Merge pull request #61 from elixir-europe/elixir-bsc

Elixir bsc
elixir-europe · Feb 14, 2024 · d75a183 · d75a183
2 parents 2a54ca3 + f2a1e4e
commit d75a183
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Showing 14 changed files with 1,571 additions and 1,188 deletions.
diff --git a/frontend/src/App.css b/frontend/src/App.css
@@ -499,20 +499,26 @@ html {
 }
 
 .exampleQuery:hover .text-example {
+  margin-right: 14px;
   display: flex;
   align-items: center;
   justify-content: center;
   border: solid #c8c8c8;
   background-color: #c8c8c8;
   color: black;
+  width: -moz-fit-content;
   width: fit-content;
   border-radius: 6px;
-  margin-left: 10px;
-  padding: 1px;
+  margin-left: -98px;
+
+  padding-top: 1px;
+  padding-bottom: 1px;
+  padding-left: 2px;
+  padding-right: 2px;
 }
 
 .examplesQueriesList {
-  width: 111px;
+  width: fit-content;
   display: flex;
   flex-direction: column;
   justify-content: center;
@@ -653,8 +659,9 @@ select {
   /* justify-content: center; */
   align-content: center;
   align-items: center;
-  padding-bottom: 10px;
-  min-height: 630px;
+  padding-bottom: 55px;
+  min-height: 280px;
+
 }
 
 .resultSet2 {
@@ -692,17 +699,20 @@ hr {
     sans-serif;
   text-transform: uppercase;
   font-size: 12px;
-  margin-left: 33px;
 }
 
 .exampleQueries:hover {
   color: rgb(118, 151, 228);
 }
 
 .bulbExample {
+  margin-right: 48px;
+  padding-right: 19px;
+  border-right: 1.7px solid #f1f1f1;
   display: flex;
+  justify-content: center;
   align-items: center;
-  border-left: 1.7px solid #f1f1f1;
+  flex-direction: row-reverse;
 }
 
 .helpButton {
@@ -780,10 +790,10 @@ hr {
 .example {
   display: flex;
   align-items: center;
-  margin-right: -117px;
+  /* margin-right: -117px; */
   margin-top: 22px;
   margin-bottom: 22px;
-  flex-direction: row-reverse;
+  flex-direction: row;
   align-content: space-between;
   justify-content: center;
 }
@@ -803,7 +813,7 @@ hr {
   padding: 5px;
   cursor: pointer;
   display: flex;
-  flex-direction: row-reverse;
+  flex-direction: row;
   align-content: center;
   justify-content: center;
   align-items: center;
@@ -1063,8 +1073,8 @@ h5 {
     sans-serif;
   text-transform: uppercase;
   font-size: 12px;
-  margin-right: 36px;
-  margin-left: 27px;
+  margin-right: 32px;
+  margin-left: -20px;
 }
 
 .filters:hover {
@@ -1177,7 +1187,7 @@ h5 {
     padding: 5px;
     cursor: pointer;
     display: flex;
-    flex-direction: row-reverse;
+    flex-direction: row;
     align-content: center;
     justify-content: center;
     align-items: center;
@@ -1264,10 +1274,8 @@ h5 {
       'Helvetica Neue', sans-serif;
     text-transform: uppercase;
     font-size: 10px;
-    margin-left: 2px !important;
-    margin-right: 7px !important;
-    /* margin-right: 36px; */
-    /* margin-left: 27px; */
+    margin-right: 3px;
+    margin-left: -23px;
   }
 
   .container-fluid {
@@ -1285,7 +1293,7 @@ h5 {
     margin-right: 0px;
     margin-top: 22px;
     margin-bottom: 22px;
-    flex-direction: row-reverse;
+    flex-direction: row;
     align-content: space-between;
     justify-content: center;
   }
@@ -1327,13 +1335,14 @@ h5 {
     height: 27px;
   }
   .bulbExample {
+    margin-right: 48px;
+    padding-right: 19px;
+    border-right: 1.7px solid #f1f1f1;
     display: flex;
-    border-left: 1.7px solid #f1f1f1;
-    flex-direction: column;
-    justify-content: center;
-    align-content: center;
-    align-items: center;
-    width: 112px;
+    font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', 'Roboto',
+      'Oxygen', 'Ubuntu', 'Cantarell', 'Fira Sans', 'Droid Sans',
+      'Helvetica Neue', sans-serif;
+    text-transform: uppercase;
   }
   .searchIcon {
     width: 26px;
@@ -1364,20 +1373,22 @@ h5 {
     justify-content: center;
     align-content: center;
     align-items: flex-start;
-    width: 189px;
+    width: fit-content;
     border-radius: 5px;
     font-size: 9px;
     margin-left: 10px !important;
     background: #8dbde0;
   }
 
   .bulbExample {
+    margin-right: 49px;
     display: flex;
-    border-left: 1.7px solid #f1f1f1;
-    flex-direction: column;
-    justify-content: center;
-    align-content: center;
-    align-items: center;
+    padding-right: 13px;
+    border-right: 1.7px solid #f1f1f1;
+    font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', 'Roboto',
+      'Oxygen', 'Ubuntu', 'Cantarell', 'Fira Sans', 'Droid Sans',
+      'Helvetica Neue', sans-serif;
+    text-transform: uppercase;
   }
 
   .NavlinkVerifier {

diff --git a/frontend/src/components/Analyses/AnalysesResults.js b/frontend/src/components/Analyses/AnalysesResults.js
@@ -94,10 +94,21 @@ function AnalysesResults (props) {
               }
               arrayFilter.push(alphaNumFilter)
             } else {
-              const filter2 = {
+              let filter2 = {
                 id: element,
                 includeDescendantTerms: props.descendantTerm
               }
+              props.filteringTerms.data.response.filteringTerms.forEach(
+                element2 => {
+                  if (element === element2.label) {
+                    filter2 = {
+                      id: element2.id,
+                      includeDescendantTerms: props.descendantTerm
+                    }
+                  }
+                }
+              )
+
               arrayFilter.push(filter2)
             }
           })
@@ -133,9 +144,18 @@ function AnalysesResults (props) {
             }
             arrayFilter.push(alphaNumFilter)
           } else {
-            const filter = {
-              id: props.query
-            }
+            let filter = { id: props.query }
+            let labelToOntology = 0
+            props.filteringTerms.data.response.filteringTerms.forEach(
+              element => {
+                if (props.query === element.label) {
+                  labelToOntology = element.id
+                  filter = {
+                    id: labelToOntology
+                  }
+                }
+              }
+            )
             arrayFilter.push(filter)
           }
         }
@@ -178,7 +198,10 @@ function AnalysesResults (props) {
           }
 
           if (token === null) {
-            res = await axios.post(configData.API_URL + '/analyses', jsonData1)
+            res = await axios.post(
+              configData.API_URL + '/analyses',
+              jsonData1
+            )
           } else {
             const headers = { Authorization: `Bearer ${token}` }
 
@@ -215,7 +238,6 @@ function AnalysesResults (props) {
                         [element.resultsCount]
                       ]
                       let found = false
-
                       resultsPerDataset.forEach(element => {
                         if (element[0] === arrayResultsPerDataset[0]) {
                           found = true
@@ -233,14 +255,14 @@ function AnalysesResults (props) {
                     [element.exists],
                     [element.resultsCount]
                   ]
-
                   resultsPerDataset.push(arrayResultsPerDataset)
                 }
               }
 
               if (element.id === undefined || element.id === '') {
                 let arrayResultsNoDatasets = [element.beaconId]
                 resultsNotPerDataset.push(arrayResultsNoDatasets)
+                console.log(arrayResultsNoDatasets)
               }
 
               if (res.data.response.resultSets[index].results) {
@@ -273,6 +295,7 @@ function AnalysesResults (props) {
             }
           }
           jsonData2 = JSON.stringify(jsonData2)
+          console.log(jsonData2)
           let token = null
           if (auth.userData === null) {
             token = getStoredToken()
@@ -282,25 +305,28 @@ function AnalysesResults (props) {
 
           if (token === null) {
             console.log('Querying without token')
-            res = await axios.post(configData.API_URL + '/analyses', jsonData2)
+            res = await axios.post(
+              configData.API_URL + '/analyses',
+              jsonData2
+            )
           } else {
             console.log('Querying WITH token')
             const headers = { Authorization: `Bearer ${token}` }
-
             res = await axios.post(
               configData.API_URL + '/analyses',
               jsonData2,
               { headers: headers }
             )
           }
-          setTimeOut(true)
 
+          setTimeOut(true)
+          console.log(res.data)
           if (
             (res.data.responseSummary.numTotalResults < 1 ||
               res.data.responseSummary.numTotalResults === undefined) &&
             props.resultSets !== 'MISS'
           ) {
-            setError('. Please try another query')
+            setError('No results. Please try another query')
             setNumberResults(0)
             setBoolean(false)
           } else {
@@ -361,9 +387,7 @@ function AnalysesResults (props) {
           }
         }
       } catch (error) {
-        setError(
-          'No results. Please check the query and the connection and retry'
-        )
+        setError('Connection error. Please retry')
         setTimeOut(true)
       }
     }

diff --git a/frontend/src/components/Biosamples/BiosamplesResults.js b/frontend/src/components/Biosamples/BiosamplesResults.js
@@ -94,10 +94,21 @@ function BiosamplesResults (props) {
               }
               arrayFilter.push(alphaNumFilter)
             } else {
-              const filter2 = {
+              let filter2 = {
                 id: element,
                 includeDescendantTerms: props.descendantTerm
               }
+              props.filteringTerms.data.response.filteringTerms.forEach(
+                element2 => {
+                  if (element === element2.label) {
+                    filter2 = {
+                      id: element2.id,
+                      includeDescendantTerms: props.descendantTerm
+                    }
+                  }
+                }
+              )
+
               arrayFilter.push(filter2)
             }
           })
@@ -133,9 +144,18 @@ function BiosamplesResults (props) {
             }
             arrayFilter.push(alphaNumFilter)
           } else {
-            const filter = {
-              id: props.query
-            }
+            let filter = { id: props.query }
+            let labelToOntology = 0
+            props.filteringTerms.data.response.filteringTerms.forEach(
+              element => {
+                if (props.query === element.label) {
+                  labelToOntology = element.id
+                  filter = {
+                    id: labelToOntology
+                  }
+                }
+              }
+            )
             arrayFilter.push(filter)
           }
         }
@@ -242,6 +262,7 @@ function BiosamplesResults (props) {
               if (element.id === undefined || element.id === '') {
                 let arrayResultsNoDatasets = [element.beaconId]
                 resultsNotPerDataset.push(arrayResultsNoDatasets)
+                console.log(arrayResultsNoDatasets)
               }
 
               if (res.data.response.resultSets[index].results) {
@@ -274,6 +295,7 @@ function BiosamplesResults (props) {
             }
           }
           jsonData2 = JSON.stringify(jsonData2)
+          console.log(jsonData2)
           let token = null
           if (auth.userData === null) {
             token = getStoredToken()
@@ -290,15 +312,15 @@ function BiosamplesResults (props) {
           } else {
             console.log('Querying WITH token')
             const headers = { Authorization: `Bearer ${token}` }
-
             res = await axios.post(
               configData.API_URL + '/biosamples',
               jsonData2,
               { headers: headers }
             )
           }
-          setTimeOut(true)
 
+          setTimeOut(true)
+          console.log(res.data)
           if (
             (res.data.responseSummary.numTotalResults < 1 ||
               res.data.responseSummary.numTotalResults === undefined) &&
@@ -324,7 +346,6 @@ function BiosamplesResults (props) {
                         [element.resultsCount]
                       ]
                       let found = false
-
                       resultsPerDataset.forEach(element => {
                         if (element[0] === arrayResultsPerDataset[0]) {
                           found = true