Merge pull request #893 from BV-BRC/beta

Prod update Oct 17 2024
BV-BRC · Oct 17, 2024 · 2c281bf · 2c281bf
2 parents 615621f + 35dbb3a
commit 2c281bf
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Showing 8 changed files with 146 additions and 20 deletions.
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "p3-web",
-  "version": "3.40.2",
+  "version": "3.41.1",
   "private": true,
   "scripts": {
     "start": "node ./bin/p3-web",

diff --git a/public/js/p3/widget/AdvancedSearchFields.js b/public/js/p3/widget/AdvancedSearchFields.js
@@ -881,7 +881,10 @@ define([], function () {
       },
       {
         field: 'segment', type: 'str', facet: true, facet_hidden: false, search: true
-      }
+      },
+      {
+        field: 'additional_metadata', type: 'str', facet: true, facet_hidden: false, search: true
+      },
     ],
     'subsystem': [
       {

diff --git a/public/js/p3/widget/SFVTGrid.js b/public/js/p3/widget/SFVTGrid.js
@@ -35,10 +35,12 @@ define([
       sf_category: {label: 'SF Category', field: 'sf_category', hidden: false},
       segments: {label: 'Reference Positions', field: 'segments', hidden: false},
       source_strain: {label: 'Source Strain', field: 'source_strain', hidden: false},
+      product: {label: 'Product', field: 'product', hidden: false},
 
+      additional_metadata: {label: 'Additional Metadata', field: 'additional_metadata', hidden: true},
       segment: {label: 'Segment', field: 'segment', hidden: true},
       subtype: {label: 'Subtype', field: 'subtype', hidden: true},
-      comments: {label: 'Comments', field: 'comments', hidden: true},
+      comments: {label: 'Comments', field: 'comments', hidden: true}
       //feature_type: {label: 'Evidence', field: 'feature_type', hidden: false}
     },
     startup: function () {

diff --git a/public/js/p3/widget/search/SFVTSearch.js b/public/js/p3/widget/search/SFVTSearch.js
@@ -1,11 +1,11 @@
 define([
   'dojo/_base/declare', 'dojo/_base/lang', 'dojo/store/Memory', 'dojo/text!./templates/SFVTSearch.html', 'dojo/query',
   './TextInputEncoder', './SearchBase', './FacetStoreBuilder', './PathogenGroups', '../../util/PathJoin', 'dojo/request/xhr',
-  'dijit/Dialog', 'dojo/on'
+  'dijit/Dialog', 'dojo/on', 'dojo/when', 'dojo/dom-construct'
 ], function (
   declare, lang, Memory, template, query,
   TextInputEncoder, SearchBase, storeBuilder, pathogenGroupStore, PathJoin, xhr,
-  Dialog, on
+  Dialog, on, when, domConstruct
 ) {
 
   const influenzaSegmentMapping = {
@@ -22,6 +22,10 @@ define([
     'NS2': '8'
   };
 
+  const otherPathogenGroups = {
+    '10244': 'Monkeypox virus'
+  };
+
   function sanitizeInput(str) {
     return str.replace(/\(|\)|\.|\*|\||\[|\]/g, '');
   }
@@ -42,6 +46,7 @@ define([
     segmentOptions: ['11320'],
     sfvtSequenceErrorMessage: 'There are too many Sequence Feature hits. Please refine Sequence Feature Variant Type Sequence pattern to narrow down the results.',
     sfvtMaxLimit: 300,
+    mpoxGeneProductMapping: {},
 
     startup: function () {
       let sfvtSeqSearchButton = query('#sfvt-seq-search')[0];
@@ -80,12 +85,23 @@ define([
     postCreate: function () {
       this.inherited(arguments);
 
+      this.additionalMetadataNode.addOption([
+        {
+          value: 'Clade I',
+          label: 'Clade I'
+        }, {
+          value: 'Clade II',
+          label: 'Clade II'
+        }
+      ]);
       storeBuilder('sequence_feature', 'taxon_id').then(lang.hitch(this, (store) => {
         // Display correct names based on taxon id
         for (let item of store.data) {
           const taxon = pathogenGroupStore.data.find(pathogen => pathogen.id == item.id);
           if (taxon) {
             item.name = taxon.name;
+          } else if (otherPathogenGroups[item.id]) {
+            item.name = otherPathogenGroups[item.id];
           }
         }
         this.pathogenGroupNode.store = store;
@@ -103,6 +119,27 @@ define([
             });
         }
       }));
+
+      // Retrieve product values for gene
+      let self = this;
+      when(xhr.post(PathJoin(window.App.dataAPI, '/sequence_feature/'), {
+        handleAs: 'json',
+        headers: {
+          Accept: 'application/solr+json',
+          'Content-Type': 'application/solrquery+x-www-form-urlencoded',
+          'X-Requested-With': null,
+          Authorization: (window.App.authorizationToken || '')
+        },
+        data: 'q=taxon_id:10244&fl=gene,product&group=true&group.field=gene'
+      }), function (response) {
+        if (response && response.grouped && response.grouped.gene) {
+          response.grouped.gene.groups.forEach(group => {
+            const gene = group.groupValue;
+            const product = group.doclist.docs[0].product;
+            self.mpoxGeneProductMapping[gene] = product;
+          });
+        }
+      });
     },
 
     onPathogenChange: function () {
@@ -118,6 +155,10 @@ define([
       this.subtypeNNode.reset();
       this.geneNode.set('options', []);
       this.geneNode.reset();
+      this.additionalMetadataNode.set('value', []);
+      this.additionalMetadataNode._updateSelection();
+      //this.additionalMetadataNode.set('options', []);
+      //this.additionalMetadataNode.reset();
 
       //Update virus type multi select values with selected pathogen
       const condition = 'taxon_id:' + taxonId;
@@ -150,33 +191,79 @@ define([
       }));
 
       storeBuilder('sequence_feature', 'gene', condition).then(lang.hitch(this, (store) => {
-        let geneOptions = []
+        let geneOptions = [];
         for (let item of store.data) {
-          const segmentNo = influenzaSegmentMapping[item.name];
-          geneOptions.push(
-            {
-              value: item.name,
-              label: segmentNo ? `${segmentNo} / ${item.name}` : item.name
-            });
+          if (taxonId === this.defaultTaxonId) { // Influenza
+            const segmentNo = influenzaSegmentMapping[item.name];
+            geneOptions.push(
+              {
+                value: item.name,
+                label: segmentNo ? `${segmentNo} / ${item.name}` : item.name
+              });
+          } else {
+            const product = this.mpoxGeneProductMapping[item.name];
+            geneOptions.push(
+              {
+                value: item.name,
+                label: product ? `${item.name} - ${product}` : item.name
+              });
+          }
         }
 
         geneOptions.sort((a, b) => a.label.localeCompare(b.label));
 
         this.geneNode.addOption(geneOptions);
       }));
 
+      const customFilters = query('.customFilter');
       if (this.segmentOptions.includes(taxonId)) {
+        const options = query('#options1')[0];
+        customFilters.forEach(function (container) {
+          domConstruct.place(container, options, 'last');
+        });
+
         query('.proteinOptions').style('display', 'none');
         query('.segmentOptions').style('display', 'block');
       } else {
+        const options = query('#options2')[0];
+        customFilters.forEach(function (container) {
+          domConstruct.place(container, options, 'last');
+        });
+
         query('.segmentOptions').style('display', 'none');
         query('.proteinOptions').style('display', 'block');
       }
 
+      // Specific monkeypox option
+      if (taxonId === '10244') {
+        /*storeBuilder('sequence_feature', 'additional_metadata', condition).then(lang.hitch(this, (store) => {
+          let metadataOptions = [];
+          for (let item of store.data) {
+            metadataOptions.push({
+              value: item.name,
+              label: item.name
+            });
+          }
+
+          this.additionalMetadataNode.addOption(metadataOptions);
+        }));*/
+
+        query('.monkeypox').style('display', 'block');
+      } else {
+        query('.monkeypox').style('display', 'none');
+      }
+
       query('.sfvtOptions').style('display', 'block');
       query('#pathogenInfoDiv').style('display', 'none');
     },
 
+    buildDefaultColumns: function () {
+      const taxonId = this.pathogenGroupNode.value;
+
+      // Reorganize table columns for Monkeypox virus
+      return taxonId === '10244' ? '-source_strain,additional_metadata' : '';
+    },
+
     buildFilter: async function () {
       this.sfvtSequenceMessage.innerHTML = '';
 
@@ -250,6 +337,15 @@ define([
         sfQueryArr.push(`in(sf_category,(${sequenceFeatureTypeValue.join(',')}))`);
       }
 
+      const additionalMetadataValue = this.additionalMetadataNode.get('value');
+      if (additionalMetadataValue.length === 1) {
+        filterArr.push(`eq(additional_metadata,"${TextInputEncoder(sanitizeInput(additionalMetadataValue[0]))}")`);
+        sfQueryArr.push(`eq(additional_metadata,${TextInputEncoder(sanitizeInput(additionalMetadataValue[0]))})`);
+      } else if (additionalMetadataValue.length > 1) {
+        filterArr.push(`or(${additionalMetadataValue.map(v => `eq(additional_metadata,"${TextInputEncoder(sanitizeInput(v))}")`)})`);
+        sfQueryArr.push(`in(additional_metadata,(${additionalMetadataValue.join(',')}))`);
+      }
+
       /*const startValue = parseInt(this.aaCoordinatesStartNode.get('value'));
       if (!isNaN(startValue)) {
         // gt

diff --git a/public/js/p3/widget/search/SearchBase.js b/public/js/p3/widget/search/SearchBase.js
@@ -69,6 +69,8 @@ define([
     },
     buildFilter: function () {
     },
+    buildDefaultColumns: function () {
+    },
     _buildAdvancedQuery: function () {
       return Object.keys(this._Searches).map((idx) => {
         const col = this._Searches[idx]
@@ -143,11 +145,15 @@ define([
 
       const query = this.buildQuery();
       const filter = await this.buildFilter();
+      const defaultColumns = this.buildDefaultColumns();
 
       let url = this.resultUrlBase + query + this.resultUrlHash;
       if (filter) {
         url += '&filter=' + filter;
       }
+      if (defaultColumns) {
+        url += '&defaultColumns=' + defaultColumns;
+      }
       Topic.publish('/navigate', { href: url });
     }
   })

diff --git a/public/js/p3/widget/search/templates/SFVTSearch.html b/public/js/p3/widget/search/templates/SFVTSearch.html
@@ -3,6 +3,7 @@
         .dojoxCheckedMultiSelectWrapper {
             width: 100%;
             height: 100% !important;
+            max-height: 250px;
         }
     </style>
     <div class="appTemplate">
@@ -54,21 +55,24 @@ <h3>${searchAppName}</h3>
                                 data-dojo-attach-point="virusTypeNode" multiple style="height: 100%"></select>
                     </div>
                 </div>-->
-                <div class="appFieldLong" style="display: flex;">
+                <div class="appFieldLong" style="display: flex;" id="options1">
                     <div style="box-sizing: border-box;margin-right: 50px;min-width: 120px;">
                         <div class="headerrow segmentOptions">
                             <label class="appBoxLabel">Segment / Protein</label>
                         </div>
+                        <div class="headerrow proteinOptions">
+                            <label class="appBoxLabel">Gene - Protein</label>
+                        </div>
                         <div class="appRow">
                             <div class="appFieldLong">
                                 <select data-dojo-type="dojox/form/CheckedMultiSelect" name="genes"
                                         data-dojo-props="disabled:false"
                                         data-dojo-attach-event="onChange: onSegmentChange"
-                                        data-dojo-attach-point="geneNode" multiple style="height: 100%"></select>
+                                        data-dojo-attach-point="geneNode" multiple style="height: 100%;"></select>
                             </div>
                         </div>
                     </div>
-                    <div style="flex: 1; box-sizing: border-box;">
+                    <div id="sequenceFeatureType" class="customFilter" style="flex: 1; box-sizing: border-box;">
                         <div class="headerrow">
                             <label class="appBoxLabel">Sequence Feature Type</label>
                         </div>
@@ -81,7 +85,21 @@ <h3>${searchAppName}</h3>
                             </div>
                         </div>
                     </div>
+                    <div id="cladeType" class="monkeypox customFilter" style="flex: 1; box-sizing: border-box;">
+                        <div class="headerrow ">
+                            <label class="appBoxLabel">Clade</label>
+                        </div>
+                        <div class="appRow monkeypox">
+                            <div class="appFieldLong">
+                                <select data-dojo-type="dojox/form/CheckedMultiSelect" name="additional_metadata"
+                                        data-dojo-props="disabled:false"
+                                        data-dojo-attach-point="additionalMetadataNode" multiple
+                                        style="height: 100%"></select>
+                            </div>
+                        </div>
+                    </div>
                 </div>
+                <div class="appFieldLong" style="display: flex;" id="options2"></div>
                 <div class="headerrow subtypeOptions" style="display: none;">
                     <label class="appBoxLabel">Subtype</label>
                 </div>
@@ -114,7 +132,8 @@ <h3>${searchAppName}</h3>
                     <div class="appFieldLong">
                         <div data-dojo-type="dijit/form/TextBox" data-dojo-props="placeHolder:'eg. *RERE*'"
                              data-dojo-attach-point="sfvtSequenceNode" name="sfvtSequence" style="width: 500px"></div>
-                        <div class="warning" data-dojo-attach-point="sfvtSequenceMessage" style="font-size: 0.9em"></div>
+                        <div class="warning" data-dojo-attach-point="sfvtSequenceMessage"
+                             style="font-size: 0.9em"></div>
                     </div>
                 </div>
                 <!--<div class="headerrow">
@@ -141,7 +160,8 @@ <h3>${searchAppName}</h3>
         <div class="appSubmissionArea sfvtOptions" style="display: none;">
             <div style="margin-top: 10px; text-align:center;">
                 <div data-dojo-type="dijit/form/Button"
-                     data-dojo-attach-event="onClick: onReset">Reset</div>
+                     data-dojo-attach-event="onClick: onReset">Reset
+                </div>
                 <div data-dojo-attach-point="submitButton"
                      type="submit" data-dojo-type="dijit/form/Button">Search
                 </div>

diff --git a/public/js/p3/widget/viewer/Taxonomy.js b/public/js/p3/widget/viewer/Taxonomy.js
@@ -96,7 +96,8 @@ define([
         }
 
         // SFVT
-        if (this.taxonomy.lineage_names.includes('Influenza A virus')) {
+        if (this.taxonomy.lineage_names.includes('Influenza A virus') ||
+          this.taxonomy.lineage_names.includes('Monkeypox virus')) {
           if (!this.sfvt) {
             this.viewer.addChild(this.sfvt);
           }

diff --git a/views/pages/team.ejs b/views/pages/team.ejs
@@ -40,8 +40,6 @@
                                 <li>Roshni Bhattacharya</li>
                                 <li>Anna Capria</li>
                                 <li>Mehmet Kuscuoglu</li>
-                                <li>Jian Lu</li>
-                                <li>Catherine Macken</li>
                                 <li>Lucy Stewart</li>
                                 <li>Gene Tan</li>
                                 <li>Christian Zmasek</li>
-Original file line number
+Diff line change
@@ Expand Up / @@ -881,7 +881,10 @@ define([], function () { @@
           },
           {
             field: 'segment', type: 'str', facet: true, facet_hidden: false, search: true
-          }
+          },
+          {
+            field: 'additional_metadata', type: 'str', facet: true, facet_hidden: false, search: true
+          },
         ],
         'subsystem': [
           {
@@ Expand Down @@