Pigean geneset fix (#811)

* fixes issue where empty genes do not display but instead leave preexisting data

* working toward a geneset page for all traits

* remove superfluous console log

* bioindex util constant for the list of all trait groups

* correct autocomplete options

* gene and geneset single search

src/utils/bioIndexUtils.js

@@ -141,6 +141,7 @@ async function processRequest(req, onResolve, onError, onLoad, limitWhile) {
 export const DEFAULT_SIGMA = 2;
 export const DEFAULT_GENESET_SIZE = "small";
 export const DEFAULT_TRAIT_GROUP = "all";
+export const TRAIT_GROUPS = ["portal", "gcat_trait", "rare_v2"];
 
 export default {
     query,
@@ -152,5 +153,6 @@ export default {
     BIO_INDEX_HOST_PRIVATE,
     DEFAULT_SIGMA,
     DEFAULT_GENESET_SIZE,
-    DEFAULT_TRAIT_GROUP
+    DEFAULT_TRAIT_GROUP,
+    TRAIT_GROUPS
 };

src/views/PIGEAN/Gene/Template.vue

@@ -105,7 +105,7 @@
                             :field="'phenotype'"
                             placeholder="Select a phenotype ..."
                             :options="
-                                $store.state.pigeanGene.data.map(
+                                $parent.phewasAllData.map(
                                     (d) => d.phenotype
                                 )
                             "

src/views/PIGEAN/Gene/store.js

@@ -48,7 +48,7 @@ export default new Vuex.Store({
             state.aliasName = aliasName || state.aliasName;
         },
         setPhewasData(state, phewasData){
-            state.phewasData = phewasData || state.phewasData;
+            state.phewasData = phewasData;
         }
     },
 
@@ -77,6 +77,7 @@ export default new Vuex.Store({
 
     actions: {
         async queryGeneName(context, symbol) {
+            await context.commit("setPhewasData", []);
             let name = context.state.geneToQuery || context.state.geneName;
             let genesetSize = context.state.genesetSizeToQuery || context.state.genesetSize;
             let traitGroup = context.state.traitGroupToQuery || context.state.traitGroup;
@@ -91,10 +92,9 @@ export default new Vuex.Store({
                     context.commit("setPhewasData", context.state.pigeanGene.data);
                 } else {
                     // If ALL is selected, query all trait groups and get top results across all
-                    const TRAIT_GROUPS = ["portal", "gcat_trait", "rare_v2"];
                     let traitsData = [];
-                    for (let i = 0; i < TRAIT_GROUPS.length; i++){
-                        let group = TRAIT_GROUPS[i];
+                    for (let i = 0; i < bioIndexUtils.TRAIT_GROUPS.length; i++){
+                        let group = bioIndexUtils.TRAIT_GROUPS[i];
                         let traitQuery = `${group},${context.state.geneName},${
                             bioIndexUtils.DEFAULT_SIGMA},${context.state.genesetSize}`;
                         let groupData = await bioIndexUtils.query("pigean-gene", traitQuery);

src/views/PIGEAN/GeneSet/Template.vue

@@ -85,7 +85,7 @@
                             :field="'phenotype'"
                             placeholder="Select a phenotype ..."
                             :options="
-                                $store.state.pigeanGeneset.data.map(
+                                $parent.phewasAllData.map(
                                     (d) => d.phenotype
                                 )
                             "
@@ -130,9 +130,7 @@
                                 <div class="col-md-4">
                                     <pigean-plot
                                         v-if="$parent.plotReady"
-                                        :pigean-data="
-                                            $store.state.pigeanGeneset.data
-                                        "
+                                        :pigean-data="$parent.phewasAllData"
                                         :config="$parent.pigeanPlotConfig"
                                         :phenotype-map="$parent.pigeanMap"
                                         :filter="filter"
@@ -142,9 +140,7 @@
                                 <div class="card-body pigean-table">
                                     <pigean-table
                                         v-if="$parent.plotReady"
-                                        :pigean-data="
-                                            $store.state.pigeanGeneset.data
-                                        "
+                                        :pigean-data="$parent.phewasAllData"
                                         :phenotype-map="$parent.pigeanMap"
                                         :config="$parent.tableConfig"
                                         :filter="filter"

src/views/PIGEAN/GeneSet/main.js

@@ -125,14 +125,12 @@ new Vue({
         },
         plotReady() {
             return (
-                this.$store.state.pigeanGeneset.data.length > 0 &&
+                this.phewasAllData.length > 0 &&
                 Object.keys(this.pigeanPhenotypeMap).length > 0
             );
         },
         phewasAdjustedData() {
-            let adjustedData = JSON.parse(
-                JSON.stringify(this.$store.state.pigeanGeneset.data)
-            ); // Deep copy
+            let adjustedData = structuredClone(this.phewasAllData);
             for (let i = 0; i < adjustedData.length; i++) {
                 if (adjustedData[i].beta_uncorrected < 0) {
                     adjustedData[i].beta_uncorrected = 0;
@@ -142,6 +140,9 @@ new Vue({
         },
         pigeanMap(){
             return this.pigeanPhenotypeMap;
+        },
+        phewasAllData(){
+            return this.$store.state.phewasData;
         }
     },
     watch: {

src/views/PIGEAN/GeneSet/store.js

@@ -24,6 +24,7 @@ export default new Vuex.Store({
         aliasName: null,
         traitGroup: keyParams.traitGroup || bioIndexUtils.DEFAULT_TRAIT_GROUP,
         traitGroupToQuery: null,
+        phewasData: [],
     },
 
     mutations: {
@@ -39,23 +40,40 @@ export default new Vuex.Store({
             state.traitGroup = traitGroup || state.traitGroup;
             keyParams.set({ traitGroup: state.traitGroup });
         },
+        setPhewasData(state, phewasData){
+            state.phewasData = phewasData;
+        }
     },
 
     getters: {
     },
 
     actions: {
         async queryGeneset(context, symbol) {
+            await context.commit("setPhewasData", []);
             let name = context.state.genesetToQuery || context.state.geneset;
             let genesetSize = context.state.genesetSizeToQuery || context.state.genesetSize;
             let traitGroup = context.state.traitGroupToQuery || context.state.traitGroup;
             context.commit("setGeneset", name);
             context.commit("setGenesetSize", genesetSize);
             context.commit("setTraitGroup", traitGroup);
 
-            if (!!name) {
-                context.dispatch("pigeanGeneset/query", { q: 
-                    `${traitGroup},${name},${bioIndexUtils.DEFAULT_SIGMA},${genesetSize}` });
+            if (traitGroup !== 'all'){
+                await context.dispatch("pigeanGeneset/query", { q: 
+                    `${traitGroup},${name},${bioIndexUtils.DEFAULT_SIGMA},${genesetSize}`});
+                context.commit("setPhewasData", context.state.pigeanGeneset.data);
+            } else {
+                // If ALL is selected, query all trait groups and get top results across all
+                let traitsData = [];
+                for (let i = 0; i < bioIndexUtils.TRAIT_GROUPS.length; i++){
+                    let group = bioIndexUtils.TRAIT_GROUPS[i];
+                    let traitQuery = `${group},${name},${
+                        bioIndexUtils.DEFAULT_SIGMA},${genesetSize}`;
+                    let groupData = await bioIndexUtils.query("pigean-gene-set", traitQuery);
+                    traitsData = traitsData.concat(groupData);
+                }
+                traitsData = traitsData.sort((a,b) => b.combined - a.combined);
+                context.commit("setPhewasData", traitsData.slice(0,1500));
             }
         },
         async getPigeanPhenotypes(context) {

src/views/PIGEAN/Index/main.js

@@ -69,7 +69,7 @@ new Vue({
                     parameter: "gene",
                     "data point": {
                         type: "api",
-                        url: `${BIO_INDEX_HOST}/api/bio/keys/pigean-gene/3?columns=gene`,
+                        url: `${BIO_INDEX_HOST}/api/bio/keys/pigean-gene/4?columns=gene`,
                         "data type": "json",
                         "data wrapper": ["keys"],
                     },
@@ -82,7 +82,7 @@ new Vue({
                     parameter: "geneset",
                     "data point": {
                         type: "api",
-                        url: `${BIO_INDEX_HOST}/api/bio/keys/pigean-gene-set/3?columns=gene_set`,
+                        url: `${BIO_INDEX_HOST}/api/bio/keys/pigean-gene-set/4?columns=gene_set`,
                         "data type": "json",
                         "data wrapper": ["keys"],
                     },