Merge pull request #1049 from iobio/gene_4.9

Gene 4.9
iobio · Feb 23, 2024 · 995b471 · 995b471
2 parents 841564d + b85d297
commit 995b471
Show file tree

Hide file tree

Showing 8 changed files with 47 additions and 20 deletions.
diff --git a/client/app/components/pages/GeneHome.vue b/client/app/components/pages/GeneHome.vue
@@ -2335,6 +2335,9 @@ export default {
             var options = {'getKnownVariants': self.showKnownVariantsCard,
                 'getSfariVariants': (self.showSfariVariantsCard && !self.blacklistedGeneSelected),
                 'blacklistedGeneSelected': self.blacklistedGeneSelected };
+            options.analyzeCodingVariantsOnly = self.cohortModel.analyzeCodingVariantsOnly;
+            options.isBackground = false;
+
 
             self.cohortModel.promiseLoadData(self.selectedGene, self.selectedTranscript, options)
                 .then(function(resultMap) {

diff --git a/client/app/components/partials/GeneDiseaseTable.vue b/client/app/components/partials/GeneDiseaseTable.vue
@@ -70,7 +70,7 @@
       </v-badge>
     </div>
     <div  class="disease-table-body" style="padding-top:5px">
-      <div class="hpo-row" v-for="entry in entries" :key="entry.diseaseId">
+      <div class="hpo-row" v-for="entry in entries" :key="entry.key">
           <span class="hpo-launch" >
             <a :href="entry.url" target="_hpo">
               {{ entry.diseaseId }}
@@ -133,7 +133,9 @@ export default {
           self.entries.push({'diseaseId': geneDisorder.disease_id, 
                         'phenotypeInheritance': geneDisorder.inheritance,
                         'diseaseName': geneDisorder.disorder,
-                        'url': url })
+                        'url': url,
+                        'key':
+                           geneDisorder.disease_id + "-" + geneDisorder.disorder.replaceAll(" ", "_")})
 
         })
         self.entryCount = self.entries.length > 0 ? self.entries.length : ""

diff --git a/client/app/components/partials/GenePhenotypeTable.vue b/client/app/components/partials/GenePhenotypeTable.vue
@@ -280,7 +280,7 @@
     </div>
 
     <div  :class="`hpo-table-body` + ' ' + viewMode">
-      <div class="hpo-row patient-match" v-for="entry in hpoEntries" :key="entry.ontologyId">
+      <div class="hpo-row patient-match" v-for="entry in hpoEntries" :key="entry.key">
         <v-chip v-if="highlightMatches  && entry.match != ''" :class="`match-chip match-level-` + entry.matchLevel">
           {{ entry.match }}
         </v-chip>
@@ -354,7 +354,10 @@ export default {
       self.hasMatches = false;
 
       if (self.genePatientPhenotypes) {
-        self.hpoEntries = self.genePatientPhenotypes;
+        self.hpoEntries = self.genePatientPhenotypes.map(function(entry) {
+          entry.key = entry.ontologyId + "-" + entry.name.replaceAll(" ", "_")
+          return entry;
+        })
         self.entryCount = self.hpoEntries.length > 0 ? self.hpoEntries.length : ""
         self.hasMatches = self.hpoEntries.filter(function(hpoEntry) {
           return hpoEntry.match != ""
@@ -369,6 +372,7 @@ export default {
           let idx = 0;
           self.hpoEntries = data.hpoEntries.map(function(entry) {
             entry.ordinal = idx++;
+            entry.key = entry.ontologyId + "-" + entry.name.replaceAll(" ", "_")
             return entry;
           })
           self.hpoEntriesAll = self.hpoEntries;

diff --git a/client/app/components/viz/VariantInspectCard.vue b/client/app/components/viz/VariantInspectCard.vue
@@ -2253,7 +2253,7 @@ export default {
             return gnomAD;
 
         }
-        else if (this.globalApp.gnomADExtraMethod == this.globalApp.GNOMAD_METHOD_MERGED_ANNOTS &&
+        else if (this.globalApp.gnomADExtraMethod == this.globalApp.GNOMAD_METHOD_MERGE_ANNOTS &&
           (this.globalApp.gnomADExtraAll || (this.globalApp.gnomADExtra && this.selectedVariant.extraAnnot))) {
           let source      =  "gnomAD genomes"
           let infoPopup   = "gnomAD"

diff --git a/client/app/globals/GlobalApp.js b/client/app/globals/GlobalApp.js
@@ -9,7 +9,7 @@ class GlobalApp {
     this.tour                  = "";
     this.completedTour         = "";
 
-    this.version               = "4.9";
+    this.version               = "4.9a";
 
     this.GREEN_IOBIO           = "nv-green.iobio.io/";  // Must always stay at green to accommodate VEP service
 
@@ -53,10 +53,10 @@ class GlobalApp {
     // get gnomad extra info for all variants
     this.gnomADExtraAll       = true;
 
-    // how should we get the gnomad extra info?  'bcftools' or 'vepcustom'
-    this.GNOMAD_METHOD_BCFTOOLS   = "gnomad_merge_annots";
-    this.GNOMAD_METHOD_CUSTOM_VEP = "gnomad_custom_vep";
-    this.gnomADExtraMethod        = this.GNOMAD_METHOD_MERGE_ANNOTS;
+    // how should we get the gnomad extra info?  'merge annots' or 'cust vep'
+    this.GNOMAD_METHOD_MERGE_ANNOTS   = "gnomad_merge_annots";
+    this.GNOMAD_METHOD_CUSTOM_VEP     = "gnomad_custom_vep";
+    this.gnomADExtraMethod            = this.GNOMAD_METHOD_MERGE_ANNOTS;
 
 
     // How many genes can be analyzed in one session.  Set to null if no limitation.

diff --git a/client/app/models/CohortModel.js b/client/app/models/CohortModel.js
@@ -1069,7 +1069,7 @@ class CohortModel {
         })
 
       } else {
-        let theOptions = $.extend({'isMultiSample': self.mode == 'trio' && self.samplesInSingleVcf(), 'isBackground': false}, options);
+        let theOptions = $.extend(options, {'isMultiSample': self.mode == 'trio' && self.samplesInSingleVcf(), 'isBackground': false});
         self.promiseAnnotateVariants(theGene, theTranscript, theOptions)
         .then(function(resultMap) {
           // Flag bookmarked variants
@@ -1545,8 +1545,12 @@ class CohortModel {
             model.inProgress.loadingVariants = true;
           }
         })
-        options.analyzeCodingVariantsOnly = self.analyzeCodingVariantsOnly;
-        p = self.sampleMap['proband'].model.promiseAnnotateVariants(theGene, theTranscript, self.getCanonicalModels(), options)
+        let theOptions = $.extend({}, options)
+        theOptions.analyzeCodingVariantsOnly = self.analyzeCodingVariantsOnly;
+        theOptions.getKnownVariants = false;
+        theOptions.getSfariVariants = false;
+        theOptions.blacklistedGeneSelected = false;
+        p = self.sampleMap['proband'].model.promiseAnnotateVariants(theGene, theTranscript, self.getCanonicalModels(), theOptions)
         .then(function(resultMap) {
           if (!options.isBackground) {
             self.getCanonicalModels().forEach(function(model) {
@@ -1555,6 +1559,9 @@ class CohortModel {
           }
           theResultMap = resultMap;
         })
+        .catch(function(error) {
+          console.log(error)
+        })
         annotatePromises.push(p);
       } else {
         for (var rel in self.sampleMap) {
@@ -1564,8 +1571,13 @@ class CohortModel {
               model.inProgress.loadingVariants = true;
             }
             if (rel !== 'known-variants' && rel !== 'sfari-variants') {
-              options.analyzeCodingVariantsOnly = self.analyzeCodingVariantsOnly;
-              var p = model.promiseAnnotateVariants(theGene, theTranscript, [model], options)
+              let theOptions = $.extend({}, options)
+              theOptions.analyzeCodingVariantsOnly = self.analyzeCodingVariantsOnly;
+              theOptions.getKnownVariants = false;
+              theOptions.getSfariVariants = false;
+              theOptions.blacklistedGeneSelected = false;
+
+              var p = model.promiseAnnotateVariants(theGene, theTranscript, [model], theOptions)
                 .then(function(resultMap) {
                     for (var theRelationship in resultMap) {
                         if (!options.isBackground) {
@@ -1586,13 +1598,14 @@ class CohortModel {
       if (options.getKnownVariants && (!options.hasOwnProperty('bypassAnnotate') || options.bypassAnnotate == false)) {
         let p = self.promiseLoadKnownVariants(theGene, theTranscript)
         .then(function(resultMap) {
-          if (self.knownVariantViz === 'variants') {
+          if (self.knownVariantsViz === 'variants') {
             for (var rel in resultMap) {
               theResultMap[rel] = resultMap[rel];
             }
           }
         })
         .catch(function(error) {
+          console.log(error)
           reject(error)
         })
         annotatePromises.push(p);
@@ -1606,7 +1619,9 @@ class CohortModel {
                   theResultMap[rel] = resultMap[rel];
               }
             }
-          });
+           }).catch(function(error) {
+              console.log(error)
+           })
         annotatePromises.push(p);
       }
 
@@ -1617,7 +1632,10 @@ class CohortModel {
           self.promiseAnnotateWithClinvar(theResultMap, theGene, theTranscript, options.isBackground)
           .then(function(data) {
             resolve(data)
-          })          
+          })
+          .catch(function(error) {
+            console.log(error)
+          })
         } else {
           resolve(theResultMap)
         }

diff --git a/client/app/models/GeneModel.js b/client/app/models/GeneModel.js
@@ -1939,7 +1939,7 @@ class GeneModel {
   isKnownGene(geneName) {
     if (geneName in this.allKnownGeneNames) {
       return true;
-    } else if (geneName.toUpperCase() in allKnowGeneNames) {
+    } else if (geneName.toUpperCase() in this.allKnownGeneNames) {
       return true;
     } else {
       return false;

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "gene-iobio-vue",
-  "version": "4.9.0",
+  "version": "4.9.0a",
   "scripts": {
     "start": "DEBUG=http ./node_modules/nodemon/bin/nodemon.js --inspect --ignore client/ www.js",
     "build": "./node_modules/webpack/bin/webpack.js",