Merge pull request #285 from CSCfi/dev

Release 1.4.0
CSCfi · Dec 8, 2021 · 06b2e45 · 06b2e45
2 parents a60f68a + 367bb4a
commit 06b2e45
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Showing 12 changed files with 2,094 additions and 4,303 deletions.
diff --git a/babel.config.js b/babel.config.js
@@ -1,3 +1,3 @@
 module.exports = {
-  presets: ["@vue/app"]
+  presets: ["@vue/app"],
 };
diff --git a/jest.config.js b/jest.config.js
@@ -4,12 +4,12 @@ module.exports = {
   moduleFileExtensions: ["js", "ts", "tsx", "json", "vue"],
   transform: {
     ".*\\.(vue)$": "vue-jest",
-    "^.+\\.tsx?$": "ts-jest"
+    "^.+\\.tsx?$": "ts-jest",
   },
   testURL: "http://localhost/",
   collectCoverage: true,
   preset: "@vue/cli-plugin-unit-jest/presets/typescript-and-babel",
   setupFilesAfterEnv: ["<rootDir>/tests/unit/vueSetup.js"],
   coverageReporters: ["text", "html", "lcov"],
-  coverageDirectory: "jest-coverage"
+  coverageDirectory: "jest-coverage",
 };
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "beacon-network-ui",
-  "version": "1.3.1",
+  "version": "1.4.0",
   "private": true,
   "scripts": {
     "serve": "vue-cli-service serve",
@@ -11,47 +11,47 @@
     "start": "serve -l 8080 -s dist"
   },
   "dependencies": {
-    "@vue/cli-plugin-babel": "^5.0.0-rc.0",
-    "@vue/cli-plugin-eslint": "^5.0.0-rc.0",
-    "@vue/cli-plugin-typescript": "^5.0.0-rc.0",
-    "@vue/cli-plugin-unit-jest": "^5.0.0-rc.0",
-    "@vue/cli-service": "^5.0.0-rc.0",
-    "@vue/test-utils": "^1.2.2",
-    "acorn": "^8.5.0",
+    "@vue/cli-plugin-babel": "^5.0.0-rc.1",
+    "@vue/cli-plugin-eslint": "^5.0.0-rc.1",
+    "@vue/cli-plugin-typescript": "^5.0.0-rc.1",
+    "@vue/cli-plugin-unit-jest": "^5.0.0-rc.1",
+    "@vue/cli-service": "^5.0.0-rc.1",
+    "@vue/test-utils": "^1.3.0",
+    "acorn": "^8.6.0",
     "axios": "^0.24.0",
     "babel-eslint": "^10.1.0",
     "buefy": "^0.9.13",
     "bulma": "^0.9.2",
-    "core-js": "^3.19.1",
-    "cypress-localstorage-commands": "^1.6.0",
+    "core-js": "^3.19.3",
+    "cypress-localstorage-commands": "^1.6.1",
     "eslint": "^7.32.0",
     "eslint-config-prettier": "^8.3.0",
     "eslint-plugin-prettier": "^4.0.0",
     "eslint-plugin-vue": "^7.19.1",
     "minimist": "^1.2.5",
     "node-sass": "^6.0.1",
-    "prettier": "^2.4.1",
+    "prettier": "^2.5.1",
     "regenerator-runtime": "^0.13.9",
     "sass-loader": "^12.3.0",
     "serve": "^13.0.2",
     "vue": "^2.6.14",
     "vue-cookies": "^1.7.4",
-    "vue-material-design-icons": "^4.13.0",
+    "vue-material-design-icons": "^5.0.0",
     "vue-matomo": "^4.1.0",
     "vue-router": "^3.5.3"
   },
   "devDependencies": {
     "@babel/core": "^7.16.0",
-    "@cypress/code-coverage": "^3.9.11",
-    "@types/jest": "^27.0.0",
+    "@cypress/code-coverage": "^3.9.12",
+    "@types/jest": "^27.0.3",
     "@typescript-eslint/eslint-plugin": "^4.33.0",
     "@typescript-eslint/parser": "^4.33.0",
     "@vue/eslint-config-typescript": "^7.0.0",
-    "@vue/vue2-jest": "^27.0.0-alpha.3",
+    "@vue/vue2-jest": "^27.0.0-alpha.4",
     "babel-core": "^7.0.0-bridge.0",
-    "cypress": "^9.0.0",
-    "ts-jest": "^27.0.4",
-    "typescript": "~4.4.4",
+    "cypress": "^9.1.1",
+    "ts-jest": "^27.1.0",
+    "typescript": "~4.5.2",
     "vue-jest": "^3.0.7",
     "vue-template-compiler": "^2.6.14"
   }

diff --git a/postcss.config.js b/postcss.config.js
@@ -1,5 +1,5 @@
 module.exports = {
   plugins: {
-    autoprefixer: {}
-  }
+    autoprefixer: {},
+  },
 };
diff --git a/src/components/BasicSearch.vue b/src/components/BasicSearch.vue
@@ -87,7 +87,7 @@ export default {
       errorMessage: "",
       errorTooltip: false,
       regex:
-        /^(X|Y|MT|[1-9]|1[0-9]|2[0-2])\s:\s(\d+) ([ATCGN]+)\s>\s(DEL:ME|INS:ME|DUP:TANDEM|DUP|DEL|INS|INV|CNV|SNP|MNP|[ATCGN]+)$/i,
+        /^(X|Y|MT|[1-9]|1[0-9]|2[0-2])\s?:\s?(\d+)\s?([ATCGN]+)\s?>\s?(DEL:ME|INS:ME|DUP:TANDEM|DUP|DEL|INS|INV|CNV|SNP|MNP|[ATCGN]+)$/i,
       variantTypes: [
         "DEL:ME",
         "INS:ME",
@@ -123,22 +123,11 @@ export default {
       vm.validateInput();
       if (vm.validated) {
         // Query string
-        var queryObj = {
-          searchType: "basic",
-          includeDatasetResponses: "HIT",
-          assemblyId: vm.assembly,
-          referenceName: vm.query.split(" ")[0],
-          start: vm.query.split(" ")[2] > 0 ? vm.query.split(" ")[2] - 1 : 0,
-          referenceBases: vm.query.split(" ")[3],
-        };
-        // Determine if last element is a base of a variant type
-        if (vm.variantTypes.includes(vm.query.split(" ")[5])) {
-          // vm.query.split(" ")[5]) is a variantType
-          queryObj["variantType"] = vm.query.split(" ")[5];
-        } else {
-          // vm.query.split(" ")[5]) is an alternateBases
-          queryObj["alternateBases"] = vm.query.split(" ")[5];
-        }
+        var queryObj = {};
+        queryObj.searchType = "basic";
+        queryObj.includeDatasetResponses = "HIT";
+        queryObj.assemblyId = vm.assembly;
+        queryObj = Object.assign(queryObj, vm.buildQueryObj());
         // Change view to results and send GET query string
         this.$router.push(
           {
@@ -158,9 +147,34 @@ export default {
       vm.query = "MT : 10 T > C";
       document.getElementById("searchBar").focus();
     },
+    buildQueryObj: function () {
+      var vm = this;
+      var temp = vm.query.split(vm.regex).filter(Boolean);
+      var tempArray = [];
+      for (var i = 0; i < temp.length; i++) {
+        if (temp[i] != ":" && temp[i] != ">") {
+          tempArray.push(temp[i]);
+        }
+      }
+      var queryObj = {
+        referenceName: tempArray[0],
+        start: tempArray[1] > 0 ? tempArray[1] - 1 : 0,
+        referenceBases: tempArray[2],
+      };
+      // Determine if last element is a base of a variant type
+      if (vm.variantTypes.includes(tempArray[3])) {
+        // tempArray[3] is a variantType
+        queryObj["variantType"] = tempArray[3];
+      } else {
+        // tempArray[3] is an alternateBases
+        queryObj["alternateBases"] = tempArray[3];
+      }
+
+      return queryObj;
+    },
     validateInput: function () {
       var vm = this;
-      if (vm.regex.exec(vm.query)) {
+      if (vm.regex.test(vm.query)) {
         vm.validated = true;
       } else {
         vm.validated = false;

diff --git a/src/components/BasicSearchV2.vue b/src/components/BasicSearchV2.vue
@@ -113,7 +113,7 @@ export default {
       errorMessage: "",
       errorTooltip: false,
       regex:
-        /^(X|Y|MT|[1-9]|1[0-9]|2[0-2])\s:\s(\d+) ([ATCGN]+)\s>\s(DEL:ME|INS:ME|DUP:TANDEM|DUP|DEL|INS|INV|CNV|SNP|MNP|[ATCGN]+)$/i,
+        /^(X|Y|MT|[1-9]|1[0-9]|2[0-2])\s?:\s?(\d+)\s?([ATCGN]+)\s?>\s?(DEL:ME|INS:ME|DUP:TANDEM|DUP|DEL|INS|INV|CNV|SNP|MNP|[ATCGN]+)$/i,
       variantTypes: [
         "DEL:ME",
         "INS:ME",
@@ -159,24 +159,12 @@ export default {
       vm.validateInput();
       if (vm.validated) {
         // Query string
-        var queryObj = {
-          searchInInput: vm.searchInInput,
-          searchType: "basic",
-          includeDatasetResponses: "HIT",
-          assemblyId: vm.assembly,
-          referenceName: vm.query.split(" ")[0],
-          start: vm.query.split(" ")[2] > 0 ? vm.query.split(" ")[2] - 1 : 0,
-          referenceBases: vm.query.split(" ")[3],
-        };
-
-        // Determine if last element is a base of a variant type
-        if (vm.variantTypes.includes(vm.query.split(" ")[5])) {
-          // vm.query.split(" ")[5]) is a variantType
-          queryObj["variantType"] = vm.query.split(" ")[5];
-        } else {
-          // vm.query.split(" ")[5]) is an alternateBases
-          queryObj["alternateBases"] = vm.query.split(" ")[5];
-        }
+        var queryObj = {};
+        queryObj.searchInInput = vm.searchInInput;
+        queryObj.searchType = "basic";
+        queryObj.includeDatasetResponses = "HIT";
+        queryObj.assemblyId = vm.assembly;
+        queryObj = Object.assign(queryObj, vm.buildQueryObj());
         // Change view to results and send GET query string
         this.$router.push(
           {
@@ -198,9 +186,34 @@ export default {
       vm.query = "MT : 151 T > C";
       document.getElementById("searchBar").focus();
     },
+    buildQueryObj: function () {
+      var vm = this;
+      var temp = vm.query.split(vm.regex).filter(Boolean);
+      var tempArray = [];
+      for (var i = 0; i < temp.length; i++) {
+        if (temp[i] != ":" && temp[i] != ">") {
+          tempArray.push(temp[i]);
+        }
+      }
+      var queryObj = {
+        referenceName: tempArray[0],
+        start: tempArray[1] > 0 ? tempArray[1] - 1 : 0,
+        referenceBases: tempArray[2],
+      };
+      // Determine if last element is a base of a variant type
+      if (vm.variantTypes.includes(tempArray[3])) {
+        // tempArray[3] is a variantType
+        queryObj["variantType"] = tempArray[3];
+      } else {
+        // tempArray[3] is an alternateBases
+        queryObj["alternateBases"] = tempArray[3];
+      }
+
+      return queryObj;
+    },
     validateInput: function () {
       var vm = this;
-      if (vm.regex.exec(vm.query)) {
+      if (vm.regex.test(vm.query)) {
         vm.validated = true;
       } else {
         vm.validated = false;

diff --git a/src/components/BeaconResultTileDetails.vue b/src/components/BeaconResultTileDetails.vue
@@ -145,9 +145,6 @@ export default {
 </script>
 
 <style scoped>
-.results-section {
-  /* text-align: center; */
-}
 .show-more {
   display: block;
   margin: 0 auto;

diff --git a/src/components/BeaconResultTileDetailsV2.vue b/src/components/BeaconResultTileDetailsV2.vue
@@ -149,8 +149,8 @@
                               "
                             >
                               <b-table-column v-slot="props">
-                                <b v-if="typeof props.row.key != 'number'"
-                                  >{{ props.row.key }}
+                                <b v-if="typeof props.row.key != 'number'">
+                                  {{ props.row.key }}
                                 </b>
                                 <b v-else>{{ getResultId(props.row.value) }}</b>
                               </b-table-column>
@@ -360,9 +360,6 @@ export default {
 #resultContent {
   border-bottom: 1px solid black;
 }
-.results-section {
-  /* text-align: center; */
-}
 .show-more {
   display: block;
   margin: 0 auto;

diff --git a/src/components/Footer.vue b/src/components/Footer.vue
@@ -142,7 +142,7 @@
               >
             </p>
             <p class="legal">
-              Copyright © ELIXIR 2019 |
+              Copyright © ELIXIR 2019 - {{ new Date().getFullYear() }} |
               <router-link
                 to="/tos"
                 title="Read the Terms of Service of ELIXIR Beacon Network"

diff --git a/src/views/Guide.vue b/src/views/Guide.vue
@@ -29,7 +29,7 @@
       system, while datasets may use either a 0- or a 1-based coordinate system
       depending on the dataset file type. 1-based queries made from the Beacon
       Network UI are substracted by one, and received at the Beacon APIs as
-      0-based.
+      0-based. <b>Note that:</b> Spaces are not enforced.
     </p>
     <h3>Advanced Search</h3>
     <p>

diff --git a/vue.config.js b/vue.config.js
@@ -1,7 +1,7 @@
 module.exports = {
   pages: {
     index: {
-      entry: "src/main.js"
-    }
-  }
+      entry: "src/main.js",
+    },
+  },
 };