Merge pull request #1278 from sagely1/AG-1221-add-srm-evidence-to-gct…

…-proteomics AG-1221 add SRM option to GCT subcategory dropdown options
Sage-Bionetworks · Jan 24, 2024 · d85512d · d85512d
2 parents d1ea464 + 6179e88
commit d85512d
Show file tree

Hide file tree

Showing 8 changed files with 160 additions and 30 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
@@ -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()"
@@ -312,7 +313,7 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
                     <div class="gene-controls">
                       <div>
                         {{ gene.hgnc_symbol || gene.ensembl_gene_id }}
-                        <ng-container *ngIf="gene.uniprotid">
+                        <ng-container *ngIf="gene.uniprotid && this.subCategory !== 'SRM'">
                           ({{ gene.uniprotid }})
                         </ng-container>
                       </div>
@@ -441,7 +442,7 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
                     <div class="gene-controls">
                       <div>
                         {{ gene.hgnc_symbol || gene.ensembl_gene_id }}
-                        <ng-container *ngIf="gene.uniprotid">
+                        <ng-container *ngIf="gene.uniprotid && this.subCategory !== 'SRM'">
                           ({{ gene.uniprotid }})
                         </ng-container>
                       </div>

diff --git a/...app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts b/...app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.spec.ts
@@ -14,6 +14,8 @@ import { MessageService, SortEvent } from 'primeng/api';
 import { Table } from 'primeng/table';
 import { Checkbox } from 'primeng/checkbox';
 
+import * as helpers from './gene-comparison-tool.helpers';
+
 import {
   GeneComparisonToolComponent,
   GeneComparisonToolDetailsPanelComponent,
@@ -24,7 +26,7 @@ import {
 import { ApiService, HelperService } from '../../../../core/services';
 import { GeneService } from '../../../../features/genes/services';
 import { routes } from '../../../../app.routing';
-import { comparisonGeneMock1, comparisonGeneMock2 } from '../../../../testing';
+import { comparisonGeneEmptyHGNCMock, comparisonGeneMock1, comparisonGeneMock2 } from '../../../../testing';
 
 const DEFAULT_SIGNIFICANCE_THRESHOLD = 0.05;
 
@@ -506,5 +508,15 @@ describe('Component: GeneComparisonToolComponent', () => {
 
       expectSignificanceThresholdIsApplied(newValue);
     }));
+
+    it('should have a label for SRM popup', () => {
+      const label = helpers.getGeneLabelForSRM(comparisonGeneMock1);
+      const expected = 'MSN - ENSG00000147065';
+      expect(label).toBe(expected);
+
+      const label2 = helpers.getGeneLabelForSRM(comparisonGeneEmptyHGNCMock);
+      const expected2 = 'ENSG00000147065';
+      expect(label2).toBe(expected2);
+    });
   });
 });
diff --git a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.helpers.ts b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.helpers.ts
@@ -68,6 +68,12 @@ export function getGeneLabelForProteinDifferentialExpression(gene: GCTGene) {
   gene.ensembl_gene_id;
 }
 
+export function getGeneLabelForSRM(gene: GCTGene) {
+  let label = gene.hgnc_symbol ? `${ gene.hgnc_symbol } - ` : '';
+  label += gene.ensembl_gene_id;
+  return label;
+}
+
 export function getScore(columnName: string, gene: GCTGene) {
   columnName = columnName.toUpperCase();
   if (columnName === 'RISK SCORE')
@@ -140,17 +146,13 @@ export const getDetailsPanelData = function (
   };
 
   if (category === 'Protein - Differential Expression') {
-    data.label = getGeneLabelForProteinDifferentialExpression(gene);
+    if (subCategory === 'SRM') {
+      data.label = getGeneLabelForSRM(gene);
+    } else {
+      data.label = getGeneLabelForProteinDifferentialExpression(gene);
+    }
     data.heading = 'Differential Protein Expression (' + tissue.name + ')';
     data.allTissueLink = false;
-
-    // if ('TMT' === subCategory) {
-    //   data.min = -35;
-    //   data.max = 35;
-    // } else {
-    //   data.min = -4;
-    //   data.max = 4;
-    // }
   } else {
     data.label = getGeneLabel(gene);
     data.heading = 'Differential RNA Expression (' + tissue.name + ')';

diff --git a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.variables.ts b/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',
+    },
   ],
 };
 

diff --git a/src/app/testing/gene-comparison-tool-mocks.ts b/src/app/testing/gene-comparison-tool-mocks.ts
@@ -173,6 +173,92 @@ export const comparisonGeneMock2: GCTGene = {
   multi_omics_score: 1.3
 };
 
+export const comparisonGeneEmptyHGNCMock: GCTGene = {
+  ensembl_gene_id: 'ENSG00000147065',
+  hgnc_symbol: '',
+  tissues: [
+    {
+      name: 'ACC',
+      logfc: -0.0144678061734664,
+      adj_p_val: 0.893263674388766,
+      ci_l: -0.133332670728704,
+      ci_r: 0.104397058381771,
+    },
+    {
+      name: 'CBE',
+      logfc: -0.0751554371582435,
+      adj_p_val: 0.530889774959758,
+      ci_l: -0.247449816301241,
+      ci_r: 0.0971389419847545,
+    },
+    {
+      name: 'DLPFC',
+      logfc: 0.0349940606540153,
+      adj_p_val: 0.604655110745068,
+      ci_l: -0.0564780903179806,
+      ci_r: 0.126466211626011,
+    },
+    {
+      name: 'FP',
+      logfc: 0.235992067764791,
+      adj_p_val: 0.0293685880983672,
+      ci_l: 0.0813918568317721,
+      ci_r: 0.390592278697809,
+    },
+    {
+      name: 'IFG',
+      logfc: 0.393613393602616,
+      adj_p_val: 0.0000468370819411619,
+      ci_l: 0.236604395922642,
+      ci_r: 0.550622391282589,
+    },
+    {
+      name: 'PCC',
+      logfc: 0.0870992749746771,
+      adj_p_val: 0.275931011190809,
+      ci_l: -0.0292845799777793,
+      ci_r: 0.203483129927133,
+    },
+    {
+      name: 'PHG',
+      logfc: 0.6626818751507,
+      adj_p_val: 9.688467425132421e-14,
+      ci_l: 0.506746460875332,
+      ci_r: 0.818617289426068,
+    },
+    {
+      name: 'STG',
+      logfc: 0.421363564302165,
+      adj_p_val: 0.0000165742209158385,
+      ci_l: 0.26315969917125,
+      ci_r: 0.57956742943308,
+    },
+    {
+      name: 'TCX',
+      logfc: 0.450452869099202,
+      adj_p_val: 0.00000476005829762979,
+      ci_l: 0.275315930793305,
+      ci_r: 0.625589807405099,
+    },
+  ],
+  nominations: {
+    count: 4,
+    year: 2018,
+    teams: ['Chang Lab', 'Emory', 'MSSM', 'MSSM'],
+    studies: ['ROSMAP', 'Kronos', 'MSBB', 'ACT', 'BLSA', 'Banner'],
+    inputs: ['Genetics', 'RNA', 'Protein'],
+    programs: ['Community Contributed', 'AMP-AD'],
+    validations: [
+      'validation studies ongoing',
+      'not prioritized for experimental validation',
+    ],
+  },
+  associations: [3, 4],
+  target_risk_score: 3.1,
+  genetics_score: 2.2,
+  multi_omics_score: 3.3
+};
+
 export const gctDetailsPanelDataMock: GCTDetailsPanelData = {
   label: 'label',
   heading: 'heading',

diff --git a/src/server/api.ts b/src/server/api.ts
@@ -38,23 +38,9 @@ const database = { url: '' };
         doc && ('doc => ' + util.inspect(doc)), '\n');
 }); */
 
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
-console.log('HELLLLLLOOOOOOOO');
 console.log(process.env);
 console.log(process.env.MONGODB_HOST);
 console.log(process.env.MONGODB_PORT);
-console.log('DONE!');
-console.log('DONE!');
-console.log('DONE!');
-console.log('DONE!');
-console.log('DONE!');
-console.log('DONE!');
 
 // Set the database url
 if (

diff --git a/src/server/components/comparison.ts b/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 +209,19 @@ 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();
+  } else {
+    // TODO capture corner scenarios
+    throw 'unknown method selected: ' + method;
   }
 
   if (items) {

diff --git a/tests/gene-comparison-tool.spec.ts b/tests/gene-comparison-tool.spec.ts
@@ -0,0 +1,30 @@
+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 }) => {
+    // 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 = page.locator('#subCategory');
+    await expect(dropdown).toHaveText('Targeted Selected Reaction Monitoring (SRM)');
+  });
+});