Merge pull request #983 from Sage-Bionetworks/staging

2.4.0 to production

.ebextensions/eb-options.config

@@ -1,7 +1,6 @@
 option_settings:
   aws:elasticbeanstalk:container:nodejs:
     ProxyServer: "nginx"
-    NodeCommand: "node --max_old_space_size=2000  ./dist/server.js"
 
   aws:elasticbeanstalk:command:
     Timeout: 2700

package.json

@@ -1,8 +1,8 @@
 {
   "name": "agora",
-  "version": "2.3.0",
+  "version": "2.4.0",
   "data-file": "syn13363290",
-  "data-version": "34",
+  "data-version": "35",
   "description": "An application to aggregate genomic evidence supporting candidate gene and module targets nominated by members of the AMP-AD consortium.",
   "keywords": [
     "angular8",
@@ -206,7 +206,7 @@
     "inline-manifest-webpack-plugin": "^4.0.2",
     "istanbul-instrumenter-loader": "^3.0.1",
     "jasmine-core": "^3.5.0",
-    "karma": "^6.3.2",
+    "karma": "^6.3.16",
     "karma-chrome-launcher": "^2.2.0",
     "karma-coverage": "^1.1.2",
     "karma-coverage-istanbul-reporter": "^2.1.1",
@@ -269,8 +269,8 @@
     "url": "https://github.com/Sage-Bionetworks/Agora/issues"
   },
   "engines": {
-    "node": ">= 10.13.0",
-    "npm": ">= 5"
+    "node": "12.22.3",
+    "npm": "6.14.13"
   },
   "browserslist": [
     "iOS >= 7",

src/app/charts/box-plot/box-plot-view/box-plot-view.component.ts

@@ -338,7 +338,8 @@ export class BoxPlotViewComponent implements OnInit, OnDestroy, AfterViewInit {
             logVals.push(self.dataService.getSignificantFigures(g.logfc));
             significanceTexts.push((g.adj_p_val <= 0.05) ?
             ' ' : 'not ');
-            phrases.push(g.hgnc_symbol + ' is ' + significanceTexts[significanceTexts.length - 1] +
+            phrases.push((g.hgnc_symbol || g.ensembl_gene_id) +
+                ' is ' + significanceTexts[significanceTexts.length - 1] +
                 'significantly differentially expressed in ' +
                 g.tissue +
                 ' with a log fold change value of ' + g.logfc + ' and an adjusted p-value of ' +

src/app/charts/box-plot/pbox-plot-view/pbox-plot-view.component.ts

@@ -328,7 +328,8 @@ export class PBoxPlotViewComponent implements OnInit, OnDestroy, AfterViewInit {
             logVals.push(p.log2_fc);
             significanceTexts.push((p.cor_pval <= 0.05) ?
             ' ' : 'not ');
-            phrases.push(p.hgnc_symbol + ' is ' + significanceTexts[significanceTexts.length - 1] +
+            phrases.push((p.hgnc_symbol || p.ensembl_gene_id) +
+                ' is ' + significanceTexts[significanceTexts.length - 1] +
                 'significantly differentially expressed in ' +
                 p.tissue +
                 ' with a log fold change value of ' + p.log2_fc + ' and an adjusted p-value of ' +

src/app/charts/candlestick-chart/candlestick-chart-view/candlestick-chart-view.component.ts

@@ -25,7 +25,7 @@ import * as d3 from 'd3';
 export class CandlestickChartViewComponent implements OnInit, OnDestroy, AfterViewInit {
 
     @ViewChild('chart', {static: false}) candleStickChart: ElementRef;
-    @Input() hgicId: string = '';
+    @Input() geneId: string = '';
 
     dataEmpty: boolean = true;
     rawData: any;
@@ -195,7 +195,7 @@ export class CandlestickChartViewComponent implements OnInit, OnDestroy, AfterVi
             .style('fill', color)
             .on('mouseover', d => {
                 const isOrNot = d.value.pval_adj <= 0.05 ? 'is' : 'is not';
-                const msg = `${this.hgicId} ${isOrNot} significantly correlated with ${d.key}, with an odds ratio of ${d.value.mean} and an adjusted p-value of ${d.value.pval_adj}.`;
+                const msg = `${this.geneId} ${isOrNot} significantly correlated with ${d.key}, with an odds ratio of ${d.value.mean} and an adjusted p-value of ${d.value.pval_adj}.`;
                 this.showTooltip(this.tooltip, msg);
             })
             .on('mouseout', d => this.hideTooltip(this.tooltip));

src/app/charts/force-chart/force-chart-view/force-chart-view.component.spec.ts

@@ -78,7 +78,7 @@ describe('Component: ForceChartView', () => {
             ensembl_gene_id: 'ENSG00000169436',
             group: 2,
             hgnc_symbol: 'COL22A1',
-            id: 'ENSG00000128564',
+            id: 'ENSG00000169436',
             index: 1,
             vx: 0.6383193392459895,
             vy: -4.464810585759529,
@@ -93,8 +93,8 @@ describe('Component: ForceChartView', () => {
             links: [
                 {
                     brainregions: ['DLPFC'],
-                    hgnc_symbolA: 'VGF',
-                    hgnc_symbolB: 'COL22A1',
+                    geneIdA: 'VGF',
+                    geneIdB: 'COL22A1',
                     source: mockNode1,
                     target: mockNode2,
                     value: 1

src/app/charts/force-chart/force-chart-view/force-chart-view.component.ts

@@ -250,7 +250,7 @@ export class ForceChartViewComponent implements OnInit, AfterViewInit, OnChanges
             .selectAll('text')
             .data(this.networkData.nodes, (d) =>  d.id)
             .enter().append('text')
-            .text((node: any) => node.hgnc_symbol)
+            .text((node: any) => (node.hgnc_symbol || node.ensembl_gene_id))
             .attr('font-size', 12)
             .attr('dx', 13)
             .attr('dy', 4);
@@ -271,7 +271,7 @@ export class ForceChartViewComponent implements OnInit, AfterViewInit, OnChanges
                     // A font size of 12 has 16 pixels per letter, so we pick
                     // half the word and make a negative dx. The anchor is in
                     // the middle so we half the result again
-                    return (((-node.hgnc_symbol.length * 16) / 2) / 2);
+                    return (((-(node.hgnc_symbol.length || node.ensembl_gene_id.length) * 16) / 2) / 2);
                 })
                 .attr('dy', (node: any) => {
                     return 35;
@@ -367,7 +367,7 @@ export class ForceChartViewComponent implements OnInit, AfterViewInit, OnChanges
             .data(this.networkData.nodes, (d) =>  d.id);
         this.textElements.exit().remove();
         this.textElements = this.textElements.enter().append('text')
-            .text((node: any) => node.hgnc_symbol)
+            .text((node: any) => (node.hgnc_symbol || node.ensembl_gene_id))
             .attr('font-size', 12)
             .attr('dx', 23)
             .attr('dy', 4)

src/app/charts/row-chart/row-chart-view/row-chart-view.component.spec.ts

@@ -11,8 +11,8 @@ import { Router } from '@angular/router';
 import {
     RouterStub,
     GeneServiceStub,
-    DataServiceStub,
     ChartServiceStub,
+    DataServiceStub,
     mockModels,
     mockTissues
 } from '../../../testing';
@@ -28,7 +28,6 @@ describe('Component: RowChartView', () => {
     let router: RouterStub;
     let geneService: GeneServiceStub;
     let chartService: ChartServiceStub;
-    let dataService: DataServiceStub;
     let location: SpyLocation;
 
     beforeEach(async(() => {
@@ -54,7 +53,6 @@ describe('Component: RowChartView', () => {
         // Get the injected instances
         router = fixture.debugElement.injector.get(Router);
         geneService = fixture.debugElement.injector.get(GeneService);
-        dataService = fixture.debugElement.injector.get(DataService);
         chartService = fixture.debugElement.injector.get(ChartService);
         location = fixture.debugElement.injector.get(SpyLocation);
 

src/app/charts/row-chart/row-chart-view/row-chart-view.component.ts

@@ -356,8 +356,11 @@ export class RowChartViewComponent implements OnInit, OnDestroy, AfterViewInit,
         const allTicks = chart.selectAll('g.axis g.tick');
         allTicks.each(function(t, i) {
             let value = parseFloat(d3.select(this).select('text').text());
-            // Handle UTF-8 characters, if text is not a number, then replace all non-numeric values with the empty string
-            value = isNaN(value) ? parseFloat('-' + d3.select(this).select('text').text().replace(/[^,.0-9]/g, '')) : value;
+            // Handle UTF-8 characters, if text is not a number,
+            // then replace all non-numeric values with the empty string
+            value = isNaN(value) ?
+                parseFloat('-' + d3.select(this).select('text').text().replace(/[^,.0-9]/g, '')) :
+                value;
 
             if (i > 0 && i < allTicks.size() - 1) {
                 if (value) {

src/app/charts/select-menu/select-menu-view/select-menu-view.component.spec.ts

@@ -64,7 +64,7 @@ describe('Component: SelectMenuView', () => {
         geneService = fixture.debugElement.injector.get(GeneService);
         chartService = fixture.debugElement.injector.get(ChartService);
         activatedRoute = fixture.debugElement.injector.get(ActivatedRoute);
-        activatedRoute.setParamMap({ id: mockInfo1.hgnc_symbol });
+        activatedRoute.setParamMap({ id: mockInfo1.ensembl_gene_id });
         location = fixture.debugElement.injector.get(SpyLocation);
 
         component = fixture.componentInstance; // Component test instance

src/app/charts/select-menu/select-menu-view/select-menu-view.component.ts

@@ -446,11 +446,11 @@ export class SelectMenuViewComponent implements OnInit, OnDestroy {
                 const cPromise = new Promise(async (resolve, reject) => {
                     if (self.type === 'RNA') {
                         self.chartService.queryFilter.smGroup = c.innerHTML;
-                        const gene = self.geneService.getCurrentGene().hgnc_symbol;
                         self.isActive = false;
 
                         await self.apiService.refreshChartsData(
-                            self.chartService.queryFilter.smGroup, gene
+                            self.chartService.queryFilter.smGroup,
+                            self.geneService.getCurrentGene().ensembl_gene_id
                         )
                             .subscribe((results) => {
                             self.chartService.filteredData = results;
@@ -459,11 +459,13 @@ export class SelectMenuViewComponent implements OnInit, OnDestroy {
                         });
                     } else if (self.type === 'Proteomics') {
                         self.chartService.pQueryFilter.spGroup = c.innerHTML;
-                        const gene = self.geneService.getCurrentGene().hgnc_symbol;
                         self.isActive = false;
 
                         await self.apiService.refreshChartsData(
-                            self.chartService.pQueryFilter.spGroup, gene, self.type)
+                            self.chartService.pQueryFilter.spGroup,
+                            self.geneService.getCurrentGene().ensembl_gene_id,
+                            self.type
+                        )
                             .subscribe((results) => {
                             self.chartService.filteredData = results;
                             self.isActive = true;

src/app/core/core-routing.module.ts

@@ -6,15 +6,13 @@ import { HelpComponent } from './help';
 import { NoContentComponent } from './no-content';
 import { SynapseAccountComponent } from './synapse-account';
 import { ContribTeamsPageComponent } from './contrib-teams';
-import { TermsComponent } from './terms';
 import { NewsComponent } from './news';
 
 export const routes: Routes = [
     { path: '', loadChildren: '../genes/genes.module#GenesModule'},
     { path: 'about', component: AboutComponent },
     { path: 'news', component: NewsComponent },
     { path: 'help', component: HelpComponent },
-    { path: 'terms', component: TermsComponent },
     { path: 'teams-contributing', component: ContribTeamsPageComponent },
     { path: 'synapse-account', component: SynapseAccountComponent },
     { path: 'no-content', component: NoContentComponent },

src/app/core/core.module.ts

@@ -18,7 +18,6 @@ import {
 import { AboutComponent } from './about';
 import { NewsComponent } from './news';
 import { HelpComponent } from './help';
-import { TermsComponent } from './terms';
 import { SynapseAccountComponent } from './synapse-account';
 import { NavbarComponent } from './navbar';
 import { MenubarComponent } from './menubar';
@@ -43,7 +42,6 @@ import '../../styles/headings.scss';
         AboutComponent,
         NewsComponent,
         HelpComponent,
-        TermsComponent,
         ContribTeamsPageComponent,
         SynapseAccountComponent
     ],
@@ -55,7 +53,6 @@ import '../../styles/headings.scss';
         NoContentComponent,
         AboutComponent,
         HelpComponent,
-        TermsComponent,
         ContribTeamsPageComponent,
         SynapseAccountComponent
     ],

src/app/core/services/api.service.spec.ts

@@ -55,11 +55,11 @@ describe('Service: Api: TestBed', () => {
     it('should get the genes data from the server', () => {
         const dummyGenes = mockGenesResponse;
 
-        apiService.getGenes('VGF').subscribe((response) => {
+        apiService.getGenes('ENSG00000128564').subscribe((response) => {
             expect(response).toEqual(mockGenesResponse);
         });
 
-        const req = httpMock.expectOne('/api/genes?id=VGF');
+        const req = httpMock.expectOne('/api/genes?id=ENSG00000128564');
         expect(req.request.method).toBe('GET');
         req.flush(dummyGenes);
     });
@@ -102,7 +102,7 @@ describe('Service: Api: TestBed', () => {
 
     it('should get the gene data from the server', () => {
         const res = { mockInfo1, mockGene1 };
-        apiService.getGene('VGF', 'DLPFC', 'AD+Diagnosis+%28males+and+females%29')
+        apiService.getGene('ENSG00000128564', 'DLPFC', 'AD+Diagnosis+%28males+and+females%29')
             .subscribe((response) => {
             expect(response).toEqual(res);
         });
@@ -178,13 +178,13 @@ describe('Service: Api: TestBed', () => {
     it('should trigger a refresh for the charts on the server', () => {
         const res: string[] = mockModels;
 
-        apiService.refreshChartsData('AD Diagnosis (males and females)', 'VGF').subscribe(
+        apiService.refreshChartsData('AD Diagnosis (males and females)', 'ENSG00000128564').subscribe(
             (response) => {
             expect(response).toEqual(res);
         });
 
         const req = httpMock.expectOne(
-            '/api/refresh?filter=' + JSON.stringify('AD Diagnosis (males and females)') + '&id=VGF'
+            '/api/refresh?filter=' + JSON.stringify('AD Diagnosis (males and females)') + '&id=ENSG00000128564'
         );
         expect(req.request.method).toBe('GET');
         req.flush(res);

src/app/core/services/data.service.ts

@@ -38,7 +38,7 @@ export class DataService {
     ) {}
 
     loadData(gene: Gene): Observable<any[]> {
-        const genesResponse = this.apiService.getGenes(gene.hgnc_symbol);
+        const genesResponse = this.apiService.getGenes(gene.ensembl_gene_id);
         const nodesResponse = this.apiService.getLinksList(gene);
 
         return forkJoin([

src/app/core/services/force.service.ts

@@ -169,8 +169,8 @@ export class ForceService {
                 source: obj.geneA_ensembl_gene_id,
                 target: obj.geneB_ensembl_gene_id,
                 brainregions: [obj.brainRegion],
-                hgnc_symbolA: obj.geneA_external_gene_name,
-                hgnc_symbolB: obj.geneB_external_gene_name
+                geneIdA: obj.geneA_external_gene_name || obj.geneA_ensembl_gene_id,
+                geneIdB: obj.geneB_external_gene_name || obj.geneB_ensembl_gene_id
             };
             dicL[obj.geneA_ensembl_gene_id + obj.geneB_ensembl_gene_id] = link;
             genes.links = [...genes.links,

src/app/core/services/gene.service.spec.ts

@@ -3,7 +3,12 @@ import {
 } from '@angular/core/testing';
 
 import {
-    ApiServiceStub, mockGene1, mockGeneResponse1, mockGeneResponseNoGeneItem, mockGeneResponseNoExpValidation, mockGeneResponseNoScores
+    ApiServiceStub,
+    mockGene1,
+    mockGeneResponse1,
+    mockGeneResponseNoGeneItem,
+    mockGeneResponseNoExpValidation,
+    mockGeneResponseNoScores
 } from '../../testing';
 
 import { ApiService, GeneService } from './';

src/app/core/services/gene.service.ts

@@ -65,7 +65,7 @@ export class GeneService {
 
     updatePreviousGene() {
         // Only update the previous gene if we already have a current one
-        if (this.getCurrentGene() && this.getCurrentGene().hgnc_symbol) {
+        if (this.getCurrentGene() && this.getCurrentGene().ensembl_gene_id) {
             this.setPreviousGene(this.getCurrentGene());
         }
     }
@@ -275,7 +275,7 @@ export class GeneService {
 
     hasGeneChanged(): boolean {
         return (this.getPreviousGene() && this.getCurrentGene()) ?
-            this.getPreviousGene().hgnc_symbol !== this.getCurrentGene().hgnc_symbol :
+            this.getPreviousGene().ensembl_gene_id !== this.getCurrentGene().ensembl_gene_id :
             false;
     }