AG-959-ensembl-release-version

.github/workflows/node.js.yml

@@ -49,4 +49,4 @@ jobs:
       # with:
       #   name: playwright-report
       #   path: playwright-report/
-      #   retention-days: 30
+      #   retention-days: 30

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
@@ -24,7 +26,7 @@ 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',
@@ -69,9 +71,9 @@ 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

@@ -14,17 +14,31 @@ <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 *ngIf="getAlias() || getEnsemblUrl() !== ''" 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>
+          <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>
             {{ getAlias() }}
           </p>

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

@@ -110,4 +110,14 @@ 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 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)
+      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 +99,8 @@ export interface Gene {
   input_data_display_value?: string;
 
   bio_domains?: BioDomains;
+
+  ensembl_info: EnsemblInfo[];
 }
 
 export interface GenesResponse {

src/app/testing/gene-mocks.ts

@@ -2934,7 +2934,14 @@ export const geneMock1: Gene = {
   },
   is_adi: false,
   is_tep: true,
-  resource_url: 'https://adknowledgeportal.synapse.org/Explore/Target%20Enabling%20Resources?QueryWrapper0=%7B%22sql%22%3A%22select%20*%20from%20syn26146692%20WHERE%20%60isPublic%60%20%3D%20true%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22target%22%2C%22facetValues%22%3A%5B%22MSN%22%5D%7D%5D%7D'
+  resource_url: 'https://adknowledgeportal.synapse.org/Explore/Target%20Enabling%20Resources?QueryWrapper0=%7B%22sql%22%3A%22select%20*%20from%20syn26146692%20WHERE%20%60isPublic%60%20%3D%20true%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22target%22%2C%22facetValues%22%3A%5B%22MSN%22%5D%7D%5D%7D',
+  ensembl_info: [
+    {
+      ensembl_release: 84,
+      ensembl_possible_replacements: ['ENSG00000283172'],
+      ensembl_permalink: 'https://may2015.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264794'
+    }
+  ]
 };
 
 export const geneMock2: Gene = {
@@ -3121,7 +3128,14 @@ export const geneMock2: Gene = {
   total_nominations: 3,
   is_adi: false,
   is_tep: true,
-  resource_url: 'https://adknowledgeportal.synapse.org/Explore/Target%20Enabling%20Resources?QueryWrapper0=%7B%22sql%22%3A%22select%20*%20from%20syn26146692%20WHERE%20%60isPublic%60%20%3D%20true%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22target%22%2C%22facetValues%22%3A%5B%22PLEC%22%5D%7D%5D%7D'
+  resource_url: 'https://adknowledgeportal.synapse.org/Explore/Target%20Enabling%20Resources?QueryWrapper0=%7B%22sql%22%3A%22select%20*%20from%20syn26146692%20WHERE%20%60isPublic%60%20%3D%20true%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22target%22%2C%22facetValues%22%3A%5B%22PLEC%22%5D%7D%5D%7D',
+  ensembl_info: [
+    {
+      ensembl_release: 84,
+      ensembl_possible_replacements: ['ENSG00000283172, ENSG00000283172'],
+      ensembl_permalink: 'https://may2015.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264794'
+    }
+  ]
 };
 
 export const geneMock3: Gene = {
@@ -3243,7 +3257,14 @@ export const geneMock3: Gene = {
   total_nominations: null,
   is_adi: false,
   is_tep: true,
-  resource_url: null
+  resource_url: null,
+  ensembl_info: [
+    {
+      ensembl_release: 84,
+      ensembl_possible_replacements: ['ENSG00000283172, ENSG00000283172'],
+      ensembl_permalink: 'https://may2015.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264794'
+    }
+  ]
 };
 
 export const gctGeneMock1: GCTGene = {
@@ -3421,7 +3442,14 @@ export const nominatedGeneMock1: Gene = {
   total_nominations: 4,
   is_adi: false,
   is_tep: false,
-  resource_url: null
+  resource_url: null,
+  ensembl_info: [
+    {
+      ensembl_release: 84,
+      ensembl_possible_replacements: ['ENSG00000283172, ENSG00000283172'],
+      ensembl_permalink: 'https://may2015.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264794'
+    }
+  ]
 } as Gene;
 
 export const noHGNCgeneMock: Gene = {
@@ -3518,5 +3546,12 @@ export const noHGNCgeneMock: Gene = {
   total_nominations: 4,
   is_adi: false,
   is_tep: false,
-  resource_url: null
+  resource_url: null,
+  ensembl_info: [
+    {
+      ensembl_release: 84,
+      ensembl_possible_replacements: ['ENSG00000283172, ENSG00000283172'],
+      ensembl_permalink: 'https://may2015.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000264794'
+    }
+  ]
 } as Gene;

src/server/api.ts

@@ -51,7 +51,7 @@ if (
     ],
     { region: 'us-east-1' }
   );
-
+  
   if (results && results.Parameters) {
     database.url =
       'mongodb://' +

src/server/models/genes.ts

@@ -12,6 +12,7 @@ import {
   TargetNomination,
   Druggability,
 } from '../../app/models';
+import { EnsemblInfo } from '../../app/models/EnsemblInfo';
 export { Gene } from '../../app/models';
 
 // -------------------------------------------------------------------------- //
@@ -42,6 +43,12 @@ const MedianExpressionSchema = new Schema<MedianExpression>({
   tissue: { type: String, required: true },
 });
 
+const EnsemblInfoSchema = new Schema<EnsemblInfo>({
+  ensembl_release: { type: Number, required: true },
+  ensembl_possible_replacements: { type: [String], required: true },
+  ensembl_permalink: { type: String, required: true }
+});
+
 const DruggabilitySchema = new Schema<Druggability>({
   sm_druggability_bucket: { type: Number, required: true },
   safety_bucket: { type: Number, required: true },
@@ -70,6 +77,7 @@ const GeneSchema = new Schema<Gene>(
     median_expression: { type: [MedianExpressionSchema], required: true },
     druggability: { type: [DruggabilitySchema], required: true },
     total_nominations: { type: Number, required: true },
+    ensembl_info: { type: [EnsemblInfoSchema], required: true }
   },
   { collection: 'geneinfo' }
 );