Pigean cleanup (#797)

* gene page moved stuff to module * refactored all pigean pages to use utils * label fix
broadinstitute · Dec 3, 2024 · cac59ff · cac59ff
1 parent eb34995
commit cac59ff
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Showing 6 changed files with 41 additions and 79 deletions.
diff --git a/src/utils/pigeanUtils.js b/src/utils/pigeanUtils.js
@@ -0,0 +1,23 @@
+/* PIGeAN Utilities
+*/
+
+export function toOldStyle(newStylePhenotype){
+    let oldStyle = structuredClone(newStylePhenotype);
+    oldStyle.description = newStylePhenotype.phenotype_name;
+    oldStyle.name = newStylePhenotype.phenotype;
+    oldStyle.group = newStylePhenotype.display_group;
+    return oldStyle;
+}
+
+export function mapPhenotypes(allPhenotypes){
+    let phenotypeMap = {};
+    allPhenotypes.forEach(item => {
+        phenotypeMap[item.phenotype] = toOldStyle(item);
+    });
+    return phenotypeMap;
+}
+
+export default {
+    toOldStyle,
+    mapPhenotypes
+};
diff --git a/src/views/PIGEAN/Gene/main.js b/src/views/PIGEAN/Gene/main.js
@@ -20,6 +20,7 @@ import sortUtils from "@/utils/sortUtils";
 import alertUtils from "@/utils/alertUtils";
 import Formatters from "@/utils/formatters";
 import dataConvert from "@/utils/dataConvert";
+import pigeanUtils from "@/utils/pigeanUtils.js";
 import { pageMixin } from "@/mixins/pageMixin.js";
 
 new Vue({
@@ -44,8 +45,8 @@ new Vue({
             pigeanPhenotypeMap: {},
             filterFields: [
                 { key: "combined", label: "Combined genetic support" },
-                { key: "huge_score", label: "GWAS unweighted" },
-                { key: "log_bf", label: "GWAS weighted" },
+                { key: "huge_score", label: "Direct support w/o gene sets" },
+                { key: "log_bf", label: "Direct support w/ gene sets" },
                 { key: "prior", label: "Indirect support" },
             ],
             tableConfig: {
@@ -175,7 +176,8 @@ new Vue({
         this.$store.dispatch("bioPortal/getDiseaseGroups");
         this.$store.dispatch("bioPortal/getPhenotypes");
         await this.$store.dispatch("getPigeanPhenotypes");
-        this.pigeanPhenotypeMap = this.mapPhenotypes();
+        this.pigeanPhenotypeMap = 
+            pigeanUtils.mapPhenotypes(this.$store.state.pigeanAllPhenotypes.data);
     },
     methods: {
         // go to region page
@@ -188,21 +190,6 @@ new Vue({
                 }&start=${r.start - expanded}&end=${r.end + expanded}`;
             }
         },
-        mapPhenotypes(){
-            let phenotypeMap = {};
-            let phenotypes = this.$store.state.pigeanAllPhenotypes.data
-            phenotypes.forEach(item => {
-                phenotypeMap[item.phenotype] = this.toOldStyle(item);
-            });
-            return phenotypeMap;
-        },
-        toOldStyle(newStylePhenotype){
-            let oldStyle = structuredClone(newStylePhenotype);
-            oldStyle.description = newStylePhenotype.phenotype_name;
-            oldStyle.name = newStylePhenotype.phenotype;
-            oldStyle.group = newStylePhenotype.display_group;
-            return oldStyle;
-        },
     },
 
     render(createElement, context) {

diff --git a/src/views/PIGEAN/GeneSet/main.js b/src/views/PIGEAN/GeneSet/main.js
@@ -18,6 +18,7 @@ import uiUtils from "@/utils/uiUtils";
 import plotUtils from "@/utils/plotUtils";
 import sortUtils from "@/utils/sortUtils";
 import alertUtils from "@/utils/alertUtils";
+import pigeanUtils from "@/utils/pigeanUtils.js";
 import Formatters from "@/utils/formatters";
 import dataConvert from "@/utils/dataConvert";
 import { pageMixin } from "@/mixins/pageMixin.js";
@@ -148,30 +149,13 @@ new Vue({
             this.$store.dispatch("kp4cd/getFrontContents", group.name);
         },
     },
-    methods: {
-        mapPhenotypes(){
-            let phenotypeMap = {};
-            let phenotypes = this.$store.state.pigeanAllPhenotypes.data
-            phenotypes.forEach(item => {
-                phenotypeMap[item.phenotype] = this.toOldStyle(item);
-            });
-            return phenotypeMap;
-        },
-        toOldStyle(newStylePhenotype){
-            let oldStyle = structuredClone(newStylePhenotype);
-            oldStyle.description = newStylePhenotype.phenotype_name;
-            oldStyle.name = newStylePhenotype.phenotype;
-            oldStyle.group = newStylePhenotype.display_group;
-            return oldStyle;
-        },
-    },
-
     async created() {
         this.$store.dispatch("queryGeneset", this.$store.state.geneset);
         this.$store.dispatch("bioPortal/getDiseaseGroups");
         this.$store.dispatch("bioPortal/getPhenotypes");
         await this.$store.dispatch("getPigeanPhenotypes");
-        this.pigeanPhenotypeMap = this.mapPhenotypes();
+        this.pigeanPhenotypeMap = 
+            pigeanUtils.mapPhenotypes(this.$store.state.pigeanAllPhenotypes.data);
     },
 
     render(createElement, context) {

diff --git a/src/views/PIGEAN/Index/main.js b/src/views/PIGEAN/Index/main.js
@@ -15,6 +15,7 @@ import uiUtils from "@/utils/uiUtils";
 import plotUtils from "@/utils/plotUtils";
 import sortUtils from "@/utils/sortUtils";
 import alertUtils from "@/utils/alertUtils";
+import pigeanUtils from "@/utils/pigeanUtils.js";
 import Formatters from "@/utils/formatters";
 import dataConvert from "@/utils/dataConvert";
 import keyParams from "@/utils/keyParams";
@@ -402,18 +403,11 @@ new Vue({
                 return char.toUpperCase();
             });
         },
-        toOldStyle(newStylePhenotype){
-            let oldStyle = structuredClone(newStylePhenotype);
-            oldStyle.description = newStylePhenotype.phenotype_name;
-            oldStyle.name = newStylePhenotype.phenotype;
-            oldStyle.group = newStylePhenotype.display_group;
-            return oldStyle;
-        },
         formatAllPhenotypes(){
             let newPhenotypes = this.$store.state.pigeanAllPhenotypes.data;
             let output = [];
             for (let i = 0; i < newPhenotypes.length; i++){
-                output.push(this.toOldStyle(newPhenotypes[i]));
+                output.push(pigeanUtils.toOldStyle(newPhenotypes[i]));
             }
             this.$store.dispatch("phenotypesInSession", output);
         }

diff --git a/src/views/PIGEAN/NetworkGraph/main.js b/src/views/PIGEAN/NetworkGraph/main.js
@@ -6,6 +6,7 @@ import NetworkGraph from "@/components/NetworkGraph.vue";
 import SearchHeaderWrapper from "@/components/SearchHeaderWrapper.vue";
 import GenesetSizeSelectPicker from "@/components/GenesetSizeSelectPicker.vue";
 import keyParams from "@/utils/keyParams";
+import pigeanUtils from "@/utils/pigeanUtils.js";
 import { pageMixin } from "@/mixins/pageMixin.js";
 new Vue({
     store,
@@ -35,7 +36,7 @@ new Vue({
     },
     methods: {
         setSelectedPhenotype(PHENOTYPE) {
-            let oldStylePhenotype = this.toOldStyle(PHENOTYPE);
+            let oldStylePhenotype = pigeanUtils.toOldStyle(PHENOTYPE);
             this.newPhenotypeSearchKey = oldStylePhenotype.description;
             this.phenotypeSearchKey = null;
             this.selectedPhenotype = oldStylePhenotype;
@@ -52,33 +53,19 @@ new Vue({
 
             return isInPhenotype == searchKeys.length ? true : null;
         },
-        toOldStyle(newStylePhenotype){
-            let oldStyle = structuredClone(newStylePhenotype);
-            oldStyle.description = newStylePhenotype.phenotype_name;
-            oldStyle.name = newStylePhenotype.phenotype;
-            oldStyle.group = newStylePhenotype.display_group;
-            return oldStyle;
-        },
         searchPhenotype(){
             let phenotypeToSearch = this.selectedPhenotype 
                 || this.pigeanPhenotypeMap[keyParams.phenotype];
             this.$store.dispatch("sendSearch", phenotypeToSearch);
         },
-        mapPhenotypes(){
-            let phenotypeMap = {};
-            let phenotypes = this.$store.state.pigeanAllPhenotypes.data
-            phenotypes.forEach(item => {
-                phenotypeMap[item.phenotype] = this.toOldStyle(item);
-            });
-            return phenotypeMap;
-        },
     },
     async created() {
         this.$store.dispatch("bioPortal/getDiseaseSystems");
         this.$store.dispatch("bioPortal/getDiseaseGroups");
         this.$store.dispatch("bioPortal/getPhenotypes");
         await this.$store.dispatch("getPigeanPhenotypes");
-        this.pigeanPhenotypeMap = this.mapPhenotypes();
+        this.pigeanPhenotypeMap = 
+            pigeanUtils.mapPhenotypes(this.$store.state.pigeanAllPhenotypes.data);
         let initialPhenotype = this.pigeanPhenotypeMap[keyParams.phenotype];
         this.$store.dispatch("sendSearch", initialPhenotype)
     },

diff --git a/src/views/PIGEAN/Phenotype/main.js b/src/views/PIGEAN/Phenotype/main.js
@@ -9,6 +9,7 @@ import Formatters from "@/utils/formatters";
 import uiUtils from "@/utils/uiUtils";
 import alertUtils from "@/utils/alertUtils";
 import plotUtils from "@/utils/plotUtils";
+import pigeanUtils from "@/utils/pigeanUtils.js";
 import sessionUtils from "@/utils/sessionUtils";
 import sortUtils from "@/utils/sortUtils";
 import dataConvert from "@/utils/dataConvert";
@@ -362,7 +363,8 @@ new Vue({
         this.$store.dispatch("bioPortal/getPhenotypes");
         this.$store.dispatch("bioPortal/getDatasets");
         await this.$store.dispatch("getPigeanPhenotypes");
-        this.pigeanPhenotypeMap = this.mapPhenotypes();
+        this.pigeanPhenotypeMap = 
+            pigeanUtils.mapPhenotypes(this.$store.state.pigeanAllPhenotypes.data);
         this.lookupInPigeanMap();
     },
     methods: {
@@ -372,7 +374,7 @@ new Vue({
             uiUtils.getToolTipPosition(ELEMENT);
         },
         setSelectedPhenotype(PHENOTYPE) {
-            let oldStylePhenotype = this.toOldStyle(PHENOTYPE);
+            let oldStylePhenotype = pigeanUtils.toOldStyle(PHENOTYPE);
             this.newPhenotypeSearchKey = oldStylePhenotype.description;
             this.phenotypeSearchKey = null;
             this.$store.dispatch("selectedPhenotype", oldStylePhenotype);
@@ -420,21 +422,6 @@ new Vue({
             });
             return data;
         },
-        mapPhenotypes(){
-            let phenotypeMap = {};
-            let phenotypes = this.$store.state.pigeanAllPhenotypes.data
-            phenotypes.forEach(item => {
-                phenotypeMap[item.phenotype] = this.toOldStyle(item);
-            });
-            return phenotypeMap;
-        },
-        toOldStyle(newStylePhenotype){
-            let oldStyle = structuredClone(newStylePhenotype);
-            oldStyle.description = newStylePhenotype.phenotype_name;
-            oldStyle.name = newStylePhenotype.phenotype;
-            oldStyle.group = newStylePhenotype.display_group;
-            return oldStyle;
-        },
         lookupInPigeanMap(){
             let name = keyParams.phenotype;
             let phenotype = this.pigeanPhenotypeMap[name];