Merge pull request #847 from broadinstitute/master

Merge remote-tracking branch 'origin/master' into pankbase-main

configs/vue.config.radiant.js

@@ -0,0 +1,317 @@
+/* We define all the pages first in an object that can be modified BEFORE being
+ * exported so we can add/remove pages based on build type.
+ */
+
+let pages = {
+    index: {
+        entry: "src/portals/Radiant/views/Index/main.js",
+        template: "public/index.html",
+        filename: "index.html",
+        title: "Home",
+        chunks: ["chunk-vendors", "chunk-common", "index"],
+    },
+    debug: {
+        entry: "src/views/Debug/main.js",
+        template: "public/index.html",
+        filename: "debug.html",
+        title: "Debug Page",
+        chunks: ["chunk-vendors", "chunk-common", "debug"],
+    },
+    phenotype: {
+        entry: "src/views/Phenotype/main.js",
+        template: "public/index.html",
+        filename: "phenotype.html",
+        title: "Phenotype",
+        chunks: ["chunk-vendors", "chunk-common", "phenotype"],
+    },
+    region: {
+        entry: "src/views/Region/main.js",
+        template: "public/index.html",
+        filename: "region.html",
+        title: "Region Info",
+        chunks: ["chunk-vendors", "chunk-common", "region"],
+    },
+    variant: {
+        entry: "src/portals/Radiant/views/Variant/main.js",
+        template: "public/index.html",
+        filename: "variant.html",
+        title: "Variant Info",
+        chunks: ["chunk-vendors", "chunk-common", "variant"],
+    },
+    gene: {
+        entry: "src/portals/Radiant/views/Gene/main.js",
+        template: "public/index.html",
+        filename: "gene.html",
+        title: "Gene Info",
+        chunks: ["chunk-vendors", "chunk-common", "gene"],
+    },
+    datasets: {
+        entry: "src/views/Datasets/main.js",
+        template: "public/index.html",
+        filename: "datasets.html",
+        title: "Datasets",
+        chunks: ["chunk-vendors", "chunk-common", "datasets"],
+    },
+    dinspector: {
+        entry: "src/views/DatasetInspector/main.js",
+        template: "public/index.html",
+        filename: "dinspector.html",
+        title: "Dataset Inspector",
+        chunks: ["chunk-vendors", "chunk-common", "dinspector"],
+    },
+    downloads: {
+        entry: "src/views/Downloads/main.js",
+        template: "public/index.html",
+        filename: "downloads.html",
+        title: "Downloads",
+        chunks: ["chunk-vendors", "chunk-common", "downloads"],
+    },
+    policies: {
+        entry: "src/views/Policies/main.js",
+        template: "public/index.html",
+        filename: "policies.html",
+        title: "Policies",
+        chunks: ["chunk-vendors", "chunk-common", "policies"],
+    },
+    about: {
+        entry: "src/views/About/main.js",
+        template: "public/index.html",
+        filename: "about.html",
+        title: "About",
+        chunks: ["chunk-vendors", "chunk-common", "about"],
+    },
+    collaborate: {
+        entry: "src/views/Collaborate/main.js",
+        template: "public/index.html",
+        filename: "collaborate.html",
+        title: "Collaborate",
+        chunks: ["chunk-vendors", "chunk-common", "collaborate"],
+    },
+    resources: {
+        entry: "src/views/Resources/main.js",
+        template: "public/index.html",
+        filename: "resources.html",
+        title: "Resources",
+        chunks: ["chunk-vendors", "chunk-common", "resources"],
+    },
+    publications: {
+        entry: "src/views/Publications/main.js",
+        template: "public/index.html",
+        filename: "publications.html",
+        title: "Publications",
+        chunks: ["chunk-vendors", "chunk-common", "publications"],
+    },
+    news: {
+        entry: "src/views/News/main.js",
+        template: "public/index.html",
+        filename: "news.html",
+        title: "News",
+        chunks: ["chunk-vendors", "chunk-common", "news"],
+    },
+    contacts: {
+        entry: "src/views/Contacts/main.js",
+        template: "public/index.html",
+        filename: "contacts.html",
+        title: "Contacts",
+        chunks: ["chunk-vendors", "chunk-common", "contacts"],
+    },
+    kplab: {
+        entry: "src/views/KPLab/main.js",
+        template: "public/index.html",
+        filename: "kplab.html",
+        title: "KP Lab",
+        chunks: ["chunk-vendors", "chunk-common", "kplab"],
+    },
+    apis: {
+        entry: "src/views/Apis/main.js",
+        template: "public/index.html",
+        filename: "apis.html",
+        title: "APIs",
+        chunks: ["chunk-vendors", "chunk-common", "apis"],
+    },
+    epigeneticdatasets: {
+        entry: "src/views/EpigeneticDatasets/main.js",
+        template: "public/index.html",
+        filename: "epigeneticdatasets.html",
+        title: "Epigenetic Datasets",
+        chunks: ["chunk-vendors", "chunk-common", "epigeneticdatasets"],
+    },
+    epigenomicdatasets: {
+        entry: "src/views/EpigenomicDatasets/main.js",
+        template: "public/index.html",
+        filename: "epigenomicdatasets.html",
+        title: "Epigenomic Datasets",
+        chunks: ["chunk-vendors", "chunk-common", "epigenomicdatasets"],
+    },
+    ampt2dpartnership: {
+        entry: "src/views/AmpT2dPartnership/main.js",
+        template: "public/index.html",
+        filename: "ampt2dpartnership.html",
+        title: "AMP T2D Partnership",
+        chunks: ["chunk-vendors", "chunk-common", "ampt2dpartnership"],
+    },
+    effectorgenes: {
+        entry: "src/views/EffectorGenes/main.js",
+        template: "public/index.html",
+        filename: "effectorgenes.html",
+        title: "Predicted Effector Genes Research Methods",
+        chunks: ["chunk-vendors", "chunk-common", "effectorgenes"],
+    },
+    eglmethod: {
+        entry: "src/views/EglMethod/main.js",
+        template: "public/index.html",
+        filename: "method.html",
+        title: "Research Method",
+        chunks: ["chunk-vendors", "chunk-common", "eglmethod"],
+    },
+    hugecalculator: {
+        entry: "src/views/HuGeCalculator/main.js",
+        template: "public/index.html",
+        filename: "hugecalculator.html",
+        title: "HuGe Calculator",
+        chunks: ["chunk-vendors", "chunk-common", "hugecalculator"],
+    },
+
+    genefinder: {
+        entry: "src/views/GeneFinder/main.js",
+        template: "public/index.html",
+        filename: "genefinder.html",
+        title: "Gene Finder",
+        chunks: ["chunk-vendors", "chunk-common", "genefinder"],
+    },
+    signalsifter: {
+        entry: "src/views/SignalSifter/main.js",
+        template: "public/index.html",
+        filename: "signalsifter.html",
+        title: "Signal Sifter",
+        chunks: ["chunk-vendors", "chunk-common", "signalsifter"],
+    },
+    complicationsviewer: {
+        entry: "src/views/ComplicationsViewer/main.js",
+        template: "public/index.html",
+        filename: "complicationsviewer.html",
+        title: "Complications Viewer",
+        chunks: ["chunk-vendors", "chunk-common", "complicationsviewer"],
+    },
+
+    page404: {
+        entry: "src/views/404/main.js",
+        template: "public/index.html",
+        filename: "404.html",
+        title: "Page Not Found",
+        chunks: ["chunk-vendors", "chunk-common", "page404"],
+    },
+    gait: {
+        entry: "src/views/GAIT/main.js",
+        template: "public/index.html",
+        filename: "gait.html",
+        title: "Genetic Association Interactive Tool",
+        chunks: ["chunk-vendors", "chunk-common", "gait"],
+    },
+    gait2: {
+        entry: "src/views/GAIT2/main.js",
+        template: "public/index.html",
+        filename: "ncgait.html",
+        title: "Non-Coding Genetic Association Interactive Tool",
+        chunks: ["chunk-vendors", "chunk-common", "gait2"],
+    },
+    project: {
+        entry: "src/views/Project/main.js",
+        template: "public/index.html",
+        filename: "project.html",
+        title: "Project",
+        chunks: ["chunk-vendors", "chunk-common", "project"],
+    },
+    variantsearch: {
+        entry: "src/views/VariantSearch/main.js",
+        template: "public/index.html",
+        filename: "variantsearch.html",
+        title: "Variant Search",
+        chunks: ["chunk-vendors", "chunk-common", "variantsearch"],
+    },
+    research: {
+        entry: "src/views/Papers/Research/main.js",
+        template: "public/index.html",
+        filename: "research.html",
+        title: "Research",
+        chunks: ["chunk-vendors", "chunk-common", "research"],
+    },
+    egggenerator: {
+        entry: "src/views/EggGenerator/main.js",
+        template: "public/index.html",
+        filename: "egggenerator.html",
+        title: "Exome Gene-Level Group-file Generator",
+        chunks: ["chunk-vendors", "chunk-common", "egggenerator"],
+    },
+    help: {
+        entry: "src/views/Help/main.js",
+        template: "public/index.html",
+        filename: "help.html",
+        title: "Help",
+        chunks: ["chunk-vendors", "chunk-common", "help"],
+    },
+};
+
+// remove the debug page in production
+if (process.env.NODE_ENV === "production") {
+    delete pages.debug;
+}
+
+module.exports = {
+    devServer: {
+        writeToDisk: true, // https://webpack.js.org/configuration/dev-server/#devserverwritetodisk-
+    },
+    configureWebpack: (config) => {
+        let bioindex_dev = process.env.BIOINDEX_DEV;
+        let bioindex_host = "https://bioindex.hugeamp.org"; // production by default
+        //set private bioindex host if variable is defined, otherwise use default
+        let bioindex_host_private =
+            process.env.BIOINDEX_HOST_PRIVATE || "https://bioindex.hugeamp.org";
+
+        if (!!bioindex_dev) {
+            bioindex_host =
+                bioindex_dev == "localhost"
+                    ? "http://localhost:5000"
+                    : "https://bioindex-dev.hugeamp.org";
+        }
+
+        // output which vue config file and bioindex is being used
+        console.log(
+            `VUE_CONFIG_PATH=${process.env.VUE_CLI_SERVICE_CONFIG_PATH}; BIOINDEX_DEV=${process.env.BIOINDEX_DEV}; using ${bioindex_host} and ${bioindex_host_private}`
+        );
+
+        // add the transform rule for bioindex
+        config.module.rules.push({
+            test: /bioIndexUtils\.js$/,
+            loader: "string-replace-loader",
+            options: {
+                search: "SERVER_IP_ADDRESS",
+                replace: bioindex_host,
+                flags: "g",
+            },
+        });
+
+        // add the transform rule for bioindex
+        // Helen 2021-06-17
+        config.module.rules.push({
+            test: /bioIndexUtils\.js$/,
+            loader: "string-replace-loader",
+            options: {
+                search: "SERVER_IP_PRIVATE",
+                replace: bioindex_host_private,
+                flags: "g",
+            },
+        });
+
+        // create inline maps for dev builds
+        if (process.env.NODE_ENV !== "production") {
+            //config.devtool = "inline-source-map";
+
+            //https://stackoverflow.com/questions/48047150/chrome-extension-compiled-by-webpack-throws-unsafe-eval-error
+            config.devtool = "cheap-module-source-map";
+        }
+    },
+    outputDir: "portals/Radiant/dist",
+    productionSourceMap: false,
+    pages,
+};

src/components/GeneAssociationsMasks.vue

@@ -132,14 +132,15 @@ export default Vue.component("GeneAssociationsMasks", {
         },
         //filter associations that only exist in the phenotypeMap
         filteredAssociations() {
-            let assocs = !this.filter
+            return this.associations;
+            /*let assocs = !this.filter
                 ? this.associations
                 : this.associations.filter(this.filter);
             return (
                 assocs.filter((row) => {
                     return this.phenotypeMap[row.phenotype];
                 }) || []
-            );
+            );*/
         },
     },
     methods: {

src/components/researchPortal/ResearchInSectionSearch.vue

@@ -16,8 +16,7 @@
 						<span v-html="parameter.label"></span>
 					</div>
 
-					<select v-if="parameter.type == 'api list' &&
-						parameterOptions[paramIndex].length <= 10"
+					<select v-if="parameter.type == 'api list'"
 							:id="'section_search_param_' + parameter.parameter"  class="custom-select custom-select-search"
 							@change="updateSearchInputByEvent($event, paramIndex, parameter.parameter)">
 
@@ -27,11 +26,11 @@
 									v-html="param.label.trim()"></option>
 					</select>
 
-					<template v-if="parameter.type == 'api list' && parameterOptions[paramIndex].length > 10">
+					<!--<template v-if="parameter.type == 'api list' && parameterOptions[paramIndex].length > 10">
 						<input v-model="paramSearch[paramIndex]" class="form-control"
 							@keyup="getListOptions($event, parameter)" :id="'section_search_param_' + parameter.parameter" />
 
-						<!--<div :id="'listOptions' + parameter.parameter" class="custom-select custom-select-search long-list"
+						<div :id="'listOptions' + parameter.parameter" class="custom-select custom-select-search long-list"
 							:size="!!listOptions[parameter.parameter] && listOptions[parameter.parameter].length >= 5 ? 5 : 'auto'"
 							:style="!listOptions[parameter.parameter] || listOptions[parameter.parameter].length == 0
 								? 'display:none !important;'
@@ -46,8 +45,8 @@
 								)
 									" class="custom-select-a-option"></a>
 							</template>
-						</div>-->
-					</template>
+						</div>
+					</template>-->
 
 					<select
 						v-if="parameter.type == 'list' &&

src/components/researchPortal/ResearchMultiSectionsSearch.vue

@@ -59,7 +59,7 @@
 							<input v-model="paramSearch[paramIndex]" class="form-control" @keyup="getGenes($event)"
 								:id="'search_param_' + parameter.parameter" />
 
-							<div class="custom-select custom-select-search" :size="kpGenes.length >= 5 ? 5 : 'auto'" :style="kpGenes.length == 0
+							<div class="custom-select custom-select-search" :size="kpGenes.length >= 5 ? 5 : 'auto'" :style="kpGenes.length == 0 || checkFocus('search_param_' + parameter.parameter) == false
 								? 'display:none !important;'
 								: ''
 								">
@@ -202,6 +202,13 @@ export default Vue.component("research-multi-sections-search", {
 		
 	},
 	methods: {
+		checkFocus(ID) {
+			if (!document.getElementById(ID).matches(':focus')) {
+				return false;
+			} else {
+				return true;
+			}
+		},
 		async getList(apiPoint, INDEX) {
 			
 			let searchPoint = apiPoint.url;