   3 +-
 .../MappingsFunctions/GetMappingsModal.jsx    |   1 -
 .../MappingsFunctions/OntologyCheckboxes.jsx  | 103 ++++++++++--------
 5 files changed, 63 insertions(+), 50 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index d7098af..1266910 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -16,6 +16,8 @@ export function SearchContextRoot() {
   const [apiPreferencesCode, setApiPreferencesCode] = useState(undefined);
   const [unformattedPref, setUnformattedPref] = useState([]);
   const [facetCounts, setFacetCounts] = useState([]);
+  const [ontologyApis, setOntologyApis] = useState([]);
+
   const defaultOntologies = 'mondo,hp,maxo,ncit';
 
   const context = {
@@ -44,6 +46,8 @@ export function SearchContextRoot() {
     setFacetCounts,
     unformattedPref,
     setUnformattedPref,
+    ontologyApis,
+    setOntologyApis,
   };
 
   return (
diff --git a/src/components/Manager/MappingsFunctions/FilterReset.jsx b/src/components/Manager/MappingsFunctions/FilterReset.jsx
index ac37e40..d1229fe 100644
--- a/src/components/Manager/MappingsFunctions/FilterReset.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterReset.jsx
@@ -12,7 +12,7 @@ export const FilterReset = ({ table }) => {
   const [remove, setRemove] = useState(false);
 
   const deleteOntologies = evt => {
-    return fetch(`${vocabUrl}/${table?.terminology?.reference}/filter`, {
+    return fetch(`${vocabUrl}/${table?.terminology?.reference}/filter/self`, {
       method: 'DELETE',
       headers: {
         'Content-Type': 'application/json',
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index 538f380..d763a39 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -5,6 +5,7 @@ import { myContext } from '../../../App';
 import { FilterAPI } from './FilterAPI';
 import { getOntologies } from '../FetchManager';
 import { ModalSpinner } from '../Spinner';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
   const [form] = Form.useForm();
@@ -19,7 +20,7 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
   const [active, setActive] = useState(null);
   const [loading, setLoading] = useState(false);
   const { user, vocabUrl, ontologyForPagination } = useContext(myContext);
-  const [ontologyApis, setOntologyApis] = useState([]);
+  const { ontologyApis, setOntologyApis } = useContext(SearchContext);
   const [searchText, setSearchText] = useState('');
 
   // Gets the ontologyAPIs on first load, automatically sets active to the first of the list to display on the page
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 902328d..2f7dcb7 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -119,7 +119,6 @@ export const GetMappingsModal = ({
     setSelectedMappings([]);
     setDisplaySelectedMappings([]);
     setApiPreferencesCode(undefined);
-    setApiPreferences([]);
     setSelectedBoxes([]);
     setSelectedKey(null);
   };
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index e6085d9..61482ed 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -4,8 +4,12 @@ import { useContext, useEffect, useState } from 'react';
 import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const OntologyCheckboxes = ({ apiPreferences }) => {
-  const { apiPreferencesCode, setApiPreferencesCode, facetCounts } =
-    useContext(SearchContext);
+  const {
+    apiPreferencesCode,
+    setApiPreferencesCode,
+    facetCounts,
+    ontologyApis,
+  } = useContext(SearchContext);
   const [checkedOntologies, setCheckedOntologies] = useState([]);
 
   const defaultOntologies = ['mondo', 'hp', 'maxo', 'ncit'];
@@ -21,35 +25,26 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
     setCheckedOntologies(existingOntologies);
   }, [apiPreferences]);
 
-  console.log('default', defaultOntologies);
-  console.log('exsiting', existingOntologies);
-  console.log('checked', checkedOntologies);
-
   const onCheckboxChange = e => {
     const { value, checked } = e.target;
 
     setCheckedOntologies(existingOntologies => {
-      // Ensure existingOntologies is always an array
       const newCheckedOntologies = Array.isArray(existingOntologies)
         ? checked
-          ? [...existingOntologies, value] // Add value if checked
-          : existingOntologies.filter(key => key !== value) // Remove value if unchecked
-        : []; // Fallback to an empty array if it's not an array
+          ? [...existingOntologies, value]
+          : existingOntologies.filter(key => key !== value)
+        : [];
 
-      // Update apiPreferencesCode
       setApiPreferencesCode(existingCode => {
         if (checked) {
-          // Add value if checked, and avoid duplications
           return existingCode ? `${existingCode},${value}` : value;
         } else {
-          // Remove value if unchecked, handling cases where the string might be empty
           const updatedCode = existingCode
             .split(',')
-            .filter(code => code !== value) // Remove the unchecked value
+            .filter(code => code !== value)
             .join(',');
 
-          // Ensure there's no trailing comma
-          return updatedCode.replace(/,$/, '');
+          return updatedCode;
         }
       });
 
@@ -59,19 +54,35 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
 
   const formattedFacetCounts = ontologyCounts(facetCounts);
 
-  const existingOntologiesArray = Array.isArray(existingOntologies)
-    ? existingOntologies
-    : [];
+  const sortedData = ontologyApis.map(api => {
+    const sortedOntologies = Object.fromEntries(
+      Object.entries(api.ontologies).sort((a, b) =>
+        a[1].ontology_code > b[1].ontology_code ? 1 : -1
+      )
+    );
+
+    return {
+      ...api,
+      ontologies: sortedOntologies,
+    };
+  });
+
+  const countsMap = formattedFacetCounts.reduce((acc, item) => {
+    const key = Object.keys(item)[0];
+    acc[key] = parseInt(item[key], 10);
+    return acc;
+  }, {});
+
+  // // Build the new data structure
+  const countsResult = Object.keys(sortedData[0].ontologies).map(key => {
+    return { [key]: countsMap[key] || 0 };
+  });
 
   const checkedOntologiesArray = Array.isArray(checkedOntologies)
     ? checkedOntologies
     : [];
-  // Sort the `formattedFacetCounts` before rendering, not inside the `map()`
-  const sortedFacetCounts = formattedFacetCounts?.sort(
-    (a, b) =>
-      (existingOntologiesArray?.includes(Object.keys(a)[0]) ? -1 : 1) -
-      (existingOntologiesArray?.includes(Object.keys(b)[0]) ? -1 : 1)
-  );
+
+  console.log(checkedOntologiesArray);
 
   return (
     <div className="ontology_form">
@@ -81,28 +92,26 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
         rules={[{ required: false }]}
       >
         <div className="modal_display_results">
-          {sortedFacetCounts?.map((fc, i) => {
-            const key = Object.keys(fc)[0];
-            const value = fc[key];
-            formattedFacetCounts.sort(
-              (a, b) =>
-                (existingOntologiesArray?.includes(Object.keys(a)[0])
-                  ? -1
-                  : 1) -
-                (existingOntologiesArray?.includes(Object.keys(b)[0]) ? -1 : 1)
-            );
-
-            return (
-              <Checkbox
-                key={i}
-                value={key}
-                checked={checkedOntologiesArray?.includes(key)} // Check if key is in checkedOntologies array
-                onChange={onCheckboxChange}
-              >
-                {`${key.toUpperCase()} ${value !== '0' ? `(${value})` : ''}`}
-              </Checkbox>
-            );
-          })}
+          {countsResult
+            ?.sort((a, b) => {
+              const aValue = Object.values(a)[0];
+              const bValue = Object.values(b)[0];
+              return bValue - aValue;
+            })
+            .map((fc, i) => {
+              const key = Object.keys(fc)[0];
+              const value = fc[key];
+              return (
+                <Checkbox
+                  key={i}
+                  value={key}
+                  checked={checkedOntologiesArray?.includes(key)}
+                  onChange={onCheckboxChange}
+                >
+                  {`${key.toUpperCase()} ${value !== 0 ? `(${value})` : ''}`}
+                </Checkbox>
+              );
+            })}
         </div>
       </Form.Item>
     </div>

From 674320612443a6c8f24e7841784d38c43eb71034 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 22 Oct 2024 16:04:25 -0500
Subject: [PATCH 041/180] checkboxes checking and updating apiPreferencesCode

---
 .../MappingsFunctions/OntologyCheckboxes.jsx       | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 61482ed..addba01 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -13,6 +13,7 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
   const [checkedOntologies, setCheckedOntologies] = useState([]);
 
   const defaultOntologies = ['mondo', 'hp', 'maxo', 'ncit'];
+
   const existingOntologies = apiPreferencesCode
     ? apiPreferencesCode
     : apiPreferences &&
@@ -35,18 +36,7 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
           : existingOntologies.filter(key => key !== value)
         : [];
 
-      setApiPreferencesCode(existingCode => {
-        if (checked) {
-          return existingCode ? `${existingCode},${value}` : value;
-        } else {
-          const updatedCode = existingCode
-            .split(',')
-            .filter(code => code !== value)
-            .join(',');
-
-          return updatedCode;
-        }
-      });
+      setApiPreferencesCode(newCheckedOntologies);
 
       return newCheckedOntologies;
     });

From f0f3d9e7f7c2444fdd9458e011ae4d7de4fa0f22 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 08:45:39 -0500
Subject: [PATCH 042/180] adding delete mapping from table

---
 .../Projects/Tables/TableDetails.jsx          | 76 ++++++++++++++++---
 1 file changed, 67 insertions(+), 9 deletions(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 71de573..a8b353b 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -4,7 +4,7 @@ import './TableStyling.scss';
 import { Link, useNavigate, useParams } from 'react-router-dom';
 import { Spinner } from '../../Manager/Spinner';
 import { getById } from '../../Manager/FetchManager';
-import { Card, Col, Form, notification, Row, Table, Tooltip } from 'antd';
+import { Card, Col, Form, notification, Row, Table, Button } from 'antd';
 import { EditTableDetails } from './EditTableDetails';
 import { DeleteTable } from './DeleteTable';
 import { LoadVariables } from './LoadVariables';
@@ -52,6 +52,51 @@ export const TableDetails = () => {
     setDataSource(tableData(table));
   }, [table, mapping]);
 
+
+  const updateMappings = (mapArr,mappingCode ) => {
+    
+    // setLoading(true);
+    const mappingsDTO = {
+      mappings: mapArr,
+      editor: user.email,
+    };
+    console.log(mappingsDTO,"mappingsDTO");
+    
+    fetch(`${vocabUrl}/Table/${tableId}/mapping/${mappingCode}`, {
+      method: 'PUT',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify(mappingsDTO),
+    })
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .then(data => {
+        setMapping(data.codes);
+        setEditMappings(null);
+        form.resetFields();
+        notification.success({ description:'Mapping removed.'});
+      })
+      .catch(error => {
+        console.log(error,'error');
+        
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred. Please try again.',
+          });
+        }
+        return error;
+      })
+      .finally(() => setLoading(false));
+  };
+
+
   const alphabetizeOntologies = ontologies => {
     // Sort the keys alphabetically
     const sortedKeys = Object.keys(ontologies).sort();
@@ -79,6 +124,8 @@ export const TableDetails = () => {
               .then(data => setMapping(data.codes))
               .catch(error => {
                 if (error) {
+                  console.log(error,"error");
+                  
                   notification.error({
                     message: 'Error',
                     description: 'An error occurred loading mappings.',
@@ -178,26 +225,37 @@ The function maps through the mapping array. For each variable, if the mapping v
 variable in the table, AND the mappings array length for the variable is > 0, the mappings array is mapped through
 and returns the length of the mapping array (i.e. returns the number of variables mapped to the table variable). 
 There is then a tooltip that displays the variables on hover.*/
-const noMapping = variable => {
-return <button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
-    Set Mapping
-  </button>
+  const noMapping = variable => {
+    return <Button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
+      Get Mapping
+    </Button>
   }
 
   const matchCode = variable => {
+
+
     if (!mapping?.length) {
       return noMapping(variable);
     }
-  
-    const variableMappings = mapping.find(item => item?.code === variable?.code); 
-  
+
+    const variableMappings = mapping.find(item => item?.code === variable?.code);
+
     if (variableMappings && variableMappings.mappings?.length) {
-      return variableMappings.mappings.map(code => <div key={code.id}>{code.display}</div>);
+      return variableMappings.mappings.map(code => <div key={code.display}><span onClick={() => handleRemoveMapping(variableMappings,code)}>X </span>{code.display}</div>);
     } else {
       return noMapping(variable);
     }
   };
 
+  const handleRemoveMapping = (variableMappings,code) => {
+    // console.log(variableMappings,"variableMappings");
+    const mappingToRemove = variableMappings.mappings.indexOf(code);
+    //remove mapping from mappings
+    {mappingToRemove !== -1 && variableMappings.mappings.splice(mappingToRemove,1)}   
+    updateMappings(variableMappings?.mappings,variableMappings?.code);    
+  
+  }
+
 
 
   // data for the table columns. Each table has an array of variables. Each variable has a name, description, and data type.

From 16832f2a0507f0e29ee1fb5072cede2433c47215 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 08:47:09 -0500
Subject: [PATCH 043/180] adding ant icons

---
 package-lock.json | 15 ++++++++-------
 package.json      |  1 +
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index e277d09..419d30d 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -8,6 +8,7 @@
       "name": "vocab-management-tool",
       "version": "0.0.0",
       "dependencies": {
+        "@ant-design/icons": "^5.5.1",
         "@react-oauth/google": "^0.12.1",
         "antd": "^5.15.2",
         "jwt-decode": "^4.0.0",
@@ -77,13 +78,13 @@
       }
     },
     "node_modules/@ant-design/icons": {
-      "version": "5.3.7",
-      "resolved": "https://registry.npmjs.org/@ant-design/icons/-/icons-5.3.7.tgz",
-      "integrity": "sha512-bCPXTAg66f5bdccM4TT21SQBDO1Ek2gho9h3nO9DAKXJP4sq+5VBjrQMSxMVXSB3HyEz+cUbHQ5+6ogxCOpaew==",
+      "version": "5.5.1",
+      "resolved": "https://registry.npmjs.org/@ant-design/icons/-/icons-5.5.1.tgz",
+      "integrity": "sha512-0UrM02MA2iDIgvLatWrj6YTCYe0F/cwXvVE0E2SqGrL7PZireQwgEKTKBisWpZyal5eXZLvuM98kju6YtYne8w==",
       "dependencies": {
         "@ant-design/colors": "^7.0.0",
         "@ant-design/icons-svg": "^4.4.0",
-        "@babel/runtime": "^7.11.2",
+        "@babel/runtime": "^7.24.8",
         "classnames": "^2.2.6",
         "rc-util": "^5.31.1"
       },
@@ -394,9 +395,9 @@
       }
     },
     "node_modules/@babel/runtime": {
-      "version": "7.24.7",
-      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.24.7.tgz",
-      "integrity": "sha512-UwgBRMjJP+xv857DCngvqXI3Iq6J4v0wXmwc6sapg+zyhbwmQX67LUEFrkK5tbyJ30jGuG3ZvWpBiB9LCy1kWw==",
+      "version": "7.25.9",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.25.9.tgz",
+      "integrity": "sha512-4zpTHZ9Cm6L9L+uIqghQX8ZXg8HKFcjYO3qHoO8zTmRm6HQUJ8SSJ+KRvbMBZn0EGVlT4DRYeQ/6hjlyXBh+Kg==",
       "dependencies": {
         "regenerator-runtime": "^0.14.0"
       },
diff --git a/package.json b/package.json
index 5855550..38334e7 100644
--- a/package.json
+++ b/package.json
@@ -12,6 +12,7 @@
     "preview": "vite preview"
   },
   "dependencies": {
+    "@ant-design/icons": "^5.5.1",
     "@react-oauth/google": "^0.12.1",
     "antd": "^5.15.2",
     "jwt-decode": "^4.0.0",

From d0be76d103d33a4320b68279d838d499640fba5b Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 09:13:04 -0500
Subject: [PATCH 044/180] adding styling

---
 .../Projects/Tables/TableDetails.jsx           |  3 ++-
 .../Projects/Tables/TableStyling.scss          | 18 ++++++++++++++++++
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index a8b353b..d5f93e5 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -5,6 +5,7 @@ import { Link, useNavigate, useParams } from 'react-router-dom';
 import { Spinner } from '../../Manager/Spinner';
 import { getById } from '../../Manager/FetchManager';
 import { Card, Col, Form, notification, Row, Table, Button } from 'antd';
+import { CloseCircleOutlined } from '@ant-design/icons';
 import { EditTableDetails } from './EditTableDetails';
 import { DeleteTable } from './DeleteTable';
 import { LoadVariables } from './LoadVariables';
@@ -241,7 +242,7 @@ There is then a tooltip that displays the variables on hover.*/
     const variableMappings = mapping.find(item => item?.code === variable?.code);
 
     if (variableMappings && variableMappings.mappings?.length) {
-      return variableMappings.mappings.map(code => <div key={code.display}><span onClick={() => handleRemoveMapping(variableMappings,code)}>X </span>{code.display}</div>);
+      return variableMappings.mappings.map(code => <div className='mapping' key={code.display}><span className='mapping-display'>{code.display}</span><span className='remove-mapping' onClick={() => handleRemoveMapping(variableMappings,code)}><CloseCircleOutlined  style={{color:"red", }} /></span></div>);
     } else {
       return noMapping(variable);
     }
diff --git a/src/components/Projects/Tables/TableStyling.scss b/src/components/Projects/Tables/TableStyling.scss
index 4cf5288..4767acb 100644
--- a/src/components/Projects/Tables/TableStyling.scss
+++ b/src/components/Projects/Tables/TableStyling.scss
@@ -54,6 +54,7 @@ input::file-selector-button:hover {
   border: 1px solid darkgrey;
   color: gray;
   border-radius: 25px;
+
   font: {
     size: 0.7rem;
     weight: 800;
@@ -74,3 +75,20 @@ input::file-selector-button:hover {
   gap: 10px;
   margin-left: 50px;
 }
+
+.mapping {
+  &-display{
+    white-space: nowrap;
+  }
+  display: flex;
+  .remove-mapping {
+    padding-left:.25rem;
+    cursor: pointer;
+    opacity: 0;
+
+    &:hover {
+      transition: all .4s linear;
+      opacity: 1;
+    }
+  }
+}
\ No newline at end of file

From 7e229972e793c996eb3d31ea29c047ad9d324745 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 09:29:40 -0500
Subject: [PATCH 045/180] Get MappingS

---
 src/components/Projects/Tables/TableDetails.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index d5f93e5..f0f2afb 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -228,7 +228,7 @@ and returns the length of the mapping array (i.e. returns the number of variable
 There is then a tooltip that displays the variables on hover.*/
   const noMapping = variable => {
     return <Button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
-      Get Mapping
+      Get Mappings
     </Button>
   }
 

From 7fb589c289d7ba886b5ad336823209e6fa996d15 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 09:31:07 -0500
Subject: [PATCH 046/180] updating comment

---
 src/components/Projects/Tables/TableDetails.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index f0f2afb..f570285 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -225,7 +225,7 @@ The variables in the mappings need to be matched up to each variable in the tabl
 The function maps through the mapping array. For each variable, if the mapping variable is equal to the 
 variable in the table, AND the mappings array length for the variable is > 0, the mappings array is mapped through
 and returns the length of the mapping array (i.e. returns the number of variables mapped to the table variable). 
-There is then a tooltip that displays the variables on hover.*/
+It then shows the mappings as table data and alows the user to delete a mapping from the table.*/
   const noMapping = variable => {
     return <Button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
       Get Mappings

From 7624d02aa2fcbdb7b01dc54573e477a52ef4a274 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 23 Oct 2024 12:22:07 -0500
Subject: [PATCH 047/180] Ontology filter payload for code

---
 .../OntologyFilterCodeSubmit.jsx              | 71 +++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx

diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
new file mode 100644
index 0000000..6750a98
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
@@ -0,0 +1,71 @@
+import { notification } from 'antd';
+
+export const OntologyFilterCodeSubmit = (
+  apiPreferencesCode,
+  setApiPreferencesCode,
+  apiPreferences,
+  mappingProp,
+  table,
+  vocabUrl
+) => {
+  const apiPreference = {
+    api_preference: { 'ols': [] },
+  };
+
+  if (
+    apiPreferencesCode &&
+    JSON.stringify(
+      Object.values(apiPreferences?.self?.api_preference)[0].sort()
+    ) !== JSON.stringify(apiPreferencesCode?.sort())
+  ) {
+    apiPreference.api_preference.ols = apiPreferencesCode;
+
+    fetch(
+      `${vocabUrl}/${table?.terminology?.reference}/filter/${mappingProp}`,
+      {
+        method: 'POST',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify(apiPreference),
+      }
+    )
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .then(() =>
+        fetch(
+          `${vocabUrl}/${table?.terminology?.reference}/filter/${mappingProp}`,
+          {
+            method: 'GET',
+            headers: {
+              'Content-Type': 'application/json',
+            },
+          }
+        )
+      )
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .then(data => {
+        setApiPreferencesCode(data);
+      })
+      .catch(error => {
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred saving the ontology preferences.',
+          });
+        }
+        return error;
+      });
+  }
+};

From 1d567fe0180deb76217868bd677c3bba12585ebb Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 14:02:56 -0500
Subject: [PATCH 048/180] sticky nav

---
 src/AppRouter.jsx                  | 2 ++
 src/components/Nav/Breadcrumbs.jsx | 3 +++
 src/components/Nav/NavBar.scss     | 2 +-
 3 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 src/components/Nav/Breadcrumbs.jsx

diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index 4892b4b..813839c 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -1,6 +1,7 @@
 import { OntologySearch } from './components/Search/OntologySearch';
 import { BrowserRouter, Outlet, Route, Routes } from 'react-router-dom';
 import { NavBar } from './components/Nav/NavBar';
+import { Breadcrumbs } from './components/Nav/Breadcrumbs.jsx';
 import { Footer } from './components/Nav/Footer';
 import { SearchResults } from './components/Search/SearchResults';
 import { Terminology } from './components/Projects/Terminologies/Terminology';
@@ -27,6 +28,7 @@ export const AppRouter = () => {
             <>
               <div className="approuter_div">
                 <NavBar />
+                <Breadcrumbs/>
                 <div className="outlet_div">
                   <Outlet />
                 </div>
diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
new file mode 100644
index 0000000..6e32a4b
--- /dev/null
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -0,0 +1,3 @@
+export const Breadcrumbs = () =>{
+   return <h1>sup breadcrumb</h1>
+}
\ No newline at end of file
diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index 25c21e9..b5cc79a 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -11,7 +11,7 @@ nav {
   display: flex;
   flex-direction: row;
   justify-content: center;
-  position: fixed;
+  position: sticky;
   top: 0;
   li {
     list-style-type: none;

From 04e6b32a3f8676a81a727f722c8bfddb1bf9ac8a Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 23 Oct 2024 15:21:58 -0500
Subject: [PATCH 049/180] Saving preferred ontologies for code

---
 src/components/Manager/FetchManager.jsx       |   4 +-
 .../Manager/MappingsFunctions/FilterAPI.jsx   |   7 -
 .../MappingsFunctions/FilterOntology.jsx      |   3 +-
 .../MappingsFunctions/GetMappingsModal.jsx    |  25 +-
 .../MappingsFunctions/MappingReset.jsx        | 207 ++++++++------
 .../MappingsFunctions/MappingSearch.jsx       | 265 ++++++++++--------
 .../MappingsFunctions/OntologyCheckboxes.jsx  |  22 +-
 src/components/Nav/NavBar.jsx                 |   4 +-
 .../Tables/EditMappingsTableModal.jsx         |  10 +
 .../Projects/Tables/TableDetails.jsx          |   1 +
 10 files changed, 326 insertions(+), 222 deletions(-)

diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 013c11c..57c5b86 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -224,7 +224,7 @@ export const olsFilterOntologiesSearch = (
       setResultsCount(res.results.length);
       setFacetCounts(data?.facet_counts?.facet_fields?.ontologyPreferredPrefix);
     })
-    .then(() => setLoading(false));
+    .finally(() => setLoading(false));
 };
 
 export const getFiltersByCode = (
@@ -241,7 +241,7 @@ export const getFiltersByCode = (
     `${vocabUrl}/${
       component === table
         ? component?.terminology?.reference
-        : `Terminology/${component.id}`
+        : `Terminology/${component?.id}`
     }/filter/${mappingProp}`,
     {
       method: 'GET',
diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 8998711..183cd3b 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -43,13 +43,6 @@ export const FilterAPI = ({
     )
     .flat();
 
-  // The initial value for the form. The checkboxes for the filters that have already been selected will be checked by default
-  const initialChecked = flattenedFilters?.map(ef =>
-    JSON.stringify({
-      ontology: ef,
-    })
-  );
-
   // Fetches the active ontologyAPI each time the active API changes
   useEffect(() => {
     active && getOntologyApiById();
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 9ed6e40..d62a5a3 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -17,8 +17,7 @@ export const FilterOntology = ({
   table,
 }) => {
   const [allCheckboxes, setAllCheckboxes] = useState([]);
-  const { ontologyForPagination, setOntologyForPagination } =
-    useContext(myContext);
+  const { setOntologyForPagination } = useContext(myContext);
 
   useEffect(() => {
     setOntologyForPagination(ontology);
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 2f7dcb7..03dd47f 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -15,6 +15,7 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
+import { OntologyFilterCodeSubmit } from './OntologyFilterCodeSubmit';
 
 export const GetMappingsModal = ({
   componentString,
@@ -31,7 +32,6 @@ export const GetMappingsModal = ({
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
   const {
     apiPreferences,
-    setApiPreferences,
     defaultOntologies,
     setFacetCounts,
     setApiPreferencesCode,
@@ -83,6 +83,12 @@ export const GetMappingsModal = ({
     if (apiPreferencesCode !== undefined) fetchResults(0, searchProp);
   }, [apiPreferencesCode, searchProp]);
 
+  useEffect(() => {
+    if (!!currentSearchProp) {
+      fetchResults(page, currentSearchProp);
+    }
+  }, [page, currentSearchProp]);
+
   /* Pagination is handled via a "View More" link at the bottom of the page. 
   Each click on the "View More" link makes an API call to fetch the next 15 results.
   This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
@@ -143,7 +149,7 @@ export const GetMappingsModal = ({
       mappings: selectedMappings,
       editor: user.email,
     };
-
+    setLoading(true);
     fetch(
       `${vocabUrl}/${componentString}/${component.id}/mapping/${mappingProp}`,
       {
@@ -166,7 +172,18 @@ export const GetMappingsModal = ({
         form.resetFields();
         setGetMappings(null);
         message.success('Changes saved successfully.');
-      });
+      })
+      .then(() =>
+        OntologyFilterCodeSubmit(
+          apiPreferencesCode,
+          setApiPreferencesCode,
+          apiPreferences,
+          mappingProp,
+          table,
+          vocabUrl
+        )
+      )
+      .finally(() => setLoading(false));
   };
 
   const fetchResults = (page, query) => {
@@ -350,7 +367,7 @@ export const GetMappingsModal = ({
         okText="Save"
         onOk={() => {
           form.validateFields().then(values => {
-            // handleSubmit(values);
+            handleSubmit(values);
             console.log(values);
             onClose();
           });
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 2da7ae0..ed05747 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -1,21 +1,31 @@
-import { Checkbox, Form, Input, Tooltip } from 'antd';
+import { Checkbox, Form, Input, notification, Tooltip } from 'antd';
 import { useContext, useEffect, useRef, useState } from 'react';
 import { myContext } from '../../../App';
 import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
-import { olsFilterOntologiesSearch } from '../FetchManager';
+import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import { OntologyCheckboxes } from './OntologyCheckboxes';
 
 export const MappingReset = ({
   searchProp,
   setEditMappings,
   form,
   onClose,
+  component,
+  mappingProp,
+  table,
 }) => {
-  const { searchUrl } = useContext(myContext);
-  const { apiPreferences, defaultOntologies, facetCounts, setFacetCounts } =
-    useContext(SearchContext);
+  const { searchUrl, vocabUrl } = useContext(myContext);
+  const {
+    apiPreferences,
+    defaultOntologies,
+    setFacetCounts,
+    setApiPreferencesCode,
+    apiPreferencesCode,
+    setUnformattedPref,
+  } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 15;
   const [loading, setLoading] = useState(true);
@@ -46,10 +56,23 @@ export const MappingReset = ({
     setCurrentSearchProp(searchProp);
     setPage(0);
     if (!!searchProp) {
-      fetchResults(0, searchProp);
+      getFiltersByCode(
+        vocabUrl,
+        component,
+        mappingProp,
+        setApiPreferencesCode,
+        notification,
+        apiPreferencesCode,
+        setUnformattedPref,
+        table
+      );
     }
   }, [searchProp]);
 
+  useEffect(() => {
+    if (apiPreferencesCode !== undefined) fetchResults(0, searchProp);
+  }, [apiPreferencesCode, searchProp]);
+
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the code and when the page changes.
@@ -64,7 +87,7 @@ export const MappingReset = ({
   This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
   Because the content is in a modal and not the window, the closest class name to the modal is used for the location of the ref. */
   useEffect(() => {
-    if (results && page > 0) {
+    if (results?.length > 0 && page > 0) {
       const container = ref.current.closest('.ant-modal-body');
       const scrollTop = ref.current.offsetTop - container.offsetTop;
       container.scrollTop = scrollTop;
@@ -124,7 +147,9 @@ export const MappingReset = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferenceOntologies(),
+        apiPreferencesCode !== ''
+          ? apiPreferencesCode
+          : apiPreferenceOntologies(),
         page,
         entriesPerPage,
         pageStart,
@@ -141,7 +166,7 @@ export const MappingReset = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        defaultOntologies,
+        apiPreferencesCode !== '' ? apiPreferencesCode : defaultOntologies,
         page,
         entriesPerPage,
         pageStart,
@@ -292,91 +317,101 @@ export const MappingReset = ({
                   </div>
                 </div>
                 {/* ant.design form displaying the checkboxes with the search results.  */}
-                {results?.length > 0 ? (
-                  <div className="result_container">
-                    <Form form={form} layout="vertical">
-                      {displaySelectedMappings?.length > 0 && (
-                        <Form.Item
-                          name="selected_mappings"
-                          valuePropName="value"
-                          rules={[{ required: false }]}
-                        >
-                          {' '}
-                          <div className="modal_display_results">
-                            {displaySelectedMappings?.map((sm, i) => (
-                              <Checkbox
-                                key={i}
-                                onChange={e => onCheckboxChange(e, sm)}
-                                checked={selectedBoxes.some(
-                                  box => box.obo_id === sm.obo_id
-                                )}
-                                value={sm}
+                <div className="result_container">
+                  <Form form={form} layout="vertical" preserve={false}>
+                    <div className="all_checkboxes_container">
+                      <OntologyCheckboxes apiPreferences={apiPreferences} />
+                      <div className="result_form">
+                        {results?.length > 0 ? (
+                          <>
+                            {displaySelectedMappings?.length > 0 && (
+                              <Form.Item
+                                name="selected_mappings"
+                                valuePropName="value"
+                                rules={[{ required: false }]}
                               >
-                                {selectedTermsDisplay(sm, i)}
-                              </Checkbox>
-                            ))}
-                          </div>
-                        </Form.Item>
-                      )}
-                      <Form.Item
-                        name={['filtered_mappings']}
-                        valuePropName="value"
-                        rules={[
-                          {
-                            required: true,
-                            message: 'Please make a selection.',
-                          },
-                        ]}
-                      >
-                        {filteredResultsArray?.length > 0 ? (
-                          <Checkbox.Group
-                            className="mappings_checkbox"
-                            options={filteredResultsArray?.map((d, index) => {
-                              return {
-                                value: JSON.stringify({
-                                  code: d.obo_id,
-                                  display: d.label,
-                                  // description: d.description[0],
-                                  system: systemsMatch(d?.obo_id.split(':')[0]),
-                                }),
-                                label: checkBoxDisplay(d, index),
-                              };
-                            })}
-                            onChange={onSelectedChange}
-                          />
+                                <div className="modal_display_results">
+                                  {displaySelectedMappings?.map((sm, i) => (
+                                    <Checkbox
+                                      key={i}
+                                      onChange={e => onCheckboxChange(e, sm)}
+                                      checked={selectedBoxes.some(
+                                        box => box.obo_id === sm.obo_id
+                                      )}
+                                      value={sm}
+                                    >
+                                      {selectedTermsDisplay(sm, i)}
+                                    </Checkbox>
+                                  ))}
+                                </div>
+                              </Form.Item>
+                            )}
+                            <Form.Item
+                              name={['filtered_mappings']}
+                              valuePropName="value"
+                              rules={[
+                                {
+                                  required: true,
+                                  message: 'Please make a selection.',
+                                },
+                              ]}
+                            >
+                              {filteredResultsArray?.length > 0 ? (
+                                <Checkbox.Group
+                                  className="mappings_checkbox"
+                                  options={filteredResultsArray?.map(
+                                    (d, index) => {
+                                      return {
+                                        value: JSON.stringify({
+                                          code: d.obo_id,
+                                          display: d.label,
+                                          // description: d.description[0],
+                                          system: systemsMatch(
+                                            d?.obo_id.split(':')[0]
+                                          ),
+                                        }),
+                                        label: checkBoxDisplay(d, index),
+                                      };
+                                    }
+                                  )}
+                                  onChange={onSelectedChange}
+                                />
+                              ) : (
+                                ''
+                              )}
+                            </Form.Item>
+                          </>
                         ) : (
-                          ''
+                          <h3>No results found</h3>
                         )}
-                      </Form.Item>
-                    </Form>
-                    <div>
-                      {/* 'View More' pagination displaying the number of results being displayed
+                      </div>
+                    </div>
+                  </Form>
+                  <div className="view_more_wrapper">
+                    {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
                       inconsistencies in results numbers per page. */}
-                      <Tooltip
-                        placement="bottom"
-                        title="Redundant entries have been removed"
+                    <Tooltip
+                      placement="bottom"
+                      title="Redundant entries have been removed"
+                    >
+                      Displaying {resultsCount}
+                      &nbsp;of&nbsp;{totalCount}
+                    </Tooltip>
+                    {totalCount - filteredResultsCount !== resultsCount && (
+                      <span
+                        className="view_more_link"
+                        onClick={e => {
+                          handleViewMore(e);
+                          setLastCount(resultsCount);
+                        }}
                       >
-                        Displaying {resultsCount}
-                        &nbsp;of&nbsp;{totalCount}
-                      </Tooltip>
-                      {totalCount - filteredResultsCount !== resultsCount && (
-                        <span
-                          className="view_more_link"
-                          onClick={e => {
-                            handleViewMore(e);
-                            setLastCount(resultsCount);
-                          }}
-                        >
-                          View More
-                        </span>
-                      )}
-                    </div>
+                        View More
+                      </span>
+                    )}
                   </div>
-                ) : (
-                  <h3>No results found.</h3>
-                )}
+                </div>
               </div>
             </>
           ) : (
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index a98cd90..c640087 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -5,7 +5,8 @@ import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
 import { ModalSpinner } from '../Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
-import { olsFilterOntologiesSearch } from '../FetchManager';
+import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
+import { OntologyCheckboxes } from './OntologyCheckboxes';
 
 export const MappingSearch = ({
   setEditMappings,
@@ -13,13 +14,22 @@ export const MappingSearch = ({
   mappingsForSearch,
   onClose,
   searchProp,
+  component,
+  mappingProp,
+  table,
 }) => {
-  const { searchUrl } = useContext(myContext);
-  const { apiPreferences, defaultOntologies, facetCounts, setFacetCounts } =
-    useContext(SearchContext);
+  const { searchUrl, vocabUrl } = useContext(myContext);
+  const {
+    apiPreferences,
+    defaultOntologies,
+    setFacetCounts,
+    setApiPreferencesCode,
+    apiPreferencesCode,
+    setUnformattedPref,
+  } = useContext(SearchContext);
 
   const [page, setPage] = useState(0);
-  const entriesPerPage = 15;
+  const entriesPerPage = 2500;
   const [loading, setLoading] = useState(true);
   const [results, setResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
@@ -50,10 +60,23 @@ export const MappingSearch = ({
     setCurrentSearchProp(searchProp);
     setPage(0);
     if (!!searchProp) {
-      fetchResults(0, searchProp);
+      getFiltersByCode(
+        vocabUrl,
+        component,
+        mappingProp,
+        setApiPreferencesCode,
+        notification,
+        apiPreferencesCode,
+        setUnformattedPref,
+        table
+      );
     }
   }, [searchProp]);
 
+  useEffect(() => {
+    if (apiPreferencesCode !== undefined) fetchResults(0, searchProp);
+  }, [apiPreferencesCode, searchProp]);
+
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the code and when the page changes.
@@ -68,13 +91,12 @@ export const MappingSearch = ({
   This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
   Because the content is in a modal and not the window, the closest class name to the modal is used for the location of the ref. */
   useEffect(() => {
-    if (results && page > 0) {
+    if (results?.length > 0 && page > 0) {
       const container = ref.current.closest('.ant-modal-body');
       const scrollTop = ref.current.offsetTop - container.offsetTop;
       container.scrollTop = scrollTop;
     }
   }, [results]);
-
   // Sets the value of the selected_mappings in the form to the checkboxes that are selected
   useEffect(() => {
     form.setFieldsValue({
@@ -127,7 +149,9 @@ export const MappingSearch = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferenceOntologies(),
+        apiPreferencesCode !== ''
+          ? apiPreferencesCode
+          : apiPreferenceOntologies(),
         page,
         entriesPerPage,
         pageStart,
@@ -144,7 +168,7 @@ export const MappingSearch = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        defaultOntologies,
+        apiPreferencesCode !== '' ? apiPreferencesCode : defaultOntologies,
         page,
         entriesPerPage,
         pageStart,
@@ -356,119 +380,130 @@ export const MappingSearch = ({
                   </div>
                 </div>
                 {/* ant.design form displaying the checkboxes with the search results.  */}
-                {results?.length > 0 ? (
-                  <div className="result_container">
-                    <Form form={form} layout="vertical">
-                      <Form.Item
-                        initialValue={initialChecked}
-                        name={['existing_mappings']}
-                        valuePropName="value"
-                        rules={[
-                          {
-                            required: false,
-                          },
-                        ]}
-                      >
-                        {mappingsForSearch?.length > 0 && (
-                          <Checkbox.Group
-                            className="mappings_checkbox"
-                            options={mappingsForSearch?.map((d, index) => {
-                              return {
-                                value: JSON.stringify({
-                                  code: d.code,
-                                  display: d.display,
-                                  description: d.description,
-                                  system: d.system,
-                                }),
-                                label: existingMappingDisplay(d, index),
-                              };
-                            })}
-                            onChange={onExistingChange}
-                          />
-                        )}
-                      </Form.Item>
+                <div className="result_container">
+                  <Form form={form} layout="vertical" preserve={false}>
+                    <div className="all_checkboxes_container">
+                      <OntologyCheckboxes apiPreferences={apiPreferences} />
+                      <div className="result_form">
+                        {results?.length > 0 ? (
+                          <>
+                            <Form.Item
+                              initialValue={initialChecked}
+                              name={['existing_mappings']}
+                              valuePropName="value"
+                              rules={[
+                                {
+                                  required: false,
+                                },
+                              ]}
+                            >
+                              {mappingsForSearch?.length > 0 && (
+                                <Checkbox.Group
+                                  className="mappings_checkbox"
+                                  options={mappingsForSearch?.map(
+                                    (d, index) => {
+                                      return {
+                                        value: JSON.stringify({
+                                          code: d.code,
+                                          display: d.display,
+                                          description: d.description,
+                                          system: d.system,
+                                        }),
+                                        label: existingMappingDisplay(d, index),
+                                      };
+                                    }
+                                  )}
+                                  onChange={onExistingChange}
+                                />
+                              )}
+                            </Form.Item>
 
-                      {displaySelectedMappings?.length > 0 && (
-                        <Form.Item
-                          name="selected_mappings"
-                          valuePropName="value"
-                          rules={[{ required: false }]}
-                        >
-                          {' '}
-                          <div className="modal_display_results">
-                            {displaySelectedMappings?.map((sm, i) => (
-                              <Checkbox
-                                key={i}
-                                onChange={e => onCheckboxChange(e, sm)}
-                                checked={selectedBoxes.some(
-                                  box => box.obo_id === sm.obo_id
-                                )}
-                                value={sm}
+                            {displaySelectedMappings?.length > 0 && (
+                              <Form.Item
+                                name="selected_mappings"
+                                valuePropName="value"
+                                rules={[{ required: false }]}
                               >
-                                {selectedTermsDisplay(sm, i)}
-                              </Checkbox>
-                            ))}
-                          </div>
-                        </Form.Item>
-                      )}
-                      <Form.Item
-                        name={['filtered_mappings']}
-                        valuePropName="value"
-                        rules={[
-                          {
-                            required: false,
-                          },
-                        ]}
-                      >
-                        {filteredResultsArray?.length > 0 && (
-                          <Checkbox.Group
-                            className="mappings_checkbox"
-                            options={filteredResultsArray?.map((d, index) => {
-                              return {
-                                value: JSON.stringify({
-                                  code: d.obo_id,
-                                  display: d.label,
-                                  description: d.description[0],
-                                  system: systemsMatch(
-                                    d?.obo_id?.split(':')[0]
-                                  ),
-                                }),
-                                label: newSearchDisplay(d, index),
-                              };
-                            })}
-                            onChange={onSelectedChange}
-                          />
+                                {' '}
+                                <div className="modal_display_results">
+                                  {displaySelectedMappings?.map((sm, i) => (
+                                    <Checkbox
+                                      key={i}
+                                      onChange={e => onCheckboxChange(e, sm)}
+                                      checked={selectedBoxes.some(
+                                        box => box.obo_id === sm.obo_id
+                                      )}
+                                      value={sm}
+                                    >
+                                      {selectedTermsDisplay(sm, i)}
+                                    </Checkbox>
+                                  ))}
+                                </div>
+                              </Form.Item>
+                            )}
+                            <Form.Item
+                              name={['filtered_mappings']}
+                              valuePropName="value"
+                              rules={[
+                                {
+                                  required: false,
+                                },
+                              ]}
+                            >
+                              {filteredResultsArray?.length > 0 && (
+                                <Checkbox.Group
+                                  className="mappings_checkbox"
+                                  options={filteredResultsArray?.map(
+                                    (d, index) => {
+                                      return {
+                                        value: JSON.stringify({
+                                          code: d.obo_id,
+                                          display: d.label,
+                                          description: d.description[0],
+                                          system: systemsMatch(
+                                            d?.obo_id?.split(':')[0]
+                                          ),
+                                        }),
+                                        label: newSearchDisplay(d, index),
+                                      };
+                                    }
+                                  )}
+                                  onChange={onSelectedChange}
+                                />
+                              )}
+                            </Form.Item>
+                          </>
+                        ) : (
+                          <h3>No results found</h3>
                         )}
-                      </Form.Item>
-                    </Form>
-                    <div>
-                      {/* 'View More' pagination displaying the number of results being displayed
+                      </div>
+                    </div>
+                  </Form>
+                  <div className="view_more_wrapper">
+                    {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
                       inconsistencies in results numbers per page. */}
-                      <Tooltip
-                        placement="bottom"
-                        title="Redundant entries have been removed"
+                    <Tooltip
+                      placement="bottom"
+                      title="Redundant entries have been removed"
+                    >
+                      Displaying {resultsCount}
+                      &nbsp;of&nbsp;{totalCount}
+                    </Tooltip>
+                    {totalCount - filteredResultsCount !== resultsCount && (
+                      <span
+                        className="view_more_link"
+                        onClick={e => {
+                          handleViewMore(e);
+                          setLastCount(resultsCount);
+                        }}
                       >
-                        Displaying {resultsCount}
-                        &nbsp;of&nbsp;{totalCount}
-                      </Tooltip>
-                      {totalCount - filteredResultsCount !== resultsCount && (
-                        <span
-                          className="view_more_link"
-                          onClick={e => {
-                            handleViewMore(e);
-                            setLastCount(resultsCount);
-                          }}
-                        >
-                          View More
-                        </span>
-                      )}
-                    </div>
+                        View More
+                      </span>
+                    )}
                   </div>
-                ) : (
-                  <h3>No results found.</h3>
-                )}
+                </div>
               </div>
             </>
           ) : (
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index addba01..58ab005 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -9,13 +9,22 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
     setApiPreferencesCode,
     facetCounts,
     ontologyApis,
+    component,
   } = useContext(SearchContext);
   const [checkedOntologies, setCheckedOntologies] = useState([]);
 
   const defaultOntologies = ['mondo', 'hp', 'maxo', 'ncit'];
 
+  let processedApiPreferencesCode;
+
+  if (Array.isArray(apiPreferencesCode)) {
+    processedApiPreferencesCode = apiPreferencesCode;
+  } else if (typeof apiPreferencesCode === 'string') {
+    processedApiPreferencesCode = apiPreferencesCode.split(',');
+  }
+
   const existingOntologies = apiPreferencesCode
-    ? apiPreferencesCode
+    ? processedApiPreferencesCode
     : apiPreferences &&
       apiPreferences?.self &&
       apiPreferences?.self?.api_preference
@@ -57,6 +66,13 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
     };
   });
 
+  // console.log('sorted', sortedData);
+  // console.log('ontologyapi', ontologyApis);
+  console.log('pref', Object.values(apiPreferences?.self?.api_preference));
+  // console.log('code', apiPreferencesCode);
+  console.log('default', defaultOntologies);
+  console.log('checked onts', checkedOntologies);
+
   const countsMap = formattedFacetCounts.reduce((acc, item) => {
     const key = Object.keys(item)[0];
     acc[key] = parseInt(item[key], 10);
@@ -65,15 +81,13 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
 
   // // Build the new data structure
   const countsResult = Object.keys(sortedData[0].ontologies).map(key => {
-    return { [key]: countsMap[key] || 0 };
+    return { [key]: countsMap[key] || 0, api: sortedData[0]?.api_id };
   });
 
   const checkedOntologiesArray = Array.isArray(checkedOntologies)
     ? checkedOntologies
     : [];
 
-  console.log(checkedOntologiesArray);
-
   return (
     <div className="ontology_form">
       <Form.Item
diff --git a/src/components/Nav/NavBar.jsx b/src/components/Nav/NavBar.jsx
index 80e39ff..13a0c11 100644
--- a/src/components/Nav/NavBar.jsx
+++ b/src/components/Nav/NavBar.jsx
@@ -27,11 +27,11 @@ export const NavBar = () => {
             </NavLink>
             {/* Placeholder elements below. No functionality at this time.*/}
             <NavLink to="/help">
-              <li className="nav_link">About</li>
+              <li className="nav_link">Help</li>
             </NavLink>
 
             <NavLink to="/about">
-              <li className="nav_link">Ontologies</li>
+              <li className="nav_link">About</li>
             </NavLink>
           </div>
           <div className="login">
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index 3408f96..ce7a71c 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -16,12 +16,14 @@ import { MappingReset } from '../../Manager/MappingsFunctions/MappingReset';
 import { ResetTableMappings } from './ResetTableMappings';
 import { ellipsisString, systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const EditMappingsTableModal = ({
   editMappings,
   setEditMappings,
   tableId,
   setMapping,
+  table,
 }) => {
   const [form] = Form.useForm();
   const [termMappings, setTermMappings] = useState([]);
@@ -33,6 +35,7 @@ export const EditMappingsTableModal = ({
   const [editSearch, setEditSearch] = useState(false);
   const { setSelectedMappings, setDisplaySelectedMappings } =
     useContext(MappingContext);
+  const { setApiPreferencesCode } = useContext(SearchContext);
 
   useEffect(() => {
     fetchMappings();
@@ -45,6 +48,7 @@ export const EditMappingsTableModal = ({
     setReset(false);
     setEditSearch(false);
     setSelectedKey(null);
+    setApiPreferencesCode(undefined);
   };
 
   const fetchMappings = () => {
@@ -337,6 +341,9 @@ export const EditMappingsTableModal = ({
           reset={reset}
           onClose={form.resetFields}
           searchProp={editMappings.name}
+          component={table}
+          mappingProp={editMappings.code}
+          table={table}
         />
       ) : (
         reset && (
@@ -347,6 +354,9 @@ export const EditMappingsTableModal = ({
             form={form}
             reset={reset}
             onClose={form.resetFields}
+            component={table}
+            mappingProp={editMappings.code}
+            table={table}
           />
         )
       )}
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index f1edf07..c85bf9a 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -355,6 +355,7 @@ There is then a tooltip that displays the variables on hover.*/
         setEditMappings={setEditMappings}
         tableId={tableId}
         setMapping={setMapping}
+        table={table}
       />
       <GetMappingsModal
         component={table}

From b3c61bc0d4a0c87b051dbe0e4f63f51473bf23ec Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 15:46:47 -0500
Subject: [PATCH 050/180] using pathname for labels

---
 src/components/Nav/Breadcrumbs.jsx |  17 ++++-
 src/components/Nav/NavBar.scss     | 109 ++++++++++++++++-------------
 2 files changed, 76 insertions(+), 50 deletions(-)

diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
index 6e32a4b..0ba833b 100644
--- a/src/components/Nav/Breadcrumbs.jsx
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -1,3 +1,16 @@
-export const Breadcrumbs = () =>{
-   return <h1>sup breadcrumb</h1>
+import { Breadcrumb } from "antd"
+import { useLocation } from 'react-router-dom';
+export const Breadcrumbs = () => {
+   const location = useLocation();
+   const pathParts = location.pathname.split('/').filter(Boolean);
+   const pathArr = []
+   pathParts.forEach(path => {
+      pathArr.push({title:path});
+   });
+   return <span className="breadcrumbs">
+      <Breadcrumb
+         items={pathArr}
+         params={{ id: 1 }}
+      />
+   </span>
 }
\ No newline at end of file
diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index b5cc79a..20f18e2 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -3,7 +3,7 @@
 $navColor: #080705;
 $linkColor: #fffc31;
 
-nav {
+nav.navbar {
   z-index: 1;
   width: 100%;
   background-color: $navColor;
@@ -13,72 +13,85 @@ nav {
   justify-content: center;
   position: sticky;
   top: 0;
+
   li {
     list-style-type: none;
   }
+
   a:not(.nav_logo) {
     text-decoration: none;
     color: $navColor;
+
     font: {
       size: 1em;
       weight: 800;
     }
   }
-}
 
-.nav_body {
-  width: 100%;
-  display: grid;
-  grid-template-columns: 1fr auto 1fr;
-}
 
-.logo_container {
-  left: 0;
-  padding-left: 100px;
-}
+  .nav_body {
+    width: 100%;
+    display: grid;
+    grid-template-columns: 1fr auto 1fr;
+  }
 
-.nav_logo {
-  width: 81px;
-  color: white;
-  font: {
-    weight: 800;
-    size: 1.3rem;
+  .logo_container {
+    left: 0;
+    padding-left: 100px;
   }
-  text-align: left;
-  text-decoration: none;
-}
 
-.nav_links {
-  margin: auto;
-  display: flex;
-  flex-direction: row;
-  gap: 2rem;
-  grid-column-start: 2;
-}
+  .nav_logo {
+    width: 81px;
+    color: white;
 
-.nav_link {
-  display: flex;
-  flex-direction: row;
-  align-items: center;
-  justify-content: center;
-  background-color: $linkColor;
-  height: 75px;
-  padding: 0 4px;
-  width: $navHeight;
-  border-radius: 10px;
-}
+    font: {
+      weight: 800;
+      size: 1.3rem;
+    }
+
+    text-align: left;
+    text-decoration: none;
+  }
+
+  .nav_links {
+    margin: auto;
+    display: flex;
+    flex-direction: row;
+    gap: 2rem;
+    grid-column-start: 2;
+  }
+
+  .nav_link {
+    display: flex;
+    flex-direction: row;
+    align-items: center;
+    justify-content: center;
+    background-color: $linkColor;
+    height: 75px;
+    padding: 0 4px;
+    width: $navHeight;
+    border-radius: 10px;
+  }
 
-.nav_link:hover {
-  color: rgb(45, 42, 34);
-  box-shadow: 0 5px 15px rgba(178, 182, 92, 0.8);
+  .nav_link:hover {
+    color: rgb(45, 42, 34);
+    box-shadow: 0 5px 15px rgba(178, 182, 92, 0.8);
+  }
+
+  .login {
+    display: flex;
+    flex-direction: row;
+    justify-content: flex-end;
+    align-items: center;
+    margin: 0 100px 0 0;
+  }
 }
 
-.login {
-  display: flex;
-  flex-direction: row;
-  justify-content: flex-end;
-  align-items: center;
-  margin: 0 100px 0 0;
+.breadcrumbs {
+
+  position: sticky;
+  top: 115px;
+ 
 }
 
 footer {
@@ -88,4 +101,4 @@ footer {
   height: 50px;
   margin-top: -50px;
   background-color: $navColor;
-}
+}
\ No newline at end of file

From 8286622c2e25d2c46918a1dc8be837f31ec2dd59 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 21:39:42 -0500
Subject: [PATCH 051/180] working breadcrumbs and redirect

---
 src/AppRouter.jsx                  | 18 +++++++++++++-----
 src/components/Nav/Breadcrumbs.jsx | 22 ++++++++++++++++------
 src/components/Nav/NavBar.scss     | 10 ++++++----
 3 files changed, 35 insertions(+), 15 deletions(-)

diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index 813839c..b01e2eb 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -28,7 +28,7 @@ export const AppRouter = () => {
             <>
               <div className="approuter_div">
                 <NavBar />
-                <Breadcrumbs/>
+                <Breadcrumbs />
                 <div className="outlet_div">
                   <Outlet />
                 </div>
@@ -46,14 +46,22 @@ export const AppRouter = () => {
             <Route element={<MappingContextRoot />}>
               <Route element={<SearchContextRoot />}>
                 <Route path="/studies" element={<StudyList />} />
+                <Route path="/study" element={<StudyList />} />
                 <Route path="/Study/:studyId">
                   <Route index element={<StudyDetails />} />
-                  <Route path="/Study/:studyId/DataDictionary/:DDId">
-                    <Route index element={<DDDetails />} />
+                  <Route path="DataDictionary">
+                    <Route index element={<StudyDetails />} />
                     <Route
-                      path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId"
-                      element={<TableDetails />}
+                      path="/Study/:studyId/DataDictionary/:DDId/Table/"
+                      element={<DDDetails />}
                     />
+                    <Route path="/Study/:studyId/DataDictionary/:DDId">
+                      <Route index element={<DDDetails />} />
+                      <Route
+                        path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId"
+                        element={<TableDetails />}
+                      />
+                    </Route>
                   </Route>
                 </Route>
                 <Route
diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
index 0ba833b..8e064fb 100644
--- a/src/components/Nav/Breadcrumbs.jsx
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -1,16 +1,26 @@
 import { Breadcrumb } from "antd"
-import { useLocation } from 'react-router-dom';
+import { useLocation, Link } from 'react-router-dom';
+// import { Link } from 'react-router';
 export const Breadcrumbs = () => {
    const location = useLocation();
    const pathParts = location.pathname.split('/').filter(Boolean);
    const pathArr = []
    pathParts.forEach(path => {
-      pathArr.push({title:path});
+      pathArr.push({ title: path, path: path });
    });
+   console.log(itemRender);
+   
+
    return <span className="breadcrumbs">
-      <Breadcrumb
-         items={pathArr}
-         params={{ id: 1 }}
-      />
+      <Breadcrumb itemRender={itemRender} items={pathArr} />
    </span>
+}
+function itemRender(currentRoute, params, items, pathArr) {
+   const isLast = currentRoute?.path === items[items.length - 1]?.path;
+
+   return isLast ? (
+      <span>{currentRoute.title}</span>
+   ) : (
+      <Link to={`/${pathArr.join("/")}`}>{currentRoute.title}</Link>
+   );
 }
\ No newline at end of file
diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index 20f18e2..7796e63 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -88,10 +88,12 @@ nav.navbar {
 }
 
 .breadcrumbs {
-
-  position: sticky;
-  top: 115px;
- 
+  padding:.5rem;
+  & * {text-transform: capitalize;}
+  nav {
+    position: sticky;
+    top: 115px;
+  }
 }
 
 footer {

From 953563bd37a678cfe1cdf9950d8525cb838ba374 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 22:30:17 -0500
Subject: [PATCH 052/180] redirects + styles

---
 src/App.scss                       |  2 ++
 src/AppRouter.jsx                  |  5 ++--
 src/components/Nav/Breadcrumbs.jsx | 10 +++++---
 src/components/Nav/NavBar.scss     | 38 ++++++++++++++++++++++++++----
 4 files changed, 45 insertions(+), 10 deletions(-)

diff --git a/src/App.scss b/src/App.scss
index 5ea8142..4245aa4 100644
--- a/src/App.scss
+++ b/src/App.scss
@@ -6,4 +6,6 @@
 .outlet_div {
   height: 100%;
   min-height: 100vh;
+  position: relative;
+  top:-2.5rem;
 }
diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index b01e2eb..5a5008e 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -1,5 +1,5 @@
 import { OntologySearch } from './components/Search/OntologySearch';
-import { BrowserRouter, Outlet, Route, Routes } from 'react-router-dom';
+import { BrowserRouter, Outlet, Route, Routes, Navigate } from 'react-router-dom';
 import { NavBar } from './components/Nav/NavBar';
 import { Breadcrumbs } from './components/Nav/Breadcrumbs.jsx';
 import { Footer } from './components/Nav/Footer';
@@ -43,10 +43,11 @@ export const AppRouter = () => {
             <Route path="/404" element={<Error404 />} />
             <Route path="/about" element={<OntologyInfo />} />
             <Route path="/terminologies" element={<TerminologyList />} />
+            <Route path="/terminology" element={<Navigate to="/terminologies" />} />
             <Route element={<MappingContextRoot />}>
               <Route element={<SearchContextRoot />}>
                 <Route path="/studies" element={<StudyList />} />
-                <Route path="/study" element={<StudyList />} />
+                <Route path="/study" element={<Navigate to="/studies" />} />
                 <Route path="/Study/:studyId">
                   <Route index element={<StudyDetails />} />
                   <Route path="DataDictionary">
diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
index 8e064fb..f6b29ee 100644
--- a/src/components/Nav/Breadcrumbs.jsx
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -8,19 +8,23 @@ export const Breadcrumbs = () => {
    pathParts.forEach(path => {
       pathArr.push({ title: path, path: path });
    });
-   console.log(itemRender);
+  
+   console.log(location,'location');
    
 
    return <span className="breadcrumbs">
+       <li><Link to={'/'}>Home</Link> {location.pathname != '/' && <span>&nbsp;&nbsp;/&nbsp;&nbsp;</span>}</li>
       <Breadcrumb itemRender={itemRender} items={pathArr} />
    </span>
 }
 function itemRender(currentRoute, params, items, pathArr) {
    const isLast = currentRoute?.path === items[items.length - 1]?.path;
 
-   return isLast ? (
+   return <>
+   {isLast ? (
       <span>{currentRoute.title}</span>
    ) : (
       <Link to={`/${pathArr.join("/")}`}>{currentRoute.title}</Link>
-   );
+   )}
+   </>
 }
\ No newline at end of file
diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index 7796e63..e707377 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -88,12 +88,40 @@ nav.navbar {
 }
 
 .breadcrumbs {
-  padding:.5rem;
-  & * {text-transform: capitalize;}
-  nav {
-    position: sticky;
-    top: 115px;
+  display: flex;
+  align-items: baseline;
+  z-index: 1;
+  padding: 0 .5rem;
+  position: sticky;
+  top: 115px;
+  background:#eeee;
+
+  li {
+    font-size: 14px;
+    line-height: 1.5714285714285714;
+    color: rgba(0, 0, 0, 0.45);
+    
+    &>a {
+      color: rgba(0, 0, 0, 0.45);
+      text-decoration: none;
+      transition: color 0.2s;
+      padding: 0 4px;
+      border-radius: 4px;
+      height: 22px;
+      display: inline-block;
+      margin-inline: -4px;
+
+      &:hover {
+        color: rgba(0, 0, 0, 0.88);
+        background-color: rgba(0, 0, 0, 0.06);
+      }
+    }
+  }
+
+  & * {
+    text-transform: capitalize;
   }
+
 }
 
 footer {

From 946e36e69531c0a38db43d59449e8ab75cf5289b Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 22:32:46 -0500
Subject: [PATCH 053/180] style tweak

---
 src/index.css | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/index.css b/src/index.css
index e777e9d..7af083f 100644
--- a/src/index.css
+++ b/src/index.css
@@ -2,4 +2,8 @@ body {
   margin: 0;
   font-size: 14px;
   font-family: 'Wix Madefor Display', sans-serif;
+  background:white;
 }
+html {
+  background:black
+}
\ No newline at end of file

From 4b66f4d25be86e8720452cfc2c910f4c260e3460 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 22:33:14 -0500
Subject: [PATCH 054/180] revert style tweak

---
 src/index.css | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/index.css b/src/index.css
index 7af083f..e777e9d 100644
--- a/src/index.css
+++ b/src/index.css
@@ -2,8 +2,4 @@ body {
   margin: 0;
   font-size: 14px;
   font-family: 'Wix Madefor Display', sans-serif;
-  background:white;
 }
-html {
-  background:black
-}
\ No newline at end of file

From 64ce09a66696e74df88d46ff6fc43eb715722fa4 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 23:01:16 -0500
Subject: [PATCH 055/180] container style tweaks

---
 src/App.scss                                           | 6 +++---
 src/components/Nav/NavBar.scss                         | 5 +----
 src/components/Projects/Studies/StudyStyling.scss      | 3 ++-
 src/components/Projects/Terminologies/Terminology.scss | 2 +-
 4 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/src/App.scss b/src/App.scss
index 4245aa4..b7d7961 100644
--- a/src/App.scss
+++ b/src/App.scss
@@ -1,11 +1,11 @@
 .approuter_div {
   display: flex;
   flex-direction: column;
+  justify-content: space-between;
 }
 
 .outlet_div {
-  height: 100%;
-  min-height: 100vh;
+
   position: relative;
-  top:-2.5rem;
+  // top:-2.5rem;
 }
diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index e707377..f509801 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -93,7 +93,7 @@ nav.navbar {
   z-index: 1;
   padding: 0 .5rem;
   position: sticky;
-  top: 115px;
+  top: 100px;
   background:#eeee;
 
   li {
@@ -125,10 +125,7 @@ nav.navbar {
 }
 
 footer {
-  margin-top: auto;
-  bottom: 0;
   width: 100%;
   height: 50px;
-  margin-top: -50px;
   background-color: $navColor;
 }
\ No newline at end of file
diff --git a/src/components/Projects/Studies/StudyStyling.scss b/src/components/Projects/Studies/StudyStyling.scss
index 62eca80..f454aed 100644
--- a/src/components/Projects/Studies/StudyStyling.scss
+++ b/src/components/Projects/Studies/StudyStyling.scss
@@ -1,6 +1,7 @@
 .studies_container {
-  margin: 17vh 10vw 10vh 10vw;
+  margin: 5rem 10vw 10vh 10vw;
   line-height: 1.5rem;
+  height: 100vh;
 }
 
 .cards_container {
diff --git a/src/components/Projects/Terminologies/Terminology.scss b/src/components/Projects/Terminologies/Terminology.scss
index 09485e7..a73c8ef 100644
--- a/src/components/Projects/Terminologies/Terminology.scss
+++ b/src/components/Projects/Terminologies/Terminology.scss
@@ -1,6 +1,6 @@
 @import '../../Styling/Variables';
 .terminology_container {
-  margin: 17vh 10vw 10vh 10vw;
+  margin: 5rem 10vw 10vh 5rem;
   width: 66vw;
 }
 

From 78b107719a23d3ddbd38ee8ace516f81c8e2da8c Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Wed, 23 Oct 2024 23:02:17 -0500
Subject: [PATCH 056/180] breadcrumb style tweaks

---
 src/components/Nav/NavBar.scss | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index f509801..e57f82b 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -93,7 +93,7 @@ nav.navbar {
   z-index: 1;
   padding: 0 .5rem;
   position: sticky;
-  top: 100px;
+  top: 115px;
   background:#eeee;
 
   li {

From 87aa2090e5022302bcacf8bf8c47aa6c296f1c79 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 23 Oct 2024 23:05:39 -0500
Subject: [PATCH 057/180] Filter ontologies for terminology codes

---
 .../MappingsFunctions/FilterSelect.jsx        |  2 +-
 .../MappingsFunctions/GetMappingsModal.jsx    |  8 ++----
 .../MappingsFunctions/OntologyCheckboxes.jsx  |  9 +-----
 .../OntologyFilterCodeSubmit.jsx              | 28 ++++---------------
 .../Projects/Tables/TableDetails.jsx          | 15 ++++++----
 .../Terminologies/EditMappingModal.jsx        |  4 +++
 .../Projects/Terminologies/Terminology.jsx    |  2 +-
 7 files changed, 24 insertions(+), 44 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index d763a39..031396b 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -134,7 +134,7 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
         }
       })
       .then(() =>
-        fetch(`${vocabUrl}/${table?.terminology?.reference}/filter`, {
+        fetch(`${vocabUrl}/${table?.terminology?.reference}/filter/self`, {
           method: 'GET',
           headers: {
             'Content-Type': 'application/json',
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 03dd47f..a6e3974 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -28,7 +28,6 @@ export const GetMappingsModal = ({
 }) => {
   const [form] = Form.useForm();
   const { Search } = Input;
-
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
   const {
     apiPreferences,
@@ -139,7 +138,7 @@ export const GetMappingsModal = ({
   // Each mapping in the mappings array being edited is JSON.parsed and pushed to the blank mappings array.
   // The mappings are turned into objects in the mappings array.
   const handleSubmit = values => {
-    const selectedMappings = values?.selected_mappings?.map(item => ({
+    const selectedMappings = selectedBoxes?.map(item => ({
       code: item.obo_id,
       display: item.label,
       description: item.description[0],
@@ -180,7 +179,8 @@ export const GetMappingsModal = ({
           apiPreferences,
           mappingProp,
           table,
-          vocabUrl
+          vocabUrl,
+          component
         )
       )
       .finally(() => setLoading(false));
@@ -319,7 +319,6 @@ export const GetMappingsModal = ({
       setSelectedBoxes(prevState => prevState.filter(val => val !== code));
     }
   };
-
   const onSelectedChange = checkedValues => {
     const selected = JSON.parse(checkedValues?.[0]);
     const selectedMapping = results.find(
@@ -368,7 +367,6 @@ export const GetMappingsModal = ({
         onOk={() => {
           form.validateFields().then(values => {
             handleSubmit(values);
-            console.log(values);
             onClose();
           });
         }}
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 58ab005..123f96c 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -66,13 +66,6 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
     };
   });
 
-  // console.log('sorted', sortedData);
-  // console.log('ontologyapi', ontologyApis);
-  console.log('pref', Object.values(apiPreferences?.self?.api_preference));
-  // console.log('code', apiPreferencesCode);
-  console.log('default', defaultOntologies);
-  console.log('checked onts', checkedOntologies);
-
   const countsMap = formattedFacetCounts.reduce((acc, item) => {
     const key = Object.keys(item)[0];
     acc[key] = parseInt(item[key], 10);
@@ -80,7 +73,7 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
   }, {});
 
   // // Build the new data structure
-  const countsResult = Object.keys(sortedData[0].ontologies).map(key => {
+  const countsResult = Object.keys(sortedData[0]?.ontologies).map(key => {
     return { [key]: countsMap[key] || 0, api: sortedData[0]?.api_id };
   });
 
diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
index 6750a98..84050dc 100644
--- a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
@@ -6,7 +6,8 @@ export const OntologyFilterCodeSubmit = (
   apiPreferences,
   mappingProp,
   table,
-  vocabUrl
+  vocabUrl,
+  component
 ) => {
   const apiPreference = {
     api_preference: { 'ols': [] },
@@ -21,7 +22,9 @@ export const OntologyFilterCodeSubmit = (
     apiPreference.api_preference.ols = apiPreferencesCode;
 
     fetch(
-      `${vocabUrl}/${table?.terminology?.reference}/filter/${mappingProp}`,
+      `${vocabUrl}/${(component = table
+        ? table?.terminology?.reference
+        : `Terminology/${component?.id}`)}/filter/${mappingProp}`,
       {
         method: 'POST',
         headers: {
@@ -37,27 +40,6 @@ export const OntologyFilterCodeSubmit = (
           throw new Error('An unknown error occurred.');
         }
       })
-      .then(() =>
-        fetch(
-          `${vocabUrl}/${table?.terminology?.reference}/filter/${mappingProp}`,
-          {
-            method: 'GET',
-            headers: {
-              'Content-Type': 'application/json',
-            },
-          }
-        )
-      )
-      .then(res => {
-        if (res.ok) {
-          return res.json();
-        } else {
-          throw new Error('An unknown error occurred.');
-        }
-      })
-      .then(data => {
-        setApiPreferencesCode(data);
-      })
       .catch(error => {
         if (error) {
           notification.error({
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index c85bf9a..75e5f3c 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -86,12 +86,15 @@ export const TableDetails = () => {
                 return error;
               })
               .then(() =>
-                fetch(`${vocabUrl}/${data?.terminology?.reference}/filter`, {
-                  method: 'GET',
-                  headers: {
-                    'Content-Type': 'application/json',
-                  },
-                })
+                fetch(
+                  `${vocabUrl}/${data?.terminology?.reference}/filter/self`,
+                  {
+                    method: 'GET',
+                    headers: {
+                      'Content-Type': 'application/json',
+                    },
+                  }
+                )
               )
               .then(res => {
                 if (res.ok) {
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index ecc352c..27bb93a 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -15,17 +15,20 @@ import { ResetMappings } from './ResetMappings';
 import { MappingReset } from '../../Manager/MappingsFunctions/MappingReset';
 import { ellipsisString, systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const EditMappingsModal = ({
   editMappings,
   setEditMappings,
   terminologyId,
   setMapping,
+  terminology,
 }) => {
   const [form] = Form.useForm();
   const [termMappings, setTermMappings] = useState([]);
   const [options, setOptions] = useState([]);
   const { vocabUrl, setSelectedKey, user } = useContext(myContext);
+  const { setApiPreferencesCode } = useContext(SearchContext);
   const [loading, setLoading] = useState(false);
   const [reset, setReset] = useState(false);
   const [mappingsForSearch, setMappingsForSearch] = useState([]);
@@ -39,6 +42,7 @@ export const EditMappingsModal = ({
     setTermMappings([]);
     setOptions([]);
     setSelectedKey(null);
+    setApiPreferencesCode(undefined);
   };
 
   const fetchMappings = () => {
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index a7c49b3..e6dcc85 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -256,9 +256,9 @@ There is then a tooltip that displays the codes on hover.*/
           <EditMappingsModal
             editMappings={editMappings}
             setEditMappings={setEditMappings}
-            mapping={mapping}
             terminologyId={terminologyId}
             setMapping={setMapping}
+            terminology={terminology}
           />
           <GetMappingsModal
             componentString={'Terminology'}

From ccf1eacf961e7aa8cd95be1fa10e46baf342e0b4 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 24 Oct 2024 01:09:07 -0500
Subject: [PATCH 058/180] crumb color

---
 src/components/Nav/NavBar.scss | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index e57f82b..02b9884 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -94,7 +94,7 @@ nav.navbar {
   padding: 0 .5rem;
   position: sticky;
   top: 115px;
-  background:#eeee;
+  background:#eeeeee;
 
   li {
     font-size: 14px;

From 810ae2ee6cac0a58784f0d0119917ad7aac7d06f Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 24 Oct 2024 02:36:25 -0500
Subject: [PATCH 059/180] adding to terminology

---
 .../Projects/Terminologies/Terminology.jsx    | 105 ++++++++++++++----
 1 file changed, 84 insertions(+), 21 deletions(-)

diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 65970cf..75fd6c8 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -4,7 +4,8 @@ import { myContext } from '../../../App';
 import './Terminology.scss';
 import { Spinner } from '../../Manager/Spinner';
 import { getById } from '../../Manager/FetchManager';
-import { Col, Form, notification, Row, Table, Tooltip } from 'antd';
+import { Col, Form, notification, Row, Table, Button } from 'antd';
+import { CloseCircleOutlined } from '@ant-design/icons';
 import { EditMappingsModal } from './EditMappingModal';
 import { EditTerminologyDetails } from './EditTerminologyDetails';
 import { SettingsDropdownTerminology } from '../../Manager/Dropdown/SettingsDropdownTerminology';
@@ -21,15 +22,15 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 export const Terminology = () => {
   const [form] = Form.useForm();
 
-  const { terminologyId } = useParams();
-  const { vocabUrl } = useContext(myContext);
+  const { terminologyId , tableId } = useParams();
+  const { vocabUrl, user } = useContext(myContext);
   const { setPrefTerminologies, prefTerminologies } = useContext(SearchContext);
   const {
     editMappings,
     setEditMappings,
     getMappings,
     setGetMappings,
-    mapping,
+    mapping, 
     setMapping,
   } = useContext(MappingContext);
 
@@ -37,28 +38,90 @@ export const Terminology = () => {
   const initialTerminology = { url: '', description: '', name: '', codes: [] }; //initial state of terminology
   const [terminology, setTerminology] = useState(initialTerminology);
   const navigate = useNavigate();
+  
+  
+  const updateMappings = (mapArr,mappingCode ) => {
+    // setLoading(true);
+    const mappingsDTO = {
+      mappings: mapArr,
+      editor: user.email,
+    };
+    console.log(tableId,"tableId");
+    
+    fetch(`${vocabUrl}/Terminology/${terminologyId}/mapping/${mappingCode}`, {
+      method: 'PUT',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify(mappingsDTO),
+    })
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .then(data => {
+        setMapping(data.codes);
+        setEditMappings(null);
+        form.resetFields();
+        notification.success({ description:'Mapping removed.'});
+      })
+      .catch(error => {
+        console.log(error,'error');
+        
+        if (error) {
+          console.log(error,'error');
+          
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred. Please try again.',
+          });
+        }
+        return error;
+      })
+      .finally(() => setLoading(false));
+  };
+
   /* The terminology may have numerous codes. The API call to fetch the mappings returns all mappings for the terminology.
 The codes in the mappings need to be matched up to each code in the terminology.
 The function maps through the mapping array. For each code, if the mapping code is equal to the 
 code in the terminology, AND the mappings array length for the code is > 0, the mappings array is mapped through
 and returns the length of the mapping array (i.e. returns the number of codes mapped to the terminology code). 
-There is then a tooltip that displays the codes on hover.*/
-  const matchCode = code =>
-    mapping?.length > 0 &&
-    mapping?.map(
-      (item, index) =>
-        item.code === code.code &&
-        item?.mappings?.length > 0 && (
-          <Tooltip
-            title={item.mappings.map(code => {
-              return <div key={index}>{code.code}</div>;
-            })}
-            key={index}
-          >
-            {item.mappings.length}
-          </Tooltip>
-        )
-    );
+It then shows the mappings as table data and alows the user to delete a mapping from the table.*/
+
+  const noMapping = variable => {
+    return <Button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
+      Get Mappings
+    </Button>
+  }
+
+  const matchCode = variable => {
+
+
+    if (!mapping?.length) {
+      return noMapping(variable);
+    }
+
+    const variableMappings = mapping.find(item => item?.code === variable?.code);
+
+    if (variableMappings && variableMappings.mappings?.length) {
+      return variableMappings.mappings.map(code => <div className='mapping' key={code.display}><span className='mapping-display'>{code.display}</span><span className='remove-mapping' onClick={() => handleRemoveMapping(variableMappings,code)}><CloseCircleOutlined  style={{color:"red", }} /></span></div>);
+    } else {
+      return noMapping(variable);
+    }
+  };
+
+  const handleRemoveMapping = (variableMappings,code) => {
+    // console.log(variableMappings,"variableMappings");
+    const mappingToRemove = variableMappings.mappings.indexOf(code);
+    //remove mapping from mappings
+    {mappingToRemove !== -1 && variableMappings.mappings.splice(mappingToRemove,1)}   
+    updateMappings(variableMappings?.mappings,variableMappings?.code);    
+  
+  }
+
 
   // data for each column in the table.
   // Map through the codes in the terminology and display the code, display, number of mapped terms,

From 954e2772c0afd28fbe5d390d24e6d756515cf3bf Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 24 Oct 2024 08:39:36 -0500
Subject: [PATCH 060/180] margins

---
 src/components/Nav/NavBar.scss                         | 3 ++-
 src/components/Projects/Terminologies/Terminology.scss | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index 02b9884..95459e7 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -91,12 +91,13 @@ nav.navbar {
   display: flex;
   align-items: baseline;
   z-index: 1;
-  padding: 0 .5rem;
+  padding: 0 10vw;
   position: sticky;
   top: 115px;
   background:#eeeeee;
 
   li {
+    list-style: none;
     font-size: 14px;
     line-height: 1.5714285714285714;
     color: rgba(0, 0, 0, 0.45);
diff --git a/src/components/Projects/Terminologies/Terminology.scss b/src/components/Projects/Terminologies/Terminology.scss
index a73c8ef..7a7405b 100644
--- a/src/components/Projects/Terminologies/Terminology.scss
+++ b/src/components/Projects/Terminologies/Terminology.scss
@@ -1,6 +1,6 @@
 @import '../../Styling/Variables';
 .terminology_container {
-  margin: 5rem 10vw 10vh 5rem;
+  margin: 5rem 10vw 10vh 10vw;
   width: 66vw;
 }
 

From d431cd00fa0010e17fd8d4759c0fc8886a2373e0 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 24 Oct 2024 08:44:33 -0500
Subject: [PATCH 061/180] rm fixed ontology table

---
 src/components/About/OntologyInfo.scss | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/components/About/OntologyInfo.scss b/src/components/About/OntologyInfo.scss
index 226e395..db5a8b1 100644
--- a/src/components/About/OntologyInfo.scss
+++ b/src/components/About/OntologyInfo.scss
@@ -13,7 +13,6 @@
 .api_list {
   width: 12vw;
   height: fit-content;
-  position: fixed;
   display: flex;
   flex-flow: column wrap;
   gap: 2px;
@@ -40,7 +39,6 @@
 }
 .ontology_list {
   margin: 0 0 0 15vw;
-  position: fixed;
   top: 20vh;
   height: 20%;
   width: 70vw;

From a04663807380d32eafde7af6903ea7cee62aa8e6 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 24 Oct 2024 08:47:43 -0500
Subject: [PATCH 062/180] about_container margin

---
 src/components/About/OntologyInfo.scss | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/About/OntologyInfo.scss b/src/components/About/OntologyInfo.scss
index db5a8b1..249f4de 100644
--- a/src/components/About/OntologyInfo.scss
+++ b/src/components/About/OntologyInfo.scss
@@ -1,7 +1,7 @@
 @import '../Styling/Variables';
 
 .about_container {
-  margin: 17vh 10vw 10vh 10vw;
+  margin: 0 10vw;
   line-height: 1.5rem;
 }
 

From 120e23721ed182833085157f5e2a2f78ecb9d4fd Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 24 Oct 2024 09:23:57 -0500
Subject: [PATCH 063/180] moved 'no results found' to still display any
 selected mappings

---
 .../MappingsFunctions/GetMappingsModal.jsx    |  44 ++++----
 .../MappingsFunctions/MappingReset.jsx        |  44 ++++----
 .../MappingsFunctions/MappingSearch.jsx       | 105 +++++++++---------
 3 files changed, 95 insertions(+), 98 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index a6e3974..74dc182 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -402,30 +402,30 @@ export const GetMappingsModal = ({
                     <div className="all_checkboxes_container">
                       <OntologyCheckboxes apiPreferences={apiPreferences} />
                       <div className="result_form">
+                        {displaySelectedMappings?.length > 0 && (
+                          <Form.Item
+                            name="selected_mappings"
+                            valuePropName="value"
+                            rules={[{ required: false }]}
+                          >
+                            <div className="modal_display_results">
+                              {displaySelectedMappings?.map((sm, i) => (
+                                <Checkbox
+                                  key={i}
+                                  checked={selectedBoxes.some(
+                                    box => box.obo_id === sm.obo_id
+                                  )}
+                                  value={sm}
+                                  onChange={e => onCheckboxChange(e, sm, i)}
+                                >
+                                  {selectedTermsDisplay(sm, i)}
+                                </Checkbox>
+                              ))}
+                            </div>
+                          </Form.Item>
+                        )}
                         {results?.length > 0 ? (
                           <>
-                            {displaySelectedMappings?.length > 0 && (
-                              <Form.Item
-                                name="selected_mappings"
-                                valuePropName="value"
-                                rules={[{ required: false }]}
-                              >
-                                <div className="modal_display_results">
-                                  {displaySelectedMappings?.map((sm, i) => (
-                                    <Checkbox
-                                      key={i}
-                                      checked={selectedBoxes.some(
-                                        box => box.obo_id === sm.obo_id
-                                      )}
-                                      value={sm}
-                                      onChange={e => onCheckboxChange(e, sm, i)}
-                                    >
-                                      {selectedTermsDisplay(sm, i)}
-                                    </Checkbox>
-                                  ))}
-                                </div>
-                              </Form.Item>
-                            )}
                             <Form.Item
                               name={['filtered_mappings']}
                               valuePropName="value"
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index ed05747..d789a27 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -322,30 +322,30 @@ export const MappingReset = ({
                     <div className="all_checkboxes_container">
                       <OntologyCheckboxes apiPreferences={apiPreferences} />
                       <div className="result_form">
+                        {displaySelectedMappings?.length > 0 && (
+                          <Form.Item
+                            name="selected_mappings"
+                            valuePropName="value"
+                            rules={[{ required: false }]}
+                          >
+                            <div className="modal_display_results">
+                              {displaySelectedMappings?.map((sm, i) => (
+                                <Checkbox
+                                  key={i}
+                                  onChange={e => onCheckboxChange(e, sm)}
+                                  checked={selectedBoxes.some(
+                                    box => box.obo_id === sm.obo_id
+                                  )}
+                                  value={sm}
+                                >
+                                  {selectedTermsDisplay(sm, i)}
+                                </Checkbox>
+                              ))}
+                            </div>
+                          </Form.Item>
+                        )}{' '}
                         {results?.length > 0 ? (
                           <>
-                            {displaySelectedMappings?.length > 0 && (
-                              <Form.Item
-                                name="selected_mappings"
-                                valuePropName="value"
-                                rules={[{ required: false }]}
-                              >
-                                <div className="modal_display_results">
-                                  {displaySelectedMappings?.map((sm, i) => (
-                                    <Checkbox
-                                      key={i}
-                                      onChange={e => onCheckboxChange(e, sm)}
-                                      checked={selectedBoxes.some(
-                                        box => box.obo_id === sm.obo_id
-                                      )}
-                                      value={sm}
-                                    >
-                                      {selectedTermsDisplay(sm, i)}
-                                    </Checkbox>
-                                  ))}
-                                </div>
-                              </Form.Item>
-                            )}
                             <Form.Item
                               name={['filtered_mappings']}
                               valuePropName="value"
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index c640087..b738931 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -385,62 +385,59 @@ export const MappingSearch = ({
                     <div className="all_checkboxes_container">
                       <OntologyCheckboxes apiPreferences={apiPreferences} />
                       <div className="result_form">
+                        <Form.Item
+                          initialValue={initialChecked}
+                          name={['existing_mappings']}
+                          valuePropName="value"
+                          rules={[
+                            {
+                              required: false,
+                            },
+                          ]}
+                        >
+                          {mappingsForSearch?.length > 0 && (
+                            <Checkbox.Group
+                              className="mappings_checkbox"
+                              options={mappingsForSearch?.map((d, index) => {
+                                return {
+                                  value: JSON.stringify({
+                                    code: d.code,
+                                    display: d.display,
+                                    description: d.description,
+                                    system: d.system,
+                                  }),
+                                  label: existingMappingDisplay(d, index),
+                                };
+                              })}
+                              onChange={onExistingChange}
+                            />
+                          )}
+                        </Form.Item>
+                        {displaySelectedMappings?.length > 0 && (
+                          <Form.Item
+                            name="selected_mappings"
+                            valuePropName="value"
+                            rules={[{ required: false }]}
+                          >
+                            {' '}
+                            <div className="modal_display_results">
+                              {displaySelectedMappings?.map((sm, i) => (
+                                <Checkbox
+                                  key={i}
+                                  onChange={e => onCheckboxChange(e, sm)}
+                                  checked={selectedBoxes.some(
+                                    box => box.obo_id === sm.obo_id
+                                  )}
+                                  value={sm}
+                                >
+                                  {selectedTermsDisplay(sm, i)}
+                                </Checkbox>
+                              ))}
+                            </div>
+                          </Form.Item>
+                        )}{' '}
                         {results?.length > 0 ? (
                           <>
-                            <Form.Item
-                              initialValue={initialChecked}
-                              name={['existing_mappings']}
-                              valuePropName="value"
-                              rules={[
-                                {
-                                  required: false,
-                                },
-                              ]}
-                            >
-                              {mappingsForSearch?.length > 0 && (
-                                <Checkbox.Group
-                                  className="mappings_checkbox"
-                                  options={mappingsForSearch?.map(
-                                    (d, index) => {
-                                      return {
-                                        value: JSON.stringify({
-                                          code: d.code,
-                                          display: d.display,
-                                          description: d.description,
-                                          system: d.system,
-                                        }),
-                                        label: existingMappingDisplay(d, index),
-                                      };
-                                    }
-                                  )}
-                                  onChange={onExistingChange}
-                                />
-                              )}
-                            </Form.Item>
-
-                            {displaySelectedMappings?.length > 0 && (
-                              <Form.Item
-                                name="selected_mappings"
-                                valuePropName="value"
-                                rules={[{ required: false }]}
-                              >
-                                {' '}
-                                <div className="modal_display_results">
-                                  {displaySelectedMappings?.map((sm, i) => (
-                                    <Checkbox
-                                      key={i}
-                                      onChange={e => onCheckboxChange(e, sm)}
-                                      checked={selectedBoxes.some(
-                                        box => box.obo_id === sm.obo_id
-                                      )}
-                                      value={sm}
-                                    >
-                                      {selectedTermsDisplay(sm, i)}
-                                    </Checkbox>
-                                  ))}
-                                </div>
-                              </Form.Item>
-                            )}
                             <Form.Item
                               name={['filtered_mappings']}
                               valuePropName="value"

From db26d7b0ffec83c5c80184ce960ca4d962de7b70 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 24 Oct 2024 09:42:49 -0500
Subject: [PATCH 064/180] Styling fix for FilterAPIs to stop results from
 appearing mid-page

---
 .../Manager/MappingsFunctions/FilterAPI.jsx   | 92 ++++++++++---------
 1 file changed, 48 insertions(+), 44 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 183cd3b..faee0ea 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -1,5 +1,5 @@
 import { useContext, useEffect, useState } from 'react';
-import { Checkbox, Form, Tooltip } from 'antd';
+import { Checkbox, Form } from 'antd';
 import { ModalSpinner, OntologySpinner } from '../Spinner';
 import { myContext } from '../../../App';
 import { FilterOntology } from './FilterOntology';
@@ -43,6 +43,13 @@ export const FilterAPI = ({
     )
     .flat();
 
+  // The initial value for the form. The checkboxes for the filters that have already been selected will be checked by default
+  const initialChecked = flattenedFilters?.map(ef =>
+    JSON.stringify({
+      ontology: ef,
+    })
+  );
+
   // Fetches the active ontologyAPI each time the active API changes
   useEffect(() => {
     active && getOntologyApiById();
@@ -115,51 +122,48 @@ export const FilterAPI = ({
     <div>
       <div className="api_list">
         <Form form={form} preserve={false}>
-          <div>
-            <Tooltip
-              placement="top"
-              title="Default search through OLS using HPO, MAXO, MONDO, NCIT"
-            >
+          <div style={{ display: 'flex' }}>
+            <div style={{ flex: '0 0 25%' }}>
               <div className="api_label">APIs</div>
-            </Tooltip>
 
-            <Form.Item name={'selected_apis'} valuePropName="value">
-              <Checkbox.Group
-                className="mappings_checkbox"
-                options={ontologyApis.map((api, index) => {
-                  return {
-                    value: JSON.stringify({ api_preference: api?.api_id }),
-                    label: checkboxDisplay(api, index),
-                  };
-                })}
-              />
-            </Form.Item>
-          </div>
-          <div className="ontology_list">
-            {tableLoading ? (
-              <div className="ontology_spinner_div">
-                <OntologySpinner />
-              </div>
-            ) : (
-              <FilterOntology
-                ontology={ontology}
-                form={form}
-                selectedOntologies={selectedOntologies}
-                setSelectedOntologies={setSelectedOntologies}
-                selectedBoxes={selectedBoxes}
-                setSelectedBoxes={setSelectedBoxes}
-                displaySelectedOntologies={displaySelectedOntologies}
-                setDisplaySelectedOntologies={setDisplaySelectedOntologies}
-                searchText={searchText}
-                currentPage={currentPage}
-                setCurrentPage={setCurrentPage}
-                pageSize={pageSize}
-                setPageSize={setPageSize}
-                paginatedOntologies={paginatedOntologies}
-                apiPreferences={apiPreferences}
-                table={table}
-              />
-            )}
+              <Form.Item name={'selected_apis'} valuePropName="value">
+                <Checkbox.Group
+                  className="mappings_checkbox"
+                  options={ontologyApis.map((api, index) => {
+                    return {
+                      value: JSON.stringify({ api_preference: api?.api_id }),
+                      label: checkboxDisplay(api, index),
+                    };
+                  })}
+                />
+              </Form.Item>
+            </div>
+            <div style={{ flex: '0 0 70%' }}>
+              {tableLoading ? (
+                <div className="ontology_spinner_div">
+                  <OntologySpinner />
+                </div>
+              ) : (
+                <FilterOntology
+                  ontology={ontology}
+                  form={form}
+                  selectedOntologies={selectedOntologies}
+                  setSelectedOntologies={setSelectedOntologies}
+                  selectedBoxes={selectedBoxes}
+                  setSelectedBoxes={setSelectedBoxes}
+                  displaySelectedOntologies={displaySelectedOntologies}
+                  setDisplaySelectedOntologies={setDisplaySelectedOntologies}
+                  searchText={searchText}
+                  currentPage={currentPage}
+                  setCurrentPage={setCurrentPage}
+                  pageSize={pageSize}
+                  setPageSize={setPageSize}
+                  paginatedOntologies={paginatedOntologies}
+                  apiPreferences={apiPreferences}
+                  table={table}
+                />
+              )}
+            </div>
           </div>
         </Form>
       </div>

From 3070bb026966eb00b02991add6f86976621f5c69 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 24 Oct 2024 09:48:32 -0500
Subject: [PATCH 065/180] changed labels in nav bar for accuracy

---
 src/components/Nav/NavBar.jsx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/components/Nav/NavBar.jsx b/src/components/Nav/NavBar.jsx
index 13a0c11..80e39ff 100644
--- a/src/components/Nav/NavBar.jsx
+++ b/src/components/Nav/NavBar.jsx
@@ -27,11 +27,11 @@ export const NavBar = () => {
             </NavLink>
             {/* Placeholder elements below. No functionality at this time.*/}
             <NavLink to="/help">
-              <li className="nav_link">Help</li>
+              <li className="nav_link">About</li>
             </NavLink>
 
             <NavLink to="/about">
-              <li className="nav_link">About</li>
+              <li className="nav_link">Ontologies</li>
             </NavLink>
           </div>
           <div className="login">

From d7ee7c22af39397a8d83cabe8afa3bd13cfd5245 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 24 Oct 2024 10:24:53 -0500
Subject: [PATCH 066/180] modified endpoint in .env

---
 .env | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.env b/.env
index 0815b66..0f6c051 100644
--- a/.env
+++ b/.env
@@ -1,6 +1,6 @@
 VITE_SEARCH_ENDPOINT = https://www.ebi.ac.uk/ols4/api/search?
 VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
 # VITE_VOCAB_ENDPOINT = http://127.0.0.1:5000/api # local
-VITE_VOCAB_ENDPOINT = https://locutus-110109177269.us-central1.run.app/api # dev
-# VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
+# VITE_VOCAB_ENDPOINT = https://locutus-110109177269.us-central1.run.app/api # dev
+VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
 VITE_CLIENT_ID = 907694787484-36jr4oaf04mmniik6482batc87ejemm8.apps.googleusercontent.com

From 292bc5d163f8eba7691e6a0bc152f524a3aaf327 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 24 Oct 2024 10:36:08 -0500
Subject: [PATCH 067/180] adding 
 /Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/:terminologyId

---
 src/AppRouter.jsx                               | 5 +++++
 src/components/Projects/Tables/TableDetails.jsx | 4 +++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index 5a5008e..1ca5075 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -62,6 +62,11 @@ export const AppRouter = () => {
                         path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId"
                         element={<TableDetails />}
                       />
+                      <Route
+                        path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/:terminologyId"
+                        element={<Terminology />}
+                      />
+                      <Route path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/" element={<Terminology />} />
                     </Route>
                   </Route>
                 </Route>
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 69eddd6..7d7a54a 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -217,7 +217,9 @@ There is then a tooltip that displays the variables on hover.*/
         max: variable.max,
         units: variable.units,
         enumeration: variable.data_type === 'ENUMERATION' && (
-          <Link to={`/${variable.enumerations.reference}`}>View/Edit</Link>
+          console.log(variable.enumerations.reference,"variable.enumerations.reference"),
+          
+          <Link to={`/Study/${studyId}/DataDictionary/${DDId}/Table/${tableId}/${variable.enumerations.reference}`}>View/Edit</Link>
         ),
         mapped_terms: matchCode(variable),
       };

From f81dc803364a7574fa25e433c09f689fd59927fe Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 24 Oct 2024 11:17:00 -0500
Subject: [PATCH 068/180] Merged main with new main

---
 package-lock.json                             |  15 +-
 package.json                                  |   1 +
 src/components/About/OntologyTable.jsx        |  19 +-
 .../MappingsFunctions/GetMappingsModal.jsx    |   2 +
 .../MappingsFunctions/MappingReset.jsx        | 174 +++++++++---------
 .../MappingsFunctions/MappingSearch.jsx       |   2 +
 .../MappingsFunctions/MappingsFunctions.scss  |  23 ++-
 .../Tables/EditMappingsTableModal.jsx         |  10 +
 .../Projects/Tables/TableDetails.jsx          | 115 ++++++++++--
 .../Projects/Tables/TableStyling.scss         |  18 ++
 .../Terminologies/EditMappingModal.jsx        |   4 +
 .../Projects/Terminologies/Terminology.jsx    | 148 +++++++++++++--
 .../Terminologies/TerminologyList.jsx         |  16 +-
 13 files changed, 407 insertions(+), 140 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index e277d09..419d30d 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -8,6 +8,7 @@
       "name": "vocab-management-tool",
       "version": "0.0.0",
       "dependencies": {
+        "@ant-design/icons": "^5.5.1",
         "@react-oauth/google": "^0.12.1",
         "antd": "^5.15.2",
         "jwt-decode": "^4.0.0",
@@ -77,13 +78,13 @@
       }
     },
     "node_modules/@ant-design/icons": {
-      "version": "5.3.7",
-      "resolved": "https://registry.npmjs.org/@ant-design/icons/-/icons-5.3.7.tgz",
-      "integrity": "sha512-bCPXTAg66f5bdccM4TT21SQBDO1Ek2gho9h3nO9DAKXJP4sq+5VBjrQMSxMVXSB3HyEz+cUbHQ5+6ogxCOpaew==",
+      "version": "5.5.1",
+      "resolved": "https://registry.npmjs.org/@ant-design/icons/-/icons-5.5.1.tgz",
+      "integrity": "sha512-0UrM02MA2iDIgvLatWrj6YTCYe0F/cwXvVE0E2SqGrL7PZireQwgEKTKBisWpZyal5eXZLvuM98kju6YtYne8w==",
       "dependencies": {
         "@ant-design/colors": "^7.0.0",
         "@ant-design/icons-svg": "^4.4.0",
-        "@babel/runtime": "^7.11.2",
+        "@babel/runtime": "^7.24.8",
         "classnames": "^2.2.6",
         "rc-util": "^5.31.1"
       },
@@ -394,9 +395,9 @@
       }
     },
     "node_modules/@babel/runtime": {
-      "version": "7.24.7",
-      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.24.7.tgz",
-      "integrity": "sha512-UwgBRMjJP+xv857DCngvqXI3Iq6J4v0wXmwc6sapg+zyhbwmQX67LUEFrkK5tbyJ30jGuG3ZvWpBiB9LCy1kWw==",
+      "version": "7.25.9",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.25.9.tgz",
+      "integrity": "sha512-4zpTHZ9Cm6L9L+uIqghQX8ZXg8HKFcjYO3qHoO8zTmRm6HQUJ8SSJ+KRvbMBZn0EGVlT4DRYeQ/6hjlyXBh+Kg==",
       "dependencies": {
         "regenerator-runtime": "^0.14.0"
       },
diff --git a/package.json b/package.json
index 5855550..38334e7 100644
--- a/package.json
+++ b/package.json
@@ -12,6 +12,7 @@
     "preview": "vite preview"
   },
   "dependencies": {
+    "@ant-design/icons": "^5.5.1",
     "@react-oauth/google": "^0.12.1",
     "antd": "^5.15.2",
     "jwt-decode": "^4.0.0",
diff --git a/src/components/About/OntologyTable.jsx b/src/components/About/OntologyTable.jsx
index 905d099..a326572 100644
--- a/src/components/About/OntologyTable.jsx
+++ b/src/components/About/OntologyTable.jsx
@@ -1,10 +1,19 @@
 import { Button, Input, Space, Table } from 'antd';
 import { SearchOutlined } from '@ant-design/icons';
-import { useState } from 'react';
+import { useState, useEffect } from 'react';
 
 export const OntologyTable = ({ ontology }) => {
   const [filter, setFilter] = useState(null);
 
+  const [pageSize, setPageSize] = useState(
+    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+  const handleTableChange = (current, size) => {
+    setPageSize(size);
+  };
+  useEffect(() => {
+    localStorage.setItem('pageSize', pageSize);
+  }, [pageSize]);
+
   const ontologyTitle = () => {
     return (
       <div className="ontology_filter">
@@ -85,6 +94,8 @@ export const OntologyTable = ({ ontology }) => {
     }))
   );
 
+
+
   return (
     <Table
       columns={columns}
@@ -92,6 +103,12 @@ export const OntologyTable = ({ ontology }) => {
       scroll={{
         y: 470,
       }}
+      pagination={{
+        showSizeChanger: true,
+        pageSizeOptions: ['10', '20', '30'],
+        pageSize: pageSize, // Use the stored pageSize
+        onChange: handleTableChange, // Capture pagination changes
+      }}
     />
   );
 };
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 74dc182..474f5c8 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -24,6 +24,7 @@ export const GetMappingsModal = ({
   searchProp,
   component,
   mappingProp,
+  mappingDesc,
   table,
 }) => {
   const [form] = Form.useForm();
@@ -395,6 +396,7 @@ export const GetMappingsModal = ({
                       onChange={handleChange}
                     />
                   </div>
+                  <span className="search-desc">{mappingDesc}</span>
                 </div>
                 {/* ant.design form displaying the checkboxes with the search results.  */}
                 <div className="result_container">
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index d789a27..552f9c3 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -10,6 +10,7 @@ import { OntologyCheckboxes } from './OntologyCheckboxes';
 
 export const MappingReset = ({
   searchProp,
+  mappingDesc,
   setEditMappings,
   form,
   onClose,
@@ -315,102 +316,103 @@ export const MappingReset = ({
                       onChange={handleChange}
                     />
                   </div>
+                  <span className="search-desc">{mappingDesc}</span>
                 </div>
-                {/* ant.design form displaying the checkboxes with the search results.  */}
-                <div className="result_container">
-                  <Form form={form} layout="vertical" preserve={false}>
-                    <div className="all_checkboxes_container">
-                      <OntologyCheckboxes apiPreferences={apiPreferences} />
-                      <div className="result_form">
-                        {displaySelectedMappings?.length > 0 && (
+              </div>
+              {/* ant.design form displaying the checkboxes with the search results.  */}
+              <div className="result_container">
+                <Form form={form} layout="vertical" preserve={false}>
+                  <div className="all_checkboxes_container">
+                    <OntologyCheckboxes apiPreferences={apiPreferences} />
+                    <div className="result_form">
+                      {displaySelectedMappings?.length > 0 && (
+                        <Form.Item
+                          name="selected_mappings"
+                          valuePropName="value"
+                          rules={[{ required: false }]}
+                        >
+                          <div className="modal_display_results">
+                            {displaySelectedMappings?.map((sm, i) => (
+                              <Checkbox
+                                key={i}
+                                onChange={e => onCheckboxChange(e, sm)}
+                                checked={selectedBoxes.some(
+                                  box => box.obo_id === sm.obo_id
+                                )}
+                                value={sm}
+                              >
+                                {selectedTermsDisplay(sm, i)}
+                              </Checkbox>
+                            ))}
+                          </div>
+                        </Form.Item>
+                      )}{' '}
+                      {results?.length > 0 ? (
+                        <>
                           <Form.Item
-                            name="selected_mappings"
+                            name={['filtered_mappings']}
                             valuePropName="value"
-                            rules={[{ required: false }]}
+                            rules={[
+                              {
+                                required: true,
+                                message: 'Please make a selection.',
+                              },
+                            ]}
                           >
-                            <div className="modal_display_results">
-                              {displaySelectedMappings?.map((sm, i) => (
-                                <Checkbox
-                                  key={i}
-                                  onChange={e => onCheckboxChange(e, sm)}
-                                  checked={selectedBoxes.some(
-                                    box => box.obo_id === sm.obo_id
-                                  )}
-                                  value={sm}
-                                >
-                                  {selectedTermsDisplay(sm, i)}
-                                </Checkbox>
-                              ))}
-                            </div>
+                            {filteredResultsArray?.length > 0 ? (
+                              <Checkbox.Group
+                                className="mappings_checkbox"
+                                options={filteredResultsArray?.map(
+                                  (d, index) => {
+                                    return {
+                                      value: JSON.stringify({
+                                        code: d.obo_id,
+                                        display: d.label,
+                                        // description: d.description[0],
+                                        system: systemsMatch(
+                                          d?.obo_id.split(':')[0]
+                                        ),
+                                      }),
+                                      label: checkBoxDisplay(d, index),
+                                    };
+                                  }
+                                )}
+                                onChange={onSelectedChange}
+                              />
+                            ) : (
+                              ''
+                            )}
                           </Form.Item>
-                        )}{' '}
-                        {results?.length > 0 ? (
-                          <>
-                            <Form.Item
-                              name={['filtered_mappings']}
-                              valuePropName="value"
-                              rules={[
-                                {
-                                  required: true,
-                                  message: 'Please make a selection.',
-                                },
-                              ]}
-                            >
-                              {filteredResultsArray?.length > 0 ? (
-                                <Checkbox.Group
-                                  className="mappings_checkbox"
-                                  options={filteredResultsArray?.map(
-                                    (d, index) => {
-                                      return {
-                                        value: JSON.stringify({
-                                          code: d.obo_id,
-                                          display: d.label,
-                                          // description: d.description[0],
-                                          system: systemsMatch(
-                                            d?.obo_id.split(':')[0]
-                                          ),
-                                        }),
-                                        label: checkBoxDisplay(d, index),
-                                      };
-                                    }
-                                  )}
-                                  onChange={onSelectedChange}
-                                />
-                              ) : (
-                                ''
-                              )}
-                            </Form.Item>
-                          </>
-                        ) : (
-                          <h3>No results found</h3>
-                        )}
-                      </div>
+                        </>
+                      ) : (
+                        <h3>No results found</h3>
+                      )}
                     </div>
-                  </Form>
-                  <div className="view_more_wrapper">
-                    {/* 'View More' pagination displaying the number of results being displayed
+                  </div>
+                </Form>
+                <div className="view_more_wrapper">
+                  {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
                       inconsistencies in results numbers per page. */}
-                    <Tooltip
-                      placement="bottom"
-                      title="Redundant entries have been removed"
+                  <Tooltip
+                    placement="bottom"
+                    title="Redundant entries have been removed"
+                  >
+                    Displaying {resultsCount}
+                    &nbsp;of&nbsp;{totalCount}
+                  </Tooltip>
+                  {totalCount - filteredResultsCount !== resultsCount && (
+                    <span
+                      className="view_more_link"
+                      onClick={e => {
+                        handleViewMore(e);
+                        setLastCount(resultsCount);
+                      }}
                     >
-                      Displaying {resultsCount}
-                      &nbsp;of&nbsp;{totalCount}
-                    </Tooltip>
-                    {totalCount - filteredResultsCount !== resultsCount && (
-                      <span
-                        className="view_more_link"
-                        onClick={e => {
-                          handleViewMore(e);
-                          setLastCount(resultsCount);
-                        }}
-                      >
-                        View More
-                      </span>
-                    )}
-                  </div>
+                      View More
+                    </span>
+                  )}
                 </div>
               </div>
             </>
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index b738931..88d8db4 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -14,6 +14,7 @@ export const MappingSearch = ({
   mappingsForSearch,
   onClose,
   searchProp,
+  mappingDesc,
   component,
   mappingProp,
   table,
@@ -378,6 +379,7 @@ export const MappingSearch = ({
                       onChange={handleChange}
                     />
                   </div>
+                  <span className="search-desc">{mappingDesc}</span>
                 </div>
                 {/* ant.design form displaying the checkboxes with the search results.  */}
                 <div className="result_container">
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index 001d127..170c28b 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -25,15 +25,28 @@
   position: sticky;
   margin: 0 0 15px 0;
   display: flex;
+  flex-wrap: wrap;
   flex-direction: row;
-  align-items: center;
-  gap: 20px;
+  justify-content: flex-start;
+  align-items: end;
   z-index: 10;
+  flex: 1;
+  border-bottom: solid 1px #eeee;
+  h4 {
+    margin:0;
+    padding-right:1rem;
+  }
+  .mappings_search_bar {
+    width: 60%;
+  }
+  .search-desc {
+    flex: 0 0 100%;
+    margin-bottom:1rem;
+  }
 }
 
-.mappings_search_bar {
-  width: 50%;
-}
+
+
 
 .inactive_term,
 .active_term {
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index ce7a71c..15fdc98 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -341,6 +341,11 @@ export const EditMappingsTableModal = ({
           reset={reset}
           onClose={form.resetFields}
           searchProp={editMappings.name}
+          mappingDesc={
+            editMappings.description
+              ? editMappings.description
+              : 'No Description'
+          }
           component={table}
           mappingProp={editMappings.code}
           table={table}
@@ -349,6 +354,11 @@ export const EditMappingsTableModal = ({
         reset && (
           <MappingReset
             searchProp={editMappings.name}
+            mappingDesc={
+              editMappings.description
+                ? editMappings.description
+                : 'No Description'
+            }
             setEditMappings={setEditMappings}
             mappingsForSearch={mappingsForSearch}
             form={form}
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 75e5f3c..6da13b8 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -4,7 +4,8 @@ import './TableStyling.scss';
 import { Link, useNavigate, useParams } from 'react-router-dom';
 import { Spinner } from '../../Manager/Spinner';
 import { getById } from '../../Manager/FetchManager';
-import { Card, Col, Form, notification, Row, Table, Tooltip } from 'antd';
+import { Card, Col, Form, notification, Row, Table, Button } from 'antd';
+import { CloseCircleOutlined } from '@ant-design/icons';
 import { EditTableDetails } from './EditTableDetails';
 import { DeleteTable } from './DeleteTable';
 import { LoadVariables } from './LoadVariables';
@@ -40,6 +41,11 @@ export const TableDetails = () => {
   const [loading, setLoading] = useState(true);
   const [load, setLoad] = useState(false);
 
+  const [pageSize, setPageSize] = useState(
+    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+  const handleTableChange = (current, size) => {
+    setPageSize(size);
+  };
   const navigate = useNavigate();
 
   const handleSuccess = () => {
@@ -48,8 +54,55 @@ export const TableDetails = () => {
   const login = RequiredLogin({ handleSuccess: handleSuccess });
 
   useEffect(() => {
+
     setDataSource(tableData(table));
-  }, [table, mapping]);
+    localStorage.setItem('pageSize', pageSize);
+  }, [table, mapping, pageSize]);
+
+
+  const updateMappings = (mapArr,mappingCode ) => {
+    
+    // setLoading(true);
+    const mappingsDTO = {
+      mappings: mapArr,
+      editor: user.email,
+    };
+    console.log(mappingsDTO,"mappingsDTO");
+    
+    fetch(`${vocabUrl}/Table/${tableId}/mapping/${mappingCode}`, {
+      method: 'PUT',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify(mappingsDTO),
+    })
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .then(data => {
+        setMapping(data.codes);
+        setEditMappings(null);
+        form.resetFields();
+        notification.success({ description:'Mapping removed.'});
+      })
+      .catch(error => {
+        console.log(error,'error');
+        
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred. Please try again.',
+          });
+        }
+        return error;
+      })
+      .finally(() => setLoading(false));
+  };
+
 
   const alphabetizeOntologies = ontologies => {
     // Sort the keys alphabetically
@@ -78,6 +131,8 @@ export const TableDetails = () => {
               .then(data => setMapping(data.codes))
               .catch(error => {
                 if (error) {
+                  console.log(error,"error");
+                  
                   notification.error({
                     message: 'Error',
                     description: 'An error occurred loading mappings.',
@@ -179,23 +234,39 @@ The variables in the mappings need to be matched up to each variable in the tabl
 The function maps through the mapping array. For each variable, if the mapping variable is equal to the 
 variable in the table, AND the mappings array length for the variable is > 0, the mappings array is mapped through
 and returns the length of the mapping array (i.e. returns the number of variables mapped to the table variable). 
-There is then a tooltip that displays the variables on hover.*/
-  const matchCode = variable =>
-    mapping?.length > 0 &&
-    mapping?.map(
-      (item, index) =>
-        item?.code === variable?.code &&
-        item?.mappings?.length > 0 && (
-          <Tooltip
-            title={item.mappings.map(code => {
-              return <div key={index}>{code.code}</div>;
-            })}
-            key={index}
-          >
-            {item?.mappings?.length}
-          </Tooltip>
-        )
-    );
+It then shows the mappings as table data and alows the user to delete a mapping from the table.*/
+  const noMapping = variable => {
+    return <Button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
+      Get Mappings
+    </Button>
+  }
+
+  const matchCode = variable => {
+
+
+    if (!mapping?.length) {
+      return noMapping(variable);
+    }
+
+    const variableMappings = mapping.find(item => item?.code === variable?.code);
+
+    if (variableMappings && variableMappings.mappings?.length) {
+      return variableMappings.mappings.map(code => <div className='mapping' key={code.display}><span className='mapping-display'>{code.display}</span><span className='remove-mapping' onClick={() => handleRemoveMapping(variableMappings,code)}><CloseCircleOutlined  style={{color:"red", }} /></span></div>);
+    } else {
+      return noMapping(variable);
+    }
+  };
+
+  const handleRemoveMapping = (variableMappings,code) => {
+    // console.log(variableMappings,"variableMappings");
+    const mappingToRemove = variableMappings.mappings.indexOf(code);
+    //remove mapping from mappings
+    {mappingToRemove !== -1 && variableMappings.mappings.splice(mappingToRemove,1)}   
+    updateMappings(variableMappings?.mappings,variableMappings?.code);    
+  
+  }
+
+
 
   // data for the table columns. Each table has an array of variables. Each variable has a name, description, and data type.
   // The integer and quantity data types include additional details.
@@ -312,6 +383,12 @@ There is then a tooltip that displays the variables on hover.*/
                         record.data_type === 'INTEGER' ||
                         record.data_type === 'QUANTITY',
                     }}
+                    pagination={{
+                      showSizeChanger: true,
+                      pageSizeOptions: ['10', '20', '30'],
+                      pageSize: pageSize, // Use the stored pageSize
+                      onChange: handleTableChange, // Capture pagination changes
+                    }}
                   />
                 </Form>
                 <ExportFile table={table} />
diff --git a/src/components/Projects/Tables/TableStyling.scss b/src/components/Projects/Tables/TableStyling.scss
index 4cf5288..4767acb 100644
--- a/src/components/Projects/Tables/TableStyling.scss
+++ b/src/components/Projects/Tables/TableStyling.scss
@@ -54,6 +54,7 @@ input::file-selector-button:hover {
   border: 1px solid darkgrey;
   color: gray;
   border-radius: 25px;
+
   font: {
     size: 0.7rem;
     weight: 800;
@@ -74,3 +75,20 @@ input::file-selector-button:hover {
   gap: 10px;
   margin-left: 50px;
 }
+
+.mapping {
+  &-display{
+    white-space: nowrap;
+  }
+  display: flex;
+  .remove-mapping {
+    padding-left:.25rem;
+    cursor: pointer;
+    opacity: 0;
+
+    &:hover {
+      transition: all .4s linear;
+      opacity: 1;
+    }
+  }
+}
\ No newline at end of file
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 27bb93a..6eb19b5 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -22,6 +22,7 @@ export const EditMappingsModal = ({
   setEditMappings,
   terminologyId,
   setMapping,
+  mappingDesc,
   terminology,
 }) => {
   const [form] = Form.useForm();
@@ -324,6 +325,7 @@ export const EditMappingsModal = ({
                 ? editMappings.display
                 : editMappings?.code}
             </h3>
+            <span className="search-desc">{mappingDesc}</span>
           </div>
           <Form form={form} layout="vertical" preserve={false}>
             <Form.Item
@@ -348,6 +350,7 @@ export const EditMappingsModal = ({
           searchProp={
             editMappings?.display ? editMappings.display : editMappings?.code
           }
+          mappingDesc={editMappings?.description}
         />
       ) : (
         reset && (
@@ -360,6 +363,7 @@ export const EditMappingsModal = ({
             form={form}
             reset={reset}
             onClose={form.resetFields}
+            mappingDesc={editMappings?.description}
           />
         )
       )}
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index e6dcc85..5316c5f 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -4,7 +4,8 @@ import { myContext } from '../../../App';
 import './Terminology.scss';
 import { Spinner } from '../../Manager/Spinner';
 import { getById } from '../../Manager/FetchManager';
-import { Col, Form, notification, Row, Table, Tooltip } from 'antd';
+import { Col, Form, notification, Row, Table, Button } from 'antd';
+import { CloseCircleOutlined } from '@ant-design/icons';
 import { EditMappingsModal } from './EditMappingModal';
 import { EditTerminologyDetails } from './EditTerminologyDetails';
 import { SettingsDropdownTerminology } from '../../Manager/Dropdown/SettingsDropdownTerminology';
@@ -21,8 +22,8 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 export const Terminology = () => {
   const [form] = Form.useForm();
 
-  const { terminologyId } = useParams();
-  const { vocabUrl } = useContext(myContext);
+  const { terminologyId, tableId } = useParams();
+  const { vocabUrl, user } = useContext(myContext);
   const { setPrefTerminologies, prefTerminologies } = useContext(SearchContext);
   const {
     editMappings,
@@ -33,33 +34,121 @@ export const Terminology = () => {
     setMapping,
   } = useContext(MappingContext);
 
+  const [pageSize, setPageSize] = useState(
+    parseInt(localStorage.getItem('pageSize'), 10) || 10
+  );
+  const handleTableChange = (current, size) => {
+    setPageSize(size);
+  };
+  useEffect(() => {
+    localStorage.setItem('pageSize', pageSize);
+  }, [pageSize]);
+
   const [loading, setLoading] = useState(true);
   const initialTerminology = { url: '', description: '', name: '', codes: [] }; //initial state of terminology
   const [terminology, setTerminology] = useState(initialTerminology);
   const navigate = useNavigate();
+
+  const updateMappings = (mapArr, mappingCode) => {
+    // setLoading(true);
+    const mappingsDTO = {
+      mappings: mapArr,
+      editor: user.email,
+    };
+    console.log(tableId, 'tableId');
+
+    fetch(`${vocabUrl}/Terminology/${terminologyId}/mapping/${mappingCode}`, {
+      method: 'PUT',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify(mappingsDTO),
+    })
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .then(data => {
+        setMapping(data.codes);
+        setEditMappings(null);
+        form.resetFields();
+        notification.success({ description: 'Mapping removed.' });
+      })
+      .catch(error => {
+        console.log(error, 'error');
+
+        if (error) {
+          console.log(error, 'error');
+
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred. Please try again.',
+          });
+        }
+        return error;
+      })
+      .finally(() => setLoading(false));
+  };
+
   /* The terminology may have numerous codes. The API call to fetch the mappings returns all mappings for the terminology.
 The codes in the mappings need to be matched up to each code in the terminology.
 The function maps through the mapping array. For each code, if the mapping code is equal to the 
 code in the terminology, AND the mappings array length for the code is > 0, the mappings array is mapped through
 and returns the length of the mapping array (i.e. returns the number of codes mapped to the terminology code). 
-There is then a tooltip that displays the codes on hover.*/
-  const matchCode = code =>
-    mapping?.length > 0 &&
-    mapping?.map(
-      (item, index) =>
-        item.code === code.code &&
-        item?.mappings?.length > 0 && (
-          <Tooltip
-            title={item.mappings.map(code => {
-              return <div key={index}>{code.code}</div>;
-            })}
-            key={index}
-          >
-            {item.mappings.length}
-          </Tooltip>
-        )
+It then shows the mappings as table data and alows the user to delete a mapping from the table.*/
+
+  const noMapping = variable => {
+    return (
+      <Button
+        onClick={() =>
+          setGetMappings({ name: variable.name, code: variable.code })
+        }
+      >
+        Get Mappings
+      </Button>
+    );
+  };
+
+  const matchCode = variable => {
+    if (!mapping?.length) {
+      return noMapping(variable);
+    }
+
+    const variableMappings = mapping.find(
+      item => item?.code === variable?.code
     );
 
+    if (variableMappings && variableMappings.mappings?.length) {
+      return variableMappings.mappings.map(code => (
+        <div className="mapping" key={code.display}>
+          <span className="mapping-display">{code.display}</span>
+          <span
+            className="remove-mapping"
+            onClick={() => handleRemoveMapping(variableMappings, code)}
+          >
+            <CloseCircleOutlined style={{ color: 'red' }} />
+          </span>
+        </div>
+      ));
+    } else {
+      return noMapping(variable);
+    }
+  };
+
+  const handleRemoveMapping = (variableMappings, code) => {
+    // console.log(variableMappings,"variableMappings");
+    const mappingToRemove = variableMappings.mappings.indexOf(code);
+    //remove mapping from mappings
+    {
+      mappingToRemove !== -1 &&
+        variableMappings.mappings.splice(mappingToRemove, 1);
+    }
+    updateMappings(variableMappings?.mappings, variableMappings?.code);
+  };
+
   // data for each column in the table.
   // Map through the codes in the terminology and display the code, display, number of mapped terms,
   // and an edit or get mappings button depending on the condition.
@@ -248,7 +337,16 @@ There is then a tooltip that displays the codes on hover.*/
               <Spinner />
             ) : (
               <Form form={form}>
-                <Table columns={columns} dataSource={dataSource} />
+                <Table
+                  columns={columns}
+                  dataSource={dataSource}
+                  pagination={{
+                    showSizeChanger: true,
+                    pageSizeOptions: ['10', '20', '30'],
+                    pageSize: pageSize, // Use the stored pageSize
+                    onChange: handleTableChange, // Capture pagination changes
+                  }}
+                />
               </Form>
             )}
           </div>
@@ -258,6 +356,11 @@ There is then a tooltip that displays the codes on hover.*/
             setEditMappings={setEditMappings}
             terminologyId={terminologyId}
             setMapping={setMapping}
+            mappingDesc={
+              editMappings?.description
+                ? editMappings?.description
+                : 'No Description'
+            }
             terminology={terminology}
           />
           <GetMappingsModal
@@ -271,6 +374,11 @@ There is then a tooltip that displays the codes on hover.*/
             setMapping={setMapping}
             terminologyId={terminologyId}
             mappingProp={getMappings?.code}
+            mappingDesc={
+              getMappings?.description
+                ? getMappings?.description
+                : 'No Description'
+            }
           />
 
           {/* Displays the edit form */}
diff --git a/src/components/Projects/Terminologies/TerminologyList.jsx b/src/components/Projects/Terminologies/TerminologyList.jsx
index 5b3ca6f..99d0cbf 100644
--- a/src/components/Projects/Terminologies/TerminologyList.jsx
+++ b/src/components/Projects/Terminologies/TerminologyList.jsx
@@ -14,7 +14,8 @@ export const TerminologyList = () => {
   const [terms, setTerms] = useState([]);
   const [filter, setFilter] = useState(null);
   const [deleteId, setDeleteId] = useState(null);
-
+  const [pageSize, setPageSize] = useState(
+    parseInt(localStorage.getItem('pageSize'), 10) || 10);
   const { vocabUrl } = useContext(myContext);
 
   const navigate = useNavigate();
@@ -28,7 +29,8 @@ export const TerminologyList = () => {
         setTerms(data);
       })
       .finally(() => setLoading(false));
-  }, []);
+      localStorage.setItem('pageSize', pageSize);
+  }, [pageSize]);
 
   const terminologyTitle = () => {
     return (
@@ -44,6 +46,9 @@ export const TerminologyList = () => {
       {item.name ? item.name : item.id}
     </Link>
   );
+  const handleTableChange = (current, size) => { 
+    setPageSize(size);     
+  };
 
   const columns = [
     {
@@ -140,9 +145,16 @@ export const TerminologyList = () => {
         <h2>Terminology Index</h2>
         <AddTerminology />
         <Table
+          showSizeChanger={true}
           columns={columns}
           dataSource={dataSource}
           getPopupContainer={trigger => trigger.parentNode}
+          pagination={{ 
+            showSizeChanger: true,
+            pageSizeOptions: ['10', '20', '30'],
+            pageSize: pageSize, // Use the stored pageSize
+            onChange: handleTableChange, // Capture pagination changes
+          }} 
         />
       </div>
       <DeleteTerminology

From f4822ff5211a0bc6f8f4da0874c6744dfe653885 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 24 Oct 2024 11:47:27 -0500
Subject: [PATCH 069/180] CSS styling for footer and main content

---
 .env                                          |   4 +-
 src/App.scss                                  |   3 +
 src/AppRouter.jsx                             |  26 +++-
 src/components/About/OntologyInfo.scss        |   4 +-
 src/components/Nav/Breadcrumbs.jsx            |  30 ++++
 src/components/Nav/NavBar.scss                | 143 +++++++++++-------
 .../Projects/Studies/StudyStyling.scss        |   3 +-
 .../Projects/Tables/TableDetails.jsx          |   4 +-
 .../Projects/Tables/TableStyling.scss         |  10 +-
 .../Projects/Terminologies/Terminology.scss   |   2 +-
 10 files changed, 160 insertions(+), 69 deletions(-)
 create mode 100644 src/components/Nav/Breadcrumbs.jsx

diff --git a/.env b/.env
index 0f6c051..0815b66 100644
--- a/.env
+++ b/.env
@@ -1,6 +1,6 @@
 VITE_SEARCH_ENDPOINT = https://www.ebi.ac.uk/ols4/api/search?
 VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
 # VITE_VOCAB_ENDPOINT = http://127.0.0.1:5000/api # local
-# VITE_VOCAB_ENDPOINT = https://locutus-110109177269.us-central1.run.app/api # dev
-VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
+VITE_VOCAB_ENDPOINT = https://locutus-110109177269.us-central1.run.app/api # dev
+# VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
 VITE_CLIENT_ID = 907694787484-36jr4oaf04mmniik6482batc87ejemm8.apps.googleusercontent.com
diff --git a/src/App.scss b/src/App.scss
index 5ea8142..6a5342c 100644
--- a/src/App.scss
+++ b/src/App.scss
@@ -1,9 +1,12 @@
 .approuter_div {
   display: flex;
   flex-direction: column;
+  justify-content: space-between;
 }
 
 .outlet_div {
   height: 100%;
   min-height: 100vh;
+  position: relative;
+  // top:-2.5rem;
 }
diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index 4892b4b..1ca5075 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -1,6 +1,7 @@
 import { OntologySearch } from './components/Search/OntologySearch';
-import { BrowserRouter, Outlet, Route, Routes } from 'react-router-dom';
+import { BrowserRouter, Outlet, Route, Routes, Navigate } from 'react-router-dom';
 import { NavBar } from './components/Nav/NavBar';
+import { Breadcrumbs } from './components/Nav/Breadcrumbs.jsx';
 import { Footer } from './components/Nav/Footer';
 import { SearchResults } from './components/Search/SearchResults';
 import { Terminology } from './components/Projects/Terminologies/Terminology';
@@ -27,6 +28,7 @@ export const AppRouter = () => {
             <>
               <div className="approuter_div">
                 <NavBar />
+                <Breadcrumbs />
                 <div className="outlet_div">
                   <Outlet />
                 </div>
@@ -41,17 +43,31 @@ export const AppRouter = () => {
             <Route path="/404" element={<Error404 />} />
             <Route path="/about" element={<OntologyInfo />} />
             <Route path="/terminologies" element={<TerminologyList />} />
+            <Route path="/terminology" element={<Navigate to="/terminologies" />} />
             <Route element={<MappingContextRoot />}>
               <Route element={<SearchContextRoot />}>
                 <Route path="/studies" element={<StudyList />} />
+                <Route path="/study" element={<Navigate to="/studies" />} />
                 <Route path="/Study/:studyId">
                   <Route index element={<StudyDetails />} />
-                  <Route path="/Study/:studyId/DataDictionary/:DDId">
-                    <Route index element={<DDDetails />} />
+                  <Route path="DataDictionary">
+                    <Route index element={<StudyDetails />} />
                     <Route
-                      path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId"
-                      element={<TableDetails />}
+                      path="/Study/:studyId/DataDictionary/:DDId/Table/"
+                      element={<DDDetails />}
                     />
+                    <Route path="/Study/:studyId/DataDictionary/:DDId">
+                      <Route index element={<DDDetails />} />
+                      <Route
+                        path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId"
+                        element={<TableDetails />}
+                      />
+                      <Route
+                        path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/:terminologyId"
+                        element={<Terminology />}
+                      />
+                      <Route path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/" element={<Terminology />} />
+                    </Route>
                   </Route>
                 </Route>
                 <Route
diff --git a/src/components/About/OntologyInfo.scss b/src/components/About/OntologyInfo.scss
index 226e395..249f4de 100644
--- a/src/components/About/OntologyInfo.scss
+++ b/src/components/About/OntologyInfo.scss
@@ -1,7 +1,7 @@
 @import '../Styling/Variables';
 
 .about_container {
-  margin: 17vh 10vw 10vh 10vw;
+  margin: 0 10vw;
   line-height: 1.5rem;
 }
 
@@ -13,7 +13,6 @@
 .api_list {
   width: 12vw;
   height: fit-content;
-  position: fixed;
   display: flex;
   flex-flow: column wrap;
   gap: 2px;
@@ -40,7 +39,6 @@
 }
 .ontology_list {
   margin: 0 0 0 15vw;
-  position: fixed;
   top: 20vh;
   height: 20%;
   width: 70vw;
diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
new file mode 100644
index 0000000..f6b29ee
--- /dev/null
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -0,0 +1,30 @@
+import { Breadcrumb } from "antd"
+import { useLocation, Link } from 'react-router-dom';
+// import { Link } from 'react-router';
+export const Breadcrumbs = () => {
+   const location = useLocation();
+   const pathParts = location.pathname.split('/').filter(Boolean);
+   const pathArr = []
+   pathParts.forEach(path => {
+      pathArr.push({ title: path, path: path });
+   });
+  
+   console.log(location,'location');
+   
+
+   return <span className="breadcrumbs">
+       <li><Link to={'/'}>Home</Link> {location.pathname != '/' && <span>&nbsp;&nbsp;/&nbsp;&nbsp;</span>}</li>
+      <Breadcrumb itemRender={itemRender} items={pathArr} />
+   </span>
+}
+function itemRender(currentRoute, params, items, pathArr) {
+   const isLast = currentRoute?.path === items[items.length - 1]?.path;
+
+   return <>
+   {isLast ? (
+      <span>{currentRoute.title}</span>
+   ) : (
+      <Link to={`/${pathArr.join("/")}`}>{currentRoute.title}</Link>
+   )}
+   </>
+}
\ No newline at end of file
diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index 25c21e9..95459e7 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -3,7 +3,7 @@
 $navColor: #080705;
 $linkColor: #fffc31;
 
-nav {
+nav.navbar {
   z-index: 1;
   width: 100%;
   background-color: $navColor;
@@ -11,81 +11,122 @@ nav {
   display: flex;
   flex-direction: row;
   justify-content: center;
-  position: fixed;
+  position: sticky;
   top: 0;
+
   li {
     list-style-type: none;
   }
+
   a:not(.nav_logo) {
     text-decoration: none;
     color: $navColor;
+
     font: {
       size: 1em;
       weight: 800;
     }
   }
-}
 
-.nav_body {
-  width: 100%;
-  display: grid;
-  grid-template-columns: 1fr auto 1fr;
-}
 
-.logo_container {
-  left: 0;
-  padding-left: 100px;
-}
+  .nav_body {
+    width: 100%;
+    display: grid;
+    grid-template-columns: 1fr auto 1fr;
+  }
 
-.nav_logo {
-  width: 81px;
-  color: white;
-  font: {
-    weight: 800;
-    size: 1.3rem;
+  .logo_container {
+    left: 0;
+    padding-left: 100px;
   }
-  text-align: left;
-  text-decoration: none;
-}
 
-.nav_links {
-  margin: auto;
-  display: flex;
-  flex-direction: row;
-  gap: 2rem;
-  grid-column-start: 2;
-}
+  .nav_logo {
+    width: 81px;
+    color: white;
 
-.nav_link {
-  display: flex;
-  flex-direction: row;
-  align-items: center;
-  justify-content: center;
-  background-color: $linkColor;
-  height: 75px;
-  padding: 0 4px;
-  width: $navHeight;
-  border-radius: 10px;
-}
+    font: {
+      weight: 800;
+      size: 1.3rem;
+    }
+
+    text-align: left;
+    text-decoration: none;
+  }
+
+  .nav_links {
+    margin: auto;
+    display: flex;
+    flex-direction: row;
+    gap: 2rem;
+    grid-column-start: 2;
+  }
+
+  .nav_link {
+    display: flex;
+    flex-direction: row;
+    align-items: center;
+    justify-content: center;
+    background-color: $linkColor;
+    height: 75px;
+    padding: 0 4px;
+    width: $navHeight;
+    border-radius: 10px;
+  }
+
+  .nav_link:hover {
+    color: rgb(45, 42, 34);
+    box-shadow: 0 5px 15px rgba(178, 182, 92, 0.8);
+  }
 
-.nav_link:hover {
-  color: rgb(45, 42, 34);
-  box-shadow: 0 5px 15px rgba(178, 182, 92, 0.8);
+  .login {
+    display: flex;
+    flex-direction: row;
+    justify-content: flex-end;
+    align-items: center;
+    margin: 0 100px 0 0;
+  }
 }
 
-.login {
+.breadcrumbs {
   display: flex;
-  flex-direction: row;
-  justify-content: flex-end;
-  align-items: center;
-  margin: 0 100px 0 0;
+  align-items: baseline;
+  z-index: 1;
+  padding: 0 10vw;
+  position: sticky;
+  top: 115px;
+  background:#eeeeee;
+
+  li {
+    list-style: none;
+    font-size: 14px;
+    line-height: 1.5714285714285714;
+    color: rgba(0, 0, 0, 0.45);
+    
+    &>a {
+      color: rgba(0, 0, 0, 0.45);
+      text-decoration: none;
+      transition: color 0.2s;
+      padding: 0 4px;
+      border-radius: 4px;
+      height: 22px;
+      display: inline-block;
+      margin-inline: -4px;
+
+      &:hover {
+        color: rgba(0, 0, 0, 0.88);
+        background-color: rgba(0, 0, 0, 0.06);
+      }
+    }
+  }
+
+  & * {
+    text-transform: capitalize;
+  }
+
 }
 
 footer {
-  margin-top: auto;
-  bottom: 0;
   width: 100%;
   height: 50px;
-  margin-top: -50px;
   background-color: $navColor;
-}
+}
\ No newline at end of file
diff --git a/src/components/Projects/Studies/StudyStyling.scss b/src/components/Projects/Studies/StudyStyling.scss
index 62eca80..7a2cae2 100644
--- a/src/components/Projects/Studies/StudyStyling.scss
+++ b/src/components/Projects/Studies/StudyStyling.scss
@@ -1,6 +1,7 @@
 .studies_container {
-  margin: 17vh 10vw 10vh 10vw;
+  margin: 5vh 10vw 10vh 10vw;
   line-height: 1.5rem;
+  height: 100vh;
 }
 
 .cards_container {
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 6da13b8..ca17c9d 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -285,7 +285,9 @@ It then shows the mappings as table data and alows the user to delete a mapping
         max: variable.max,
         units: variable.units,
         enumeration: variable.data_type === 'ENUMERATION' && (
-          <Link to={`/${variable.enumerations.reference}`}>View/Edit</Link>
+          console.log(variable.enumerations.reference,"variable.enumerations.reference"),
+          
+          <Link to={`/Study/${studyId}/DataDictionary/${DDId}/Table/${tableId}/${variable.enumerations.reference}`}>View/Edit</Link>
         ),
         mapped_terms: matchCode(variable),
       };
diff --git a/src/components/Projects/Tables/TableStyling.scss b/src/components/Projects/Tables/TableStyling.scss
index 4767acb..22dd6f1 100644
--- a/src/components/Projects/Tables/TableStyling.scss
+++ b/src/components/Projects/Tables/TableStyling.scss
@@ -2,7 +2,7 @@
 @import '../../Styling/Variables';
 
 .table_id_container {
-  margin: 17vh 10vw 13vh 10vw; //Make 10vh bottom without export button
+  margin: 5vh 10vw 13vh 10vw; //Make 10vh bottom without export button
   width: 66vw;
 }
 
@@ -77,18 +77,18 @@ input::file-selector-button:hover {
 }
 
 .mapping {
-  &-display{
+  &-display {
     white-space: nowrap;
   }
   display: flex;
   .remove-mapping {
-    padding-left:.25rem;
+    padding-left: 0.25rem;
     cursor: pointer;
     opacity: 0;
 
     &:hover {
-      transition: all .4s linear;
+      transition: all 0.4s linear;
       opacity: 1;
     }
   }
-}
\ No newline at end of file
+}
diff --git a/src/components/Projects/Terminologies/Terminology.scss b/src/components/Projects/Terminologies/Terminology.scss
index 09485e7..ca3ad43 100644
--- a/src/components/Projects/Terminologies/Terminology.scss
+++ b/src/components/Projects/Terminologies/Terminology.scss
@@ -1,6 +1,6 @@
 @import '../../Styling/Variables';
 .terminology_container {
-  margin: 17vh 10vw 10vh 10vw;
+  margin: 5vh 10vw 10vh 10vw;
   width: 66vw;
 }
 

From cd0ae9b7762e6364d7f6d2c41c10bfc38d624bce Mon Sep 17 00:00:00 2001
From: Yelena Cox <107718499+yelenacox@users.noreply.github.com>
Date: Thu, 24 Oct 2024 12:59:38 -0500
Subject: [PATCH 070/180] Update Terminology.jsx

---
 .../Projects/Terminologies/Terminology.jsx    | 55 ++++++-------------
 1 file changed, 16 insertions(+), 39 deletions(-)

diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 9f1a245..5316c5f 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -23,7 +23,6 @@ export const Terminology = () => {
   const [form] = Form.useForm();
 
   const { terminologyId, tableId } = useParams();
-
   const { vocabUrl, user } = useContext(myContext);
   const { setPrefTerminologies, prefTerminologies } = useContext(SearchContext);
   const {
@@ -31,13 +30,13 @@ export const Terminology = () => {
     setEditMappings,
     getMappings,
     setGetMappings,
-    mapping, 
+    mapping,
     setMapping,
   } = useContext(MappingContext);
 
   const [pageSize, setPageSize] = useState(
-
-    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+    parseInt(localStorage.getItem('pageSize'), 10) || 10
+  );
   const handleTableChange = (current, size) => {
     setPageSize(size);
   };
@@ -51,7 +50,6 @@ export const Terminology = () => {
   const navigate = useNavigate();
 
   const updateMappings = (mapArr, mappingCode) => {
-
     // setLoading(true);
     const mappingsDTO = {
       mappings: mapArr,
@@ -59,7 +57,6 @@ export const Terminology = () => {
     };
     console.log(tableId, 'tableId');
 
-
     fetch(`${vocabUrl}/Terminology/${terminologyId}/mapping/${mappingCode}`, {
       method: 'PUT',
       headers: {
@@ -86,7 +83,6 @@ export const Terminology = () => {
         if (error) {
           console.log(error, 'error');
 
-
           notification.error({
             message: 'Error',
             description: 'An error occurred. Please try again.',
@@ -117,30 +113,13 @@ It then shows the mappings as table data and alows the user to delete a mapping
   };
 
   const matchCode = variable => {
-
     if (!mapping?.length) {
       return noMapping(variable);
     }
 
-
-    const variableMappings = mapping.find(item => item?.code === variable?.code);
-
-    if (variableMappings && variableMappings.mappings?.length) {
-      return variableMappings.mappings.map(code => <div className='mapping' key={code.display}><span className='mapping-display'>{code.display}</span><span className='remove-mapping' onClick={() => handleRemoveMapping(variableMappings,code)}><CloseCircleOutlined  style={{color:"red", }} /></span></div>);
-    } else {
-      return noMapping(variable);
-    }
-  };
-
-  const handleRemoveMapping = (variableMappings,code) => {
-    // console.log(variableMappings,"variableMappings");
-    const mappingToRemove = variableMappings.mappings.indexOf(code);
-    //remove mapping from mappings
-    {mappingToRemove !== -1 && variableMappings.mappings.splice(mappingToRemove,1)}   
-    updateMappings(variableMappings?.mappings,variableMappings?.code);    
-  
-  }
-
+    const variableMappings = mapping.find(
+      item => item?.code === variable?.code
+    );
 
     if (variableMappings && variableMappings.mappings?.length) {
       return variableMappings.mappings.map(code => (
@@ -358,16 +337,16 @@ It then shows the mappings as table data and alows the user to delete a mapping
               <Spinner />
             ) : (
               <Form form={form}>
-
-                <Table 
-                columns={columns} 
-                dataSource={dataSource}
-                pagination={{ 
-                  showSizeChanger: true,
-                  pageSizeOptions: ['10', '20', '30'],
-                  pageSize: pageSize, // Use the stored pageSize
-                  onChange: handleTableChange, // Capture pagination changes
-                }}  />
+                <Table
+                  columns={columns}
+                  dataSource={dataSource}
+                  pagination={{
+                    showSizeChanger: true,
+                    pageSizeOptions: ['10', '20', '30'],
+                    pageSize: pageSize, // Use the stored pageSize
+                    onChange: handleTableChange, // Capture pagination changes
+                  }}
+                />
               </Form>
             )}
           </div>
@@ -383,7 +362,6 @@ It then shows the mappings as table data and alows the user to delete a mapping
                 : 'No Description'
             }
             terminology={terminology}
-
           />
           <GetMappingsModal
             componentString={'Terminology'}
@@ -401,7 +379,6 @@ It then shows the mappings as table data and alows the user to delete a mapping
                 ? getMappings?.description
                 : 'No Description'
             }
-
           />
 
           {/* Displays the edit form */}

From b667d18925eff672ec56bfaff93375aaa96ba2ba Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 24 Oct 2024 13:22:09 -0500
Subject: [PATCH 071/180] fixed it

---
 src/components/Manager/MappingsFunctions/MappingReset.jsx | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index f87c1b7..10d91fd 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -417,12 +417,6 @@ export const MappingReset = ({
               </div>
             </>
           ) : (
-            <div className="loading_spinner">
-              <ModalSpinner />
-
-            </div>
-        </>
-        ) : (
         <div className="loading_spinner">
           <ModalSpinner />
         </div>
@@ -432,3 +426,4 @@ export const MappingReset = ({
     </>
   );
 };
+ 
\ No newline at end of file

From 88ff11851b1b736d154560064b9e4981b91ec626 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 24 Oct 2024 15:39:45 -0500
Subject: [PATCH 072/180] Search bar for ontologies in OntologyCheckboxes

---
 .../MappingsFunctions/MappingsFunctions.scss  | 18 +++--
 .../MappingsFunctions/OntologyCheckboxes.jsx  | 25 +++++-
 src/components/Nav/Breadcrumbs.jsx            | 50 ++++++------
 .../Projects/Tables/TableDetails.jsx          | 77 +++++++++++--------
 .../Projects/Terminologies/Terminology.jsx    |  2 -
 5 files changed, 104 insertions(+), 68 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index 170c28b..b24fc07 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -10,7 +10,7 @@
   flex-direction: row;
 }
 .ontology_form {
-  width: 10vw;
+  width: 10.5vw;
   height: 50vh;
   overflow: auto;
   position: fixed;
@@ -28,26 +28,24 @@
   flex-wrap: wrap;
   flex-direction: row;
   justify-content: flex-start;
-  align-items: end;
+  align-items: center;
   z-index: 10;
   flex: 1;
   border-bottom: solid 1px #eeee;
   h4 {
-    margin:0;
-    padding-right:1rem;
+    margin: 0;
+    padding-right: 1rem;
   }
   .mappings_search_bar {
+    margin: 0 0 0 8px;
     width: 60%;
   }
   .search-desc {
     flex: 0 0 100%;
-    margin-bottom:1rem;
+    margin-bottom: 1rem;
   }
 }
 
-
-
-
 .inactive_term,
 .active_term {
   padding: 10px;
@@ -120,3 +118,7 @@
 .view_more_wrapper {
   margin-left: 11vw;
 }
+
+.onto_search_bar {
+  margin-bottom: 8px;
+}
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 123f96c..14d33ad 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -1,4 +1,4 @@
-import { Checkbox, Form } from 'antd';
+import { Checkbox, Form, Input } from 'antd';
 import { ontologyCounts } from '../Utilitiy';
 import { useContext, useEffect, useState } from 'react';
 import { SearchContext } from '../../../Contexts/SearchContext';
@@ -9,14 +9,19 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
     setApiPreferencesCode,
     facetCounts,
     ontologyApis,
-    component,
   } = useContext(SearchContext);
+  const { Search } = Input;
+
   const [checkedOntologies, setCheckedOntologies] = useState([]);
+  const [searchText, setSearchText] = useState('');
 
   const defaultOntologies = ['mondo', 'hp', 'maxo', 'ncit'];
 
   let processedApiPreferencesCode;
 
+  // Ensures the data sent to the API is in the correct format.
+  // If apiPreferencesCode is an array, sets processedApiPreferencesCode equal to it.
+  // If it is a comma-separated string, it splits it by the commas and adds them to an array
   if (Array.isArray(apiPreferencesCode)) {
     processedApiPreferencesCode = apiPreferencesCode;
   } else if (typeof apiPreferencesCode === 'string') {
@@ -81,15 +86,29 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
     ? checkedOntologies
     : [];
 
+  const getFilteredItems = searchText => {
+    const filtered = countsResult?.filter(item => {
+      const key = Object.keys(item)[0];
+      return key.startsWith(searchText);
+    });
+    return filtered;
+  };
+
   return (
     <div className="ontology_form">
+      <Search
+        placeholder="Ontologies"
+        className="onto_search_bar"
+        value={searchText}
+        onChange={e => setSearchText(e.target.value)}
+      />
       <Form.Item
         name="selected_ontologies"
         valuePropName="value"
         rules={[{ required: false }]}
       >
         <div className="modal_display_results">
-          {countsResult
+          {getFilteredItems(searchText)
             ?.sort((a, b) => {
               const aValue = Object.values(a)[0];
               const bValue = Object.values(b)[0];
diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
index f6b29ee..245d2f0 100644
--- a/src/components/Nav/Breadcrumbs.jsx
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -1,30 +1,34 @@
-import { Breadcrumb } from "antd"
+import { Breadcrumb } from 'antd';
 import { useLocation, Link } from 'react-router-dom';
 // import { Link } from 'react-router';
 export const Breadcrumbs = () => {
-   const location = useLocation();
-   const pathParts = location.pathname.split('/').filter(Boolean);
-   const pathArr = []
-   pathParts.forEach(path => {
-      pathArr.push({ title: path, path: path });
-   });
-  
-   console.log(location,'location');
-   
+  const location = useLocation();
+  const pathParts = location.pathname.split('/').filter(Boolean);
+  const pathArr = [];
+  pathParts.forEach(path => {
+    pathArr.push({ title: path, path: path });
+  });
 
-   return <span className="breadcrumbs">
-       <li><Link to={'/'}>Home</Link> {location.pathname != '/' && <span>&nbsp;&nbsp;/&nbsp;&nbsp;</span>}</li>
+  return (
+    <span className="breadcrumbs">
+      <li>
+        <Link to={'/'}>Home</Link>{' '}
+        {location.pathname != '/' && <span>&nbsp;&nbsp;/&nbsp;&nbsp;</span>}
+      </li>
       <Breadcrumb itemRender={itemRender} items={pathArr} />
-   </span>
-}
+    </span>
+  );
+};
 function itemRender(currentRoute, params, items, pathArr) {
-   const isLast = currentRoute?.path === items[items.length - 1]?.path;
+  const isLast = currentRoute?.path === items[items.length - 1]?.path;
 
-   return <>
-   {isLast ? (
-      <span>{currentRoute.title}</span>
-   ) : (
-      <Link to={`/${pathArr.join("/")}`}>{currentRoute.title}</Link>
-   )}
-   </>
-}
\ No newline at end of file
+  return (
+    <>
+      {isLast ? (
+        <span>{currentRoute.title}</span>
+      ) : (
+        <Link to={`/${pathArr.join('/')}`}>{currentRoute.title}</Link>
+      )}
+    </>
+  );
+}
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index ca17c9d..327a105 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -42,7 +42,8 @@ export const TableDetails = () => {
   const [load, setLoad] = useState(false);
 
   const [pageSize, setPageSize] = useState(
-    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+    parseInt(localStorage.getItem('pageSize'), 10) || 10
+  );
   const handleTableChange = (current, size) => {
     setPageSize(size);
   };
@@ -54,21 +55,17 @@ export const TableDetails = () => {
   const login = RequiredLogin({ handleSuccess: handleSuccess });
 
   useEffect(() => {
-
     setDataSource(tableData(table));
     localStorage.setItem('pageSize', pageSize);
   }, [table, mapping, pageSize]);
 
-
-  const updateMappings = (mapArr,mappingCode ) => {
-    
+  const updateMappings = (mapArr, mappingCode) => {
     // setLoading(true);
     const mappingsDTO = {
       mappings: mapArr,
       editor: user.email,
     };
-    console.log(mappingsDTO,"mappingsDTO");
-    
+
     fetch(`${vocabUrl}/Table/${tableId}/mapping/${mappingCode}`, {
       method: 'PUT',
       headers: {
@@ -87,11 +84,11 @@ export const TableDetails = () => {
         setMapping(data.codes);
         setEditMappings(null);
         form.resetFields();
-        notification.success({ description:'Mapping removed.'});
+        notification.success({ description: 'Mapping removed.' });
       })
       .catch(error => {
-        console.log(error,'error');
-        
+        console.log(error, 'error');
+
         if (error) {
           notification.error({
             message: 'Error',
@@ -103,7 +100,6 @@ export const TableDetails = () => {
       .finally(() => setLoading(false));
   };
 
-
   const alphabetizeOntologies = ontologies => {
     // Sort the keys alphabetically
     const sortedKeys = Object.keys(ontologies).sort();
@@ -131,8 +127,8 @@ export const TableDetails = () => {
               .then(data => setMapping(data.codes))
               .catch(error => {
                 if (error) {
-                  console.log(error,"error");
-                  
+                  console.log(error, 'error');
+
                   notification.error({
                     message: 'Error',
                     description: 'An error occurred loading mappings.',
@@ -236,37 +232,52 @@ variable in the table, AND the mappings array length for the variable is > 0, th
 and returns the length of the mapping array (i.e. returns the number of variables mapped to the table variable). 
 It then shows the mappings as table data and alows the user to delete a mapping from the table.*/
   const noMapping = variable => {
-    return <Button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
-      Get Mappings
-    </Button>
-  }
+    return (
+      <Button
+        onClick={() =>
+          setGetMappings({ name: variable.name, code: variable.code })
+        }
+      >
+        Get Mappings
+      </Button>
+    );
+  };
 
   const matchCode = variable => {
-
-
     if (!mapping?.length) {
       return noMapping(variable);
     }
 
-    const variableMappings = mapping.find(item => item?.code === variable?.code);
+    const variableMappings = mapping.find(
+      item => item?.code === variable?.code
+    );
 
     if (variableMappings && variableMappings.mappings?.length) {
-      return variableMappings.mappings.map(code => <div className='mapping' key={code.display}><span className='mapping-display'>{code.display}</span><span className='remove-mapping' onClick={() => handleRemoveMapping(variableMappings,code)}><CloseCircleOutlined  style={{color:"red", }} /></span></div>);
+      return variableMappings.mappings.map(code => (
+        <div className="mapping" key={code.display}>
+          <span className="mapping-display">{code.display}</span>
+          <span
+            className="remove-mapping"
+            onClick={() => handleRemoveMapping(variableMappings, code)}
+          >
+            <CloseCircleOutlined style={{ color: 'red' }} />
+          </span>
+        </div>
+      ));
     } else {
       return noMapping(variable);
     }
   };
 
-  const handleRemoveMapping = (variableMappings,code) => {
-    // console.log(variableMappings,"variableMappings");
+  const handleRemoveMapping = (variableMappings, code) => {
     const mappingToRemove = variableMappings.mappings.indexOf(code);
     //remove mapping from mappings
-    {mappingToRemove !== -1 && variableMappings.mappings.splice(mappingToRemove,1)}   
-    updateMappings(variableMappings?.mappings,variableMappings?.code);    
-  
-  }
-
-
+    {
+      mappingToRemove !== -1 &&
+        variableMappings.mappings.splice(mappingToRemove, 1);
+    }
+    updateMappings(variableMappings?.mappings, variableMappings?.code);
+  };
 
   // data for the table columns. Each table has an array of variables. Each variable has a name, description, and data type.
   // The integer and quantity data types include additional details.
@@ -285,9 +296,11 @@ It then shows the mappings as table data and alows the user to delete a mapping
         max: variable.max,
         units: variable.units,
         enumeration: variable.data_type === 'ENUMERATION' && (
-          console.log(variable.enumerations.reference,"variable.enumerations.reference"),
-          
-          <Link to={`/Study/${studyId}/DataDictionary/${DDId}/Table/${tableId}/${variable.enumerations.reference}`}>View/Edit</Link>
+          <Link
+            to={`/Study/${studyId}/DataDictionary/${DDId}/Table/${tableId}/${variable.enumerations.reference}`}
+          >
+            View/Edit
+          </Link>
         ),
         mapped_terms: matchCode(variable),
       };
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 5316c5f..b3c4709 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -55,7 +55,6 @@ export const Terminology = () => {
       mappings: mapArr,
       editor: user.email,
     };
-    console.log(tableId, 'tableId');
 
     fetch(`${vocabUrl}/Terminology/${terminologyId}/mapping/${mappingCode}`, {
       method: 'PUT',
@@ -139,7 +138,6 @@ It then shows the mappings as table data and alows the user to delete a mapping
   };
 
   const handleRemoveMapping = (variableMappings, code) => {
-    // console.log(variableMappings,"variableMappings");
     const mappingToRemove = variableMappings.mappings.indexOf(code);
     //remove mapping from mappings
     {

From b40ab4ab825a8dd100499827066a5a1759705d57 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 25 Oct 2024 12:47:43 -0500
Subject: [PATCH 073/180] Changed 'url' to 'system'

---
 src/components/Nav/Breadcrumbs.jsx            | 50 ++++++------
 src/components/Projects/Studies/AddStudy.jsx  |  4 +-
 .../Projects/Studies/EditStudyDetails.jsx     |  6 +-
 .../Projects/Studies/StudyDetails.jsx         |  2 +-
 .../Projects/Tables/EditTableDetails.jsx      | 14 +++-
 .../Projects/Tables/TableDetails.jsx          | 77 +++++++++++--------
 .../Projects/Tables/UploadTable.jsx           |  6 +-
 .../Projects/Terminologies/AddTerminology.jsx |  4 +-
 .../Terminologies/EditTerminologyDetails.jsx  |  6 +-
 .../Projects/Terminologies/Terminology.jsx    |  2 -
 10 files changed, 99 insertions(+), 72 deletions(-)

diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
index f6b29ee..245d2f0 100644
--- a/src/components/Nav/Breadcrumbs.jsx
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -1,30 +1,34 @@
-import { Breadcrumb } from "antd"
+import { Breadcrumb } from 'antd';
 import { useLocation, Link } from 'react-router-dom';
 // import { Link } from 'react-router';
 export const Breadcrumbs = () => {
-   const location = useLocation();
-   const pathParts = location.pathname.split('/').filter(Boolean);
-   const pathArr = []
-   pathParts.forEach(path => {
-      pathArr.push({ title: path, path: path });
-   });
-  
-   console.log(location,'location');
-   
+  const location = useLocation();
+  const pathParts = location.pathname.split('/').filter(Boolean);
+  const pathArr = [];
+  pathParts.forEach(path => {
+    pathArr.push({ title: path, path: path });
+  });
 
-   return <span className="breadcrumbs">
-       <li><Link to={'/'}>Home</Link> {location.pathname != '/' && <span>&nbsp;&nbsp;/&nbsp;&nbsp;</span>}</li>
+  return (
+    <span className="breadcrumbs">
+      <li>
+        <Link to={'/'}>Home</Link>{' '}
+        {location.pathname != '/' && <span>&nbsp;&nbsp;/&nbsp;&nbsp;</span>}
+      </li>
       <Breadcrumb itemRender={itemRender} items={pathArr} />
-   </span>
-}
+    </span>
+  );
+};
 function itemRender(currentRoute, params, items, pathArr) {
-   const isLast = currentRoute?.path === items[items.length - 1]?.path;
+  const isLast = currentRoute?.path === items[items.length - 1]?.path;
 
-   return <>
-   {isLast ? (
-      <span>{currentRoute.title}</span>
-   ) : (
-      <Link to={`/${pathArr.join("/")}`}>{currentRoute.title}</Link>
-   )}
-   </>
-}
\ No newline at end of file
+  return (
+    <>
+      {isLast ? (
+        <span>{currentRoute.title}</span>
+      ) : (
+        <Link to={`/${pathArr.join('/')}`}>{currentRoute.title}</Link>
+      )}
+    </>
+  );
+}
diff --git a/src/components/Projects/Studies/AddStudy.jsx b/src/components/Projects/Studies/AddStudy.jsx
index 8517ba0..23422c5 100644
--- a/src/components/Projects/Studies/AddStudy.jsx
+++ b/src/components/Projects/Studies/AddStudy.jsx
@@ -109,8 +109,8 @@ export const AddStudy = ({ addStudy, setAddStudy }) => {
           </Form.Item>
           <Form.Item
             name="url"
-            label="URL"
-            rules={[{ required: true, message: 'Please input Study URL.' }]}
+            label="System"
+            rules={[{ required: true, message: 'Please input Study system.' }]}
           >
             <Input />
           </Form.Item>
diff --git a/src/components/Projects/Studies/EditStudyDetails.jsx b/src/components/Projects/Studies/EditStudyDetails.jsx
index bc10e8e..ba11754 100644
--- a/src/components/Projects/Studies/EditStudyDetails.jsx
+++ b/src/components/Projects/Studies/EditStudyDetails.jsx
@@ -87,8 +87,10 @@ export const EditStudyDetails = ({ form, study, setStudy, edit, setEdit }) => {
             </Form.Item>
             <Form.Item
               name="url"
-              label="URL"
-              rules={[{ required: true, message: 'Please input Study URL.' }]}
+              label="System"
+              rules={[
+                { required: true, message: 'Please input Study system.' },
+              ]}
             >
               <Input />
             </Form.Item>
diff --git a/src/components/Projects/Studies/StudyDetails.jsx b/src/components/Projects/Studies/StudyDetails.jsx
index 3066ece..786c8c6 100644
--- a/src/components/Projects/Studies/StudyDetails.jsx
+++ b/src/components/Projects/Studies/StudyDetails.jsx
@@ -107,7 +107,7 @@ export const StudyDetails = () => {
                   <div className="study_dropdown">
                     <SettingsDropdownStudy study={study} />
                   </div>
-                  <div className="study_url">URL: {study?.url}</div>
+                  <div className="study_url">System: {study?.url}</div>
                 </div>
               </Col>
             </div>
diff --git a/src/components/Projects/Tables/EditTableDetails.jsx b/src/components/Projects/Tables/EditTableDetails.jsx
index d31f344..cae5c4c 100644
--- a/src/components/Projects/Tables/EditTableDetails.jsx
+++ b/src/components/Projects/Tables/EditTableDetails.jsx
@@ -1,4 +1,4 @@
-import { Form, Input, message, Modal } from 'antd';
+import { Form, Input, message, Modal, notification } from 'antd';
 import { useContext, useState } from 'react';
 import { myContext } from '../../../App';
 import { handleUpdate } from '../../Manager/FetchManager';
@@ -35,6 +35,12 @@ export const EditTableDetails = ({ table, setTable, edit, setEdit }) => {
       })
       // Displays a self-closing message that the udpates have been successfully saved.
       .then(() => message.success('Changes saved successfully.'))
+      .catch(error => {
+        notification.error({
+          message: 'Error',
+          description: 'An error occurred editing the Table.',
+        });
+      })
       .finally(() => setLoading(false));
   };
   return (
@@ -84,8 +90,10 @@ export const EditTableDetails = ({ table, setTable, edit, setEdit }) => {
             </Form.Item>
             <Form.Item
               name="url"
-              label="URL"
-              rules={[{ required: true, message: 'Please input Table URL.' }]}
+              label="System"
+              rules={[
+                { required: true, message: 'Please input Table system.' },
+              ]}
             >
               <Input />
             </Form.Item>{' '}
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index ca17c9d..327a105 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -42,7 +42,8 @@ export const TableDetails = () => {
   const [load, setLoad] = useState(false);
 
   const [pageSize, setPageSize] = useState(
-    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+    parseInt(localStorage.getItem('pageSize'), 10) || 10
+  );
   const handleTableChange = (current, size) => {
     setPageSize(size);
   };
@@ -54,21 +55,17 @@ export const TableDetails = () => {
   const login = RequiredLogin({ handleSuccess: handleSuccess });
 
   useEffect(() => {
-
     setDataSource(tableData(table));
     localStorage.setItem('pageSize', pageSize);
   }, [table, mapping, pageSize]);
 
-
-  const updateMappings = (mapArr,mappingCode ) => {
-    
+  const updateMappings = (mapArr, mappingCode) => {
     // setLoading(true);
     const mappingsDTO = {
       mappings: mapArr,
       editor: user.email,
     };
-    console.log(mappingsDTO,"mappingsDTO");
-    
+
     fetch(`${vocabUrl}/Table/${tableId}/mapping/${mappingCode}`, {
       method: 'PUT',
       headers: {
@@ -87,11 +84,11 @@ export const TableDetails = () => {
         setMapping(data.codes);
         setEditMappings(null);
         form.resetFields();
-        notification.success({ description:'Mapping removed.'});
+        notification.success({ description: 'Mapping removed.' });
       })
       .catch(error => {
-        console.log(error,'error');
-        
+        console.log(error, 'error');
+
         if (error) {
           notification.error({
             message: 'Error',
@@ -103,7 +100,6 @@ export const TableDetails = () => {
       .finally(() => setLoading(false));
   };
 
-
   const alphabetizeOntologies = ontologies => {
     // Sort the keys alphabetically
     const sortedKeys = Object.keys(ontologies).sort();
@@ -131,8 +127,8 @@ export const TableDetails = () => {
               .then(data => setMapping(data.codes))
               .catch(error => {
                 if (error) {
-                  console.log(error,"error");
-                  
+                  console.log(error, 'error');
+
                   notification.error({
                     message: 'Error',
                     description: 'An error occurred loading mappings.',
@@ -236,37 +232,52 @@ variable in the table, AND the mappings array length for the variable is > 0, th
 and returns the length of the mapping array (i.e. returns the number of variables mapped to the table variable). 
 It then shows the mappings as table data and alows the user to delete a mapping from the table.*/
   const noMapping = variable => {
-    return <Button onClick={() => setGetMappings({ name: variable.name, code: variable.code })}>
-      Get Mappings
-    </Button>
-  }
+    return (
+      <Button
+        onClick={() =>
+          setGetMappings({ name: variable.name, code: variable.code })
+        }
+      >
+        Get Mappings
+      </Button>
+    );
+  };
 
   const matchCode = variable => {
-
-
     if (!mapping?.length) {
       return noMapping(variable);
     }
 
-    const variableMappings = mapping.find(item => item?.code === variable?.code);
+    const variableMappings = mapping.find(
+      item => item?.code === variable?.code
+    );
 
     if (variableMappings && variableMappings.mappings?.length) {
-      return variableMappings.mappings.map(code => <div className='mapping' key={code.display}><span className='mapping-display'>{code.display}</span><span className='remove-mapping' onClick={() => handleRemoveMapping(variableMappings,code)}><CloseCircleOutlined  style={{color:"red", }} /></span></div>);
+      return variableMappings.mappings.map(code => (
+        <div className="mapping" key={code.display}>
+          <span className="mapping-display">{code.display}</span>
+          <span
+            className="remove-mapping"
+            onClick={() => handleRemoveMapping(variableMappings, code)}
+          >
+            <CloseCircleOutlined style={{ color: 'red' }} />
+          </span>
+        </div>
+      ));
     } else {
       return noMapping(variable);
     }
   };
 
-  const handleRemoveMapping = (variableMappings,code) => {
-    // console.log(variableMappings,"variableMappings");
+  const handleRemoveMapping = (variableMappings, code) => {
     const mappingToRemove = variableMappings.mappings.indexOf(code);
     //remove mapping from mappings
-    {mappingToRemove !== -1 && variableMappings.mappings.splice(mappingToRemove,1)}   
-    updateMappings(variableMappings?.mappings,variableMappings?.code);    
-  
-  }
-
-
+    {
+      mappingToRemove !== -1 &&
+        variableMappings.mappings.splice(mappingToRemove, 1);
+    }
+    updateMappings(variableMappings?.mappings, variableMappings?.code);
+  };
 
   // data for the table columns. Each table has an array of variables. Each variable has a name, description, and data type.
   // The integer and quantity data types include additional details.
@@ -285,9 +296,11 @@ It then shows the mappings as table data and alows the user to delete a mapping
         max: variable.max,
         units: variable.units,
         enumeration: variable.data_type === 'ENUMERATION' && (
-          console.log(variable.enumerations.reference,"variable.enumerations.reference"),
-          
-          <Link to={`/Study/${studyId}/DataDictionary/${DDId}/Table/${tableId}/${variable.enumerations.reference}`}>View/Edit</Link>
+          <Link
+            to={`/Study/${studyId}/DataDictionary/${DDId}/Table/${tableId}/${variable.enumerations.reference}`}
+          >
+            View/Edit
+          </Link>
         ),
         mapped_terms: matchCode(variable),
       };
diff --git a/src/components/Projects/Tables/UploadTable.jsx b/src/components/Projects/Tables/UploadTable.jsx
index cf2749c..850976e 100644
--- a/src/components/Projects/Tables/UploadTable.jsx
+++ b/src/components/Projects/Tables/UploadTable.jsx
@@ -152,8 +152,10 @@ export const UploadTable = ({ addTable, setAddTable }) => {
             </Form.Item>
             <Form.Item
               name="url"
-              label="URL"
-              rules={[{ required: true, message: 'Please input Table URL.' }]}
+              label="System"
+              rules={[
+                { required: true, message: 'Please input Table system.' },
+              ]}
             >
               <Input />
             </Form.Item>
diff --git a/src/components/Projects/Terminologies/AddTerminology.jsx b/src/components/Projects/Terminologies/AddTerminology.jsx
index f85e77e..8e0c36a 100644
--- a/src/components/Projects/Terminologies/AddTerminology.jsx
+++ b/src/components/Projects/Terminologies/AddTerminology.jsx
@@ -149,9 +149,9 @@ export const AddTerminology = () => {
             </Form.Item>
             <Form.Item
               name="url"
-              label="URL"
+              label="System"
               rules={[
-                { required: true, message: 'Please input Terminology URL.' },
+                { required: true, message: 'Please input Terminology system.' },
               ]}
             >
               <Input />
diff --git a/src/components/Projects/Terminologies/EditTerminologyDetails.jsx b/src/components/Projects/Terminologies/EditTerminologyDetails.jsx
index 7d9129f..18670cf 100644
--- a/src/components/Projects/Terminologies/EditTerminologyDetails.jsx
+++ b/src/components/Projects/Terminologies/EditTerminologyDetails.jsx
@@ -74,7 +74,7 @@ export const EditTerminologyDetails = ({
               name="name"
               label="Name"
               rules={[
-                { required: true, message: 'Please input terminology name.' },
+                { required: true, message: 'Please input Terminology name.' },
               ]}
             >
               <Input />
@@ -88,9 +88,9 @@ export const EditTerminologyDetails = ({
             </Form.Item>
             <Form.Item
               name="url"
-              label="URL"
+              label="System"
               rules={[
-                { required: true, message: 'Please input terminology URL.' },
+                { required: true, message: 'Please input Terminology system.' },
               ]}
             >
               <Input />
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 5316c5f..b3c4709 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -55,7 +55,6 @@ export const Terminology = () => {
       mappings: mapArr,
       editor: user.email,
     };
-    console.log(tableId, 'tableId');
 
     fetch(`${vocabUrl}/Terminology/${terminologyId}/mapping/${mappingCode}`, {
       method: 'PUT',
@@ -139,7 +138,6 @@ It then shows the mappings as table data and alows the user to delete a mapping
   };
 
   const handleRemoveMapping = (variableMappings, code) => {
-    // console.log(variableMappings,"variableMappings");
     const mappingToRemove = variableMappings.mappings.indexOf(code);
     //remove mapping from mappings
     {

From 9f2b2016d82e72e71579878cb434210b96c6db63 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 28 Oct 2024 12:04:23 -0500
Subject: [PATCH 074/180] fetching inherited ontology filters from table into
 terminology

---
 src/Contexts/SearchContext.jsx                |  3 ++
 .../MappingsFunctions/FilterSelect.jsx        |  9 ++++--
 .../OntologyFilterCodeSubmit.jsx              |  3 +-
 .../Projects/Tables/TableDetails.jsx          |  1 +
 .../Projects/Terminologies/Terminology.jsx    | 28 +++++++++++++++++--
 5 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index 1266910..bb27b88 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -17,6 +17,7 @@ export function SearchContextRoot() {
   const [unformattedPref, setUnformattedPref] = useState([]);
   const [facetCounts, setFacetCounts] = useState([]);
   const [ontologyApis, setOntologyApis] = useState([]);
+  const [apiPreferencesTerm, setApiPreferencesTerm] = useState(undefined);
 
   const defaultOntologies = 'mondo,hp,maxo,ncit';
 
@@ -48,6 +49,8 @@ export function SearchContextRoot() {
     setUnformattedPref,
     ontologyApis,
     setOntologyApis,
+    setApiPreferencesTerm,
+    apiPreferencesTerm,
   };
 
   return (
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index 031396b..87b4771 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -7,7 +7,12 @@ import { getOntologies } from '../FetchManager';
 import { ModalSpinner } from '../Spinner';
 import { SearchContext } from '../../../Contexts/SearchContext';
 
-export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
+export const FilterSelect = ({
+  component,
+  table,
+  apiPreferences,
+  setApiPreferences,
+}) => {
   const [form] = Form.useForm();
   const [addFilter, setAddFilter] = useState(false);
   const [currentPage, setCurrentPage] = useState(1);
@@ -119,7 +124,7 @@ export const FilterSelect = ({ table, apiPreferences, setApiPreferences }) => {
         ? 'POST'
         : 'PUT';
 
-    fetch(`${vocabUrl}/${table?.terminology?.reference}/filter`, {
+    fetch(`${vocabUrl}/${(component = table && terminology?.id)}/filter`, {
       method: method,
       headers: {
         'Content-Type': 'application/json',
diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
index 84050dc..807f780 100644
--- a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
@@ -2,7 +2,6 @@ import { notification } from 'antd';
 
 export const OntologyFilterCodeSubmit = (
   apiPreferencesCode,
-  setApiPreferencesCode,
   apiPreferences,
   mappingProp,
   table,
@@ -23,7 +22,7 @@ export const OntologyFilterCodeSubmit = (
 
     fetch(
       `${vocabUrl}/${(component = table
-        ? table?.terminology?.reference
+        ? `Table/${component?.id}`
         : `Terminology/${component?.id}`)}/filter/${mappingProp}`,
       {
         method: 'POST',
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 327a105..5507144 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -375,6 +375,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
                 {' '}
                 <div className="add_row_buttons">
                   <FilterSelect
+                    component={table}
                     table={table}
                     apiPreferences={apiPreferences}
                     setApiPreferences={setApiPreferences}
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index b3c4709..606d4e4 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -24,7 +24,12 @@ export const Terminology = () => {
 
   const { terminologyId, tableId } = useParams();
   const { vocabUrl, user } = useContext(myContext);
-  const { setPrefTerminologies, prefTerminologies } = useContext(SearchContext);
+  const {
+    setPrefTerminologies,
+    prefTerminologies,
+    setApiPreferencesTerm,
+    apiPreferencesTerm,
+  } = useContext(SearchContext);
   const {
     editMappings,
     setEditMappings,
@@ -180,6 +185,24 @@ It then shows the mappings as table data and alows the user to delete a mapping
         } else {
           setTerminology(data);
           if (data) {
+            const cleanedName = data?.name.toLowerCase().replaceAll(' ', '_');
+
+            fetch(`${vocabUrl}/Table/${tableId}/filter/${cleanedName}`, {
+              method: 'GET',
+              headers: {
+                'Content-Type': 'application/json',
+              },
+            })
+              .then(res => {
+                if (res.ok) {
+                  return res.json();
+                } else {
+                  throw new Error('An unknown error occurred.');
+                }
+              })
+              .then(data => {
+                setApiPreferencesTerm(data);
+              });
             getById(vocabUrl, 'Terminology', `${terminologyId}/mapping`)
               .then(data => setMapping(data.codes))
               .catch(error => {
@@ -218,7 +241,8 @@ It then shows the mappings as table data and alows the user to delete a mapping
         if (error) {
           notification.error({
             message: 'Error',
-            description: 'An error occurred loading the Terminology.',
+            description:
+              'An error occurred loading the the ontology preferences.',
           });
         }
         return error;

From b68049024058d8ba9798271c44ec4f2aeb97b4d7 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 28 Oct 2024 14:30:14 -0500
Subject: [PATCH 075/180] Showing number of preferred ontologies in api filters
 button

---
 .../MappingsFunctions/FilterOntology.jsx      | 16 +++++---
 .../MappingsFunctions/FilterSelect.jsx        | 41 ++++++++++++-------
 .../Projects/Tables/TableDetails.jsx          |  7 +---
 .../Projects/Terminologies/Terminology.jsx    |  3 ++
 4 files changed, 41 insertions(+), 26 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index d62a5a3..1cef582 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -2,6 +2,7 @@ import { Checkbox, Form, Pagination } from 'antd';
 import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
 import { FilterReset } from './FilterReset';
+import { SearchContext } from '../../../Contexts/SearchContext';
 
 export const FilterOntology = ({
   ontology,
@@ -18,6 +19,7 @@ export const FilterOntology = ({
 }) => {
   const [allCheckboxes, setAllCheckboxes] = useState([]);
   const { setOntologyForPagination } = useContext(myContext);
+  const { apiPreferencesTerm } = useContext(SearchContext);
 
   useEffect(() => {
     setOntologyForPagination(ontology);
@@ -126,7 +128,11 @@ export const FilterOntology = ({
     );
   };
 
-  const existingFilters = Object.values(apiPreferences?.self || {}).flat();
+  const preferenceType = apiPreferencesTerm
+    ? apiPreferencesTerm
+    : apiPreferences;
+
+  const existingFilters = Object.values(preferenceType?.self || {}).flat();
 
   const flattenedFilters = existingFilters
     .flatMap(item =>
@@ -148,8 +154,8 @@ export const FilterOntology = ({
   return (
     <>
       <div className="modal_checkbox_wrapper">
-        {Object.keys(apiPreferences?.self?.api_preference || {}).some(
-          key => apiPreferences?.self?.api_preference[key]?.length > 0
+        {Object.keys(preferenceType?.self?.api_preference || {}).some(
+          key => preferenceType?.self?.api_preference[key]?.length > 0
         ) && (
           <>
             <div className="onto_reset">
@@ -204,8 +210,8 @@ export const FilterOntology = ({
             </Form.Item>
           </>
         )}
-        {(Object.keys(apiPreferences?.self?.api_preference || {}).some(
-          key => apiPreferences?.self?.api_preference[key]?.length > 0
+        {(Object.keys(preferenceType?.self?.api_preference || {}).some(
+          key => preferenceType?.self?.api_preference[key]?.length > 0
         ) ||
           displaySelectedOntologies.length > 0) && <h4>Ontologies</h4>}
         <Form.Item name={'ontologies'} valuePropName="value">
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index 87b4771..82a0a60 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -7,12 +7,7 @@ import { getOntologies } from '../FetchManager';
 import { ModalSpinner } from '../Spinner';
 import { SearchContext } from '../../../Contexts/SearchContext';
 
-export const FilterSelect = ({
-  component,
-  table,
-  apiPreferences,
-  setApiPreferences,
-}) => {
+export const FilterSelect = ({ component, table, terminology }) => {
   const [form] = Form.useForm();
   const [addFilter, setAddFilter] = useState(false);
   const [currentPage, setCurrentPage] = useState(1);
@@ -25,7 +20,14 @@ export const FilterSelect = ({
   const [active, setActive] = useState(null);
   const [loading, setLoading] = useState(false);
   const { user, vocabUrl, ontologyForPagination } = useContext(myContext);
-  const { ontologyApis, setOntologyApis } = useContext(SearchContext);
+  const {
+    ontologyApis,
+    setOntologyApis,
+    apiPreferences,
+    setApiPreferences,
+    apiPreferencesTerm,
+    setApiPreferencesTerm,
+  } = useContext(SearchContext);
   const [searchText, setSearchText] = useState('');
 
   // Gets the ontologyAPIs on first load, automatically sets active to the first of the list to display on the page
@@ -124,13 +126,18 @@ export const FilterSelect = ({
         ? 'POST'
         : 'PUT';
 
-    fetch(`${vocabUrl}/${(component = table && terminology?.id)}/filter`, {
-      method: method,
-      headers: {
-        'Content-Type': 'application/json',
-      },
-      body: JSON.stringify(apiPreferenceDTO),
-    })
+    fetch(
+      `${vocabUrl}/${(component = table
+        ? `Table/${table.id}`
+        : `Terminology/${terminology.id}`)}/filter`,
+      {
+        method: method,
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify(apiPreferenceDTO),
+      }
+    )
       .then(res => {
         if (res.ok) {
           return res.json();
@@ -171,7 +178,11 @@ export const FilterSelect = ({
       .finally(() => setLoading(false));
   };
 
-  const apiPrefObject = apiPreferences?.self?.api_preference;
+  const preferenceType = apiPreferencesTerm
+    ? apiPreferencesTerm
+    : apiPreferences;
+
+  const apiPrefObject = preferenceType?.self?.api_preference;
 
   // // Calculate the total length of all arrays
   const apiPrefLength =
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 5507144..69a2a16 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -374,12 +374,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
               <>
                 {' '}
                 <div className="add_row_buttons">
-                  <FilterSelect
-                    component={table}
-                    table={table}
-                    apiPreferences={apiPreferences}
-                    setApiPreferences={setApiPreferences}
-                  />
+                  <FilterSelect component={table} table={table} />
                   <AddVariable
                     table={table}
                     setTable={setTable}
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 606d4e4..6f471ca 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -18,6 +18,7 @@ import { Submenu } from '../../Manager/Submenu';
 import { LoadCodes } from './LoadCodes';
 import { PreferredTerminology } from './PreferredTerminology';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
 
 export const Terminology = () => {
   const [form] = Form.useForm();
@@ -345,6 +346,8 @@ It then shows the mappings as table data and alows the user to delete a mapping
           </Row>
           <div className="table_container">
             <div className="add_row_buttons">
+              <FilterSelect component={terminology} terminology={terminology} />
+
               <PreferredTerminology
                 terminology={terminology}
                 setTerminology={setTerminology}

From d18e9b56cc50215ad445eb160343d7a33d9a619d Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 29 Oct 2024 13:27:52 -0500
Subject: [PATCH 076/180] Existing terminology ontology filters checking by
 default

---
 .../Manager/MappingsFunctions/FilterAPI.jsx   |  2 +
 .../MappingsFunctions/FilterOntology.jsx      | 38 +++++++++++++-----
 .../Manager/MappingsFunctions/FilterReset.jsx | 24 ++++++++----
 .../MappingsFunctions/FilterSelect.jsx        | 39 +++++++++++++------
 .../MappingsFunctions/GetMappingsModal.jsx    |  3 +-
 src/components/Manager/Utilitiy.jsx           |  2 +
 .../Projects/Terminologies/Terminology.jsx    | 26 +++++++++----
 7 files changed, 96 insertions(+), 38 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index faee0ea..e761834 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -23,6 +23,7 @@ export const FilterAPI = ({
   paginatedOntologies,
   apiPreferences,
   table,
+  terminology,
 }) => {
   const { vocabUrl } = useContext(myContext);
   const [ontology, setOntology] = useState([]);
@@ -161,6 +162,7 @@ export const FilterAPI = ({
                   paginatedOntologies={paginatedOntologies}
                   apiPreferences={apiPreferences}
                   table={table}
+                  terminology={terminology}
                 />
               )}
             </div>
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 1cef582..6b07ca7 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -16,6 +16,7 @@ export const FilterOntology = ({
   paginatedOntologies,
   apiPreferences,
   table,
+  terminology,
 }) => {
   const [allCheckboxes, setAllCheckboxes] = useState([]);
   const { setOntologyForPagination } = useContext(myContext);
@@ -132,7 +133,11 @@ export const FilterOntology = ({
     ? apiPreferencesTerm
     : apiPreferences;
 
-  const existingFilters = Object.values(preferenceType?.self || {}).flat();
+  const prefTypeKey = Object.keys(preferenceType)[0];
+
+  const existingFilters = Object.values(
+    preferenceType[prefTypeKey] || {}
+  )?.flat();
 
   const flattenedFilters = existingFilters
     .flatMap(item =>
@@ -151,15 +156,30 @@ export const FilterOntology = ({
     })
   );
 
+  useEffect(() => {
+    form.setFieldsValue({
+      existing_filters: flattenedFilters?.map((ff, index) =>
+        JSON.stringify({
+          ontology: ff,
+        })
+      ),
+    });
+  }, [apiPreferencesTerm, existingFilters, initialChecked, form]);
+
   return (
     <>
       <div className="modal_checkbox_wrapper">
-        {Object.keys(preferenceType?.self?.api_preference || {}).some(
-          key => preferenceType?.self?.api_preference[key]?.length > 0
+        {Object.keys(preferenceType[prefTypeKey]?.api_preference || {}).some(
+          key => preferenceType[prefTypeKey]?.api_preference[key]?.length > 0
         ) && (
           <>
             <div className="onto_reset">
-              <h4>Ontology Filters</h4> <FilterReset table={table} />
+              <h4>Ontology Filters</h4>{' '}
+              <FilterReset
+                table={table}
+                component={table}
+                terminology={terminology}
+              />
             </div>
             <Form.Item
               initialValue={initialChecked}
@@ -171,20 +191,18 @@ export const FilterOntology = ({
                 },
               ]}
             >
-              {flattenedFilters?.length > 0 ? (
+              {flattenedFilters?.length > 0 && (
                 <Checkbox.Group
                   className="mappings_checkbox"
-                  options={flattenedFilters?.map((po, index) => {
+                  options={flattenedFilters?.map((ff, index) => {
                     return {
                       value: JSON.stringify({
-                        ontology: po,
+                        ontology: ff,
                       }),
-                      label: existingDisplay(po, index),
+                      label: existingDisplay(ff, index),
                     };
                   })}
                 />
-              ) : (
-                ''
               )}
             </Form.Item>
           </>
diff --git a/src/components/Manager/MappingsFunctions/FilterReset.jsx b/src/components/Manager/MappingsFunctions/FilterReset.jsx
index d1229fe..83f3ed0 100644
--- a/src/components/Manager/MappingsFunctions/FilterReset.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterReset.jsx
@@ -3,22 +3,30 @@ import { ExclamationCircleFilled } from '@ant-design/icons';
 import { useContext, useState } from 'react';
 import { myContext } from '../../../App';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import { useParams } from 'react-router-dom';
+import { cleanedName } from '../Utilitiy';
 
-export const FilterReset = ({ table }) => {
+export const FilterReset = ({ table, component, terminology }) => {
   const { confirm } = Modal;
+  const { tableId } = useParams();
 
   const { user, vocabUrl } = useContext(myContext);
   const { setApiPreferences } = useContext(SearchContext);
   const [remove, setRemove] = useState(false);
 
   const deleteOntologies = evt => {
-    return fetch(`${vocabUrl}/${table?.terminology?.reference}/filter/self`, {
-      method: 'DELETE',
-      headers: {
-        'Content-Type': 'application/json',
-      },
-      body: JSON.stringify({ editor: user.email }),
-    })
+    return fetch(
+      `${vocabUrl}/Table/${tableId}/filter/${
+        component === table ? 'self' : cleanedName(terminology?.name)
+      }`,
+      {
+        method: 'DELETE',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify({ editor: user.email }),
+      }
+    )
       .then(res => {
         if (res.ok) {
           return res.json().then(data => {
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index 82a0a60..acd26e7 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -6,9 +6,13 @@ import { FilterAPI } from './FilterAPI';
 import { getOntologies } from '../FetchManager';
 import { ModalSpinner } from '../Spinner';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import { cleanedName } from '../Utilitiy';
+import { useParams } from 'react-router-dom';
 
 export const FilterSelect = ({ component, table, terminology }) => {
   const [form] = Form.useForm();
+  const { tableId } = useParams();
+
   const [addFilter, setAddFilter] = useState(false);
   const [currentPage, setCurrentPage] = useState(1);
   const [pageSize, setPageSize] = useState(10);
@@ -69,6 +73,9 @@ export const FilterSelect = ({ component, table, terminology }) => {
     setDisplaySelectedOntologies([]);
   };
 
+  const preferenceTypeSet = data =>
+    apiPreferencesTerm ? setApiPreferencesTerm(data) : setApiPreferences(data);
+
   // If the api doesn't exist in api_preference, creates an empty array for it
   // If the api_preference array for the api does not include an ontology_code, pushes the code to the array for the api
   // If there is an api in api_preferences that is not included with the ontology_code, it's added to apiPreference with an empty array
@@ -127,9 +134,11 @@ export const FilterSelect = ({ component, table, terminology }) => {
         : 'PUT';
 
     fetch(
-      `${vocabUrl}/${(component = table
-        ? `Table/${table.id}`
-        : `Terminology/${terminology.id}`)}/filter`,
+      `${vocabUrl}/Table/${(component = table
+        ? table?.id
+        : tableId)}/${(component = table
+        ? `filter`
+        : `filter/${cleanedName(terminology?.name)}`)}`,
       {
         method: method,
         headers: {
@@ -146,12 +155,17 @@ export const FilterSelect = ({ component, table, terminology }) => {
         }
       })
       .then(() =>
-        fetch(`${vocabUrl}/${table?.terminology?.reference}/filter/self`, {
-          method: 'GET',
-          headers: {
-            'Content-Type': 'application/json',
-          },
-        })
+        fetch(
+          `${vocabUrl}/Table/${tableId}/filter/${(component = table
+            ? `self`
+            : `${cleanedName(terminology?.name)}`)}`,
+          {
+            method: 'GET',
+            headers: {
+              'Content-Type': 'application/json',
+            },
+          }
+        )
       )
       .then(res => {
         if (res.ok) {
@@ -161,7 +175,7 @@ export const FilterSelect = ({ component, table, terminology }) => {
         }
       })
       .then(data => {
-        setApiPreferences(data);
+        preferenceTypeSet(data);
         form.resetFields();
         setAddFilter(false);
         message.success('Preferred ontologies saved successfully.');
@@ -182,7 +196,9 @@ export const FilterSelect = ({ component, table, terminology }) => {
     ? apiPreferencesTerm
     : apiPreferences;
 
-  const apiPrefObject = preferenceType?.self?.api_preference;
+  const prefTypeKey = Object.keys(preferenceType)[0];
+
+  const apiPrefObject = preferenceType[prefTypeKey]?.api_preference;
 
   // // Calculate the total length of all arrays
   const apiPrefLength =
@@ -300,6 +316,7 @@ export const FilterSelect = ({ component, table, terminology }) => {
               paginatedOntologies={paginatedOntologies}
               apiPreferences={apiPreferences}
               table={table}
+              terminology={terminology}
             />
           )}
         </Modal>
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 32fc530..8c26df3 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -25,7 +25,7 @@ export const GetMappingsModal = ({
   component,
   mappingProp,
   mappingDesc,
-  table
+  table,
 }) => {
   const [form] = Form.useForm();
   const { Search } = Input;
@@ -37,6 +37,7 @@ export const GetMappingsModal = ({
     setApiPreferencesCode,
     apiPreferencesCode,
     setUnformattedPref,
+    setApiPreferencesTerm,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 2500;
diff --git a/src/components/Manager/Utilitiy.jsx b/src/components/Manager/Utilitiy.jsx
index 1515f19..787a5d3 100644
--- a/src/components/Manager/Utilitiy.jsx
+++ b/src/components/Manager/Utilitiy.jsx
@@ -60,3 +60,5 @@ export const ontologyCounts = arr => {
 
   return result;
 };
+
+export const cleanedName = data => data?.toLowerCase().replaceAll(' ', '_');
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 6f471ca..a97556d 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -19,6 +19,7 @@ import { LoadCodes } from './LoadCodes';
 import { PreferredTerminology } from './PreferredTerminology';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
+import { cleanedName } from '../../Manager/Utilitiy';
 
 export const Terminology = () => {
   const [form] = Form.useForm();
@@ -50,6 +51,13 @@ export const Terminology = () => {
     localStorage.setItem('pageSize', pageSize);
   }, [pageSize]);
 
+  useEffect(
+    () => () => {
+      setApiPreferencesTerm(undefined);
+    },
+    []
+  );
+
   const [loading, setLoading] = useState(true);
   const initialTerminology = { url: '', description: '', name: '', codes: [] }; //initial state of terminology
   const [terminology, setTerminology] = useState(initialTerminology);
@@ -186,14 +194,16 @@ It then shows the mappings as table data and alows the user to delete a mapping
         } else {
           setTerminology(data);
           if (data) {
-            const cleanedName = data?.name.toLowerCase().replaceAll(' ', '_');
-
-            fetch(`${vocabUrl}/Table/${tableId}/filter/${cleanedName}`, {
-              method: 'GET',
-              headers: {
-                'Content-Type': 'application/json',
-              },
-            })
+            cleanedName(data?.name);
+            fetch(
+              `${vocabUrl}/Table/${tableId}/filter/${cleanedName(data?.name)}`,
+              {
+                method: 'GET',
+                headers: {
+                  'Content-Type': 'application/json',
+                },
+              }
+            )
               .then(res => {
                 if (res.ok) {
                   return res.json();

From dc427dc19de524d541e1bde2ca693c694692662a Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 29 Oct 2024 15:11:12 -0500
Subject: [PATCH 077/180] Ability to select ontology filters for a terminology

---
 src/Contexts/SearchContext.jsx                |  3 ++
 .../Manager/MappingsFunctions/FilterAPI.jsx   |  8 +++-
 .../MappingsFunctions/FilterOntology.jsx      | 22 +++--------
 .../Manager/MappingsFunctions/FilterReset.jsx | 38 +++++++++++++++++--
 .../MappingsFunctions/FilterSelect.jsx        | 17 +++++----
 5 files changed, 58 insertions(+), 30 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index bb27b88..e784fd6 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -20,6 +20,8 @@ export function SearchContextRoot() {
   const [apiPreferencesTerm, setApiPreferencesTerm] = useState(undefined);
 
   const defaultOntologies = 'mondo,hp,maxo,ncit';
+  const preferenceTypeSet = data =>
+    apiPreferencesTerm ? setApiPreferencesTerm(data) : setApiPreferences(data);
 
   const context = {
     prefTerminologies,
@@ -51,6 +53,7 @@ export function SearchContextRoot() {
     setOntologyApis,
     setApiPreferencesTerm,
     apiPreferencesTerm,
+    preferenceTypeSet,
   };
 
   return (
diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index e761834..538f2ea 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -1,5 +1,5 @@
 import { useContext, useEffect, useState } from 'react';
-import { Checkbox, Form } from 'antd';
+import { Checkbox, Form, Tooltip } from 'antd';
 import { ModalSpinner, OntologySpinner } from '../Spinner';
 import { myContext } from '../../../App';
 import { FilterOntology } from './FilterOntology';
@@ -125,7 +125,11 @@ export const FilterAPI = ({
         <Form form={form} preserve={false}>
           <div style={{ display: 'flex' }}>
             <div style={{ flex: '0 0 25%' }}>
-              <div className="api_label">APIs</div>
+              <div className="api_label">
+                <Tooltip title="Default search with OLS using HP, MAXO, MONDO, NCIT">
+                  APIs
+                </Tooltip>
+              </div>
 
               <Form.Item name={'selected_apis'} valuePropName="value">
                 <Checkbox.Group
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 6b07ca7..958b10b 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -1,4 +1,4 @@
-import { Checkbox, Form, Pagination } from 'antd';
+import { Checkbox, Form } from 'antd';
 import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
 import { FilterReset } from './FilterReset';
@@ -101,6 +101,7 @@ export const FilterOntology = ({
       </>
     );
   };
+
   const checkBoxDisplay = (ont, i) => {
     return (
       <>
@@ -115,6 +116,7 @@ export const FilterOntology = ({
       </>
     );
   };
+
   const existingDisplay = (ont, i) => {
     return (
       <>
@@ -129,10 +131,12 @@ export const FilterOntology = ({
     );
   };
 
+  // Checks if there are apiPreferences (table) or apiPreferencesTerm (terminology) and returns the appropriate one
   const preferenceType = apiPreferencesTerm
     ? apiPreferencesTerm
     : apiPreferences;
 
+  // The first key is different depending if it's coming from a table or terminology. This dynamically gets the first key
   const prefTypeKey = Object.keys(preferenceType)[0];
 
   const existingFilters = Object.values(
@@ -156,16 +160,6 @@ export const FilterOntology = ({
     })
   );
 
-  useEffect(() => {
-    form.setFieldsValue({
-      existing_filters: flattenedFilters?.map((ff, index) =>
-        JSON.stringify({
-          ontology: ff,
-        })
-      ),
-    });
-  }, [apiPreferencesTerm, existingFilters, initialChecked, form]);
-
   return (
     <>
       <div className="modal_checkbox_wrapper">
@@ -175,11 +169,7 @@ export const FilterOntology = ({
           <>
             <div className="onto_reset">
               <h4>Ontology Filters</h4>{' '}
-              <FilterReset
-                table={table}
-                component={table}
-                terminology={terminology}
-              />
+              <FilterReset table={table} terminology={terminology} />
             </div>
             <Form.Item
               initialValue={initialChecked}
diff --git a/src/components/Manager/MappingsFunctions/FilterReset.jsx b/src/components/Manager/MappingsFunctions/FilterReset.jsx
index 83f3ed0..122fe2e 100644
--- a/src/components/Manager/MappingsFunctions/FilterReset.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterReset.jsx
@@ -6,18 +6,20 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 import { useParams } from 'react-router-dom';
 import { cleanedName } from '../Utilitiy';
 
-export const FilterReset = ({ table, component, terminology }) => {
+export const FilterReset = ({ table, terminology }) => {
   const { confirm } = Modal;
   const { tableId } = useParams();
 
   const { user, vocabUrl } = useContext(myContext);
-  const { setApiPreferences } = useContext(SearchContext);
+  const { preferenceTypeSet } = useContext(SearchContext);
   const [remove, setRemove] = useState(false);
 
   const deleteOntologies = evt => {
+    // If deleting from a table, 'self' in endpoint
+    // If deleting from a terminology, the terminology code in endpoint
     return fetch(
       `${vocabUrl}/Table/${tableId}/filter/${
-        component === table ? 'self' : cleanedName(terminology?.name)
+        table ? 'self' : cleanedName(terminology?.name)
       }`,
       {
         method: 'DELETE',
@@ -39,7 +41,35 @@ export const FilterReset = ({ table, component, terminology }) => {
           });
         }
       })
-      .then(data => setApiPreferences(data));
+      .then(() =>
+        // Fetch the updated api preferences
+        fetch(
+          `${vocabUrl}/Table/${tableId}/filter/${
+            table ? `self` : `${cleanedName(terminology?.name)}`
+          }`,
+          {
+            method: 'GET',
+            headers: {
+              'Content-Type': 'application/json',
+            },
+          }
+        )
+      )
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          notification.error({
+            message: 'Error',
+            description: `An error occurred loading the ${
+              table ? 'table' : 'terminology'
+            }.`,
+          });
+        }
+      })
+      .then(data => {
+        preferenceTypeSet(data);
+      });
   };
 
   const showConfirm = () => {
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index acd26e7..31ff783 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -28,9 +28,8 @@ export const FilterSelect = ({ component, table, terminology }) => {
     ontologyApis,
     setOntologyApis,
     apiPreferences,
-    setApiPreferences,
     apiPreferencesTerm,
-    setApiPreferencesTerm,
+    preferenceTypeSet,
   } = useContext(SearchContext);
   const [searchText, setSearchText] = useState('');
 
@@ -47,6 +46,7 @@ export const FilterSelect = ({ component, table, terminology }) => {
       .finally(() => setLoading(false));
   }, []);
 
+  // Sets the first API in the list as active
   useEffect(() => {
     setActive(ontologyApis[0]?.api_id);
   }, [addFilter]);
@@ -73,9 +73,6 @@ export const FilterSelect = ({ component, table, terminology }) => {
     setDisplaySelectedOntologies([]);
   };
 
-  const preferenceTypeSet = data =>
-    apiPreferencesTerm ? setApiPreferencesTerm(data) : setApiPreferences(data);
-
   // If the api doesn't exist in api_preference, creates an empty array for it
   // If the api_preference array for the api does not include an ontology_code, pushes the code to the array for the api
   // If there is an api in api_preferences that is not included with the ontology_code, it's added to apiPreference with an empty array
@@ -129,7 +126,8 @@ export const FilterSelect = ({ component, table, terminology }) => {
     };
 
     const method =
-      Object.keys(apiPreferences?.self?.api_preference || {}).length === 0
+      Object.keys(preferenceType[prefTypeKey]?.api_preference || {}).length ===
+      0
         ? 'POST'
         : 'PUT';
 
@@ -192,15 +190,18 @@ export const FilterSelect = ({ component, table, terminology }) => {
       .finally(() => setLoading(false));
   };
 
+  // Checks if there are apiPreferences (table) or apiPreferencesTerm (terminology) and returns the appropriate one
   const preferenceType = apiPreferencesTerm
     ? apiPreferencesTerm
     : apiPreferences;
 
-  const prefTypeKey = Object.keys(preferenceType)[0];
+  // The first key is different depending if it's coming from a table or terminology. This dynamically gets the first key
+  const prefTypeKey = Object?.keys(preferenceType)[0];
 
+  // Creates a dynamic api preference object
   const apiPrefObject = preferenceType[prefTypeKey]?.api_preference;
 
-  // // Calculate the total length of all arrays
+  // Calculates the total length of all arrays to display number of ontology filters
   const apiPrefLength =
     apiPrefObject &&
     Object.values(apiPrefObject)?.reduce((acc, arr) => acc + arr.length, 0);

From 43b2ae76abfa1d4dab5c32ea069bbf9f15e472cb Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 29 Oct 2024 15:25:40 -0500
Subject: [PATCH 078/180] Added 'self' after table for ontology filters
 POST/PUT

---
 src/components/Manager/MappingsFunctions/FilterSelect.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index 31ff783..b5e1911 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -135,7 +135,7 @@ export const FilterSelect = ({ component, table, terminology }) => {
       `${vocabUrl}/Table/${(component = table
         ? table?.id
         : tableId)}/${(component = table
-        ? `filter`
+        ? `filter/self`
         : `filter/${cleanedName(terminology?.name)}`)}`,
       {
         method: method,

From 70239d2deb001e50e9f19c2309000dab0a48cf0a Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 30 Oct 2024 10:08:45 -0500
Subject: [PATCH 079/180] committing to change branches

---
 src/Contexts/SearchContext.jsx                |  9 +++++++
 src/components/Manager/FetchManager.jsx       | 21 ++++++----------
 .../MappingsFunctions/FilterOntology.jsx      | 10 +-------
 .../MappingsFunctions/FilterSelect.jsx        | 11 ++-------
 .../MappingsFunctions/GetMappingsModal.jsx    | 24 ++++++++++++-------
 .../MappingsFunctions/OntologyCheckboxes.jsx  | 15 ++++++------
 .../OntologyFilterCodeSubmit.jsx              |  5 ++--
 7 files changed, 45 insertions(+), 50 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index e784fd6..ab17bb6 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -23,6 +23,13 @@ export function SearchContextRoot() {
   const preferenceTypeSet = data =>
     apiPreferencesTerm ? setApiPreferencesTerm(data) : setApiPreferences(data);
 
+  // Checks if there are apiPreferences (table) or apiPreferencesTerm (terminology) and returns the appropriate one
+  const preferenceType = apiPreferencesTerm
+    ? apiPreferencesTerm
+    : apiPreferences;
+
+  const prefTypeKey = Object.keys(preferenceType)[0];
+
   const context = {
     prefTerminologies,
     setPrefTerminologies,
@@ -54,6 +61,8 @@ export function SearchContextRoot() {
     setApiPreferencesTerm,
     apiPreferencesTerm,
     preferenceTypeSet,
+    preferenceType,
+    prefTypeKey,
   };
 
   return (
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 57c5b86..1f989ec 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -235,21 +235,14 @@ export const getFiltersByCode = (
   notification,
   apiPreferencesCode,
   setUnformattedPref,
-  table
+  tableId
 ) => {
-  return fetch(
-    `${vocabUrl}/${
-      component === table
-        ? component?.terminology?.reference
-        : `Terminology/${component?.id}`
-    }/filter/${mappingProp}`,
-    {
-      method: 'GET',
-      headers: {
-        'Content-Type': 'application/json',
-      },
-    }
-  )
+  return fetch(`${vocabUrl}/Table/${tableId}/filter/${mappingProp}`, {
+    method: 'GET',
+    headers: {
+      'Content-Type': 'application/json',
+    },
+  })
     .then(res => {
       if (res.ok) {
         return res.json();
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 958b10b..10e67c2 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -12,15 +12,13 @@ export const FilterOntology = ({
   setSelectedBoxes,
   displaySelectedOntologies,
   setDisplaySelectedOntologies,
-  searchText,
   paginatedOntologies,
-  apiPreferences,
   table,
   terminology,
 }) => {
   const [allCheckboxes, setAllCheckboxes] = useState([]);
   const { setOntologyForPagination } = useContext(myContext);
-  const { apiPreferencesTerm } = useContext(SearchContext);
+  const { preferenceType, prefTypeKey } = useContext(SearchContext);
 
   useEffect(() => {
     setOntologyForPagination(ontology);
@@ -131,13 +129,7 @@ export const FilterOntology = ({
     );
   };
 
-  // Checks if there are apiPreferences (table) or apiPreferencesTerm (terminology) and returns the appropriate one
-  const preferenceType = apiPreferencesTerm
-    ? apiPreferencesTerm
-    : apiPreferences;
-
   // The first key is different depending if it's coming from a table or terminology. This dynamically gets the first key
-  const prefTypeKey = Object.keys(preferenceType)[0];
 
   const existingFilters = Object.values(
     preferenceType[prefTypeKey] || {}
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index b5e1911..f6b47eb 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -28,8 +28,9 @@ export const FilterSelect = ({ component, table, terminology }) => {
     ontologyApis,
     setOntologyApis,
     apiPreferences,
-    apiPreferencesTerm,
     preferenceTypeSet,
+    preferenceType,
+    prefTypeKey,
   } = useContext(SearchContext);
   const [searchText, setSearchText] = useState('');
 
@@ -190,14 +191,6 @@ export const FilterSelect = ({ component, table, terminology }) => {
       .finally(() => setLoading(false));
   };
 
-  // Checks if there are apiPreferences (table) or apiPreferencesTerm (terminology) and returns the appropriate one
-  const preferenceType = apiPreferencesTerm
-    ? apiPreferencesTerm
-    : apiPreferences;
-
-  // The first key is different depending if it's coming from a table or terminology. This dynamically gets the first key
-  const prefTypeKey = Object?.keys(preferenceType)[0];
-
   // Creates a dynamic api preference object
   const apiPrefObject = preferenceType[prefTypeKey]?.api_preference;
 
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 8c26df3..b245975 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -16,6 +16,7 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
 import { OntologyFilterCodeSubmit } from './OntologyFilterCodeSubmit';
+import { useParams } from 'react-router-dom';
 
 export const GetMappingsModal = ({
   componentString,
@@ -27,17 +28,19 @@ export const GetMappingsModal = ({
   mappingDesc,
   table,
 }) => {
+  const { tableId } = useParams();
   const [form] = Form.useForm();
   const { Search } = Input;
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
   const {
-    apiPreferences,
+    preferenceType,
     defaultOntologies,
     setFacetCounts,
     setApiPreferencesCode,
     apiPreferencesCode,
     setUnformattedPref,
-    setApiPreferencesTerm,
+    preferenceTypeSet,
+    prefTypeKey,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 2500;
@@ -75,11 +78,13 @@ export const GetMappingsModal = ({
         notification,
         apiPreferencesCode,
         setUnformattedPref,
-        table
+        tableId
       );
     }
   }, [searchProp]);
 
+  console.log('component', component);
+
   useEffect(() => {
     if (apiPreferencesCode !== undefined) fetchResults(0, searchProp);
   }, [apiPreferencesCode, searchProp]);
@@ -178,7 +183,8 @@ export const GetMappingsModal = ({
         OntologyFilterCodeSubmit(
           apiPreferencesCode,
           setApiPreferencesCode,
-          apiPreferences,
+          preferenceType,
+          prefTypeKey,
           mappingProp,
           table,
           vocabUrl,
@@ -199,12 +205,12 @@ export const GetMappingsModal = ({
 
     if (
       //If there are api preferences and one of them is OLS, it gets the preferred ontologies
-      apiPreferences?.self?.api_preference &&
-      'ols' in apiPreferences?.self?.api_preference
+      preferenceType[prefTypeKey]?.api_preference &&
+      'ols' in preferenceType[prefTypeKey]?.api_preference
     ) {
       const apiPreferenceOntologies = () => {
-        if (apiPreferences?.self?.api_preference?.ols) {
-          return apiPreferences.self.api_preference.ols.join(',');
+        if (preferenceType[prefTypeKey]?.api_preference?.ols) {
+          return preferenceType[prefTypeKey].api_preference.ols.join(',');
         } else {
           // else if there are no preferred ontologies, it uses the default ontologies
           return defaultOntologies;
@@ -403,7 +409,7 @@ export const GetMappingsModal = ({
                 <div className="result_container">
                   <Form form={form} layout="vertical" preserve={false}>
                     <div className="all_checkboxes_container">
-                      <OntologyCheckboxes apiPreferences={apiPreferences} />
+                      <OntologyCheckboxes preferenceType={preferenceType} />
                       <div className="result_form">
                         {displaySelectedMappings?.length > 0 && (
                           <Form.Item
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 14d33ad..fcb4c3d 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -3,15 +3,16 @@ import { ontologyCounts } from '../Utilitiy';
 import { useContext, useEffect, useState } from 'react';
 import { SearchContext } from '../../../Contexts/SearchContext';
 
-export const OntologyCheckboxes = ({ apiPreferences }) => {
+export const OntologyCheckboxes = ({ preferenceType }) => {
   const {
     apiPreferencesCode,
     setApiPreferencesCode,
     facetCounts,
     ontologyApis,
+    prefTypeKey,
   } = useContext(SearchContext);
   const { Search } = Input;
-
+  console.log('api pref code', apiPreferencesCode);
   const [checkedOntologies, setCheckedOntologies] = useState([]);
   const [searchText, setSearchText] = useState('');
 
@@ -30,15 +31,15 @@ export const OntologyCheckboxes = ({ apiPreferences }) => {
 
   const existingOntologies = apiPreferencesCode
     ? processedApiPreferencesCode
-    : apiPreferences &&
-      apiPreferences?.self &&
-      apiPreferences?.self?.api_preference
-    ? Object?.values(apiPreferences?.self?.api_preference).flat()
+    : preferenceType &&
+      preferenceType?.self &&
+      preferenceType[prefTypeKey]?.api_preference
+    ? Object?.values(preferenceType[prefTypeKey]?.api_preference).flat()
     : defaultOntologies;
 
   useEffect(() => {
     setCheckedOntologies(existingOntologies);
-  }, [apiPreferences]);
+  }, [preferenceType]);
 
   const onCheckboxChange = e => {
     const { value, checked } = e.target;
diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
index 807f780..c1cbe16 100644
--- a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
@@ -2,7 +2,8 @@ import { notification } from 'antd';
 
 export const OntologyFilterCodeSubmit = (
   apiPreferencesCode,
-  apiPreferences,
+  preferenceType,
+  prefTypeKey,
   mappingProp,
   table,
   vocabUrl,
@@ -15,7 +16,7 @@ export const OntologyFilterCodeSubmit = (
   if (
     apiPreferencesCode &&
     JSON.stringify(
-      Object.values(apiPreferences?.self?.api_preference)[0].sort()
+      Object.values(preferenceType[prefTypeKey]?.api_preference)[0].sort()
     ) !== JSON.stringify(apiPreferencesCode?.sort())
   ) {
     apiPreference.api_preference.ols = apiPreferencesCode;

From bbfe5a00a50f96a55de3101ecbf357e8a6daf01f Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 30 Oct 2024 12:44:06 -0500
Subject: [PATCH 080/180] Bean work on using terminology ontology filters for
 mapping search

---
 src/components/Manager/FetchManager.jsx       | 27 +++++++++++-------
 .../MappingsFunctions/GetMappingsModal.jsx    | 19 ++++++-------
 .../MappingsFunctions/MappingReset.jsx        | 18 ++++++------
 .../MappingsFunctions/MappingSearch.jsx       |  8 ++++--
 .../MappingsFunctions/OntologyCheckboxes.jsx  |  2 +-
 .../OntologyFilterCodeSubmit.jsx              | 28 +++++++++----------
 .../Terminologies/EditMappingModal.jsx        |  4 +--
 .../Projects/Terminologies/Terminology.jsx    |  1 +
 8 files changed, 57 insertions(+), 50 deletions(-)

diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 1f989ec..f0e8b6d 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -1,4 +1,4 @@
-import { ontologyReducer } from './Utilitiy';
+import { cleanedName, ontologyReducer } from './Utilitiy';
 
 // Fetches all elements at an endpoint
 export const getAll = (vocabUrl, name, navigate) => {
@@ -219,7 +219,9 @@ export const olsFilterOntologiesSearch = (
       //the results are set to res (the filtered, concatenated results)
 
       setResults(res.results);
-      setFilteredResultsCount(res?.filteredResults?.length);
+      setFilteredResultsCount(
+        prevState => prevState + res?.filteredResults?.length
+      );
       // resultsCount is set to the length of the filtered, concatenated results for pagination
       setResultsCount(res.results.length);
       setFacetCounts(data?.facet_counts?.facet_fields?.ontologyPreferredPrefix);
@@ -233,16 +235,21 @@ export const getFiltersByCode = (
   mappingProp,
   setApiPreferencesCode,
   notification,
-  apiPreferencesCode,
   setUnformattedPref,
-  tableId
+  tableId,
+  terminology
 ) => {
-  return fetch(`${vocabUrl}/Table/${tableId}/filter/${mappingProp}`, {
-    method: 'GET',
-    headers: {
-      'Content-Type': 'application/json',
-    },
-  })
+  return fetch(
+    `${vocabUrl}/Table/${tableId}/filter/${(component = terminology
+      ? cleanedName(terminology?.name)
+      : mappingProp)}`,
+    {
+      method: 'GET',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+    }
+  )
     .then(res => {
       if (res.ok) {
         return res.json();
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index b245975..37e4c74 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -27,6 +27,7 @@ export const GetMappingsModal = ({
   mappingProp,
   mappingDesc,
   table,
+  terminology,
 }) => {
   const { tableId } = useParams();
   const [form] = Form.useForm();
@@ -43,7 +44,7 @@ export const GetMappingsModal = ({
     prefTypeKey,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
-  const entriesPerPage = 2500;
+  const entriesPerPage = 15;
   const [loading, setLoading] = useState(false);
   const [results, setResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
@@ -76,15 +77,13 @@ export const GetMappingsModal = ({
         mappingProp,
         setApiPreferencesCode,
         notification,
-        apiPreferencesCode,
         setUnformattedPref,
-        tableId
+        tableId,
+        terminology
       );
     }
   }, [searchProp]);
 
-  console.log('component', component);
-
   useEffect(() => {
     if (apiPreferencesCode !== undefined) fetchResults(0, searchProp);
   }, [apiPreferencesCode, searchProp]);
@@ -100,7 +99,7 @@ export const GetMappingsModal = ({
   This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
   Because the content is in a modal and not the window, the closest class name to the modal is used for the location of the ref. */
   useEffect(() => {
-    if (results?.length > 0 && page > 0) {
+    if (results?.length > 0 && page > 0 && ref.current) {
       const container = ref.current.closest('.ant-modal-body');
       const scrollTop = ref.current.offsetTop - container.offsetTop;
       container.scrollTop = scrollTop;
@@ -182,13 +181,11 @@ export const GetMappingsModal = ({
       .then(() =>
         OntologyFilterCodeSubmit(
           apiPreferencesCode,
-          setApiPreferencesCode,
           preferenceType,
           prefTypeKey,
           mappingProp,
-          table,
           vocabUrl,
-          component
+          tableId
         )
       )
       .finally(() => setLoading(false));
@@ -482,12 +479,12 @@ export const GetMappingsModal = ({
                       inconsistencies in results numbers per page. */}
                     <Tooltip
                       placement="bottom"
-                      title="Redundant entries have been removed"
+                      title={`${filteredResultsCount} redundant entries have been removed`}
                     >
                       Displaying {resultsCount}
                       &nbsp;of&nbsp;{totalCount}
                     </Tooltip>
-                    {totalCount - filteredResultsCount !== resultsCount && (
+                    {resultsCount < totalCount - filteredResultsCount && (
                       <span
                         className="view_more_link"
                         onClick={e => {
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 10d91fd..3210ab7 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -7,6 +7,7 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
+import { useParams } from 'react-router-dom';
 
 export const MappingReset = ({
   searchProp,
@@ -17,8 +18,10 @@ export const MappingReset = ({
   component,
   mappingProp,
   table,
+  terminology,
 }) => {
   const { searchUrl, vocabUrl } = useContext(myContext);
+  const { tableId } = useParams();
   const {
     apiPreferences,
     defaultOntologies,
@@ -63,9 +66,9 @@ export const MappingReset = ({
         mappingProp,
         setApiPreferencesCode,
         notification,
-        apiPreferencesCode,
         setUnformattedPref,
-        table
+        tableId,
+        terminology
       );
     }
   }, [searchProp]);
@@ -417,13 +420,12 @@ export const MappingReset = ({
               </div>
             </>
           ) : (
-        <div className="loading_spinner">
-          <ModalSpinner />
-        </div>
+            <div className="loading_spinner">
+              <ModalSpinner />
+            </div>
           )}
-      </>
-    </div >
+        </>
+      </div>
     </>
   );
 };
- 
\ No newline at end of file
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 88d8db4..1d56fa5 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -7,6 +7,7 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
+import { useParams } from 'react-router-dom';
 
 export const MappingSearch = ({
   setEditMappings,
@@ -17,7 +18,7 @@ export const MappingSearch = ({
   mappingDesc,
   component,
   mappingProp,
-  table,
+  terminology,
 }) => {
   const { searchUrl, vocabUrl } = useContext(myContext);
   const {
@@ -28,6 +29,7 @@ export const MappingSearch = ({
     apiPreferencesCode,
     setUnformattedPref,
   } = useContext(SearchContext);
+  const { tableId } = useParams();
 
   const [page, setPage] = useState(0);
   const entriesPerPage = 2500;
@@ -67,9 +69,9 @@ export const MappingSearch = ({
         mappingProp,
         setApiPreferencesCode,
         notification,
-        apiPreferencesCode,
         setUnformattedPref,
-        table
+        tableId,
+        terminology
       );
     }
   }, [searchProp]);
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index fcb4c3d..3477edf 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -12,7 +12,7 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
     prefTypeKey,
   } = useContext(SearchContext);
   const { Search } = Input;
-  console.log('api pref code', apiPreferencesCode);
+
   const [checkedOntologies, setCheckedOntologies] = useState([]);
   const [searchText, setSearchText] = useState('');
 
diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
index c1cbe16..15a6ad5 100644
--- a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
@@ -5,10 +5,13 @@ export const OntologyFilterCodeSubmit = (
   preferenceType,
   prefTypeKey,
   mappingProp,
-  table,
   vocabUrl,
-  component
+  tableId
 ) => {
+  console.log('key', prefTypeKey);
+  console.log('code preferences', JSON.stringify(apiPreferencesCode?.sort()));
+  console.log('preferences', preferenceType[prefTypeKey]?.api_preference[0]);
+
   const apiPreference = {
     api_preference: { 'ols': [] },
   };
@@ -16,23 +19,18 @@ export const OntologyFilterCodeSubmit = (
   if (
     apiPreferencesCode &&
     JSON.stringify(
-      Object.values(preferenceType[prefTypeKey]?.api_preference)[0].sort()
+      Object.values(preferenceType[prefTypeKey]?.api_preference)[0]?.sort()
     ) !== JSON.stringify(apiPreferencesCode?.sort())
   ) {
     apiPreference.api_preference.ols = apiPreferencesCode;
 
-    fetch(
-      `${vocabUrl}/${(component = table
-        ? `Table/${component?.id}`
-        : `Terminology/${component?.id}`)}/filter/${mappingProp}`,
-      {
-        method: 'POST',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-        body: JSON.stringify(apiPreference),
-      }
-    )
+    fetch(`${vocabUrl}/Table/${tableId}/filter/${mappingProp}`, {
+      method: 'POST',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify(apiPreference),
+    })
       .then(res => {
         if (res.ok) {
           return res.json();
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 4845716..0fa0fe5 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -24,7 +24,6 @@ export const EditMappingsModal = ({
   setMapping,
   mappingDesc,
   terminology,
-
 }) => {
   const [form] = Form.useForm();
   const [termMappings, setTermMappings] = useState([]);
@@ -327,7 +326,6 @@ export const EditMappingsModal = ({
                 : editMappings?.code}
             </h3>
             <span className="search-desc">{mappingDesc}</span>
-
           </div>
           <Form form={form} layout="vertical" preserve={false}>
             <Form.Item
@@ -353,6 +351,7 @@ export const EditMappingsModal = ({
             editMappings?.display ? editMappings.display : editMappings?.code
           }
           mappingDesc={editMappings?.description}
+          terminology={terminology}
         />
       ) : (
         reset && (
@@ -366,6 +365,7 @@ export const EditMappingsModal = ({
             reset={reset}
             onClose={form.resetFields}
             mappingDesc={editMappings?.description}
+            terminology={terminology}
           />
         )
       )}
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index a97556d..e74e505 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -401,6 +401,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
           <GetMappingsModal
             componentString={'Terminology'}
             component={terminology}
+            terminology={terminology}
             setTerminology={setTerminology}
             searchProp={
               getMappings?.display ? getMappings.display : getMappings?.code

From d65856414c770b0f4116f836bfec7450a69b9b44 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Wed, 30 Oct 2024 13:47:10 -0500
Subject: [PATCH 081/180] [FD-1779] Add deploy_alpha workflow

---
 .github/workflows/deploy_alpha.yml | 64 ++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 .github/workflows/deploy_alpha.yml

diff --git a/.github/workflows/deploy_alpha.yml b/.github/workflows/deploy_alpha.yml
new file mode 100644
index 0000000..d7ce3cb
--- /dev/null
+++ b/.github/workflows/deploy_alpha.yml
@@ -0,0 +1,64 @@
+# This workflow build and push a Docker container to Google Artifact Registry
+# and deploy it on Cloud Run when manually triggered.
+
+name: 'Build and Deploy Alpha to  Cloud Run'
+
+on:
+    workflow_dispatch
+
+env:
+
+  PROJECT_ID: ${{ secrets.PROJECT_ID }}
+  REGION: ${{ secrets.REGION_LOC_1 }}
+  SERVICE: 'map-dragon'
+  IMAGE_NAME: 'map-dragon_img'
+  GCP_CREDENTIALS:  ${{ secrets.GCP_CREDENTIALS }}
+
+
+jobs:
+  
+  deploy:
+    runs-on: 'ubuntu-latest'
+
+    
+    environment:
+      name: alpha
+
+    permissions:
+      contents: 'read'
+      id-token: 'write'
+
+    steps:
+      - name: 'Checkout'
+        uses: 'actions/checkout@v4'
+      - id: 'auth'
+        name: 'Authenticate to Google Cloud'
+        uses: 'google-github-actions/auth@v2'
+        with:
+          credentials_json: '${{ env.GCP_CREDENTIALS }}'
+
+      - name: Generate .env.alpha file
+        run: |
+          echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.alpha
+          echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.alpha
+          echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.alpha
+      - name: 'Docker Auth'
+        run: |-
+          gcloud auth configure-docker '${{ env.REGION }}-docker.pkg.dev'
+
+      - name: 'Build Docker Image' # New step to build the image
+        run: |-
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          docker build -t "${DOCKER_TAG}" .
+
+      - name: 'Push Docker Image'
+        run: |-
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          docker push "${DOCKER_TAG}"
+
+      - name: 'Deploy to Cloud Run'
+        uses: 'google-github-actions/deploy-cloudrun@v2'
+        with:
+          service: '${{ env.SERVICE }}'
+          region: '${{ env.REGION }}'
+          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
\ No newline at end of file

From bb93780ebc09eb5e723fa1055c7de107bc455f8c Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 30 Oct 2024 14:05:48 -0500
Subject: [PATCH 082/180] Rolling back backend bug workaround

---
 src/components/Manager/FetchManager.jsx | 17 ++++++-----------
 1 file changed, 6 insertions(+), 11 deletions(-)

diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index f0e8b6d..fa0290d 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -239,17 +239,12 @@ export const getFiltersByCode = (
   tableId,
   terminology
 ) => {
-  return fetch(
-    `${vocabUrl}/Table/${tableId}/filter/${(component = terminology
-      ? cleanedName(terminology?.name)
-      : mappingProp)}`,
-    {
-      method: 'GET',
-      headers: {
-        'Content-Type': 'application/json',
-      },
-    }
-  )
+  return fetch(`${vocabUrl}/Table/${tableId}/filter/${mappingProp}`, {
+    method: 'GET',
+    headers: {
+      'Content-Type': 'application/json',
+    },
+  })
     .then(res => {
       if (res.ok) {
         return res.json();

From c3ee2cb2df65d24391fcebe8090a4434f9e2387e Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 30 Oct 2024 21:39:19 -0500
Subject: [PATCH 083/180] committing to change branches

---
 .../Manager/MappingsFunctions/FilterReset.jsx  | 16 ++++++++++++----
 .../Manager/MappingsFunctions/FilterSelect.jsx | 18 ++++++++++--------
 .../Projects/Tables/TableDetails.jsx           | 15 ++++++---------
 .../Projects/Terminologies/Terminology.jsx     |  4 +++-
 4 files changed, 31 insertions(+), 22 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterReset.jsx b/src/components/Manager/MappingsFunctions/FilterReset.jsx
index 122fe2e..536baff 100644
--- a/src/components/Manager/MappingsFunctions/FilterReset.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterReset.jsx
@@ -18,8 +18,12 @@ export const FilterReset = ({ table, terminology }) => {
     // If deleting from a table, 'self' in endpoint
     // If deleting from a terminology, the terminology code in endpoint
     return fetch(
-      `${vocabUrl}/Table/${tableId}/filter/${
-        table ? 'self' : cleanedName(terminology?.name)
+      `${vocabUrl}/${
+        table
+          ? `Table/${table.id}/filter/self`
+          : `Terminology/${terminology.id}/filter/${cleanedName(
+              terminology.name
+            )}`
       }`,
       {
         method: 'DELETE',
@@ -44,8 +48,12 @@ export const FilterReset = ({ table, terminology }) => {
       .then(() =>
         // Fetch the updated api preferences
         fetch(
-          `${vocabUrl}/Table/${tableId}/filter/${
-            table ? `self` : `${cleanedName(terminology?.name)}`
+          `${vocabUrl}/${
+            table
+              ? `Table/${table.id}/filter/self`
+              : `Terminology/${terminology.id}/filter/${cleanedName(
+                  terminology.name
+                )}`
           }`,
           {
             method: 'GET',
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index f6b47eb..cab3d55 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -133,11 +133,11 @@ export const FilterSelect = ({ component, table, terminology }) => {
         : 'PUT';
 
     fetch(
-      `${vocabUrl}/Table/${(component = table
-        ? table?.id
-        : tableId)}/${(component = table
-        ? `filter/self`
-        : `filter/${cleanedName(terminology?.name)}`)}`,
+      `${vocabUrl}/${(component = table
+        ? `Table/${table.id}/filter/self`
+        : `Terminology/${terminology.id}/filter/${cleanedName(
+            terminology.name
+          )}`)}`,
       {
         method: method,
         headers: {
@@ -155,9 +155,11 @@ export const FilterSelect = ({ component, table, terminology }) => {
       })
       .then(() =>
         fetch(
-          `${vocabUrl}/Table/${tableId}/filter/${(component = table
-            ? `self`
-            : `${cleanedName(terminology?.name)}`)}`,
+          `${vocabUrl}/${(component = table
+            ? `Table/${table.id}/filter/self`
+            : `Terminology/${terminology.id}/filter/${cleanedName(
+                terminology.name
+              )}`)}`,
           {
             method: 'GET',
             headers: {
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 69a2a16..1bd0320 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -137,15 +137,12 @@ export const TableDetails = () => {
                 return error;
               })
               .then(() =>
-                fetch(
-                  `${vocabUrl}/${data?.terminology?.reference}/filter/self`,
-                  {
-                    method: 'GET',
-                    headers: {
-                      'Content-Type': 'application/json',
-                    },
-                  }
-                )
+                fetch(`${vocabUrl}/Table/${tableId}/filter/self`, {
+                  method: 'GET',
+                  headers: {
+                    'Content-Type': 'application/json',
+                  },
+                })
               )
               .then(res => {
                 if (res.ok) {
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index e74e505..ca6e966 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -196,7 +196,9 @@ It then shows the mappings as table data and alows the user to delete a mapping
           if (data) {
             cleanedName(data?.name);
             fetch(
-              `${vocabUrl}/Table/${tableId}/filter/${cleanedName(data?.name)}`,
+              `${vocabUrl}/Terminology/${data?.id}/filter/${cleanedName(
+                data?.name
+              )}`,
               {
                 method: 'GET',
                 headers: {

From 413db9e6aa5e6005c5fed804785206a1cc33837d Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Thu, 31 Oct 2024 10:41:10 -0500
Subject: [PATCH 084/180] [FD-1779] Specify branch to deploy prod and alpha

---
 .github/workflows/deploy_alpha.yml | 4 +++-
 .github/workflows/deploy_prod.yml  | 3 +++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/deploy_alpha.yml b/.github/workflows/deploy_alpha.yml
index d7ce3cb..7f9f7fe 100644
--- a/.github/workflows/deploy_alpha.yml
+++ b/.github/workflows/deploy_alpha.yml
@@ -20,7 +20,6 @@ jobs:
   deploy:
     runs-on: 'ubuntu-latest'
 
-    
     environment:
       name: alpha
 
@@ -31,6 +30,9 @@ jobs:
     steps:
       - name: 'Checkout'
         uses: 'actions/checkout@v4'
+        with:
+          ref: release # release is deployed, not the default or working branch
+        
       - id: 'auth'
         name: 'Authenticate to Google Cloud'
         uses: 'google-github-actions/auth@v2'
diff --git a/.github/workflows/deploy_prod.yml b/.github/workflows/deploy_prod.yml
index d5fb093..7293668 100644
--- a/.github/workflows/deploy_prod.yml
+++ b/.github/workflows/deploy_prod.yml
@@ -35,6 +35,9 @@ jobs:
     steps:
       - name: 'Checkout'
         uses: 'actions/checkout@v4'
+        with:
+          ref: release # release is deployed, not the default or working branch.
+
       - id: 'auth'
         name: 'Authenticate to Google Cloud'
         uses: 'google-github-actions/auth@v2'

From 7a78f7ad9b027e3659985543b44f29d53e54af6b Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 31 Oct 2024 13:41:20 -0500
Subject: [PATCH 085/180] Ontology filters for terminology codes

---
 src/components/Manager/FetchManager.jsx       | 21 +++++---
 .../MappingsFunctions/DefaultSearch.jsx       | 52 ------------------
 .../MappingsFunctions/GetMappingsModal.jsx    | 34 ++++++++----
 .../MappingsFunctions/MappingReset.jsx        | 11 ++--
 .../MappingsFunctions/MappingSearch.jsx       | 11 ++--
 .../MappingsFunctions/OntologyCheckboxes.jsx  |  2 +-
 .../OntologyFilterCodeSubmit.jsx              | 53 ++++++++++++++++---
 .../Tables/EditMappingsTableModal.jsx         | 20 ++++++-
 .../Projects/Terminologies/APIResults.jsx     |  4 +-
 .../Projects/Terminologies/APISearchBar.jsx   |  2 +-
 .../Terminologies/EditMappingModal.jsx        | 28 +++++++++-
 11 files changed, 145 insertions(+), 93 deletions(-)
 delete mode 100644 src/components/Manager/MappingsFunctions/DefaultSearch.jsx

diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index fa0290d..f358a31 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -236,15 +236,22 @@ export const getFiltersByCode = (
   setApiPreferencesCode,
   notification,
   setUnformattedPref,
-  tableId,
+  table,
   terminology
 ) => {
-  return fetch(`${vocabUrl}/Table/${tableId}/filter/${mappingProp}`, {
-    method: 'GET',
-    headers: {
-      'Content-Type': 'application/json',
-    },
-  })
+  return fetch(
+    `${vocabUrl}/${
+      table
+        ? `Table/${table.id}/filter/${mappingProp}`
+        : `Terminology/${terminology.id}/filter/${mappingProp}`
+    }`,
+    {
+      method: 'GET',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+    }
+  )
     .then(res => {
       if (res.ok) {
         return res.json();
diff --git a/src/components/Manager/MappingsFunctions/DefaultSearch.jsx b/src/components/Manager/MappingsFunctions/DefaultSearch.jsx
deleted file mode 100644
index ef91ae6..0000000
--- a/src/components/Manager/MappingsFunctions/DefaultSearch.jsx
+++ /dev/null
@@ -1,52 +0,0 @@
-import { ontologyReducer } from '../Utilitiy';
-
-export const fetchResults = (
-  page,
-  query,
-  entriesPerPage,
-  //   setLoading,
-  setTotalCount,
-  setResults,
-  setFilteredResultsCount,
-  setResultsCount,
-  searchUrl,
-  selectedBoxes
-) => {
-  if (!query) {
-    return undefined;
-  }
-  //   setLoading(true);
-  const pageStart = page * entriesPerPage;
-
-  return fetch(
-    `${searchUrl}q=${query}&ontology=mondo,hp,maxo,ncit&rows=${entriesPerPage}&start=${pageStart}`,
-    {
-      method: 'GET',
-      headers: {
-        'Content-Type': 'application/json',
-      },
-    }
-  )
-    .then(res => res.json())
-    .then(data => {
-      let res = ontologyReducer(data?.response?.docs);
-
-      // Filter based on selectedBoxes
-      if (selectedBoxes) {
-        res.results = res.results.filter(
-          d => !selectedBoxes.some(box => box.obo_id === d.obo_id)
-        );
-      }
-
-      if (page > 0 && res.results.length > 0) {
-        res.results = results.concat(res.results);
-      } else {
-        setTotalCount(data.response.numFound);
-      }
-
-      setResults(res.results);
-      setFilteredResultsCount(res?.filteredResults?.length);
-      setResultsCount(res.results.length);
-    });
-  // .finally(() => setLoading(false));
-};
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 37e4c74..511d6d6 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -15,7 +15,10 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
-import { OntologyFilterCodeSubmit } from './OntologyFilterCodeSubmit';
+import {
+  OntologyFilterCodeSubmit,
+  OntologyFilterCodeSubmitTerm,
+} from './OntologyFilterCodeSubmit';
 import { useParams } from 'react-router-dom';
 
 export const GetMappingsModal = ({
@@ -44,7 +47,7 @@ export const GetMappingsModal = ({
     prefTypeKey,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
-  const entriesPerPage = 15;
+  const entriesPerPage = 2000;
   const [loading, setLoading] = useState(false);
   const [results, setResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
@@ -78,7 +81,7 @@ export const GetMappingsModal = ({
         setApiPreferencesCode,
         notification,
         setUnformattedPref,
-        tableId,
+        table,
         terminology
       );
     }
@@ -179,14 +182,23 @@ export const GetMappingsModal = ({
         message.success('Changes saved successfully.');
       })
       .then(() =>
-        OntologyFilterCodeSubmit(
-          apiPreferencesCode,
-          preferenceType,
-          prefTypeKey,
-          mappingProp,
-          vocabUrl,
-          tableId
-        )
+        table
+          ? OntologyFilterCodeSubmit(
+              apiPreferencesCode,
+              preferenceType,
+              prefTypeKey,
+              mappingProp,
+              vocabUrl,
+              table
+            )
+          : OntologyFilterCodeSubmitTerm(
+              apiPreferencesCode,
+              preferenceType,
+              prefTypeKey,
+              searchProp,
+              vocabUrl,
+              terminology
+            )
       )
       .finally(() => setLoading(false));
   };
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 3210ab7..15ca486 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -21,7 +21,6 @@ export const MappingReset = ({
   terminology,
 }) => {
   const { searchUrl, vocabUrl } = useContext(myContext);
-  const { tableId } = useParams();
   const {
     apiPreferences,
     defaultOntologies,
@@ -31,7 +30,7 @@ export const MappingReset = ({
     setUnformattedPref,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
-  const entriesPerPage = 15;
+  const entriesPerPage = 2000;
   const [loading, setLoading] = useState(true);
   const [results, setResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
@@ -67,7 +66,7 @@ export const MappingReset = ({
         setApiPreferencesCode,
         notification,
         setUnformattedPref,
-        tableId,
+        table,
         terminology
       );
     }
@@ -91,7 +90,7 @@ export const MappingReset = ({
   This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
   Because the content is in a modal and not the window, the closest class name to the modal is used for the location of the ref. */
   useEffect(() => {
-    if (results?.length > 0 && page > 0) {
+    if (results?.length > 0 && page > 0 && ref.current) {
       const container = ref.current.closest('.ant-modal-body');
       const scrollTop = ref.current.offsetTop - container.offsetTop;
       container.scrollTop = scrollTop;
@@ -373,7 +372,7 @@ export const MappingReset = ({
                                         display: d.label,
                                         // description: d.description[0],
                                         system: systemsMatch(
-                                          d?.obo_id.split(':')[0]
+                                          d?.obo_id?.split(':')[0]
                                         ),
                                       }),
                                       label: checkBoxDisplay(d, index),
@@ -405,7 +404,7 @@ export const MappingReset = ({
                     Displaying {resultsCount}
                     &nbsp;of&nbsp;{totalCount}
                   </Tooltip>
-                  {totalCount - filteredResultsCount !== resultsCount && (
+                  {resultsCount < totalCount - filteredResultsCount && (
                     <span
                       className="view_more_link"
                       onClick={e => {
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 1d56fa5..26b4589 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -15,10 +15,11 @@ export const MappingSearch = ({
   mappingsForSearch,
   onClose,
   searchProp,
+  mappingProp,
   mappingDesc,
   component,
-  mappingProp,
   terminology,
+  table,
 }) => {
   const { searchUrl, vocabUrl } = useContext(myContext);
   const {
@@ -32,7 +33,7 @@ export const MappingSearch = ({
   const { tableId } = useParams();
 
   const [page, setPage] = useState(0);
-  const entriesPerPage = 2500;
+  const entriesPerPage = 2000;
   const [loading, setLoading] = useState(true);
   const [results, setResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
@@ -70,7 +71,7 @@ export const MappingSearch = ({
         setApiPreferencesCode,
         notification,
         setUnformattedPref,
-        tableId,
+        table,
         terminology
       );
     }
@@ -94,7 +95,7 @@ export const MappingSearch = ({
   This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
   Because the content is in a modal and not the window, the closest class name to the modal is used for the location of the ref. */
   useEffect(() => {
-    if (results?.length > 0 && page > 0) {
+    if (results?.length > 0 && page > 0 && ref.current) {
       const container = ref.current.closest('.ant-modal-body');
       const scrollTop = ref.current.offsetTop - container.offsetTop;
       container.scrollTop = scrollTop;
@@ -492,7 +493,7 @@ export const MappingSearch = ({
                       Displaying {resultsCount}
                       &nbsp;of&nbsp;{totalCount}
                     </Tooltip>
-                    {totalCount - filteredResultsCount !== resultsCount && (
+                    {resultsCount < totalCount - filteredResultsCount && (
                       <span
                         className="view_more_link"
                         onClick={e => {
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 3477edf..89e8662 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -32,7 +32,7 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
   const existingOntologies = apiPreferencesCode
     ? processedApiPreferencesCode
     : preferenceType &&
-      preferenceType?.self &&
+      preferenceType[prefTypeKey] &&
       preferenceType[prefTypeKey]?.api_preference
     ? Object?.values(preferenceType[prefTypeKey]?.api_preference).flat()
     : defaultOntologies;
diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
index 15a6ad5..8e1b4d9 100644
--- a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
@@ -1,4 +1,5 @@
 import { notification } from 'antd';
+import { cleanedName } from '../Utilitiy';
 
 export const OntologyFilterCodeSubmit = (
   apiPreferencesCode,
@@ -6,16 +7,56 @@ export const OntologyFilterCodeSubmit = (
   prefTypeKey,
   mappingProp,
   vocabUrl,
-  tableId
+  table
 ) => {
-  console.log('key', prefTypeKey);
-  console.log('code preferences', JSON.stringify(apiPreferencesCode?.sort()));
-  console.log('preferences', preferenceType[prefTypeKey]?.api_preference[0]);
-
   const apiPreference = {
     api_preference: { 'ols': [] },
   };
+  if (
+    apiPreferencesCode &&
+    JSON.stringify(
+      Object.values(preferenceType[prefTypeKey]?.api_preference)[0]?.sort()
+    ) !== JSON.stringify(apiPreferencesCode?.sort())
+  ) {
+    apiPreference.api_preference.ols = apiPreferencesCode;
 
+    fetch(`${vocabUrl}/Table/${table.id}/filter/${mappingProp}`, {
+      method: 'POST',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify(apiPreference),
+    })
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .catch(error => {
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred saving the ontology preferences.',
+          });
+        }
+        return error;
+      });
+  }
+};
+
+export const OntologyFilterCodeSubmitTerm = (
+  apiPreferencesCode,
+  preferenceType,
+  prefTypeKey,
+  searchProp,
+  vocabUrl,
+  terminology
+) => {
+  const apiPreference = {
+    api_preference: { 'ols': [] },
+  };
   if (
     apiPreferencesCode &&
     JSON.stringify(
@@ -24,7 +65,7 @@ export const OntologyFilterCodeSubmit = (
   ) {
     apiPreference.api_preference.ols = apiPreferencesCode;
 
-    fetch(`${vocabUrl}/Table/${tableId}/filter/${mappingProp}`, {
+    fetch(`${vocabUrl}/Terminology/${terminology.id}/filter/${searchProp}`, {
       method: 'POST',
       headers: {
         'Content-Type': 'application/json',
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index 15fdc98..ca8b0d5 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -17,6 +17,7 @@ import { ResetTableMappings } from './ResetTableMappings';
 import { ellipsisString, systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import { OntologyFilterCodeSubmit } from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmit';
 
 export const EditMappingsTableModal = ({
   editMappings,
@@ -35,7 +36,12 @@ export const EditMappingsTableModal = ({
   const [editSearch, setEditSearch] = useState(false);
   const { setSelectedMappings, setDisplaySelectedMappings } =
     useContext(MappingContext);
-  const { setApiPreferencesCode } = useContext(SearchContext);
+  const {
+    apiPreferencesCode,
+    setApiPreferencesCode,
+    preferenceType,
+    prefTypeKey,
+  } = useContext(SearchContext);
 
   useEffect(() => {
     fetchMappings();
@@ -193,6 +199,7 @@ export const EditMappingsTableModal = ({
       .finally(() => setLoading(false));
   };
 
+  const mappingProp = editMappings?.code;
   // Function to send a PUT call to update the mappings after code name change.
   // The existing and new mappings are JSON.parsed and combined into one mappings array to be passed into the body of the PUT call.
   const editUpdatedMappings = values => {
@@ -240,6 +247,17 @@ export const EditMappingsTableModal = ({
         }
         return error;
       })
+      .then(() =>
+        OntologyFilterCodeSubmit(
+          apiPreferencesCode,
+          preferenceType,
+          prefTypeKey,
+          mappingProp,
+          vocabUrl,
+          table
+        )
+      )
+
       .finally(() => setLoading(false));
   };
 
diff --git a/src/components/Projects/Terminologies/APIResults.jsx b/src/components/Projects/Terminologies/APIResults.jsx
index b881ce1..cf125c1 100644
--- a/src/components/Projects/Terminologies/APIResults.jsx
+++ b/src/components/Projects/Terminologies/APIResults.jsx
@@ -21,7 +21,7 @@ export const APIResults = ({
   This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
   Because the content is in a modal and not the window, the closest class name to the modal is used for the location of the ref. */
   useEffect(() => {
-    if (apiResults && apiPage > 0) {
+    if (apiResults && apiPage > 0 && ref.current) {
       const container = ref.current.closest('.ant-modal-body');
       const scrollTop = ref.current.offsetTop - container.offsetTop;
       container.scrollTop = scrollTop;
@@ -131,7 +131,7 @@ export const APIResults = ({
               Displaying {apiResultsCount}
               &nbsp;of&nbsp;{apiTotalCount}
             </Tooltip>
-            {apiTotalCount - filteredResultsCount !== apiResultsCount && (
+            {apiResultsCount < apiTotalCount - filteredResultsCount && (
               <span
                 className="view_more_link"
                 onClick={e => {
diff --git a/src/components/Projects/Terminologies/APISearchBar.jsx b/src/components/Projects/Terminologies/APISearchBar.jsx
index 51f672e..3e25c9c 100644
--- a/src/components/Projects/Terminologies/APISearchBar.jsx
+++ b/src/components/Projects/Terminologies/APISearchBar.jsx
@@ -22,7 +22,7 @@ export const APISearchBar = ({
     setApiTotalCount,
   } = useContext(SearchContext);
   const [inputValue, setInputValue] = useState(searchProp);
-  const entriesPerPage = 15;
+  const entriesPerPage = 2000;
   const [currentSearchProp, setCurrentSearchProp] = useState(searchProp);
   const [filteredResultsCount, setFilteredResultsCount] = useState(0);
 
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 0fa0fe5..73b635d 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -16,6 +16,10 @@ import { MappingReset } from '../../Manager/MappingsFunctions/MappingReset';
 import { ellipsisString, systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import {
+  OntologyFilterCodeSubmit,
+  OntologyFilterCodeSubmitTerm,
+} from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmit';
 
 export const EditMappingsModal = ({
   editMappings,
@@ -29,7 +33,12 @@ export const EditMappingsModal = ({
   const [termMappings, setTermMappings] = useState([]);
   const [options, setOptions] = useState([]);
   const { vocabUrl, setSelectedKey, user } = useContext(myContext);
-  const { setApiPreferencesCode } = useContext(SearchContext);
+  const {
+    apiPreferencesCode,
+    setApiPreferencesCode,
+    preferenceType,
+    prefTypeKey,
+  } = useContext(SearchContext);
   const [loading, setLoading] = useState(false);
   const [reset, setReset] = useState(false);
   const [mappingsForSearch, setMappingsForSearch] = useState([]);
@@ -148,6 +157,10 @@ export const EditMappingsModal = ({
     );
   };
 
+  const searchProp = editMappings?.display
+    ? editMappings.display
+    : editMappings?.code;
+
   // Function to send a PUT call to update the mappings.
   // Each mapping in the mappings array being edited is JSON.parsed and mappings are turned into objects in the mappings array.
   const updateMappings = values => {
@@ -242,8 +255,19 @@ export const EditMappingsModal = ({
         }
         return error;
       })
+      .then(() =>
+        OntologyFilterCodeSubmitTerm(
+          apiPreferencesCode,
+          preferenceType,
+          prefTypeKey,
+          searchProp,
+          vocabUrl,
+          terminology
+        )
+      )
       .finally(() => setLoading(false));
   };
+
   return (
     <Modal
       // since the code is passed through editMappings, the '!!' forces it to be evaluated as a boolean.
@@ -350,6 +374,7 @@ export const EditMappingsModal = ({
           searchProp={
             editMappings?.display ? editMappings.display : editMappings?.code
           }
+          mappingProp={editMappings?.code}
           mappingDesc={editMappings?.description}
           terminology={terminology}
         />
@@ -365,6 +390,7 @@ export const EditMappingsModal = ({
             reset={reset}
             onClose={form.resetFields}
             mappingDesc={editMappings?.description}
+            mappingProp={editMappings?.code}
             terminology={terminology}
           />
         )

From d389437ce7d707bc7253a5440ca74005ecdd2492 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 31 Oct 2024 14:07:02 -0500
Subject: [PATCH 086/180] Update deploy_alpha.yml --build-arg ENV=qa

---
 .github/workflows/deploy_alpha.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/deploy_alpha.yml b/.github/workflows/deploy_alpha.yml
index 7f9f7fe..fba3b58 100644
--- a/.github/workflows/deploy_alpha.yml
+++ b/.github/workflows/deploy_alpha.yml
@@ -51,7 +51,7 @@ jobs:
       - name: 'Build Docker Image' # New step to build the image
         run: |-
           DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
-          docker build -t "${DOCKER_TAG}" .
+          docker build -t "${DOCKER_TAG}" --build-arg ENV=alpha .
 
       - name: 'Push Docker Image'
         run: |-
@@ -63,4 +63,4 @@ jobs:
         with:
           service: '${{ env.SERVICE }}'
           region: '${{ env.REGION }}'
-          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
\ No newline at end of file
+          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"

From 5e50c946e95f0e14e779f2362a62758ebe321569 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 31 Oct 2024 14:09:17 -0500
Subject: [PATCH 087/180] Update package.json    "build-alpha": "vite build
 --mode alpha",

---
 package.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/package.json b/package.json
index 38334e7..efb9880 100644
--- a/package.json
+++ b/package.json
@@ -8,6 +8,7 @@
     "build": "vite build",
     "build-dev": "vite build --mode dev",
     "build-qa": "vite build --mode qa",
+    "build-alpha": "vite build --mode alpha",
     "lint": "eslint . --ext js,jsx --report-unused-disable-directives --max-warnings 0",
     "preview": "vite preview"
   },

From 2a9d58e7ffb1345b73c90f0cca98c793d129264f Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 31 Oct 2024 14:34:40 -0500
Subject: [PATCH 088/180] removed pack-lock

---
 package-lock.json | 5334 ---------------------------------------------
 1 file changed, 5334 deletions(-)
 delete mode 100644 package-lock.json

diff --git a/package-lock.json b/package-lock.json
deleted file mode 100644
index 419d30d..0000000
--- a/package-lock.json
+++ /dev/null
@@ -1,5334 +0,0 @@
-{
-  "name": "vocab-management-tool",
-  "version": "0.0.0",
-  "lockfileVersion": 3,
-  "requires": true,
-  "packages": {
-    "": {
-      "name": "vocab-management-tool",
-      "version": "0.0.0",
-      "dependencies": {
-        "@ant-design/icons": "^5.5.1",
-        "@react-oauth/google": "^0.12.1",
-        "antd": "^5.15.2",
-        "jwt-decode": "^4.0.0",
-        "papaparse": "^5.4.1",
-        "react": "^18.2.0",
-        "react-dom": "^18.2.0",
-        "react-router-dom": "^6.22.3",
-        "sass": "^1.72.0"
-      },
-      "devDependencies": {
-        "@types/react": "^18.2.64",
-        "@types/react-dom": "^18.2.21",
-        "@vitejs/plugin-react": "^4.2.1",
-        "eslint": "^8.57.0",
-        "eslint-plugin-react": "^7.34.0",
-        "eslint-plugin-react-hooks": "^4.6.0",
-        "eslint-plugin-react-refresh": "^0.4.5",
-        "vite": "^5.1.6"
-      }
-    },
-    "node_modules/@aashutoshrathi/word-wrap": {
-      "version": "1.2.6",
-      "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz",
-      "integrity": "sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==",
-      "dev": true,
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
-    "node_modules/@ampproject/remapping": {
-      "version": "2.3.0",
-      "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz",
-      "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==",
-      "dev": true,
-      "dependencies": {
-        "@jridgewell/gen-mapping": "^0.3.5",
-        "@jridgewell/trace-mapping": "^0.3.24"
-      },
-      "engines": {
-        "node": ">=6.0.0"
-      }
-    },
-    "node_modules/@ant-design/colors": {
-      "version": "7.1.0",
-      "resolved": "https://registry.npmjs.org/@ant-design/colors/-/colors-7.1.0.tgz",
-      "integrity": "sha512-MMoDGWn1y9LdQJQSHiCC20x3uZ3CwQnv9QMz6pCmJOrqdgM9YxsoVVY0wtrdXbmfSgnV0KNk6zi09NAhMR2jvg==",
-      "dependencies": {
-        "@ctrl/tinycolor": "^3.6.1"
-      }
-    },
-    "node_modules/@ant-design/cssinjs": {
-      "version": "1.21.0",
-      "resolved": "https://registry.npmjs.org/@ant-design/cssinjs/-/cssinjs-1.21.0.tgz",
-      "integrity": "sha512-gIilraPl+9EoKdYxnupxjHB/Q6IHNRjEXszKbDxZdsgv4sAZ9pjkCq8yanDWNvyfjp4leir2OVAJm0vxwKK8YA==",
-      "dependencies": {
-        "@babel/runtime": "^7.11.1",
-        "@emotion/hash": "^0.8.0",
-        "@emotion/unitless": "^0.7.5",
-        "classnames": "^2.3.1",
-        "csstype": "^3.1.3",
-        "rc-util": "^5.35.0",
-        "stylis": "^4.0.13"
-      },
-      "peerDependencies": {
-        "react": ">=16.0.0",
-        "react-dom": ">=16.0.0"
-      }
-    },
-    "node_modules/@ant-design/icons": {
-      "version": "5.5.1",
-      "resolved": "https://registry.npmjs.org/@ant-design/icons/-/icons-5.5.1.tgz",
-      "integrity": "sha512-0UrM02MA2iDIgvLatWrj6YTCYe0F/cwXvVE0E2SqGrL7PZireQwgEKTKBisWpZyal5eXZLvuM98kju6YtYne8w==",
-      "dependencies": {
-        "@ant-design/colors": "^7.0.0",
-        "@ant-design/icons-svg": "^4.4.0",
-        "@babel/runtime": "^7.24.8",
-        "classnames": "^2.2.6",
-        "rc-util": "^5.31.1"
-      },
-      "engines": {
-        "node": ">=8"
-      },
-      "peerDependencies": {
-        "react": ">=16.0.0",
-        "react-dom": ">=16.0.0"
-      }
-    },
-    "node_modules/@ant-design/icons-svg": {
-      "version": "4.4.2",
-      "resolved": "https://registry.npmjs.org/@ant-design/icons-svg/-/icons-svg-4.4.2.tgz",
-      "integrity": "sha512-vHbT+zJEVzllwP+CM+ul7reTEfBR0vgxFe7+lREAsAA7YGsYpboiq2sQNeQeRvh09GfQgs/GyFEvZpJ9cLXpXA=="
-    },
-    "node_modules/@ant-design/react-slick": {
-      "version": "1.1.2",
-      "resolved": "https://registry.npmjs.org/@ant-design/react-slick/-/react-slick-1.1.2.tgz",
-      "integrity": "sha512-EzlvzE6xQUBrZuuhSAFTdsr4P2bBBHGZwKFemEfq8gIGyIQCxalYfZW/T2ORbtQx5rU69o+WycP3exY/7T1hGA==",
-      "dependencies": {
-        "@babel/runtime": "^7.10.4",
-        "classnames": "^2.2.5",
-        "json2mq": "^0.2.0",
-        "resize-observer-polyfill": "^1.5.1",
-        "throttle-debounce": "^5.0.0"
-      },
-      "peerDependencies": {
-        "react": ">=16.9.0"
-      }
-    },
-    "node_modules/@babel/code-frame": {
-      "version": "7.23.5",
-      "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.5.tgz",
-      "integrity": "sha512-CgH3s1a96LipHCmSUmYFPwY7MNx8C3avkq7i4Wl3cfa662ldtUe4VM1TPXX70pfmrlWTb6jLqTYrZyT2ZTJBgA==",
-      "dev": true,
-      "dependencies": {
-        "@babel/highlight": "^7.23.4",
-        "chalk": "^2.4.2"
-      },
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/@babel/compat-data": {
-      "version": "7.23.5",
-      "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.23.5.tgz",
-      "integrity": "sha512-uU27kfDRlhfKl+w1U6vp16IuvSLtjAxdArVXPa9BvLkrr7CYIsxH5adpHObeAGY/41+syctUWOZ140a2Rvkgjw==",
-      "dev": true,
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/@babel/core": {
-      "version": "7.24.0",
-      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.24.0.tgz",
-      "integrity": "sha512-fQfkg0Gjkza3nf0c7/w6Xf34BW4YvzNfACRLmmb7XRLa6XHdR+K9AlJlxneFfWYf6uhOzuzZVTjF/8KfndZANw==",
-      "dev": true,
-      "dependencies": {
-        "@ampproject/remapping": "^2.2.0",
-        "@babel/code-frame": "^7.23.5",
-        "@babel/generator": "^7.23.6",
-        "@babel/helper-compilation-targets": "^7.23.6",
-        "@babel/helper-module-transforms": "^7.23.3",
-        "@babel/helpers": "^7.24.0",
-        "@babel/parser": "^7.24.0",
-        "@babel/template": "^7.24.0",
-        "@babel/traverse": "^7.24.0",
-        "@babel/types": "^7.24.0",
-        "convert-source-map": "^2.0.0",
-        "debug": "^4.1.0",
-        "gensync": "^1.0.0-beta.2",
-        "json5": "^2.2.3",
-        "semver": "^6.3.1"
-      },
-      "engines": {
-        "node": ">=6.9.0"
-      },
-      "funding": {
-        "type": "opencollective",
-        "url": "https://opencollective.com/babel"
-      }
-    },
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-      "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
-      "dev": true,
-      "dependencies": {
-        "isexe": "^2.0.0"
-      },
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-        "node-which": "bin/node-which"
-      },
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-        "node": ">= 8"
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-        "which-typed-array": "^1.1.9"
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-        "node": ">= 0.4"
-      },
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-        "for-each": "^0.3.3",
-        "gopd": "^1.0.1",
-        "has-tostringtag": "^1.0.2"
-      },
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-        "node": ">= 0.4"
-      },
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-      "dev": true
-    },
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-      "dev": true
-    },
-    "node_modules/yocto-queue": {
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-      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
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-      "dev": true,
-      "engines": {
-        "node": ">=10"
-      },
-      "funding": {
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-      }
-    }
-  }
-}

From 5371d3d7ebfee1cc59bc1c59d6ba062cb322547c Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 31 Oct 2024 14:41:41 -0500
Subject: [PATCH 089/180] Update package.json QUACK test

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index efb9880..d1c195e 100644
--- a/package.json
+++ b/package.json
@@ -7,7 +7,7 @@
     "dev": "vite",
     "build": "vite build",
     "build-dev": "vite build --mode dev",
-    "build-qa": "vite build --mode qa",
+    "build-qaack": "vite build --mode qa",
     "build-alpha": "vite build --mode alpha",
     "lint": "eslint . --ext js,jsx --report-unused-disable-directives --max-warnings 0",
     "preview": "vite preview"

From 99af65d982f741461e6748e0e994eb89c7de33b1 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 31 Oct 2024 14:43:47 -0500
Subject: [PATCH 090/180] Update package.json revert qauack

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index d1c195e..efb9880 100644
--- a/package.json
+++ b/package.json
@@ -7,7 +7,7 @@
     "dev": "vite",
     "build": "vite build",
     "build-dev": "vite build --mode dev",
-    "build-qaack": "vite build --mode qa",
+    "build-qa": "vite build --mode qa",
     "build-alpha": "vite build --mode alpha",
     "lint": "eslint . --ext js,jsx --report-unused-disable-directives --max-warnings 0",
     "preview": "vite preview"

From a59ddc74c462d1bb6d493514a669de2384e84f64 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 31 Oct 2024 14:47:31 -0500
Subject: [PATCH 091/180] Update deploy_alpha.yml removed ref release

---
 .github/workflows/deploy_alpha.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/deploy_alpha.yml b/.github/workflows/deploy_alpha.yml
index fba3b58..a0f7b96 100644
--- a/.github/workflows/deploy_alpha.yml
+++ b/.github/workflows/deploy_alpha.yml
@@ -30,8 +30,8 @@ jobs:
     steps:
       - name: 'Checkout'
         uses: 'actions/checkout@v4'
-        with:
-          ref: release # release is deployed, not the default or working branch
+        # with:
+        #   ref: release # release is deployed, not the default or working branch
         
       - id: 'auth'
         name: 'Authenticate to Google Cloud'

From f84a35fe99ce5bb5ea8d62392f7d4cfb9676441d Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 1 Nov 2024 09:36:29 -0500
Subject: [PATCH 092/180] Saving ontologies in MappingSearch

---
 src/components/Manager/FetchManager.jsx       | 14 +---
 .../MappingsFunctions/GetMappingsModal.jsx    | 42 +++++------
 .../MappingsFunctions/MappingSearch.jsx       |  1 -
 .../OntologyFilterCodeSubmit.jsx              | 54 ++------------
 .../OntologyFilterCodeSubmitTerm.jsx          | 73 +++++++++++++++++++
 .../Tables/EditMappingsTableModal.jsx         | 27 +++----
 .../Terminologies/EditMappingModal.jsx        | 25 +++----
 7 files changed, 123 insertions(+), 113 deletions(-)
 create mode 100644 src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx

diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index f358a31..bf9c11a 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -256,7 +256,10 @@ export const getFiltersByCode = (
       if (res.ok) {
         return res.json();
       } else {
-        throw new Error('An unknown error occurred.');
+        notification.error({
+          message: 'Error',
+          description: 'An error occurred loading the ontology preferences.',
+        });
       }
     })
     .then(data => {
@@ -271,14 +274,5 @@ export const getFiltersByCode = (
       } else {
         setApiPreferencesCode(''); // Fallback if no ols found
       }
-    })
-    .catch(error => {
-      if (error) {
-        notification.error({
-          message: 'Error',
-          description: 'An error occurred loading the ontology preferences.',
-        });
-      }
-      return error;
     });
 };
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 511d6d6..961b100 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -15,10 +15,8 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
-import {
-  OntologyFilterCodeSubmit,
-  OntologyFilterCodeSubmitTerm,
-} from './OntologyFilterCodeSubmit';
+import { OntologyFilterCodeSubmit } from './OntologyFilterCodeSubmit';
+import { OntologyFilterCodeSubmitTerm } from './OntologyFilterCodeSubmitTerm';
 import { useParams } from 'react-router-dom';
 
 export const GetMappingsModal = ({
@@ -181,26 +179,24 @@ export const GetMappingsModal = ({
         setGetMappings(null);
         message.success('Changes saved successfully.');
       })
-      .then(() =>
-        table
-          ? OntologyFilterCodeSubmit(
-              apiPreferencesCode,
-              preferenceType,
-              prefTypeKey,
-              mappingProp,
-              vocabUrl,
-              table
-            )
-          : OntologyFilterCodeSubmitTerm(
-              apiPreferencesCode,
-              preferenceType,
-              prefTypeKey,
-              searchProp,
-              vocabUrl,
-              terminology
-            )
-      )
       .finally(() => setLoading(false));
+    table
+      ? OntologyFilterCodeSubmit(
+          apiPreferencesCode,
+          preferenceType,
+          prefTypeKey,
+          mappingProp,
+          vocabUrl,
+          table
+        )
+      : OntologyFilterCodeSubmitTerm(
+          apiPreferencesCode,
+          preferenceType,
+          prefTypeKey,
+          searchProp,
+          vocabUrl,
+          terminology
+        );
   };
 
   const fetchResults = (page, query) => {
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 26b4589..fb58be7 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -186,7 +186,6 @@ export const MappingSearch = ({
         setFacetCounts
       );
   };
-
   // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
   const handleViewMore = e => {
     e.preventDefault();
diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
index 8e1b4d9..e1c0fc5 100644
--- a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmit.jsx
@@ -1,5 +1,4 @@
 import { notification } from 'antd';
-import { cleanedName } from '../Utilitiy';
 
 export const OntologyFilterCodeSubmit = (
   apiPreferencesCode,
@@ -12,60 +11,17 @@ export const OntologyFilterCodeSubmit = (
   const apiPreference = {
     api_preference: { 'ols': [] },
   };
-  if (
-    apiPreferencesCode &&
-    JSON.stringify(
-      Object.values(preferenceType[prefTypeKey]?.api_preference)[0]?.sort()
-    ) !== JSON.stringify(apiPreferencesCode?.sort())
-  ) {
-    apiPreference.api_preference.ols = apiPreferencesCode;
 
-    fetch(`${vocabUrl}/Table/${table.id}/filter/${mappingProp}`, {
-      method: 'POST',
-      headers: {
-        'Content-Type': 'application/json',
-      },
-      body: JSON.stringify(apiPreference),
-    })
-      .then(res => {
-        if (res.ok) {
-          return res.json();
-        } else {
-          throw new Error('An unknown error occurred.');
-        }
-      })
-      .catch(error => {
-        if (error) {
-          notification.error({
-            message: 'Error',
-            description: 'An error occurred saving the ontology preferences.',
-          });
-        }
-        return error;
-      });
-  }
-};
-
-export const OntologyFilterCodeSubmitTerm = (
-  apiPreferencesCode,
-  preferenceType,
-  prefTypeKey,
-  searchProp,
-  vocabUrl,
-  terminology
-) => {
-  const apiPreference = {
-    api_preference: { 'ols': [] },
-  };
   if (
     apiPreferencesCode &&
-    JSON.stringify(
-      Object.values(preferenceType[prefTypeKey]?.api_preference)[0]?.sort()
-    ) !== JSON.stringify(apiPreferencesCode?.sort())
+    (!preferenceType[prefTypeKey]?.api_preference?.[0] ||
+      JSON.stringify(
+        Object.values(preferenceType[prefTypeKey]?.api_preference)[0]?.sort()
+      ) !== JSON.stringify(apiPreferencesCode?.sort()))
   ) {
     apiPreference.api_preference.ols = apiPreferencesCode;
 
-    fetch(`${vocabUrl}/Terminology/${terminology.id}/filter/${searchProp}`, {
+    fetch(`${vocabUrl}/Table/${table.id}/filter/${mappingProp}`, {
       method: 'POST',
       headers: {
         'Content-Type': 'application/json',
diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx
new file mode 100644
index 0000000..748b97b
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx
@@ -0,0 +1,73 @@
+import { notification } from 'antd';
+
+export const OntologyFilterCodeSubmitTerm = (
+  apiPreferencesCode,
+  preferenceType,
+  prefTypeKey,
+  searchProp,
+  vocabUrl,
+  terminology
+) => {
+  const apiPreference = {
+    api_preference: { 'ols': [] },
+  };
+
+  if (
+    apiPreferencesCode &&
+    (!preferenceType[prefTypeKey]?.api_preference ||
+      JSON.stringify(
+        Object.values(preferenceType[prefTypeKey]?.api_preference)[0]?.sort()
+      ) !== JSON.stringify(apiPreferencesCode?.sort()))
+  ) {
+    apiPreference.api_preference.ols = apiPreferencesCode;
+
+    fetch(`${vocabUrl}/Terminology/${terminology.id}/filter/${searchProp}`, {
+      method: 'POST',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify(apiPreference),
+    })
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .catch(error => {
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred saving the ontology preferences.',
+          });
+        }
+      });
+  }
+};
+
+//   apiPreference.api_preference.ols = apiPreferencesCode;
+
+//       fetch(`${vocabUrl}/Terminology/${terminology.id}/filter/${searchProp}`, {
+//         method: 'POST',
+//         headers: {
+//           'Content-Type': 'application/json',
+//         },
+//         body: JSON.stringify(apiPreference),
+//       })
+//         .then(res => {
+//           if (res.ok) {
+//             return res.json();
+//           } else {
+//             throw new Error('An unknown error occurred.');
+//           }
+//         })
+//         .catch(error => {
+//           if (error) {
+//             notification.error({
+//               message: 'Error',
+//               description: 'An error occurred saving the ontology preferences.',
+//             });
+//           }
+//           return error;
+//         });
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index ca8b0d5..474d4f0 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -247,18 +247,15 @@ export const EditMappingsTableModal = ({
         }
         return error;
       })
-      .then(() =>
-        OntologyFilterCodeSubmit(
-          apiPreferencesCode,
-          preferenceType,
-          prefTypeKey,
-          mappingProp,
-          vocabUrl,
-          table
-        )
-      )
-
       .finally(() => setLoading(false));
+    OntologyFilterCodeSubmit(
+      apiPreferencesCode,
+      preferenceType,
+      prefTypeKey,
+      mappingProp,
+      vocabUrl,
+      table
+    );
   };
 
   return (
@@ -358,14 +355,14 @@ export const EditMappingsTableModal = ({
           form={form}
           reset={reset}
           onClose={form.resetFields}
-          searchProp={editMappings.name}
+          searchProp={editMappings?.name}
           mappingDesc={
-            editMappings.description
-              ? editMappings.description
+            editMappings?.description
+              ? editMappings?.description
               : 'No Description'
           }
           component={table}
-          mappingProp={editMappings.code}
+          mappingProp={editMappings?.code}
           table={table}
         />
       ) : (
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 73b635d..6fc4916 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -16,10 +16,7 @@ import { MappingReset } from '../../Manager/MappingsFunctions/MappingReset';
 import { ellipsisString, systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
-import {
-  OntologyFilterCodeSubmit,
-  OntologyFilterCodeSubmitTerm,
-} from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmit';
+import { OntologyFilterCodeSubmitTerm } from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm';
 
 export const EditMappingsModal = ({
   editMappings,
@@ -255,17 +252,15 @@ export const EditMappingsModal = ({
         }
         return error;
       })
-      .then(() =>
-        OntologyFilterCodeSubmitTerm(
-          apiPreferencesCode,
-          preferenceType,
-          prefTypeKey,
-          searchProp,
-          vocabUrl,
-          terminology
-        )
-      )
       .finally(() => setLoading(false));
+    OntologyFilterCodeSubmitTerm(
+      apiPreferencesCode,
+      preferenceType,
+      prefTypeKey,
+      searchProp,
+      vocabUrl,
+      terminology
+    );
   };
 
   return (
@@ -372,7 +367,7 @@ export const EditMappingsModal = ({
           reset={reset}
           onClose={form.resetFields}
           searchProp={
-            editMappings?.display ? editMappings.display : editMappings?.code
+            editMappings?.display ? editMappings?.display : editMappings?.code
           }
           mappingProp={editMappings?.code}
           mappingDesc={editMappings?.description}

From 09679f5b69c8926beff55f67c4ecc60d9188b769 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 1 Nov 2024 10:17:14 -0500
Subject: [PATCH 093/180] Changed entries per page for faster loading time

---
 src/components/Manager/MappingsFunctions/GetMappingsModal.jsx | 4 ++--
 src/components/Manager/MappingsFunctions/MappingReset.jsx     | 2 +-
 src/components/Manager/MappingsFunctions/MappingSearch.jsx    | 2 +-
 .../Manager/MappingsFunctions/OntologyCheckboxes.jsx          | 2 +-
 src/components/Projects/Terminologies/APISearchBar.jsx        | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 961b100..75c7849 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -45,7 +45,7 @@ export const GetMappingsModal = ({
     prefTypeKey,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
-  const entriesPerPage = 2000;
+  const entriesPerPage = 1000;
   const [loading, setLoading] = useState(false);
   const [results, setResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
@@ -460,7 +460,7 @@ export const GetMappingsModal = ({
                                           display: d.label,
                                           description: d.description[0],
                                           system: systemsMatch(
-                                            d?.obo_id.split(':')[0]
+                                            d?.obo_id?.split(':')[0]
                                           ),
                                         }),
                                         label: checkBoxDisplay(d, index),
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 15ca486..b8274ef 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -30,7 +30,7 @@ export const MappingReset = ({
     setUnformattedPref,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
-  const entriesPerPage = 2000;
+  const entriesPerPage = 1000;
   const [loading, setLoading] = useState(true);
   const [results, setResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index fb58be7..154f770 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -33,7 +33,7 @@ export const MappingSearch = ({
   const { tableId } = useParams();
 
   const [page, setPage] = useState(0);
-  const entriesPerPage = 2000;
+  const entriesPerPage = 1000;
   const [loading, setLoading] = useState(true);
   const [results, setResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 89e8662..0ad3168 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -78,7 +78,7 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
     return acc;
   }, {});
 
-  // // Build the new data structure
+  // Build the new data structure
   const countsResult = Object.keys(sortedData[0]?.ontologies).map(key => {
     return { [key]: countsMap[key] || 0, api: sortedData[0]?.api_id };
   });
diff --git a/src/components/Projects/Terminologies/APISearchBar.jsx b/src/components/Projects/Terminologies/APISearchBar.jsx
index 3e25c9c..05441dc 100644
--- a/src/components/Projects/Terminologies/APISearchBar.jsx
+++ b/src/components/Projects/Terminologies/APISearchBar.jsx
@@ -22,7 +22,7 @@ export const APISearchBar = ({
     setApiTotalCount,
   } = useContext(SearchContext);
   const [inputValue, setInputValue] = useState(searchProp);
-  const entriesPerPage = 2000;
+  const entriesPerPage = 1000;
   const [currentSearchProp, setCurrentSearchProp] = useState(searchProp);
   const [filteredResultsCount, setFilteredResultsCount] = useState(0);
 

From 44ce18e51ae9c9a09d6739a6c52ee97b187b0ca9 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 1 Nov 2024 10:54:12 -0500
Subject: [PATCH 094/180] removed console logs

---
 src/components/Manager/FetchManager.jsx        | 18 +++++++++++-------
 .../MappingsFunctions/GetMappingsModal.jsx     |  1 -
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index bf9c11a..307abe3 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -264,15 +264,19 @@ export const getFiltersByCode = (
     })
     .then(data => {
       setUnformattedPref(data);
+      const codeToSearch = Object.keys(data)?.[0];
 
-      // Dynamically derive the mappingProp based on a condition or the structure of the data
-      const codeToSearch = Object.keys(data)[0]; // Example: get the first key in the object
-      if (data?.[codeToSearch]?.api_preference?.ols) {
-        const joinedOntologies =
-          data[codeToSearch].api_preference.ols.join(',');
-        setApiPreferencesCode(joinedOntologies); // Set state to the comma-separated string
+      const ols = data?.[codeToSearch]?.api_preference?.ols;
+
+      if (Array.isArray(ols)) {
+        // If ols in api_preference is an array, use it as is
+        setApiPreferencesCode(ols); // Set state to the array
+      } else if (typeof ols === 'string') {
+        // If ols in api_preference is a string, split it into an array
+        const splitOntologies = ols.split(',');
+        setApiPreferencesCode(splitOntologies); // Set state to the array
       } else {
-        setApiPreferencesCode(''); // Fallback if no ols found
+        setApiPreferencesCode([]); // Fallback if no ols found
       }
     });
 };
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 75c7849..c7b5ffa 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -368,7 +368,6 @@ export const GetMappingsModal = ({
   };
 
   const filteredResultsArray = getFilteredResults();
-
   return (
     <>
       <Modal

From c8e7ae70bfdd6794fc62f19785cdd22dffd97ef1 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 1 Nov 2024 15:54:47 -0500
Subject: [PATCH 095/180] Search bar for selecting ontology filters for a
 Table/Terminology

---
 src/Contexts/SearchContext.jsx                   |  3 +++
 .../Manager/MappingsFunctions/FilterAPI.jsx      |  2 --
 .../Manager/MappingsFunctions/FilterOntology.jsx | 12 ++++++++++--
 .../Manager/MappingsFunctions/FilterSelect.jsx   | 16 +++++++++++-----
 .../MappingsFunctions/MappingsFunctions.scss     |  5 +++++
 5 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/src/Contexts/SearchContext.jsx b/src/Contexts/SearchContext.jsx
index ab17bb6..2de70e4 100644
--- a/src/Contexts/SearchContext.jsx
+++ b/src/Contexts/SearchContext.jsx
@@ -18,6 +18,7 @@ export function SearchContextRoot() {
   const [facetCounts, setFacetCounts] = useState([]);
   const [ontologyApis, setOntologyApis] = useState([]);
   const [apiPreferencesTerm, setApiPreferencesTerm] = useState(undefined);
+  const [searchText, setSearchText] = useState('');
 
   const defaultOntologies = 'mondo,hp,maxo,ncit';
   const preferenceTypeSet = data =>
@@ -63,6 +64,8 @@ export function SearchContextRoot() {
     preferenceTypeSet,
     preferenceType,
     prefTypeKey,
+    searchText,
+    setSearchText,
   };
 
   return (
diff --git a/src/components/Manager/MappingsFunctions/FilterAPI.jsx b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
index 538f2ea..281151a 100644
--- a/src/components/Manager/MappingsFunctions/FilterAPI.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterAPI.jsx
@@ -15,7 +15,6 @@ export const FilterAPI = ({
   ontologyApis,
   active,
   setActive,
-  searchText,
   currentPage,
   setCurrentPage,
   pageSize,
@@ -158,7 +157,6 @@ export const FilterAPI = ({
                   setSelectedBoxes={setSelectedBoxes}
                   displaySelectedOntologies={displaySelectedOntologies}
                   setDisplaySelectedOntologies={setDisplaySelectedOntologies}
-                  searchText={searchText}
                   currentPage={currentPage}
                   setCurrentPage={setCurrentPage}
                   pageSize={pageSize}
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 10e67c2..0b1da87 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -1,4 +1,4 @@
-import { Checkbox, Form } from 'antd';
+import { Checkbox, Form, Input } from 'antd';
 import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
 import { FilterReset } from './FilterReset';
@@ -16,9 +16,11 @@ export const FilterOntology = ({
   table,
   terminology,
 }) => {
+  const { Search } = Input;
   const [allCheckboxes, setAllCheckboxes] = useState([]);
   const { setOntologyForPagination } = useContext(myContext);
-  const { preferenceType, prefTypeKey } = useContext(SearchContext);
+  const { preferenceType, prefTypeKey, searchText, setSearchText } =
+    useContext(SearchContext);
 
   useEffect(() => {
     setOntologyForPagination(ontology);
@@ -155,6 +157,12 @@ export const FilterOntology = ({
   return (
     <>
       <div className="modal_checkbox_wrapper">
+        <Search
+          placeholder="Search ontologies"
+          className="api_onto_search_bar"
+          value={searchText}
+          onChange={e => setSearchText(e.target.value)}
+        />
         {Object.keys(preferenceType[prefTypeKey]?.api_preference || {}).some(
           key => preferenceType[prefTypeKey]?.api_preference[key]?.length > 0
         ) && (
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index cab3d55..8addb6d 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -31,8 +31,9 @@ export const FilterSelect = ({ component, table, terminology }) => {
     preferenceTypeSet,
     preferenceType,
     prefTypeKey,
+    searchText,
+    setSearchText,
   } = useContext(SearchContext);
-  const [searchText, setSearchText] = useState('');
 
   // Gets the ontologyAPIs on first load, automatically sets active to the first of the list to display on the page
   useEffect(() => {
@@ -72,6 +73,7 @@ export const FilterSelect = ({ component, table, terminology }) => {
     setSelectedOntologies([]);
     setSelectedBoxes([]);
     setDisplaySelectedOntologies([]);
+    setSearchText('');
   };
 
   // If the api doesn't exist in api_preference, creates an empty array for it
@@ -201,8 +203,9 @@ export const FilterSelect = ({ component, table, terminology }) => {
     apiPrefObject &&
     Object.values(apiPrefObject)?.reduce((acc, arr) => acc + arr.length, 0);
 
-  // Makes a set of ontologies to exclude from the list of available ones to select(excludes those that have already been selected)
-  // Converts the ontologies object into an array and filter based on the ontologiesToExclude
+  // Makes a set of ontologies to exclude from the list of available (excludes those that have already been selected)
+  // Converts the ontologies object into an array and filters based on the ontologiesToExclude
+  // Then filters that object based on the searchText in the search bar
   const filterOntologies = () => {
     if (ontologyForPagination) {
       const firstOntology = ontologyForPagination[0];
@@ -218,7 +221,10 @@ export const FilterSelect = ({ component, table, terminology }) => {
           }))
           .filter(obj => {
             return !ontologiesToExclude.has(obj.ontology_code);
-          });
+          })
+          .filter(item =>
+            item?.curie.toLowerCase().includes(searchText.toLowerCase())
+          );
 
         return filteredOntologies;
       }
@@ -227,7 +233,7 @@ export const FilterSelect = ({ component, table, terminology }) => {
 
   const filteredOntologiesArray = filterOntologies();
 
-  // // Pagination
+  // Pagination
   const paginatedOntologies = filteredOntologiesArray?.slice(
     (currentPage - 1) * pageSize,
     currentPage * pageSize
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index b24fc07..c573bfa 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -119,6 +119,11 @@
   margin-left: 11vw;
 }
 
+.api_onto_search_bar,
 .onto_search_bar {
   margin-bottom: 8px;
 }
+
+.api_onto_search_bar {
+  width: 400px;
+}

From 83d4f1085f472c7493075e03d8dde28c8f87bed9 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 4 Nov 2024 11:10:27 -0600
Subject: [PATCH 096/180] Hover to display code for mapped terms

---
 src/components/Projects/Tables/TableDetails.jsx  | 16 ++++++++++++++--
 .../Projects/Terminologies/Terminology.jsx       |  6 ++++--
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 1bd0320..cdf90b7 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -4,7 +4,16 @@ import './TableStyling.scss';
 import { Link, useNavigate, useParams } from 'react-router-dom';
 import { Spinner } from '../../Manager/Spinner';
 import { getById } from '../../Manager/FetchManager';
-import { Card, Col, Form, notification, Row, Table, Button } from 'antd';
+import {
+  Button,
+  Card,
+  Col,
+  Form,
+  notification,
+  Row,
+  Table,
+  Tooltip,
+} from 'antd';
 import { CloseCircleOutlined } from '@ant-design/icons';
 import { EditTableDetails } from './EditTableDetails';
 import { DeleteTable } from './DeleteTable';
@@ -252,7 +261,10 @@ It then shows the mappings as table data and alows the user to delete a mapping
     if (variableMappings && variableMappings.mappings?.length) {
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.display}>
-          <span className="mapping-display">{code.display}</span>
+          <span className="mapping-display">
+            {' '}
+            <Tooltip title={code.code}>{code.display}</Tooltip>
+          </span>
           <span
             className="remove-mapping"
             onClick={() => handleRemoveMapping(variableMappings, code)}
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index ca6e966..33824ba 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -4,7 +4,7 @@ import { myContext } from '../../../App';
 import './Terminology.scss';
 import { Spinner } from '../../Manager/Spinner';
 import { getById } from '../../Manager/FetchManager';
-import { Col, Form, notification, Row, Table, Button } from 'antd';
+import { Button, Col, Form, notification, Row, Table, Tooltip } from 'antd';
 import { CloseCircleOutlined } from '@ant-design/icons';
 import { EditMappingsModal } from './EditMappingModal';
 import { EditTerminologyDetails } from './EditTerminologyDetails';
@@ -137,7 +137,9 @@ It then shows the mappings as table data and alows the user to delete a mapping
     if (variableMappings && variableMappings.mappings?.length) {
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.display}>
-          <span className="mapping-display">{code.display}</span>
+          <span className="mapping-display">
+            <Tooltip title={code.code}>{code.display}</Tooltip>
+          </span>
           <span
             className="remove-mapping"
             onClick={() => handleRemoveMapping(variableMappings, code)}

From 9f5d552d2d89198d8fa5e99108f7173e6ac124fa Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 4 Nov 2024 11:31:47 -0600
Subject: [PATCH 097/180] Loading spinner stays on screen while results set in
 modal

---
 .../Manager/MappingsFunctions/GetMappingsModal.jsx       | 2 +-
 .../Manager/MappingsFunctions/MappingReset.jsx           | 9 ++-------
 .../Manager/MappingsFunctions/MappingSearch.jsx          | 2 +-
 3 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index c7b5ffa..f6e00dc 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -90,7 +90,7 @@ export const GetMappingsModal = ({
   }, [apiPreferencesCode, searchProp]);
 
   useEffect(() => {
-    if (!!currentSearchProp) {
+    if (!!currentSearchProp && apiPreferencesCode !== undefined) {
       fetchResults(page, currentSearchProp);
     }
   }, [page, currentSearchProp]);
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index b8274ef..de99925 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -80,7 +80,7 @@ export const MappingReset = ({
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the code and when the page changes.
   useEffect(() => {
-    if (!!currentSearchProp) {
+    if (!!currentSearchProp && apiPreferencesCode !== undefined) {
       fetchResults(page, currentSearchProp);
     }
   }, [page, currentSearchProp]);
@@ -354,12 +354,7 @@ export const MappingReset = ({
                           <Form.Item
                             name={['filtered_mappings']}
                             valuePropName="value"
-                            rules={[
-                              {
-                                required: true,
-                                message: 'Please make a selection.',
-                              },
-                            ]}
+                            rules={[{ required: false }]}
                           >
                             {filteredResultsArray?.length > 0 ? (
                               <Checkbox.Group
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 154f770..4fd6fe7 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -85,7 +85,7 @@ export const MappingSearch = ({
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the code and when the page changes.
   useEffect(() => {
-    if (!!currentSearchProp) {
+    if (!!currentSearchProp && apiPreferencesCode !== undefined) {
       fetchResults(page, currentSearchProp);
     }
   }, [page, currentSearchProp]);

From ce4061c8e70e4ffa7f86e7017caadefd138da6da Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 4 Nov 2024 13:57:34 -0600
Subject: [PATCH 098/180] Changed 'name' to 'short code' for studies

---
 .../Manager/MappingsFunctions/MappingReset.jsx  |  2 +-
 src/components/Projects/Studies/AddStudy.jsx    | 17 +++++++++--------
 .../Projects/Studies/EditStudyDetails.jsx       |  6 ++++--
 3 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index de99925..5d2d3ad 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -348,7 +348,7 @@ export const MappingReset = ({
                             ))}
                           </div>
                         </Form.Item>
-                      )}{' '}
+                      )}
                       {results?.length > 0 ? (
                         <>
                           <Form.Item
diff --git a/src/components/Projects/Studies/AddStudy.jsx b/src/components/Projects/Studies/AddStudy.jsx
index 23422c5..df32bbc 100644
--- a/src/components/Projects/Studies/AddStudy.jsx
+++ b/src/components/Projects/Studies/AddStudy.jsx
@@ -9,6 +9,7 @@ export const AddStudy = ({ addStudy, setAddStudy }) => {
   const [loading, setLoading] = useState(false);
   const [form] = Form.useForm();
   const { vocabUrl, setStudy } = useContext(myContext);
+  const { TextArea } = Input;
 
   const navigate = useNavigate();
   // Submit function for adding a new study.
@@ -75,19 +76,12 @@ export const AddStudy = ({ addStudy, setAddStudy }) => {
           <h2>Create Study</h2>
           <Form.Item
             name="name"
-            label="Name"
+            label="Name / Short Code"
             rules={[{ required: true, message: 'Please input Study name.' }]}
           >
             <Input />
           </Form.Item>
 
-          <Form.Item
-            name="description"
-            label="Description"
-            rules={[{ required: false }]}
-          >
-            <Input />
-          </Form.Item>
           <Form.Item
             name="title"
             label="Title"
@@ -95,6 +89,13 @@ export const AddStudy = ({ addStudy, setAddStudy }) => {
           >
             <Input />
           </Form.Item>
+          <Form.Item
+            name="description"
+            label="Description"
+            rules={[{ required: false }]}
+          >
+            <TextArea />
+          </Form.Item>
           <Form.Item
             name="identifier_prefix"
             label="Identifier Prefix"
diff --git a/src/components/Projects/Studies/EditStudyDetails.jsx b/src/components/Projects/Studies/EditStudyDetails.jsx
index ba11754..a2360b5 100644
--- a/src/components/Projects/Studies/EditStudyDetails.jsx
+++ b/src/components/Projects/Studies/EditStudyDetails.jsx
@@ -7,6 +7,8 @@ import { myContext } from '../../../App';
 export const EditStudyDetails = ({ form, study, setStudy, edit, setEdit }) => {
   const [loading, setLoading] = useState(false);
   const { vocabUrl } = useContext(myContext);
+  const { TextArea } = Input;
+
   // Sets the initial values displayed in the form and esnures they are current
   const changeHandler = () => {
     form.setFieldsValue({
@@ -66,7 +68,7 @@ export const EditStudyDetails = ({ form, study, setStudy, edit, setEdit }) => {
             <h2>{study.name ? study.name : study.id}</h2>
             <Form.Item
               name="name"
-              label="Name"
+              label="Name / Short Code"
               rules={[{ required: true, message: 'Please input Study name.' }]}
             >
               <Input />
@@ -83,7 +85,7 @@ export const EditStudyDetails = ({ form, study, setStudy, edit, setEdit }) => {
               label="Description"
               rules={[{ required: false }]}
             >
-              <Input />
+              <TextArea />
             </Form.Item>
             <Form.Item
               name="url"

From e92c5172708c675ccaa9869b9547bb5cb74f8e12 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 4 Nov 2024 21:14:19 -0600
Subject: [PATCH 099/180] committing to switch branches

---
 .../MappingsFunctions/GetMappingsModal.jsx       | 15 ++++++++++++---
 .../Manager/MappingsFunctions/MappingReset.jsx   | 15 ++++++++++-----
 .../Manager/MappingsFunctions/MappingSearch.jsx  | 16 ++++++++++------
 3 files changed, 32 insertions(+), 14 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index f6e00dc..91f1998 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -86,14 +86,23 @@ export const GetMappingsModal = ({
   }, [searchProp]);
 
   useEffect(() => {
-    if (apiPreferencesCode !== undefined) fetchResults(0, searchProp);
-  }, [apiPreferencesCode, searchProp]);
+    if (apiPreferencesCode !== undefined) {
+      fetchResults(0, searchProp);
+    }
+  }, [searchProp]);
+
+  useEffect(() => {
+    fetchResults(page, currentSearchProp);
+  }, [page]);
 
+  // The '!!' forces currentSearchProp to be evaluated as a boolean.
+  // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
+  // The function is run when the query changes and when the preferred ontology changes.
   useEffect(() => {
     if (!!currentSearchProp && apiPreferencesCode !== undefined) {
       fetchResults(page, currentSearchProp);
     }
-  }, [page, currentSearchProp]);
+  }, [currentSearchProp, apiPreferencesCode]);
 
   /* Pagination is handled via a "View More" link at the bottom of the page. 
   Each click on the "View More" link makes an API call to fetch the next 15 results.
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 5d2d3ad..c527a03 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -7,7 +7,6 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
-import { useParams } from 'react-router-dom';
 
 export const MappingReset = ({
   searchProp,
@@ -73,17 +72,23 @@ export const MappingReset = ({
   }, [searchProp]);
 
   useEffect(() => {
-    if (apiPreferencesCode !== undefined) fetchResults(0, searchProp);
-  }, [apiPreferencesCode, searchProp]);
+    if (apiPreferencesCode !== undefined) {
+      fetchResults(0, searchProp);
+    }
+  }, [searchProp]);
+
+  useEffect(() => {
+    fetchResults(page, currentSearchProp);
+  }, [page]);
 
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
-  // The function is run when the code and when the page changes.
+  // The function is run when the query changes and when the preferred ontology changes.
   useEffect(() => {
     if (!!currentSearchProp && apiPreferencesCode !== undefined) {
       fetchResults(page, currentSearchProp);
     }
-  }, [page, currentSearchProp]);
+  }, [currentSearchProp, apiPreferencesCode]);
 
   /* Pagination is handled via a "View More" link at the bottom of the page. 
   Each click on the "View More" link makes an API call to fetch the next 15 results.
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 4fd6fe7..c5db61e 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -7,7 +7,6 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
-import { useParams } from 'react-router-dom';
 
 export const MappingSearch = ({
   setEditMappings,
@@ -30,7 +29,6 @@ export const MappingSearch = ({
     apiPreferencesCode,
     setUnformattedPref,
   } = useContext(SearchContext);
-  const { tableId } = useParams();
 
   const [page, setPage] = useState(0);
   const entriesPerPage = 1000;
@@ -78,17 +76,23 @@ export const MappingSearch = ({
   }, [searchProp]);
 
   useEffect(() => {
-    if (apiPreferencesCode !== undefined) fetchResults(0, searchProp);
-  }, [apiPreferencesCode, searchProp]);
+    if (apiPreferencesCode !== undefined) {
+      fetchResults(0, searchProp);
+    }
+  }, [searchProp]);
+
+  useEffect(() => {
+    fetchResults(page, currentSearchProp);
+  }, [page]);
 
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
-  // The function is run when the code and when the page changes.
+  // The function is run when the query changes and when the preferred ontology changes.
   useEffect(() => {
     if (!!currentSearchProp && apiPreferencesCode !== undefined) {
       fetchResults(page, currentSearchProp);
     }
-  }, [page, currentSearchProp]);
+  }, [currentSearchProp, apiPreferencesCode]);
 
   /* Pagination is handled via a "View More" link at the bottom of the page. 
   Each click on the "View More" link makes an API call to fetch the next 15 results.

From 402d8c0fcb66d8759e02296079aeefb0174ef114 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 5 Nov 2024 10:53:55 -0600
Subject: [PATCH 100/180] Corrected error with original query being search on
 ontology change

---
 .../MappingsFunctions/MappingReset.jsx        |  4 ++-
 .../MappingsFunctions/MappingSearch.jsx       |  4 ++-
 .../MappingsFunctions/MappingsFunctions.scss  | 28 +++++++++----------
 3 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index c527a03..c17c002 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -78,7 +78,9 @@ export const MappingReset = ({
   }, [searchProp]);
 
   useEffect(() => {
-    fetchResults(page, currentSearchProp);
+    if (apiPreferencesCode !== undefined) {
+      fetchResults(page, currentSearchProp);
+    }
   }, [page]);
 
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index c5db61e..441e227 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -82,7 +82,9 @@ export const MappingSearch = ({
   }, [searchProp]);
 
   useEffect(() => {
-    fetchResults(page, currentSearchProp);
+    if (apiPreferencesCode !== undefined) {
+      fetchResults(page, currentSearchProp);
+    }
   }, [page]);
 
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index c573bfa..32c00d8 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -5,20 +5,6 @@
   top: 25vh;
 }
 
-.all_checkboxes_container {
-  display: flex;
-  flex-direction: row;
-}
-.ontology_form {
-  width: 10.5vw;
-  height: 50vh;
-  overflow: auto;
-  position: fixed;
-}
-.result_form {
-  margin-left: 11vw;
-}
-
 .modal_search_results_header {
   background-color: white;
   top: 0;
@@ -46,6 +32,20 @@
   }
 }
 
+.all_checkboxes_container {
+  display: flex;
+  flex-direction: row;
+}
+.ontology_form {
+  width: 10.5vw;
+  height: 50vh;
+  overflow: auto;
+  position: fixed;
+}
+.result_form {
+  margin-left: 11vw;
+}
+
 .inactive_term,
 .active_term {
   padding: 10px;

From d4f12528b09ad85ebba56173998ee78ae8b76a68 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 5 Nov 2024 12:17:34 -0600
Subject: [PATCH 101/180] Fixed issue with header not sticking in MappingReset

---
 .../MappingsFunctions/GetMappingsModal.jsx    |   4 +-
 .../MappingsFunctions/MappingReset.jsx        | 160 +++++++++---------
 .../MappingsFunctions/OntologyCheckboxes.jsx  |   1 +
 3 files changed, 84 insertions(+), 81 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 91f1998..57e0407 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -92,7 +92,9 @@ export const GetMappingsModal = ({
   }, [searchProp]);
 
   useEffect(() => {
-    fetchResults(page, currentSearchProp);
+    if (apiPreferencesCode !== undefined) {
+      fetchResults(page, currentSearchProp);
+    }
   }, [page]);
 
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index c17c002..9205451 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -327,96 +327,96 @@ export const MappingReset = ({
                   </div>
                   <span className="search-desc">{mappingDesc}</span>
                 </div>
-              </div>
-              {/* ant.design form displaying the checkboxes with the search results.  */}
-              <div className="result_container">
-                <Form form={form} layout="vertical" preserve={false}>
-                  <div className="all_checkboxes_container">
-                    <OntologyCheckboxes apiPreferences={apiPreferences} />
-                    <div className="result_form">
-                      {displaySelectedMappings?.length > 0 && (
-                        <Form.Item
-                          name="selected_mappings"
-                          valuePropName="value"
-                          rules={[{ required: false }]}
-                        >
-                          <div className="modal_display_results">
-                            {displaySelectedMappings?.map((sm, i) => (
-                              <Checkbox
-                                key={i}
-                                onChange={e => onCheckboxChange(e, sm)}
-                                checked={selectedBoxes.some(
-                                  box => box.obo_id === sm.obo_id
-                                )}
-                                value={sm}
-                              >
-                                {selectedTermsDisplay(sm, i)}
-                              </Checkbox>
-                            ))}
-                          </div>
-                        </Form.Item>
-                      )}
-                      {results?.length > 0 ? (
-                        <>
+                {/* ant.design form displaying the checkboxes with the search results.  */}
+                <div className="result_container">
+                  <Form form={form} layout="vertical" preserve={false}>
+                    <div className="all_checkboxes_container">
+                      <OntologyCheckboxes apiPreferences={apiPreferences} />
+                      <div className="result_form">
+                        {displaySelectedMappings?.length > 0 && (
                           <Form.Item
-                            name={['filtered_mappings']}
+                            name="selected_mappings"
                             valuePropName="value"
                             rules={[{ required: false }]}
                           >
-                            {filteredResultsArray?.length > 0 ? (
-                              <Checkbox.Group
-                                className="mappings_checkbox"
-                                options={filteredResultsArray?.map(
-                                  (d, index) => {
-                                    return {
-                                      value: JSON.stringify({
-                                        code: d.obo_id,
-                                        display: d.label,
-                                        // description: d.description[0],
-                                        system: systemsMatch(
-                                          d?.obo_id?.split(':')[0]
-                                        ),
-                                      }),
-                                      label: checkBoxDisplay(d, index),
-                                    };
-                                  }
-                                )}
-                                onChange={onSelectedChange}
-                              />
-                            ) : (
-                              ''
-                            )}
+                            <div className="modal_display_results">
+                              {displaySelectedMappings?.map((sm, i) => (
+                                <Checkbox
+                                  key={i}
+                                  onChange={e => onCheckboxChange(e, sm)}
+                                  checked={selectedBoxes.some(
+                                    box => box.obo_id === sm.obo_id
+                                  )}
+                                  value={sm}
+                                >
+                                  {selectedTermsDisplay(sm, i)}
+                                </Checkbox>
+                              ))}
+                            </div>
                           </Form.Item>
-                        </>
-                      ) : (
-                        <h3>No results found</h3>
-                      )}
+                        )}
+                        {results?.length > 0 ? (
+                          <>
+                            <Form.Item
+                              name={['filtered_mappings']}
+                              valuePropName="value"
+                              rules={[{ required: false }]}
+                            >
+                              {filteredResultsArray?.length > 0 ? (
+                                <Checkbox.Group
+                                  className="mappings_checkbox"
+                                  options={filteredResultsArray?.map(
+                                    (d, index) => {
+                                      return {
+                                        value: JSON.stringify({
+                                          code: d.obo_id,
+                                          display: d.label,
+                                          // description: d.description[0],
+                                          system: systemsMatch(
+                                            d?.obo_id?.split(':')[0]
+                                          ),
+                                        }),
+                                        label: checkBoxDisplay(d, index),
+                                      };
+                                    }
+                                  )}
+                                  onChange={onSelectedChange}
+                                />
+                              ) : (
+                                ''
+                              )}
+                            </Form.Item>
+                          </>
+                        ) : (
+                          <h3>No results found</h3>
+                        )}
+                      </div>
                     </div>
-                  </div>
-                </Form>
-                <div className="view_more_wrapper">
-                  {/* 'View More' pagination displaying the number of results being displayed
+                  </Form>
+                  <div className="view_more_wrapper">
+                    {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
                       inconsistencies in results numbers per page. */}
-                  <Tooltip
-                    placement="bottom"
-                    title="Redundant entries have been removed"
-                  >
-                    Displaying {resultsCount}
-                    &nbsp;of&nbsp;{totalCount}
-                  </Tooltip>
-                  {resultsCount < totalCount - filteredResultsCount && (
-                    <span
-                      className="view_more_link"
-                      onClick={e => {
-                        handleViewMore(e);
-                        setLastCount(resultsCount);
-                      }}
+                    <Tooltip
+                      placement="bottom"
+                      title="Redundant entries have been removed"
                     >
-                      View More
-                    </span>
-                  )}
+                      Displaying {resultsCount}
+                      &nbsp;of&nbsp;{totalCount}
+                    </Tooltip>
+                    {resultsCount < totalCount - filteredResultsCount && (
+                      <span
+                        className="view_more_link"
+                        onClick={e => {
+                          handleViewMore(e);
+                          setLastCount(resultsCount);
+                        }}
+                      >
+                        View More
+                      </span>
+                    )}
+                  </div>
                 </div>
               </div>
             </>
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 0ad3168..d304944 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -2,6 +2,7 @@ import { Checkbox, Form, Input } from 'antd';
 import { ontologyCounts } from '../Utilitiy';
 import { useContext, useEffect, useState } from 'react';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import './MappingsFunctions.scss';
 
 export const OntologyCheckboxes = ({ preferenceType }) => {
   const {

From 9159ac0f6f0f6db76139828bb621a42a0d8ddde4 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 5 Nov 2024 14:15:52 -0600
Subject: [PATCH 102/180] Sorting preferred ontologies to the top of ontology
 display box

---
 .../MappingsFunctions/OntologyCheckboxes.jsx     | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index d304944..c2430dd 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -112,8 +112,20 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
         <div className="modal_display_results">
           {getFilteredItems(searchText)
             ?.sort((a, b) => {
-              const aValue = Object.values(a)[0];
-              const bValue = Object.values(b)[0];
+              const aKey = Object.keys(a)[0]; // gets the key from the first object in array
+              const bKey = Object.keys(b)[0]; // gets the key from the second object in array
+              const aValue = a[aKey]; // gets the value from the first key
+              const bValue = b[bKey]; // gets the value from the second key
+
+              // checks if one or both keys are in apiPreferencesCode
+              const aInPreferences = apiPreferencesCode?.includes(aKey);
+              const bInPreferences = apiPreferencesCode?.includes(bKey);
+
+              // If one of them is in apiPreferencesCode and the other isn't, prioritizes the one in apiPreferencesCode
+              if (aInPreferences && !bInPreferences) return -1; // if a is in apiPreferencesCode, it comes before b
+              if (!aInPreferences && bInPreferences) return 1; //if b is in apiPreferencesCode, it comes before a
+
+              // If both are in apiPreferencesCode or both are not, sorts by value
               return bValue - aValue;
             })
             .map((fc, i) => {

From 1edf6699fc5d8eb0bee8c682b8b860f0e35634dd Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 5 Nov 2024 20:10:45 -0600
Subject: [PATCH 103/180] added dividers to mappings modals

---
 .../Manager/MappingsFunctions/MappingSearch.jsx  |  3 +--
 .../MappingsFunctions/MappingsFunctions.scss     |  4 ++++
 src/components/Projects/Tables/TableDetails.jsx  | 16 ++--------------
 .../Projects/Terminologies/Terminology.jsx       | 13 +++++++++++--
 .../Projects/Terminologies/Terminology.scss      |  1 +
 5 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 441e227..f719af9 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -407,7 +407,7 @@ export const MappingSearch = ({
                         >
                           {mappingsForSearch?.length > 0 && (
                             <Checkbox.Group
-                              className="mappings_checkbox"
+                              className="mappings_checkbox existing_display"
                               options={mappingsForSearch?.map((d, index) => {
                                 return {
                                   value: JSON.stringify({
@@ -429,7 +429,6 @@ export const MappingSearch = ({
                             valuePropName="value"
                             rules={[{ required: false }]}
                           >
-                            {' '}
                             <div className="modal_display_results">
                               {displaySelectedMappings?.map((sm, i) => (
                                 <Checkbox
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index 32c00d8..35ddb0f 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -127,3 +127,7 @@
 .api_onto_search_bar {
   width: 400px;
 }
+
+.existing_display {
+  border-bottom: solid 1px #eeee;
+}
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index cdf90b7..2041bae 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -9,6 +9,7 @@ import {
   Card,
   Col,
   Form,
+  message,
   notification,
   Row,
   Table,
@@ -93,7 +94,7 @@ export const TableDetails = () => {
         setMapping(data.codes);
         setEditMappings(null);
         form.resetFields();
-        notification.success({ description: 'Mapping removed.' });
+        message.success('Mapping removed.');
       })
       .catch(error => {
         console.log(error, 'error');
@@ -109,19 +110,6 @@ export const TableDetails = () => {
       .finally(() => setLoading(false));
   };
 
-  const alphabetizeOntologies = ontologies => {
-    // Sort the keys alphabetically
-    const sortedKeys = Object.keys(ontologies).sort();
-
-    // Rebuild object using the sorted keys
-    const sortedOntologies = {};
-    sortedKeys.forEach(key => {
-      sortedOntologies[key] = ontologies[key];
-    });
-
-    return sortedOntologies;
-  };
-
   // fetches the table and sets 'table' to the response
   useEffect(() => {
     setLoading(true);
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 33824ba..629a289 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -4,7 +4,16 @@ import { myContext } from '../../../App';
 import './Terminology.scss';
 import { Spinner } from '../../Manager/Spinner';
 import { getById } from '../../Manager/FetchManager';
-import { Button, Col, Form, notification, Row, Table, Tooltip } from 'antd';
+import {
+  Button,
+  Col,
+  Form,
+  message,
+  notification,
+  Row,
+  Table,
+  Tooltip,
+} from 'antd';
 import { CloseCircleOutlined } from '@ant-design/icons';
 import { EditMappingsModal } from './EditMappingModal';
 import { EditTerminologyDetails } from './EditTerminologyDetails';
@@ -88,7 +97,7 @@ export const Terminology = () => {
         setMapping(data.codes);
         setEditMappings(null);
         form.resetFields();
-        notification.success({ description: 'Mapping removed.' });
+        message.success('Mapping removed.');
       })
       .catch(error => {
         console.log(error, 'error');
diff --git a/src/components/Projects/Terminologies/Terminology.scss b/src/components/Projects/Terminologies/Terminology.scss
index ca3ad43..0953ec4 100644
--- a/src/components/Projects/Terminologies/Terminology.scss
+++ b/src/components/Projects/Terminologies/Terminology.scss
@@ -101,6 +101,7 @@
 .modal_display_results {
   display: flex;
   flex-direction: column;
+  border-bottom: solid 1px #eeee;
 }
 .modal_display_result {
   margin: 0 0 10px 0;

From e4b59a0f71d668ebcc4c79e2c4d1ed3e26891606 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 6 Nov 2024 15:36:44 -0600
Subject: [PATCH 104/180] Created about page and added version number to it

---
 src/AppRouter.jsx                             | 24 ++++++--
 src/components/About/About.jsx                | 55 +++++++++++++++++++
 src/components/About/About.scss               |  3 +
 src/components/Manager/FetchManager.jsx       |  6 +-
 .../MappingsFunctions/FilterOntology.jsx      |  4 +-
 .../MappingsFunctions/GetMappingsModal.jsx    |  7 +--
 .../MappingsFunctions/MappingReset.jsx        |  5 +-
 .../MappingsFunctions/MappingSearch.jsx       |  5 +-
 src/components/Nav/NavBar.jsx                 |  4 +-
 .../{About => Ontologies}/OntologyAPIs.jsx    |  2 +-
 .../{About => Ontologies}/OntologyInfo.scss   |  0
 .../{About => Ontologies}/OntologyTable.jsx   |  0
 12 files changed, 92 insertions(+), 23 deletions(-)
 create mode 100644 src/components/About/About.jsx
 create mode 100644 src/components/About/About.scss
 rename src/components/{About => Ontologies}/OntologyAPIs.jsx (98%)
 rename src/components/{About => Ontologies}/OntologyInfo.scss (100%)
 rename src/components/{About => Ontologies}/OntologyTable.jsx (100%)

diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index 1ca5075..6db2e0c 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -1,5 +1,11 @@
 import { OntologySearch } from './components/Search/OntologySearch';
-import { BrowserRouter, Outlet, Route, Routes, Navigate } from 'react-router-dom';
+import {
+  BrowserRouter,
+  Outlet,
+  Route,
+  Routes,
+  Navigate,
+} from 'react-router-dom';
 import { NavBar } from './components/Nav/NavBar';
 import { Breadcrumbs } from './components/Nav/Breadcrumbs.jsx';
 import { Footer } from './components/Nav/Footer';
@@ -14,9 +20,10 @@ import './App.scss';
 import { PageLayout } from './components/Styling/PageLayout.jsx';
 import { MappingContextRoot } from './Contexts/MappingContext.jsx';
 import { Error404 } from './components/Error/Error404';
-import { OntologyInfo } from './components/About/OntologyAPIs';
+import { OntologyInfo } from './components/Ontologies/OntologyAPIs.jsx';
 import { TerminologyList } from './components/Projects/Terminologies/TerminologyList';
 import { SearchContextRoot } from './Contexts/SearchContext.jsx';
+import { About } from './components/About/About.jsx';
 
 export const AppRouter = () => {
   return (
@@ -41,9 +48,13 @@ export const AppRouter = () => {
           <Route element={<PageLayout />}>
             <Route path="/search/:query" element={<SearchResults />} />
             <Route path="/404" element={<Error404 />} />
-            <Route path="/about" element={<OntologyInfo />} />
+            <Route path="/ontologies" element={<OntologyInfo />} />
+            <Route path="/about" element={<About />} />
             <Route path="/terminologies" element={<TerminologyList />} />
-            <Route path="/terminology" element={<Navigate to="/terminologies" />} />
+            <Route
+              path="/terminology"
+              element={<Navigate to="/terminologies" />}
+            />
             <Route element={<MappingContextRoot />}>
               <Route element={<SearchContextRoot />}>
                 <Route path="/studies" element={<StudyList />} />
@@ -66,7 +77,10 @@ export const AppRouter = () => {
                         path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/:terminologyId"
                         element={<Terminology />}
                       />
-                      <Route path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/" element={<Terminology />} />
+                      <Route
+                        path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/"
+                        element={<Terminology />}
+                      />
                     </Route>
                   </Route>
                 </Route>
diff --git a/src/components/About/About.jsx b/src/components/About/About.jsx
new file mode 100644
index 0000000..c93fab4
--- /dev/null
+++ b/src/components/About/About.jsx
@@ -0,0 +1,55 @@
+import { useContext, useEffect, useState } from 'react';
+import { Descriptions, notification, Spin } from 'antd';
+import { getAll } from '../Manager/FetchManager';
+import { myContext } from '../../App';
+import { useNavigate } from 'react-router-dom';
+import { Spinner } from '../Manager/Spinner';
+import './About.scss';
+
+export const About = () => {
+  const { vocabUrl } = useContext(myContext);
+  const navigate = useNavigate();
+  const [loading, setLoading] = useState(true);
+  const [version, setVersion] = useState({});
+
+  useEffect(() => {
+    setLoading(true);
+    getAll(vocabUrl, 'version', navigate)
+      .then(data => setVersion(data))
+      .catch(error => {
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred. Please try again.',
+          });
+        }
+        return error;
+      })
+      .finally(() => setLoading(false));
+  }, []);
+
+  const items = [
+    {
+      key: '1',
+      label: 'Version',
+      children: `${version?.version}`,
+      labelStyle: { width: '150px' },
+      contentStyle: { width: '150px' },
+    },
+  ];
+
+  return (
+    <>
+      {loading ? (
+        <Spinner />
+      ) : (
+        <div className="studies_container">
+          <h2>About</h2>
+          <div className="about_description">
+            <Descriptions title="Version" bordered items={items} />
+          </div>
+        </div>
+      )}
+    </>
+  );
+};
diff --git a/src/components/About/About.scss b/src/components/About/About.scss
new file mode 100644
index 0000000..8377e8e
--- /dev/null
+++ b/src/components/About/About.scss
@@ -0,0 +1,3 @@
+.about_description {
+  width: 500px;
+}
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 307abe3..e6f2eb6 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -184,7 +184,6 @@ export const olsFilterOntologiesSearch = (
   results,
   setFacetCounts
 ) => {
-  setLoading(true);
   return fetch(
     `${searchUrl}q=${query}&ontology=${ontologiesToSearch}&rows=${entriesPerPage}&start=${pageStart}`,
     {
@@ -231,14 +230,15 @@ export const olsFilterOntologiesSearch = (
 
 export const getFiltersByCode = (
   vocabUrl,
-  component,
   mappingProp,
   setApiPreferencesCode,
   notification,
   setUnformattedPref,
   table,
-  terminology
+  terminology,
+  setLoading
 ) => {
+  setLoading(true);
   return fetch(
     `${vocabUrl}/${
       table
diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 0b1da87..595e074 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -60,7 +60,7 @@ export const FilterOntology = ({
   const onSelectedChange = checkedValues => {
     if (checkedValues.length > 0) {
       const selected = JSON.parse(checkedValues[0]);
-      const selectedOntology = ontologyForCheckboxes().find(
+      const selectedOntology = allCheckboxes?.find(
         item => item.ontology_code === selected.ontology
       );
 
@@ -80,7 +80,7 @@ export const FilterOntology = ({
       ]);
 
       // Filters out the selected ontologies from the available ones
-      const updatedOntologies = ontologyForCheckboxes().filter(
+      const updatedOntologies = allCheckboxes?.filter(
         ont => ont.ontology_code !== selected.ontology
       );
       setOntologiesForSelection(updatedOntologies);
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 57e0407..123a761 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -41,12 +41,11 @@ export const GetMappingsModal = ({
     setApiPreferencesCode,
     apiPreferencesCode,
     setUnformattedPref,
-    preferenceTypeSet,
     prefTypeKey,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 1000;
-  const [loading, setLoading] = useState(false);
+  const [loading, setLoading] = useState(true);
   const [results, setResults] = useState([]);
   const [totalCount, setTotalCount] = useState();
   const [resultsCount, setResultsCount] = useState();
@@ -74,13 +73,13 @@ export const GetMappingsModal = ({
     if (!!searchProp) {
       getFiltersByCode(
         vocabUrl,
-        component,
         mappingProp,
         setApiPreferencesCode,
         notification,
         setUnformattedPref,
         table,
-        terminology
+        terminology,
+        setLoading
       );
     }
   }, [searchProp]);
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 9205451..1d5772c 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -14,7 +14,6 @@ export const MappingReset = ({
   setEditMappings,
   form,
   onClose,
-  component,
   mappingProp,
   table,
   terminology,
@@ -60,13 +59,13 @@ export const MappingReset = ({
     if (!!searchProp) {
       getFiltersByCode(
         vocabUrl,
-        component,
         mappingProp,
         setApiPreferencesCode,
         notification,
         setUnformattedPref,
         table,
-        terminology
+        terminology,
+        setLoading
       );
     }
   }, [searchProp]);
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index f719af9..0eccb3c 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -16,7 +16,6 @@ export const MappingSearch = ({
   searchProp,
   mappingProp,
   mappingDesc,
-  component,
   terminology,
   table,
 }) => {
@@ -64,13 +63,13 @@ export const MappingSearch = ({
     if (!!searchProp) {
       getFiltersByCode(
         vocabUrl,
-        component,
         mappingProp,
         setApiPreferencesCode,
         notification,
         setUnformattedPref,
         table,
-        terminology
+        terminology,
+        setLoading
       );
     }
   }, [searchProp]);
diff --git a/src/components/Nav/NavBar.jsx b/src/components/Nav/NavBar.jsx
index 80e39ff..155727e 100644
--- a/src/components/Nav/NavBar.jsx
+++ b/src/components/Nav/NavBar.jsx
@@ -26,11 +26,11 @@ export const NavBar = () => {
               <li className="nav_link">Terminologies</li>
             </NavLink>
             {/* Placeholder elements below. No functionality at this time.*/}
-            <NavLink to="/help">
+            <NavLink to="/about">
               <li className="nav_link">About</li>
             </NavLink>
 
-            <NavLink to="/about">
+            <NavLink to="/ontologies">
               <li className="nav_link">Ontologies</li>
             </NavLink>
           </div>
diff --git a/src/components/About/OntologyAPIs.jsx b/src/components/Ontologies/OntologyAPIs.jsx
similarity index 98%
rename from src/components/About/OntologyAPIs.jsx
rename to src/components/Ontologies/OntologyAPIs.jsx
index f325044..1feb1d2 100644
--- a/src/components/About/OntologyAPIs.jsx
+++ b/src/components/Ontologies/OntologyAPIs.jsx
@@ -61,7 +61,7 @@ export const OntologyInfo = () => {
   return loading ? (
     <Spinner />
   ) : (
-    <div className="about_container">
+    <div className="studies_container">
       <h2>Ontology Information</h2>
 
       <div className="ontology_container">
diff --git a/src/components/About/OntologyInfo.scss b/src/components/Ontologies/OntologyInfo.scss
similarity index 100%
rename from src/components/About/OntologyInfo.scss
rename to src/components/Ontologies/OntologyInfo.scss
diff --git a/src/components/About/OntologyTable.jsx b/src/components/Ontologies/OntologyTable.jsx
similarity index 100%
rename from src/components/About/OntologyTable.jsx
rename to src/components/Ontologies/OntologyTable.jsx

From f84a293a639dc6b59cd585c95bb2de500f844d27 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Thu, 7 Nov 2024 13:26:04 -0600
Subject: [PATCH 105/180] [FD-1791] Edit workflow dispatch

---
 .github/workflows/deploy_alpha.yml | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/deploy_alpha.yml b/.github/workflows/deploy_alpha.yml
index a0f7b96..b40a151 100644
--- a/.github/workflows/deploy_alpha.yml
+++ b/.github/workflows/deploy_alpha.yml
@@ -4,7 +4,18 @@
 name: 'Build and Deploy Alpha to  Cloud Run'
 
 on:
-    workflow_dispatch
+  workflow_dispatch:
+    inputs:
+      environment:
+        description: 'Deployment environment (e.g., dev, qa, prod, alpha)'
+        required: true
+        type: string
+        default: 'dev'
+      tag:
+        description: 'Optional version for the deployment'
+        required: false
+        type: string
+        default: 'dispatch'
 
 env:
 
@@ -21,7 +32,7 @@ jobs:
     runs-on: 'ubuntu-latest'
 
     environment:
-      name: alpha
+      name: ${{ github.event.inputs.environment }}
 
     permissions:
       contents: 'read'
@@ -44,18 +55,19 @@ jobs:
           echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.alpha
           echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.alpha
           echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.alpha
+          echo "VITE_MAPDRAGON_VERSION= ${{ github.event.inputs.tag }}" >> .env.alpha
       - name: 'Docker Auth'
         run: |-
           gcloud auth configure-docker '${{ env.REGION }}-docker.pkg.dev'
 
       - name: 'Build Docker Image' # New step to build the image
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
-          docker build -t "${DOCKER_TAG}" --build-arg ENV=alpha .
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          docker build -t "${DOCKER_TAG}" --build-arg ENV=${{ github.event.inputs.environment }} .
 
       - name: 'Push Docker Image'
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           docker push "${DOCKER_TAG}"
 
       - name: 'Deploy to Cloud Run'
@@ -63,4 +75,4 @@ jobs:
         with:
           service: '${{ env.SERVICE }}'
           region: '${{ env.REGION }}'
-          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"

From 78494103e26cd8873a0fe5b18615e83d49324fd4 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Thu, 7 Nov 2024 13:55:54 -0600
Subject: [PATCH 106/180] [FD-1791] Edit service

---
 .github/workflows/deploy_alpha.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/deploy_alpha.yml b/.github/workflows/deploy_alpha.yml
index b40a151..fe83389 100644
--- a/.github/workflows/deploy_alpha.yml
+++ b/.github/workflows/deploy_alpha.yml
@@ -21,7 +21,7 @@ env:
 
   PROJECT_ID: ${{ secrets.PROJECT_ID }}
   REGION: ${{ secrets.REGION_LOC_1 }}
-  SERVICE: 'map-dragon'
+  SERVICE: 'mapdragon'
   IMAGE_NAME: 'map-dragon_img'
   GCP_CREDENTIALS:  ${{ secrets.GCP_CREDENTIALS }}
 

From 0cf93148ccd4d743628568304d36cf00ce4dd6b1 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Thu, 7 Nov 2024 14:03:15 -0600
Subject: [PATCH 107/180] [FD-1791] Edit service

---
 .github/workflows/deploy_alpha.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/deploy_alpha.yml b/.github/workflows/deploy_alpha.yml
index fe83389..6e1fc35 100644
--- a/.github/workflows/deploy_alpha.yml
+++ b/.github/workflows/deploy_alpha.yml
@@ -73,6 +73,6 @@ jobs:
       - name: 'Deploy to Cloud Run'
         uses: 'google-github-actions/deploy-cloudrun@v2'
         with:
-          service: '${{ env.SERVICE }}'
+          service: '${{ env.SERVICE }}-${{ github.event.inputs.environment }}'
           region: '${{ env.REGION }}'
           image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"

From 4933af5239d4e29159bbc2fa7880d5eed20b9b15 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 7 Nov 2024 14:10:43 -0600
Subject: [PATCH 108/180] Added version to about page. Bug fixes for
 GetMappings button on table

---
 .env                                          |  1 +
 src/App.jsx                                   |  2 ++
 src/App.scss                                  |  3 +-
 src/components/About/About.jsx                | 20 ++++++++---
 .../MappingsFunctions/GetMappingsModal.jsx    |  2 +-
 .../MappingsFunctions/OntologyCheckboxes.jsx  |  2 +-
 .../OntologyFilterCodeSubmitTerm.jsx          |  4 +--
 src/components/Manager/Spinner.scss           |  1 -
 src/components/Manager/Submenu.jsx            | 19 -----------
 src/components/Nav/NavBar.scss                | 10 +++---
 .../Projects/DataDictionaries/DDDetails.jsx   |  2 --
 .../Projects/Studies/StudyDetails.jsx         |  2 --
 .../Projects/Tables/TableDetails.jsx          |  2 --
 .../Terminologies/EditMappingModal.jsx        |  2 +-
 .../Projects/Terminologies/Terminology.jsx    | 33 ++++++++-----------
 15 files changed, 41 insertions(+), 64 deletions(-)
 delete mode 100644 src/components/Manager/Submenu.jsx

diff --git a/.env b/.env
index 0815b66..85f0aac 100644
--- a/.env
+++ b/.env
@@ -4,3 +4,4 @@ VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
 VITE_VOCAB_ENDPOINT = https://locutus-110109177269.us-central1.run.app/api # dev
 # VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
 VITE_CLIENT_ID = 907694787484-36jr4oaf04mmniik6482batc87ejemm8.apps.googleusercontent.com
+VITE_MAPDRAGON_VERSION = "Development"
\ No newline at end of file
diff --git a/src/App.jsx b/src/App.jsx
index 4769f37..6363339 100644
--- a/src/App.jsx
+++ b/src/App.jsx
@@ -10,6 +10,7 @@ function App() {
   const monarchUrl = import.meta.env.VITE_MONARCH_SEARCH;
   const vocabUrl = import.meta.env.VITE_VOCAB_ENDPOINT;
   const clientId = import.meta.env.VITE_CLIENT_ID;
+  const mapDragonVersion = import.meta.env.VITE_MAPDRAGON_VERSION;
 
   const [results, setResults] = useState({}); //search results for mappings
   const [tablesDD, setTablesDD] = useState([]); //the tables in a data dictionary
@@ -49,6 +50,7 @@ function App() {
           searchUrl,
           monarchUrl,
           vocabUrl,
+          mapDragonVersion,
           tablesDD,
           setTablesDD,
           studyDDs,
diff --git a/src/App.scss b/src/App.scss
index 6a5342c..d453759 100644
--- a/src/App.scss
+++ b/src/App.scss
@@ -5,8 +5,7 @@
 }
 
 .outlet_div {
-  height: 100%;
   min-height: 100vh;
+  height: 100%;
   position: relative;
-  // top:-2.5rem;
 }
diff --git a/src/components/About/About.jsx b/src/components/About/About.jsx
index c93fab4..8144e99 100644
--- a/src/components/About/About.jsx
+++ b/src/components/About/About.jsx
@@ -7,7 +7,7 @@ import { Spinner } from '../Manager/Spinner';
 import './About.scss';
 
 export const About = () => {
-  const { vocabUrl } = useContext(myContext);
+  const { vocabUrl, mapDragonVersion } = useContext(myContext);
   const navigate = useNavigate();
   const [loading, setLoading] = useState(true);
   const [version, setVersion] = useState({});
@@ -31,13 +31,23 @@ export const About = () => {
   const items = [
     {
       key: '1',
-      label: 'Version',
+      label: 'Locutus version',
       children: `${version?.version}`,
-      labelStyle: { width: '150px' },
-      contentStyle: { width: '150px' },
+      labelStyle: { width: '120px' },
+      contentStyle: { width: '170px' },
     },
   ];
 
+  if (mapDragonVersion) {
+    items.push({
+      key: '2',
+      label: 'Map Dragon version',
+      children: `${mapDragonVersion}`,
+      labelStyle: { width: '120px' },
+      contentStyle: { width: '170px' },
+    });
+  }
+
   return (
     <>
       {loading ? (
@@ -46,7 +56,7 @@ export const About = () => {
         <div className="studies_container">
           <h2>About</h2>
           <div className="about_description">
-            <Descriptions title="Version" bordered items={items} />
+            <Descriptions title="Version" bordered column={1} items={items} />
           </div>
         </div>
       )}
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 123a761..37ddc73 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -203,7 +203,7 @@ export const GetMappingsModal = ({
           apiPreferencesCode,
           preferenceType,
           prefTypeKey,
-          searchProp,
+          mappingProp,
           vocabUrl,
           terminology
         );
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index c2430dd..f6d4c37 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -29,7 +29,7 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
   } else if (typeof apiPreferencesCode === 'string') {
     processedApiPreferencesCode = apiPreferencesCode.split(',');
   }
-
+  console.log(apiPreferencesCode);
   const existingOntologies = apiPreferencesCode
     ? processedApiPreferencesCode
     : preferenceType &&
diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx
index 748b97b..89680c8 100644
--- a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx
@@ -4,7 +4,7 @@ export const OntologyFilterCodeSubmitTerm = (
   apiPreferencesCode,
   preferenceType,
   prefTypeKey,
-  searchProp,
+  mappingProp,
   vocabUrl,
   terminology
 ) => {
@@ -21,7 +21,7 @@ export const OntologyFilterCodeSubmitTerm = (
   ) {
     apiPreference.api_preference.ols = apiPreferencesCode;
 
-    fetch(`${vocabUrl}/Terminology/${terminology.id}/filter/${searchProp}`, {
+    fetch(`${vocabUrl}/Terminology/${terminology.id}/filter/${mappingProp}`, {
       method: 'POST',
       headers: {
         'Content-Type': 'application/json',
diff --git a/src/components/Manager/Spinner.scss b/src/components/Manager/Spinner.scss
index 18f8aa1..a3833b8 100644
--- a/src/components/Manager/Spinner.scss
+++ b/src/components/Manager/Spinner.scss
@@ -2,7 +2,6 @@
 
 .loading_screen {
   margin-top: $navHeight;
-  height: calc(100vh - $navHeight);
   display: flex;
   flex-direction: row;
   align-items: center;
diff --git a/src/components/Manager/Submenu.jsx b/src/components/Manager/Submenu.jsx
deleted file mode 100644
index ff60aa0..0000000
--- a/src/components/Manager/Submenu.jsx
+++ /dev/null
@@ -1,19 +0,0 @@
-import { Col, Row } from 'antd';
-
-export const Submenu = ({ prop }) => {
-  return (
-    <Row gutter={30}>
-      <Col span={24}>
-        <div
-          className="submenu"
-          style={{
-            fontSize: '16px',
-            fontWeight: '600',
-          }}
-        >
-          {prop?.resource_type}
-        </div>
-      </Col>
-    </Row>
-  );
-};
diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index 95459e7..a48d239 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -28,7 +28,6 @@ nav.navbar {
     }
   }
 
-
   .nav_body {
     width: 100%;
     display: grid;
@@ -94,15 +93,15 @@ nav.navbar {
   padding: 0 10vw;
   position: sticky;
   top: 115px;
-  background:#eeeeee;
+  background: #eeeeee;
 
   li {
     list-style: none;
     font-size: 14px;
     line-height: 1.5714285714285714;
     color: rgba(0, 0, 0, 0.45);
-    
-    &>a {
+
+    & > a {
       color: rgba(0, 0, 0, 0.45);
       text-decoration: none;
       transition: color 0.2s;
@@ -122,11 +121,10 @@ nav.navbar {
   & * {
     text-transform: capitalize;
   }
-
 }
 
 footer {
   width: 100%;
   height: 50px;
   background-color: $navColor;
-}
\ No newline at end of file
+}
diff --git a/src/components/Projects/DataDictionaries/DDDetails.jsx b/src/components/Projects/DataDictionaries/DDDetails.jsx
index e0ef78e..bb63ab0 100644
--- a/src/components/Projects/DataDictionaries/DDDetails.jsx
+++ b/src/components/Projects/DataDictionaries/DDDetails.jsx
@@ -21,7 +21,6 @@ import { EditDDDetails } from './EditDDDetails';
 import { UploadTable } from '../Tables/UploadTable';
 import { RemoveTableDD } from './RemoveTableDD';
 import { DeleteDD } from './DeleteDD';
-import { Submenu } from '../../Manager/Submenu';
 import { RequiredLogin } from '../../Auth/RequiredLogin';
 
 export const DDDetails = () => {
@@ -100,7 +99,6 @@ export const DDDetails = () => {
         <Spinner />
       ) : (
         <div className="studies_container">
-          <Submenu prop={dataDictionary} />
           <Row gutter={30}>
             <div className="study_details_container">
               <Col span={15}>
diff --git a/src/components/Projects/Studies/StudyDetails.jsx b/src/components/Projects/Studies/StudyDetails.jsx
index 786c8c6..8f3274e 100644
--- a/src/components/Projects/Studies/StudyDetails.jsx
+++ b/src/components/Projects/Studies/StudyDetails.jsx
@@ -12,7 +12,6 @@ import { EditStudyDetails } from './EditStudyDetails';
 import { DeleteStudy } from './DeleteStudy';
 import { AddDD } from '../DataDictionaries/AddDD';
 import { RemoveStudyDD } from './RemoveStudyDD';
-import { Submenu } from '../../Manager/Submenu';
 const { Meta } = Card;
 
 export const StudyDetails = () => {
@@ -79,7 +78,6 @@ export const StudyDetails = () => {
         <Spinner />
       ) : (
         <div className="studies_container">
-          <Submenu prop={study} />
           <Row gutter={30}>
             <div className="study_details_container">
               <Col span={15}>
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 2041bae..15a0b45 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -27,7 +27,6 @@ import { GetMappingsModal } from '../../Manager/MappingsFunctions/GetMappingsMod
 import { AddVariable } from './AddVariable';
 import { ExpandedRowTable } from './ExpandedRowTable';
 import { TableMenu } from './TableMenu';
-import { Submenu } from '../../Manager/Submenu';
 import { SettingsDropdownTable } from '../../Manager/Dropdown/SettingsDropdownTable';
 import { RequiredLogin } from '../../Auth/RequiredLogin';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
@@ -320,7 +319,6 @@ It then shows the mappings as table data and alows the user to delete a mapping
         <Spinner />
       ) : (
         <div className="table_id_container">
-          <Submenu prop={table} />
           <Row gutter={30}>
             <div className="study_details_container">
               <Col span={15}>
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 6fc4916..2bb49c0 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -257,7 +257,7 @@ export const EditMappingsModal = ({
       apiPreferencesCode,
       preferenceType,
       prefTypeKey,
-      searchProp,
+      editMappings.code,
       vocabUrl,
       terminology
     );
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 629a289..6f1d009 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -23,7 +23,6 @@ import { AddCode } from './AddCode';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { GetMappingsModal } from '../../Manager/MappingsFunctions/GetMappingsModal';
 import { TerminologyMenu } from './TerminologyMenu';
-import { Submenu } from '../../Manager/Submenu';
 import { LoadCodes } from './LoadCodes';
 import { PreferredTerminology } from './PreferredTerminology';
 import { SearchContext } from '../../../Contexts/SearchContext';
@@ -35,12 +34,8 @@ export const Terminology = () => {
 
   const { terminologyId, tableId } = useParams();
   const { vocabUrl, user } = useContext(myContext);
-  const {
-    setPrefTerminologies,
-    prefTerminologies,
-    setApiPreferencesTerm,
-    apiPreferencesTerm,
-  } = useContext(SearchContext);
+  const { setPrefTerminologies, prefTerminologies, setApiPreferencesTerm } =
+    useContext(SearchContext);
   const {
     editMappings,
     setEditMappings,
@@ -48,6 +43,7 @@ export const Terminology = () => {
     setGetMappings,
     mapping,
     setMapping,
+    setAssignMappings,
   } = useContext(MappingContext);
 
   const [pageSize, setPageSize] = useState(
@@ -122,18 +118,16 @@ code in the terminology, AND the mappings array length for the code is > 0, the
 and returns the length of the mapping array (i.e. returns the number of codes mapped to the terminology code). 
 It then shows the mappings as table data and alows the user to delete a mapping from the table.*/
 
-  const noMapping = variable => {
-    return (
-      <Button
-        onClick={() =>
-          setGetMappings({ name: variable.name, code: variable.code })
-        }
-      >
-        Get Mappings
-      </Button>
-    );
-  };
-
+  const noMapping = variable => (
+    <Button
+      onClick={() => {
+        setGetMappings({ display: variable.display, code: variable.code });
+      }}
+    >
+      {prefTerminologies.length > 0 ? 'Assign Mappings' : 'Get Mappings'}
+    </Button>
+  );
+  console.log(prefTerminologies);
   const matchCode = variable => {
     if (!mapping?.length) {
       return noMapping(variable);
@@ -330,7 +324,6 @@ It then shows the mappings as table data and alows the user to delete a mapping
         <Spinner />
       ) : (
         <div className="terminology_container">
-          <Submenu prop={terminology} />
           <Row gutter={30}>
             <div className="study_details_container">
               <Col span={15}>

From a9bcc32a31e7b8471a71d23eb6b396652a1c0e78 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 7 Nov 2024 14:59:27 -0600
Subject: [PATCH 109/180] Started working on pref. terminology functionality in
 get mappings button

---
 .../Terminologies/AssignMappingsViaButton.jsx | 137 ++++++++++++++++++
 .../Projects/Terminologies/Terminology.jsx    |  30 +++-
 2 files changed, 162 insertions(+), 5 deletions(-)
 create mode 100644 src/components/Projects/Terminologies/AssignMappingsViaButton.jsx

diff --git a/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx b/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx
new file mode 100644
index 0000000..7524929
--- /dev/null
+++ b/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx
@@ -0,0 +1,137 @@
+import { useContext, useEffect, useState } from 'react';
+import { Form, message, Modal, notification } from 'antd';
+import { AssignMappingsCheckboxes } from '../../Manager/MappingsFunctions/AssignMappingsCheckboxes';
+import { myContext } from '../../../App';
+import { SearchContext } from '../../../Contexts/SearchContext';
+import { MappingContext } from '../../../Contexts/MappingContext';
+import { ModalSpinner } from '../../Manager/Spinner';
+
+export const AssignMappingsViaButton = ({
+  assignMappingsViaButton,
+  setAssignMappingsViaButton,
+  terminology,
+}) => {
+  const [form] = Form.useForm();
+
+  const { vocabUrl, user } = useContext(myContext);
+  const { prefTerminologies, setApiResults } = useContext(SearchContext);
+  const { setMapping } = useContext(MappingContext);
+  const [terminologiesToMap, setTerminologiesToMap] = useState([]);
+  const [loading, setLoading] = useState(false);
+  const [mappingProp, setMappingProp] = useState('');
+  const [selectedBoxes, setSelectedBoxes] = useState([]);
+
+  const onClose = () => {
+    setApiResults([]);
+  };
+  const fetchTerminologies = () => {
+    setLoading(true);
+    const fetchPromises = prefTerminologies?.map(pref =>
+      fetch(`${vocabUrl}/${pref?.reference}`).then(response => response.json())
+    );
+
+    Promise.all(fetchPromises)
+      .then(results => {
+        // Once all fetch calls are resolved, set the combined data
+        setTerminologiesToMap(results);
+      })
+      .catch(error => {
+        notification.error({
+          message: 'Error',
+          description: 'An error occurred. Please try again.',
+        });
+      })
+      .finally(() => setLoading(false));
+  };
+
+  useEffect(() => {
+    fetchTerminologies();
+  }, [assignMappingsViaButton]);
+
+  const handleSubmit = values => {
+    setLoading(true);
+    const selectedMappings = selectedBoxes?.map(item => ({
+      code: item.code,
+      display: item.display,
+      description: Array.isArray(item.description)
+        ? item.description[0]
+        : item.description,
+      system: item.system,
+    }));
+    const mappingsDTO = {
+      mappings: selectedMappings,
+      editor: user.email,
+    };
+
+    fetch(
+      `${vocabUrl}/Terminology/${terminology.id}/mapping/${assignMappingsViaButton.code}`,
+      {
+        method: 'PUT',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify(mappingsDTO),
+      }
+    )
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .then(data => {
+        setMapping(data.codes);
+        form.resetFields();
+        setAssignMappingsViaButton(false);
+        message.success('Changes saved successfully.');
+      })
+      .finally(() => setLoading(false));
+  };
+
+  return (
+    <Modal
+      open={!!assignMappingsViaButton}
+      width={'60%'}
+      onOk={() => {
+        form.validateFields().then(values => {
+          handleSubmit(values);
+          onClose();
+        });
+      }}
+      onCancel={() => {
+        form.resetFields();
+        onClose();
+        setAssignMappingsViaButton(false);
+      }}
+      styles={{
+        body: {
+          minHeight: '55vh',
+          maxHeight: '55vh',
+          overflowY: 'auto',
+        },
+      }}
+      closeIcon={false}
+      maskClosable={false}
+      destroyOnClose={true}
+      cancelButtonProps={{ disabled: loading }}
+      okButtonProps={{ disabled: loading }}
+    >
+      {loading ? (
+        <ModalSpinner />
+      ) : (
+        <AssignMappingsCheckboxes
+          form={form}
+          terminologiesToMap={terminologiesToMap}
+          selectedBoxes={selectedBoxes}
+          setSelectedBoxes={setSelectedBoxes}
+          searchProp={
+            assignMappingsViaButton?.display
+              ? assignMappingsViaButton.display
+              : assignMappingsViaButton?.code
+          }
+        />
+      )}
+    </Modal>
+  );
+};
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 6f1d009..48c5e5d 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -28,6 +28,7 @@ import { PreferredTerminology } from './PreferredTerminology';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
 import { cleanedName } from '../../Manager/Utilitiy';
+import { AssignMappingsViaButton } from './AssignMappingsViaButton';
 
 export const Terminology = () => {
   const [form] = Form.useForm();
@@ -43,12 +44,12 @@ export const Terminology = () => {
     setGetMappings,
     mapping,
     setMapping,
-    setAssignMappings,
   } = useContext(MappingContext);
 
   const [pageSize, setPageSize] = useState(
     parseInt(localStorage.getItem('pageSize'), 10) || 10
   );
+  const [assignMappingsViaButton, setAssignMappingsViaButton] = useState(false);
   const handleTableChange = (current, size) => {
     setPageSize(size);
   };
@@ -63,6 +64,8 @@ export const Terminology = () => {
     []
   );
 
+  console.log(prefTerminologies);
+
   const [loading, setLoading] = useState(true);
   const initialTerminology = { url: '', description: '', name: '', codes: [] }; //initial state of terminology
   const [terminology, setTerminology] = useState(initialTerminology);
@@ -121,13 +124,23 @@ It then shows the mappings as table data and alows the user to delete a mapping
   const noMapping = variable => (
     <Button
       onClick={() => {
-        setGetMappings({ display: variable.display, code: variable.code });
+        prefTerminologies.length > 0
+          ? setAssignMappingsViaButton({
+              display: variable.display,
+              code: variable.code,
+            })
+          : setGetMappings({
+              display: variable.display,
+              code: variable.code,
+            });
       }}
     >
-      {prefTerminologies.length > 0 ? 'Assign Mappings' : 'Get Mappings'}
+      {prefTerminologies && prefTerminologies.length > 0
+        ? 'Assign Mappings'
+        : 'Get Mappings'}
     </Button>
   );
-  console.log(prefTerminologies);
+
   const matchCode = variable => {
     if (!mapping?.length) {
       return noMapping(variable);
@@ -141,7 +154,9 @@ It then shows the mappings as table data and alows the user to delete a mapping
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.display}>
           <span className="mapping-display">
-            <Tooltip title={code.code}>{code.display}</Tooltip>
+            <Tooltip title={code.code}>
+              {code.display ? code.display : code.code}
+            </Tooltip>
           </span>
           <span
             className="remove-mapping"
@@ -434,6 +449,11 @@ It then shows the mappings as table data and alows the user to delete a mapping
             terminology={terminology}
             setTerminology={setTerminology}
           />
+          <AssignMappingsViaButton
+            assignMappingsViaButton={assignMappingsViaButton}
+            setAssignMappingsViaButton={setAssignMappingsViaButton}
+            terminology={terminology}
+          />
         </div>
       )}
     </>

From 370b0071c1e69a06eaa54a6956a922587988bc3d Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Thu, 7 Nov 2024 15:13:16 -0600
Subject: [PATCH 110/180] [FD-1791] Update name

---
 .github/workflows/{deploy_alpha.yml => dispatch_deploy.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{deploy_alpha.yml => dispatch_deploy.yml} (100%)

diff --git a/.github/workflows/deploy_alpha.yml b/.github/workflows/dispatch_deploy.yml
similarity index 100%
rename from .github/workflows/deploy_alpha.yml
rename to .github/workflows/dispatch_deploy.yml

From 7588d6951b670e35446d6f2cb01cad8a6e9b4b6b Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 7 Nov 2024 15:56:02 -0600
Subject: [PATCH 111/180] committing to change branches

---
 src/components/Manager/MappingsFunctions/FilterSelect.jsx | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index 8addb6d..ce5680a 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -137,9 +137,7 @@ export const FilterSelect = ({ component, table, terminology }) => {
     fetch(
       `${vocabUrl}/${(component = table
         ? `Table/${table.id}/filter/self`
-        : `Terminology/${terminology.id}/filter/${cleanedName(
-            terminology.name
-          )}`)}`,
+        : `Terminology/${terminology.id}/filter`)}`,
       {
         method: method,
         headers: {

From 60f3827e940e82fbfb323f03274c86550c36a1ff Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 7 Nov 2024 16:03:08 -0600
Subject: [PATCH 112/180] Terminology codes inheriting terminology ontology
 filters

---
 src/components/Manager/MappingsFunctions/FilterSelect.jsx     | 4 +---
 .../Manager/MappingsFunctions/OntologyCheckboxes.jsx          | 1 -
 src/components/Projects/Terminologies/Terminology.jsx         | 3 +--
 3 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index 8addb6d..ce5680a 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -137,9 +137,7 @@ export const FilterSelect = ({ component, table, terminology }) => {
     fetch(
       `${vocabUrl}/${(component = table
         ? `Table/${table.id}/filter/self`
-        : `Terminology/${terminology.id}/filter/${cleanedName(
-            terminology.name
-          )}`)}`,
+        : `Terminology/${terminology.id}/filter`)}`,
       {
         method: method,
         headers: {
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index f6d4c37..db0c32a 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -29,7 +29,6 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
   } else if (typeof apiPreferencesCode === 'string') {
     processedApiPreferencesCode = apiPreferencesCode.split(',');
   }
-  console.log(apiPreferencesCode);
   const existingOntologies = apiPreferencesCode
     ? processedApiPreferencesCode
     : preferenceType &&
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 6f1d009..f74767c 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -124,10 +124,9 @@ It then shows the mappings as table data and alows the user to delete a mapping
         setGetMappings({ display: variable.display, code: variable.code });
       }}
     >
-      {prefTerminologies.length > 0 ? 'Assign Mappings' : 'Get Mappings'}
+      Get Mappings
     </Button>
   );
-  console.log(prefTerminologies);
   const matchCode = variable => {
     if (!mapping?.length) {
       return noMapping(variable);

From 643e12a9c87bbca0f9d4e6bf83444f0bd46fc377 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 7 Nov 2024 20:34:50 -0600
Subject: [PATCH 113/180] Added preferred terminology mapping capability to
 mapping button in terminology

---
 .../{deploy_alpha.yml => dispatch_deploy.yml} | 28 +++++++++++++------
 .../MappingsFunctions/OntologyCheckboxes.jsx  |  1 -
 .../Projects/Terminologies/Terminology.jsx    |  8 ++----
 3 files changed, 22 insertions(+), 15 deletions(-)
 rename .github/workflows/{deploy_alpha.yml => dispatch_deploy.yml} (63%)

diff --git a/.github/workflows/deploy_alpha.yml b/.github/workflows/dispatch_deploy.yml
similarity index 63%
rename from .github/workflows/deploy_alpha.yml
rename to .github/workflows/dispatch_deploy.yml
index a0f7b96..6e1fc35 100644
--- a/.github/workflows/deploy_alpha.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -4,13 +4,24 @@
 name: 'Build and Deploy Alpha to  Cloud Run'
 
 on:
-    workflow_dispatch
+  workflow_dispatch:
+    inputs:
+      environment:
+        description: 'Deployment environment (e.g., dev, qa, prod, alpha)'
+        required: true
+        type: string
+        default: 'dev'
+      tag:
+        description: 'Optional version for the deployment'
+        required: false
+        type: string
+        default: 'dispatch'
 
 env:
 
   PROJECT_ID: ${{ secrets.PROJECT_ID }}
   REGION: ${{ secrets.REGION_LOC_1 }}
-  SERVICE: 'map-dragon'
+  SERVICE: 'mapdragon'
   IMAGE_NAME: 'map-dragon_img'
   GCP_CREDENTIALS:  ${{ secrets.GCP_CREDENTIALS }}
 
@@ -21,7 +32,7 @@ jobs:
     runs-on: 'ubuntu-latest'
 
     environment:
-      name: alpha
+      name: ${{ github.event.inputs.environment }}
 
     permissions:
       contents: 'read'
@@ -44,23 +55,24 @@ jobs:
           echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.alpha
           echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.alpha
           echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.alpha
+          echo "VITE_MAPDRAGON_VERSION= ${{ github.event.inputs.tag }}" >> .env.alpha
       - name: 'Docker Auth'
         run: |-
           gcloud auth configure-docker '${{ env.REGION }}-docker.pkg.dev'
 
       - name: 'Build Docker Image' # New step to build the image
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
-          docker build -t "${DOCKER_TAG}" --build-arg ENV=alpha .
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          docker build -t "${DOCKER_TAG}" --build-arg ENV=${{ github.event.inputs.environment }} .
 
       - name: 'Push Docker Image'
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           docker push "${DOCKER_TAG}"
 
       - name: 'Deploy to Cloud Run'
         uses: 'google-github-actions/deploy-cloudrun@v2'
         with:
-          service: '${{ env.SERVICE }}'
+          service: '${{ env.SERVICE }}-${{ github.event.inputs.environment }}'
           region: '${{ env.REGION }}'
-          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index f6d4c37..db0c32a 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -29,7 +29,6 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
   } else if (typeof apiPreferencesCode === 'string') {
     processedApiPreferencesCode = apiPreferencesCode.split(',');
   }
-  console.log(apiPreferencesCode);
   const existingOntologies = apiPreferencesCode
     ? processedApiPreferencesCode
     : preferenceType &&
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 48c5e5d..3f77b9e 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -64,8 +64,6 @@ export const Terminology = () => {
     []
   );
 
-  console.log(prefTerminologies);
-
   const [loading, setLoading] = useState(true);
   const initialTerminology = { url: '', description: '', name: '', codes: [] }; //initial state of terminology
   const [terminology, setTerminology] = useState(initialTerminology);
@@ -135,9 +133,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
             });
       }}
     >
-      {prefTerminologies && prefTerminologies.length > 0
-        ? 'Assign Mappings'
-        : 'Get Mappings'}
+      {prefTerminologies?.length > 0 ? 'Assign Mappings' : 'Get Mappings'}
     </Button>
   );
 
@@ -200,7 +196,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
 
   useEffect(() => {
     setDataSource(tableData(terminology));
-  }, [terminology, mapping]);
+  }, [terminology, mapping, prefTerminologies]);
 
   // Fetches the terminology using the terminologyId param and sets 'terminology' to the response.
   // Fetches the mappings for the terminology and sets the response to 'mapping'

From 24d2cd2f0f23d8ee34fdcd3ed903682c771016a6 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Fri, 8 Nov 2024 08:20:41 -0600
Subject: [PATCH 114/180] [FD-1791] Update dispatch workflow

---
 .github/workflows/dispatch_deploy.yml | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index 6e1fc35..e4b3587 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -1,7 +1,7 @@
 # This workflow build and push a Docker container to Google Artifact Registry
 # and deploy it on Cloud Run when manually triggered.
 
-name: 'Build and Deploy Alpha to  Cloud Run'
+name: 'Dispatch Deploy'
 
 on:
   workflow_dispatch:
@@ -13,9 +13,14 @@ on:
         default: 'dev'
       tag:
         description: 'Optional version for the deployment'
-        required: false
+        required: true
+        type: string
+        default: 'v0.0.0-env'
+      deploy_branch:
+        description: 'Branch to deploy to the environment'
+        required: true
         type: string
-        default: 'dispatch'
+        default: 'main'
 
 env:
 
@@ -41,8 +46,8 @@ jobs:
     steps:
       - name: 'Checkout'
         uses: 'actions/checkout@v4'
-        # with:
-        #   ref: release # release is deployed, not the default or working branch
+        with:
+          ref: ${{ github.event.inputs.environment }} # This branch is deployed
         
       - id: 'auth'
         name: 'Authenticate to Google Cloud'
@@ -50,12 +55,12 @@ jobs:
         with:
           credentials_json: '${{ env.GCP_CREDENTIALS }}'
 
-      - name: Generate .env.alpha file
+      - name: Generate .env.${{ github.event.inputs.environment }} file
         run: |
-          echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.alpha
-          echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.alpha
-          echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.alpha
-          echo "VITE_MAPDRAGON_VERSION= ${{ github.event.inputs.tag }}" >> .env.alpha
+          echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.${{ github.event.inputs.environment }}
+          echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.${{ github.event.inputs.environment }}
+          echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.${{ github.event.inputs.environment }}
+          echo "VITE_MAPDRAGON_VERSION= ${{ github.event.inputs.tag }}" >> .env.${{ github.event.inputs.environment }}
       - name: 'Docker Auth'
         run: |-
           gcloud auth configure-docker '${{ env.REGION }}-docker.pkg.dev'

From 2723b61ab6e744390b55ee5676788bf160d9413b Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Fri, 8 Nov 2024 08:29:35 -0600
Subject: [PATCH 115/180] [FD-1791] Update checkout in dispatch

---
 .github/workflows/dispatch_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index e4b3587..6be12c7 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -47,7 +47,7 @@ jobs:
       - name: 'Checkout'
         uses: 'actions/checkout@v4'
         with:
-          ref: ${{ github.event.inputs.environment }} # This branch is deployed
+          ref: ${{ github.event.inputs.deploy_branch }} # This branch is deployed
         
       - id: 'auth'
         name: 'Authenticate to Google Cloud'

From 2eeb2128bb38be9da3dab0dddfd7b10a8d8a55ae Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Fri, 8 Nov 2024 08:51:53 -0600
Subject: [PATCH 116/180] [FD-1791] Update dev workflow trigger and version

---
 .github/workflows/deploy_dev.yml | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/deploy_dev.yml b/.github/workflows/deploy_dev.yml
index a67b7b9..80e94a9 100644
--- a/.github/workflows/deploy_dev.yml
+++ b/.github/workflows/deploy_dev.yml
@@ -4,9 +4,7 @@
 name: 'Build and Deploy to Cloud Run'
 on:
   pull_request_review:
-    branches:
-      - main
-    types: [submitted]
+    types: [submitted, edited] # submitted, reviewer edits the PR (ex comments)
     
 env:
 
@@ -22,7 +20,8 @@ jobs:
   deploy:
     runs-on: 'ubuntu-latest'
     
-    if: github.event.review.state == 'approved'
+    # If PR is approved and the PR is for the 'main' branch
+    if: github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'main'
     
     environment:
       name: dev
@@ -41,11 +40,18 @@ jobs:
         with:
           credentials_json: '${{ env.GCP_CREDENTIALS }}'
 
+      - name: Extract Version from PR Number
+        id: extract_version
+        run: |
+          VERSION=${{ github.event.pull_request.number }} 
+          echo "Extracted Version: ${VERSION}"
+
       - name: Generate .env.dev file
         run: |
           echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.dev
           echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.dev
           echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.dev
+          echo "VITE_MAPDRAGON_VERSION=${VERSION}" >> .env.dev
       
       - name: 'Docker Auth'
         run: |-

From d113f7d8bb8cca9bcb1cab2aabd17b7ade13cbf0 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Fri, 8 Nov 2024 11:21:15 -0600
Subject: [PATCH 117/180] [FD-1791] Edit url names

---
 .github/workflows/deploy_dev.yml      | 10 +++++-----
 .github/workflows/deploy_qa.yml       | 18 ++++++++++++------
 .github/workflows/dispatch_deploy.yml |  4 ++--
 3 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/deploy_dev.yml b/.github/workflows/deploy_dev.yml
index 80e94a9..757163b 100644
--- a/.github/workflows/deploy_dev.yml
+++ b/.github/workflows/deploy_dev.yml
@@ -10,7 +10,7 @@ env:
 
   PROJECT_ID: ${{ secrets.PROJECT_ID }}
   REGION: ${{ secrets.REGION_LOC_1 }}
-  SERVICE: 'map-dragon'
+  SERVICE: 'mapdragon'
   IMAGE_NAME: 'map-dragon_img'
   GCP_CREDENTIALS:  ${{ secrets.GCP_CREDENTIALS }}
 
@@ -60,17 +60,17 @@ jobs:
       - name: 'Build Docker Image' # New step to build the image
 
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-dev/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           docker build -t "${DOCKER_TAG}" --build-arg ENV=dev .
 
       - name: 'Push Docker Image'
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-dev/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           docker push "${DOCKER_TAG}"
 
       - name: 'Deploy to Cloud Run'
         uses: 'google-github-actions/deploy-cloudrun@v2'
         with:
-          service: '${{ env.SERVICE }}'
+          service: '${{ env.SERVICE }}-dev'
           region: '${{ env.REGION }}'
-          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-dev/${{ env.IMAGE_NAME }}:${{ github.sha }}"
diff --git a/.github/workflows/deploy_qa.yml b/.github/workflows/deploy_qa.yml
index 3dfe34c..06e99a3 100644
--- a/.github/workflows/deploy_qa.yml
+++ b/.github/workflows/deploy_qa.yml
@@ -7,8 +7,7 @@ on:
   pull_request:
     branches:
       - release
-    types:
-      - closed
+    types: [opened, edited, synchronize] # PR opened, edited(PR title, etc), new commits are pushed.
 
 
 env:
@@ -43,11 +42,18 @@ jobs:
         with:
           credentials_json: '${{ env.GCP_CREDENTIALS }}'
 
+      - name: Extract Version from PR Title # Assumes PR title contains the tag. ex v0.0.0 or v0.0.0-abc
+        run: |
+          VERSION=$(echo "${{ github.event.pull_request.title }}" | grep -o 'v[0-9]\+\.[0-9]\+\.[0-9]\+\(-[a-zA-Z]*\)\?') 
+          echo "Extracted Version: ${VERSION}"
+
       - name: Generate .env.qa file
         run: |
           echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.qa
           echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.qa
           echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.qa
+          echo "VITE_MAPDRAGON_VERSION=${VERSION}" >> .env.qa
+
 
       - name: 'Docker Auth'
         run: |-
@@ -55,17 +61,17 @@ jobs:
 
       - name: 'Build Docker Image' # New step to build the image
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-uat/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           docker build -t "${DOCKER_TAG}" --build-arg ENV=qa .
 
       - name: 'Push Docker Image'
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-uat/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           docker push "${DOCKER_TAG}"
 
       - name: 'Deploy to Cloud Run'
         uses: 'google-github-actions/deploy-cloudrun@v2'
         with:
-          service: '${{ env.SERVICE }}'
+          service: '${{ env.SERVICE }}-uat'
           region: '${{ env.REGION }}'
-          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
\ No newline at end of file
+          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-uat/${{ env.IMAGE_NAME }}:${{ github.sha }}"
\ No newline at end of file
diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index 6be12c7..e84d343 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -11,7 +11,7 @@ on:
         required: true
         type: string
         default: 'dev'
-      tag:
+      version:
         description: 'Optional version for the deployment'
         required: true
         type: string
@@ -60,7 +60,7 @@ jobs:
           echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.${{ github.event.inputs.environment }}
           echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.${{ github.event.inputs.environment }}
           echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.${{ github.event.inputs.environment }}
-          echo "VITE_MAPDRAGON_VERSION= ${{ github.event.inputs.tag }}" >> .env.${{ github.event.inputs.environment }}
+          echo "VITE_MAPDRAGON_VERSION= ${{ github.event.inputs.version }}" >> .env.${{ github.event.inputs.environment }}
       - name: 'Docker Auth'
         run: |-
           gcloud auth configure-docker '${{ env.REGION }}-docker.pkg.dev'

From cdf472ef2a01731f0895cf744d527e5805318b79 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 8 Nov 2024 13:20:25 -0600
Subject: [PATCH 118/180] Page location in browser tab

---
 src/components/About/About.jsx                |  1 +
 src/components/Manager/FetchManager.jsx       |  2 +-
 .../Manager/MappingsFunctions/FilterReset.jsx |  9 ++-----
 .../MappingsFunctions/FilterSelect.jsx        |  5 +---
 src/components/Manager/ShowHistory.jsx        |  2 +-
 src/components/Ontologies/OntologyTable.jsx   |  9 ++++---
 .../Projects/DataDictionaries/DDDetails.jsx   |  4 +++-
 .../Projects/Studies/StudyDetails.jsx         |  3 +++
 src/components/Projects/Studies/StudyList.jsx |  1 +
 .../Projects/Tables/TableDetails.jsx          |  4 ++++
 .../Projects/Terminologies/Terminology.jsx    | 24 +++++++++----------
 .../Terminologies/TerminologyList.jsx         | 17 ++++++++-----
 src/components/Search/OntologySearch.jsx      |  5 +++-
 src/components/Search/SearchResults.jsx       |  3 +++
 14 files changed, 52 insertions(+), 37 deletions(-)

diff --git a/src/components/About/About.jsx b/src/components/About/About.jsx
index 8144e99..8e68818 100644
--- a/src/components/About/About.jsx
+++ b/src/components/About/About.jsx
@@ -13,6 +13,7 @@ export const About = () => {
   const [version, setVersion] = useState({});
 
   useEffect(() => {
+    document.title = 'About - Map Dragon';
     setLoading(true);
     getAll(vocabUrl, 'version', navigate)
       .then(data => setVersion(data))
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index e6f2eb6..cde1309 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -1,4 +1,4 @@
-import { cleanedName, ontologyReducer } from './Utilitiy';
+import { ontologyReducer } from './Utilitiy';
 
 // Fetches all elements at an endpoint
 export const getAll = (vocabUrl, name, navigate) => {
diff --git a/src/components/Manager/MappingsFunctions/FilterReset.jsx b/src/components/Manager/MappingsFunctions/FilterReset.jsx
index 536baff..8efc0f4 100644
--- a/src/components/Manager/MappingsFunctions/FilterReset.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterReset.jsx
@@ -4,7 +4,6 @@ import { useContext, useState } from 'react';
 import { myContext } from '../../../App';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { useParams } from 'react-router-dom';
-import { cleanedName } from '../Utilitiy';
 
 export const FilterReset = ({ table, terminology }) => {
   const { confirm } = Modal;
@@ -21,9 +20,7 @@ export const FilterReset = ({ table, terminology }) => {
       `${vocabUrl}/${
         table
           ? `Table/${table.id}/filter/self`
-          : `Terminology/${terminology.id}/filter/${cleanedName(
-              terminology.name
-            )}`
+          : `Terminology/${terminology.id}/filter}`
       }`,
       {
         method: 'DELETE',
@@ -51,9 +48,7 @@ export const FilterReset = ({ table, terminology }) => {
           `${vocabUrl}/${
             table
               ? `Table/${table.id}/filter/self`
-              : `Terminology/${terminology.id}/filter/${cleanedName(
-                  terminology.name
-                )}`
+              : `Terminology/${terminology.id}/filter}`
           }`,
           {
             method: 'GET',
diff --git a/src/components/Manager/MappingsFunctions/FilterSelect.jsx b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
index ce5680a..5de5553 100644
--- a/src/components/Manager/MappingsFunctions/FilterSelect.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterSelect.jsx
@@ -6,7 +6,6 @@ import { FilterAPI } from './FilterAPI';
 import { getOntologies } from '../FetchManager';
 import { ModalSpinner } from '../Spinner';
 import { SearchContext } from '../../../Contexts/SearchContext';
-import { cleanedName } from '../Utilitiy';
 import { useParams } from 'react-router-dom';
 
 export const FilterSelect = ({ component, table, terminology }) => {
@@ -157,9 +156,7 @@ export const FilterSelect = ({ component, table, terminology }) => {
         fetch(
           `${vocabUrl}/${(component = table
             ? `Table/${table.id}/filter/self`
-            : `Terminology/${terminology.id}/filter/${cleanedName(
-                terminology.name
-              )}`)}`,
+            : `Terminology/${terminology.id}/filter`)}`,
           {
             method: 'GET',
             headers: {
diff --git a/src/components/Manager/ShowHistory.jsx b/src/components/Manager/ShowHistory.jsx
index 5d2cdf2..8459afb 100644
--- a/src/components/Manager/ShowHistory.jsx
+++ b/src/components/Manager/ShowHistory.jsx
@@ -92,7 +92,7 @@ export const ShowHistory = ({
         maskClosable={true}
         footer={[
           <Button type="primary" onClick={handleOk}>
-            OK
+            Close
           </Button>,
         ]}
       >
diff --git a/src/components/Ontologies/OntologyTable.jsx b/src/components/Ontologies/OntologyTable.jsx
index a326572..c3cf948 100644
--- a/src/components/Ontologies/OntologyTable.jsx
+++ b/src/components/Ontologies/OntologyTable.jsx
@@ -6,7 +6,8 @@ export const OntologyTable = ({ ontology }) => {
   const [filter, setFilter] = useState(null);
 
   const [pageSize, setPageSize] = useState(
-    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+    parseInt(localStorage.getItem('pageSize'), 10) || 10
+  );
   const handleTableChange = (current, size) => {
     setPageSize(size);
   };
@@ -14,6 +15,10 @@ export const OntologyTable = ({ ontology }) => {
     localStorage.setItem('pageSize', pageSize);
   }, [pageSize]);
 
+  useEffect(() => {
+    document.title = 'Ontologies - Map Dragon';
+  }, []);
+
   const ontologyTitle = () => {
     return (
       <div className="ontology_filter">
@@ -94,8 +99,6 @@ export const OntologyTable = ({ ontology }) => {
     }))
   );
 
-
-
   return (
     <Table
       columns={columns}
diff --git a/src/components/Projects/DataDictionaries/DDDetails.jsx b/src/components/Projects/DataDictionaries/DDDetails.jsx
index bb63ab0..ef70ea6 100644
--- a/src/components/Projects/DataDictionaries/DDDetails.jsx
+++ b/src/components/Projects/DataDictionaries/DDDetails.jsx
@@ -61,7 +61,9 @@ export const DDDetails = () => {
   // fetches the specified DD. Sets response to 'dataDictionary'.
   // if a DD was fetched, calls the getDDTables function to fetch the tables.
   // otherwise sets loading to false.
-
+  useEffect(() => {
+    document.title = 'Data Dictionary - Map Dragon';
+  }, []);
   useEffect(() => {
     setLoading(true);
     getById(vocabUrl, 'DataDictionary', DDId)
diff --git a/src/components/Projects/Studies/StudyDetails.jsx b/src/components/Projects/Studies/StudyDetails.jsx
index 8f3274e..eec70b7 100644
--- a/src/components/Projects/Studies/StudyDetails.jsx
+++ b/src/components/Projects/Studies/StudyDetails.jsx
@@ -23,6 +23,9 @@ export const StudyDetails = () => {
   const [loading, setLoading] = useState(true);
   const navigate = useNavigate();
 
+  useEffect(() => {
+    document.title = 'Study - Map Dragon';
+  }, []);
   /* Function that maps through the datadictionary array in a study.
   For each DD, it makes a fetch call to the id of the DD.
   Promise.all fulfills all of the fetch calls. The response is set to studyDDs  */
diff --git a/src/components/Projects/Studies/StudyList.jsx b/src/components/Projects/Studies/StudyList.jsx
index 426fc79..ffd7fdf 100644
--- a/src/components/Projects/Studies/StudyList.jsx
+++ b/src/components/Projects/Studies/StudyList.jsx
@@ -24,6 +24,7 @@ export const StudyList = () => {
   const login = RequiredLogin({ handleSuccess: handleSuccess });
   // API call to fetch all studies. Sets response to 'studies' then sets loading to false
   useEffect(() => {
+    document.title = 'Studies - Map Dragon';
     setLoading(true);
     getAll(vocabUrl, 'Study', navigate)
       .then(data => setStudies(data))
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 15a0b45..e722a53 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -63,6 +63,10 @@ export const TableDetails = () => {
   };
   const login = RequiredLogin({ handleSuccess: handleSuccess });
 
+  useEffect(() => {
+    document.title = 'Table - Map Dragon';
+  }, []);
+
   useEffect(() => {
     setDataSource(tableData(table));
     localStorage.setItem('pageSize', pageSize);
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 3f77b9e..6c7699b 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -27,7 +27,6 @@ import { LoadCodes } from './LoadCodes';
 import { PreferredTerminology } from './PreferredTerminology';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
-import { cleanedName } from '../../Manager/Utilitiy';
 import { AssignMappingsViaButton } from './AssignMappingsViaButton';
 
 export const Terminology = () => {
@@ -53,6 +52,11 @@ export const Terminology = () => {
   const handleTableChange = (current, size) => {
     setPageSize(size);
   };
+
+  useEffect(() => {
+    document.title = 'Terminology - Map Dragon';
+  }, []);
+
   useEffect(() => {
     localStorage.setItem('pageSize', pageSize);
   }, [pageSize]);
@@ -210,18 +214,12 @@ It then shows the mappings as table data and alows the user to delete a mapping
         } else {
           setTerminology(data);
           if (data) {
-            cleanedName(data?.name);
-            fetch(
-              `${vocabUrl}/Terminology/${data?.id}/filter/${cleanedName(
-                data?.name
-              )}`,
-              {
-                method: 'GET',
-                headers: {
-                  'Content-Type': 'application/json',
-                },
-              }
-            )
+            fetch(`${vocabUrl}/Terminology/${data?.id}/filter`, {
+              method: 'GET',
+              headers: {
+                'Content-Type': 'application/json',
+              },
+            })
               .then(res => {
                 if (res.ok) {
                   return res.json();
diff --git a/src/components/Projects/Terminologies/TerminologyList.jsx b/src/components/Projects/Terminologies/TerminologyList.jsx
index 99d0cbf..743d806 100644
--- a/src/components/Projects/Terminologies/TerminologyList.jsx
+++ b/src/components/Projects/Terminologies/TerminologyList.jsx
@@ -15,11 +15,16 @@ export const TerminologyList = () => {
   const [filter, setFilter] = useState(null);
   const [deleteId, setDeleteId] = useState(null);
   const [pageSize, setPageSize] = useState(
-    parseInt(localStorage.getItem('pageSize'), 10) || 10);
+    parseInt(localStorage.getItem('pageSize'), 10) || 10
+  );
   const { vocabUrl } = useContext(myContext);
 
   const navigate = useNavigate();
 
+  useEffect(() => {
+    document.title = 'Terminology Index - Map Dragon';
+  }, []);
+
   const inputRef = useRef(null);
 
   useEffect(() => {
@@ -29,7 +34,7 @@ export const TerminologyList = () => {
         setTerms(data);
       })
       .finally(() => setLoading(false));
-      localStorage.setItem('pageSize', pageSize);
+    localStorage.setItem('pageSize', pageSize);
   }, [pageSize]);
 
   const terminologyTitle = () => {
@@ -46,8 +51,8 @@ export const TerminologyList = () => {
       {item.name ? item.name : item.id}
     </Link>
   );
-  const handleTableChange = (current, size) => { 
-    setPageSize(size);     
+  const handleTableChange = (current, size) => {
+    setPageSize(size);
   };
 
   const columns = [
@@ -149,12 +154,12 @@ export const TerminologyList = () => {
           columns={columns}
           dataSource={dataSource}
           getPopupContainer={trigger => trigger.parentNode}
-          pagination={{ 
+          pagination={{
             showSizeChanger: true,
             pageSizeOptions: ['10', '20', '30'],
             pageSize: pageSize, // Use the stored pageSize
             onChange: handleTableChange, // Capture pagination changes
-          }} 
+          }}
         />
       </div>
       <DeleteTerminology
diff --git a/src/components/Search/OntologySearch.jsx b/src/components/Search/OntologySearch.jsx
index 5d21402..f1bf66f 100644
--- a/src/components/Search/OntologySearch.jsx
+++ b/src/components/Search/OntologySearch.jsx
@@ -1,4 +1,4 @@
-import { useRef, useState } from 'react';
+import { useEffect, useRef, useState } from 'react';
 import './OntologySearch.scss';
 import { useNavigate } from 'react-router-dom';
 
@@ -8,6 +8,9 @@ export const OntologySearch = () => {
   const navigate = useNavigate();
   const ref = useRef();
 
+  useEffect(() => {
+    document.title = 'Map Dragon';
+  }, []);
   const searchOnEnter = e => {
     /* if the input field has a value (i.e. term being searched), the value is transposed into the address bar. 
     The user is then redirected to the search page, which completes the search for the search term.
diff --git a/src/components/Search/SearchResults.jsx b/src/components/Search/SearchResults.jsx
index ed0811f..1c03825 100644
--- a/src/components/Search/SearchResults.jsx
+++ b/src/components/Search/SearchResults.jsx
@@ -19,6 +19,9 @@ export const SearchResults = () => {
   const navigate = useNavigate();
   const ref = useRef();
 
+  useEffect(() => {
+    document.title = 'Map Dragon';
+  }, []);
   // sets the page and current page to the page number of the paginator
   const onChange = page => {
     setCurrent(page);

From 54405a3e8fdea3fbcae94f2bae4e8dec1924e607 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Fri, 8 Nov 2024 14:31:19 -0600
Subject: [PATCH 119/180] [FD-1791] Edit version and triggers for uat and prod
 workflows

---
 .github/workflows/deploy_dev.yml      |  2 +-
 .github/workflows/deploy_prod.yml     | 21 ++++++++++++++-------
 .github/workflows/deploy_qa.yml       | 16 ++++++++--------
 .github/workflows/dispatch_deploy.yml |  2 +-
 4 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/deploy_dev.yml b/.github/workflows/deploy_dev.yml
index 757163b..03b6d61 100644
--- a/.github/workflows/deploy_dev.yml
+++ b/.github/workflows/deploy_dev.yml
@@ -1,5 +1,5 @@
 # This workflow build and push a Docker container to Google Artifact Registry
-# and deploy it on Cloud Run when a PR has been approved by a reviewer.
+# and deploy it on Cloud Run when a PR to 'main' has been approved by a reviewer.
 
 name: 'Build and Deploy to Cloud Run'
 on:
diff --git a/.github/workflows/deploy_prod.yml b/.github/workflows/deploy_prod.yml
index 7293668..8b8f600 100644
--- a/.github/workflows/deploy_prod.yml
+++ b/.github/workflows/deploy_prod.yml
@@ -4,17 +4,16 @@
 name: 'Build and Deploy PROD to  Cloud Run'
 
 on:
-    pull_request:
-      branches:
-        - release
-      types:
-        - closed
+  pull_request:
+    branches:
+      - release
+    types: [closed, edited] # PR opened, edited(PR title, etc)
 
 env:
 
   PROJECT_ID: ${{ secrets.PROJECT_ID }}
   REGION: ${{ secrets.REGION_LOC_1 }}
-  SERVICE: 'map-dragon'
+  SERVICE: 'mapdragon'
   IMAGE_NAME: 'map-dragon_img'
   GCP_CREDENTIALS:  ${{ secrets.GCP_CREDENTIALS }}
 
@@ -24,7 +23,8 @@ jobs:
   deploy:
     runs-on: 'ubuntu-latest'
 
-    
+    if: github.event.pull_request.merged == true && github.event.pull_request.base.ref == 'release'
+
     environment:
       name: prod
 
@@ -44,11 +44,18 @@ jobs:
         with:
           credentials_json: '${{ env.GCP_CREDENTIALS }}'
 
+      - name: Extract Version from PR Title # Assumes PR title contains the tag. ex v0.0.0 or v0.0.0-abc
+        run: |
+          VERSION=$(echo "${{ github.event.pull_request.title }}" | grep -o 'v[0-9]\+\.[0-9]\+\.[0-9]\+\(-[a-zA-Z]*\)\?') 
+          echo "Extracted Version: ${VERSION}"
+
       - name: Generate .env.prod file
         run: |
           echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.prod
           echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.prod
           echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.prod
+          echo "VITE_MAPDRAGON_VERSION=${VERSION}" >> .env.prod
+
       - name: 'Docker Auth'
         run: |-
           gcloud auth configure-docker '${{ env.REGION }}-docker.pkg.dev'
diff --git a/.github/workflows/deploy_qa.yml b/.github/workflows/deploy_qa.yml
index 06e99a3..5a03580 100644
--- a/.github/workflows/deploy_qa.yml
+++ b/.github/workflows/deploy_qa.yml
@@ -1,7 +1,7 @@
 # This workflow build and push a Docker container to Google Artifact Registry
 # and deploy it on Cloud Run when a PR to the `release` branch is made.
 
-name: 'Build and Deploy QA to Cloud Run'
+name: 'Build and Deploy UAT to Cloud Run'
 
 on:
   pull_request:
@@ -25,7 +25,7 @@ jobs:
     runs-on: 'ubuntu-latest'
 
     environment:
-      name: qa
+      name: uat
 
     permissions:
       contents: 'read'
@@ -47,12 +47,12 @@ jobs:
           VERSION=$(echo "${{ github.event.pull_request.title }}" | grep -o 'v[0-9]\+\.[0-9]\+\.[0-9]\+\(-[a-zA-Z]*\)\?') 
           echo "Extracted Version: ${VERSION}"
 
-      - name: Generate .env.qa file
+      - name: Generate .env.uat file
         run: |
-          echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.qa
-          echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.qa
-          echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.qa
-          echo "VITE_MAPDRAGON_VERSION=${VERSION}" >> .env.qa
+          echo "VITE_CLIENT_ID = ${{ secrets.VITE_CLIENT_ID }}" > .env.uat
+          echo "VITE_SEARCH_ENDPOINT = ${{ secrets.VITE_SEARCH_ENDPOINT }}" >> .env.uat
+          echo "VITE_VOCAB_ENDPOINT= ${{ secrets.VITE_VOCAB_ENDPOINT }}" >> .env.uat
+          echo "VITE_MAPDRAGON_VERSION=${VERSION}" >> .env.uat
 
 
       - name: 'Docker Auth'
@@ -62,7 +62,7 @@ jobs:
       - name: 'Build Docker Image' # New step to build the image
         run: |-
           DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-uat/${{ env.IMAGE_NAME }}:${{ github.sha }}"
-          docker build -t "${DOCKER_TAG}" --build-arg ENV=qa .
+          docker build -t "${DOCKER_TAG}" --build-arg ENV=uat .
 
       - name: 'Push Docker Image'
         run: |-
diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index e84d343..f400a48 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -7,7 +7,7 @@ on:
   workflow_dispatch:
     inputs:
       environment:
-        description: 'Deployment environment (e.g., dev, qa, prod, alpha)'
+        description: 'Deployment environment (e.g., dev, uat, prod, alpha)'
         required: true
         type: string
         default: 'dev'

From 953766b1a116452a245ae6e534e6f381c01752e2 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 8 Nov 2024 15:19:24 -0600
Subject: [PATCH 120/180] fd-1796 default ontologies used for search when none
 are specified

---
 src/components/Manager/FetchManager.jsx       |  1 +
 .../MappingsFunctions/GetMappingsModal.jsx    |  4 +--
 .../MappingsFunctions/MappingReset.jsx        |  4 +--
 .../MappingsFunctions/MappingSearch.jsx       |  4 +--
 .../MappingsFunctions/OntologyCheckboxes.jsx  | 29 ++++++++++++++-----
 5 files changed, 29 insertions(+), 13 deletions(-)

diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index cde1309..374d1cd 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -184,6 +184,7 @@ export const olsFilterOntologiesSearch = (
   results,
   setFacetCounts
 ) => {
+  setLoading(true);
   return fetch(
     `${searchUrl}q=${query}&ontology=${ontologiesToSearch}&rows=${entriesPerPage}&start=${pageStart}`,
     {
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 37ddc73..cc55698 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -235,7 +235,7 @@ export const GetMappingsModal = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferencesCode !== ''
+        apiPreferencesCode?.length > 0
           ? apiPreferencesCode
           : apiPreferenceOntologies(),
         page,
@@ -254,7 +254,7 @@ export const GetMappingsModal = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferencesCode !== '' ? apiPreferencesCode : defaultOntologies,
+        apiPreferencesCode?.length > 0 ? apiPreferencesCode : defaultOntologies,
         page,
         entriesPerPage,
         pageStart,
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 1d5772c..8b954ff 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -156,7 +156,7 @@ export const MappingReset = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferencesCode !== ''
+        apiPreferencesCode?.length > 0
           ? apiPreferencesCode
           : apiPreferenceOntologies(),
         page,
@@ -175,7 +175,7 @@ export const MappingReset = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferencesCode !== '' ? apiPreferencesCode : defaultOntologies,
+        apiPreferencesCode?.length > 0 ? apiPreferencesCode : defaultOntologies,
         page,
         entriesPerPage,
         pageStart,
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 0eccb3c..6c1d7e3 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -158,7 +158,7 @@ export const MappingSearch = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferencesCode !== ''
+        apiPreferencesCode?.length > 0
           ? apiPreferencesCode
           : apiPreferenceOntologies(),
         page,
@@ -177,7 +177,7 @@ export const MappingSearch = ({
       return olsFilterOntologiesSearch(
         searchUrl,
         query,
-        apiPreferencesCode !== '' ? apiPreferencesCode : defaultOntologies,
+        apiPreferencesCode?.length > 0 ? apiPreferencesCode : defaultOntologies,
         page,
         entriesPerPage,
         pageStart,
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index db0c32a..a6900d2 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -29,13 +29,28 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
   } else if (typeof apiPreferencesCode === 'string') {
     processedApiPreferencesCode = apiPreferencesCode.split(',');
   }
-  const existingOntologies = apiPreferencesCode
-    ? processedApiPreferencesCode
-    : preferenceType &&
-      preferenceType[prefTypeKey] &&
-      preferenceType[prefTypeKey]?.api_preference
-    ? Object?.values(preferenceType[prefTypeKey]?.api_preference).flat()
-    : defaultOntologies;
+
+  let existingOntologies;
+
+  // Checks if apiPreferencesCode exists and is non-empty, if so, assigns processedApiPreferencesCode to existingOntologies
+  if (Array.isArray(apiPreferencesCode) && apiPreferencesCode.length > 0) {
+    existingOntologies = processedApiPreferencesCode;
+  }
+  // Checks if preferenceType[prefTypeKey].api_preference exists and is non-empty, if so, assigns the values to existingOntologies
+  else if (
+    preferenceType &&
+    preferenceType[prefTypeKey] &&
+    preferenceType[prefTypeKey].api_preference &&
+    Object.keys(preferenceType[prefTypeKey].api_preference).length > 0
+  ) {
+    existingOntologies = Object.values(
+      preferenceType[prefTypeKey].api_preference
+    ).flat();
+  }
+  // If the above are false, defaultOntologies are used for the search
+  else {
+    existingOntologies = defaultOntologies;
+  }
 
   useEffect(() => {
     setCheckedOntologies(existingOntologies);

From 7560c3ede7f118841e35619c9af0d98438cc8e27 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 8 Nov 2024 15:38:44 -0600
Subject: [PATCH 121/180] Search on tab for mapping search modals

---
 .../Manager/MappingsFunctions/GetMappingsModal.jsx     | 10 ++++++++++
 .../Manager/MappingsFunctions/MappingReset.jsx         |  8 ++++++++
 .../Manager/MappingsFunctions/MappingSearch.jsx        |  9 +++++++++
 3 files changed, 27 insertions(+)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index cc55698..80d8005 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -378,6 +378,15 @@ export const GetMappingsModal = ({
   };
 
   const filteredResultsArray = getFilteredResults();
+
+  // Peforms search on Tab key press
+  const searchOnTab = e => {
+    if (e.key === 'Tab') {
+      e.preventDefault();
+      handleSearch(e.target.value);
+    }
+  };
+
   return (
     <>
       <Modal
@@ -415,6 +424,7 @@ export const GetMappingsModal = ({
                       onSearch={handleSearch}
                       value={inputValue}
                       onChange={handleChange}
+                      onKeyDown={searchOnTab}
                     />
                   </div>
                   <span className="search-desc">{mappingDesc}</span>
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index 8b954ff..dfb508e 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -308,6 +308,13 @@ export const MappingReset = ({
   };
 
   const filteredResultsArray = getFilteredResults();
+  // Peforms search on Tab key press
+  const searchOnTab = e => {
+    if (e.key === 'Tab') {
+      e.preventDefault();
+      handleSearch(e.target.value);
+    }
+  };
   return (
     <>
       <div className="results_modal_container">
@@ -322,6 +329,7 @@ export const MappingReset = ({
                       onSearch={handleSearch}
                       value={inputValue}
                       onChange={handleChange}
+                      onKeyDown={searchOnTab}
                     />
                   </div>
                   <span className="search-desc">{mappingDesc}</span>
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 6c1d7e3..18c8e96 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -370,6 +370,14 @@ export const MappingSearch = ({
 
   const filteredResultsArray = getFilteredResults();
 
+  // Peforms search on Tab key press
+  const searchOnTab = e => {
+    if (e.key === 'Tab') {
+      e.preventDefault();
+      handleSearch(e.target.value);
+    }
+  };
+
   return (
     <>
       <div className="results_modal_container">
@@ -384,6 +392,7 @@ export const MappingSearch = ({
                       onSearch={handleSearch}
                       value={inputValue}
                       onChange={handleChange}
+                      onKeyDown={searchOnTab}
                     />
                   </div>
                   <span className="search-desc">{mappingDesc}</span>

From 863c8b0bd69adf7847c992958b9e5232d050731b Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Fri, 8 Nov 2024 17:10:22 -0600
Subject: [PATCH 122/180] [FD-1791] Exchange qa for uat

---
 .gitignore   | 2 +-
 package.json | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 13a3147..d9ffc16 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,6 +25,6 @@ dist-ssr
 
 # Environment variables
 .env.local
-.env.qa
+.env.uat
 .env.dev
 .env
diff --git a/package.json b/package.json
index efb9880..34885eb 100644
--- a/package.json
+++ b/package.json
@@ -7,7 +7,7 @@
     "dev": "vite",
     "build": "vite build",
     "build-dev": "vite build --mode dev",
-    "build-qa": "vite build --mode qa",
+    "build-uat": "vite build --mode uat",
     "build-alpha": "vite build --mode alpha",
     "lint": "eslint . --ext js,jsx --report-unused-disable-directives --max-warnings 0",
     "preview": "vite preview"

From b8418d518dad709cba338736721013b6db8aa925 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 11 Nov 2024 14:11:12 -0600
Subject: [PATCH 123/180] FD-1680 -- Preferred Terminology Filtering by Name
 and System

---
 .../Projects/Terminologies/PreferredTerminology.jsx | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/components/Projects/Terminologies/PreferredTerminology.jsx b/src/components/Projects/Terminologies/PreferredTerminology.jsx
index dacf0f5..ef66b10 100644
--- a/src/components/Projects/Terminologies/PreferredTerminology.jsx
+++ b/src/components/Projects/Terminologies/PreferredTerminology.jsx
@@ -144,14 +144,17 @@ export const PreferredTerminology = ({ terminology, setTerminology }) => {
     setPreferredData([]);
   };
 
-  // Filters the terminologies that have already been selected out of the main terminology array to avoid duplicates
+  // Filters terminologies that have already been selected (by combination of name and url) out of the main terminology array to avoid duplicates
   const filterTerminologies = () => {
     const terminologiesToExclude = new Set([
-      ...prefTerminologies?.map(pt => pt?.id),
-      ...displaySelectedTerminologies?.map(dst => dst?.id),
-      ...preferredData?.map(ep => ep?.id),
+      ...prefTerminologies?.map(pt => `${pt?.name}|${pt?.url}`),
+      ...displaySelectedTerminologies?.map(dst => `${dst?.name}|${dst?.url}`),
+      ...preferredData?.map(ep => `${ep?.name}|${ep?.url}`),
     ]);
-    return terminologies.filter(t => !terminologiesToExclude?.has(t.id));
+
+    return terminologies.filter(
+      t => !terminologiesToExclude.has(`${t?.name}|${t?.url}`)
+    );
   };
 
   const filteredTerminologyArray = filterTerminologies();

From 90de21269baa5a46a46c61e75a6e2782c4c65e96 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 11 Nov 2024 14:30:28 -0600
Subject: [PATCH 124/180] login gateing studies teminologies and ontologies

---
 src/AppRouter.jsx                 | 40 +++++++++++++++++++++----------
 src/components/Auth/Login.jsx     |  1 +
 src/components/Auth/LoginPage.jsx |  8 +++++++
 src/components/Auth/Logout.jsx    |  1 +
 4 files changed, 37 insertions(+), 13 deletions(-)
 create mode 100644 src/components/Auth/LoginPage.jsx

diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index 6db2e0c..d169a87 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -4,9 +4,11 @@ import {
   Outlet,
   Route,
   Routes,
-  Navigate,
+  Navigate, 
 } from 'react-router-dom';
 import { NavBar } from './components/Nav/NavBar';
+import { Login } from './components/Auth/Login.jsx';
+import { LoginPage } from './components/Auth/LoginPage.jsx';
 import { Breadcrumbs } from './components/Nav/Breadcrumbs.jsx';
 import { Footer } from './components/Nav/Footer';
 import { SearchResults } from './components/Search/SearchResults';
@@ -15,7 +17,6 @@ import { TableDetails } from './components/Projects/Tables/TableDetails';
 import { DDDetails } from './components/Projects/DataDictionaries/DDDetails';
 import { StudyDetails } from './components/Projects/Studies/StudyDetails';
 import { StudyList } from './components/Projects/Studies/StudyList';
-
 import './App.scss';
 import { PageLayout } from './components/Styling/PageLayout.jsx';
 import { MappingContextRoot } from './Contexts/MappingContext.jsx';
@@ -26,6 +27,18 @@ import { SearchContextRoot } from './Contexts/SearchContext.jsx';
 import { About } from './components/About/About.jsx';
 
 export const AppRouter = () => {
+
+  const isLoggedIn = () => {
+    const token = localStorage.getItem('googleToken');
+    if (token) {
+      return true;
+    } else {
+      return false;
+    }
+  }
+
+  
+
   return (
     <BrowserRouter>
       <Routes>
@@ -48,45 +61,46 @@ export const AppRouter = () => {
           <Route element={<PageLayout />}>
             <Route path="/search/:query" element={<SearchResults />} />
             <Route path="/404" element={<Error404 />} />
-            <Route path="/ontologies" element={<OntologyInfo />} />
+            <Route path="/ontologies" element={isLoggedIn() ? <OntologyInfo />: <Navigate to="/login" />} />
             <Route path="/about" element={<About />} />
-            <Route path="/terminologies" element={<TerminologyList />} />
+            <Route path="/terminologies" element={isLoggedIn() ? <TerminologyList />: <Navigate to="/login" />} />
+            <Route path="/login" element={isLoggedIn() ? <Navigate to="/"/> : <LoginPage />} />
             <Route
               path="/terminology"
               element={<Navigate to="/terminologies" />}
             />
             <Route element={<MappingContextRoot />}>
               <Route element={<SearchContextRoot />}>
-                <Route path="/studies" element={<StudyList />} />
+                <Route path="/studies" element={isLoggedIn() ? <StudyList />: <Navigate to="/login" />} />
                 <Route path="/study" element={<Navigate to="/studies" />} />
                 <Route path="/Study/:studyId">
-                  <Route index element={<StudyDetails />} />
+                  <Route index element={isLoggedIn() ? <StudyDetails />: <Navigate to="/login" />} />
                   <Route path="DataDictionary">
-                    <Route index element={<StudyDetails />} />
+                    <Route index element={isLoggedIn() ? <StudyDetails />: <Navigate to="/login" />} />
                     <Route
                       path="/Study/:studyId/DataDictionary/:DDId/Table/"
-                      element={<DDDetails />}
+                      element={isLoggedIn() ? <DDDetails />: <Navigate to="/login" />}
                     />
                     <Route path="/Study/:studyId/DataDictionary/:DDId">
-                      <Route index element={<DDDetails />} />
+                      <Route index element={isLoggedIn() ? <DDDetails />: <Navigate to="/login" />} />
                       <Route
                         path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId"
-                        element={<TableDetails />}
+                        element={isLoggedIn() ? <TableDetails />: <Navigate to="/login" />}
                       />
                       <Route
                         path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/:terminologyId"
-                        element={<Terminology />}
+                        element={isLoggedIn() ? <Terminology />: <Navigate to="/login" />}
                       />
                       <Route
                         path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/"
-                        element={<Terminology />}
+                        element={isLoggedIn() ? <Terminology />: <Navigate to="/login" />}
                       />
                     </Route>
                   </Route>
                 </Route>
                 <Route
                   path="/Terminology/:terminologyId"
-                  element={<Terminology />}
+                  element={isLoggedIn() ? <Terminology />: <Navigate to="/login" />}
                 />
               </Route>
             </Route>
diff --git a/src/components/Auth/Login.jsx b/src/components/Auth/Login.jsx
index 9534a4a..19405d0 100644
--- a/src/components/Auth/Login.jsx
+++ b/src/components/Auth/Login.jsx
@@ -22,6 +22,7 @@ export const Login = () => {
       <GoogleLogin
         theme="filled_black"
         onSuccess={credentialResponse => {
+          localStorage.setItem('googleToken', credentialResponse.access_token); 
           const credentialResponseDecoded = jwtDecode(
             credentialResponse.credential
           );
diff --git a/src/components/Auth/LoginPage.jsx b/src/components/Auth/LoginPage.jsx
new file mode 100644
index 0000000..8dc8395
--- /dev/null
+++ b/src/components/Auth/LoginPage.jsx
@@ -0,0 +1,8 @@
+import { Login } from "./Login"
+export const LoginPage = () => {
+    return <>
+        <div style={{ height:"25rem",display:"flex",flexDirection:"column",justifyContent:"space-around",alignItems:"center"}}>
+            <Login />
+        </div>
+    </>
+}
\ No newline at end of file
diff --git a/src/components/Auth/Logout.jsx b/src/components/Auth/Logout.jsx
index 6ff80c0..38e0920 100644
--- a/src/components/Auth/Logout.jsx
+++ b/src/components/Auth/Logout.jsx
@@ -7,6 +7,7 @@ export const Logout = ({ user, setUser }) => {
   const logOut = () => {
     googleLogout();
     setUser(null);
+    localStorage.removeItem('googleToken');
     localStorage.removeItem('user');
   };
 

From f4163cc94f1cba651cfb5e56163c425e391ef2a2 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 11 Nov 2024 14:52:46 -0600
Subject: [PATCH 125/180] fixing spacing bug

---
 src/App.scss                                      | 9 +++++++--
 src/AppRouter.jsx                                 | 6 ++++--
 src/components/Nav/NavBar.scss                    | 2 --
 src/components/Projects/Studies/StudyStyling.scss | 1 -
 src/components/Search/OntologySearch.scss         | 3 +--
 5 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/src/App.scss b/src/App.scss
index d453759..f90502e 100644
--- a/src/App.scss
+++ b/src/App.scss
@@ -1,11 +1,16 @@
 .approuter_div {
   display: flex;
+  min-height: 100vh;
   flex-direction: column;
   justify-content: space-between;
 }
 
 .outlet_div {
-  min-height: 100vh;
-  height: 100%;
   position: relative;
 }
+
+.header {
+  z-index: 100;
+  position: sticky;
+  top:0;
+}
diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index 6db2e0c..01d9447 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -34,8 +34,10 @@ export const AppRouter = () => {
           element={
             <>
               <div className="approuter_div">
-                <NavBar />
-                <Breadcrumbs />
+                <div className="header">
+                  <NavBar />
+                  <Breadcrumbs />
+                </div>
                 <div className="outlet_div">
                   <Outlet />
                 </div>
diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index a48d239..48efebd 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -11,8 +11,6 @@ nav.navbar {
   display: flex;
   flex-direction: row;
   justify-content: center;
-  position: sticky;
-  top: 0;
 
   li {
     list-style-type: none;
diff --git a/src/components/Projects/Studies/StudyStyling.scss b/src/components/Projects/Studies/StudyStyling.scss
index 7a2cae2..a0d63ba 100644
--- a/src/components/Projects/Studies/StudyStyling.scss
+++ b/src/components/Projects/Studies/StudyStyling.scss
@@ -1,7 +1,6 @@
 .studies_container {
   margin: 5vh 10vw 10vh 10vw;
   line-height: 1.5rem;
-  height: 100vh;
 }
 
 .cards_container {
diff --git a/src/components/Search/OntologySearch.scss b/src/components/Search/OntologySearch.scss
index 3b7753f..4bb37fd 100644
--- a/src/components/Search/OntologySearch.scss
+++ b/src/components/Search/OntologySearch.scss
@@ -1,8 +1,7 @@
 @import '../Styling/Variables';
 
 .search_page {
-  height: 100%;
-  min-height: 100vh;
+
   display: flex;
   flex-direction: column;
   align-items: center;

From 85997e9b33347d55c3105814535c871a659b5a90 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 11 Nov 2024 15:32:30 -0600
Subject: [PATCH 126/180] Bug not recognizing spaces in enumerated dropdown on
 var edit

---
 .../Projects/Tables/EditDataTypeSubForm.jsx         | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/components/Projects/Tables/EditDataTypeSubForm.jsx b/src/components/Projects/Tables/EditDataTypeSubForm.jsx
index 19f91e6..fd47948 100644
--- a/src/components/Projects/Tables/EditDataTypeSubForm.jsx
+++ b/src/components/Projects/Tables/EditDataTypeSubForm.jsx
@@ -57,13 +57,16 @@ function EditDataTypeSubForm({ type, form, editRow, tableData }) {
               }}
               placeholder="Search to Select"
               optionFilterProp="children"
-              filterOption={(input, option) =>
-                (option?.label ?? '').includes(input)
-              }
+              // Searches by terminology name, accounting for spaces in the name
+              filterOption={(input, option) => {
+                const trimmedInput = input.toLowerCase().trim();
+                const optionLabel = (option?.label).toLowerCase().trim();
+                return optionLabel.includes(trimmedInput);
+              }}
               filterSort={(optionA, optionB) =>
-                (optionA?.label ?? '')
+                (optionA?.label)
                   .toLowerCase()
-                  .localeCompare((optionB?.label ?? '').toLowerCase())
+                  .localeCompare((optionB?.label).toLowerCase())
               }
               options={terminologies.map(term => {
                 return {

From cb6e028aaa71e9fe959dd3c755fb00c5e78ee303 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 12 Nov 2024 10:31:22 -0600
Subject: [PATCH 127/180] committing to change branches

---
 src/components/Projects/Tables/TableStyling.scss    | 11 +++++------
 .../Projects/Terminologies/Terminology.jsx          | 13 ++++++++++++-
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/src/components/Projects/Tables/TableStyling.scss b/src/components/Projects/Tables/TableStyling.scss
index 64e5b6e..3e9e654 100644
--- a/src/components/Projects/Tables/TableStyling.scss
+++ b/src/components/Projects/Tables/TableStyling.scss
@@ -81,14 +81,13 @@ input::file-selector-button:hover {
     white-space: nowrap;
   }
   display: flex;
+  &:hover .remove-mapping {
+    transition: all 0.4s linear;
+    opacity: 1;
+  }
   .remove-mapping {
-    padding-left:.25rem;
+    padding-left: 0.25rem;
     cursor: pointer;
     opacity: 0;
-
-    &:hover {
-      transition: all .4s linear;
-      opacity: 1;
-    }
   }
 }
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 6c7699b..4488e1d 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -14,7 +14,11 @@ import {
   Table,
   Tooltip,
 } from 'antd';
-import { CloseCircleOutlined } from '@ant-design/icons';
+import {
+  CloseCircleOutlined,
+  DownOutlined,
+  UpOutlined,
+} from '@ant-design/icons';
 import { EditMappingsModal } from './EditMappingModal';
 import { EditTerminologyDetails } from './EditTerminologyDetails';
 import { SettingsDropdownTerminology } from '../../Manager/Dropdown/SettingsDropdownTerminology';
@@ -153,6 +157,13 @@ It then shows the mappings as table data and alows the user to delete a mapping
     if (variableMappings && variableMappings.mappings?.length) {
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.display}>
+          <span className="mapping_votes remove-mapping">
+            {/* <span
+            id="remove-mapping"
+          > */}
+            <UpOutlined style={{ color: 'blue' }} />
+            <DownOutlined style={{ color: 'green' }} />
+          </span>
           <span className="mapping-display">
             <Tooltip title={code.code}>
               {code.display ? code.display : code.code}

From ef6d90deed5f1cd5b32e6a06238e0440b10b81a5 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 12 Nov 2024 11:37:57 -0600
Subject: [PATCH 128/180] committing to go back to main

---
 src/components/Manager/Utilitiy.jsx           | 11 +++++++
 .../Projects/Tables/TableDetails.jsx          | 27 ++++++++++++----
 .../Projects/Tables/TableStyling.scss         | 10 ++++--
 .../Projects/Terminologies/Terminology.jsx    | 32 +++++++++++--------
 4 files changed, 58 insertions(+), 22 deletions(-)

diff --git a/src/components/Manager/Utilitiy.jsx b/src/components/Manager/Utilitiy.jsx
index 787a5d3..0cbe232 100644
--- a/src/components/Manager/Utilitiy.jsx
+++ b/src/components/Manager/Utilitiy.jsx
@@ -62,3 +62,14 @@ export const ontologyCounts = arr => {
 };
 
 export const cleanedName = data => data?.toLowerCase().replaceAll(' ', '_');
+
+export const mappingTooltip = code => {
+  return (
+    <>
+      <div className="mapping_tooltip">
+        <div>{code.code}</div>
+        <div>{code?.display}</div>
+      </div>
+    </>
+  );
+};
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index e722a53..e3e9aea 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -15,7 +15,11 @@ import {
   Table,
   Tooltip,
 } from 'antd';
-import { CloseCircleOutlined } from '@ant-design/icons';
+import {
+  CloseCircleOutlined,
+  UpCircleOutlined,
+  DownCircleOutlined,
+} from '@ant-design/icons';
 import { EditTableDetails } from './EditTableDetails';
 import { DeleteTable } from './DeleteTable';
 import { LoadVariables } from './LoadVariables';
@@ -31,6 +35,7 @@ import { SettingsDropdownTable } from '../../Manager/Dropdown/SettingsDropdownTa
 import { RequiredLogin } from '../../Auth/RequiredLogin';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
 import { SearchContext } from '../../../Contexts/SearchContext';
+import { ellipsisString } from '../../Manager/Utilitiy';
 
 export const TableDetails = () => {
   const [form] = Form.useForm();
@@ -248,16 +253,26 @@ It then shows the mappings as table data and alows the user to delete a mapping
     const variableMappings = mapping.find(
       item => item?.code === variable?.code
     );
-
     if (variableMappings && variableMappings.mappings?.length) {
       return variableMappings.mappings.map(code => (
-        <div className="mapping" key={code.display}>
+        <div className="mapping" key={code.code}>
+          <span className="mapping_votes mapping_actions">
+            <UpCircleOutlined style={{ color: 'blue' }} />
+            <DownCircleOutlined style={{ color: 'green' }} />
+          </span>
           <span className="mapping-display">
-            {' '}
-            <Tooltip title={code.code}>{code.display}</Tooltip>
+            <Tooltip
+              title={
+                (code.display ? code.display : code.code).length > 25
+                  ? mappingTooltip(code)
+                  : code.code
+              }
+            >
+              {ellipsisString(code.display ? code.display : code.code, '25')}
+            </Tooltip>
           </span>
           <span
-            className="remove-mapping"
+            className="mapping_actions"
             onClick={() => handleRemoveMapping(variableMappings, code)}
           >
             <CloseCircleOutlined style={{ color: 'red' }} />
diff --git a/src/components/Projects/Tables/TableStyling.scss b/src/components/Projects/Tables/TableStyling.scss
index 3e9e654..f6adc5e 100644
--- a/src/components/Projects/Tables/TableStyling.scss
+++ b/src/components/Projects/Tables/TableStyling.scss
@@ -81,13 +81,19 @@ input::file-selector-button:hover {
     white-space: nowrap;
   }
   display: flex;
-  &:hover .remove-mapping {
+  &:hover .mapping_actions {
     transition: all 0.4s linear;
     opacity: 1;
   }
-  .remove-mapping {
+  .mapping_actions {
     padding-left: 0.25rem;
     cursor: pointer;
     opacity: 0;
   }
 }
+
+.mapping_votes {
+  display: flex;
+  gap: 2px;
+  padding-right: 0.25rem;
+}
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 4488e1d..234c6dd 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -16,8 +16,8 @@ import {
 } from 'antd';
 import {
   CloseCircleOutlined,
-  DownOutlined,
-  UpOutlined,
+  DownCircleOutlined,
+  UpCircleOutlined,
 } from '@ant-design/icons';
 import { EditMappingsModal } from './EditMappingModal';
 import { EditTerminologyDetails } from './EditTerminologyDetails';
@@ -32,6 +32,7 @@ import { PreferredTerminology } from './PreferredTerminology';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
 import { AssignMappingsViaButton } from './AssignMappingsViaButton';
+import { ellipsisString, mappingTooltip } from '../../Manager/Utilitiy';
 
 export const Terminology = () => {
   const [form] = Form.useForm();
@@ -153,24 +154,26 @@ It then shows the mappings as table data and alows the user to delete a mapping
     const variableMappings = mapping.find(
       item => item?.code === variable?.code
     );
-
     if (variableMappings && variableMappings.mappings?.length) {
       return variableMappings.mappings.map(code => (
-        <div className="mapping" key={code.display}>
-          <span className="mapping_votes remove-mapping">
-            {/* <span
-            id="remove-mapping"
-          > */}
-            <UpOutlined style={{ color: 'blue' }} />
-            <DownOutlined style={{ color: 'green' }} />
+        <div className="mapping" key={code.code}>
+          <span className="mapping_votes mapping_actions">
+            <UpCircleOutlined style={{ color: 'blue' }} />
+            <DownCircleOutlined style={{ color: 'green' }} />
           </span>
           <span className="mapping-display">
-            <Tooltip title={code.code}>
-              {code.display ? code.display : code.code}
+            <Tooltip
+              title={
+                (code.display ? code.display : code.code).length > 25
+                  ? mappingTooltip(code)
+                  : code.code
+              }
+            >
+              {ellipsisString(code.display ? code.display : code.code, '25')}
             </Tooltip>
           </span>
           <span
-            className="remove-mapping"
+            className="mapping_actions"
             onClick={() => handleRemoveMapping(variableMappings, code)}
           >
             <CloseCircleOutlined style={{ color: 'red' }} />
@@ -304,8 +307,9 @@ It then shows the mappings as table data and alows the user to delete a mapping
     {
       title: 'Description',
       dataIndex: 'description',
+      width: 300,
     },
-    { title: 'Mapped Terms', dataIndex: 'mapped_terms', width: 90 },
+    { title: 'Mapped Terms', dataIndex: 'mapped_terms', width: 120 },
     {
       title: '',
       dataIndex: 'delete_column',

From fed2769f6082f592061bfba83ae6df78c5446353 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 12 Nov 2024 22:08:16 -0600
Subject: [PATCH 129/180] Began work on voting on a mapping

---
 .../MappingsFunctions/MappingVotes.jsx        | 41 +++++++++++
 .../Projects/Tables/TableDetails.jsx          | 16 +++--
 .../Projects/Tables/TableStyling.scss         | 10 ++-
 .../Projects/Terminologies/Terminology.jsx    | 68 +++++++++++++------
 4 files changed, 108 insertions(+), 27 deletions(-)
 create mode 100644 src/components/Manager/MappingsFunctions/MappingVotes.jsx

diff --git a/src/components/Manager/MappingsFunctions/MappingVotes.jsx b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
new file mode 100644
index 0000000..84512a8
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
@@ -0,0 +1,41 @@
+export const MappingVotes = (
+  variableMappings,
+  code,
+  user,
+  vote,
+  vocabUrl,
+  terminologyId,
+  notification
+) => {
+  const mappingVoteDTO = {
+    editor: user?.email,
+    vote: vote,
+  };
+
+  return fetch(
+    `${vocabUrl}/Terminology/${terminologyId}/user_input/${variableMappings?.code}/${code?.code}/mapping_votes`,
+    {
+      method: 'PUT',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify(mappingVoteDTO),
+    }
+  )
+    .then(res => {
+      if (res.ok) {
+        return res.json();
+      } else {
+        throw new Error('An unknown error occurred.');
+      }
+    })
+    .catch(error => {
+      if (error) {
+        notification.error({
+          message: 'Error',
+          description: 'An error occurred saving the ontology preferences.',
+        });
+      }
+      return error;
+    });
+};
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index e3e9aea..c8f9398 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -235,13 +235,15 @@ and returns the length of the mapping array (i.e. returns the number of variable
 It then shows the mappings as table data and alows the user to delete a mapping from the table.*/
   const noMapping = variable => {
     return (
-      <Button
-        onClick={() =>
-          setGetMappings({ name: variable.name, code: variable.code })
-        }
-      >
-        Get Mappings
-      </Button>
+      <div className="no_mapping_button">
+        <Button
+          onClick={() =>
+            setGetMappings({ name: variable.name, code: variable.code })
+          }
+        >
+          Get Mappings
+        </Button>
+      </div>
     );
   };
 
diff --git a/src/components/Projects/Tables/TableStyling.scss b/src/components/Projects/Tables/TableStyling.scss
index f6adc5e..89ad784 100644
--- a/src/components/Projects/Tables/TableStyling.scss
+++ b/src/components/Projects/Tables/TableStyling.scss
@@ -81,6 +81,7 @@ input::file-selector-button:hover {
     white-space: nowrap;
   }
   display: flex;
+  align-items: center;
   &:hover .mapping_actions {
     transition: all 0.4s linear;
     opacity: 1;
@@ -94,6 +95,13 @@ input::file-selector-button:hover {
 
 .mapping_votes {
   display: flex;
-  gap: 2px;
+  flex-direction: column;
+  align-items: center;
+  // gap: 2px;
   padding-right: 0.25rem;
+  font-size: 0.7rem;
+}
+
+.no_mapping_button {
+  padding-left: 2rem;
 }
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 234c6dd..8bb2d56 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -16,8 +16,8 @@ import {
 } from 'antd';
 import {
   CloseCircleOutlined,
-  DownCircleOutlined,
-  UpCircleOutlined,
+  DownOutlined,
+  UpOutlined,
 } from '@ant-design/icons';
 import { EditMappingsModal } from './EditMappingModal';
 import { EditTerminologyDetails } from './EditTerminologyDetails';
@@ -33,6 +33,7 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
 import { AssignMappingsViaButton } from './AssignMappingsViaButton';
 import { ellipsisString, mappingTooltip } from '../../Manager/Utilitiy';
+import { MappingVotes } from '../../Manager/MappingsFunctions/MappingVotes';
 
 export const Terminology = () => {
   const [form] = Form.useForm();
@@ -129,21 +130,23 @@ and returns the length of the mapping array (i.e. returns the number of codes ma
 It then shows the mappings as table data and alows the user to delete a mapping from the table.*/
 
   const noMapping = variable => (
-    <Button
-      onClick={() => {
-        prefTerminologies.length > 0
-          ? setAssignMappingsViaButton({
-              display: variable.display,
-              code: variable.code,
-            })
-          : setGetMappings({
-              display: variable.display,
-              code: variable.code,
-            });
-      }}
-    >
-      {prefTerminologies?.length > 0 ? 'Assign Mappings' : 'Get Mappings'}
-    </Button>
+    <div className="no_mapping_button">
+      <Button
+        onClick={() => {
+          prefTerminologies.length > 0
+            ? setAssignMappingsViaButton({
+                display: variable.display,
+                code: variable.code,
+              })
+            : setGetMappings({
+                display: variable.display,
+                code: variable.code,
+              });
+        }}
+      >
+        {prefTerminologies?.length > 0 ? 'Assign Mappings' : 'Get Mappings'}
+      </Button>
+    </div>
   );
 
   const matchCode = variable => {
@@ -158,8 +161,35 @@ It then shows the mappings as table data and alows the user to delete a mapping
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.code}>
           <span className="mapping_votes mapping_actions">
-            <UpCircleOutlined style={{ color: 'blue' }} />
-            <DownCircleOutlined style={{ color: 'green' }} />
+            <UpOutlined
+              style={{ color: 'blue' }}
+              onClick={() =>
+                MappingVotes(
+                  variableMappings,
+                  code,
+                  user,
+                  'up',
+                  vocabUrl,
+                  terminologyId,
+                  notification
+                )
+              }
+            />
+            0
+            <DownOutlined
+              style={{ color: 'green' }}
+              onClick={() =>
+                MappingVotes(
+                  variableMappings,
+                  code,
+                  user,
+                  'down',
+                  vocabUrl,
+                  terminologyId,
+                  notification
+                )
+              }
+            />
           </span>
           <span className="mapping-display">
             <Tooltip

From 2155c5d96aa1db4292ab2bb6ebe5c52ea8de021e Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 13 Nov 2024 12:48:58 -0600
Subject: [PATCH 130/180] Began work on adding mapping comments

---
 .../MappingsFunctions/FilterOntology.jsx      |  17 +--
 .../MappingsFunctions/MappingComments.jsx     | 101 ++++++++++++++++++
 .../MappingsFunctions/MappingVotes.jsx        |   2 +-
 .../SelectPreferredTerminologies.jsx          |  33 +-----
 .../Projects/Terminologies/Terminology.jsx    |  19 ++++
 5 files changed, 123 insertions(+), 49 deletions(-)
 create mode 100644 src/components/Manager/MappingsFunctions/MappingComments.jsx

diff --git a/src/components/Manager/MappingsFunctions/FilterOntology.jsx b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
index 595e074..167d012 100644
--- a/src/components/Manager/MappingsFunctions/FilterOntology.jsx
+++ b/src/components/Manager/MappingsFunctions/FilterOntology.jsx
@@ -87,21 +87,6 @@ export const FilterOntology = ({
     }
   };
 
-  const selectedOntDisplay = (ont, i) => {
-    return (
-      <>
-        <div key={i} className="modal_search_result">
-          <div>
-            <div className="modal_term_ontology">
-              <div>{ont?.curie}</div>
-            </div>
-            <div>{ont?.ontology_title}</div>
-          </div>
-        </div>
-      </>
-    );
-  };
-
   const checkBoxDisplay = (ont, i) => {
     return (
       <>
@@ -211,7 +196,7 @@ export const FilterOntology = ({
                     value={selected}
                     onChange={e => onCheckboxChange(e, selected)}
                   >
-                    {selectedOntDisplay(selected, i)}
+                    {checkBoxDisplay(selected, i)}
                   </Checkbox>
                 ))}
               </div>
diff --git a/src/components/Manager/MappingsFunctions/MappingComments.jsx b/src/components/Manager/MappingsFunctions/MappingComments.jsx
new file mode 100644
index 0000000..6b6ce4d
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/MappingComments.jsx
@@ -0,0 +1,101 @@
+import { Button, Form, Input, Modal, notification } from 'antd';
+import { useContext } from 'react';
+import { myContext } from '../../../App';
+
+export const MappingComments = ({
+  code,
+  variableMappings,
+  setComment,
+  terminologyId,
+}) => {
+  const [form] = Form.useForm();
+  const { vocabUrl, user } = useContext(myContext);
+  const { TextArea } = Input;
+
+  const onClose = () => {
+    setComment(null);
+  };
+
+  const onFinish = values => {
+    const mappingCommentDTO = {
+      editor: user?.email,
+      note: values.comment,
+    };
+
+    return fetch(
+      `${vocabUrl}/Terminology/${terminologyId}/user_input/${variableMappings}/${code}/mapping_conversations`,
+      {
+        method: 'PUT',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify(mappingCommentDTO),
+      }
+    )
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .catch(error => {
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred saving the comment.',
+          });
+        }
+        return error;
+      });
+  };
+
+  return (
+    <>
+      <Modal
+        open={!!code}
+        width={'70%'}
+        styles={{
+          body: {
+            minHeight: '60vh',
+            maxHeight: '60vh',
+          },
+        }}
+        footer={[<Button onClick={onClose}>Close</Button>]}
+        maskClosable={false}
+        closeIcon={false}
+        destroyOnClose={true}
+      >
+        <Form
+          form={form}
+          layout="inline"
+          onFinish={() => {
+            form.validateFields().then(values => {
+              onFinish(values);
+              onClose();
+            });
+          }}
+          preserve={false}
+        >
+          <Form.Item name="comment">
+            <TextArea
+              rows={1}
+              style={{
+                width: 500,
+                resize: 'both',
+              }}
+              showCount
+              maxLength={1000}
+              autoFocus
+            />
+          </Form.Item>
+          <Form.Item>
+            <Button type="primary" htmlType="submit">
+              Comment
+            </Button>
+          </Form.Item>
+        </Form>
+      </Modal>
+    </>
+  );
+};
diff --git a/src/components/Manager/MappingsFunctions/MappingVotes.jsx b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
index 84512a8..e15d5ff 100644
--- a/src/components/Manager/MappingsFunctions/MappingVotes.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
@@ -33,7 +33,7 @@ export const MappingVotes = (
       if (error) {
         notification.error({
           message: 'Error',
-          description: 'An error occurred saving the ontology preferences.',
+          description: 'An error occurred saving the vote.',
         });
       }
       return error;
diff --git a/src/components/Projects/Terminologies/SelectPreferredTerminologies.jsx b/src/components/Projects/Terminologies/SelectPreferredTerminologies.jsx
index a7fdaa1..1062e83 100644
--- a/src/components/Projects/Terminologies/SelectPreferredTerminologies.jsx
+++ b/src/components/Projects/Terminologies/SelectPreferredTerminologies.jsx
@@ -96,37 +96,6 @@ export const SelectPreferredTerminologies = ({
     setTerminologies(updatedTerminologies);
   };
 
-  const selectedTermsDisplay = (selected, index) => {
-    return (
-      <>
-        <div key={index} className="modal_display_result">
-          <div>
-            <div className="modal_term_ontology">
-              <div>
-                <Link
-                  to={`/Terminology/${selected.id}`}
-                  target="_blank"
-                  className="terminology_link"
-                >
-                  <b>{selected?.name ? selected.name : selected.id}</b>
-                </Link>
-              </div>
-            </div>
-            <div>
-              {selected?.description?.length > 125 ? (
-                <Tooltip title={selected?.description} mouseEnterDelay={0.5}>
-                  {ellipsisString(selected?.description, '125')}
-                </Tooltip>
-              ) : (
-                ellipsisString(selected?.description, '125')
-              )}
-            </div>
-          </div>
-        </div>
-      </>
-    );
-  };
-
   const checkBoxDisplay = (item, index) => {
     return (
       <>
@@ -238,7 +207,7 @@ export const SelectPreferredTerminologies = ({
                         value={selected}
                         onChange={e => onCheckboxChange(e, selected)}
                       >
-                        {selectedTermsDisplay(selected, i)}
+                        {checkBoxDisplay(selected, i)}
                       </Checkbox>
                     ))}
                   </div>
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 8bb2d56..6d6b218 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -17,6 +17,7 @@ import {
 import {
   CloseCircleOutlined,
   DownOutlined,
+  MessageOutlined,
   UpOutlined,
 } from '@ant-design/icons';
 import { EditMappingsModal } from './EditMappingModal';
@@ -34,6 +35,7 @@ import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
 import { AssignMappingsViaButton } from './AssignMappingsViaButton';
 import { ellipsisString, mappingTooltip } from '../../Manager/Utilitiy';
 import { MappingVotes } from '../../Manager/MappingsFunctions/MappingVotes';
+import { MappingComments } from '../../Manager/MappingsFunctions/MappingComments';
 
 export const Terminology = () => {
   const [form] = Form.useForm();
@@ -55,6 +57,7 @@ export const Terminology = () => {
     parseInt(localStorage.getItem('pageSize'), 10) || 10
   );
   const [assignMappingsViaButton, setAssignMappingsViaButton] = useState(false);
+  const [comment, setComment] = useState(false);
   const handleTableChange = (current, size) => {
     setPageSize(size);
   };
@@ -160,6 +163,16 @@ It then shows the mappings as table data and alows the user to delete a mapping
     if (variableMappings && variableMappings.mappings?.length) {
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.code}>
+          <span className="mapping_actions">
+            <MessageOutlined
+              onClick={() =>
+                setComment({
+                  code: code.code,
+                  variableMappings: variableMappings.code,
+                })
+              }
+            />
+          </span>
           <span className="mapping_votes mapping_actions">
             <UpOutlined
               style={{ color: 'blue' }}
@@ -493,6 +506,12 @@ It then shows the mappings as table data and alows the user to delete a mapping
             setAssignMappingsViaButton={setAssignMappingsViaButton}
             terminology={terminology}
           />
+          <MappingComments
+            code={comment?.code}
+            variableMappings={comment?.variableMappings}
+            setComment={setComment}
+            terminologyId={terminologyId}
+          />
         </div>
       )}
     </>

From 8b7df8ebea8dbc60c93bcc9ad19988989f08656a Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 14 Nov 2024 06:04:46 -0600
Subject: [PATCH 131/180] main routes are protected

---
 src/AppRouter.jsx             | 24 +++++++++++++++++++-----
 src/components/Auth/Login.jsx |  8 ++++++--
 2 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index d169a87..c198640 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -4,7 +4,8 @@ import {
   Outlet,
   Route,
   Routes,
-  Navigate, 
+  Navigate,
+  useLocation
 } from 'react-router-dom';
 import { NavBar } from './components/Nav/NavBar';
 import { Login } from './components/Auth/Login.jsx';
@@ -37,7 +38,19 @@ export const AppRouter = () => {
     }
   }
 
+ 
+
+  function ProtectedRoute({ children }) {
+    const location = useLocation();
+  
+    // If the user is not logged in, redirect to login with the intended destination path
+    if (!isLoggedIn()) {
+      return <Navigate to="/login" replace state={{ from: location }} />;
+    }
   
+    // Otherwise, render the child component (e.g., DDDetails)
+    return children;
+  }
 
   return (
     <BrowserRouter>
@@ -61,17 +74,18 @@ export const AppRouter = () => {
           <Route element={<PageLayout />}>
             <Route path="/search/:query" element={<SearchResults />} />
             <Route path="/404" element={<Error404 />} />
-            <Route path="/ontologies" element={isLoggedIn() ? <OntologyInfo />: <Navigate to="/login" />} />
+            
+            <Route path="/ontologies" element={ <ProtectedRoute><OntologyInfo /></ProtectedRoute>} />
             <Route path="/about" element={<About />} />
-            <Route path="/terminologies" element={isLoggedIn() ? <TerminologyList />: <Navigate to="/login" />} />
-            <Route path="/login" element={isLoggedIn() ? <Navigate to="/"/> : <LoginPage />} />
+            <Route path="/terminologies" element={<ProtectedRoute><TerminologyList /></ProtectedRoute>} />
+            <Route path="/login" element={<LoginPage/>}/>
             <Route
               path="/terminology"
               element={<Navigate to="/terminologies" />}
             />
             <Route element={<MappingContextRoot />}>
               <Route element={<SearchContextRoot />}>
-                <Route path="/studies" element={isLoggedIn() ? <StudyList />: <Navigate to="/login" />} />
+                <Route path="/studies" element={<ProtectedRoute><StudyList /></ProtectedRoute>} />
                 <Route path="/study" element={<Navigate to="/studies" />} />
                 <Route path="/Study/:studyId">
                   <Route index element={isLoggedIn() ? <StudyDetails />: <Navigate to="/login" />} />
diff --git a/src/components/Auth/Login.jsx b/src/components/Auth/Login.jsx
index 19405d0..7daa5fb 100644
--- a/src/components/Auth/Login.jsx
+++ b/src/components/Auth/Login.jsx
@@ -3,10 +3,12 @@ import { jwtDecode } from 'jwt-decode';
 import { useContext, useEffect } from 'react';
 import { Logout } from './Logout';
 import { myContext } from '../../App';
-
+import { useLocation, useNavigate } from 'react-router-dom';
 export const Login = () => {
   const { user, setUser } = useContext(myContext);
-
+  const location = useLocation();
+  const navigate = useNavigate();
+  const from = location.state?.from?.pathname || '/'
   useEffect(() => {
     const storedUser = localStorage.getItem('user');
     if (storedUser) {
@@ -31,6 +33,8 @@ export const Login = () => {
             'user',
             JSON.stringify(credentialResponseDecoded)
           );
+          navigate(from, { replace: true });
+          
         }}
         onError={() => {
           console.log('Login Failed');

From bf0bdf18856ad0a055ce311eb0a96fddc21b5bef Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 14 Nov 2024 06:12:33 -0600
Subject: [PATCH 132/180] fixed background issue

---
 src/App.scss                              | 11 +++++++++++
 src/components/Search/OntologySearch.scss |  8 +-------
 src/components/Styling/PageLayout.jsx     |  7 ++-----
 3 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/App.scss b/src/App.scss
index f90502e..7fa32b7 100644
--- a/src/App.scss
+++ b/src/App.scss
@@ -1,3 +1,11 @@
+body{
+
+    background: url('./assets/Background.png');
+    background-size: 100vw;
+    background-repeat: no-repeat;
+    background-position: calc(50% - 50px) 50%;
+
+}
 .approuter_div {
   display: flex;
   min-height: 100vh;
@@ -7,6 +15,7 @@
 
 .outlet_div {
   position: relative;
+  background-color: rgba(255,255,255,.6);
 }
 
 .header {
@@ -14,3 +23,5 @@
   position: sticky;
   top:0;
 }
+
+
diff --git a/src/components/Search/OntologySearch.scss b/src/components/Search/OntologySearch.scss
index 4bb37fd..02814e6 100644
--- a/src/components/Search/OntologySearch.scss
+++ b/src/components/Search/OntologySearch.scss
@@ -6,13 +6,7 @@
   flex-direction: column;
   align-items: center;
   justify-content: center;
-  background: {
-    image: url('../../assets/Background.png');
-    size: 100vw;
-    repeat: no-repeat;
-    position: calc(50% - 50px) 50%;
-  }
-  z-index: -1;
+padding:10rem 0rem;
 }
 
 .search_field {
diff --git a/src/components/Styling/PageLayout.jsx b/src/components/Styling/PageLayout.jsx
index d95aab8..fec5483 100644
--- a/src/components/Styling/PageLayout.jsx
+++ b/src/components/Styling/PageLayout.jsx
@@ -3,11 +3,8 @@ import Background from '../../assets/Background.png';
 
 export const PageLayout = () => {
   return (
-    <div>
-      <div className="image_container">
-        <img className="background_image_results" src={Background} />
-      </div>
+    <>
       <Outlet />
-    </div>
+    </>
   );
 };

From d9ff52f2d5d0f1fd396ba5105c0f347099f9fe36 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 14 Nov 2024 06:30:18 -0600
Subject: [PATCH 133/180] Pagination on history

---
 src/components/Manager/ShowHistory.jsx | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/components/Manager/ShowHistory.jsx b/src/components/Manager/ShowHistory.jsx
index 8459afb..306afd3 100644
--- a/src/components/Manager/ShowHistory.jsx
+++ b/src/components/Manager/ShowHistory.jsx
@@ -16,6 +16,7 @@ export const ShowHistory = ({
   const { vocabUrl } = useContext(myContext);
   const [provData, setProvData] = useState([]);
   const [loading, setLoading] = useState(true);
+  const [pageSize, setPageSize] = useState(10);
 
   // If the showHistory key matches the key of the row clicked, the provenance data is fetched
   useEffect(() => {
@@ -81,6 +82,12 @@ export const ShowHistory = ({
       new_value: prov.new_value,
       editor: prov.editor,
     })) ?? [];
+
+  const handleTableChange = (current, size) => {
+    setPageSize(size);
+  };
+
+
   return (
     showHistory === tableData.key && (
       <Modal
@@ -107,7 +114,12 @@ export const ShowHistory = ({
             <Table
               columns={columns}
               dataSource={dataSource}
-              pagination={false}
+              pagination={{
+                showSizeChanger: true,
+                pageSizeOptions: ['10', '20', '30'],
+                pageSize: pageSize, // Use the stored pageSize
+                onChange: handleTableChange
+              }} // Capture pagination changes
               size="small"
             />
           </>

From ef35028ff6e95d3aade9935c8db30e570c610663 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Thu, 14 Nov 2024 09:35:58 -0600
Subject: [PATCH 134/180] sorting date

---
 src/components/Manager/ShowHistory.jsx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/components/Manager/ShowHistory.jsx b/src/components/Manager/ShowHistory.jsx
index 306afd3..0d99bab 100644
--- a/src/components/Manager/ShowHistory.jsx
+++ b/src/components/Manager/ShowHistory.jsx
@@ -81,7 +81,11 @@ export const ShowHistory = ({
       old_value: prov.old_value,
       new_value: prov.new_value,
       editor: prov.editor,
-    })) ?? [];
+    })).sort((a, b) => {
+      const dateA = new Date(a.timestamp);
+      const dateB = new Date(b.timestamp);
+      return dateB - dateA;
+    }) ?? [];
 
   const handleTableChange = (current, size) => {
     setPageSize(size);
@@ -110,7 +114,6 @@ export const ShowHistory = ({
             <div>
               <h4>{code}</h4>
             </div>
-
             <Table
               columns={columns}
               dataSource={dataSource}

From d96237f78bfccac35c1c0bcfc4445dbd10561bee Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 14 Nov 2024 11:17:16 -0600
Subject: [PATCH 135/180] Added mapping display to mapping comments

---
 src/components/Manager/MappingsFunctions/MappingComments.jsx | 2 ++
 src/components/Projects/Terminologies/Terminology.jsx        | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/src/components/Manager/MappingsFunctions/MappingComments.jsx b/src/components/Manager/MappingsFunctions/MappingComments.jsx
index 6b6ce4d..fa58ed9 100644
--- a/src/components/Manager/MappingsFunctions/MappingComments.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingComments.jsx
@@ -4,6 +4,7 @@ import { myContext } from '../../../App';
 
 export const MappingComments = ({
   code,
+  codeDisplay,
   variableMappings,
   setComment,
   terminologyId,
@@ -66,6 +67,7 @@ export const MappingComments = ({
         closeIcon={false}
         destroyOnClose={true}
       >
+        {variableMappings} : {codeDisplay}
         <Form
           form={form}
           layout="inline"
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 6d6b218..5714b6c 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -168,6 +168,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
               onClick={() =>
                 setComment({
                   code: code.code,
+                  display: code.display,
                   variableMappings: variableMappings.code,
                 })
               }
@@ -508,6 +509,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
           />
           <MappingComments
             code={comment?.code}
+            codeDisplay={comment?.display}
             variableMappings={comment?.variableMappings}
             setComment={setComment}
             terminologyId={terminologyId}

From f39e6d13acb3673b011aeeddbfc0abd2328c5966 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 18 Nov 2024 14:23:20 -0600
Subject: [PATCH 136/180] bread crumbs names corrected

---
 src/components/Nav/Breadcrumbs.jsx | 82 +++++++++++++++++++++++-------
 1 file changed, 64 insertions(+), 18 deletions(-)

diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
index 245d2f0..a69b81c 100644
--- a/src/components/Nav/Breadcrumbs.jsx
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -1,34 +1,80 @@
 import { Breadcrumb } from 'antd';
 import { useLocation, Link } from 'react-router-dom';
-// import { Link } from 'react-router';
+import { useEffect, useContext, useState, useMemo } from 'react';
+import { getById } from '../Manager/FetchManager';
+import { myContext } from '../../App';
+
 export const Breadcrumbs = () => {
+  const { vocabUrl } = useContext(myContext);
   const location = useLocation();
-  const pathParts = location.pathname.split('/').filter(Boolean);
-  const pathArr = [];
-  pathParts.forEach(path => {
-    pathArr.push({ title: path, path: path });
-  });
+
+  // Memoize path parts to avoid unnecessary recalculations
+  const pathParts = useMemo(() => location.pathname.split('/').filter(Boolean), [location.pathname]);
+  const [updatedPathArr, setUpdatedPathArr] = useState([]);
+
+  useEffect(() => {
+    const controller = new AbortController(); // For canceling stale requests
+
+    const fetchBreadcrumbData = async () => {
+      const pathArr = pathParts.map((path) => ({ title: path, path: path }));
+
+      try {
+        const promises = [];
+        for (let i = 0; i < pathArr.length; i += 2) {
+          if (i + 1 < pathArr.length) {
+            promises.push(
+              getById(vocabUrl, pathArr[i].path, pathArr[i + 1].path, { signal: controller.signal }).then((result) => {
+                pathArr[i + 1] = { ...pathArr[i + 1], title: result.name };
+              })
+            );
+          }
+        }
+
+        await Promise.all(promises); // Wait for all `getById` calls to finish
+        setUpdatedPathArr([...pathArr]);
+      } catch (error) {
+        if (error.name === 'AbortError') {
+          console.log('Request aborted:', error); // Ignore aborted fetches
+        } else {
+          console.error('Fetch error:', error);
+        }
+      }
+    };
+
+    fetchBreadcrumbData();
+
+    return () => {
+      controller.abort(); // Cleanup stale requests
+    };
+  }, [vocabUrl, pathParts]); // Dependencies: vocabUrl and pathParts
+
+  if (!updatedPathArr.length) {
+    return null; // Show nothing until breadcrumbs are loaded
+  }
 
   return (
     <span className="breadcrumbs">
       <li>
-        <Link to={'/'}>Home</Link>{' '}
-        {location.pathname != '/' && <span>&nbsp;&nbsp;/&nbsp;&nbsp;</span>}
+        <Link to="/">Home</Link>{' '}
+        {location.pathname !== '/' && <span>&nbsp;&nbsp;/&nbsp;&nbsp;</span>}
       </li>
-      <Breadcrumb itemRender={itemRender} items={pathArr} />
+      <Breadcrumb itemRender={(route, params, items) => itemRender(route, params, items)} items={updatedPathArr} />
     </span>
   );
 };
-function itemRender(currentRoute, params, items, pathArr) {
+
+function itemRender(currentRoute, params, items) {
   const isLast = currentRoute?.path === items[items.length - 1]?.path;
 
-  return (
-    <>
-      {isLast ? (
-        <span>{currentRoute.title}</span>
-      ) : (
-        <Link to={`/${pathArr.join('/')}`}>{currentRoute.title}</Link>
-      )}
-    </>
+  // Build cumulative path
+  const cumulativePath = items
+    .slice(0, items.findIndex((item) => item.path === currentRoute.path) + 1)
+    .map((item) => item.path)
+    .join('/');
+
+  return isLast ? (
+    <span>{currentRoute.title}</span>
+  ) : (
+    <Link to={`/${cumulativePath}`}>{currentRoute.title}</Link>
   );
 }

From cfc58b8a462f92aa3a5027905b465ac14c3715d7 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 18 Nov 2024 14:26:00 -0600
Subject: [PATCH 137/180] both pref terminologies and ols search mappings
 showing up when selected

---
 .../Error/AssignMappingsCheckboxes.jsx        | 166 ---------
 .../MappingsFunctions/MappingSearch.jsx       | 345 ++++++++++++++----
 .../MappingsFunctions/MappingsFunctions.scss  |  23 +-
 .../MappingsFunctions/OntologyCheckboxes.jsx  |   6 +-
 .../Terminologies/EditMappingModal.jsx        |   3 -
 5 files changed, 301 insertions(+), 242 deletions(-)
 delete mode 100644 src/components/Error/AssignMappingsCheckboxes.jsx

diff --git a/src/components/Error/AssignMappingsCheckboxes.jsx b/src/components/Error/AssignMappingsCheckboxes.jsx
deleted file mode 100644
index caaf518..0000000
--- a/src/components/Error/AssignMappingsCheckboxes.jsx
+++ /dev/null
@@ -1,166 +0,0 @@
-import { useEffect, useState } from 'react';
-import { Checkbox, Form, Tooltip } from 'antd';
-import { ellipsisString } from '../Utilitiy';
-import { APISearchBar } from '../../Projects/Terminologies/APISearchBar';
-import { DisplaySelected } from './DisplaySelected';
-import { APIResults } from '../../Projects/Terminologies/APIResults';
-
-export const AssignMappingsCheckboxes = ({
-  terminologiesToMap,
-  form,
-  selectedBoxes,
-  setSelectedBoxes,
-  searchProp,
-}) => {
-  const [active, setActive] = useState(null);
-  const [displaySelectedMappings, setDisplaySelectedMappings] = useState([]);
-  const [allCheckboxes, setAllCheckboxes] = useState([]);
-  const [loading, setLoading] = useState(false);
-
-  useEffect(() => {
-    setActive(terminologiesToMap?.[0]?.id);
-  }, [terminologiesToMap]);
-
-  useEffect(() => {
-    setAllCheckboxes(
-      terminologiesToMap.find(term => term.id === active)?.codes ?? []
-    );
-  }, [active]);
-
-  useEffect(() => {
-    form.setFieldsValue({
-      selected_terminologies: selectedBoxes,
-    });
-  }, [selectedBoxes, form]);
-
-  const onSelectedChange = checkedValues => {
-    const selected = JSON.parse(checkedValues?.[checkedValues.length - 1]);
-
-    // Adds the selectedMappings to the selectedBoxes to ensure they are checked
-    setSelectedBoxes(prevState => {
-      const updated = [...prevState, selected];
-      // Sets the values for the form to the selectedMappings checkboxes that are checked
-      form.setFieldsValue({ selected_mappings: updated });
-      return updated;
-    });
-
-    setDisplaySelectedMappings(prevState => [...prevState, selected]);
-  };
-
-  const checkBoxDisplay = (item, index) => {
-    return (
-      <>
-        <div key={index} className="modal_search_result">
-          <div key={index} className="modal_display_result">
-            <div>
-              <div className="modal_term_ontology">
-                <div>{item.code}</div>
-              </div>
-              <div>{item.display}</div>
-              <div>
-                {item?.description?.length > 85 ? (
-                  <Tooltip
-                    placement="topRight"
-                    mouseEnterDelay={0.5}
-                    title={item?.description}
-                  >
-                    {ellipsisString(item?.description, '85')}
-                  </Tooltip>
-                ) : (
-                  ellipsisString(item?.description, '85')
-                )}
-              </div>
-            </div>
-          </div>
-        </div>
-      </>
-    );
-  };
-  const mappedTerminology = () => {
-    return (
-      <Form form={form} layout="vertical">
-        {displaySelectedMappings?.length > 0 && (
-          <>
-            <h4>Selected</h4>
-            <DisplaySelected
-              displaySelectedMappings={displaySelectedMappings}
-              form={form}
-              selectedBoxes={selectedBoxes}
-              setSelectedBoxes={setSelectedBoxes}
-            />
-          </>
-        )}
-        <h4>Codes</h4>
-        {active === 'search' ? (
-          <APIResults
-            loading={loading}
-            displaySelectedMappings={displaySelectedMappings}
-            onSelectedChange={onSelectedChange}
-          />
-        ) : (
-          <>
-            <Form.Item
-              name={['mappings']}
-              valuePropName="value"
-              rules={[
-                {
-                  required: false,
-                },
-              ]}
-            >
-              <Checkbox.Group
-                className="mappings_checkbox"
-                options={allCheckboxes
-                  .filter(
-                    checkbox =>
-                      !displaySelectedMappings.some(
-                        dsm => checkbox.code === dsm.code
-                      )
-                  )
-                  .map((code, index) => ({
-                    value: JSON.stringify({
-                      code: code.code,
-                      display: code.display,
-                      description: code.description,
-                      system: code.system,
-                    }),
-                    label: checkBoxDisplay(code, index),
-                  }))}
-                onChange={onSelectedChange}
-              />
-            </Form.Item>
-          </>
-        )}
-      </Form>
-    );
-  };
-
-  return (
-    <>
-      <h4>{searchProp}</h4>
-      {terminologiesToMap?.length && (
-        <div className="assign_map_checkbox_container">
-          <div className="assign_map_checkbox_wrapper">
-            {terminologiesToMap.map((term, i) => (
-              <div
-                key={i}
-                className={active === term.id ? 'active_term' : 'inactive_term'}
-                onClick={() => setActive(term.id)}
-              >
-                {term.name}
-              </div>
-            ))}
-            <APISearchBar
-              active={active}
-              setActive={setActive}
-              searchProp={searchProp}
-              selectedBoxes={selectedBoxes}
-              setLoading={setLoading}
-            />
-          </div>
-          <div className="assign_map_checkboxes">{mappedTerminology()}</div>
-        </div>
-      )}
-    </>
-  );
-};
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 18c8e96..0305f3c 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -7,6 +7,7 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
+import { APISearchBar } from '../../Projects/Terminologies/APISearchBar';
 
 export const MappingSearch = ({
   setEditMappings,
@@ -27,6 +28,8 @@ export const MappingSearch = ({
     setApiPreferencesCode,
     apiPreferencesCode,
     setUnformattedPref,
+    prefTerminologies,
+    setApiResults,
   } = useContext(SearchContext);
 
   const [page, setPage] = useState(0);
@@ -39,6 +42,9 @@ export const MappingSearch = ({
   const [filteredResultsCount, setFilteredResultsCount] = useState(0);
   const [inputValue, setInputValue] = useState(searchProp); //Sets the value of the search bar
   const [currentSearchProp, setCurrentSearchProp] = useState(searchProp);
+  const [terminologiesToMap, setTerminologiesToMap] = useState([]);
+  const [active, setActive] = useState(null);
+  const [allCheckboxes, setAllCheckboxes] = useState([]);
 
   const {
     setExistingMappings,
@@ -52,6 +58,25 @@ export const MappingSearch = ({
   let ref = useRef();
   const { Search } = Input;
 
+  const fetchTerminologies = () => {
+    setLoading(true);
+    const fetchPromises = prefTerminologies?.map(pref =>
+      fetch(`${vocabUrl}/${pref?.reference}`).then(response => response.json())
+    );
+
+    Promise.all(fetchPromises)
+      .then(results => {
+        // Once all fetch calls are resolved, set the combined data
+        setTerminologiesToMap(results);
+      })
+      .catch(error => {
+        notification.error({
+          message: 'Error',
+          description: 'An error occurred. Please try again.',
+        });
+      })
+      .finally(() => setLoading(false));
+  };
   // since the code is passed through searchProp, the '!!' forces it to be evaluated as a boolean.
   // if there is a searchProp being passed, it evaluates to true and runs the search function.
   // inputValue and currentSearchProp for the search bar is set to the passed searchProp.
@@ -86,6 +111,22 @@ export const MappingSearch = ({
     }
   }, [page]);
 
+  useEffect(() => {
+    if (prefTerminologies.length > 0) {
+      fetchTerminologies();
+    }
+  }, []);
+
+  useEffect(() => {
+    setAllCheckboxes(
+      terminologiesToMap.find(term => term.id === active)?.codes ?? []
+    );
+  }, [active]);
+
+  useEffect(() => {
+    setActive(terminologiesToMap?.[0]?.id);
+  }, [terminologiesToMap]);
+
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the query changes and when the preferred ontology changes.
@@ -121,6 +162,7 @@ export const MappingSearch = ({
       setSelectedMappings([]);
       setDisplaySelectedMappings([]);
       setSelectedBoxes([]);
+      setApiResults([]);
     },
     []
   );
@@ -217,30 +259,44 @@ export const MappingSearch = ({
   };
 
   const onSelectedChange = checkedValues => {
-    const selected = JSON.parse(checkedValues?.[0]);
-    const selectedMapping = results.find(
-      result => result.obo_id === selected.code
-    );
-
-    // Updates selectedMappings and displaySelectedMappings to include the new selected items
-    setSelectedMappings(prevState => [...prevState, selectedMapping]);
+    const selected = JSON.parse(checkedValues?.[checkedValues.length - 1]);
 
     // Adds the selectedMappings to the selectedBoxes to ensure they are checked
     setSelectedBoxes(prevState => {
-      const updated = [...prevState, selectedMapping];
+      const updated = [...prevState, selected];
+      // Sets the values for the form to the selectedMappings checkboxes that are checked
       form.setFieldsValue({ selected_mappings: updated });
       return updated;
     });
 
-    setDisplaySelectedMappings(prevState => [...prevState, selectedMapping]);
-
-    // Filters out the selected checkboxes from the results being displayed
-    const updatedResults = results.filter(
-      result => result.obo_id !== selected.code
-    );
-    setResults(updatedResults);
+    setDisplaySelectedMappings(prevState => [...prevState, selected]);
   };
 
+  // const onSelectedChange = checkedValues => {
+  //   const selected = JSON.parse(checkedValues?.[0]);
+  //   const selectedMapping = results.find(
+  //     result => result.obo_id === selected.code
+  //   );
+
+  //   // Updates selectedMappings and displaySelectedMappings to include the new selected items
+  //   setSelectedMappings(prevState => [...prevState, selectedMapping]);
+
+  //   // Adds the selectedMappings to the selectedBoxes to ensure they are checked
+  //   setSelectedBoxes(prevState => {
+  //     const updated = [...prevState, selectedMapping];
+  //     form.setFieldsValue({ selected_mappings: updated });
+  //     return updated;
+  //   });
+
+  //   setDisplaySelectedMappings(prevState => [...prevState, selectedMapping]);
+
+  //   // Filters out the selected checkboxes from the results being displayed
+  //   const updatedResults = results.filter(
+  //     result => result.obo_id !== selected.code
+  //   );
+  //   setResults(updatedResults);
+  // };
+
   // The display for the checkboxes. The index is set to the count of the results before you fetch the new batch of results
   // again + 1, to move the scrollbar to the first result of the new batch.
   const newSearchDisplay = (d, index) => {
@@ -289,15 +345,41 @@ export const MappingSearch = ({
           <div>
             <div className="modal_term_ontology">
               <div>
-                <b>{d?.label}</b>
+                <div>
+                  <b>{d?.display || d?.label}</b>
+                </div>
               </div>
               <div>
-                <a href={d?.iri} target="_blank">
-                  {d?.obo_id}
-                </a>
+                {d?.code || (
+                  <a href={d?.iri} target="_blank">
+                    {d?.obo_id}
+                  </a>
+                )}
               </div>
             </div>
-            <div>{ellipsisString(d?.description[0], '100')}</div>
+            <div>
+              {d?.description?.length > 85 ? (
+                <Tooltip
+                  placement="topRight"
+                  mouseEnterDelay={0.5}
+                  title={d?.description}
+                >
+                  {ellipsisString(
+                    Array.isArray(d.description)
+                      ? d.description[0]
+                      : d.description,
+                    '85'
+                  )}
+                </Tooltip>
+              ) : (
+                ellipsisString(
+                  Array.isArray(d.description)
+                    ? d.description[0]
+                    : d.description,
+                  '85'
+                )
+              )}
+            </div>
           </div>
         </div>
       </>
@@ -318,11 +400,7 @@ export const MappingSearch = ({
               <div>
                 <b>{d.display}</b>
               </div>
-              <div>
-                {/* <a href={d.iri} target="_blank"> */}
-                {d.code}
-                {/* </a> */}
-              </div>
+              <div>{d.code}</div>
             </div>
             <div>
               {d?.description?.length > 100 ? (
@@ -378,6 +456,36 @@ export const MappingSearch = ({
     }
   };
 
+  const checkBoxDisplay = (item, index) => {
+    return (
+      <>
+        <div key={index} className="modal_search_result">
+          <div key={index} className="modal_display_result">
+            <div>
+              <div className="modal_term_ontology">
+                <div>{item.code}</div>
+              </div>
+              <div>{item.display}</div>
+              <div>
+                {item?.description?.length > 85 ? (
+                  <Tooltip
+                    placement="topRight"
+                    mouseEnterDelay={0.5}
+                    title={item?.description}
+                  >
+                    {ellipsisString(item?.description, '85')}
+                  </Tooltip>
+                ) : (
+                  ellipsisString(item?.description, '85')
+                )}
+              </div>
+            </div>
+          </div>
+        </div>
+      </>
+    );
+  };
+
   return (
     <>
       <div className="results_modal_container">
@@ -388,12 +496,14 @@ export const MappingSearch = ({
                 <div className="modal_search_results_header">
                   <h4>{searchProp}</h4>
                   <div className="mappings_search_bar">
-                    <Search
-                      onSearch={handleSearch}
-                      value={inputValue}
-                      onChange={handleChange}
-                      onKeyDown={searchOnTab}
-                    />
+                    {!prefTerminologies.length > 0 && (
+                      <Search
+                        onSearch={handleSearch}
+                        value={inputValue}
+                        onChange={handleChange}
+                        onKeyDown={searchOnTab}
+                      />
+                    )}
                   </div>
                   <span className="search-desc">{mappingDesc}</span>
                 </div>
@@ -401,7 +511,61 @@ export const MappingSearch = ({
                 <div className="result_container">
                   <Form form={form} layout="vertical" preserve={false}>
                     <div className="all_checkboxes_container">
-                      <OntologyCheckboxes apiPreferences={apiPreferences} />
+                      <div className="mapping_modal_left">
+                        {terminologiesToMap?.length > 0 && (
+                          <div className="assign_map_checkbox_container">
+                            <div className="assign_map_checkbox_wrapper">
+                              <div
+                                className="pref_tab"
+                                onClick={() =>
+                                  setActive(terminologiesToMap?.[0]?.id)
+                                }
+                              >
+                                <b>Preferred Terminologies</b>
+                              </div>
+                              {terminologiesToMap.map((term, i) => (
+                                <div
+                                  key={i}
+                                  className={
+                                    active === term.id
+                                      ? 'active_term'
+                                      : active !== term.id &&
+                                        active !== 'search'
+                                      ? 'inactive_term'
+                                      : active === 'search' && 'hidden_term'
+                                  }
+                                  onClick={() => setActive(term.id)}
+                                >
+                                  {term.name}
+                                </div>
+                              ))}
+                              <div
+                                onClick={() => setActive('search')}
+                                className={
+                                  active === 'search'
+                                    ? 'active_term'
+                                    : 'inactive_term'
+                                }
+                              >
+                                <Search
+                                  onSearch={handleSearch}
+                                  value={inputValue}
+                                  onChange={handleChange}
+                                  onKeyDown={searchOnTab}
+                                />
+                              </div>
+                            </div>
+                          </div>
+                        )}
+                        {active === 'search' && (
+                          <OntologyCheckboxes
+                            apiPreferences={apiPreferences}
+                            active={active}
+                          />
+                        )}
+                      </div>
+                    </div>
+                    <div>
                       <div className="result_form">
                         <Form.Item
                           initialValue={initialChecked}
@@ -442,9 +606,15 @@ export const MappingSearch = ({
                                 <Checkbox
                                   key={i}
                                   onChange={e => onCheckboxChange(e, sm)}
-                                  checked={selectedBoxes.some(
-                                    box => box.obo_id === sm.obo_id
-                                  )}
+                                  checked={
+                                    active === 'search'
+                                      ? selectedBoxes.some(
+                                          box => box.obo_id === sm.obo_id
+                                        )
+                                      : selectedBoxes.some(
+                                          box => box.code === sm.code
+                                        )
+                                  }
                                   value={sm}
                                 >
                                   {selectedTermsDisplay(sm, i)}
@@ -452,43 +622,76 @@ export const MappingSearch = ({
                               ))}
                             </div>
                           </Form.Item>
-                        )}{' '}
-                        {results?.length > 0 ? (
-                          <>
-                            <Form.Item
-                              name={['filtered_mappings']}
-                              valuePropName="value"
-                              rules={[
-                                {
-                                  required: false,
-                                },
-                              ]}
-                            >
-                              {filteredResultsArray?.length > 0 && (
-                                <Checkbox.Group
-                                  className="mappings_checkbox"
-                                  options={filteredResultsArray?.map(
-                                    (d, index) => {
-                                      return {
-                                        value: JSON.stringify({
-                                          code: d.obo_id,
-                                          display: d.label,
-                                          description: d.description[0],
-                                          system: systemsMatch(
-                                            d?.obo_id?.split(':')[0]
-                                          ),
-                                        }),
-                                        label: newSearchDisplay(d, index),
-                                      };
-                                    }
-                                  )}
-                                  onChange={onSelectedChange}
-                                />
-                              )}
-                            </Form.Item>
-                          </>
+                        )}
+                        {active === 'search' ? (
+                          results?.length > 0 ? (
+                            <>
+                              <Form.Item
+                                name={['filtered_mappings']}
+                                valuePropName="value"
+                                rules={[
+                                  {
+                                    required: false,
+                                  },
+                                ]}
+                              >
+                                {filteredResultsArray?.length > 0 && (
+                                  <Checkbox.Group
+                                    className="mappings_checkbox"
+                                    options={filteredResultsArray?.map(
+                                      (d, index) => {
+                                        return {
+                                          value: JSON.stringify({
+                                            code: d.obo_id,
+                                            display: d.label,
+                                            description: d.description[0],
+                                            system: systemsMatch(
+                                              d?.obo_id?.split(':')[0]
+                                            ),
+                                          }),
+                                          label: newSearchDisplay(d, index),
+                                        };
+                                      }
+                                    )}
+                                    onChange={onSelectedChange}
+                                  />
+                                )}
+                              </Form.Item>
+                            </>
+                          ) : (
+                            <h3>No results found</h3>
+                          )
                         ) : (
-                          <h3>No results found</h3>
+                          <Form.Item
+                            name={['mappings']}
+                            valuePropName="value"
+                            rules={[
+                              {
+                                required: false,
+                              },
+                            ]}
+                          >
+                            <Checkbox.Group
+                              className="mappings_checkbox"
+                              options={allCheckboxes
+                                .filter(
+                                  checkbox =>
+                                    !displaySelectedMappings.some(
+                                      dsm => checkbox.code === dsm.code
+                                    )
+                                )
+                                .map((code, index) => ({
+                                  value: JSON.stringify({
+                                    code: code.code,
+                                    display: code.display,
+                                    description: code.description,
+                                    system: code.system,
+                                  }),
+                                  label: checkBoxDisplay(code, index),
+                                }))}
+                              onChange={onSelectedChange}
+                            />
+                          </Form.Item>
                         )}
                       </div>
                     </div>
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index 35ddb0f..89cf6d8 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -32,6 +32,11 @@
   }
 }
 
+.result_container {
+  // display: flex;
+  // flex-direction: row;
+  background-color: lightcoral;
+}
 .all_checkboxes_container {
   display: flex;
   flex-direction: row;
@@ -42,12 +47,21 @@
   overflow: auto;
   position: fixed;
 }
+
+.ontology_form_pref {
+  width: 10.5vw;
+  height: 45vh;
+  overflow: auto;
+  position: fixed;
+}
+
 .result_form {
   margin-left: 11vw;
 }
 
 .inactive_term,
-.active_term {
+.active_term,
+.pref_tab {
   padding: 10px;
   cursor: pointer;
   width: 15vw;
@@ -63,6 +77,13 @@
   background-color: $lightBlue;
 }
 
+.hidden_term {
+  display: none;
+}
+.pref_tab {
+  background-color: rgb(233, 233, 233);
+}
+
 .assign_map_checkbox_container {
   display: flex;
 }
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index a6900d2..dd12b53 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -11,6 +11,8 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
     facetCounts,
     ontologyApis,
     prefTypeKey,
+    prefTerminologies,
+    active,
   } = useContext(SearchContext);
   const { Search } = Input;
 
@@ -111,7 +113,9 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
   };
 
   return (
-    <div className="ontology_form">
+    <div
+      className={active === 'search' ? 'ontology_form' : 'ontology_form_pref'}
+    >
       <Search
         placeholder="Ontologies"
         className="onto_search_bar"
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 2bb49c0..44d5d66 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -275,9 +275,6 @@ export const EditMappingsModal = ({
         form
           .validateFields()
           .then(values => {
-            {
-              /* Performs the updateMappings PUT call on 'Save' button click */
-            }
             editSearch || reset
               ? editUpdatedMappings(values)
               : updateMappings(values);

From aac54a9d942f2c96ca5038ef0b6d96146da4fe88 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 18 Nov 2024 14:49:47 -0600
Subject: [PATCH 138/180] committing to switch branches

---
 .../MappingsFunctions/MappingSearch.jsx       | 67 +++++++------------
 .../MappingsFunctions/MappingsFunctions.scss  |  5 +-
 2 files changed, 27 insertions(+), 45 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 0305f3c..3e0c507 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -131,10 +131,14 @@ export const MappingSearch = ({
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the query changes and when the preferred ontology changes.
   useEffect(() => {
-    if (!!currentSearchProp && apiPreferencesCode !== undefined) {
+    if (
+      active === 'search' &&
+      !!currentSearchProp &&
+      apiPreferencesCode !== undefined
+    ) {
       fetchResults(page, currentSearchProp);
     }
-  }, [currentSearchProp, apiPreferencesCode]);
+  }, [currentSearchProp, apiPreferencesCode, active]);
 
   /* Pagination is handled via a "View More" link at the bottom of the page. 
   Each click on the "View More" link makes an API call to fetch the next 15 results.
@@ -272,31 +276,6 @@ export const MappingSearch = ({
     setDisplaySelectedMappings(prevState => [...prevState, selected]);
   };
 
-  // const onSelectedChange = checkedValues => {
-  //   const selected = JSON.parse(checkedValues?.[0]);
-  //   const selectedMapping = results.find(
-  //     result => result.obo_id === selected.code
-  //   );
-
-  //   // Updates selectedMappings and displaySelectedMappings to include the new selected items
-  //   setSelectedMappings(prevState => [...prevState, selectedMapping]);
-
-  //   // Adds the selectedMappings to the selectedBoxes to ensure they are checked
-  //   setSelectedBoxes(prevState => {
-  //     const updated = [...prevState, selectedMapping];
-  //     form.setFieldsValue({ selected_mappings: updated });
-  //     return updated;
-  //   });
-
-  //   setDisplaySelectedMappings(prevState => [...prevState, selectedMapping]);
-
-  //   // Filters out the selected checkboxes from the results being displayed
-  //   const updatedResults = results.filter(
-  //     result => result.obo_id !== selected.code
-  //   );
-  //   setResults(updatedResults);
-  // };
-
   // The display for the checkboxes. The index is set to the count of the results before you fetch the new batch of results
   // again + 1, to move the scrollbar to the first result of the new batch.
   const newSearchDisplay = (d, index) => {
@@ -523,22 +502,24 @@ export const MappingSearch = ({
                               >
                                 <b>Preferred Terminologies</b>
                               </div>
-                              {terminologiesToMap.map((term, i) => (
-                                <div
-                                  key={i}
-                                  className={
-                                    active === term.id
-                                      ? 'active_term'
-                                      : active !== term.id &&
-                                        active !== 'search'
-                                      ? 'inactive_term'
-                                      : active === 'search' && 'hidden_term'
-                                  }
-                                  onClick={() => setActive(term.id)}
-                                >
-                                  {term.name}
-                                </div>
-                              ))}
+                              <div className="">
+                                {terminologiesToMap.map((term, i) => (
+                                  <div
+                                    key={i}
+                                    className={
+                                      active === term.id
+                                        ? 'active_term'
+                                        : active !== term.id &&
+                                          active !== 'search'
+                                        ? 'inactive_term'
+                                        : active === 'search' && 'hidden_term'
+                                    }
+                                    onClick={() => setActive(term.id)}
+                                  >
+                                    {term.name}
+                                  </div>
+                                ))}
+                              </div>
                               <div
                                 onClick={() => setActive('search')}
                                 className={
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index 89cf6d8..a43ce4b 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -35,7 +35,7 @@
 .result_container {
   // display: flex;
   // flex-direction: row;
-  background-color: lightcoral;
+  background-color: forestgreen;
 }
 .all_checkboxes_container {
   display: flex;
@@ -64,8 +64,9 @@
 .pref_tab {
   padding: 10px;
   cursor: pointer;
-  width: 15vw;
+  width: 13vw;
   border-bottom: white 2px solid;
+  text-wrap: wrap;
 }
 
 .active_term {

From 65ca8b9874481f08d7c1d4964f93fcfd7e3f87d4 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 18 Nov 2024 15:52:06 -0600
Subject: [PATCH 139/180] removed the catigories in breadcrumbs

---
 src/components/Nav/Breadcrumbs.jsx | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
index a69b81c..40d4da4 100644
--- a/src/components/Nav/Breadcrumbs.jsx
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -14,7 +14,6 @@ export const Breadcrumbs = () => {
 
   useEffect(() => {
     const controller = new AbortController(); // For canceling stale requests
-
     const fetchBreadcrumbData = async () => {
       const pathArr = pathParts.map((path) => ({ title: path, path: path }));
 
@@ -24,13 +23,18 @@ export const Breadcrumbs = () => {
           if (i + 1 < pathArr.length) {
             promises.push(
               getById(vocabUrl, pathArr[i].path, pathArr[i + 1].path, { signal: controller.signal }).then((result) => {
-                pathArr[i + 1] = { ...pathArr[i + 1], title: result.name };
+                pathArr[i + 1] = { path: pathArr[i].path + '/' + result.id, title: result.name };
               })
             );
           }
         }
 
         await Promise.all(promises); // Wait for all `getById` calls to finish
+        if (pathArr.length !== 1) {
+          pathArr.splice(0, 1);
+          pathArr.splice(1, 1);
+          pathArr.splice(2, 1);
+        }
         setUpdatedPathArr([...pathArr]);
       } catch (error) {
         if (error.name === 'AbortError') {

From a9b5f3a2dfc8239528713ceac3377188f2d68522 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 18 Nov 2024 15:54:44 -0600
Subject: [PATCH 140/180] pref term mappings and ols mappings saving

---
 .../MappingsFunctions/MappingSearch.jsx       | 282 +++++++++---------
 .../MappingsFunctions/MappingsFunctions.scss  |  21 +-
 .../Terminologies/EditMappingModal.jsx        |   8 +-
 3 files changed, 157 insertions(+), 154 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 3e0c507..9591071 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -545,106 +545,11 @@ export const MappingSearch = ({
                           />
                         )}
                       </div>
-                    </div>
-                    <div>
-                      <div className="result_form">
-                        <Form.Item
-                          initialValue={initialChecked}
-                          name={['existing_mappings']}
-                          valuePropName="value"
-                          rules={[
-                            {
-                              required: false,
-                            },
-                          ]}
-                        >
-                          {mappingsForSearch?.length > 0 && (
-                            <Checkbox.Group
-                              className="mappings_checkbox existing_display"
-                              options={mappingsForSearch?.map((d, index) => {
-                                return {
-                                  value: JSON.stringify({
-                                    code: d.code,
-                                    display: d.display,
-                                    description: d.description,
-                                    system: d.system,
-                                  }),
-                                  label: existingMappingDisplay(d, index),
-                                };
-                              })}
-                              onChange={onExistingChange}
-                            />
-                          )}
-                        </Form.Item>
-                        {displaySelectedMappings?.length > 0 && (
-                          <Form.Item
-                            name="selected_mappings"
-                            valuePropName="value"
-                            rules={[{ required: false }]}
-                          >
-                            <div className="modal_display_results">
-                              {displaySelectedMappings?.map((sm, i) => (
-                                <Checkbox
-                                  key={i}
-                                  onChange={e => onCheckboxChange(e, sm)}
-                                  checked={
-                                    active === 'search'
-                                      ? selectedBoxes.some(
-                                          box => box.obo_id === sm.obo_id
-                                        )
-                                      : selectedBoxes.some(
-                                          box => box.code === sm.code
-                                        )
-                                  }
-                                  value={sm}
-                                >
-                                  {selectedTermsDisplay(sm, i)}
-                                </Checkbox>
-                              ))}
-                            </div>
-                          </Form.Item>
-                        )}
-                        {active === 'search' ? (
-                          results?.length > 0 ? (
-                            <>
-                              <Form.Item
-                                name={['filtered_mappings']}
-                                valuePropName="value"
-                                rules={[
-                                  {
-                                    required: false,
-                                  },
-                                ]}
-                              >
-                                {filteredResultsArray?.length > 0 && (
-                                  <Checkbox.Group
-                                    className="mappings_checkbox"
-                                    options={filteredResultsArray?.map(
-                                      (d, index) => {
-                                        return {
-                                          value: JSON.stringify({
-                                            code: d.obo_id,
-                                            display: d.label,
-                                            description: d.description[0],
-                                            system: systemsMatch(
-                                              d?.obo_id?.split(':')[0]
-                                            ),
-                                          }),
-                                          label: newSearchDisplay(d, index),
-                                        };
-                                      }
-                                    )}
-                                    onChange={onSelectedChange}
-                                  />
-                                )}
-                              </Form.Item>
-                            </>
-                          ) : (
-                            <h3>No results found</h3>
-                          )
-                        ) : (
+                      <div>
+                        <div className="result_form">
                           <Form.Item
-                            name={['mappings']}
+                            initialValue={initialChecked}
+                            name={['existing_mappings']}
                             valuePropName="value"
                             rules={[
                               {
@@ -652,55 +557,152 @@ export const MappingSearch = ({
                               },
                             ]}
                           >
-                            <Checkbox.Group
-                              className="mappings_checkbox"
-                              options={allCheckboxes
-                                .filter(
-                                  checkbox =>
-                                    !displaySelectedMappings.some(
-                                      dsm => checkbox.code === dsm.code
-                                    )
-                                )
-                                .map((code, index) => ({
-                                  value: JSON.stringify({
-                                    code: code.code,
-                                    display: code.display,
-                                    description: code.description,
-                                    system: code.system,
-                                  }),
-                                  label: checkBoxDisplay(code, index),
-                                }))}
-                              onChange={onSelectedChange}
-                            />
+                            {mappingsForSearch?.length > 0 && (
+                              <Checkbox.Group
+                                className="mappings_checkbox existing_display"
+                                options={mappingsForSearch?.map((d, index) => {
+                                  return {
+                                    value: JSON.stringify({
+                                      code: d.code,
+                                      display: d.display,
+                                      description: d.description,
+                                      system: d.system,
+                                    }),
+                                    label: existingMappingDisplay(d, index),
+                                  };
+                                })}
+                                onChange={onExistingChange}
+                              />
+                            )}
                           </Form.Item>
-                        )}
+                          {displaySelectedMappings?.length > 0 && (
+                            <Form.Item
+                              name="selected_mappings"
+                              valuePropName="value"
+                              rules={[{ required: false }]}
+                            >
+                              <div className="modal_display_results">
+                                {displaySelectedMappings?.map((sm, i) => (
+                                  <Checkbox
+                                    key={i}
+                                    onChange={e => onCheckboxChange(e, sm)}
+                                    checked={
+                                      active === 'search'
+                                        ? selectedBoxes.some(
+                                            box => box.obo_id === sm.obo_id
+                                          )
+                                        : selectedBoxes.some(
+                                            box => box.code === sm.code
+                                          )
+                                    }
+                                    value={sm}
+                                  >
+                                    {selectedTermsDisplay(sm, i)}
+                                  </Checkbox>
+                                ))}
+                              </div>
+                            </Form.Item>
+                          )}
+                          {active === 'search' ? (
+                            results?.length > 0 ? (
+                              <>
+                                <Form.Item
+                                  name={['filtered_mappings']}
+                                  valuePropName="value"
+                                  rules={[
+                                    {
+                                      required: false,
+                                    },
+                                  ]}
+                                >
+                                  {filteredResultsArray?.length > 0 && (
+                                    <Checkbox.Group
+                                      className="mappings_checkbox"
+                                      options={filteredResultsArray?.map(
+                                        (d, index) => {
+                                          return {
+                                            value: JSON.stringify({
+                                              code: d.obo_id,
+                                              display: d.label,
+                                              description: d.description[0],
+                                              system: systemsMatch(
+                                                d?.obo_id?.split(':')[0]
+                                              ),
+                                            }),
+                                            label: newSearchDisplay(d, index),
+                                          };
+                                        }
+                                      )}
+                                      onChange={onSelectedChange}
+                                    />
+                                  )}
+                                </Form.Item>
+                              </>
+                            ) : (
+                              <h3>No results found</h3>
+                            )
+                          ) : (
+                            <Form.Item
+                              name={['mappings']}
+                              valuePropName="value"
+                              rules={[
+                                {
+                                  required: false,
+                                },
+                              ]}
+                            >
+                              <Checkbox.Group
+                                className="mappings_checkbox"
+                                options={allCheckboxes
+                                  .filter(
+                                    checkbox =>
+                                      !displaySelectedMappings.some(
+                                        dsm => checkbox.code === dsm.code
+                                      )
+                                  )
+                                  .map((code, index) => ({
+                                    value: JSON.stringify({
+                                      code: code.code,
+                                      display: code.display,
+                                      description: code.description,
+                                      system: code.system,
+                                    }),
+                                    label: checkBoxDisplay(code, index),
+                                  }))}
+                                onChange={onSelectedChange}
+                              />
+                            </Form.Item>
+                          )}
+                        </div>
                       </div>
                     </div>
                   </Form>
-                  <div className="view_more_wrapper">
-                    {/* 'View More' pagination displaying the number of results being displayed
+                  {active === 'search' && (
+                    <div className="view_more_wrapper">
+                      {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
                       inconsistencies in results numbers per page. */}
-                    <Tooltip
-                      placement="bottom"
-                      title="Redundant entries have been removed"
-                    >
-                      Displaying {resultsCount}
-                      &nbsp;of&nbsp;{totalCount}
-                    </Tooltip>
-                    {resultsCount < totalCount - filteredResultsCount && (
-                      <span
-                        className="view_more_link"
-                        onClick={e => {
-                          handleViewMore(e);
-                          setLastCount(resultsCount);
-                        }}
+                      <Tooltip
+                        placement="bottom"
+                        title="Redundant entries have been removed"
                       >
-                        View More
-                      </span>
-                    )}
-                  </div>
+                        Displaying {resultsCount}
+                        &nbsp;of&nbsp;{totalCount}
+                      </Tooltip>
+                      {resultsCount < totalCount - filteredResultsCount && (
+                        <span
+                          className="view_more_link"
+                          onClick={e => {
+                            handleViewMore(e);
+                            setLastCount(resultsCount);
+                          }}
+                        >
+                          View More
+                        </span>
+                      )}
+                    </div>
+                  )}
                 </div>
               </div>
             </>
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index a43ce4b..488f557 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -32,31 +32,31 @@
   }
 }
 
-.result_container {
-  // display: flex;
-  // flex-direction: row;
-  background-color: forestgreen;
-}
 .all_checkboxes_container {
   display: flex;
   flex-direction: row;
 }
+
+.mapping_modal_left {
+  position: fixed;
+}
 .ontology_form {
-  width: 10.5vw;
+  width: 13vw;
   height: 50vh;
   overflow: auto;
   position: fixed;
 }
 
 .ontology_form_pref {
-  width: 10.5vw;
-  height: 45vh;
+  width: 13vw;
+  padding-right: 20px;
+  height: 44%;
   overflow: auto;
   position: fixed;
 }
 
 .result_form {
-  margin-left: 11vw;
+  margin-left: 15vw;
 }
 
 .inactive_term,
@@ -87,6 +87,7 @@
 
 .assign_map_checkbox_container {
   display: flex;
+  position: sticky;
 }
 
 .assign_map_checkboxes {
@@ -138,7 +139,7 @@
 }
 
 .view_more_wrapper {
-  margin-left: 11vw;
+  margin-left: 15vw;
 }
 
 .api_onto_search_bar,
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 44d5d66..e50b55b 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -207,10 +207,10 @@ export const EditMappingsModal = ({
   const editUpdatedMappings = values => {
     setLoading(true);
     const selectedMappings = values?.selected_mappings?.map(item => ({
-      code: item.obo_id,
-      display: item.label,
-      description: item.description[0],
-      system: systemsMatch(item.obo_id.split(':')[0]),
+      code: item.code,
+      display: item.display,
+      description: item.description,
+      system: item.system || systemsMatch(item.code.split(':')?.[0]),
     }));
     const mappingsDTO = {
       mappings: [

From 0fbd3056b1bc9902e33c4ceb173c93bffcb94f74 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Mon, 18 Nov 2024 16:03:25 -0600
Subject: [PATCH 141/180] one more splice

---
 src/components/Nav/Breadcrumbs.jsx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/components/Nav/Breadcrumbs.jsx b/src/components/Nav/Breadcrumbs.jsx
index 40d4da4..adf99bb 100644
--- a/src/components/Nav/Breadcrumbs.jsx
+++ b/src/components/Nav/Breadcrumbs.jsx
@@ -34,6 +34,7 @@ export const Breadcrumbs = () => {
           pathArr.splice(0, 1);
           pathArr.splice(1, 1);
           pathArr.splice(2, 1);
+          pathArr.splice(3, 1);
         }
         setUpdatedPathArr([...pathArr]);
       } catch (error) {

From 90409599b0c196b7bffe61c5e96b4c80cd67ad08 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 18 Nov 2024 22:09:28 -0600
Subject: [PATCH 142/180] fixed systems match to use ontologyApis

---
 .../MappingsFunctions/GetMappingsModal.jsx    |  7 +++---
 .../MappingsFunctions/MappingReset.jsx        |  4 +++-
 .../MappingsFunctions/MappingSearch.jsx       | 15 ++++++++++---
 .../MappingsFunctions/OntologyCheckboxes.jsx  |  1 -
 src/components/Manager/Utilitiy.jsx           | 22 +++++++++----------
 .../Tables/EditMappingsTableModal.jsx         |  3 ++-
 .../Projects/Terminologies/APIResults.jsx     | 15 ++++++++++---
 .../Terminologies/EditMappingModal.jsx        |  4 +++-
 8 files changed, 46 insertions(+), 25 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 80d8005..4594795 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -42,6 +42,7 @@ export const GetMappingsModal = ({
     apiPreferencesCode,
     setUnformattedPref,
     prefTypeKey,
+    ontologyApis,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 1000;
@@ -61,7 +62,6 @@ export const GetMappingsModal = ({
     setSelectedBoxes,
   } = useContext(MappingContext);
   let ref = useRef();
-
   // since the code is passed through searchProp, the '!!' forces it to be evaluated as a boolean.
   // if there is a searchProp being passed, it evaluates to true and runs the search function.
   // inputValue and currentSearchProp for the search bar is set to the passed searchProp.
@@ -159,7 +159,7 @@ export const GetMappingsModal = ({
       code: item.obo_id,
       display: item.label,
       description: item.description[0],
-      system: systemsMatch(item.obo_id.split(':')[0]),
+      system: systemsMatch(item.obo_id.split(':')[0], ontologyApis),
     }));
     const mappingsDTO = {
       mappings: selectedMappings,
@@ -479,7 +479,8 @@ export const GetMappingsModal = ({
                                           display: d.label,
                                           description: d.description[0],
                                           system: systemsMatch(
-                                            d?.obo_id?.split(':')[0]
+                                            d?.obo_id?.split(':')[0],
+                                            ontologyApis
                                           ),
                                         }),
                                         label: checkBoxDisplay(d, index),
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index dfb508e..a36f2d7 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -26,6 +26,7 @@ export const MappingReset = ({
     setApiPreferencesCode,
     apiPreferencesCode,
     setUnformattedPref,
+    ontologyApis,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 1000;
@@ -380,7 +381,8 @@ export const MappingReset = ({
                                           display: d.label,
                                           // description: d.description[0],
                                           system: systemsMatch(
-                                            d?.obo_id?.split(':')[0]
+                                            d.obo_id.split(':')[0],
+                                            ontologyApis
                                           ),
                                         }),
                                         label: checkBoxDisplay(d, index),
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 9591071..b6eef2b 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -30,6 +30,7 @@ export const MappingSearch = ({
     setUnformattedPref,
     prefTerminologies,
     setApiResults,
+    ontologyApis,
   } = useContext(SearchContext);
 
   const [page, setPage] = useState(0);
@@ -132,11 +133,14 @@ export const MappingSearch = ({
   // The function is run when the query changes and when the preferred ontology changes.
   useEffect(() => {
     if (
+      prefTerminologies.length > 0 &&
       active === 'search' &&
       !!currentSearchProp &&
       apiPreferencesCode !== undefined
     ) {
       fetchResults(page, currentSearchProp);
+    } else if (!!currentSearchProp && apiPreferencesCode !== undefined) {
+      fetchResults(page, currentSearchProp);
     }
   }, [currentSearchProp, apiPreferencesCode, active]);
 
@@ -538,7 +542,9 @@ export const MappingSearch = ({
                             </div>
                           </div>
                         )}
-                        {active === 'search' && (
+                        {((prefTerminologies.length > 0 &&
+                          active === 'search') ||
+                          prefTerminologies.length === 0) && (
                           <OntologyCheckboxes
                             apiPreferences={apiPreferences}
                             active={active}
@@ -603,7 +609,9 @@ export const MappingSearch = ({
                               </div>
                             </Form.Item>
                           )}
-                          {active === 'search' ? (
+                          {(prefTerminologies.length > 0 &&
+                            active === 'search') ||
+                          prefTerminologies.length === 0 ? (
                             results?.length > 0 ? (
                               <>
                                 <Form.Item
@@ -626,7 +634,8 @@ export const MappingSearch = ({
                                               display: d.label,
                                               description: d.description[0],
                                               system: systemsMatch(
-                                                d?.obo_id?.split(':')[0]
+                                                d?.obo_id?.split(':')[0],
+                                                ontologyApis
                                               ),
                                             }),
                                             label: newSearchDisplay(d, index),
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index dd12b53..872111b 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -11,7 +11,6 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
     facetCounts,
     ontologyApis,
     prefTypeKey,
-    prefTerminologies,
     active,
   } = useContext(SearchContext);
   const { Search } = Input;
diff --git a/src/components/Manager/Utilitiy.jsx b/src/components/Manager/Utilitiy.jsx
index 787a5d3..4c3dd29 100644
--- a/src/components/Manager/Utilitiy.jsx
+++ b/src/components/Manager/Utilitiy.jsx
@@ -27,20 +27,18 @@ export const ontologyReducer = d =>
     { results: [], filteredResults: [] }
   );
 
-/* The backend API does not yet have a way to affix the system URL to each ontology. 
-  This displays the system for each ontology searched. */
-export const ontologySystems = {
-  MONDO: 'http://purl.obolibrary.org/obo/mondo.owl',
-  HP: 'http://purl.obolibrary.org/obo/hp.owl',
-  MAXO: 'http://purl.obolibrary.org/obo/maxo.owl',
-  NCIT: 'http://purl.obolibrary.org/obo/ncit.owl',
-};
-
 // This function matches the ontology prop to its system (listed in object above) in the object that will be sent to the API
-export const systemsMatch = ont => {
-  return ontologySystems[ont];
+export const systemsMatch = (ontologyCode, ontologyApis) => {
+  // Search for the ontology that contains the requested ontology code
+  const ontologyApi = ontologyApis.find(
+    api => api.ontologies[ontologyCode.toLowerCase()]
+  );
+  if (ontologyApi) {
+    // Return the system URL for the matching ontology
+    return ontologyApi.ontologies[ontologyCode.toLowerCase()].system;
+  }
+  return null; // If not found, return null or handle accordingly
 };
-
 // Iterates over the facet counts in the result to make an object of search results per ontology
 export const ontologyCounts = arr => {
   let result = [];
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index 474d4f0..4ad2682 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -41,6 +41,7 @@ export const EditMappingsTableModal = ({
     setApiPreferencesCode,
     preferenceType,
     prefTypeKey,
+    ontologyApis,
   } = useContext(SearchContext);
 
   useEffect(() => {
@@ -208,7 +209,7 @@ export const EditMappingsTableModal = ({
       code: item.obo_id,
       display: item.label,
       description: item.description[0],
-      system: systemsMatch(item.obo_id.split(':')[0]),
+      system: systemsMatch(item.obo_id.split(':')[0], ontologyApis),
     }));
     const mappingsDTO = {
       mappings: [
diff --git a/src/components/Projects/Terminologies/APIResults.jsx b/src/components/Projects/Terminologies/APIResults.jsx
index cf125c1..5a21ccb 100644
--- a/src/components/Projects/Terminologies/APIResults.jsx
+++ b/src/components/Projects/Terminologies/APIResults.jsx
@@ -9,8 +9,14 @@ export const APIResults = ({
   displaySelectedMappings,
   onSelectedChange,
 }) => {
-  const { apiResults, apiResultsCount, apiPage, setApiPage, apiTotalCount } =
-    useContext(SearchContext);
+  const {
+    apiResults,
+    apiResultsCount,
+    apiPage,
+    setApiPage,
+    apiTotalCount,
+    ontologyApis,
+  } = useContext(SearchContext);
   const [filteredResultsCount, setFilteredResultsCount] = useState(0);
   const [lastCount, setLastCount] = useState(0); //save last count as count of the results before you fetch data again
 
@@ -108,7 +114,10 @@ export const APIResults = ({
                       code: d.obo_id,
                       display: d.label,
                       description: d.description[0],
-                      system: systemsMatch(d?.obo_id?.split(':')[0]),
+                      system: systemsMatch(
+                        d?.obo_id.split(':')[0],
+                        ontologyApis
+                      ),
                     }),
                     label: checkBoxDisplay(d, index),
                   };
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index e50b55b..8c1d63c 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -35,6 +35,7 @@ export const EditMappingsModal = ({
     setApiPreferencesCode,
     preferenceType,
     prefTypeKey,
+    ontologyApis,
   } = useContext(SearchContext);
   const [loading, setLoading] = useState(false);
   const [reset, setReset] = useState(false);
@@ -210,7 +211,8 @@ export const EditMappingsModal = ({
       code: item.code,
       display: item.display,
       description: item.description,
-      system: item.system || systemsMatch(item.code.split(':')?.[0]),
+      system:
+        item.system || systemsMatch(item.obo_id.split(':')[0], ontologyApis),
     }));
     const mappingsDTO = {
       mappings: [

From 4c041a6feb079f2f83227f7937990527436bcee0 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 19 Nov 2024 10:01:45 -0600
Subject: [PATCH 143/180] Removed duplicate OLS search from MappingSearch

---
 .../Manager/MappingsFunctions/MappingSearch.jsx          | 9 +++++++--
 .../Manager/MappingsFunctions/OntologyCheckboxes.jsx     | 7 ++++++-
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index b6eef2b..82197c2 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -127,7 +127,8 @@ export const MappingSearch = ({
   useEffect(() => {
     setActive(terminologiesToMap?.[0]?.id);
   }, [terminologiesToMap]);
-
+  console.log(active);
+  console.log(prefTerminologies.length);
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the query changes and when the preferred ontology changes.
@@ -139,7 +140,11 @@ export const MappingSearch = ({
       apiPreferencesCode !== undefined
     ) {
       fetchResults(page, currentSearchProp);
-    } else if (!!currentSearchProp && apiPreferencesCode !== undefined) {
+    } else if (
+      prefTerminologies.length === 0 &&
+      !!currentSearchProp &&
+      apiPreferencesCode !== undefined
+    ) {
       fetchResults(page, currentSearchProp);
     }
   }, [currentSearchProp, apiPreferencesCode, active]);
diff --git a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
index 872111b..cd59049 100644
--- a/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyCheckboxes.jsx
@@ -12,6 +12,7 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
     ontologyApis,
     prefTypeKey,
     active,
+    prefTerminologies,
   } = useContext(SearchContext);
   const { Search } = Input;
 
@@ -113,7 +114,11 @@ export const OntologyCheckboxes = ({ preferenceType }) => {
 
   return (
     <div
-      className={active === 'search' ? 'ontology_form' : 'ontology_form_pref'}
+      className={
+        active === 'search' || prefTerminologies.length === 0
+          ? 'ontology_form'
+          : 'ontology_form_pref'
+      }
     >
       <Search
         placeholder="Ontologies"

From f84c7e5ee532039243b9314804c1263c3b6f40ab Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Tue, 19 Nov 2024 11:43:21 -0600
Subject: [PATCH 144/180] fixed backgound

---
 src/App.scss | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/App.scss b/src/App.scss
index 7fa32b7..38d8058 100644
--- a/src/App.scss
+++ b/src/App.scss
@@ -4,6 +4,7 @@ body{
     background-size: 100vw;
     background-repeat: no-repeat;
     background-position: calc(50% - 50px) 50%;
+    background-attachment: fixed;
 
 }
 .approuter_div {
@@ -15,7 +16,7 @@ body{
 
 .outlet_div {
   position: relative;
-  background-color: rgba(255,255,255,.6);
+  background-color: rgba(255,255,255,.3);
 }
 
 .header {

From 4ea054c972707d78585bbddf7111e9eee141171e Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 19 Nov 2024 13:02:25 -0600
Subject: [PATCH 145/180] committing to switch branches

---
 .../MappingsFunctions/GetMappingsModal.jsx    |   1 -
 .../MappingsFunctions/MappingReset.jsx        | 406 +++++++++++++-----
 .../MappingsFunctions/MappingSearch.jsx       |  32 +-
 src/components/Manager/Utilitiy.jsx           |   4 +-
 .../Terminologies/EditMappingModal.jsx        |   1 +
 5 files changed, 323 insertions(+), 121 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 4594795..e056170 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -30,7 +30,6 @@ export const GetMappingsModal = ({
   table,
   terminology,
 }) => {
-  const { tableId } = useParams();
   const [form] = Form.useForm();
   const { Search } = Input;
   const { searchUrl, vocabUrl, setSelectedKey, user } = useContext(myContext);
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index a36f2d7..bc13608 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -27,6 +27,7 @@ export const MappingReset = ({
     apiPreferencesCode,
     setUnformattedPref,
     ontologyApis,
+    prefTerminologies,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 1000;
@@ -38,6 +39,9 @@ export const MappingReset = ({
   const [filteredResultsCount, setFilteredResultsCount] = useState(0);
   const [inputValue, setInputValue] = useState(searchProp); //Sets the value of the search bar
   const [currentSearchProp, setCurrentSearchProp] = useState(searchProp);
+  const [terminologiesToMap, setTerminologiesToMap] = useState([]);
+  const [active, setActive] = useState(null);
+  const [allCheckboxes, setAllCheckboxes] = useState([]);
 
   const {
     setSelectedMappings,
@@ -49,6 +53,26 @@ export const MappingReset = ({
   let ref = useRef();
   const { Search } = Input;
 
+  const fetchTerminologies = () => {
+    setLoading(true);
+    const fetchPromises = prefTerminologies?.map(pref =>
+      fetch(`${vocabUrl}/${pref?.reference}`).then(response => response.json())
+    );
+
+    Promise.all(fetchPromises)
+      .then(results => {
+        // Once all fetch calls are resolved, set the combined data
+        setTerminologiesToMap(results);
+      })
+      .catch(error => {
+        notification.error({
+          message: 'Error',
+          description: 'An error occurred. Please try again.',
+        });
+      })
+      .finally(() => setLoading(false));
+  };
+
   // since the code is passed through searchProp, the '!!' forces it to be evaluated as a boolean.
   // if there is a searchProp being passed, it evaluates to true and runs the search function.
   // inputValue and currentSearchProp for the search bar is set to the passed searchProp.
@@ -83,14 +107,42 @@ export const MappingReset = ({
     }
   }, [page]);
 
+  useEffect(() => {
+    if (prefTerminologies.length > 0) {
+      fetchTerminologies();
+    }
+  }, []);
+
+  useEffect(() => {
+    setAllCheckboxes(
+      terminologiesToMap.find(term => term.id === active)?.codes ?? []
+    );
+  }, [active]);
+
+  useEffect(() => {
+    setActive(terminologiesToMap?.[0]?.id);
+  }, [terminologiesToMap]);
+
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the query changes and when the preferred ontology changes.
+  // If there are preferred terminologies, it runs when the OLS search bar is clicked (i.e. active)
   useEffect(() => {
-    if (!!currentSearchProp && apiPreferencesCode !== undefined) {
+    if (
+      prefTerminologies.length > 0 &&
+      active === 'search' &&
+      !!currentSearchProp &&
+      apiPreferencesCode !== undefined
+    ) {
+      fetchResults(page, currentSearchProp);
+    } else if (
+      prefTerminologies.length === 0 &&
+      !!currentSearchProp &&
+      apiPreferencesCode !== undefined
+    ) {
       fetchResults(page, currentSearchProp);
     }
-  }, [currentSearchProp, apiPreferencesCode]);
+  }, [currentSearchProp, apiPreferencesCode, active]);
 
   /* Pagination is handled via a "View More" link at the bottom of the page. 
   Each click on the "View More" link makes an API call to fetch the next 15 results.
@@ -199,29 +251,30 @@ export const MappingReset = ({
 
   // The display for the checkboxes. The index is set to the count of the results before you fetch the new batch of results
   // again + 1, to move the scrollbar to the first result of the new batch.
-  const checkBoxDisplay = (d, index) => {
-    index === lastCount + 1;
+  const checkBoxDisplay = (item, index) => {
     return (
       <>
-        <div
-          key={index}
-          // prettier-ignore
-          ref={index === lastCount + 1 ? ref : undefined}
-          className="modal_search_result"
-          id="scrollbar"
-        >
-          <div>
-            <div className="modal_term_ontology">
-              <div>
-                <b>{d.label}</b>
+        <div key={index} className="modal_search_result">
+          <div key={index} className="modal_display_result">
+            <div>
+              <div className="modal_term_ontology">
+                <div>{item.code}</div>
               </div>
+              <div>{item.display}</div>
               <div>
-                <a href={d.iri} target="_blank">
-                  {d.obo_id}
-                </a>
+                {item?.description?.length > 85 ? (
+                  <Tooltip
+                    placement="topRight"
+                    mouseEnterDelay={0.5}
+                    title={item?.description}
+                  >
+                    {ellipsisString(item?.description, '85')}
+                  </Tooltip>
+                ) : (
+                  ellipsisString(item?.description, '85')
+                )}
               </div>
             </div>
-            <div>{ellipsisString(d?.description[0], '100')}</div>
           </div>
         </div>
       </>
@@ -232,10 +285,19 @@ export const MappingReset = ({
     setInputValue(e.target.value);
   };
 
-  const selectedTermsDisplay = (d, index) => {
+  // The display for the checkboxes. The index is set to the count of the results before you fetch the new batch of results
+  // again + 1, to move the scrollbar to the first result of the new batch.
+  const newSearchDisplay = (d, index) => {
+    index === lastCount + 1;
     return (
       <>
-        <div key={index} className="modal_search_result" id="scrollbar">
+        <div
+          key={index}
+          // prettier-ignore
+          ref={index === lastCount + 1 ? ref : undefined}
+          className="modal_search_result"
+          id="scrollbar"
+        >
           <div>
             <div className="modal_term_ontology">
               <div>
@@ -253,10 +315,10 @@ export const MappingReset = ({
                 title={d?.description}
                 placement="topRight"
               >
-                {ellipsisString(d?.description, '100')}
+                {ellipsisString(d?.description[0], '100')}
               </Tooltip>
             ) : (
-              ellipsisString(d?.description, '100')
+              ellipsisString(d?.description[0], '100')
             )}{' '}
           </div>
         </div>
@@ -264,6 +326,53 @@ export const MappingReset = ({
     );
   };
 
+  const selectedTermsDisplay = (d, index) => {
+    return (
+      <>
+        <div key={index} className="modal_search_result" id="scrollbar">
+          <div>
+            <div className="modal_term_ontology">
+              <div>
+                <div>
+                  <b>{d?.display || d?.label}</b>
+                </div>
+              </div>
+              <div>
+                {d?.code || (
+                  <a href={d?.iri} target="_blank">
+                    {d?.obo_id}
+                  </a>
+                )}
+              </div>
+            </div>
+            <div>
+              {d?.description?.length > 85 ? (
+                <Tooltip
+                  placement="topRight"
+                  mouseEnterDelay={0.5}
+                  title={d?.description}
+                >
+                  {ellipsisString(
+                    Array.isArray(d.description)
+                      ? d.description[0]
+                      : d.description,
+                    '85'
+                  )}
+                </Tooltip>
+              ) : (
+                ellipsisString(
+                  Array.isArray(d.description)
+                    ? d.description[0]
+                    : d.description,
+                  '85'
+                )
+              )}
+            </div>
+          </div>
+        </div>
+      </>
+    );
+  };
   // If the checkbox is checked, it adds the object to the selectedBoxes array
   // If it is unchecked, it filters it out of the selectedBoxes array.
   const onCheckboxChange = (event, code) => {
@@ -275,28 +384,17 @@ export const MappingReset = ({
   };
 
   const onSelectedChange = checkedValues => {
-    const selected = JSON.parse(checkedValues?.[0]);
-    const selectedMapping = results.find(
-      result => result.obo_id === selected.code
-    );
-
-    // Updates selectedMappings and displaySelectedMappings to include the new selected items
-    setSelectedMappings(prevState => [...prevState, selectedMapping]);
+    const selected = JSON.parse(checkedValues?.[checkedValues.length - 1]);
 
     // Adds the selectedMappings to the selectedBoxes to ensure they are checked
     setSelectedBoxes(prevState => {
-      const updated = [...prevState, selectedMapping];
+      const updated = [...prevState, selected];
+      // Sets the values for the form to the selectedMappings checkboxes that are checked
       form.setFieldsValue({ selected_mappings: updated });
       return updated;
     });
 
-    setDisplaySelectedMappings(prevState => [...prevState, selectedMapping]);
-
-    // Filters out the selected checkboxes from the results being displayed
-    const updatedResults = results.filter(
-      result => result.obo_id !== selected.code
-    );
-    setResults(updatedResults);
+    setDisplaySelectedMappings(prevState => [...prevState, selected]);
   };
 
   // Creates a Set that excludes the mappings that have already been selected.
@@ -326,12 +424,14 @@ export const MappingReset = ({
                 <div className="modal_search_results_header">
                   <h4>{searchProp}</h4>
                   <div className="mappings_search_bar">
-                    <Search
-                      onSearch={handleSearch}
-                      value={inputValue}
-                      onChange={handleChange}
-                      onKeyDown={searchOnTab}
-                    />
+                    {!prefTerminologies.length > 0 && (
+                      <Search
+                        onSearch={handleSearch}
+                        value={inputValue}
+                        onChange={handleChange}
+                        onKeyDown={searchOnTab}
+                      />
+                    )}
                   </div>
                   <span className="search-desc">{mappingDesc}</span>
                 </div>
@@ -339,7 +439,63 @@ export const MappingReset = ({
                 <div className="result_container">
                   <Form form={form} layout="vertical" preserve={false}>
                     <div className="all_checkboxes_container">
-                      <OntologyCheckboxes apiPreferences={apiPreferences} />
+                      <div className="mapping_modal_left">
+                        {terminologiesToMap?.length > 0 && (
+                          <div className="assign_map_checkbox_container">
+                            <div className="assign_map_checkbox_wrapper">
+                              <div
+                                className="pref_tab"
+                                onClick={() =>
+                                  setActive(terminologiesToMap?.[0]?.id)
+                                }
+                              >
+                                <b>Preferred Terminologies</b>
+                              </div>
+                              <div className="">
+                                {terminologiesToMap.map((term, i) => (
+                                  <div
+                                    key={i}
+                                    className={
+                                      active === term.id
+                                        ? 'active_term'
+                                        : active !== term.id &&
+                                          active !== 'search'
+                                        ? 'inactive_term'
+                                        : active === 'search' && 'hidden_term'
+                                    }
+                                    onClick={() => setActive(term.id)}
+                                  >
+                                    {term.name}
+                                  </div>
+                                ))}
+                              </div>
+                              <div
+                                onClick={() => setActive('search')}
+                                className={
+                                  active === 'search'
+                                    ? 'active_term'
+                                    : 'inactive_term'
+                                }
+                              >
+                                <Search
+                                  onSearch={handleSearch}
+                                  value={inputValue}
+                                  onChange={handleChange}
+                                  onKeyDown={searchOnTab}
+                                />
+                              </div>
+                            </div>
+                          </div>
+                        )}
+                        {((prefTerminologies.length > 0 &&
+                          active === 'search') ||
+                          prefTerminologies.length === 0) && (
+                          <OntologyCheckboxes
+                            apiPreferences={apiPreferences}
+                            active={active}
+                          />
+                        )}
+                      </div>
                       <div className="result_form">
                         {displaySelectedMappings?.length > 0 && (
                           <Form.Item
@@ -352,9 +508,15 @@ export const MappingReset = ({
                                 <Checkbox
                                   key={i}
                                   onChange={e => onCheckboxChange(e, sm)}
-                                  checked={selectedBoxes.some(
-                                    box => box.obo_id === sm.obo_id
-                                  )}
+                                  checked={
+                                    active === 'search'
+                                      ? selectedBoxes.some(
+                                          box => box.obo_id === sm.obo_id
+                                        )
+                                      : selectedBoxes.some(
+                                          box => box.code === sm.code
+                                        )
+                                  }
                                   value={sm}
                                 >
                                   {selectedTermsDisplay(sm, i)}
@@ -363,69 +525,109 @@ export const MappingReset = ({
                             </div>
                           </Form.Item>
                         )}
-                        {results?.length > 0 ? (
-                          <>
-                            <Form.Item
-                              name={['filtered_mappings']}
-                              valuePropName="value"
-                              rules={[{ required: false }]}
-                            >
-                              {filteredResultsArray?.length > 0 ? (
-                                <Checkbox.Group
-                                  className="mappings_checkbox"
-                                  options={filteredResultsArray?.map(
-                                    (d, index) => {
-                                      return {
-                                        value: JSON.stringify({
-                                          code: d.obo_id,
-                                          display: d.label,
-                                          // description: d.description[0],
-                                          system: systemsMatch(
-                                            d.obo_id.split(':')[0],
-                                            ontologyApis
-                                          ),
-                                        }),
-                                        label: checkBoxDisplay(d, index),
-                                      };
-                                    }
-                                  )}
-                                  onChange={onSelectedChange}
-                                />
-                              ) : (
-                                ''
-                              )}
-                            </Form.Item>
-                          </>
+                        {(prefTerminologies.length > 0 &&
+                          active === 'search') ||
+                        prefTerminologies.length === 0 ? (
+                          results?.length > 0 ? (
+                            <>
+                              <Form.Item
+                                name={['filtered_mappings']}
+                                valuePropName="value"
+                                rules={[
+                                  {
+                                    required: false,
+                                  },
+                                ]}
+                              >
+                                {filteredResultsArray?.length > 0 && (
+                                  <Checkbox.Group
+                                    className="mappings_checkbox"
+                                    options={filteredResultsArray?.map(
+                                      (d, index) => {
+                                        return {
+                                          value: JSON.stringify({
+                                            code: d.obo_id,
+                                            display: d.label,
+                                            description: d.description[0],
+                                            system: systemsMatch(
+                                              d?.obo_id?.split(':')[0],
+                                              ontologyApis
+                                            ),
+                                          }),
+                                          label: newSearchDisplay(d, index),
+                                        };
+                                      }
+                                    )}
+                                    onChange={onSelectedChange}
+                                  />
+                                )}
+                              </Form.Item>
+                            </>
+                          ) : (
+                            <h3>No results found</h3>
+                          )
                         ) : (
-                          <h3>No results found</h3>
+                          <Form.Item
+                            name={['mappings']}
+                            valuePropName="value"
+                            rules={[
+                              {
+                                required: false,
+                              },
+                            ]}
+                          >
+                            <Checkbox.Group
+                              className="mappings_checkbox"
+                              options={allCheckboxes
+                                .filter(
+                                  checkbox =>
+                                    !displaySelectedMappings.some(
+                                      dsm => checkbox.code === dsm.code
+                                    )
+                                )
+                                .map((code, index) => ({
+                                  value: JSON.stringify({
+                                    code: code.code,
+                                    display: code.display,
+                                    description: code.description,
+                                    system: code.system,
+                                  }),
+                                  label: checkBoxDisplay(code, index),
+                                }))}
+                              onChange={onSelectedChange}
+                            />
+                          </Form.Item>
                         )}
                       </div>
                     </div>
                   </Form>
-                  <div className="view_more_wrapper">
-                    {/* 'View More' pagination displaying the number of results being displayed
+                  {((prefTerminologies.length > 0 && active === 'search') ||
+                    prefTerminologies.length === 0) && (
+                    <div className="view_more_wrapper">
+                      {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
                       there is a tooltip informing the user that redundant entries have been removed to explain any
                       inconsistencies in results numbers per page. */}
-                    <Tooltip
-                      placement="bottom"
-                      title="Redundant entries have been removed"
-                    >
-                      Displaying {resultsCount}
-                      &nbsp;of&nbsp;{totalCount}
-                    </Tooltip>
-                    {resultsCount < totalCount - filteredResultsCount && (
-                      <span
-                        className="view_more_link"
-                        onClick={e => {
-                          handleViewMore(e);
-                          setLastCount(resultsCount);
-                        }}
+                      <Tooltip
+                        placement="bottom"
+                        title="Redundant entries have been removed"
                       >
-                        View More
-                      </span>
-                    )}
-                  </div>
+                        Displaying {resultsCount}
+                        &nbsp;of&nbsp;{totalCount}
+                      </Tooltip>
+                      {resultsCount < totalCount - filteredResultsCount && (
+                        <span
+                          className="view_more_link"
+                          onClick={e => {
+                            handleViewMore(e);
+                            setLastCount(resultsCount);
+                          }}
+                        >
+                          View More
+                        </span>
+                      )}
+                    </div>
+                  )}
                 </div>
               </div>
             </>
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 82197c2..358f04b 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -127,11 +127,10 @@ export const MappingSearch = ({
   useEffect(() => {
     setActive(terminologiesToMap?.[0]?.id);
   }, [terminologiesToMap]);
-  console.log(active);
-  console.log(prefTerminologies.length);
   // The '!!' forces currentSearchProp to be evaluated as a boolean.
   // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
   // The function is run when the query changes and when the preferred ontology changes.
+  // If there are preferred terminologies, it runs when the OLS search bar is clicked (i.e. active)
   useEffect(() => {
     if (
       prefTerminologies.length > 0 &&
@@ -558,17 +557,17 @@ export const MappingSearch = ({
                       </div>
                       <div>
                         <div className="result_form">
-                          <Form.Item
-                            initialValue={initialChecked}
-                            name={['existing_mappings']}
-                            valuePropName="value"
-                            rules={[
-                              {
-                                required: false,
-                              },
-                            ]}
-                          >
-                            {mappingsForSearch?.length > 0 && (
+                          {mappingsForSearch?.length > 0 && (
+                            <Form.Item
+                              initialValue={initialChecked}
+                              name={['existing_mappings']}
+                              valuePropName="value"
+                              rules={[
+                                {
+                                  required: false,
+                                },
+                              ]}
+                            >
                               <Checkbox.Group
                                 className="mappings_checkbox existing_display"
                                 options={mappingsForSearch?.map((d, index) => {
@@ -584,8 +583,8 @@ export const MappingSearch = ({
                                 })}
                                 onChange={onExistingChange}
                               />
-                            )}
-                          </Form.Item>
+                            </Form.Item>
+                          )}
                           {displaySelectedMappings?.length > 0 && (
                             <Form.Item
                               name="selected_mappings"
@@ -691,7 +690,8 @@ export const MappingSearch = ({
                       </div>
                     </div>
                   </Form>
-                  {active === 'search' && (
+                  {((prefTerminologies.length > 0 && active === 'search') ||
+                    prefTerminologies.length === 0) && (
                     <div className="view_more_wrapper">
                       {/* 'View More' pagination displaying the number of results being displayed
                       out of the total number of results. Because of the filter to filter out the duplicates,
diff --git a/src/components/Manager/Utilitiy.jsx b/src/components/Manager/Utilitiy.jsx
index 4c3dd29..0180d09 100644
--- a/src/components/Manager/Utilitiy.jsx
+++ b/src/components/Manager/Utilitiy.jsx
@@ -27,9 +27,9 @@ export const ontologyReducer = d =>
     { results: [], filteredResults: [] }
   );
 
-// This function matches the ontology prop to its system (listed in object above) in the object that will be sent to the API
+// This function matches the ontology prop to its system in the object that will be sent to the API
 export const systemsMatch = (ontologyCode, ontologyApis) => {
-  // Search for the ontology that contains the requested ontology code
+  // Searches for the ontology that contains the requested ontology code
   const ontologyApi = ontologyApis.find(
     api => api.ontologies[ontologyCode.toLowerCase()]
   );
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 8c1d63c..8eb849f 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -207,6 +207,7 @@ export const EditMappingsModal = ({
   // The existing and new mappings are JSON.parsed combined into one mappings array to be passed into the body of the PUT call.
   const editUpdatedMappings = values => {
     setLoading(true);
+    console.log(values);
     const selectedMappings = values?.selected_mappings?.map(item => ({
       code: item.code,
       display: item.display,

From 849b9d13fde1f4bc2620dd689de9eaa721e3e3b5 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 19 Nov 2024 13:09:36 -0600
Subject: [PATCH 146/180] Using system from ontologyAPI endpoint

---
 .../MappingsFunctions/GetMappingsModal.jsx    |  6 +++--
 .../MappingsFunctions/MappingReset.jsx        |  4 +++-
 .../MappingsFunctions/MappingSearch.jsx       |  4 +++-
 src/components/Manager/Utilitiy.jsx           | 23 +++++++++----------
 .../Tables/EditMappingsTableModal.jsx         |  3 ++-
 .../Projects/Terminologies/APIResults.jsx     | 15 +++++++++---
 .../Terminologies/EditMappingModal.jsx        |  3 ++-
 7 files changed, 37 insertions(+), 21 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 80d8005..f741e3c 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -42,6 +42,7 @@ export const GetMappingsModal = ({
     apiPreferencesCode,
     setUnformattedPref,
     prefTypeKey,
+    ontologyApis,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 1000;
@@ -159,7 +160,7 @@ export const GetMappingsModal = ({
       code: item.obo_id,
       display: item.label,
       description: item.description[0],
-      system: systemsMatch(item.obo_id.split(':')[0]),
+      system: systemsMatch(item.obo_id.split(':')[0], ontologyApis),
     }));
     const mappingsDTO = {
       mappings: selectedMappings,
@@ -479,7 +480,8 @@ export const GetMappingsModal = ({
                                           display: d.label,
                                           description: d.description[0],
                                           system: systemsMatch(
-                                            d?.obo_id?.split(':')[0]
+                                            d?.obo_id?.split(':')[0],
+                                            ontologyApis
                                           ),
                                         }),
                                         label: checkBoxDisplay(d, index),
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index dfb508e..df686b7 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -26,6 +26,7 @@ export const MappingReset = ({
     setApiPreferencesCode,
     apiPreferencesCode,
     setUnformattedPref,
+    ontologyApis,
   } = useContext(SearchContext);
   const [page, setPage] = useState(0);
   const entriesPerPage = 1000;
@@ -380,7 +381,8 @@ export const MappingReset = ({
                                           display: d.label,
                                           // description: d.description[0],
                                           system: systemsMatch(
-                                            d?.obo_id?.split(':')[0]
+                                            d?.obo_id?.split(':')[0],
+                                            ontologyApis
                                           ),
                                         }),
                                         label: checkBoxDisplay(d, index),
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 18c8e96..90938c8 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -27,6 +27,7 @@ export const MappingSearch = ({
     setApiPreferencesCode,
     apiPreferencesCode,
     setUnformattedPref,
+    ontologyApis,
   } = useContext(SearchContext);
 
   const [page, setPage] = useState(0);
@@ -475,7 +476,8 @@ export const MappingSearch = ({
                                           display: d.label,
                                           description: d.description[0],
                                           system: systemsMatch(
-                                            d?.obo_id?.split(':')[0]
+                                            d?.obo_id?.split(':')[0],
+                                            ontologyApis
                                           ),
                                         }),
                                         label: newSearchDisplay(d, index),
diff --git a/src/components/Manager/Utilitiy.jsx b/src/components/Manager/Utilitiy.jsx
index 787a5d3..0f4ef32 100644
--- a/src/components/Manager/Utilitiy.jsx
+++ b/src/components/Manager/Utilitiy.jsx
@@ -27,18 +27,17 @@ export const ontologyReducer = d =>
     { results: [], filteredResults: [] }
   );
 
-/* The backend API does not yet have a way to affix the system URL to each ontology. 
-  This displays the system for each ontology searched. */
-export const ontologySystems = {
-  MONDO: 'http://purl.obolibrary.org/obo/mondo.owl',
-  HP: 'http://purl.obolibrary.org/obo/hp.owl',
-  MAXO: 'http://purl.obolibrary.org/obo/maxo.owl',
-  NCIT: 'http://purl.obolibrary.org/obo/ncit.owl',
-};
-
-// This function matches the ontology prop to its system (listed in object above) in the object that will be sent to the API
-export const systemsMatch = ont => {
-  return ontologySystems[ont];
+// This function matches the ontology prop to its system in the object that will be sent to the API
+export const systemsMatch = (ontologyCode, ontologyApis) => {
+  // Searches for the ontology that contains the requested ontology code
+  const ontologyApi = ontologyApis.find(
+    api => api.ontologies[ontologyCode.toLowerCase()]
+  );
+  if (ontologyApi) {
+    // Return the system URL for the matching ontology
+    return ontologyApi.ontologies[ontologyCode.toLowerCase()].system;
+  }
+  return null; // If not found, return null or handle accordingly
 };
 
 // Iterates over the facet counts in the result to make an object of search results per ontology
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index 474d4f0..4ad2682 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -41,6 +41,7 @@ export const EditMappingsTableModal = ({
     setApiPreferencesCode,
     preferenceType,
     prefTypeKey,
+    ontologyApis,
   } = useContext(SearchContext);
 
   useEffect(() => {
@@ -208,7 +209,7 @@ export const EditMappingsTableModal = ({
       code: item.obo_id,
       display: item.label,
       description: item.description[0],
-      system: systemsMatch(item.obo_id.split(':')[0]),
+      system: systemsMatch(item.obo_id.split(':')[0], ontologyApis),
     }));
     const mappingsDTO = {
       mappings: [
diff --git a/src/components/Projects/Terminologies/APIResults.jsx b/src/components/Projects/Terminologies/APIResults.jsx
index cf125c1..c1e9096 100644
--- a/src/components/Projects/Terminologies/APIResults.jsx
+++ b/src/components/Projects/Terminologies/APIResults.jsx
@@ -9,8 +9,14 @@ export const APIResults = ({
   displaySelectedMappings,
   onSelectedChange,
 }) => {
-  const { apiResults, apiResultsCount, apiPage, setApiPage, apiTotalCount } =
-    useContext(SearchContext);
+  const {
+    apiResults,
+    apiResultsCount,
+    apiPage,
+    setApiPage,
+    apiTotalCount,
+    ontologyApis,
+  } = useContext(SearchContext);
   const [filteredResultsCount, setFilteredResultsCount] = useState(0);
   const [lastCount, setLastCount] = useState(0); //save last count as count of the results before you fetch data again
 
@@ -108,7 +114,10 @@ export const APIResults = ({
                       code: d.obo_id,
                       display: d.label,
                       description: d.description[0],
-                      system: systemsMatch(d?.obo_id?.split(':')[0]),
+                      system: systemsMatch(
+                        d?.obo_id?.split(':')[0],
+                        ontologyApis
+                      ),
                     }),
                     label: checkBoxDisplay(d, index),
                   };
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 2bb49c0..84232d3 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -35,6 +35,7 @@ export const EditMappingsModal = ({
     setApiPreferencesCode,
     preferenceType,
     prefTypeKey,
+    ontologyApis,
   } = useContext(SearchContext);
   const [loading, setLoading] = useState(false);
   const [reset, setReset] = useState(false);
@@ -210,7 +211,7 @@ export const EditMappingsModal = ({
       code: item.obo_id,
       display: item.label,
       description: item.description[0],
-      system: systemsMatch(item.obo_id.split(':')[0]),
+      system: systemsMatch(item.obo_id.split(':')[0], ontologyApis),
     }));
     const mappingsDTO = {
       mappings: [

From 7fa421d3052df6afea0445f6a23bc0792bb1afa7 Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Tue, 19 Nov 2024 13:45:24 -0600
Subject: [PATCH 147/180] app routes protected

---
 src/AppRouter.jsx                 | 30 +++++++----------------
 src/components/Auth/Login.jsx     | 11 +++------
 src/components/Auth/LoginPage.jsx | 12 +++++++---
 src/components/Auth/Logout.jsx    |  3 +--
 src/components/Nav/NavBar.jsx     | 40 +++++++++++++++++++++++++------
 src/components/Nav/NavBar.scss    |  2 ++
 6 files changed, 57 insertions(+), 41 deletions(-)

diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index c198640..acf9ebd 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -5,8 +5,9 @@ import {
   Route,
   Routes,
   Navigate,
-  useLocation
 } from 'react-router-dom';
+import { useContext } from 'react';
+import { myContext } from './App.jsx';
 import { NavBar } from './components/Nav/NavBar';
 import { Login } from './components/Auth/Login.jsx';
 import { LoginPage } from './components/Auth/LoginPage.jsx';
@@ -28,30 +29,17 @@ import { SearchContextRoot } from './Contexts/SearchContext.jsx';
 import { About } from './components/About/About.jsx';
 
 export const AppRouter = () => {
+ const {user} = useContext(myContext);
 
   const isLoggedIn = () => {
-    const token = localStorage.getItem('googleToken');
-    if (token) {
+    const storedUser = localStorage.getItem('user');
+    
+    if (storedUser) {
       return true;
     } else {
       return false;
     }
   }
-
- 
-
-  function ProtectedRoute({ children }) {
-    const location = useLocation();
-  
-    // If the user is not logged in, redirect to login with the intended destination path
-    if (!isLoggedIn()) {
-      return <Navigate to="/login" replace state={{ from: location }} />;
-    }
-  
-    // Otherwise, render the child component (e.g., DDDetails)
-    return children;
-  }
-
   return (
     <BrowserRouter>
       <Routes>
@@ -75,9 +63,9 @@ export const AppRouter = () => {
             <Route path="/search/:query" element={<SearchResults />} />
             <Route path="/404" element={<Error404 />} />
             
-            <Route path="/ontologies" element={ <ProtectedRoute><OntologyInfo /></ProtectedRoute>} />
+            <Route path="/ontologies" element={<OntologyInfo />} />
             <Route path="/about" element={<About />} />
-            <Route path="/terminologies" element={<ProtectedRoute><TerminologyList /></ProtectedRoute>} />
+            <Route path="/terminologies" element={ isLoggedIn() ? <TerminologyList />:<Navigate to="/login" /> } />
             <Route path="/login" element={<LoginPage/>}/>
             <Route
               path="/terminology"
@@ -85,7 +73,7 @@ export const AppRouter = () => {
             />
             <Route element={<MappingContextRoot />}>
               <Route element={<SearchContextRoot />}>
-                <Route path="/studies" element={<ProtectedRoute><StudyList /></ProtectedRoute>} />
+                <Route path="/studies" element={isLoggedIn() ? <StudyList />: <Navigate to="/login" />} />
                 <Route path="/study" element={<Navigate to="/studies" />} />
                 <Route path="/Study/:studyId">
                   <Route index element={isLoggedIn() ? <StudyDetails />: <Navigate to="/login" />} />
diff --git a/src/components/Auth/Login.jsx b/src/components/Auth/Login.jsx
index 7daa5fb..99e230a 100644
--- a/src/components/Auth/Login.jsx
+++ b/src/components/Auth/Login.jsx
@@ -3,12 +3,10 @@ import { jwtDecode } from 'jwt-decode';
 import { useContext, useEffect } from 'react';
 import { Logout } from './Logout';
 import { myContext } from '../../App';
-import { useLocation, useNavigate } from 'react-router-dom';
+
 export const Login = () => {
   const { user, setUser } = useContext(myContext);
-  const location = useLocation();
-  const navigate = useNavigate();
-  const from = location.state?.from?.pathname || '/'
+
   useEffect(() => {
     const storedUser = localStorage.getItem('user');
     if (storedUser) {
@@ -24,7 +22,6 @@ export const Login = () => {
       <GoogleLogin
         theme="filled_black"
         onSuccess={credentialResponse => {
-          localStorage.setItem('googleToken', credentialResponse.access_token); 
           const credentialResponseDecoded = jwtDecode(
             credentialResponse.credential
           );
@@ -33,8 +30,6 @@ export const Login = () => {
             'user',
             JSON.stringify(credentialResponseDecoded)
           );
-          navigate(from, { replace: true });
-          
         }}
         onError={() => {
           console.log('Login Failed');
@@ -42,4 +37,4 @@ export const Login = () => {
       />
     </div>
   );
-};
+};
\ No newline at end of file
diff --git a/src/components/Auth/LoginPage.jsx b/src/components/Auth/LoginPage.jsx
index 8dc8395..9df1e10 100644
--- a/src/components/Auth/LoginPage.jsx
+++ b/src/components/Auth/LoginPage.jsx
@@ -1,8 +1,14 @@
 import { Login } from "./Login"
+import { useContext } from 'react';
+import { myContext } from '../../App';
 export const LoginPage = () => {
-    return <>
-        <div style={{ height:"25rem",display:"flex",flexDirection:"column",justifyContent:"space-around",alignItems:"center"}}>
+    const {user} = useContext(myContext);
+    return <div style={{background:"rgba(0,0,0,.2"}}>
+        {user &&
+        <h2 style={{textAlign:"center",paddingTop:'5rem'}}>You are logged in and can navigate to the rest of the site</h2>}
+        <div style={{ height:"5rem",display:"flex",flexDirection:"column",justifyContent:"space-around",alignItems:"center"}}>
             <Login />
         </div>
-    </>
+        
+    </div>
 }
\ No newline at end of file
diff --git a/src/components/Auth/Logout.jsx b/src/components/Auth/Logout.jsx
index 38e0920..3aa8d16 100644
--- a/src/components/Auth/Logout.jsx
+++ b/src/components/Auth/Logout.jsx
@@ -7,7 +7,6 @@ export const Logout = ({ user, setUser }) => {
   const logOut = () => {
     googleLogout();
     setUser(null);
-    localStorage.removeItem('googleToken');
     localStorage.removeItem('user');
   };
 
@@ -27,4 +26,4 @@ export const Logout = ({ user, setUser }) => {
       </div>
     </>
   );
-};
+};
\ No newline at end of file
diff --git a/src/components/Nav/NavBar.jsx b/src/components/Nav/NavBar.jsx
index 155727e..2aa7411 100644
--- a/src/components/Nav/NavBar.jsx
+++ b/src/components/Nav/NavBar.jsx
@@ -1,9 +1,23 @@
-import { NavLink } from 'react-router-dom';
+import { NavLink, useNavigate } from 'react-router-dom';
 import './NavBar.scss';
 import { Login } from '../Auth/Login';
-import { GoogleOAuthProvider } from '@react-oauth/google';
+import { useContext, useState } from 'react'
+import { myContext } from '../../App';
+import { RequiredLogin } from '../Auth/RequiredLogin';
 
 export const NavBar = () => {
+  const [routeTo, setRouteTo] = useState(null);
+  const { user } = useContext(myContext);
+  const navigate = useNavigate();
+  const handleSuccess = () => {
+    navigate(routeTo);
+  };
+  const login = RequiredLogin({ handleSuccess: handleSuccess });
+  const handleLogin = (route) => {
+    setRouteTo(route);
+    login();
+  }
+  
   return (
     <>
       <nav className="navbar">
@@ -19,12 +33,24 @@ export const NavBar = () => {
             <NavLink to="/">
               <li className="nav_link">Search</li>
             </NavLink>
-            <NavLink to="/studies">
+            <div onClick={() => {
+              if (user) {
+                navigate('/studies')
+              } else {
+                handleLogin('/studies')
+              }
+            }}>
               <li className="nav_link">Studies</li>
-            </NavLink>
-            <NavLink to="/terminologies">
+            </div>
+            <div onClick={() => {
+              if (user) {
+                navigate('/terminologies')
+              } else {
+                handleLogin('/terminologies')
+              }
+            }}>
               <li className="nav_link">Terminologies</li>
-            </NavLink>
+            </div>
             {/* Placeholder elements below. No functionality at this time.*/}
             <NavLink to="/about">
               <li className="nav_link">About</li>
@@ -38,7 +64,7 @@ export const NavBar = () => {
             <Login />
           </div>
         </ul>
-      </nav>
+      </nav >
     </>
   );
 };
diff --git a/src/components/Nav/NavBar.scss b/src/components/Nav/NavBar.scss
index a48d239..b07deeb 100644
--- a/src/components/Nav/NavBar.scss
+++ b/src/components/Nav/NavBar.scss
@@ -70,6 +70,8 @@ nav.navbar {
     padding: 0 4px;
     width: $navHeight;
     border-radius: 10px;
+    font-weight: bold;
+    cursor: pointer;
   }
 
   .nav_link:hover {

From 84944cd64609aeaed7d90e3ae068f8a4eb1a3fcc Mon Sep 17 00:00:00 2001
From: Morgan Higby-Flowers <mhigbyflowers@gmail.com>
Date: Tue, 19 Nov 2024 14:07:42 -0600
Subject: [PATCH 148/180] adding scrolling

---
 src/components/Manager/ShowHistory.jsx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/components/Manager/ShowHistory.jsx b/src/components/Manager/ShowHistory.jsx
index 0d99bab..6d171d6 100644
--- a/src/components/Manager/ShowHistory.jsx
+++ b/src/components/Manager/ShowHistory.jsx
@@ -115,6 +115,10 @@ export const ShowHistory = ({
               <h4>{code}</h4>
             </div>
             <Table
+              scroll={{
+                x: 'max-content',
+                y: 60 * 5,
+              }}
               columns={columns}
               dataSource={dataSource}
               pagination={{

From 001c641dd9cf433e8a55a9f8f32ec432bf31d94b Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 25 Nov 2024 16:11:29 -0600
Subject: [PATCH 149/180] First pass at mapping relationship in
 GetMappingsModal

---
 .env                                          |  4 +--
 src/Contexts/MappingContext.jsx               |  6 ++++
 .../MappingsFunctions/GetMappingsModal.jsx    | 35 ++++++++++++++----
 .../MappingsFunctions/MappingRelationship.jsx | 36 +++++++++++++++++++
 .../Projects/Tables/TableDetails.jsx          |  6 ++++
 5 files changed, 79 insertions(+), 8 deletions(-)
 create mode 100644 src/components/Manager/MappingsFunctions/MappingRelationship.jsx

diff --git a/.env b/.env
index 85f0aac..fd0a3d4 100644
--- a/.env
+++ b/.env
@@ -1,7 +1,7 @@
 VITE_SEARCH_ENDPOINT = https://www.ebi.ac.uk/ols4/api/search?
 VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
 # VITE_VOCAB_ENDPOINT = http://127.0.0.1:5000/api # local
-VITE_VOCAB_ENDPOINT = https://locutus-110109177269.us-central1.run.app/api # dev
-# VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
+VITE_VOCAB_ENDPOINT = https://locutus-dev-110109177269.us-central1.run.app/api # dev
+# VITE_VOCAB_ENDPOINT = https://locutus-uat-1066621297011.us-central1.run.app/api # uat
 VITE_CLIENT_ID = 907694787484-36jr4oaf04mmniik6482batc87ejemm8.apps.googleusercontent.com
 VITE_MAPDRAGON_VERSION = "Development"
\ No newline at end of file
diff --git a/src/Contexts/MappingContext.jsx b/src/Contexts/MappingContext.jsx
index 97102e7..69b1884 100644
--- a/src/Contexts/MappingContext.jsx
+++ b/src/Contexts/MappingContext.jsx
@@ -13,6 +13,8 @@ export function MappingContextRoot() {
   const [selectedMappings, setSelectedMappings] = useState([]);
   const [displaySelectedMappings, setDisplaySelectedMappings] = useState([]);
   const [selectedBoxes, setSelectedBoxes] = useState([]);
+  const [relationshipOptions, setRelationshipOptions] = useState([]);
+  const [idsForSelect, setIdsForSelect] = useState([]);
 
   const context = {
     editMappings,
@@ -33,6 +35,10 @@ export function MappingContextRoot() {
     setSelectedBoxes,
     assignMappings,
     setAssignMappings,
+    relationshipOptions,
+    setRelationshipOptions,
+    idsForSelect,
+    setIdsForSelect,
   };
 
   return (
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index f71d663..911e0dc 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -17,7 +17,7 @@ import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
 import { OntologyFilterCodeSubmit } from './OntologyFilterCodeSubmit';
 import { OntologyFilterCodeSubmitTerm } from './OntologyFilterCodeSubmitTerm';
-import { useParams } from 'react-router-dom';
+import { MappingRelationship } from './MappingRelationship';
 
 export const GetMappingsModal = ({
   componentString,
@@ -54,18 +54,21 @@ export const GetMappingsModal = ({
   const [filteredResultsCount, setFilteredResultsCount] = useState(0);
   const [inputValue, setInputValue] = useState(searchProp); //Sets the value of the search bar
   const [currentSearchProp, setCurrentSearchProp] = useState(searchProp);
+
   const {
     setSelectedMappings,
     displaySelectedMappings,
     setDisplaySelectedMappings,
     selectedBoxes,
     setSelectedBoxes,
+    idsForSelect,
   } = useContext(MappingContext);
   let ref = useRef();
   // since the code is passed through searchProp, the '!!' forces it to be evaluated as a boolean.
   // if there is a searchProp being passed, it evaluates to true and runs the search function.
   // inputValue and currentSearchProp for the search bar is set to the passed searchProp.
   // The function is run when the code changes.
+
   useEffect(() => {
     setInputValue(searchProp);
     setCurrentSearchProp(searchProp);
@@ -137,11 +140,7 @@ export const GetMappingsModal = ({
 
   const onClose = () => {
     setPage(0);
-    setResults([]);
-    setSelectedMappings([]);
-    setDisplaySelectedMappings([]);
     setApiPreferencesCode(undefined);
-    setSelectedBoxes([]);
     setSelectedKey(null);
     setPrefTerminologies([]);
   };
@@ -161,11 +160,14 @@ export const GetMappingsModal = ({
       display: item.label,
       description: item.description[0],
       system: systemsMatch(item.obo_id.split(':')[0], ontologyApis),
+      mapping_relationship: idsForSelect[item.obo_id],
     }));
+
     const mappingsDTO = {
       mappings: selectedMappings,
       editor: user.email,
     };
+
     setLoading(true);
     fetch(
       `${vocabUrl}/${componentString}/${component.id}/mapping/${mappingProp}`,
@@ -186,9 +188,22 @@ export const GetMappingsModal = ({
       })
       .then(data => {
         setMapping(data.codes);
-        form.resetFields();
         setGetMappings(null);
         message.success('Changes saved successfully.');
+        form.resetFields();
+        setResults([]);
+        setSelectedMappings([]);
+        setDisplaySelectedMappings([]);
+        setSelectedBoxes([]);
+      })
+      .catch(error => {
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred saving the mapping.',
+          });
+        }
+        return error;
       })
       .finally(() => setLoading(false));
     table
@@ -321,6 +336,9 @@ export const GetMappingsModal = ({
                   {d?.obo_id}
                 </a>
               </div>
+              <div>
+                <MappingRelationship mapping={d} />
+              </div>
             </div>
             <div>{ellipsisString(d?.description[0], '100')}</div>
           </div>
@@ -404,8 +422,13 @@ export const GetMappingsModal = ({
         }}
         onCancel={() => {
           onClose();
+          setResults([]);
           form.resetFields();
           setGetMappings(null);
+          setResults([]);
+          setSelectedMappings([]);
+          setDisplaySelectedMappings([]);
+          setSelectedBoxes([]);
         }}
         maskClosable={false}
         destroyOnClose={true}
diff --git a/src/components/Manager/MappingsFunctions/MappingRelationship.jsx b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
new file mode 100644
index 0000000..375b7e4
--- /dev/null
+++ b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
@@ -0,0 +1,36 @@
+import { Select } from 'antd';
+import { useContext } from 'react';
+import { MappingContext } from '../../../Contexts/MappingContext';
+
+export const MappingRelationship = ({ mapping }) => {
+  const { relationshipOptions, idsForSelect, setIdsForSelect } =
+    useContext(MappingContext);
+
+  const handleSelectChange = (obo_id, value) => {
+    setIdsForSelect(prev => ({
+      ...prev,
+      [obo_id]: value,
+    }));
+  };
+
+  const options = relationshipOptions.map(ro => {
+    return {
+      value: ro.code,
+      label: ro.display,
+    };
+  });
+
+  return (
+    <Select
+      options={options}
+      style={{
+        width: 120,
+      }}
+      placeholder="Mapping Quality"
+      popupMatchSelectWidth={false}
+      allowClear
+      value={idsForSelect[mapping.obo_id]}
+      onChange={value => handleSelectChange(mapping.obo_id, value)}
+    />
+  );
+};
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index e722a53..6c67b6c 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -45,6 +45,8 @@ export const TableDetails = () => {
     setMapping,
     setEditMappings,
     editMappings,
+    relationshipOptions,
+    setRelationshipOptions,
   } = useContext(MappingContext);
   const { studyId, DDId, tableId } = useParams();
   const [loading, setLoading] = useState(true);
@@ -169,6 +171,10 @@ export const TableDetails = () => {
         return error;
       })
       .finally(() => setLoading(false));
+
+    getById(vocabUrl, 'Terminology', 'ftd-concept-map-relationship').then(
+      data => setRelationshipOptions(data.codes)
+    );
   }, []);
 
   // sets table to an empty object on dismount

From 9729b0a89fca51169c63f187ac909b074689e837 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 26 Nov 2024 10:03:40 -0600
Subject: [PATCH 150/180] Mapping relationships for AssignMappings and
 AssignMappingsViaButton

---
 .../Manager/MappingsFunctions/AssignMappings.jsx     |  5 ++++-
 .../Manager/MappingsFunctions/DisplaySelected.jsx    |  6 +++++-
 .../MappingsFunctions/MappingRelationship.jsx        |  6 ++++--
 src/components/Projects/Tables/TableDetails.jsx      | 12 +++++++-----
 .../Terminologies/AssignMappingsViaButton.jsx        |  5 ++++-
 .../Projects/Terminologies/Terminology.jsx           |  8 ++++++++
 6 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/AssignMappings.jsx b/src/components/Manager/MappingsFunctions/AssignMappings.jsx
index fc321f3..7c4f794 100644
--- a/src/components/Manager/MappingsFunctions/AssignMappings.jsx
+++ b/src/components/Manager/MappingsFunctions/AssignMappings.jsx
@@ -17,7 +17,8 @@ export const AssignMappings = ({
 
   const { vocabUrl, user } = useContext(myContext);
   const { prefTerminologies, setApiResults } = useContext(SearchContext);
-  const { setMapping } = useContext(MappingContext);
+  const { setMapping, idsForSelect, setIdsForSelect } =
+    useContext(MappingContext);
   const [terminologiesToMap, setTerminologiesToMap] = useState([]);
   const [loading, setLoading] = useState(false);
   const [mappingProp, setMappingProp] = useState('');
@@ -27,6 +28,7 @@ export const AssignMappings = ({
     setSelectedKey(null);
     setMappingProp('');
     setApiResults([]);
+    setIdsForSelect([]);
   };
   const fetchTerminologies = () => {
     setLoading(true);
@@ -64,6 +66,7 @@ export const AssignMappings = ({
         ? item.description[0]
         : item.description,
       system: item.system,
+      mapping_relationship: idsForSelect[item.obo_id || item.code],
     }));
     const mappingsDTO = {
       mappings: selectedMappings,
diff --git a/src/components/Manager/MappingsFunctions/DisplaySelected.jsx b/src/components/Manager/MappingsFunctions/DisplaySelected.jsx
index 97ac7ad..39c43de 100644
--- a/src/components/Manager/MappingsFunctions/DisplaySelected.jsx
+++ b/src/components/Manager/MappingsFunctions/DisplaySelected.jsx
@@ -1,5 +1,6 @@
 import { Checkbox, Form, Tooltip } from 'antd';
 import { ellipsisString } from '../Utilitiy';
+import { MappingRelationship } from './MappingRelationship';
 
 export const DisplaySelected = ({
   displaySelectedMappings,
@@ -13,8 +14,11 @@ export const DisplaySelected = ({
           <div>
             <div className="modal_term_ontology">
               <div>{selected?.code}</div>
+              <div>{selected?.display || selected?.label}</div>
+              <div>
+                <MappingRelationship mapping={selected} />
+              </div>
             </div>
-            <div>{selected?.display || selected?.label}</div>
             <div>
               {selected?.description?.length > 85 ? (
                 <Tooltip
diff --git a/src/components/Manager/MappingsFunctions/MappingRelationship.jsx b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
index 375b7e4..464ab98 100644
--- a/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
@@ -29,8 +29,10 @@ export const MappingRelationship = ({ mapping }) => {
       placeholder="Mapping Quality"
       popupMatchSelectWidth={false}
       allowClear
-      value={idsForSelect[mapping.obo_id]}
-      onChange={value => handleSelectChange(mapping.obo_id, value)}
+      value={idsForSelect[mapping.obo_id || mapping.code]}
+      onChange={value =>
+        handleSelectChange(mapping.obo_id || mapping.code, value)
+      }
     />
   );
 };
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 6c67b6c..a361c85 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -45,7 +45,6 @@ export const TableDetails = () => {
     setMapping,
     setEditMappings,
     editMappings,
-    relationshipOptions,
     setRelationshipOptions,
   } = useContext(MappingContext);
   const { studyId, DDId, tableId } = useParams();
@@ -138,6 +137,13 @@ export const TableDetails = () => {
                 }
                 return error;
               })
+              .then(() =>
+                getById(
+                  vocabUrl,
+                  'Terminology',
+                  'ftd-concept-map-relationship'
+                ).then(data => setRelationshipOptions(data.codes))
+              )
               .then(() =>
                 fetch(`${vocabUrl}/Table/${tableId}/filter/self`, {
                   method: 'GET',
@@ -171,10 +177,6 @@ export const TableDetails = () => {
         return error;
       })
       .finally(() => setLoading(false));
-
-    getById(vocabUrl, 'Terminology', 'ftd-concept-map-relationship').then(
-      data => setRelationshipOptions(data.codes)
-    );
   }, []);
 
   // sets table to an empty object on dismount
diff --git a/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx b/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx
index d475350..440b567 100644
--- a/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx
+++ b/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx
@@ -15,7 +15,8 @@ export const AssignMappingsViaButton = ({
 
   const { vocabUrl, user } = useContext(myContext);
   const { prefTerminologies, setApiResults } = useContext(SearchContext);
-  const { setMapping } = useContext(MappingContext);
+  const { setMapping, idsForSelect, setIdsForSelect } =
+    useContext(MappingContext);
   const [terminologiesToMap, setTerminologiesToMap] = useState([]);
   const [loading, setLoading] = useState(false);
   const [mappingProp, setMappingProp] = useState('');
@@ -24,6 +25,7 @@ export const AssignMappingsViaButton = ({
   const onClose = () => {
     setApiResults([]);
     setSelectedBoxes([]);
+    setIdsForSelect([]);
   };
   const fetchTerminologies = () => {
     setLoading(true);
@@ -58,6 +60,7 @@ export const AssignMappingsViaButton = ({
         ? item.description[0]
         : item.description,
       system: item.system,
+      mapping_relationship: idsForSelect[item.obo_id || item.code],
     }));
     const mappingsDTO = {
       mappings: selectedMappings,
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 6c7699b..8d87b75 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -43,6 +43,7 @@ export const Terminology = () => {
     setGetMappings,
     mapping,
     setMapping,
+    setRelationshipOptions,
   } = useContext(MappingContext);
 
   const [pageSize, setPageSize] = useState(
@@ -241,6 +242,13 @@ It then shows the mappings as table data and alows the user to delete a mapping
                 }
                 return error;
               })
+              .then(() =>
+                getById(
+                  vocabUrl,
+                  'Terminology',
+                  'ftd-concept-map-relationship'
+                ).then(data => setRelationshipOptions(data.codes))
+              )
               .then(() =>
                 getById(
                   vocabUrl,

From 349dcc0fa6067b7443ffe890c5afd04192be6b85 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 26 Nov 2024 15:47:40 -0600
Subject: [PATCH 151/180] First pass at editing mapping quality when viewing
 exisitng mappings

---
 src/Contexts/MappingContext.jsx               |  3 ++
 .../MappingsFunctions/MappingRelationship.jsx |  3 +-
 .../Tables/EditMappingsTableModal.jsx         | 53 +++++++++++++++----
 .../Projects/Tables/TableStyling.scss         | 14 ++++-
 .../Terminologies/EditMappingModal.jsx        | 31 +++++++++--
 5 files changed, 86 insertions(+), 18 deletions(-)

diff --git a/src/Contexts/MappingContext.jsx b/src/Contexts/MappingContext.jsx
index 69b1884..6a35c0f 100644
--- a/src/Contexts/MappingContext.jsx
+++ b/src/Contexts/MappingContext.jsx
@@ -15,6 +15,7 @@ export function MappingContextRoot() {
   const [selectedBoxes, setSelectedBoxes] = useState([]);
   const [relationshipOptions, setRelationshipOptions] = useState([]);
   const [idsForSelect, setIdsForSelect] = useState([]);
+  const [showOptions, setShowOptions] = useState(false);
 
   const context = {
     editMappings,
@@ -39,6 +40,8 @@ export function MappingContextRoot() {
     setRelationshipOptions,
     idsForSelect,
     setIdsForSelect,
+    showOptions,
+    setShowOptions,
   };
 
   return (
diff --git a/src/components/Manager/MappingsFunctions/MappingRelationship.jsx b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
index 464ab98..c1c8846 100644
--- a/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
@@ -23,10 +23,11 @@ export const MappingRelationship = ({ mapping }) => {
   return (
     <Select
       options={options}
+      defaultValue={mapping?.mapping_relationship || undefined}
       style={{
         width: 120,
       }}
-      placeholder="Mapping Quality"
+      placeholder="Quality"
       popupMatchSelectWidth={false}
       allowClear
       value={idsForSelect[mapping.obo_id || mapping.code]}
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index 4000478..393924b 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -18,6 +18,7 @@ import { ellipsisString, systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyFilterCodeSubmit } from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmit';
+import { MappingRelationship } from '../../Manager/MappingsFunctions/MappingRelationship';
 
 export const EditMappingsTableModal = ({
   editMappings,
@@ -34,8 +35,14 @@ export const EditMappingsTableModal = ({
   const [reset, setReset] = useState(false);
   const [mappingsForSearch, setMappingsForSearch] = useState([]);
   const [editSearch, setEditSearch] = useState(false);
-  const { setSelectedMappings, setDisplaySelectedMappings } =
-    useContext(MappingContext);
+  const {
+    setSelectedMappings,
+    setDisplaySelectedMappings,
+    relationshipOptions,
+    setShowOptions,
+    showOptions,
+    idsForSelect,
+  } = useContext(MappingContext);
   const {
     apiPreferencesCode,
     setApiPreferencesCode,
@@ -124,6 +131,16 @@ export const EditMappingsTableModal = ({
     }
   };
 
+  // Find the object in relationshipOptions where the code matches the mappings's mapping_relationship
+  // If there is a match, return the display. If not, return null.
+  const displayRelationship = item => {
+    const findDisplay = relationshipOptions.find(
+      ro => ro.code === item.mapping_relationship
+    );
+
+    return findDisplay ? findDisplay.display : null;
+  };
+
   // The label for the checkbox for each mapping. Displays JSX to show the display and code.
   // The description field is commented out to be integrated when there is API support.
   const editMappingsLabel = (item, index) => {
@@ -135,10 +152,18 @@ export const EditMappingsTableModal = ({
               <div>
                 <b>{item?.display}</b>
               </div>
-              <div>
-                {/* <a href={item.iri} target="_blank"> */}
-                {item?.code}
-                {/* </a> */}
+              <div>{item?.code}</div>
+              <div
+              // className="mapping_relationship"
+              // onClick={setShowOptions(item.mapping_relationship)}
+              >
+                <MappingRelationship mapping={item} />
+
+                {/* {item?.mapping_relationship && !showOptions
+                  ? displayRelationship(item)
+                  : (!item.mapping_relationship || !!showOptions) && (
+                      <MappingRelationship mapping={item} />
+                    )} */}
               </div>
             </div>
             <div>
@@ -164,10 +189,21 @@ export const EditMappingsTableModal = ({
   // Each mapping in the mappings array being edited is JSON.parsed and turned into objects in the mappings array.
   const updateMappings = values => {
     setLoading(true);
+    // If there are changes in the mapping relationship dropdown, the changes are matched to the code and added to the mapping object.
     const mappingsDTO = {
-      mappings: values?.mappings?.map(v => JSON.parse(v)) ?? [],
+      mappings:
+        values?.mappings?.map(v => {
+          const parsedMapping = JSON.parse(v);
+          if (idsForSelect[parsedMapping.code]) {
+            parsedMapping.mapping_relationship =
+              idsForSelect[parsedMapping.code];
+          }
+
+          return parsedMapping;
+        }) ?? [],
       editor: user.email,
     };
+
     fetch(`${vocabUrl}/Table/${tableId}/mapping/${editMappings.code}`, {
       method: 'PUT',
       headers: {
@@ -272,9 +308,6 @@ export const EditMappingsTableModal = ({
         form
           .validateFields()
           .then(values => {
-            {
-              /* Performs the updateMappings PUT call on 'Save' button click */
-            }
             editSearch || reset
               ? editUpdatedMappings(values)
               : updateMappings(values);
diff --git a/src/components/Projects/Tables/TableStyling.scss b/src/components/Projects/Tables/TableStyling.scss
index 64e5b6e..729bf44 100644
--- a/src/components/Projects/Tables/TableStyling.scss
+++ b/src/components/Projects/Tables/TableStyling.scss
@@ -82,13 +82,23 @@ input::file-selector-button:hover {
   }
   display: flex;
   .remove-mapping {
-    padding-left:.25rem;
+    padding-left: 0.25rem;
     cursor: pointer;
     opacity: 0;
 
     &:hover {
-      transition: all .4s linear;
+      transition: all 0.4s linear;
       opacity: 1;
     }
   }
 }
+
+.mapping_relationship {
+  padding: 2px 6px;
+  border: 1px solid $greyColor;
+  border-radius: 4px;
+  &:hover {
+    background-color: rgb(239, 235, 235);
+    transition: all 0.3s linear;
+  }
+}
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 8c1d63c..149c142 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -17,6 +17,8 @@ import { ellipsisString, systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyFilterCodeSubmitTerm } from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm';
+import { MappingRelationship } from '../../Manager/MappingsFunctions/MappingRelationship';
+import { MappingContext } from '../../../Contexts/MappingContext';
 
 export const EditMappingsModal = ({
   editMappings,
@@ -30,6 +32,8 @@ export const EditMappingsModal = ({
   const [termMappings, setTermMappings] = useState([]);
   const [options, setOptions] = useState([]);
   const { vocabUrl, setSelectedKey, user } = useContext(myContext);
+  const { setShowOptions, showOptions, idsForSelect } =
+    useContext(MappingContext);
   const {
     apiPreferencesCode,
     setApiPreferencesCode,
@@ -130,10 +134,18 @@ export const EditMappingsModal = ({
               <div>
                 <b>{item?.display}</b>
               </div>
-              <div>
-                {/* <a href={item.iri} target="_blank"> */}
-                {item?.code}
-                {/* </a> */}
+              <div>{item?.code}</div>
+              <div
+              // className="mapping_relationship"
+              // onClick={setShowOptions(item.mapping_relationship)}
+              >
+                <MappingRelationship mapping={item} />
+
+                {/* {item?.mapping_relationship && !showOptions
+                  ? displayRelationship(item)
+                  : (!item.mapping_relationship || !!showOptions) && (
+                      <MappingRelationship mapping={item} />
+                    )} */}
               </div>
             </div>
             <div>
@@ -164,7 +176,16 @@ export const EditMappingsModal = ({
   const updateMappings = values => {
     setLoading(true);
     const mappingsDTO = {
-      mappings: values?.mappings?.map(v => JSON.parse(v)) ?? [],
+      mappings:
+        values?.mappings?.map(v => {
+          const parsedMapping = JSON.parse(v);
+          if (idsForSelect[parsedMapping.code]) {
+            parsedMapping.mapping_relationship =
+              idsForSelect[parsedMapping.code];
+          }
+
+          return parsedMapping;
+        }) ?? [],
       editor: user.email,
     };
     fetch(

From 8208045f30969ba4a5084c5f4c40744792a9346f Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 27 Nov 2024 11:26:33 -0600
Subject: [PATCH 152/180] Mapping relationship change to dropdown menu on click

---
 .../MappingsFunctions/MappingRelationship.jsx |  1 +
 .../Projects/Tables/EditMappingsLabel.jsx     | 69 +++++++++++++++++
 .../Tables/EditMappingsTableModal.jsx         | 77 +++----------------
 .../Projects/Tables/TableStyling.scss         |  2 +-
 .../Terminologies/EditMappingModal.jsx        | 57 ++------------
 5 files changed, 87 insertions(+), 119 deletions(-)
 create mode 100644 src/components/Projects/Tables/EditMappingsLabel.jsx

diff --git a/src/components/Manager/MappingsFunctions/MappingRelationship.jsx b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
index c1c8846..451a57b 100644
--- a/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
@@ -34,6 +34,7 @@ export const MappingRelationship = ({ mapping }) => {
       onChange={value =>
         handleSelectChange(mapping.obo_id || mapping.code, value)
       }
+      onClick={e => e.preventDefault()}
     />
   );
 };
diff --git a/src/components/Projects/Tables/EditMappingsLabel.jsx b/src/components/Projects/Tables/EditMappingsLabel.jsx
new file mode 100644
index 0000000..5aceb91
--- /dev/null
+++ b/src/components/Projects/Tables/EditMappingsLabel.jsx
@@ -0,0 +1,69 @@
+import { useContext } from 'react';
+import { MappingContext } from '../../../Contexts/MappingContext';
+import { ellipsisString } from '../../Manager/Utilitiy';
+import { MappingRelationship } from '../../Manager/MappingsFunctions/MappingRelationship';
+import { Tooltip } from 'antd';
+
+export const EditMappingsLabel = ({ item, index }) => {
+  const { showOptions, setShowOptions, relationshipOptions } =
+    useContext(MappingContext);
+
+  // Find the object in relationshipOptions where the code matches the mappings's mapping_relationship
+  // If there is a match, return the display. If not, return null.
+  const displayRelationship = item => {
+    const findDisplay = relationshipOptions.find(
+      ro => ro.code === item.mapping_relationship
+    );
+
+    return findDisplay ? findDisplay.display : null;
+  };
+
+  return (
+    <>
+      <div key={index} className="modal_search_result">
+        <div>
+          <div className="modal_term_ontology">
+            <div>
+              <b>{item?.display}</b>
+            </div>
+            <div>{item?.code}</div>
+            <div
+              className={
+                !showOptions && item.mapping_relationship
+                  ? 'mapping_relationship'
+                  : ''
+              }
+              onClick={e => {
+                e.preventDefault();
+                setShowOptions(item.mapping_relationship);
+              }}
+            >
+              {item?.mapping_relationship && !showOptions ? (
+                displayRelationship(item)
+              ) : item.mapping_relationship && !!showOptions ? (
+                <MappingRelationship mapping={item} />
+              ) : (
+                !item.mapping_relationship && (
+                  <MappingRelationship mapping={item} />
+                )
+              )}
+            </div>
+          </div>
+          <div>
+            {item?.description?.length > 100 ? (
+              <Tooltip
+                mouseEnterDelay={0.5}
+                title={item?.description}
+                placement="topRight"
+              >
+                {ellipsisString(item?.description, '100')}
+              </Tooltip>
+            ) : (
+              ellipsisString(item?.description, '100')
+            )}
+          </div>
+        </div>
+      </div>
+    </>
+  );
+};
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index 393924b..f94800f 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -1,12 +1,4 @@
-import {
-  Button,
-  Checkbox,
-  Form,
-  message,
-  Modal,
-  notification,
-  Tooltip,
-} from 'antd';
+import { Button, Checkbox, Form, message, Modal, notification } from 'antd';
 import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
 import { ModalSpinner } from '../../Manager/Spinner';
@@ -14,11 +6,11 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { MappingSearch } from '../../Manager/MappingsFunctions/MappingSearch';
 import { MappingReset } from '../../Manager/MappingsFunctions/MappingReset';
 import { ResetTableMappings } from './ResetTableMappings';
-import { ellipsisString, systemsMatch } from '../../Manager/Utilitiy';
+import { systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyFilterCodeSubmit } from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmit';
-import { MappingRelationship } from '../../Manager/MappingsFunctions/MappingRelationship';
+import { EditMappingsLabel } from './EditMappingsLabel';
 
 export const EditMappingsTableModal = ({
   editMappings,
@@ -38,9 +30,7 @@ export const EditMappingsTableModal = ({
   const {
     setSelectedMappings,
     setDisplaySelectedMappings,
-    relationshipOptions,
     setShowOptions,
-    showOptions,
     idsForSelect,
   } = useContext(MappingContext);
   const {
@@ -63,6 +53,7 @@ export const EditMappingsTableModal = ({
     setEditSearch(false);
     setSelectedKey(null);
     setApiPreferencesCode(undefined);
+    setShowOptions(false);
   };
 
   const fetchMappings = () => {
@@ -112,7 +103,11 @@ export const EditMappingsTableModal = ({
             mappings.push(val); // For each mapping in the mappings array, push the stringified object above to the mappings array.
             // For each mapping in the mappings array, push the stringified object above to the options array
             // as the value for the value field for the ant.design checkbox. The label for the checkbox is returned in edditMappingsLabel function.
-            options.push({ value: val, label: editMappingsLabel(m, index) });
+            options.push({
+              value: val,
+              label: <EditMappingsLabel item={m} index={index} />,
+              // label: editMappingsLabel(m, index),
+            });
           });
           // termMappings are set to the mappings array. Options are set to the options array.
           setTermMappings(mappings);
@@ -131,60 +126,6 @@ export const EditMappingsTableModal = ({
     }
   };
 
-  // Find the object in relationshipOptions where the code matches the mappings's mapping_relationship
-  // If there is a match, return the display. If not, return null.
-  const displayRelationship = item => {
-    const findDisplay = relationshipOptions.find(
-      ro => ro.code === item.mapping_relationship
-    );
-
-    return findDisplay ? findDisplay.display : null;
-  };
-
-  // The label for the checkbox for each mapping. Displays JSX to show the display and code.
-  // The description field is commented out to be integrated when there is API support.
-  const editMappingsLabel = (item, index) => {
-    return (
-      <>
-        <div key={index} className="modal_search_result">
-          <div>
-            <div className="modal_term_ontology">
-              <div>
-                <b>{item?.display}</b>
-              </div>
-              <div>{item?.code}</div>
-              <div
-              // className="mapping_relationship"
-              // onClick={setShowOptions(item.mapping_relationship)}
-              >
-                <MappingRelationship mapping={item} />
-
-                {/* {item?.mapping_relationship && !showOptions
-                  ? displayRelationship(item)
-                  : (!item.mapping_relationship || !!showOptions) && (
-                      <MappingRelationship mapping={item} />
-                    )} */}
-              </div>
-            </div>
-            <div>
-              {item?.description?.length > 100 ? (
-                <Tooltip
-                  mouseEnterDelay={0.5}
-                  title={item?.description}
-                  placement="topRight"
-                >
-                  {ellipsisString(item?.description, '100')}
-                </Tooltip>
-              ) : (
-                ellipsisString(item?.description, '100')
-              )}
-            </div>
-          </div>
-        </div>
-      </>
-    );
-  };
-
   // Function to send a PUT call to update the mappings.
   // Each mapping in the mappings array being edited is JSON.parsed and turned into objects in the mappings array.
   const updateMappings = values => {
diff --git a/src/components/Projects/Tables/TableStyling.scss b/src/components/Projects/Tables/TableStyling.scss
index 729bf44..10cf06e 100644
--- a/src/components/Projects/Tables/TableStyling.scss
+++ b/src/components/Projects/Tables/TableStyling.scss
@@ -98,7 +98,7 @@ input::file-selector-button:hover {
   border: 1px solid $greyColor;
   border-radius: 4px;
   &:hover {
-    background-color: rgb(239, 235, 235);
+    background-color: rgb(245, 245, 245);
     transition: all 0.3s linear;
   }
 }
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 149c142..9cf4663 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -19,6 +19,7 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyFilterCodeSubmitTerm } from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm';
 import { MappingRelationship } from '../../Manager/MappingsFunctions/MappingRelationship';
 import { MappingContext } from '../../../Contexts/MappingContext';
+import { EditMappingsLabel } from '../Tables/EditMappingsLabel';
 
 export const EditMappingsModal = ({
   editMappings,
@@ -32,7 +33,7 @@ export const EditMappingsModal = ({
   const [termMappings, setTermMappings] = useState([]);
   const [options, setOptions] = useState([]);
   const { vocabUrl, setSelectedKey, user } = useContext(myContext);
-  const { setShowOptions, showOptions, idsForSelect } =
+  const { setShowOptions, showOptions, relationshipOptions, idsForSelect } =
     useContext(MappingContext);
   const {
     apiPreferencesCode,
@@ -55,6 +56,7 @@ export const EditMappingsModal = ({
     setOptions([]);
     setSelectedKey(null);
     setApiPreferencesCode(undefined);
+    setShowOptions(false);
   };
 
   const fetchMappings = () => {
@@ -104,7 +106,10 @@ export const EditMappingsModal = ({
             mappings.push(val); // For each mapping in the mappings array, push the stringified object above to the mappings array.
             // For each mapping in the mappings array, push the stringified object above to the options array
             // as the value for the value field for the ant.design checkbox. The label for the checkbox is returned in edditMappingsLabel function.
-            options.push({ value: val, label: editMappingsLabel(m, index) });
+            options.push({
+              value: val,
+              label: <EditMappingsLabel item={m} index={index} />,
+            });
           });
           // termMappings are set to the mappings array. Options are set to the options array.
           setTermMappings(mappings);
@@ -123,54 +128,6 @@ export const EditMappingsModal = ({
     }
   };
 
-  // The label for the checkbox for each mapping. Displays JSX to show the display and code.
-  // The description field is commented out to be integrated when there is API support.
-  const editMappingsLabel = (item, index) => {
-    return (
-      <>
-        <div key={index} className="modal_search_result">
-          <div>
-            <div className="modal_term_ontology">
-              <div>
-                <b>{item?.display}</b>
-              </div>
-              <div>{item?.code}</div>
-              <div
-              // className="mapping_relationship"
-              // onClick={setShowOptions(item.mapping_relationship)}
-              >
-                <MappingRelationship mapping={item} />
-
-                {/* {item?.mapping_relationship && !showOptions
-                  ? displayRelationship(item)
-                  : (!item.mapping_relationship || !!showOptions) && (
-                      <MappingRelationship mapping={item} />
-                    )} */}
-              </div>
-            </div>
-            <div>
-              {item?.description?.length > 100 ? (
-                <Tooltip
-                  title={item?.description}
-                  placement="topRight"
-                  mouseEnterDelay={0.5}
-                >
-                  {ellipsisString(item?.description, '100')}
-                </Tooltip>
-              ) : (
-                ellipsisString(item?.description, '100')
-              )}
-            </div>
-          </div>
-        </div>
-      </>
-    );
-  };
-
-  const searchProp = editMappings?.display
-    ? editMappings.display
-    : editMappings?.code;
-
   // Function to send a PUT call to update the mappings.
   // Each mapping in the mappings array being edited is JSON.parsed and mappings are turned into objects in the mappings array.
   const updateMappings = values => {

From 7e9081ad446b8067b6e64377c5f2d7613409ecbb Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 27 Nov 2024 11:54:38 -0600
Subject: [PATCH 153/180] Mapping relationship added to MappingSearch &
 MappingReset

---
 .../Manager/MappingsFunctions/MappingReset.jsx     |  4 ++++
 .../Manager/MappingsFunctions/MappingSearch.jsx    |  7 +++++++
 .../Projects/Terminologies/EditMappingModal.jsx    | 14 +++++++++++---
 3 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
index bc13608..f93ab9f 100644
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingReset.jsx
@@ -7,6 +7,7 @@ import { MappingContext } from '../../../Contexts/MappingContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
+import { MappingRelationship } from './MappingRelationship';
 
 export const MappingReset = ({
   searchProp,
@@ -344,6 +345,9 @@ export const MappingReset = ({
                   </a>
                 )}
               </div>
+              <div>
+                <MappingRelationship mapping={d} />
+              </div>
             </div>
             <div>
               {d?.description?.length > 85 ? (
diff --git a/src/components/Manager/MappingsFunctions/MappingSearch.jsx b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
index 358f04b..b21d66f 100644
--- a/src/components/Manager/MappingsFunctions/MappingSearch.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingSearch.jsx
@@ -8,6 +8,7 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
 import { OntologyCheckboxes } from './OntologyCheckboxes';
 import { APISearchBar } from '../../Projects/Terminologies/APISearchBar';
+import { MappingRelationship } from './MappingRelationship';
 
 export const MappingSearch = ({
   setEditMappings,
@@ -343,6 +344,9 @@ export const MappingSearch = ({
                   </a>
                 )}
               </div>
+              <div>
+                <MappingRelationship mapping={d} />
+              </div>
             </div>
             <div>
               {d?.description?.length > 85 ? (
@@ -388,6 +392,9 @@ export const MappingSearch = ({
                 <b>{d.display}</b>
               </div>
               <div>{d.code}</div>
+              <div>
+                <MappingRelationship mapping={d} />
+              </div>
             </div>
             <div>
               {d?.description?.length > 100 ? (
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 9cf4663..0fc6d54 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -33,8 +33,7 @@ export const EditMappingsModal = ({
   const [termMappings, setTermMappings] = useState([]);
   const [options, setOptions] = useState([]);
   const { vocabUrl, setSelectedKey, user } = useContext(myContext);
-  const { setShowOptions, showOptions, relationshipOptions, idsForSelect } =
-    useContext(MappingContext);
+  const { setShowOptions, idsForSelect } = useContext(MappingContext);
   const {
     apiPreferencesCode,
     setApiPreferencesCode,
@@ -191,10 +190,19 @@ export const EditMappingsModal = ({
       description: item.description,
       system:
         item.system || systemsMatch(item.obo_id.split(':')[0], ontologyApis),
+      mapping_relationship: idsForSelect[item.code],
     }));
     const mappingsDTO = {
       mappings: [
-        ...(values.existing_mappings?.map(v => JSON.parse(v)) ?? []),
+        ...(values.existing_mappings?.map(v => {
+          const parsedMapping = JSON.parse(v);
+          if (idsForSelect[parsedMapping.code]) {
+            parsedMapping.mapping_relationship =
+              idsForSelect[parsedMapping.code];
+          }
+
+          return parsedMapping;
+        }) ?? []),
         ...(selectedMappings ?? []),
       ],
       editor: user.email,

From 4a05f339f99fdce199e49a6ec691ccea366aa304 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Wed, 27 Nov 2024 12:06:30 -0600
Subject: [PATCH 154/180] [FD-1830] Edit dispatch deploy for prod

---
 .github/workflows/dispatch_deploy.yml | 12 ++++++++----
 package.json                          |  1 +
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index f400a48..daeb8c5 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -65,14 +65,18 @@ jobs:
         run: |-
           gcloud auth configure-docker '${{ env.REGION }}-docker.pkg.dev'
 
-      - name: 'Build Docker Image' # New step to build the image
+      - name: 'Build Docker Image'
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          if [ "${{ github.event.inputs.environment }}" == "prod" ]; then
+            DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          else
+            DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          fi
+          echo "DOCKER_TAG=${DOCKER_TAG}" >> $GITHUB_ENV 
           docker build -t "${DOCKER_TAG}" --build-arg ENV=${{ github.event.inputs.environment }} .
 
       - name: 'Push Docker Image'
         run: |-
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           docker push "${DOCKER_TAG}"
 
       - name: 'Deploy to Cloud Run'
@@ -80,4 +84,4 @@ jobs:
         with:
           service: '${{ env.SERVICE }}-${{ github.event.inputs.environment }}'
           region: '${{ env.REGION }}'
-          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          image: "${DOCKER_TAG}"
\ No newline at end of file
diff --git a/package.json b/package.json
index 34885eb..ae8a038 100644
--- a/package.json
+++ b/package.json
@@ -9,6 +9,7 @@
     "build-dev": "vite build --mode dev",
     "build-uat": "vite build --mode uat",
     "build-alpha": "vite build --mode alpha",
+    "build-prod": "vite build --mode prod",
     "lint": "eslint . --ext js,jsx --report-unused-disable-directives --max-warnings 0",
     "preview": "vite preview"
   },

From 85256f7a0e7d8d4a0e21c239df32c20da7e3e35e Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 27 Nov 2024 12:42:16 -0600
Subject: [PATCH 155/180] Added conditional to display code if there is no
 mapping display

---
 .../MappingsFunctions}/EditMappingsLabel.jsx               | 7 +++----
 src/components/Projects/Tables/EditMappingsTableModal.jsx  | 2 +-
 src/components/Projects/Tables/TableDetails.jsx            | 5 +++--
 src/components/Projects/Terminologies/EditMappingModal.jsx | 2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)
 rename src/components/{Projects/Tables => Manager/MappingsFunctions}/EditMappingsLabel.jsx (90%)

diff --git a/src/components/Projects/Tables/EditMappingsLabel.jsx b/src/components/Manager/MappingsFunctions/EditMappingsLabel.jsx
similarity index 90%
rename from src/components/Projects/Tables/EditMappingsLabel.jsx
rename to src/components/Manager/MappingsFunctions/EditMappingsLabel.jsx
index 5aceb91..a379fd8 100644
--- a/src/components/Projects/Tables/EditMappingsLabel.jsx
+++ b/src/components/Manager/MappingsFunctions/EditMappingsLabel.jsx
@@ -1,13 +1,12 @@
 import { useContext } from 'react';
 import { MappingContext } from '../../../Contexts/MappingContext';
-import { ellipsisString } from '../../Manager/Utilitiy';
-import { MappingRelationship } from '../../Manager/MappingsFunctions/MappingRelationship';
+import { ellipsisString } from '../Utilitiy';
+import { MappingRelationship } from './MappingRelationship';
 import { Tooltip } from 'antd';
 
 export const EditMappingsLabel = ({ item, index }) => {
-  const { showOptions, setShowOptions, relationshipOptions } =
+  const { showOptions, setShowOptions, relationshipOptions, idsForSelect } =
     useContext(MappingContext);
-
   // Find the object in relationshipOptions where the code matches the mappings's mapping_relationship
   // If there is a match, return the display. If not, return null.
   const displayRelationship = item => {
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index f94800f..ad92213 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -10,7 +10,7 @@ import { systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyFilterCodeSubmit } from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmit';
-import { EditMappingsLabel } from './EditMappingsLabel';
+import { EditMappingsLabel } from '../../Manager/MappingsFunctions/EditMappingsLabel';
 
 export const EditMappingsTableModal = ({
   editMappings,
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index a361c85..2b7412a 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -261,8 +261,9 @@ It then shows the mappings as table data and alows the user to delete a mapping
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.display}>
           <span className="mapping-display">
-            {' '}
-            <Tooltip title={code.code}>{code.display}</Tooltip>
+            <Tooltip title={code.code}>
+              {code.display ? code.display : code.code}
+            </Tooltip>
           </span>
           <span
             className="remove-mapping"
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 0fc6d54..6f7a3fb 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -19,7 +19,7 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyFilterCodeSubmitTerm } from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm';
 import { MappingRelationship } from '../../Manager/MappingsFunctions/MappingRelationship';
 import { MappingContext } from '../../../Contexts/MappingContext';
-import { EditMappingsLabel } from '../Tables/EditMappingsLabel';
+import { EditMappingsLabel } from '../../Manager/MappingsFunctions/EditMappingsLabel';
 
 export const EditMappingsModal = ({
   editMappings,

From 5719dc7f798e5710d0ec7f0e7ed12aec2e0bab64 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Wed, 27 Nov 2024 12:58:24 -0600
Subject: [PATCH 156/180] [FD-1830] Edits for prod

---
 .github/workflows/dispatch_deploy.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index daeb8c5..4ea7914 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -67,11 +67,15 @@ jobs:
 
       - name: 'Build Docker Image'
         run: |-
-          if [ "${{ github.event.inputs.environment }}" == "prod" ]; then
+          set -eux  # Enable debugging and exit on error
+          
+          ENVIRONMENT="${{ github.event.inputs.environment }}"
+          if [[ "$ENVIRONMENT" == "prod" ]]; then
             DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           else
-            DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${{ github.event.inputs.environment }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+            DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${ENVIRONMENT}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           fi
+          echo "Environment: $ENVIRONMENT"
           echo "DOCKER_TAG=${DOCKER_TAG}" >> $GITHUB_ENV 
           docker build -t "${DOCKER_TAG}" --build-arg ENV=${{ github.event.inputs.environment }} .
 

From acf06373aa27cf1ef11af11013b68467fc3c4f24 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Wed, 27 Nov 2024 13:01:44 -0600
Subject: [PATCH 157/180] added mapping relationship when updating Table
 mappings

---
 .../Projects/Tables/EditMappingsTableModal.jsx        | 11 ++++++++++-
 .../Projects/Terminologies/EditMappingModal.jsx       |  2 +-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index ad92213..9d2d935 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -188,10 +188,19 @@ export const EditMappingsTableModal = ({
       description: item.description,
       system:
         item.system || systemsMatch(item.obo_id.split(':')[0], ontologyApis),
+      mapping_relationship: idsForSelect[item.code],
     }));
     const mappingsDTO = {
       mappings: [
-        ...(values.existing_mappings?.map(v => JSON.parse(v)) ?? []),
+        ...(values.existing_mappings?.map(v => {
+          const parsedMapping = JSON.parse(v);
+          if (idsForSelect[parsedMapping.code]) {
+            parsedMapping.mapping_relationship =
+              idsForSelect[parsedMapping.code];
+          }
+
+          return parsedMapping;
+        }) ?? []),
         ...(selectedMappings ?? []),
       ],
       editor: user.email,
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index 6f7a3fb..b543b9e 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -13,7 +13,7 @@ import { ModalSpinner } from '../../Manager/Spinner';
 import { MappingSearch } from '../../Manager/MappingsFunctions/MappingSearch';
 import { ResetMappings } from './ResetMappings';
 import { MappingReset } from '../../Manager/MappingsFunctions/MappingReset';
-import { ellipsisString, systemsMatch } from '../../Manager/Utilitiy';
+import { systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
 import { OntologyFilterCodeSubmitTerm } from '../../Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm';

From d62ddb0d16596e497b4be12e8547a42fded6f207 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Wed, 27 Nov 2024 16:48:06 -0600
Subject: [PATCH 158/180] [FD-1830] Edits for prod

---
 .github/workflows/dispatch_deploy.yml | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index 4ea7914..a7e6cce 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -67,16 +67,14 @@ jobs:
 
       - name: 'Build Docker Image'
         run: |-
-          set -eux  # Enable debugging and exit on error
-          
-          ENVIRONMENT="${{ github.event.inputs.environment }}"
-          if [[ "$ENVIRONMENT" == "prod" ]]; then
-            DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
-          else
-            DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-${ENVIRONMENT}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          if [[ "${{ github.event.inputs.environment }}" == "prod" ]]; then
+            SERVICE='${{ env.SERVICE }}
+          else 
+            SERVICE='${{ env.SERVICE }}-${{ github.event.inputs.environment }}'
           fi
-          echo "Environment: $ENVIRONMENT"
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/SERVICE/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           echo "DOCKER_TAG=${DOCKER_TAG}" >> $GITHUB_ENV 
+          echo "SERVICE=${SERVICE}" >> $GITHUB_ENV 
           docker build -t "${DOCKER_TAG}" --build-arg ENV=${{ github.event.inputs.environment }} .
 
       - name: 'Push Docker Image'
@@ -86,6 +84,6 @@ jobs:
       - name: 'Deploy to Cloud Run'
         uses: 'google-github-actions/deploy-cloudrun@v2'
         with:
-          service: '${{ env.SERVICE }}-${{ github.event.inputs.environment }}'
+          service: "${SERVICE}"
           region: '${{ env.REGION }}'
           image: "${DOCKER_TAG}"
\ No newline at end of file

From 23f6611c30bca58bfa05a6ad1e7a2271b83a3d9f Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Wed, 27 Nov 2024 16:53:07 -0600
Subject: [PATCH 159/180] [FD-1830] Edits for prod

---
 .github/workflows/dispatch_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index a7e6cce..5142af1 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -68,7 +68,7 @@ jobs:
       - name: 'Build Docker Image'
         run: |-
           if [[ "${{ github.event.inputs.environment }}" == "prod" ]]; then
-            SERVICE='${{ env.SERVICE }}
+            SERVICE='${{ env.SERVICE }}'
           else 
             SERVICE='${{ env.SERVICE }}-${{ github.event.inputs.environment }}'
           fi

From e822ab73c5791728e864b79fc6b67fe41ab7669e Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Wed, 27 Nov 2024 16:55:22 -0600
Subject: [PATCH 160/180] [FD-1830] Edits for prod

---
 .github/workflows/dispatch_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index 5142af1..338c073 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -72,7 +72,7 @@ jobs:
           else 
             SERVICE='${{ env.SERVICE }}-${{ github.event.inputs.environment }}'
           fi
-          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/SERVICE/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${SERVICE}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
           echo "DOCKER_TAG=${DOCKER_TAG}" >> $GITHUB_ENV 
           echo "SERVICE=${SERVICE}" >> $GITHUB_ENV 
           docker build -t "${DOCKER_TAG}" --build-arg ENV=${{ github.event.inputs.environment }} .

From 57fdee48c5e61e7769c762d12970e80b840538f9 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Wed, 27 Nov 2024 16:58:32 -0600
Subject: [PATCH 161/180] [FD-1830] Edits for prod

---
 .github/workflows/dispatch_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index 338c073..d27a029 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -84,6 +84,6 @@ jobs:
       - name: 'Deploy to Cloud Run'
         uses: 'google-github-actions/deploy-cloudrun@v2'
         with:
-          service: "${SERVICE}"
+          service: ${SERVICE}
           region: '${{ env.REGION }}'
           image: "${DOCKER_TAG}"
\ No newline at end of file

From 3fe02224f2e23c630b0d5705a356fedd45563e84 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Wed, 27 Nov 2024 17:09:30 -0600
Subject: [PATCH 162/180] [FD-1830] Edits for prod

---
 .github/workflows/dispatch_deploy.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index d27a029..22797e4 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -68,13 +68,15 @@ jobs:
       - name: 'Build Docker Image'
         run: |-
           if [[ "${{ github.event.inputs.environment }}" == "prod" ]]; then
-            SERVICE='${{ env.SERVICE }}'
+            SERVICE="${{ env.SERVICE }}"
           else 
-            SERVICE='${{ env.SERVICE }}-${{ github.event.inputs.environment }}'
+            SERVICE="${{ env.SERVICE }}-${{ github.event.inputs.environment }}"
           fi
           DOCKER_TAG="${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${SERVICE}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+
           echo "DOCKER_TAG=${DOCKER_TAG}" >> $GITHUB_ENV 
           echo "SERVICE=${SERVICE}" >> $GITHUB_ENV 
+
           docker build -t "${DOCKER_TAG}" --build-arg ENV=${{ github.event.inputs.environment }} .
 
       - name: 'Push Docker Image'
@@ -84,6 +86,6 @@ jobs:
       - name: 'Deploy to Cloud Run'
         uses: 'google-github-actions/deploy-cloudrun@v2'
         with:
-          service: ${SERVICE}
+          service: ${{ env.SERVICE }}
           region: '${{ env.REGION }}'
           image: "${DOCKER_TAG}"
\ No newline at end of file

From e873fd2d16faf320de64dda0b55c2850a9018767 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Wed, 27 Nov 2024 17:16:00 -0600
Subject: [PATCH 163/180] [FD-1830] Edits for prod

---
 .github/workflows/dispatch_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index 22797e4..96f2b65 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -88,4 +88,4 @@ jobs:
         with:
           service: ${{ env.SERVICE }}
           region: '${{ env.REGION }}'
-          image: "${DOCKER_TAG}"
\ No newline at end of file
+          image: ${{ env.DOCKER_TAG }}
\ No newline at end of file

From b40855c77c30cd5a69a3e1c59bee1249263bab59 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Tue, 3 Dec 2024 21:42:44 -0600
Subject: [PATCH 164/180] Posting mapping votes and comments

---
 src/Contexts/MappingContext.jsx               |  9 ++
 .../MappingsFunctions/MappingComments.jsx     | 94 +++++++++++++++++--
 .../MappingsFunctions/MappingVotes.jsx        |  4 +-
 .../MappingsFunctions/MappingsFunctions.scss  | 24 +++++
 .../Projects/Tables/TableDetails.jsx          | 10 +-
 .../Projects/Terminologies/Terminology.jsx    | 16 ++--
 6 files changed, 130 insertions(+), 27 deletions(-)

diff --git a/src/Contexts/MappingContext.jsx b/src/Contexts/MappingContext.jsx
index 6a35c0f..b9bca8b 100644
--- a/src/Contexts/MappingContext.jsx
+++ b/src/Contexts/MappingContext.jsx
@@ -16,6 +16,9 @@ export function MappingContextRoot() {
   const [relationshipOptions, setRelationshipOptions] = useState([]);
   const [idsForSelect, setIdsForSelect] = useState([]);
   const [showOptions, setShowOptions] = useState(false);
+  const [voteCount, setVoteCount] = useState(0);
+  const [mappingComments, setMappingComments] = useState([]);
+  const [comment, setComment] = useState(false);
 
   const context = {
     editMappings,
@@ -42,6 +45,12 @@ export function MappingContextRoot() {
     setIdsForSelect,
     showOptions,
     setShowOptions,
+    voteCount,
+    setVoteCount,
+    mappingComments,
+    setMappingComments,
+    comment,
+    setComment,
   };
 
   return (
diff --git a/src/components/Manager/MappingsFunctions/MappingComments.jsx b/src/components/Manager/MappingsFunctions/MappingComments.jsx
index fa58ed9..b0a8fc3 100644
--- a/src/components/Manager/MappingsFunctions/MappingComments.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingComments.jsx
@@ -1,20 +1,62 @@
 import { Button, Form, Input, Modal, notification } from 'antd';
-import { useContext } from 'react';
+import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
+import { MappingContext } from '../../../Contexts/MappingContext';
+import { ModalSpinner } from '../Spinner';
 
 export const MappingComments = ({
-  code,
-  codeDisplay,
+  mappingCode,
+  mappingDisplay,
   variableMappings,
   setComment,
-  terminologyId,
+  idProp,
 }) => {
   const [form] = Form.useForm();
   const { vocabUrl, user } = useContext(myContext);
+  const { mappingComments, setMappingComments } = useContext(MappingContext);
+  const [loading, setLoading] = useState(false);
   const { TextArea } = Input;
 
   const onClose = () => {
     setComment(null);
+    setMappingComments([]);
+  };
+
+  useEffect(() => {
+    if (!!mappingCode) {
+      getComments();
+    }
+  }, [mappingCode]);
+
+  const getComments = () => {
+    setLoading(true);
+    return fetch(
+      `${vocabUrl}/Terminology/${idProp}/user_input/${variableMappings}/mapping/${mappingCode}/mapping_conversations`,
+      {
+        method: 'GET',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+      }
+    )
+      .then(res => {
+        if (res.ok) {
+          return res.json();
+        } else {
+          throw new Error('An unknown error occurred.');
+        }
+      })
+      .then(data => setMappingComments(data?.mapping_conversations))
+      .catch(error => {
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred saving the comment.',
+          });
+        }
+        return error;
+      })
+      .finally(() => setLoading(false));
   };
 
   const onFinish = values => {
@@ -24,7 +66,7 @@ export const MappingComments = ({
     };
 
     return fetch(
-      `${vocabUrl}/Terminology/${terminologyId}/user_input/${variableMappings}/${code}/mapping_conversations`,
+      `${vocabUrl}/Terminology/${idProp}/user_input/${variableMappings}/mapping/${mappingCode}/mapping_conversations`,
       {
         method: 'PUT',
         headers: {
@@ -40,6 +82,7 @@ export const MappingComments = ({
           throw new Error('An unknown error occurred.');
         }
       })
+      .then(data => setMappingComments(data?.mapping_conversations))
       .catch(error => {
         if (error) {
           notification.error({
@@ -51,15 +94,41 @@ export const MappingComments = ({
       });
   };
 
+  const formattedDate = dateString => {
+    const date = new Date(dateString);
+
+    return date.toLocaleString('en-US', {
+      month: 'short',
+      day: '2-digit',
+      year: 'numeric',
+      hour: '2-digit',
+      minute: '2-digit',
+      hour12: true,
+    });
+  };
+
+  const commentDisplay = (mc, i) => {
+    return (
+      <div key={i} className="comment_container">
+        <div className="comment_note">{mc.note}</div>
+        <div className="comment_date_user">
+          <div>{formattedDate(mc.date)}</div>
+          <div>{mc.user_id}</div>
+        </div>
+      </div>
+    );
+  };
+
   return (
     <>
       <Modal
-        open={!!code}
+        open={!!mappingCode}
         width={'70%'}
         styles={{
           body: {
             minHeight: '60vh',
             maxHeight: '60vh',
+            overflowY: 'auto',
           },
         }}
         footer={[<Button onClick={onClose}>Close</Button>]}
@@ -67,14 +136,15 @@ export const MappingComments = ({
         closeIcon={false}
         destroyOnClose={true}
       >
-        {variableMappings} : {codeDisplay}
+        <span className="comment_code_display">{variableMappings}: </span>
+        {mappingDisplay ? mappingDisplay : mappingCode}
         <Form
           form={form}
           layout="inline"
           onFinish={() => {
             form.validateFields().then(values => {
               onFinish(values);
-              onClose();
+              form.resetFields();
             });
           }}
           preserve={false}
@@ -84,11 +154,12 @@ export const MappingComments = ({
               rows={1}
               style={{
                 width: 500,
-                resize: 'both',
+                resize: 'vertical',
               }}
               showCount
               maxLength={1000}
               autoFocus
+              className="comment_textarea"
             />
           </Form.Item>
           <Form.Item>
@@ -97,6 +168,11 @@ export const MappingComments = ({
             </Button>
           </Form.Item>
         </Form>
+        {loading ? (
+          <ModalSpinner />
+        ) : (
+          mappingComments?.map((mc, i) => commentDisplay(mc, i))
+        )}
       </Modal>
     </>
   );
diff --git a/src/components/Manager/MappingsFunctions/MappingVotes.jsx b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
index e15d5ff..f8a5b53 100644
--- a/src/components/Manager/MappingsFunctions/MappingVotes.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
@@ -1,4 +1,4 @@
-export const MappingVotes = (
+export const mappingVotes = (
   variableMappings,
   code,
   user,
@@ -13,7 +13,7 @@ export const MappingVotes = (
   };
 
   return fetch(
-    `${vocabUrl}/Terminology/${terminologyId}/user_input/${variableMappings?.code}/${code?.code}/mapping_votes`,
+    `${vocabUrl}/Terminology/${terminologyId}/user_input/${variableMappings?.code}/mapping/${code?.code}/mapping_votes`,
     {
       method: 'PUT',
       headers: {
diff --git a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
index 488f557..ac09520 100644
--- a/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
+++ b/src/components/Manager/MappingsFunctions/MappingsFunctions.scss
@@ -154,3 +154,27 @@
 .existing_display {
   border-bottom: solid 1px #eeee;
 }
+
+.comment_code_display {
+  font-weight: 600;
+}
+
+.comment_textarea {
+  margin: 0 0 15px 0;
+}
+
+.comment_container {
+  margin: 10px 0 0 0;
+  border: 1px darkgray solid;
+  width: fit-content;
+  border-radius: 5px;
+  padding: 5px 8px;
+}
+
+.comment_date_user {
+  display: flex;
+  gap: 5px;
+  font-size: 0.7rem;
+  color: gray;
+  margin: 6px 0 0 0;
+}
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index 51d2c8e..fdaf8ec 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -15,11 +15,7 @@ import {
   Table,
   Tooltip,
 } from 'antd';
-import {
-  CloseCircleOutlined,
-  UpCircleOutlined,
-  DownCircleOutlined,
-} from '@ant-design/icons';
+import { CloseCircleOutlined } from '@ant-design/icons';
 import { EditTableDetails } from './EditTableDetails';
 import { DeleteTable } from './DeleteTable';
 import { LoadVariables } from './LoadVariables';
@@ -266,10 +262,6 @@ It then shows the mappings as table data and alows the user to delete a mapping
     if (variableMappings && variableMappings.mappings?.length) {
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.code}>
-          <span className="mapping_votes mapping_actions">
-            <UpCircleOutlined style={{ color: 'blue' }} />
-            <DownCircleOutlined style={{ color: 'green' }} />
-          </span>
           <span className="mapping-display">
             <Tooltip
               title={
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 6c942a7..534c47d 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -34,7 +34,7 @@ import { SearchContext } from '../../../Contexts/SearchContext';
 import { FilterSelect } from '../../Manager/MappingsFunctions/FilterSelect';
 import { AssignMappingsViaButton } from './AssignMappingsViaButton';
 import { ellipsisString, mappingTooltip } from '../../Manager/Utilitiy';
-import { MappingVotes } from '../../Manager/MappingsFunctions/MappingVotes';
+import { mappingVotes } from '../../Manager/MappingsFunctions/MappingVotes';
 import { MappingComments } from '../../Manager/MappingsFunctions/MappingComments';
 
 export const Terminology = () => {
@@ -52,13 +52,14 @@ export const Terminology = () => {
     mapping,
     setMapping,
     setRelationshipOptions,
+    comment,
+    setComment,
   } = useContext(MappingContext);
 
   const [pageSize, setPageSize] = useState(
     parseInt(localStorage.getItem('pageSize'), 10) || 10
   );
   const [assignMappingsViaButton, setAssignMappingsViaButton] = useState(false);
-  const [comment, setComment] = useState(false);
   const handleTableChange = (current, size) => {
     setPageSize(size);
   };
@@ -179,7 +180,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
             <UpOutlined
               style={{ color: 'blue' }}
               onClick={() =>
-                MappingVotes(
+                mappingVotes(
                   variableMappings,
                   code,
                   user,
@@ -194,7 +195,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
             <DownOutlined
               style={{ color: 'green' }}
               onClick={() =>
-                MappingVotes(
+                mappingVotes(
                   variableMappings,
                   code,
                   user,
@@ -515,12 +516,13 @@ It then shows the mappings as table data and alows the user to delete a mapping
             setAssignMappingsViaButton={setAssignMappingsViaButton}
             terminology={terminology}
           />
+
           <MappingComments
-            code={comment?.code}
-            codeDisplay={comment?.display}
+            mappingCode={comment?.code}
+            mappingDisplay={comment?.display}
             variableMappings={comment?.variableMappings}
             setComment={setComment}
-            terminologyId={terminologyId}
+            idProp={terminologyId}
           />
         </div>
       )}

From fd90c010da6f12d4548ccbc4654e2fff2f1ad229 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 5 Dec 2024 09:34:12 -0600
Subject: [PATCH 165/180] Combined MappingReset and MappingSearch, changed CSS
 for mapping votes

---
 .../MappingsFunctions/GetMappingsModal.jsx    |  4 +-
 .../MappingsFunctions/MappingRelationship.jsx |  2 +-
 .../MappingsFunctions/MappingVotes.jsx        | 24 ++++++++-
 .../OntologyFilterCodeSubmitTerm.jsx          | 26 ----------
 .../Tables/EditMappingsTableModal.jsx         | 40 ++++-----------
 .../Projects/Tables/TableStyling.scss         | 40 ---------------
 .../Terminologies/EditMappingModal.jsx        | 36 ++++---------
 .../Projects/Terminologies/Terminology.jsx    | 50 +++++++++++++++---
 .../Projects/Terminologies/Terminology.scss   | 51 +++++++++++++++++++
 9 files changed, 140 insertions(+), 133 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 911e0dc..2af90b4 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -170,7 +170,7 @@ export const GetMappingsModal = ({
 
     setLoading(true);
     fetch(
-      `${vocabUrl}/${componentString}/${component.id}/mapping/${mappingProp}`,
+      `${vocabUrl}/${componentString}/${component.id}/mapping/${mappingProp}?user_input=true`,
       {
         method: 'PUT',
         headers: {
@@ -340,7 +340,7 @@ export const GetMappingsModal = ({
                 <MappingRelationship mapping={d} />
               </div>
             </div>
-            <div>{ellipsisString(d?.description[0], '100')}</div>
+            <div>{ellipsisString(d?.description?.[0], '100')}</div>
           </div>
         </div>
       </>
diff --git a/src/components/Manager/MappingsFunctions/MappingRelationship.jsx b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
index 451a57b..1ccbcd1 100644
--- a/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingRelationship.jsx
@@ -27,7 +27,7 @@ export const MappingRelationship = ({ mapping }) => {
       style={{
         width: 120,
       }}
-      placeholder="Quality"
+      placeholder="Relationship"
       popupMatchSelectWidth={false}
       allowClear
       value={idsForSelect[mapping.obo_id || mapping.code]}
diff --git a/src/components/Manager/MappingsFunctions/MappingVotes.jsx b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
index f8a5b53..e2d34dc 100644
--- a/src/components/Manager/MappingsFunctions/MappingVotes.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
@@ -1,3 +1,5 @@
+import { getById } from '../FetchManager';
+
 export const mappingVotes = (
   variableMappings,
   code,
@@ -5,7 +7,8 @@ export const mappingVotes = (
   vote,
   vocabUrl,
   terminologyId,
-  notification
+  notification,
+  setMapping
 ) => {
   const mappingVoteDTO = {
     editor: user?.email,
@@ -37,5 +40,22 @@ export const mappingVotes = (
         });
       }
       return error;
-    });
+    })
+    .then(() =>
+      getById(
+        vocabUrl,
+        'Terminology',
+        `${terminologyId}/mapping?user_input=True`
+      )
+        .then(data => setMapping(data.codes))
+        .catch(error => {
+          if (error) {
+            notification.error({
+              message: 'Error',
+              description: 'An error occurred loading mappings.',
+            });
+          }
+          return error;
+        })
+    );
 };
diff --git a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx
index 89680c8..b294c51 100644
--- a/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx
+++ b/src/components/Manager/MappingsFunctions/OntologyFilterCodeSubmitTerm.jsx
@@ -45,29 +45,3 @@ export const OntologyFilterCodeSubmitTerm = (
       });
   }
 };
-
-//   apiPreference.api_preference.ols = apiPreferencesCode;
-
-//       fetch(`${vocabUrl}/Terminology/${terminology.id}/filter/${searchProp}`, {
-//         method: 'POST',
-//         headers: {
-//           'Content-Type': 'application/json',
-//         },
-//         body: JSON.stringify(apiPreference),
-//       })
-//         .then(res => {
-//           if (res.ok) {
-//             return res.json();
-//           } else {
-//             throw new Error('An unknown error occurred.');
-//           }
-//         })
-//         .catch(error => {
-//           if (error) {
-//             notification.error({
-//               message: 'Error',
-//               description: 'An error occurred saving the ontology preferences.',
-//             });
-//           }
-//           return error;
-//         });
diff --git a/src/components/Projects/Tables/EditMappingsTableModal.jsx b/src/components/Projects/Tables/EditMappingsTableModal.jsx
index 9d2d935..aac6938 100644
--- a/src/components/Projects/Tables/EditMappingsTableModal.jsx
+++ b/src/components/Projects/Tables/EditMappingsTableModal.jsx
@@ -4,7 +4,6 @@ import { myContext } from '../../../App';
 import { ModalSpinner } from '../../Manager/Spinner';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { MappingSearch } from '../../Manager/MappingsFunctions/MappingSearch';
-import { MappingReset } from '../../Manager/MappingsFunctions/MappingReset';
 import { ResetTableMappings } from './ResetTableMappings';
 import { systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
@@ -294,7 +293,12 @@ export const EditMappingsTableModal = ({
                   <ResetTableMappings
                     tableId={tableId}
                     editMappings={editMappings}
-                    setReset={setReset}
+                    setReset={resp => {
+                      setReset(resp);
+                      if (resp) {
+                        setMappingsForSearch([]);
+                      }
+                    }}
                   />
                   <Button onClick={() => setEditSearch(true)}>
                     Edit / Add
@@ -331,44 +335,20 @@ export const EditMappingsTableModal = ({
             </Form.Item>
           </Form>
         </>
-      ) : // If reset or editSearch is true the MappingSearch modal opens to perform the search for the table code
-      editSearch ? (
+      ) : (
+        // If reset or editSearch is true the MappingSearch modal opens to perform the search for the table code
+
         <MappingSearch
-          editMappings={editMappings}
           setEditMappings={setEditMappings}
           mappingsForSearch={mappingsForSearch}
           form={form}
-          reset={reset}
           onClose={form.resetFields}
           searchProp={editMappings?.name}
-          mappingDesc={
-            editMappings?.description
-              ? editMappings?.description
-              : 'No Description'
-          }
+          mappingDesc={editMappings?.description ?? 'No Description'}
           component={table}
           mappingProp={editMappings?.code}
           table={table}
         />
-      ) : (
-        reset && (
-          <MappingReset
-            searchProp={editMappings.name}
-            mappingDesc={
-              editMappings.description
-                ? editMappings.description
-                : 'No Description'
-            }
-            setEditMappings={setEditMappings}
-            mappingsForSearch={mappingsForSearch}
-            form={form}
-            reset={reset}
-            onClose={form.resetFields}
-            component={table}
-            mappingProp={editMappings.code}
-            table={table}
-          />
-        )
       )}
     </Modal>
   );
diff --git a/src/components/Projects/Tables/TableStyling.scss b/src/components/Projects/Tables/TableStyling.scss
index 945c2c5..609bd6b 100644
--- a/src/components/Projects/Tables/TableStyling.scss
+++ b/src/components/Projects/Tables/TableStyling.scss
@@ -75,43 +75,3 @@ input::file-selector-button:hover {
   gap: 10px;
   margin-left: 50px;
 }
-
-.mapping {
-  &-display {
-    white-space: nowrap;
-  }
-  display: flex;
-  align-items: center;
-  &:hover .mapping_actions {
-    transition: all 0.4s linear;
-    opacity: 1;
-  }
-  .mapping_actions {
-    padding-left: 0.25rem;
-    cursor: pointer;
-    opacity: 0;
-  }
-}
-
-.mapping_votes {
-  display: flex;
-  flex-direction: column;
-  align-items: center;
-  // gap: 2px;
-  padding-right: 0.25rem;
-  font-size: 0.7rem;
-}
-
-.no_mapping_button {
-  padding-left: 2rem;
-}
-
-.mapping_relationship {
-  padding: 2px 6px;
-  border: 1px solid $greyColor;
-  border-radius: 4px;
-  &:hover {
-    background-color: rgb(245, 245, 245);
-    transition: all 0.3s linear;
-  }
-}
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index b543b9e..b92d75f 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -12,7 +12,6 @@ import { myContext } from '../../../App';
 import { ModalSpinner } from '../../Manager/Spinner';
 import { MappingSearch } from '../../Manager/MappingsFunctions/MappingSearch';
 import { ResetMappings } from './ResetMappings';
-import { MappingReset } from '../../Manager/MappingsFunctions/MappingReset';
 import { systemsMatch } from '../../Manager/Utilitiy';
 import { getById } from '../../Manager/FetchManager';
 import { SearchContext } from '../../../Contexts/SearchContext';
@@ -145,7 +144,7 @@ export const EditMappingsModal = ({
       editor: user.email,
     };
     fetch(
-      `${vocabUrl}/Terminology/${terminologyId}/mapping/${editMappings.code}`,
+      `${vocabUrl}/Terminology/${terminologyId}/mapping/${editMappings.code}?user_input=true`,
       {
         method: 'PUT',
         headers: {
@@ -209,7 +208,7 @@ export const EditMappingsModal = ({
     };
 
     fetch(
-      `${vocabUrl}/Terminology/${terminologyId}/mapping/${editMappings.code}`,
+      `${vocabUrl}/Terminology/${terminologyId}/mapping/${editMappings.code}?user_input=true`,
       {
         method: 'PUT',
         headers: {
@@ -301,7 +300,12 @@ export const EditMappingsModal = ({
                   <ResetMappings
                     terminologyId={terminologyId}
                     editMappings={editMappings}
-                    setReset={setReset}
+                    setReset={resp => {
+                      setReset(resp);
+                      if (resp) {
+                        setMappingsForSearch([]);
+                      }
+                    }}
                   />
                   <Button onClick={() => setEditSearch(true)}>
                     Edit / Add
@@ -342,38 +346,20 @@ export const EditMappingsModal = ({
             </Form.Item>
           </Form>
         </>
-      ) : // If reset or editSearch is true the MappingSearch modal opens to perform the search for the terminology code
-      editSearch ? (
+      ) : (
+        // If reset or editSearch is true the MappingSearch modal opens to perform the search for the terminology code
         <MappingSearch
-          editMappings={editMappings}
           setEditMappings={setEditMappings}
           mappingsForSearch={mappingsForSearch}
           form={form}
-          reset={reset}
           onClose={form.resetFields}
           searchProp={
             editMappings?.display ? editMappings?.display : editMappings?.code
           }
           mappingProp={editMappings?.code}
-          mappingDesc={editMappings?.description}
+          mappingDesc={editMappings?.description ?? 'No description'}
           terminology={terminology}
         />
-      ) : (
-        reset && (
-          <MappingReset
-            searchProp={
-              editMappings?.display ? editMappings.display : editMappings?.code
-            }
-            setEditMappings={setEditMappings}
-            mappingsForSearch={mappingsForSearch}
-            form={form}
-            reset={reset}
-            onClose={form.resetFields}
-            mappingDesc={editMappings?.description}
-            mappingProp={editMappings?.code}
-            terminology={terminology}
-          />
-        )
       )}
     </Modal>
   );
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 534c47d..e4d887d 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -154,6 +154,12 @@ It then shows the mappings as table data and alows the user to delete a mapping
     </div>
   );
 
+  const votesCount = code => {
+    const calculatedCount =
+      code.user_input?.votes_count.up - code.user_input?.votes_count.down;
+    return calculatedCount;
+  };
+
   const matchCode = variable => {
     if (!mapping?.length) {
       return noMapping(variable);
@@ -162,11 +168,13 @@ It then shows the mappings as table data and alows the user to delete a mapping
     const variableMappings = mapping.find(
       item => item?.code === variable?.code
     );
+
     if (variableMappings && variableMappings.mappings?.length) {
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.code}>
-          <span className="mapping_actions">
+          <span>
             <MessageOutlined
+              className="mapping_actions"
               onClick={() =>
                 setComment({
                   code: code.code,
@@ -176,8 +184,9 @@ It then shows the mappings as table data and alows the user to delete a mapping
               }
             />
           </span>
-          <span className="mapping_votes mapping_actions">
+          <span className="mapping_votes">
             <UpOutlined
+              className="mapping_actions"
               style={{ color: 'blue' }}
               onClick={() =>
                 mappingVotes(
@@ -187,12 +196,30 @@ It then shows the mappings as table data and alows the user to delete a mapping
                   'up',
                   vocabUrl,
                   terminologyId,
-                  notification
+                  notification,
+                  setMapping
                 )
               }
             />
-            0
+            <Tooltip
+              title={`up: ${code.user_input?.votes_count.up},
+                down: ${code.user_input?.votes_count.down}`}
+              mouseEnterDelay={0.75}
+            >
+              <span
+                className={
+                  (code.user_input?.votes_count.down !== 0 ||
+                    code.user_input?.votes_count.up !== 0) &&
+                  votesCount(code) === 0
+                    ? 'red_votes_count'
+                    : 'votes_count'
+                }
+              >
+                {votesCount(code)}
+              </span>
+            </Tooltip>
             <DownOutlined
+              className="mapping_actions"
               style={{ color: 'green' }}
               onClick={() =>
                 mappingVotes(
@@ -202,7 +229,8 @@ It then shows the mappings as table data and alows the user to delete a mapping
                   'down',
                   vocabUrl,
                   terminologyId,
-                  notification
+                  notification,
+                  setMapping
                 )
               }
             />
@@ -214,6 +242,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
                   ? mappingTooltip(code)
                   : code.code
               }
+              mouseEnterDelay={0.75}
             >
               {ellipsisString(code.display ? code.display : code.code, '25')}
             </Tooltip>
@@ -222,7 +251,10 @@ It then shows the mappings as table data and alows the user to delete a mapping
             className="mapping_actions"
             onClick={() => handleRemoveMapping(variableMappings, code)}
           >
-            <CloseCircleOutlined style={{ color: 'red' }} />
+            <CloseCircleOutlined
+              className="mapping_actions"
+              style={{ color: 'red' }}
+            />
           </span>
         </div>
       ));
@@ -290,7 +322,11 @@ It then shows the mappings as table data and alows the user to delete a mapping
               .then(data => {
                 setApiPreferencesTerm(data);
               });
-            getById(vocabUrl, 'Terminology', `${terminologyId}/mapping`)
+            getById(
+              vocabUrl,
+              'Terminology',
+              `${terminologyId}/mapping?user_input=True`
+            )
               .then(data => setMapping(data.codes))
               .catch(error => {
                 if (error) {
diff --git a/src/components/Projects/Terminologies/Terminology.scss b/src/components/Projects/Terminologies/Terminology.scss
index 0953ec4..353bd4f 100644
--- a/src/components/Projects/Terminologies/Terminology.scss
+++ b/src/components/Projects/Terminologies/Terminology.scss
@@ -199,3 +199,54 @@ a.terminology_link:hover {
 .modal_divider {
   margin-bottom: 15px;
 }
+
+.red_votes_count,
+.votes_count {
+  background-color: rgb(230, 229, 229);
+  padding: 0 3px;
+}
+.red_votes_count {
+  color: red;
+}
+
+.mapping_votes {
+  display: flex;
+  flex-direction: column;
+  align-items: center;
+  padding-right: 0.25rem;
+  font-size: 0.7rem;
+}
+
+.no_mapping_button {
+  padding-left: 2rem;
+}
+
+.mapping_relationship {
+  padding: 2px 6px;
+  border: 1px solid $greyColor;
+  border-radius: 4px;
+  &:hover {
+    background-color: rgb(245, 245, 245);
+    transition: all 0.3s linear;
+  }
+}
+
+.mapping {
+  &-display {
+    white-space: nowrap;
+  }
+  display: flex;
+  align-items: center;
+  .mapping_actions {
+    padding-left: 0.25rem;
+    cursor: pointer;
+    opacity: 0;
+    visibility: hidden;
+    transition: opacity 0.4s linear;
+  }
+  &:hover .mapping_actions {
+    transition: all 0.4s linear;
+    opacity: 1;
+    visibility: visible;
+  }
+}

From 48f907e3c7cd36e1e090c07746ef48e72b06ad26 Mon Sep 17 00:00:00 2001
From: Eric Torstenson <eric.s.torstenson@vumc.org>
Date: Thu, 5 Dec 2024 10:02:18 -0600
Subject: [PATCH 166/180] Quick starting point for Map Dragon Help Site

---
 docs/.nojekyll         |  0
 docs/README.md         | 45 ++++++++++++++++++++++++++++++++++++++++++
 docs/_navbar.md        |  4 ++++
 docs/datadictionary.md | 31 +++++++++++++++++++++++++++++
 docs/index.html        | 23 +++++++++++++++++++++
 5 files changed, 103 insertions(+)
 create mode 100755 docs/.nojekyll
 create mode 100755 docs/README.md
 create mode 100644 docs/_navbar.md
 create mode 100644 docs/datadictionary.md
 create mode 100755 docs/index.html

diff --git a/docs/.nojekyll b/docs/.nojekyll
new file mode 100755
index 0000000..e69de29
diff --git a/docs/README.md b/docs/README.md
new file mode 100755
index 0000000..8ffc7b5
--- /dev/null
+++ b/docs/README.md
@@ -0,0 +1,45 @@
+# Map Dragon
+This application will support several user groups in submitting and validating their data, managing and tracking data definitions, and aligning data to standardized terms. 
+
+## Getting Started
+### Vite React App
+
+This is a React application bootstrapped with Vite. 
+
+### Prerequisites
+
+Make sure you have Node.js and npm installed on your machine.
+
+### Installation
+
+1. Clone the repository:
+
+   ```sh
+   git clone git@github.com:NIH-NCPI/map-dragon.git
+
+2. Navigate into the project directory:
+
+   ```sh
+   cd map-dragon
+3. Install dependencies
+
+   ```sh
+   npm i
+
+### Development
+1. To start the development server, run:
+   ```sh
+   npm run dev
+
+### Dependencies
+This project utilizes the following dependencies:
+
++ React: A JavaScript library for building user interfaces  
++ Vite: A front-end tooling for web development  
++ Ant Design: A design component library
++ Sass: A CSS preprocessor
++ React OAuth2 | Google: A React library for Google OAuth
++ jwt-decode: A JWT decoder
++ Papa Parse: A CSV parser
+
+
diff --git a/docs/_navbar.md b/docs/_navbar.md
new file mode 100644
index 0000000..b097239
--- /dev/null
+++ b/docs/_navbar.md
@@ -0,0 +1,4 @@
+* Map Dragon
+  * [Map Dragon Local Installation Directions](https://github.com/NIH-NCPI/map-dragon)
+* File Formats
+  * [Loading a Data Dictionary](datadictionary.md)
\ No newline at end of file
diff --git a/docs/datadictionary.md b/docs/datadictionary.md
new file mode 100644
index 0000000..675f3b8
--- /dev/null
+++ b/docs/datadictionary.md
@@ -0,0 +1,31 @@
+# Loading a Data Dictionary
+(TBD How to use the website to load the DD)
+
+## Expected Format for DD Table
+The following table format is currently the only format accepted by the Map Dragon "Load Table" function. When run, a new data dictionary table is instantiated along with relevant enumerations as new terminologies.
+
+Fields such as *variable_name* and *data_type* are required. Other fields such as *description* are optional but highly recommended. 
+
+The data should be a valid, ASCII only CSV file with double quotes used for "Quote Characters", commas for delimiters, etc. 
+
+| *Column Name* | *Column Descriptions* | *Column Type* |
+|  ------------ | --------------------- | ------------- |
+| *variable_name* | The human readable name associated with variable name | String |
+| *description* | Fully informative description of the contents associated with this variable/column| String |
+| *data_type* | Data type associated with column data  | integer, number, string, enumeration |
+| *min* | Minimum value (integers and numbers only) | numeric value |
+| *max* | Maximum acceptable value (integers and numbers only) | numeric value | 
+| *units* | UCUM code for units | UCUM code prefixed with the curie, UCUM. UCUM:ml for example |
+| *enumerations* | Semi-colon separated list of enumerated values. See below for more details about formatting the enumeration list. | String |
+
+### Formatting for Enumerations
+At the top level, enumerations are just a list of terms separated by semi-colons. For enumerated types with specified codes, these will be provided in the following format: 
+
+> 1=Male;2=Female;0=Unknown;-1=Preferred Not To Answer
+
+In this example, the following codes are extracted: 1, 2, 0 and -1 and assigned the following displays (in order): Male, Female, Unknown and Preferred Not To Answer.
+
+If there is no code specified, the codes will be created using the following logic: 
+> Case is dropped to lower case and potentially problematic characters, such as parenthesis, "(" or ")" will be removed. Whitespace characters will be replaced with underscores, "_". 
+
+There is currently no way to allow codes or values to include semi-colons, ";", or equal signs, "=" in them. They should be replaced prior to loading into Map Dragon. 
\ No newline at end of file
diff --git a/docs/index.html b/docs/index.html
new file mode 100755
index 0000000..00b6590
--- /dev/null
+++ b/docs/index.html
@@ -0,0 +1,23 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <title>Document</title>
+  <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
+  <meta name="description" content="Description">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0, minimum-scale=1.0">
+  <link rel="stylesheet" href="//cdn.jsdelivr.net/npm/docsify/themes/dark.css" />
+</head>
+<body>
+  <div id="app"></div>
+  <script>
+    window.$docsify = {
+      name: 'Map Dragon',
+      repo: 'https://github.com/NIH-NCPI/map-dragon',
+      loadNavbar: true
+    }
+  </script>
+  <!-- Docsify v4 -->
+  <script src="//cdn.jsdelivr.net/npm/docsify@4"></script>
+</body>
+</html>

From e982b2c40ef9cbf0bf6bfbd5de6bccc18d4c9de3 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 5 Dec 2024 12:38:06 -0600
Subject: [PATCH 167/180] Modified .env file

---
 .env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.env b/.env
index fd0a3d4..637e35e 100644
--- a/.env
+++ b/.env
@@ -3,5 +3,5 @@ VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
 # VITE_VOCAB_ENDPOINT = http://127.0.0.1:5000/api # local
 VITE_VOCAB_ENDPOINT = https://locutus-dev-110109177269.us-central1.run.app/api # dev
 # VITE_VOCAB_ENDPOINT = https://locutus-uat-1066621297011.us-central1.run.app/api # uat
-VITE_CLIENT_ID = 907694787484-36jr4oaf04mmniik6482batc87ejemm8.apps.googleusercontent.com
+VITE_CLIENT_ID = 159970607373-mvkv4lfl4ovpul5bssatuf1re4ucvg8n.apps.googleusercontent.com
 VITE_MAPDRAGON_VERSION = "Development"
\ No newline at end of file

From 2c4095c1d3a25b11e429d488c003c30e5618e7b3 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 5 Dec 2024 15:44:33 -0600
Subject: [PATCH 168/180] Corrected error with enumeration dropdown display
 returning path name

---
 src/components/Projects/Tables/EditDataTypeSubForm.jsx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/components/Projects/Tables/EditDataTypeSubForm.jsx b/src/components/Projects/Tables/EditDataTypeSubForm.jsx
index fd47948..339e165 100644
--- a/src/components/Projects/Tables/EditDataTypeSubForm.jsx
+++ b/src/components/Projects/Tables/EditDataTypeSubForm.jsx
@@ -32,11 +32,12 @@ function EditDataTypeSubForm({ type, form, editRow, tableData }) {
     if (editRow === tableData.key && tableData.data_type === 'ENUMERATION') {
       form.setFieldsValue({
         enumerations: {
-          reference: tableData.enumeration.props.to.slice(1),
+          reference: tableData?.variable?.enumerations?.reference,
         },
       });
     }
   };
+  console.log(tableData);
 
   return (
     <>

From 2db5fb0425a2c34cdac0086e77db4293e50d0609 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 5 Dec 2024 15:50:35 -0600
Subject: [PATCH 169/180] removed console log

---
 src/components/Projects/Tables/EditDataTypeSubForm.jsx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/components/Projects/Tables/EditDataTypeSubForm.jsx b/src/components/Projects/Tables/EditDataTypeSubForm.jsx
index 339e165..3b61b49 100644
--- a/src/components/Projects/Tables/EditDataTypeSubForm.jsx
+++ b/src/components/Projects/Tables/EditDataTypeSubForm.jsx
@@ -37,7 +37,6 @@ function EditDataTypeSubForm({ type, form, editRow, tableData }) {
       });
     }
   };
-  console.log(tableData);
 
   return (
     <>

From 8d5a9e447ba285dc7e6c1269cc7c531636e4618e Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 9 Dec 2024 09:22:36 -0600
Subject: [PATCH 170/180] committing to switch branches

---
 src/AppRouter.jsx                             | 85 +++++++++++++++----
 .../MappingsFunctions/GetMappingsModal.jsx    |  2 +-
 .../Projects/Terminologies/Terminology.jsx    | 20 ++---
 3 files changed, 80 insertions(+), 27 deletions(-)

diff --git a/src/AppRouter.jsx b/src/AppRouter.jsx
index 1bd9ef6..a4039a1 100644
--- a/src/AppRouter.jsx
+++ b/src/AppRouter.jsx
@@ -29,17 +29,15 @@ import { SearchContextRoot } from './Contexts/SearchContext.jsx';
 import { About } from './components/About/About.jsx';
 
 export const AppRouter = () => {
- const {user} = useContext(myContext);
-
   const isLoggedIn = () => {
     const storedUser = localStorage.getItem('user');
-    
+
     if (storedUser) {
       return true;
     } else {
       return false;
     }
-  }
+  };
   return (
     <BrowserRouter>
       <Routes>
@@ -64,47 +62,102 @@ export const AppRouter = () => {
           <Route element={<PageLayout />}>
             <Route path="/search/:query" element={<SearchResults />} />
             <Route path="/404" element={<Error404 />} />
-            
+
             <Route path="/ontologies" element={<OntologyInfo />} />
             <Route path="/about" element={<About />} />
-            <Route path="/terminologies" element={ isLoggedIn() ? <TerminologyList />:<Navigate to="/login" /> } />
-            <Route path="/login" element={<LoginPage/>}/>
+            <Route
+              path="/terminologies"
+              element={
+                isLoggedIn() ? <TerminologyList /> : <Navigate to="/login" />
+              }
+            />
+            <Route path="/login" element={<LoginPage />} />
             <Route
               path="/terminology"
               element={<Navigate to="/terminologies" />}
             />
             <Route element={<MappingContextRoot />}>
               <Route element={<SearchContextRoot />}>
-                <Route path="/studies" element={isLoggedIn() ? <StudyList />: <Navigate to="/login" />} />
+                <Route
+                  path="/studies"
+                  element={
+                    isLoggedIn() ? <StudyList /> : <Navigate to="/login" />
+                  }
+                />
                 <Route path="/study" element={<Navigate to="/studies" />} />
                 <Route path="/Study/:studyId">
-                  <Route index element={isLoggedIn() ? <StudyDetails />: <Navigate to="/login" />} />
+                  <Route
+                    index
+                    element={
+                      isLoggedIn() ? <StudyDetails /> : <Navigate to="/login" />
+                    }
+                  />
                   <Route path="DataDictionary">
-                    <Route index element={isLoggedIn() ? <StudyDetails />: <Navigate to="/login" />} />
+                    <Route
+                      index
+                      element={
+                        isLoggedIn() ? (
+                          <StudyDetails />
+                        ) : (
+                          <Navigate to="/login" />
+                        )
+                      }
+                    />
                     <Route
                       path="/Study/:studyId/DataDictionary/:DDId/Table/"
-                      element={isLoggedIn() ? <DDDetails />: <Navigate to="/login" />}
+                      element={
+                        isLoggedIn() ? <DDDetails /> : <Navigate to="/login" />
+                      }
                     />
                     <Route path="/Study/:studyId/DataDictionary/:DDId">
-                      <Route index element={isLoggedIn() ? <DDDetails />: <Navigate to="/login" />} />
+                      <Route
+                        index
+                        element={
+                          isLoggedIn() ? (
+                            <DDDetails />
+                          ) : (
+                            <Navigate to="/login" />
+                          )
+                        }
+                      />
                       <Route
                         path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId"
-                        element={isLoggedIn() ? <TableDetails />: <Navigate to="/login" />}
+                        element={
+                          isLoggedIn() ? (
+                            <TableDetails />
+                          ) : (
+                            <Navigate to="/login" />
+                          )
+                        }
                       />
                       <Route
                         path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/:terminologyId"
-                        element={isLoggedIn() ? <Terminology />: <Navigate to="/login" />}
+                        element={
+                          isLoggedIn() ? (
+                            <Terminology />
+                          ) : (
+                            <Navigate to="/login" />
+                          )
+                        }
                       />
                       <Route
                         path="/Study/:studyId/DataDictionary/:DDId/Table/:tableId/Terminology/"
-                        element={isLoggedIn() ? <Terminology />: <Navigate to="/login" />}
+                        element={
+                          isLoggedIn() ? (
+                            <Terminology />
+                          ) : (
+                            <Navigate to="/login" />
+                          )
+                        }
                       />
                     </Route>
                   </Route>
                 </Route>
                 <Route
                   path="/Terminology/:terminologyId"
-                  element={isLoggedIn() ? <Terminology />: <Navigate to="/login" />}
+                  element={
+                    isLoggedIn() ? <Terminology /> : <Navigate to="/login" />
+                  }
                 />
               </Route>
             </Route>
diff --git a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
index 2af90b4..424e43e 100644
--- a/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
+++ b/src/components/Manager/MappingsFunctions/GetMappingsModal.jsx
@@ -170,7 +170,7 @@ export const GetMappingsModal = ({
 
     setLoading(true);
     fetch(
-      `${vocabUrl}/${componentString}/${component.id}/mapping/${mappingProp}?user_input=true`,
+      `${vocabUrl}/${componentString}/${component.id}/mapping/${mappingProp}?user_input=true&user=${user?.email}`,
       {
         method: 'PUT',
         headers: {
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index e4d887d..6b05dea 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -325,18 +325,18 @@ It then shows the mappings as table data and alows the user to delete a mapping
             getById(
               vocabUrl,
               'Terminology',
-              `${terminologyId}/mapping?user_input=True`
+              `${terminologyId}/mapping?user_input=True+user=${user?.email}`
             )
               .then(data => setMapping(data.codes))
-              .catch(error => {
-                if (error) {
-                  notification.error({
-                    message: 'Error',
-                    description: 'An error occurred loading mappings.',
-                  });
-                }
-                return error;
-              })
+              // .catch(error => {
+              //   if (error) {
+              //     notification.error({
+              //       message: 'Error',
+              //       description: 'An error occurred loading mappings.',
+              //     });
+              //   }
+              //   return error;
+              // })
               .then(() =>
                 getById(
                   vocabUrl,

From dc4ffe61514d9fe654c6ad16d75cb5c4a41c050b Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Mon, 9 Dec 2024 14:11:27 -0600
Subject: [PATCH 171/180] Mapping comments updating count after making new
 comment

---
 .../MappingsFunctions/AssignMappings.jsx      |  17 +-
 .../MappingsFunctions/MappingComments.jsx     |  21 ++-
 .../MappingsFunctions/MappingVotes.jsx        |   2 +-
 .../Terminologies/AssignMappingsViaButton.jsx |   2 +-
 .../Terminologies/EditMappingModal.jsx        |   4 +-
 .../Projects/Terminologies/Terminology.jsx    | 162 +++++++++++-------
 6 files changed, 137 insertions(+), 71 deletions(-)

diff --git a/src/components/Manager/MappingsFunctions/AssignMappings.jsx b/src/components/Manager/MappingsFunctions/AssignMappings.jsx
index 7c4f794..187f8de 100644
--- a/src/components/Manager/MappingsFunctions/AssignMappings.jsx
+++ b/src/components/Manager/MappingsFunctions/AssignMappings.jsx
@@ -73,13 +73,16 @@ export const AssignMappings = ({
       editor: user.email,
     };
 
-    fetch(`${vocabUrl}/Terminology/${terminology.id}/mapping/${mappingProp}`, {
-      method: 'PUT',
-      headers: {
-        'Content-Type': 'application/json',
-      },
-      body: JSON.stringify(mappingsDTO),
-    })
+    fetch(
+      `${vocabUrl}/Terminology/${terminology.id}/mapping/${mappingProp}?user_input=true&user=${user?.email}`,
+      {
+        method: 'PUT',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify(mappingsDTO),
+      }
+    )
       .then(res => {
         if (res.ok) {
           return res.json();
diff --git a/src/components/Manager/MappingsFunctions/MappingComments.jsx b/src/components/Manager/MappingsFunctions/MappingComments.jsx
index b0a8fc3..33bcfe1 100644
--- a/src/components/Manager/MappingsFunctions/MappingComments.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingComments.jsx
@@ -3,6 +3,7 @@ import { useContext, useEffect, useState } from 'react';
 import { myContext } from '../../../App';
 import { MappingContext } from '../../../Contexts/MappingContext';
 import { ModalSpinner } from '../Spinner';
+import { getById } from '../FetchManager';
 
 export const MappingComments = ({
   mappingCode,
@@ -10,6 +11,7 @@ export const MappingComments = ({
   variableMappings,
   setComment,
   idProp,
+  setMapping,
 }) => {
   const [form] = Form.useForm();
   const { vocabUrl, user } = useContext(myContext);
@@ -91,7 +93,24 @@ export const MappingComments = ({
           });
         }
         return error;
-      });
+      })
+      .then(() =>
+        getById(
+          vocabUrl,
+          'Terminology',
+          `${idProp}/mapping?user_input=True&user=${user?.email}`
+        )
+          .then(data => setMapping(data.codes))
+          .catch(error => {
+            if (error) {
+              notification.error({
+                message: 'Error',
+                description: 'An error occurred loading mappings.',
+              });
+            }
+            return error;
+          })
+      );
   };
 
   const formattedDate = dateString => {
diff --git a/src/components/Manager/MappingsFunctions/MappingVotes.jsx b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
index e2d34dc..eb16c0b 100644
--- a/src/components/Manager/MappingsFunctions/MappingVotes.jsx
+++ b/src/components/Manager/MappingsFunctions/MappingVotes.jsx
@@ -45,7 +45,7 @@ export const mappingVotes = (
       getById(
         vocabUrl,
         'Terminology',
-        `${terminologyId}/mapping?user_input=True`
+        `${terminologyId}/mapping?user_input=True&user=${user?.email}`
       )
         .then(data => setMapping(data.codes))
         .catch(error => {
diff --git a/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx b/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx
index 440b567..4b539b7 100644
--- a/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx
+++ b/src/components/Projects/Terminologies/AssignMappingsViaButton.jsx
@@ -68,7 +68,7 @@ export const AssignMappingsViaButton = ({
     };
 
     fetch(
-      `${vocabUrl}/Terminology/${terminology.id}/mapping/${assignMappingsViaButton.code}`,
+      `${vocabUrl}/Terminology/${terminology.id}/mapping/${assignMappingsViaButton.code}?user_input=true&user=${user?.email}`,
       {
         method: 'PUT',
         headers: {
diff --git a/src/components/Projects/Terminologies/EditMappingModal.jsx b/src/components/Projects/Terminologies/EditMappingModal.jsx
index b92d75f..92b2259 100644
--- a/src/components/Projects/Terminologies/EditMappingModal.jsx
+++ b/src/components/Projects/Terminologies/EditMappingModal.jsx
@@ -144,7 +144,7 @@ export const EditMappingsModal = ({
       editor: user.email,
     };
     fetch(
-      `${vocabUrl}/Terminology/${terminologyId}/mapping/${editMappings.code}?user_input=true`,
+      `${vocabUrl}/Terminology/${terminologyId}/mapping/${editMappings.code}?user_input=true&user=${user?.email}`,
       {
         method: 'PUT',
         headers: {
@@ -208,7 +208,7 @@ export const EditMappingsModal = ({
     };
 
     fetch(
-      `${vocabUrl}/Terminology/${terminologyId}/mapping/${editMappings.code}?user_input=true`,
+      `${vocabUrl}/Terminology/${terminologyId}/mapping/${editMappings.code}?user_input=true&user=${user?.email}`,
       {
         method: 'PUT',
         headers: {
diff --git a/src/components/Projects/Terminologies/Terminology.jsx b/src/components/Projects/Terminologies/Terminology.jsx
index 6b05dea..73da018 100644
--- a/src/components/Projects/Terminologies/Terminology.jsx
+++ b/src/components/Projects/Terminologies/Terminology.jsx
@@ -15,6 +15,8 @@ import {
   Tooltip,
 } from 'antd';
 import {
+  CaretDownOutlined,
+  CaretUpOutlined,
   CloseCircleOutlined,
   DownOutlined,
   MessageOutlined,
@@ -91,13 +93,16 @@ export const Terminology = () => {
       editor: user.email,
     };
 
-    fetch(`${vocabUrl}/Terminology/${terminologyId}/mapping/${mappingCode}`, {
-      method: 'PUT',
-      headers: {
-        'Content-Type': 'application/json',
-      },
-      body: JSON.stringify(mappingsDTO),
-    })
+    fetch(
+      `${vocabUrl}/Terminology/${terminologyId}/mapping/${mappingCode}?user_input=true&user=${user?.email}`,
+      {
+        method: 'PUT',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify(mappingsDTO),
+      }
+    )
       .then(res => {
         if (res.ok) {
           return res.json();
@@ -160,6 +165,11 @@ It then shows the mappings as table data and alows the user to delete a mapping
     return calculatedCount;
   };
 
+  const userVote = code => {
+    const foundVote = code.user_input?.users_vote;
+    return foundVote;
+  };
+
   const matchCode = variable => {
     if (!mapping?.length) {
       return noMapping(variable);
@@ -173,34 +183,53 @@ It then shows the mappings as table data and alows the user to delete a mapping
       return variableMappings.mappings.map(code => (
         <div className="mapping" key={code.code}>
           <span>
-            <MessageOutlined
-              className="mapping_actions"
-              onClick={() =>
-                setComment({
-                  code: code.code,
-                  display: code.display,
-                  variableMappings: variableMappings.code,
-                })
-              }
-            />
+            <Tooltip
+              title={code?.user_input?.comments_count}
+              mouseEnterDelay={0.75}
+            >
+              <MessageOutlined
+                className="mapping_actions"
+                onClick={() =>
+                  setComment({
+                    code: code.code,
+                    display: code.display,
+                    variableMappings: variableMappings.code,
+                  })
+                }
+              />
+            </Tooltip>
           </span>
           <span className="mapping_votes">
-            <UpOutlined
-              className="mapping_actions"
-              style={{ color: 'blue' }}
-              onClick={() =>
-                mappingVotes(
-                  variableMappings,
-                  code,
-                  user,
-                  'up',
-                  vocabUrl,
-                  terminologyId,
-                  notification,
-                  setMapping
-                )
-              }
-            />
+            {userVote(code) === 'up' ? (
+              <CaretUpOutlined
+                className="mapping_actions user_vote_icon"
+                style={{
+                  color: 'blue',
+                  cursor: 'not-allowed',
+                  fontSize: '1rem',
+                }}
+              />
+            ) : (
+              <UpOutlined
+                className="mapping_actions"
+                style={{
+                  color: 'blue',
+                }}
+                onClick={() =>
+                  userVote(code) !== 'up' &&
+                  mappingVotes(
+                    variableMappings,
+                    code,
+                    user,
+                    'up',
+                    vocabUrl,
+                    terminologyId,
+                    notification,
+                    setMapping
+                  )
+                }
+              />
+            )}
             <Tooltip
               title={`up: ${code.user_input?.votes_count.up},
                 down: ${code.user_input?.votes_count.down}`}
@@ -218,22 +247,36 @@ It then shows the mappings as table data and alows the user to delete a mapping
                 {votesCount(code)}
               </span>
             </Tooltip>
-            <DownOutlined
-              className="mapping_actions"
-              style={{ color: 'green' }}
-              onClick={() =>
-                mappingVotes(
-                  variableMappings,
-                  code,
-                  user,
-                  'down',
-                  vocabUrl,
-                  terminologyId,
-                  notification,
-                  setMapping
-                )
-              }
-            />
+            {userVote(code) === 'down' ? (
+              <CaretDownOutlined
+                className="mapping_actions user_vote_icon"
+                style={{
+                  color: 'green',
+                  cursor: 'not-allowed',
+                  fontSize: '1rem',
+                }}
+              />
+            ) : (
+              <DownOutlined
+                className="mapping_actions"
+                style={{
+                  color: 'green',
+                }}
+                onClick={() =>
+                  userVote(code) !== 'down' &&
+                  mappingVotes(
+                    variableMappings,
+                    code,
+                    user,
+                    'down',
+                    vocabUrl,
+                    terminologyId,
+                    notification,
+                    setMapping
+                  )
+                }
+              />
+            )}
           </span>
           <span className="mapping-display">
             <Tooltip
@@ -325,18 +368,18 @@ It then shows the mappings as table data and alows the user to delete a mapping
             getById(
               vocabUrl,
               'Terminology',
-              `${terminologyId}/mapping?user_input=True+user=${user?.email}`
+              `${terminologyId}/mapping?user_input=True&user=${user?.email}`
             )
               .then(data => setMapping(data.codes))
-              // .catch(error => {
-              //   if (error) {
-              //     notification.error({
-              //       message: 'Error',
-              //       description: 'An error occurred loading mappings.',
-              //     });
-              //   }
-              //   return error;
-              // })
+              .catch(error => {
+                if (error) {
+                  notification.error({
+                    message: 'Error',
+                    description: 'An error occurred loading mappings.',
+                  });
+                }
+                return error;
+              })
               .then(() =>
                 getById(
                   vocabUrl,
@@ -559,6 +602,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
             variableMappings={comment?.variableMappings}
             setComment={setComment}
             idProp={terminologyId}
+            setMapping={setMapping}
           />
         </div>
       )}

From c3c47ac8fe7b64f38a41725a0bf3f8a6b35ef7c1 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Tue, 10 Dec 2024 10:42:54 -0600
Subject: [PATCH 172/180] edit -uat GHA service

---
 .env                            | 2 +-
 .github/workflows/deploy_qa.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.env b/.env
index 637e35e..3e82c01 100644
--- a/.env
+++ b/.env
@@ -2,6 +2,6 @@ VITE_SEARCH_ENDPOINT = https://www.ebi.ac.uk/ols4/api/search?
 VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
 # VITE_VOCAB_ENDPOINT = http://127.0.0.1:5000/api # local
 VITE_VOCAB_ENDPOINT = https://locutus-dev-110109177269.us-central1.run.app/api # dev
-# VITE_VOCAB_ENDPOINT = https://locutus-uat-1066621297011.us-central1.run.app/api # uat
+# VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
 VITE_CLIENT_ID = 159970607373-mvkv4lfl4ovpul5bssatuf1re4ucvg8n.apps.googleusercontent.com
 VITE_MAPDRAGON_VERSION = "Development"
\ No newline at end of file
diff --git a/.github/workflows/deploy_qa.yml b/.github/workflows/deploy_qa.yml
index 5a03580..8fdef78 100644
--- a/.github/workflows/deploy_qa.yml
+++ b/.github/workflows/deploy_qa.yml
@@ -14,7 +14,7 @@ env:
 
   PROJECT_ID: ${{ secrets.PROJECT_ID }}
   REGION: ${{ secrets.REGION_LOC_1 }}
-  SERVICE: 'map-dragon'
+  SERVICE: 'mapdragon'
   IMAGE_NAME: 'map-dragon_img'
   GCP_CREDENTIALS:  ${{ secrets.GCP_CREDENTIALS }}
 

From ed11ed79d69b055d616bcd2b5605e19bd37f0c3f Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Tue, 10 Dec 2024 10:45:54 -0600
Subject: [PATCH 173/180] edit

---
 .env | 7 -------
 1 file changed, 7 deletions(-)
 delete mode 100644 .env

diff --git a/.env b/.env
deleted file mode 100644
index 3e82c01..0000000
--- a/.env
+++ /dev/null
@@ -1,7 +0,0 @@
-VITE_SEARCH_ENDPOINT = https://www.ebi.ac.uk/ols4/api/search?
-VITE_MONARCH_SEARCH = https://api-v3.monarchinitiative.org/v3/api/search?
-# VITE_VOCAB_ENDPOINT = http://127.0.0.1:5000/api # local
-VITE_VOCAB_ENDPOINT = https://locutus-dev-110109177269.us-central1.run.app/api # dev
-# VITE_VOCAB_ENDPOINT = https://locutus-1066621297011.us-central1.run.app/api # uat
-VITE_CLIENT_ID = 159970607373-mvkv4lfl4ovpul5bssatuf1re4ucvg8n.apps.googleusercontent.com
-VITE_MAPDRAGON_VERSION = "Development"
\ No newline at end of file

From 06121791d04a189db8370304edfa8fa0c11840b8 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Thu, 12 Dec 2024 16:07:47 -0600
Subject: [PATCH 174/180] FD-1844: UCUM Codes for Units

---
 src/App.jsx                                   |   3 +
 src/components/Manager/FetchManager.jsx       |   1 +
 .../MappingsFunctions/MappingReset.jsx        | 647 ------------------
 src/components/Projects/Studies/StudyList.jsx |   2 +-
 .../Projects/Tables/AddVariable.jsx           |   2 +
 .../Projects/Tables/DataTypeNumerical.jsx     |  35 +-
 .../Projects/Tables/EditDataTypeNumerical.jsx |  36 +-
 .../Projects/Tables/EditDataTypeSubForm.jsx   |   2 +-
 .../Projects/Tables/TableDetails.jsx          |  81 ++-
 .../Terminologies/TerminologyList.jsx         |  11 +-
 10 files changed, 153 insertions(+), 667 deletions(-)
 delete mode 100644 src/components/Manager/MappingsFunctions/MappingReset.jsx

diff --git a/src/App.jsx b/src/App.jsx
index 6363339..a1db92e 100644
--- a/src/App.jsx
+++ b/src/App.jsx
@@ -37,6 +37,7 @@ function App() {
   const [selectedKey, setSelectedKey] = useState(null);
   const [user, setUser] = useState(null);
   const [ontologyForPagination, setOntologyForPagination] = useState([]);
+  const [ucumCodes, setUcumCodes] = useState([]);
 
   message.config({
     top: '25vh',
@@ -79,6 +80,8 @@ function App() {
           setImportState,
           ontologyForPagination,
           setOntologyForPagination,
+          ucumCodes,
+          setUcumCodes,
         }}
       >
         <AppRouter />
diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index 374d1cd..ff6bdfc 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -4,6 +4,7 @@ import { ontologyReducer } from './Utilitiy';
 export const getAll = (vocabUrl, name, navigate) => {
   return fetch(`${vocabUrl}/${name}`, {
     method: 'GET',
+    credentials: 'include',
     headers: {
       'Content-Type': 'application/json',
     },
diff --git a/src/components/Manager/MappingsFunctions/MappingReset.jsx b/src/components/Manager/MappingsFunctions/MappingReset.jsx
deleted file mode 100644
index f93ab9f..0000000
--- a/src/components/Manager/MappingsFunctions/MappingReset.jsx
+++ /dev/null
@@ -1,647 +0,0 @@
-import { Checkbox, Form, Input, notification, Tooltip } from 'antd';
-import { useContext, useEffect, useRef, useState } from 'react';
-import { myContext } from '../../../App';
-import { ellipsisString, ontologyReducer, systemsMatch } from '../Utilitiy';
-import { ModalSpinner } from '../Spinner';
-import { MappingContext } from '../../../Contexts/MappingContext';
-import { getFiltersByCode, olsFilterOntologiesSearch } from '../FetchManager';
-import { SearchContext } from '../../../Contexts/SearchContext';
-import { OntologyCheckboxes } from './OntologyCheckboxes';
-import { MappingRelationship } from './MappingRelationship';
-
-export const MappingReset = ({
-  searchProp,
-  mappingDesc,
-  setEditMappings,
-  form,
-  onClose,
-  mappingProp,
-  table,
-  terminology,
-}) => {
-  const { searchUrl, vocabUrl } = useContext(myContext);
-  const {
-    apiPreferences,
-    defaultOntologies,
-    setFacetCounts,
-    setApiPreferencesCode,
-    apiPreferencesCode,
-    setUnformattedPref,
-    ontologyApis,
-    prefTerminologies,
-  } = useContext(SearchContext);
-  const [page, setPage] = useState(0);
-  const entriesPerPage = 1000;
-  const [loading, setLoading] = useState(true);
-  const [results, setResults] = useState([]);
-  const [totalCount, setTotalCount] = useState();
-  const [resultsCount, setResultsCount] = useState(); //
-  const [lastCount, setLastCount] = useState(0); //save last count as count of the results before you fetch data again
-  const [filteredResultsCount, setFilteredResultsCount] = useState(0);
-  const [inputValue, setInputValue] = useState(searchProp); //Sets the value of the search bar
-  const [currentSearchProp, setCurrentSearchProp] = useState(searchProp);
-  const [terminologiesToMap, setTerminologiesToMap] = useState([]);
-  const [active, setActive] = useState(null);
-  const [allCheckboxes, setAllCheckboxes] = useState([]);
-
-  const {
-    setSelectedMappings,
-    displaySelectedMappings,
-    setDisplaySelectedMappings,
-    selectedBoxes,
-    setSelectedBoxes,
-  } = useContext(MappingContext);
-  let ref = useRef();
-  const { Search } = Input;
-
-  const fetchTerminologies = () => {
-    setLoading(true);
-    const fetchPromises = prefTerminologies?.map(pref =>
-      fetch(`${vocabUrl}/${pref?.reference}`).then(response => response.json())
-    );
-
-    Promise.all(fetchPromises)
-      .then(results => {
-        // Once all fetch calls are resolved, set the combined data
-        setTerminologiesToMap(results);
-      })
-      .catch(error => {
-        notification.error({
-          message: 'Error',
-          description: 'An error occurred. Please try again.',
-        });
-      })
-      .finally(() => setLoading(false));
-  };
-
-  // since the code is passed through searchProp, the '!!' forces it to be evaluated as a boolean.
-  // if there is a searchProp being passed, it evaluates to true and runs the search function.
-  // inputValue and currentSearchProp for the search bar is set to the passed searchProp.
-  // The function is run when the code changes.
-  useEffect(() => {
-    setInputValue(searchProp);
-    setCurrentSearchProp(searchProp);
-    setPage(0);
-    if (!!searchProp) {
-      getFiltersByCode(
-        vocabUrl,
-        mappingProp,
-        setApiPreferencesCode,
-        notification,
-        setUnformattedPref,
-        table,
-        terminology,
-        setLoading
-      );
-    }
-  }, [searchProp]);
-
-  useEffect(() => {
-    if (apiPreferencesCode !== undefined) {
-      fetchResults(0, searchProp);
-    }
-  }, [searchProp]);
-
-  useEffect(() => {
-    if (apiPreferencesCode !== undefined) {
-      fetchResults(page, currentSearchProp);
-    }
-  }, [page]);
-
-  useEffect(() => {
-    if (prefTerminologies.length > 0) {
-      fetchTerminologies();
-    }
-  }, []);
-
-  useEffect(() => {
-    setAllCheckboxes(
-      terminologiesToMap.find(term => term.id === active)?.codes ?? []
-    );
-  }, [active]);
-
-  useEffect(() => {
-    setActive(terminologiesToMap?.[0]?.id);
-  }, [terminologiesToMap]);
-
-  // The '!!' forces currentSearchProp to be evaluated as a boolean.
-  // If there is a currentSearchProp in the search bar, it evaluates to true and runs the search function.
-  // The function is run when the query changes and when the preferred ontology changes.
-  // If there are preferred terminologies, it runs when the OLS search bar is clicked (i.e. active)
-  useEffect(() => {
-    if (
-      prefTerminologies.length > 0 &&
-      active === 'search' &&
-      !!currentSearchProp &&
-      apiPreferencesCode !== undefined
-    ) {
-      fetchResults(page, currentSearchProp);
-    } else if (
-      prefTerminologies.length === 0 &&
-      !!currentSearchProp &&
-      apiPreferencesCode !== undefined
-    ) {
-      fetchResults(page, currentSearchProp);
-    }
-  }, [currentSearchProp, apiPreferencesCode, active]);
-
-  /* Pagination is handled via a "View More" link at the bottom of the page. 
-  Each click on the "View More" link makes an API call to fetch the next 15 results.
-  This useEffect moves the scroll bar on the modal to the first index of the new batch of results.
-  Because the content is in a modal and not the window, the closest class name to the modal is used for the location of the ref. */
-  useEffect(() => {
-    if (results?.length > 0 && page > 0 && ref.current) {
-      const container = ref.current.closest('.ant-modal-body');
-      const scrollTop = ref.current.offsetTop - container.offsetTop;
-      container.scrollTop = scrollTop;
-    }
-  }, [results]);
-
-  // Sets the value of the selected_mappings in the form to the checkboxes that are selected
-  useEffect(() => {
-    form.setFieldsValue({
-      selected_mappings: selectedBoxes,
-    });
-  }, [selectedBoxes, form]);
-
-  // sets the code to null on dismount.
-  useEffect(
-    () => () => {
-      onClose();
-      setEditMappings(null);
-      setSelectedMappings([]);
-      setDisplaySelectedMappings([]);
-      setSelectedBoxes([]);
-    },
-    []
-  );
-
-  // Sets currentSearchProp to the value of the search bar and sets page to 0.
-  const handleSearch = query => {
-    setCurrentSearchProp(query);
-    setPage(0);
-  };
-
-  // The function that makes the API call to search for the passed code.
-  const fetchResults = (page, query) => {
-    if (!!!query) {
-      return undefined;
-    }
-    setLoading(true);
-
-    /* The OLS API returns 10 results by default unless specified otherwise. The fetch call includes a specified
-    number of results to return per page (entriesPerPage) and a calculation of the first index to start the results
-    on each new batch of results (pageStart, calculated as the number of the page * the number of entries per page */
-    const pageStart = page * entriesPerPage;
-    if (
-      //If there are api preferences and one of them is OLS, it gets the preferred ontologies
-      apiPreferences?.self?.api_preference &&
-      'ols' in apiPreferences?.self?.api_preference
-    ) {
-      const apiPreferenceOntologies = () => {
-        if (apiPreferences?.self?.api_preference?.ols) {
-          return apiPreferences.self.api_preference.ols.join(',');
-        } else {
-          // else if there are no preferred ontologies, it uses the default ontologies
-          return defaultOntologies;
-        }
-      };
-      //fetch call to search OLS with either preferred or default ontologies
-      return olsFilterOntologiesSearch(
-        searchUrl,
-        query,
-        apiPreferencesCode?.length > 0
-          ? apiPreferencesCode
-          : apiPreferenceOntologies(),
-        page,
-        entriesPerPage,
-        pageStart,
-        selectedBoxes,
-        setTotalCount,
-        setResults,
-        setFilteredResultsCount,
-        setResultsCount,
-        setLoading,
-        results,
-        setFacetCounts
-      );
-    } else
-      return olsFilterOntologiesSearch(
-        searchUrl,
-        query,
-        apiPreferencesCode?.length > 0 ? apiPreferencesCode : defaultOntologies,
-        page,
-        entriesPerPage,
-        pageStart,
-        selectedBoxes,
-        setTotalCount,
-        setResults,
-        setFilteredResultsCount,
-        setResultsCount,
-        setLoading,
-        results,
-        setFacetCounts
-      );
-  };
-
-  // the 'View More' pagination onClick increments the page. The search function is triggered to run on page change in the useEffect.
-  const handleViewMore = e => {
-    e.preventDefault();
-    setPage(prevPage => prevPage + 1);
-  };
-
-  // The display for the checkboxes. The index is set to the count of the results before you fetch the new batch of results
-  // again + 1, to move the scrollbar to the first result of the new batch.
-  const checkBoxDisplay = (item, index) => {
-    return (
-      <>
-        <div key={index} className="modal_search_result">
-          <div key={index} className="modal_display_result">
-            <div>
-              <div className="modal_term_ontology">
-                <div>{item.code}</div>
-              </div>
-              <div>{item.display}</div>
-              <div>
-                {item?.description?.length > 85 ? (
-                  <Tooltip
-                    placement="topRight"
-                    mouseEnterDelay={0.5}
-                    title={item?.description}
-                  >
-                    {ellipsisString(item?.description, '85')}
-                  </Tooltip>
-                ) : (
-                  ellipsisString(item?.description, '85')
-                )}
-              </div>
-            </div>
-          </div>
-        </div>
-      </>
-    );
-  };
-
-  const handleChange = e => {
-    setInputValue(e.target.value);
-  };
-
-  // The display for the checkboxes. The index is set to the count of the results before you fetch the new batch of results
-  // again + 1, to move the scrollbar to the first result of the new batch.
-  const newSearchDisplay = (d, index) => {
-    index === lastCount + 1;
-    return (
-      <>
-        <div
-          key={index}
-          // prettier-ignore
-          ref={index === lastCount + 1 ? ref : undefined}
-          className="modal_search_result"
-          id="scrollbar"
-        >
-          <div>
-            <div className="modal_term_ontology">
-              <div>
-                <b>{d?.label}</b>
-              </div>
-              <div>
-                <a href={d?.iri} target="_blank">
-                  {d?.obo_id}
-                </a>
-              </div>
-            </div>
-            {d?.description?.length > 100 ? (
-              <Tooltip
-                mouseEnterDelay={0.5}
-                title={d?.description}
-                placement="topRight"
-              >
-                {ellipsisString(d?.description[0], '100')}
-              </Tooltip>
-            ) : (
-              ellipsisString(d?.description[0], '100')
-            )}{' '}
-          </div>
-        </div>
-      </>
-    );
-  };
-
-  const selectedTermsDisplay = (d, index) => {
-    return (
-      <>
-        <div key={index} className="modal_search_result" id="scrollbar">
-          <div>
-            <div className="modal_term_ontology">
-              <div>
-                <div>
-                  <b>{d?.display || d?.label}</b>
-                </div>
-              </div>
-              <div>
-                {d?.code || (
-                  <a href={d?.iri} target="_blank">
-                    {d?.obo_id}
-                  </a>
-                )}
-              </div>
-              <div>
-                <MappingRelationship mapping={d} />
-              </div>
-            </div>
-            <div>
-              {d?.description?.length > 85 ? (
-                <Tooltip
-                  placement="topRight"
-                  mouseEnterDelay={0.5}
-                  title={d?.description}
-                >
-                  {ellipsisString(
-                    Array.isArray(d.description)
-                      ? d.description[0]
-                      : d.description,
-                    '85'
-                  )}
-                </Tooltip>
-              ) : (
-                ellipsisString(
-                  Array.isArray(d.description)
-                    ? d.description[0]
-                    : d.description,
-                  '85'
-                )
-              )}
-            </div>
-          </div>
-        </div>
-      </>
-    );
-  };
-  // If the checkbox is checked, it adds the object to the selectedBoxes array
-  // If it is unchecked, it filters it out of the selectedBoxes array.
-  const onCheckboxChange = (event, code) => {
-    if (event.target.checked) {
-      setSelectedBoxes(prevState => [...prevState, code]);
-    } else {
-      setSelectedBoxes(prevState => prevState.filter(val => val !== code));
-    }
-  };
-
-  const onSelectedChange = checkedValues => {
-    const selected = JSON.parse(checkedValues?.[checkedValues.length - 1]);
-
-    // Adds the selectedMappings to the selectedBoxes to ensure they are checked
-    setSelectedBoxes(prevState => {
-      const updated = [...prevState, selected];
-      // Sets the values for the form to the selectedMappings checkboxes that are checked
-      form.setFieldsValue({ selected_mappings: updated });
-      return updated;
-    });
-
-    setDisplaySelectedMappings(prevState => [...prevState, selected]);
-  };
-
-  // Creates a Set that excludes the mappings that have already been selected.
-  // Then filteres the existing mappings out of the results to only display results that have not yet been selected.
-  const getFilteredResults = () => {
-    const codesToExclude = new Set([
-      ...displaySelectedMappings?.map(m => m?.code),
-    ]);
-    return results.filter(r => !codesToExclude?.has(r.obo_id));
-  };
-
-  const filteredResultsArray = getFilteredResults();
-  // Peforms search on Tab key press
-  const searchOnTab = e => {
-    if (e.key === 'Tab') {
-      e.preventDefault();
-      handleSearch(e.target.value);
-    }
-  };
-  return (
-    <>
-      <div className="results_modal_container">
-        <>
-          {loading === false ? (
-            <>
-              <div className="modal_search_results">
-                <div className="modal_search_results_header">
-                  <h4>{searchProp}</h4>
-                  <div className="mappings_search_bar">
-                    {!prefTerminologies.length > 0 && (
-                      <Search
-                        onSearch={handleSearch}
-                        value={inputValue}
-                        onChange={handleChange}
-                        onKeyDown={searchOnTab}
-                      />
-                    )}
-                  </div>
-                  <span className="search-desc">{mappingDesc}</span>
-                </div>
-                {/* ant.design form displaying the checkboxes with the search results.  */}
-                <div className="result_container">
-                  <Form form={form} layout="vertical" preserve={false}>
-                    <div className="all_checkboxes_container">
-                      <div className="mapping_modal_left">
-                        {terminologiesToMap?.length > 0 && (
-                          <div className="assign_map_checkbox_container">
-                            <div className="assign_map_checkbox_wrapper">
-                              <div
-                                className="pref_tab"
-                                onClick={() =>
-                                  setActive(terminologiesToMap?.[0]?.id)
-                                }
-                              >
-                                <b>Preferred Terminologies</b>
-                              </div>
-                              <div className="">
-                                {terminologiesToMap.map((term, i) => (
-                                  <div
-                                    key={i}
-                                    className={
-                                      active === term.id
-                                        ? 'active_term'
-                                        : active !== term.id &&
-                                          active !== 'search'
-                                        ? 'inactive_term'
-                                        : active === 'search' && 'hidden_term'
-                                    }
-                                    onClick={() => setActive(term.id)}
-                                  >
-                                    {term.name}
-                                  </div>
-                                ))}
-                              </div>
-                              <div
-                                onClick={() => setActive('search')}
-                                className={
-                                  active === 'search'
-                                    ? 'active_term'
-                                    : 'inactive_term'
-                                }
-                              >
-                                <Search
-                                  onSearch={handleSearch}
-                                  value={inputValue}
-                                  onChange={handleChange}
-                                  onKeyDown={searchOnTab}
-                                />
-                              </div>
-                            </div>
-                          </div>
-                        )}
-                        {((prefTerminologies.length > 0 &&
-                          active === 'search') ||
-                          prefTerminologies.length === 0) && (
-                          <OntologyCheckboxes
-                            apiPreferences={apiPreferences}
-                            active={active}
-                          />
-                        )}
-                      </div>
-                      <div className="result_form">
-                        {displaySelectedMappings?.length > 0 && (
-                          <Form.Item
-                            name="selected_mappings"
-                            valuePropName="value"
-                            rules={[{ required: false }]}
-                          >
-                            <div className="modal_display_results">
-                              {displaySelectedMappings?.map((sm, i) => (
-                                <Checkbox
-                                  key={i}
-                                  onChange={e => onCheckboxChange(e, sm)}
-                                  checked={
-                                    active === 'search'
-                                      ? selectedBoxes.some(
-                                          box => box.obo_id === sm.obo_id
-                                        )
-                                      : selectedBoxes.some(
-                                          box => box.code === sm.code
-                                        )
-                                  }
-                                  value={sm}
-                                >
-                                  {selectedTermsDisplay(sm, i)}
-                                </Checkbox>
-                              ))}
-                            </div>
-                          </Form.Item>
-                        )}
-                        {(prefTerminologies.length > 0 &&
-                          active === 'search') ||
-                        prefTerminologies.length === 0 ? (
-                          results?.length > 0 ? (
-                            <>
-                              <Form.Item
-                                name={['filtered_mappings']}
-                                valuePropName="value"
-                                rules={[
-                                  {
-                                    required: false,
-                                  },
-                                ]}
-                              >
-                                {filteredResultsArray?.length > 0 && (
-                                  <Checkbox.Group
-                                    className="mappings_checkbox"
-                                    options={filteredResultsArray?.map(
-                                      (d, index) => {
-                                        return {
-                                          value: JSON.stringify({
-                                            code: d.obo_id,
-                                            display: d.label,
-                                            description: d.description[0],
-                                            system: systemsMatch(
-                                              d?.obo_id?.split(':')[0],
-                                              ontologyApis
-                                            ),
-                                          }),
-                                          label: newSearchDisplay(d, index),
-                                        };
-                                      }
-                                    )}
-                                    onChange={onSelectedChange}
-                                  />
-                                )}
-                              </Form.Item>
-                            </>
-                          ) : (
-                            <h3>No results found</h3>
-                          )
-                        ) : (
-                          <Form.Item
-                            name={['mappings']}
-                            valuePropName="value"
-                            rules={[
-                              {
-                                required: false,
-                              },
-                            ]}
-                          >
-                            <Checkbox.Group
-                              className="mappings_checkbox"
-                              options={allCheckboxes
-                                .filter(
-                                  checkbox =>
-                                    !displaySelectedMappings.some(
-                                      dsm => checkbox.code === dsm.code
-                                    )
-                                )
-                                .map((code, index) => ({
-                                  value: JSON.stringify({
-                                    code: code.code,
-                                    display: code.display,
-                                    description: code.description,
-                                    system: code.system,
-                                  }),
-                                  label: checkBoxDisplay(code, index),
-                                }))}
-                              onChange={onSelectedChange}
-                            />
-                          </Form.Item>
-                        )}
-                      </div>
-                    </div>
-                  </Form>
-                  {((prefTerminologies.length > 0 && active === 'search') ||
-                    prefTerminologies.length === 0) && (
-                    <div className="view_more_wrapper">
-                      {/* 'View More' pagination displaying the number of results being displayed
-                      out of the total number of results. Because of the filter to filter out the duplicates,
-                      there is a tooltip informing the user that redundant entries have been removed to explain any
-                      inconsistencies in results numbers per page. */}
-                      <Tooltip
-                        placement="bottom"
-                        title="Redundant entries have been removed"
-                      >
-                        Displaying {resultsCount}
-                        &nbsp;of&nbsp;{totalCount}
-                      </Tooltip>
-                      {resultsCount < totalCount - filteredResultsCount && (
-                        <span
-                          className="view_more_link"
-                          onClick={e => {
-                            handleViewMore(e);
-                            setLastCount(resultsCount);
-                          }}
-                        >
-                          View More
-                        </span>
-                      )}
-                    </div>
-                  )}
-                </div>
-              </div>
-            </>
-          ) : (
-            <div className="loading_spinner">
-              <ModalSpinner />
-            </div>
-          )}
-        </>
-      </div>
-    </>
-  );
-};
diff --git a/src/components/Projects/Studies/StudyList.jsx b/src/components/Projects/Studies/StudyList.jsx
index ffd7fdf..4a76215 100644
--- a/src/components/Projects/Studies/StudyList.jsx
+++ b/src/components/Projects/Studies/StudyList.jsx
@@ -32,7 +32,7 @@ export const StudyList = () => {
         if (error) {
           notification.error({
             message: 'Error',
-            description: 'An error occurred. Please try again.',
+            description: 'An error occurred loading studies.',
           });
         }
         return error;
diff --git a/src/components/Projects/Tables/AddVariable.jsx b/src/components/Projects/Tables/AddVariable.jsx
index 8b22e62..54cf7db 100644
--- a/src/components/Projects/Tables/AddVariable.jsx
+++ b/src/components/Projects/Tables/AddVariable.jsx
@@ -89,6 +89,8 @@ export const AddVariable = ({ table, setTable }) => {
         }}
         maskClosable={false}
         closeIcon={false}
+        cancelButtonProps={{ disabled: loading }}
+        okButtonProps={{ disabled: loading }}
       >
         {loading ? (
           <ModalSpinner />
diff --git a/src/components/Projects/Tables/DataTypeNumerical.jsx b/src/components/Projects/Tables/DataTypeNumerical.jsx
index 4836348..88e6ec2 100644
--- a/src/components/Projects/Tables/DataTypeNumerical.jsx
+++ b/src/components/Projects/Tables/DataTypeNumerical.jsx
@@ -1,8 +1,20 @@
-import { Form, Input, InputNumber, Space } from 'antd';
+import { Form, Input, InputNumber, Select, Space } from 'antd';
+import { getById } from '../../Manager/FetchManager';
+import { useContext, useEffect, useState } from 'react';
+import { myContext } from '../../../App';
 
 export const DataTypeNumerical = ({ form, type }) => {
-  // Validation function to ensure values are numbers and min is less than max
+  const { ucumCodes } = useContext(myContext);
+
+  const options = ucumCodes.map((uc, i) => {
+    return {
+      key: i,
+      value: `ucum:${uc.code}`,
+      label: uc.display,
+    };
+  });
 
+  // Validation function to ensure values are numbers and min is less than max
   const validateMinMax = () => {
     const min = parseFloat(form.getFieldValue('min'));
     const max = parseFloat(form.getFieldValue('max'));
@@ -75,11 +87,24 @@ export const DataTypeNumerical = ({ form, type }) => {
           />
         </Form.Item>
         <Form.Item preserve={false} label="Units" name="units">
-          <Input
+          <Select
+            showSearch
             style={{
-              width: '15vw',
+              width: '100%',
+            }}
+            placeholder="Select UCUM units"
+            optionFilterProp="children"
+            popupMatchSelectWidth={false}
+            filterOption={(input, option) => {
+              const labelMatch = (option?.label ?? '')
+                .toLowerCase()
+                .includes(input.toLowerCase());
+              const valueMatch = (option?.value ?? '')
+                .toLowerCase()
+                .includes(input.toLowerCase());
+              return labelMatch || valueMatch;
             }}
-            placeholder="Units"
+            options={options}
           />
         </Form.Item>
       </Space>
diff --git a/src/components/Projects/Tables/EditDataTypeNumerical.jsx b/src/components/Projects/Tables/EditDataTypeNumerical.jsx
index 1c88578..c619f6a 100644
--- a/src/components/Projects/Tables/EditDataTypeNumerical.jsx
+++ b/src/components/Projects/Tables/EditDataTypeNumerical.jsx
@@ -1,6 +1,18 @@
-import { Form, Input, InputNumber, Space } from 'antd';
+import { Form, InputNumber, Select, Space } from 'antd';
+import { useContext } from 'react';
+import { myContext } from '../../../App';
+
+export const EditDataTypeNumerical = ({ type, form, tableData }) => {
+  const { ucumCodes } = useContext(myContext);
+
+  const options = ucumCodes.map((uc, i) => {
+    return {
+      key: i,
+      value: `ucum:${uc.code}`,
+      label: uc.display,
+    };
+  });
 
-export const EditDataTypeNumerical = ({ type, form }) => {
   // Validation function to ensure values are numbers and min is less than max
   const validateMinMax = () => {
     const min = parseFloat(form.getFieldValue('min'));
@@ -82,11 +94,25 @@ export const EditDataTypeNumerical = ({ type, form }) => {
           />
         </Form.Item>
         <Form.Item preserve={false} label="Units" name={['units']}>
-          <Input
+          <Select
+            showSearch
             style={{
-              width: '15vw',
+              width: '100%',
+            }}
+            defaultValue={tableData?.units || undefined}
+            placeholder="Select UCUM units"
+            optionFilterProp="children"
+            popupMatchSelectWidth={false}
+            filterOption={(input, option) => {
+              const labelMatch = (option?.label ?? '')
+                .toLowerCase()
+                .includes(input.toLowerCase());
+              const valueMatch = (option?.value ?? '')
+                .toLowerCase()
+                .includes(input.toLowerCase());
+              return labelMatch || valueMatch;
             }}
-            placeholder="Units"
+            options={options}
           />
         </Form.Item>
       </Space>
diff --git a/src/components/Projects/Tables/EditDataTypeSubForm.jsx b/src/components/Projects/Tables/EditDataTypeSubForm.jsx
index 3b61b49..d07b141 100644
--- a/src/components/Projects/Tables/EditDataTypeSubForm.jsx
+++ b/src/components/Projects/Tables/EditDataTypeSubForm.jsx
@@ -41,7 +41,7 @@ function EditDataTypeSubForm({ type, form, editRow, tableData }) {
   return (
     <>
       {type === 'INTEGER' || type === 'QUANTITY' ? (
-        <EditDataTypeNumerical type={type} form={form} />
+        <EditDataTypeNumerical type={type} form={form} tableData={tableData} />
       ) : (
         type === 'ENUMERATION' &&
         (!terminologyLoading ? (
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index fdaf8ec..d6e57f2 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -36,8 +36,16 @@ import { ellipsisString, mappingTooltip } from '../../Manager/Utilitiy';
 export const TableDetails = () => {
   const [form] = Form.useForm();
 
-  const { vocabUrl, edit, setEdit, table, setTable, user } =
-    useContext(myContext);
+  const {
+    vocabUrl,
+    edit,
+    setEdit,
+    table,
+    setTable,
+    user,
+    ucumCodes,
+    setUcumCodes,
+  } = useContext(myContext);
   const { apiPreferences, setApiPreferences } = useContext(SearchContext);
   const {
     getMappings,
@@ -75,7 +83,7 @@ export const TableDetails = () => {
   }, [table, mapping, pageSize]);
 
   const updateMappings = (mapArr, mappingCode) => {
-    // setLoading(true);
+    setLoading(true);
     const mappingsDTO = {
       mappings: mapArr,
       editor: user.email,
@@ -117,6 +125,10 @@ export const TableDetails = () => {
 
   // fetches the table and sets 'table' to the response
   useEffect(() => {
+    tableApiCalls();
+  }, []);
+
+  const tableApiCalls = async () => {
     setLoading(true);
     getById(vocabUrl, 'Table', tableId)
       .then(data => {
@@ -162,7 +174,8 @@ export const TableDetails = () => {
               })
               .then(data => {
                 setApiPreferences(data);
-              });
+              })
+              .finally(() => setLoading(false));
           } else {
             setLoading(false);
           }
@@ -172,13 +185,26 @@ export const TableDetails = () => {
         if (error) {
           notification.error({
             message: 'Error',
-            description: 'An error occurred loading the ontology preferences.',
+            description: 'An error occurred loading table details.',
           });
         }
         return error;
       })
       .finally(() => setLoading(false));
-  }, []);
+  };
+
+  useEffect(() => {
+    table && tableTypes();
+  }, [table]);
+
+  const tableTypes = () => {
+    const varTypes = table?.variables?.map(tv => tv.data_type);
+    if (varTypes?.includes('INTEGER' || 'QUANTITY')) {
+      getById(vocabUrl, 'Terminology', 'ucum-common').then(data =>
+        setUcumCodes(data.codes)
+      );
+    }
+  };
 
   // sets table to an empty object on dismount
   useEffect(
@@ -296,6 +322,11 @@ It then shows the mappings as table data and alows the user to delete a mapping
     updateMappings(variableMappings?.mappings, variableMappings?.code);
   };
 
+  const findType = variable => {
+    const unit = variable?.units?.split(':')[1];
+    const foundType = ucumCodes.filter(item => item.code === unit);
+    return foundType.length > 0 ? foundType[0].display : variable?.units;
+  };
   // data for the table columns. Each table has an array of variables. Each variable has a name, description, and data type.
   // The integer and quantity data types include additional details.
   // The enumeration data type includes a reference to a terminology, which includes further codes with the capability to match the
@@ -311,7 +342,7 @@ It then shows the mappings as table data and alows the user to delete a mapping
         data_type: variable.data_type,
         min: variable.min,
         max: variable.max,
-        units: variable.units,
+        units: findType(variable),
         enumeration: variable.data_type === 'ENUMERATION' && (
           <Link
             to={`/Study/${studyId}/DataDictionary/${DDId}/Table/${tableId}/${variable.enumerations.reference}`}
@@ -479,3 +510,39 @@ It then shows the mappings as table data and alows the user to delete a mapping
     </>
   );
 };
+
+// const tableApiCalls = async () => {
+//   const tableData = await getById(vocabUrl, 'Table', tableId);
+
+//   if (!tableData) {
+//     navigate('/404');
+//   } else {
+//     setTable(tableData);
+
+//     const [tableMappings, tableFilters, mappingRelationships] =
+//       await Promise.all([
+//         getById(vocabUrl, 'Table', `${tableId}/mapping`),
+//         fetch(`${vocabUrl}/Table/${tableId}/filter/self`, {
+//           method: 'GET',
+//           headers: {
+//             'Content-Type': 'application/json',
+//           },
+//         }),
+//         getById(vocabUrl, 'Terminology', 'ftd-concept-map-relationship'),
+//       ]);
+
+//     if (tableMappings) {
+//       setMapping(tableMappings.codes);
+//     }
+
+//     if (tableFilters.ok) {
+//       setApiPreferences(tableFilters.json());
+//     } else {
+//       throw new Error('An unknown error occurred.');
+//     }
+//     if (mappingRelationships) {
+//       setRelationshipOptions(mappingRelationships.codes);
+//     }
+//   }
+//   setLoading(false);
+// };
diff --git a/src/components/Projects/Terminologies/TerminologyList.jsx b/src/components/Projects/Terminologies/TerminologyList.jsx
index 743d806..8b1309e 100644
--- a/src/components/Projects/Terminologies/TerminologyList.jsx
+++ b/src/components/Projects/Terminologies/TerminologyList.jsx
@@ -1,4 +1,4 @@
-import { Button, Input, Space, Table } from 'antd';
+import { Button, Input, notification, Space, Table } from 'antd';
 import { SearchOutlined } from '@ant-design/icons';
 import { useContext, useEffect, useRef, useState } from 'react';
 import { myContext } from '../../../App';
@@ -33,6 +33,15 @@ export const TerminologyList = () => {
       .then(data => {
         setTerms(data);
       })
+      .catch(error => {
+        if (error) {
+          notification.error({
+            message: 'Error',
+            description: 'An error occurred loading terminologies.',
+          });
+        }
+        return error;
+      })
       .finally(() => setLoading(false));
     localStorage.setItem('pageSize', pageSize);
   }, [pageSize]);

From ebe32235b82b7dce1428c98e37b8f26d0586afb6 Mon Sep 17 00:00:00 2001
From: Yelena Cox <yelenacox@gmail.com>
Date: Fri, 13 Dec 2024 10:08:29 -0600
Subject: [PATCH 175/180] Removed credentials from headers causing CORS error

---
 src/components/Manager/FetchManager.jsx       |  1 -
 .../Projects/Tables/TableDetails.jsx          | 94 +++++++++----------
 2 files changed, 45 insertions(+), 50 deletions(-)

diff --git a/src/components/Manager/FetchManager.jsx b/src/components/Manager/FetchManager.jsx
index ff6bdfc..374d1cd 100644
--- a/src/components/Manager/FetchManager.jsx
+++ b/src/components/Manager/FetchManager.jsx
@@ -4,7 +4,6 @@ import { ontologyReducer } from './Utilitiy';
 export const getAll = (vocabUrl, name, navigate) => {
   return fetch(`${vocabUrl}/${name}`, {
     method: 'GET',
-    credentials: 'include',
     headers: {
       'Content-Type': 'application/json',
     },
diff --git a/src/components/Projects/Tables/TableDetails.jsx b/src/components/Projects/Tables/TableDetails.jsx
index d6e57f2..422cd1a 100644
--- a/src/components/Projects/Tables/TableDetails.jsx
+++ b/src/components/Projects/Tables/TableDetails.jsx
@@ -132,65 +132,61 @@ export const TableDetails = () => {
     setLoading(true);
     getById(vocabUrl, 'Table', tableId)
       .then(data => {
-        if (data === null) {
-          navigate('/404');
-        } else {
-          setTable(data);
-          if (data) {
-            getById(vocabUrl, 'Table', `${tableId}/mapping`)
-              .then(data => setMapping(data.codes))
-              .catch(error => {
-                if (error) {
-                  console.log(error, 'error');
-
-                  notification.error({
-                    message: 'Error',
-                    description: 'An error occurred loading mappings.',
-                  });
-                }
-                return error;
-              })
-              .then(() =>
-                getById(
-                  vocabUrl,
-                  'Terminology',
-                  'ftd-concept-map-relationship'
-                ).then(data => setRelationshipOptions(data.codes))
-              )
-              .then(() =>
-                fetch(`${vocabUrl}/Table/${tableId}/filter/self`, {
-                  method: 'GET',
-                  headers: {
-                    'Content-Type': 'application/json',
-                  },
-                })
-              )
-              .then(res => {
-                if (res.ok) {
-                  return res.json();
-                } else {
-                  throw new Error('An unknown error occurred.');
-                }
-              })
-              .then(data => {
-                setApiPreferences(data);
+        setTable(data);
+        if (data) {
+          getById(vocabUrl, 'Table', `${tableId}/mapping`)
+            .then(data => setMapping(data.codes))
+            .catch(error => {
+              if (error) {
+                console.log(error, 'error');
+
+                notification.error({
+                  message: 'Error',
+                  description: 'An error occurred loading mappings.',
+                });
+              }
+              return error;
+            })
+            .then(() =>
+              getById(
+                vocabUrl,
+                'Terminology',
+                'ftd-concept-map-relationship'
+              ).then(data => setRelationshipOptions(data.codes))
+            )
+            .then(() =>
+              fetch(`${vocabUrl}/Table/${tableId}/filter/self`, {
+                method: 'GET',
+                headers: {
+                  'Content-Type': 'application/json',
+                },
               })
-              .finally(() => setLoading(false));
-          } else {
-            setLoading(false);
-          }
+            )
+            .then(res => {
+              if (res.ok) {
+                return res.json();
+              } else {
+                throw new Error('An unknown error occurred.');
+              }
+            })
+            .then(data => {
+              setApiPreferences(data);
+            })
+            .finally(() => setLoading(false));
+        } else {
+          setLoading(false);
         }
       })
       .catch(error => {
         if (error) {
           notification.error({
             message: 'Error',
-            description: 'An error occurred loading table details.',
+            description: 'An error occurred loading the table.',
           });
+          setLoading(false);
         }
         return error;
-      })
-      .finally(() => setLoading(false));
+      });
   };
 
   useEffect(() => {

From 7804312cf5277d6c34a40ca957c7c3c8d80e44b4 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Fri, 13 Dec 2024 11:37:30 -0600
Subject: [PATCH 176/180] [FD-1869] test dispatch deploy version

---
 .github/workflows/dispatch_deploy.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/dispatch_deploy.yml b/.github/workflows/dispatch_deploy.yml
index 96f2b65..5e7358d 100644
--- a/.github/workflows/dispatch_deploy.yml
+++ b/.github/workflows/dispatch_deploy.yml
@@ -88,4 +88,5 @@ jobs:
         with:
           service: ${{ env.SERVICE }}
           region: '${{ env.REGION }}'
-          image: ${{ env.DOCKER_TAG }}
\ No newline at end of file
+          image: ${{ env.DOCKER_TAG }}
+          env_vars: ${{ github.event.inputs.version }}
\ No newline at end of file

From c3d9b7f944b5a7945b7a3dea02d0238d4bf84962 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Fri, 13 Dec 2024 11:44:46 -0600
Subject: [PATCH 177/180] [FD-1869] test dev version

---
 .github/workflows/deploy_dev.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/deploy_dev.yml b/.github/workflows/deploy_dev.yml
index 03b6d61..83eea98 100644
--- a/.github/workflows/deploy_dev.yml
+++ b/.github/workflows/deploy_dev.yml
@@ -20,8 +20,7 @@ jobs:
   deploy:
     runs-on: 'ubuntu-latest'
     
-    # If PR is approved and the PR is for the 'main' branch
-    if: github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'main'
+    # If PR is approved and the PR is for the 'main' branchif: github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'main'
     
     environment:
       name: dev
@@ -44,6 +43,7 @@ jobs:
         id: extract_version
         run: |
           VERSION=${{ github.event.pull_request.number }} 
+          echo "VERSION=${VERSION}" >> $GITHUB_ENV
           echo "Extracted Version: ${VERSION}"
 
       - name: Generate .env.dev file
@@ -74,3 +74,4 @@ jobs:
           service: '${{ env.SERVICE }}-dev'
           region: '${{ env.REGION }}'
           image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-dev/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          env_vars: VERSION=${VERSION}
\ No newline at end of file

From 14797bea394d24106d345f7c63b462dfed6abac1 Mon Sep 17 00:00:00 2001
From: brendagutman <77469967+brendagutman@users.noreply.github.com>
Date: Fri, 13 Dec 2024 14:07:46 -0600
Subject: [PATCH 178/180] add workflow dispatch to dev

---
 .github/workflows/deploy_dev.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/deploy_dev.yml b/.github/workflows/deploy_dev.yml
index 83eea98..bcb2b4a 100644
--- a/.github/workflows/deploy_dev.yml
+++ b/.github/workflows/deploy_dev.yml
@@ -5,7 +5,8 @@ name: 'Build and Deploy to Cloud Run'
 on:
   pull_request_review:
     types: [submitted, edited] # submitted, reviewer edits the PR (ex comments)
-    
+    workflow_dispatch: # This enables manual triggers
+
 env:
 
   PROJECT_ID: ${{ secrets.PROJECT_ID }}
@@ -74,4 +75,4 @@ jobs:
           service: '${{ env.SERVICE }}-dev'
           region: '${{ env.REGION }}'
           image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-dev/${{ env.IMAGE_NAME }}:${{ github.sha }}"
-          env_vars: VERSION=${VERSION}
\ No newline at end of file
+          env_vars: VERSION=${VERSION}

From 16d3cdda63bf751eb22820cdeb25525e2338e629 Mon Sep 17 00:00:00 2001
From: brendagutman <77469967+brendagutman@users.noreply.github.com>
Date: Fri, 13 Dec 2024 14:13:29 -0600
Subject: [PATCH 179/180] test dev version

---
 .github/workflows/deploy_dev.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/deploy_dev.yml b/.github/workflows/deploy_dev.yml
index bcb2b4a..289f7df 100644
--- a/.github/workflows/deploy_dev.yml
+++ b/.github/workflows/deploy_dev.yml
@@ -5,7 +5,11 @@ name: 'Build and Deploy to Cloud Run'
 on:
   pull_request_review:
     types: [submitted, edited] # submitted, reviewer edits the PR (ex comments)
-    workflow_dispatch: # This enables manual triggers
+  workflow_dispatch: # This enables manual triggers
+  pull_request:
+    branches:
+      - main
+    types: [closed, edited] # PR opened, edited(PR title, etc)
 
 env:
 

From 6f56c28dbb826632bfb1c597bc0cab7c463150a6 Mon Sep 17 00:00:00 2001
From: brendagutman <brenda.gutman@gmail.com>
Date: Fri, 13 Dec 2024 14:26:01 -0600
Subject: [PATCH 180/180] [FD-1869]Edit qa and prod version

---
 .github/workflows/deploy_dev.yml  | 9 +++------
 .github/workflows/deploy_prod.yml | 3 ++-
 .github/workflows/deploy_qa.yml   | 3 ++-
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/deploy_dev.yml b/.github/workflows/deploy_dev.yml
index 289f7df..b05f400 100644
--- a/.github/workflows/deploy_dev.yml
+++ b/.github/workflows/deploy_dev.yml
@@ -6,10 +6,6 @@ on:
   pull_request_review:
     types: [submitted, edited] # submitted, reviewer edits the PR (ex comments)
   workflow_dispatch: # This enables manual triggers
-  pull_request:
-    branches:
-      - main
-    types: [closed, edited] # PR opened, edited(PR title, etc)
 
 env:
 
@@ -25,7 +21,8 @@ jobs:
   deploy:
     runs-on: 'ubuntu-latest'
     
-    # If PR is approved and the PR is for the 'main' branchif: github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'main'
+    # If PR is approved and the PR is for the 'main' branch
+    if: github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'main'
     
     environment:
       name: dev
@@ -79,4 +76,4 @@ jobs:
           service: '${{ env.SERVICE }}-dev'
           region: '${{ env.REGION }}'
           image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-dev/${{ env.IMAGE_NAME }}:${{ github.sha }}"
-          env_vars: VERSION=${VERSION}
+          env_vars: VERSION=${VERSION}
\ No newline at end of file
diff --git a/.github/workflows/deploy_prod.yml b/.github/workflows/deploy_prod.yml
index 8b8f600..019584d 100644
--- a/.github/workflows/deploy_prod.yml
+++ b/.github/workflows/deploy_prod.yml
@@ -75,4 +75,5 @@ jobs:
         with:
           service: '${{ env.SERVICE }}'
           region: '${{ env.REGION }}'
-          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
\ No newline at end of file
+          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          env_vars: VERSION=${VERSION}
\ No newline at end of file
diff --git a/.github/workflows/deploy_qa.yml b/.github/workflows/deploy_qa.yml
index 8fdef78..748a9e6 100644
--- a/.github/workflows/deploy_qa.yml
+++ b/.github/workflows/deploy_qa.yml
@@ -74,4 +74,5 @@ jobs:
         with:
           service: '${{ env.SERVICE }}-uat'
           region: '${{ env.REGION }}'
-          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-uat/${{ env.IMAGE_NAME }}:${{ github.sha }}"
\ No newline at end of file
+          image: "${{ env.REGION }}-docker.pkg.dev/${{ env.PROJECT_ID }}/${{ env.SERVICE }}-uat/${{ env.IMAGE_NAME }}:${{ github.sha }}"
+          env_vars: VERSION=${VERSION}
\ No newline at end of file