#43 Now that we are using async service for gene typeahead, we can de…

…crease the memory footprint of the app significantly by removing genes.json (~10MB). Also, GeneModel was upgraded based on the latest functionality in gene.iobio (v 4.11), which utilizes HGNC gene synonymns in the latest version of the geneinfo service. The GeneModel also contains new functionality for gene:phenotype and gene:disease associations, which can now be shown in the rnasplice app's gene card.
iobio · Sep 24, 2024 · 1324ad0 · 1324ad0
1 parent 6059994
commit 1324ad0
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Showing 6 changed files with 1,029 additions and 354 deletions.
diff --git a/src/App.vue b/src/App.vue
@@ -5,7 +5,6 @@
       ref="ref_Navigation"
       :geneModel="geneModel"
       :appVersion="appVersion"
-      :genes="genes"
       :alerts="appAlerts"
       :alertCounts="appAlertCounts"
       :sampleNames="sampleNames"
@@ -81,7 +80,6 @@
          <SpliceJunctionHome
           ref="ref_SpliceJunctionHome"
           :loadInfo="loadInfo"
-          :genes="genes"
           :searchedGene="searchedGene"
           :selectedGene="selectedGene"
           :alerts="appAlerts"
@@ -126,9 +124,6 @@ import ObjectDetails      from './components/ObjectDetails.vue';
 import LegendPanel        from './components/LegendPanel.vue';
 
 
-import genesData          from '@/data/genes.json'
-
-
 import  qs  from 'qs'
 
 
@@ -147,8 +142,6 @@ export default {
   data: () => ({
     appVersion:  import.meta.env.PACKAGE_VERSION,
 
-    genes:       genesData,
-
     geneModel: null,
 
     searchedGene: null,

diff --git a/src/components/Navigation.vue b/src/components/Navigation.vue
@@ -18,20 +18,6 @@
 
       <v-spacer></v-spacer>
 
-      <!--<div id="search-gene-box" style="min-width:200px">
-        <v-text-field id="search-gene-input" class="pl-2"
-        hide-details
-        v-model="searchedGeneInput"
-        density="compact"
-        label="Gene"
-        prepend-icon="mdi-magnify"
-        />
-        <Typeahead  v-model="searchedGene"
-        target="#search-gene-input"
-        :data="genes"
-        item-key="gene_name" />
-      </div>
-      -->
 
       <div id="search-gene-box" style="min-width:200px">
           <v-text-field id="search-gene-name"

diff --git a/src/components/SpliceJunctionHome.vue b/src/components/SpliceJunctionHome.vue
@@ -90,7 +90,6 @@ import { reject } from 'async'
     },
     props: {
       loadInfo: Object,
-      genes: Array,
       genomeBuild: Array,
 
       searchedGene: Object,
@@ -171,8 +170,9 @@ import { reject } from 'async'
                                                       true,
                                                       { DEFAULT_BUILD: 'GRCh38' });
         self.geneModel =         new GeneModel(self.globalApp,
-                                              self.genomeBuildHelper)
-        self.geneModel.setAllKnownGenes(self.genes)
+                                              self.genomeBuildHelper,
+                                              self.launchedFromMosaic)
+
         self.geneModel.addEventListener("alertIssued", function(eventArgs) {
           let [type, message, genes, details] = eventArgs
           self.addAppAlert(type, message, genes, details)
@@ -243,15 +243,8 @@ import { reject } from 'async'
             loadInfo.genes = genes;
             let promises = []
             if (genes && genes.length > 0) {
-              genes.forEach(function(geneName){
-                if (self.geneModel.isKnownGene(geneName)) {
-                  let p = self.geneModel.promiseAddGeneName(geneName)
-                  promises.push(p)
-                } else {
-                  self.addAppAlert("warn", "Bypassing unknown gene <pre>" + geneName + "</pre>.")
-                }
-              })
-              return Promise.all(promises)
+              return self.geneModel.promiseAddGenesOrAliases(genes);
+              
             } else {
               return Promise.resolve();
             }
@@ -297,7 +290,7 @@ import { reject } from 'async'
         let self = this;
         self.geneModel.promiseAddGeneName(geneName)
         .then(function() {
-          self.geneModel.promiseGetGeneObject(geneName)
+          self.geneModel.promiseGetCachedGeneObject(geneName, true)
           .then(function(theGeneObject) {
             self.geneModel.adjustGeneRegion(theGeneObject);
             self.geneRegionStart = theGeneObject.start;

diff --git a/src/data/genes.json b/src/data/genes.json
diff --git a/src/globals/GlobalApp.js b/src/globals/GlobalApp.js
@@ -11,8 +11,10 @@ class GlobalApp {
     this.HTTP_SERVICES          = null;
     this.useSSL                = true;
     this.geneInfoServer        = null;
+    this.geneToPhenoServer     = null;
     this.genomeBuildServer     = null;
-
+    this.phenolyzerOnlyServer  = null;
+    this.hpoLookupUrl          = null;
   }
 
 
@@ -24,7 +26,12 @@ class GlobalApp {
       }
 
       this.geneInfoServer            = this.HTTP_SERVICES + "/geneinfo/";
+      this.geneToPhenoServer         = this.HTTP_SERVICES + "/gene2pheno/";
       this.genomeBuildServer         = this.HTTP_SERVICES + "/genomebuild/"
+      this.phenolyzerOnlyServer      = this.HTTP_SERVICES + "/phenolyzer/";
+      this.hpoLookupUrl              = this.HTTP_SERVICES + "/hpo/hot/lookup/?term=";
+
+
   }
 
   initServices(useMosaicBackend) {