AG-1221 add SRM option to GCT

src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html

@@ -231,6 +231,7 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
                 <div class="gct-filter-label">{{ subCategoryLabel }}</div>
                 <div class="gct-sub-category-selector">
                   <p-dropdown
+                  id="subCategory"
                     [options]="subCategories"
                     [(ngModel)]="subCategory"
                     (onChange)="onSubCategoryChange()"

src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.variables.ts

@@ -32,13 +32,17 @@ export const subCategories: { [key: string]: GCTSelectOption[] } = {
   ],
   'Protein - Differential Expression': [
     {
-      label: 'Label-free Quantification (LFQ)',
-      value: 'LFQ',
+      label: 'Targeted Selected Reaction Monitoring (SRM)',
+      value: 'SRM',
     },
     {
-      label: 'Tandem Mass Tag (TMT)',
+      label: 'Genome-wide Tandem Mass Tag (TMT)',
       value: 'TMT',
     },
+    {
+      label: 'Genome-wide Label-free Quantification (LFQ)',
+      value: 'LFQ',
+    },
   ],
 };
 

src/server/components/comparison.ts

@@ -18,6 +18,7 @@ import {
   ProteomicsLFQCollection,
   ProteomicsTMTCollection,
   Team,
+  ProteomicsSRMCollection,
 } from '../models';
 import { BioDomains, TargetNomination, Scores } from '../../app/models';
 
@@ -208,11 +209,16 @@ export async function getProteinComparisonGenes(method: string) {
       .lean()
       .sort({ hgnc_symbol: 1, tissue: 1 })
       .exec();
-  } else {
+  } else if ('LFQ' === method) {
     items = await ProteomicsLFQCollection.find()
       .lean()
       .sort({ hgnc_symbol: 1, tissue: 1 })
       .exec();
+  } else if ('SRM' === method) {
+    items = await ProteomicsSRMCollection.find()
+      .lean()
+      .sort({ hgnc_symbol: 1, tissue: 1 })
+      .exec();
   }
 
   if (items) {

tests/gene-comparison-tool.spec.ts

@@ -0,0 +1,31 @@
+import { test, expect } from '@playwright/test';
+
+test.describe('specific viewport block', () => {
+  test.slow();
+  test.use({ viewport: { width: 1600, height: 1200 } });
+
+  test('has title', async ({ page }) => {
+    await page.goto('/genes/comparison?category=Protein+-+Differential+Expression');
+
+    // wait for page to load (i.e. spinner to disappear)
+    await expect(page.locator('div:nth-child(4) > div > .spinner'))
+      .not.toBeVisible({ timeout: 250000});
+
+    // Expect a title "to contain" a substring.
+    await expect(page).toHaveTitle('Gene Comparison | Visual comparison tool for AD genes');
+  });
+
+  test('sub-category is SRM by default', async ({ page }) => {
+    test.slow();
+    // set category for Protein - Differential Expression
+    await page.goto('/genes/comparison?category=Protein+-+Differential+Expression');
+
+    // wait for page to load (i.e. spinner to disappear)
+    await expect(page.locator('div:nth-child(4) > div > .spinner'))
+      .not.toBeVisible({ timeout: 150000});
+
+    // expect sub-category dropdown to be SRM
+    const dropdown = await page.locator('#subCategory');
+    await expect(dropdown).toHaveText('Targeted Selected Reaction Monitoring (SRM)');
+  });
+});