From abae471662ddeefc3efa5fdd66e2cfde70532872 Mon Sep 17 00:00:00 2001
From: sagely1 <114952739+sagely1@users.noreply.github.com>
Date: Thu, 9 May 2024 15:51:23 -0700
Subject: [PATCH] AG-1425 updating variables and comments for clarity, fixing
 plural bug for protein header label

---
 .../gene-comparison-tool.component.html       |  14 +--
 .../gene-comparison-tool.component.spec.ts    |  10 +-
 .../gene-comparison-tool.component.ts         | 113 +++++++++---------
 3 files changed, 70 insertions(+), 67 deletions(-)

diff --git a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html
index 50f85963..987a12e5 100644
--- a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html
+++ b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html
@@ -284,20 +284,20 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
             </p-table>
 
             <div
-              *ngIf="pinnedGenes.length > 0"
+              *ngIf="pinnedItems.length > 0"
               class="table-divider table-divider-1"
             >
               <div class="table-divider-inner">
                 <div id="pinned-genes-header">
                   <span *ngIf="category === 'RNA - Differential Expression'">
-                    Pinned Genes ({{ pinnedGenes.length }}/50)
+                    Pinned Genes ({{ pinnedItems.length }}/50)
                   </span>
                   <div *ngIf="category === 'Protein - Differential Expression'">
                     <div>
                     Pinned Genes ({{ uniquePinnedGenesCount }}/50)&nbsp;&nbsp;&nbsp;
                     </div>
                     <div id="pinned-proteins">
-                      {{ pinnedGenes.length }} Proteins
+                      {{ pinnedItems.length }} Protein<ng-container *ngIf="pinnedItems.length > 1">s</ng-container>
                     </div>
                   </div>
                 </div>
@@ -314,7 +314,7 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
             </div>
             <p-table
               #pinnedTable
-              [value]="pinnedGenes"
+              [value]="pinnedItems"
               [customSort]="true"
               (sortFunction)="sortCallback($event)"
               breakpoint="0"
@@ -425,7 +425,7 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
             </div>
             <div
               *ngIf="
-                !searchTerm && !hasSelectedFilters() && pinnedGenes.length > 0
+                !searchTerm && !hasSelectedFilters() && pinnedItems.length > 0
               "
               class="table-divider"
             >
@@ -573,8 +573,8 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
     <gene-comparison-tool-pinned-genes-modal
       #pinnedGenesModal
       (onChange)="onPinnedGenesModalChange($event)"
-      [pinnedGenes]="pinnedGenes"
-      [pendingPinnedGenes]="pendingPinnedGenes"
+      [pinnedGenes]="pinnedItems"
+      [pendingPinnedGenes]="pendingPinnedItems"
       [maxPinnedGenes]="maxPinnedGenes"
     ></gene-comparison-tool-pinned-genes-modal>
   </div>
diff --git a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts
index da5e0f7c..c754110b 100644
--- a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts
+++ b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts
@@ -106,7 +106,7 @@ describe('Component: GeneComparisonToolComponent', () => {
     fixture.detectChanges();
 
     expect(component.genes).toEqual([comparisonGeneMock1, comparisonGeneMock2]);
-    expect(component.pinnedGenes).toEqual([comparisonGeneMock1]);
+    expect(component.pinnedItems).toEqual([comparisonGeneMock1]);
     flush();
   }));
 
@@ -190,15 +190,15 @@ describe('Component: GeneComparisonToolComponent', () => {
 
     component.clearPinnedGenes();
     fixture.detectChanges();
-    expect(component.pinnedGenes.length).toEqual(0);
+    expect(component.pinnedItems.length).toEqual(0);
 
     component.onPinGeneClick(comparisonGeneMock1);
     fixture.detectChanges();
-    expect(component.pinnedGenes.length).toEqual(1);
+    expect(component.pinnedItems.length).toEqual(1);
     
     component.onUnPinGeneClick(comparisonGeneMock1, true);
     fixture.detectChanges();
-    expect(component.pinnedGenes.length).toEqual(0);
+    expect(component.pinnedItems.length).toEqual(0);
   });
 
   it('should clear pinned genes', fakeAsync(() => {
@@ -207,7 +207,7 @@ describe('Component: GeneComparisonToolComponent', () => {
 
     component.clearPinnedGenes();
     fixture.detectChanges();
-    expect(component.pinnedGenes.length).toEqual(0);
+    expect(component.pinnedItems.length).toEqual(0);
     flush();
   }));
 
diff --git a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.ts b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.ts
index 2364d357..153a8c16 100644
--- a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.ts
+++ b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.ts
@@ -100,10 +100,10 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
   lastPinnedCategory = '';
   lastPinnedSubCategory = '';
 
-  pinnedGenes: GCTGene[] = [];
+  pinnedItems: GCTGene[] = [];
   uniquePinnedGenesCount = 0;
-  pinnedGenesCache: GCTGene[] = [];
-  pendingPinnedGenes: GCTGene[] = [];
+  pinnedItemsCache: GCTGene[] = [];
+  pendingPinnedItems: GCTGene[] = [];
   maxPinnedGenes = 50;
 
   /* ----------------------------------------------------------------------- */
@@ -240,53 +240,56 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
   getGeneProperty(gene: GCTGene, property: string) {
     return property.split('.').reduce((o: any, i: any) => o[i], gene);
   }
-  
-  initData(genes: GCTGene[]) {
-    // hide brain region columns initially
-    this.brainRegionsColumns.forEach(c => c.visible = false);
-    
-    const pinnedGenes: GCTGene[] = [];
-    
-    const currentPinnedGenesCache = this.pinnedGenesCache;
 
-    let previousPins: (string | undefined)[] = [];
+  getUid(item: GCTGene) {
+    // rna is just the ensembl gene id
+    // protein is a combination of ensembl gene id and uniprotid
+    if (this.category === 'RNA - Differential Expression')
+      return item.ensembl_gene_id;
+    else
+      return item.ensembl_gene_id + item.uniprotid;
+  }
 
+  getPreviousPins() {
     if (this.currentCategoriesMatchLastPinnedCategories()) {
-      // no need to load from cache if it was last pinned from the current page
-      // previousPins = this.getUrlParam('pinned', true);
-      previousPins = currentPinnedGenesCache.map((g: GCTGene) => g.uid);
+      // load from cache since it has been previously cached
+      return this.pinnedItemsCache.map((g: GCTGene) => g.uid);
     } else {
-      // if it is the initial load, the categories will not match since the last pinned categories 
-      // will be empty strings.  In this case we want to check the url to see if this was a shared url
-      // with pinned genes/proteins.
-      
-      // since the last pinned category is blank, we don't need to check the subcategory
+      // if the last pinned category is blank, then this means this is the initial load
+      // note: we only need to check the category for blank but subcategory will also be blank
+      // In this scenario, we check the url to see if this was a shared url with pinned genes/proteins
       if (this.lastPinnedCategory === '') {
         // check the url for pinned genes/proteins
-        previousPins = this.getUrlParam('pinned', true);
         this.setLastPinnedCategories();
+        return this.getUrlParam('pinned', true);
       } else {
         // categories don't match, so grab it from the cache
         if (this.category === 'RNA - Differential Expression') {
-          previousPins = currentPinnedGenesCache
-            .map((g: GCTGene) => g.uid?.substring(0, 15));
+          return this.pinnedItemsCache.map((g: GCTGene) => g.ensembl_gene_id);
         } else {
-          previousPins = currentPinnedGenesCache.map((g: GCTGene) => g.uid);
+          return this.pinnedItemsCache.map((g: GCTGene) => g.uid);
         }
       }
     }
-
+  }
+  
+  initData(genes: GCTGene[]) {
+    // hide brain region columns initially
+    this.brainRegionsColumns.forEach(c => c.visible = false);
+    
+    const pinnedGenes: GCTGene[] = [];
+    
+    // load the previous pins and format previousPins to match the current category
+    const previousPins = this.getPreviousPins();
+    
     genes.forEach((gene: GCTGene) => {
-      gene.uid = gene.ensembl_gene_id;
+      gene.uid = this.getUid(gene);
       gene.search_array = [
         gene.ensembl_gene_id.toLowerCase(),
         gene.hgnc_symbol.toLowerCase(),
       ];
 
       if (this.category === 'Protein - Differential Expression') {
-        // for this category, the uid will be ensg + uniprotid
-        gene.uid += gene.uniprotid;
-        
         gene.search_array.push(gene.uniprotid?.toLowerCase() || '');
 
         // if there is a match on uid or ensembl_gene_id, add it to pinnedGenes
@@ -356,16 +359,16 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
         'Protein - Differential Expression' === this.category &&
         this.uniquePinnedGenesCount > this.maxPinnedGenes
       ) {
-        this.pendingPinnedGenes = pinnedGenes;
+        this.pendingPinnedItems = pinnedGenes;
         this.pinnedGenesModal.show();
       } else {
-        this.pinnedGenes = [];
-        this.pendingPinnedGenes = [];
+        this.pinnedItems = [];
+        this.pendingPinnedItems = [];
         this.uniquePinnedGenesCount = this.getCountOfUniqueGenes();
         this.pinGenes(pinnedGenes);
       }
     } else {
-      this.pinnedGenes = [];
+      this.pinnedItems = [];
     }
 
     this.genes = genes;
@@ -659,16 +662,16 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
   }
 
   setPinnedGenesCache(genes: GCTGene[]) {
-    this.pinnedGenesCache = genes;
+    this.pinnedItemsCache = genes;
   }
 
   clearPinnedGenesCache() {
-    this.pinnedGenesCache = [];
+    this.pinnedItemsCache = [];
     this.uniquePinnedGenesCount = this.getCountOfUniqueGenes();
   }
 
   refreshPinnedGenes() {
-    this.setPinnedGenesCache(this.pinnedGenes);
+    this.setPinnedGenesCache(this.pinnedItems);
     this.filter();
     this.updateUrl();
   }
@@ -684,11 +687,11 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
   }
 
   pinGene(gene: GCTGene, refresh = true) {
-    const index = this.pinnedGenes.findIndex(
+    const index = this.pinnedItems.findIndex(
       (g: GCTGene) => g.uid === gene.uid
     );    
     if (this.category === 'RNA - Differential Expression') {
-      if (index > -1 || this.pinnedGenes.length >= this.maxPinnedGenes)
+      if (index > -1 || this.pinnedItems.length >= this.maxPinnedGenes)
         return;
     } else {
       // the same unique id exists, so don't allow it to be added
@@ -698,7 +701,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
         // border condition: if we are at the max allowable pinned genes
         // check if the pinned genes list has a gene with the ensembl id, 
         // in which case the protein can be added
-        const ensemblIndex = this.pinnedGenes.findIndex(
+        const ensemblIndex = this.pinnedItems.findIndex(
           (g: GCTGene) => g.ensembl_gene_id === gene.ensembl_gene_id
         );
         if (ensemblIndex < 0) {
@@ -708,7 +711,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
       }
     }
 
-    this.pinnedGenes.push(gene);
+    this.pinnedItems.push(gene);
     
     if (refresh) {
       this.clearPinnedGenesCache();
@@ -720,7 +723,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
     // this method is used for protein views since there can be multiple pinned proteins
     // that have the same ensg value but different uniprotids
     // so this will return the count of genes with unique ensgs
-    const uids = this.pinnedGenes.map(g => g.ensembl_gene_id);
+    const uids = this.pinnedItems.map(g => g.ensembl_gene_id);
     const uniqueUids = new Set(uids);
     return uniqueUids.size;
   }
@@ -752,7 +755,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
   }
 
   pinGenes(genes: GCTGene[]) {
-    const remaining = this.maxPinnedGenes - this.pinnedGenes.length;
+    const remaining = this.maxPinnedGenes - this.pinnedItems.length;
 
     if (remaining < 1) {
       return;
@@ -793,7 +796,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
   }
 
   ensgExistsInProteins(ensemblGeneId: string) {
-    const ensemblIndex = this.pinnedGenes.findIndex(
+    const ensemblIndex = this.pinnedItems.findIndex(
       (g: GCTGene) => g.ensembl_gene_id === ensemblGeneId
     );
     if (ensemblIndex < 0) {
@@ -837,7 +840,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
   onUnPinGeneClick(gene: GCTGene, refresh = true) {
     this.setLastPinnedCategories();
 
-    const index = this.pinnedGenes.findIndex(
+    const index = this.pinnedItems.findIndex(
       (g: GCTGene) => g.uid === gene.uid
     );
 
@@ -845,7 +848,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
       return;
     }
 
-    this.pinnedGenes.splice(index, 1);
+    this.pinnedItems.splice(index, 1);
 
     if (refresh) {
       this.clearPinnedGenesCache();
@@ -862,22 +865,22 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
   }
 
   clearPinnedGenes() {
-    this.pinnedGenes = [];
+    this.pinnedItems = [];
     this.clearPinnedGenesCache();
     this.refreshPinnedGenes();
   }
 
   getPinnedEnsemblGeneIds() {
-    return this.pinnedGenes.map((g: GCTGene) => g.ensembl_gene_id);
+    return this.pinnedItems.map((g: GCTGene) => g.ensembl_gene_id);
   }
 
   getPinnedUniProtIds() {
-    return this.pinnedGenes.map((g: GCTGene) => g.uniprotid);
+    return this.pinnedItems.map((g: GCTGene) => g.uniprotid);
   }
 
   getPinDisabledStatus() {
     if (this.category === 'RNA - Differential Expression')
-      return this.pinnedGenes.length >= this.maxPinnedGenes;
+      return this.pinnedItems.length >= this.maxPinnedGenes;
     else {
       // default to showing pin all button for protein view
       return false;
@@ -904,13 +907,13 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
 
   onPinnedGenesModalChange(response: boolean) {
     if (response) {
-      this.pinnedGenes = [];
-      this.pinGenes(this.pendingPinnedGenes);
+      this.pinnedItems = [];
+      this.pinGenes(this.pendingPinnedItems);
     } else {
       this.category = this.categories[0].value;
       this.onCategoryChange();
     }
-    this.pendingPinnedGenes = [];
+    this.pendingPinnedItems = [];
   }
 
   /* ----------------------------------------------------------------------- */
@@ -945,8 +948,8 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
       params['sortOrder'] = this.sortOrder;
     }
 
-    if (this.pinnedGenes.length > 0) {
-      params['pinned'] = this.pinnedGenes.map(
+    if (this.pinnedItems.length > 0) {
+      params['pinned'] = this.pinnedItems.map(
         (g: GCTGene) => g.uid
       );
       params['pinned'].sort();
@@ -1167,7 +1170,7 @@ export class GeneComparisonToolComponent implements OnInit, AVI, OnDestroy {
     ];
     const data: any[][] = [];
 
-    this.pinnedGenes.forEach((g: GCTGene) => {
+    this.pinnedItems.forEach((g: GCTGene) => {
       const baseRow = [
         g.ensembl_gene_id, 
         g.hgnc_symbol,