Merge pull request #1267 from sagely1/AG-959-gene-hero-surface-ensemb…

…l-version

AG-959 Surface Ensembl version in gene hero

.github/workflows/node.js.yml

@@ -5,18 +5,19 @@ name: Node.js CI
 
 on:
   push:
-    branches: [ "develop" ]
+    branches: [ develop, main ]
   pull_request:
-    branches: [ "develop" ]
+    branches: [ develop, main ]
 
 jobs:
   build:
-
+    timeout-minutes: 60
+
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        node-version: [16.x, 18.x]
+        node-version: [16.x]
         # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
     # Allow OIDC Integration (so we can assume the AWS role to deploy)
     # permissions:

playwright.config.ts

@@ -1,5 +1,7 @@
 import { defineConfig, devices } from '@playwright/test';
 
+export const baseURL = 'http://localhost:8080';
+
 /**
  * Read environment variables from file.
  * https://github.com/motdotla/dotenv
@@ -26,7 +28,7 @@ export default defineConfig({
   /* Shared settings for all the projects below. See https://playwright.dev/docs/api/class-testoptions. */
   use: {
     /* Base URL to use in actions like `await page.goto('/')`. */
-    baseURL: 'http://127.0.0.1:8080',
+    baseURL: baseURL,
 
     /* Collect trace when retrying the failed test. See https://playwright.dev/docs/trace-viewer */
     trace: 'on-first-retry',
@@ -71,9 +73,9 @@ export default defineConfig({
   ],
 
   /* Run your local dev server before starting the tests */
-  // webServer: {
-  //   command: 'npm run start',
-  //   url: 'http://127.0.0.1:3000',
-  //   reuseExistingServer: !process.env.CI,
-  // },
+  webServer: {
+    command: 'npm run start',
+    url: baseURL,
+    reuseExistingServer: !process.env.CI,
+  },
 });

src/app/features/genes/components/gene-hero/gene-hero.component.html

@@ -14,18 +14,32 @@ <h2 class="gene-hero-name">
       <p class="gene-hero-provider">
         {{ getSummary() }}
       </p>
-      <ng-container *ngIf="gene.bio_domains || getAlias()">
+      <ng-container *ngIf="gene.bio_domains || getAlias() || getEnsemblUrl() !== ''">
         <hr />
         <div *ngIf="gene.bio_domains" class="gene-hero-biodomains">
           <h4 class="gene-hero-biodomains-heading">Biological Domains</h4>
           <p>
             {{ getBiodomains() }}
           </p>
         </div>
-        <div *ngIf="getAlias()" class="gene-hero-aliases">
+        <div class="gene-hero-aliases">
           <h4 class="gene-hero-aliases-heading">Also known as</h4>
-          <p *ngIf="gene.hgnc_symbol" class="mb-0">{{ gene.ensembl_gene_id }}</p>
-          <p>
+          <ng-container *ngIf="getEnsemblUrl() !== ''">
+            <p>
+              <a [href]="getEnsemblUrl()" target="_blank">{{ gene.ensembl_gene_id }}</a>
+              <span *ngIf="gene.ensembl_info[0].ensembl_release">
+                (Ensembl Release {{ gene.ensembl_info[0].ensembl_release }})
+              </span>
+            </p>
+          </ng-container>
+          <ng-container *ngIf="getEnsemblUrl() === ''">
+            <span *ngIf="getEnsemblUrl() === ''">{{ gene.ensembl_gene_id }}</span>
+          </ng-container>
+          <p *ngIf="gene.ensembl_info[0].ensembl_possible_replacements.length > 0">
+            <a [href]="getPossibleReplacementsURL()">Possible replacement value<span *ngIf="gene.ensembl_info[0].ensembl_possible_replacements.length > 1">s</span></a>:
+            {{ gene.ensembl_info[0].ensembl_possible_replacements.join(', ')}}
+          </p>
+          <p *ngIf="getAlias() !== ''">
             {{ getAlias() }}
           </p>
         </div>

src/app/features/genes/components/gene-hero/gene-hero.component.scss

@@ -53,3 +53,7 @@ hr {
   text-transform: uppercase;
   margin-bottom: 15px;
 }
+
+.possible-replacements {
+  margin-bottom: 15px;
+}

src/app/features/genes/components/gene-hero/gene-hero.component.spec.ts

@@ -8,7 +8,7 @@ import { RouterTestingModule } from '@angular/router/testing';
 // Internal
 // -------------------------------------------------------------------------- //
 import { GeneHeroComponent } from './';
-import { geneMock1, geneMock3 } from '../../../../testing';
+import { geneMissingEnsemblInfo, geneMock1, geneMock3 } from '../../../../testing';
 
 // -------------------------------------------------------------------------- //
 // Tests
@@ -110,4 +110,20 @@ describe('Component: Gene Hero', () => {
     const expected = 'Immune Response, Lipid Metabolism, Structural Stabilization, Synapse, Vasculature';
     expect(component.getBiodomains()).toBe(expected);
   });
+
+  it('should return the ensembl permalink', () => {
+    component.gene = geneMock1;
+    expect(component.getEnsemblUrl()).toBe('https://may2015.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264794');
+  });
+
+  it('should return an empty string if the gene is missing ensembl info', () => {
+    // if gene does not have a url
+    component.gene = geneMissingEnsemblInfo;
+    expect(component.getEnsemblUrl()).toBe('');
+  });
+
+  it('should return a url with ensembl id', () => {
+    component.gene = geneMock1;
+    expect(component.getPossibleReplacementsURL()).toBe('https://useast.ensembl.org/Homo_sapiens/Gene/Idhistory?g=ENSG00000147065');
+  });
 });

src/app/features/genes/components/gene-hero/gene-hero.component.ts

@@ -101,4 +101,15 @@ export class GeneHeroComponent {
       .sort(ascending);
     return biodomains.join(', ');
   }
+
+  getEnsemblUrl() {
+    if (!this.gene?.ensembl_info || this.gene.ensembl_info.length <= 0)
+      return '';
+    return this.gene?.ensembl_info[0].ensembl_permalink;
+  }
+
+  getPossibleReplacementsURL() {
+    let url = 'https://useast.ensembl.org/Homo_sapiens/Gene/Idhistory?g=';
+    return url += this.gene?.ensembl_gene_id;
+  }
 }

src/app/models/EnsemblInfo.ts

@@ -0,0 +1,5 @@
+export interface EnsemblInfo {
+  ensembl_release: number;
+  ensembl_possible_replacements: string[];
+  ensembl_permalink: string;
+}

src/app/models/genes.ts

@@ -8,6 +8,7 @@ import {
   SimilarGenesNetwork,
   BioDomains
 } from './';
+import { EnsemblInfo } from './EnsemblInfo';
 
 export interface TargetNomination {
   source: string;
@@ -98,6 +99,9 @@ export interface Gene {
   input_data_display_value?: string;
 
   bio_domains?: BioDomains;
+
+  // FIXME Will be fixed by AG-1324 in a future data release as it doesn't make sense to have an array here
+  ensembl_info: EnsemblInfo[];
 }
 
 export interface GenesResponse {