From 5fa5246f442d67b21c5a4acaf89aad7f045d05fe Mon Sep 17 00:00:00 2001 From: el-rabies Date: Wed, 1 Apr 2026 13:31:17 -0400 Subject: [PATCH] chore: Removed logging from all files to clear console. --- .../tabs/result-tab/result-tab.component.ts | 20 +++++++------- .../src/app/diagram/diagram.component.ts | 4 +-- .../event-hierarchy.component.ts | 6 ++--- .../src/app/reacfoam/reacfoam.component.ts | 2 +- .../src/app/reacfoam/reacfoam.service.ts | 4 +-- .../src/app/services/analysis.service.ts | 4 +-- .../src/app/services/data-state.service.ts | 6 ++--- .../src/app/services/diagram.service.ts | 26 +++++++++---------- .../src/app/services/event.service.ts | 2 +- .../src/app/services/species.service.ts | 2 +- .../src/app/services/url-state.service.ts | 8 +++--- .../src/app/shared/logger/logger.component.ts | 2 +- .../expandable-virtual-scroll.strategy.ts | 6 ++--- .../qualitative-analysis.component.ts | 2 +- .../app/viewport/search/search.component.ts | 2 +- .../src/app/viewport/viewport.component.ts | 2 +- .../src/lib/interactivity.ts | 4 +-- .../reactome-cytoscape-style/src/lib/style.ts | 2 +- .../src/scripts/generate-index.ts | 6 ++--- projects/website-angular/src/server.ts | 2 +- 20 files changed, 56 insertions(+), 56 deletions(-) diff --git a/projects/pathway-browser/src/app/details/tabs/result-tab/result-tab.component.ts b/projects/pathway-browser/src/app/details/tabs/result-tab/result-tab.component.ts index 8cfd617..cd9f4e4 100644 --- a/projects/pathway-browser/src/app/details/tabs/result-tab/result-tab.component.ts +++ b/projects/pathway-browser/src/app/details/tabs/result-tab/result-tab.component.ts @@ -148,29 +148,29 @@ export class ResultTabComponent { let size = data.length if (this.includeGrouping() === false) { data = data.filter(p => p.llp) - console.log('Filter llp', size, '==>', data.length) + //console.log('Filter llp', size, '==>', data.length) size = data.length } if (this.includeDisease() === false) { data = data.filter(p => !p.inDisease) - console.log('Filter disease', size, '==>', data.length) + //console.log('Filter disease', size, '==>', data.length) size = data.length } if (this.state.fdrFilter() !== undefined) { data = data.filter(p => p.entities.fdr <= this.state.fdrFilter()!) - console.log('Filter fdr', size, '==>', data.length) + //console.log('Filter fdr', size, '==>', data.length) } if (this.state.minExpressionFilter() !== undefined) { data = data.filter(p => p.entities.exp[this.analysis.sampleIndex()] >= this.state.minExpressionFilter()!) - console.log('Filter minExpression', size, '==>', data.length) + //console.log('Filter minExpression', size, '==>', data.length) } if (this.state.maxExpressionFilter() !== undefined) { data = data.filter(p => p.entities.exp[this.analysis.sampleIndex()] <= this.state.maxExpressionFilter()!) - console.log('Filter minExpression', size, '==>', data.length) + //console.log('Filter minExpression', size, '==>', data.length) } if (this.state.gsaFilter().length !== 0) { data = data.filter(p => this.gsaFilterSet().has(p.entities.exp[this.analysis.sampleIndex()])) - console.log('Filter gsa', size, '==>', data.length) + //console.log('Filter gsa', size, '==>', data.length) } return data }) @@ -182,15 +182,15 @@ export class ResultTabComponent { let size = data.length if (this.state.pathwayMinSizeFilter()) { data = data.filter(p => p.entities.total >= this.state.pathwayMinSizeFilter()!) - console.log('Filter min size', size, '==>', data.length) + //console.log('Filter min size', size, '==>', data.length) size = data.length } if (this.state.pathwayMaxSizeFilter()) { data = data.filter(p => p.entities.total <= this.state.pathwayMaxSizeFilter()!) - console.log('Filter max size', size, '==>', data.length) + //console.log('Filter max size', size, '==>', data.length) size = data.length } - console.log("Total filter", this.analysis.result()?.pathways.length, '==>', size) + //console.log("Total filter", this.analysis.result()?.pathways.length, '==>', size) return data; }) @@ -276,7 +276,7 @@ export class ResultTabComponent { visitPathway(pathway: Analysis.Pathway) { this.data.selectedPathwayStId.set(pathway.stId) - console.log("Navigating to " + pathway.stId) + //console.log("Navigating to " + pathway.stId) this.state.navigateTo(pathway.stId, {queryParamsHandling: 'preserve', preserveFragment: true}) } diff --git a/projects/pathway-browser/src/app/diagram/diagram.component.ts b/projects/pathway-browser/src/app/diagram/diagram.component.ts index a838fa1..1322e64 100644 --- a/projects/pathway-browser/src/app/diagram/diagram.component.ts +++ b/projects/pathway-browser/src/app/diagram/diagram.component.ts @@ -964,7 +964,7 @@ export class DiagramComponent implements AfterViewInit, OnDestroy { const resource = this.state.overlay(); if (resource) { - console.log('Resource not null', resource) + //console.log('Resource not null', resource) this.interactorsComponent()?.getInteractors(resource) } @@ -1064,7 +1064,7 @@ export class DiagramComponent implements AfterViewInit, OnDestroy { filter((e) => e.detail.cy !== this.legend && e.type === ReactomeEventTypes.unselect) ).subscribe(e => { if (this.state.select() === e.detail.element.data('graph.stId')) { - console.log('Unselect', e.detail.reactomeId) + //console.log('Unselect', e.detail.reactomeId) this.state.select.set(null) } }) diff --git a/projects/pathway-browser/src/app/event-hierarchy/event-hierarchy.component.ts b/projects/pathway-browser/src/app/event-hierarchy/event-hierarchy.component.ts index 762ac02..9856baf 100644 --- a/projects/pathway-browser/src/app/event-hierarchy/event-hierarchy.component.ts +++ b/projects/pathway-browser/src/app/event-hierarchy/event-hierarchy.component.ts @@ -250,7 +250,7 @@ export class EventHierarchyComponent implements AfterViewInit, OnDestroy { // Combine all data and merged into one object initialData$.pipe( - tap(d => console.log('Initial data', d)), + //tap(d => console.log('Initial data', d)), switchMap(initialData => enhancedEventData$.pipe( combineLatestWith( @@ -265,14 +265,14 @@ export class EventHierarchyComponent implements AfterViewInit, OnDestroy { })) ) ), - tap(d => console.log('Combined data', d)), + //tap(d => console.log('Combined data', d)), // Build the tree with all data switchMap(({ enhancedEvent, hitReactions }) => this.eventService.buildTree(enhancedEvent, this.pathwayId(), this.tree, hitReactions)), - tap(d => console.log('Final data', d)), + //tap(d => console.log('Final data', d)), ).subscribe({ next: () => { // Give pathway id when idToUse is PEs diff --git a/projects/pathway-browser/src/app/reacfoam/reacfoam.component.ts b/projects/pathway-browser/src/app/reacfoam/reacfoam.component.ts index e28aa6f..f397229 100644 --- a/projects/pathway-browser/src/app/reacfoam/reacfoam.component.ts +++ b/projects/pathway-browser/src/app/reacfoam/reacfoam.component.ts @@ -207,7 +207,7 @@ export class ReacfoamComponent implements OnDestroy { if (selectedElement && isRLE(selectedElement)) { const flaggingResult = await firstValueFrom(this.data.getReacfoamFlagging(selectedElement.stId, this.species.currentSpecies().displayName)); if (flaggingResult.matches && flaggingResult.matches.length === 1) { - console.log('Selecting in reacfoam the parent pathway of a reaction as it is only contained in one pathway') + //console.log('Selecting in reacfoam the parent pathway of a reaction as it is only contained in one pathway') this.select.set(flaggingResult.matches[0]); } } diff --git a/projects/pathway-browser/src/app/reacfoam/reacfoam.service.ts b/projects/pathway-browser/src/app/reacfoam/reacfoam.service.ts index 9853f06..1175218 100644 --- a/projects/pathway-browser/src/app/reacfoam/reacfoam.service.ts +++ b/projects/pathway-browser/src/app/reacfoam/reacfoam.service.ts @@ -115,13 +115,13 @@ export class ReacfoamService { fetchEventsHierarchy(species: Species, params: Partial): Observable { cleanObject(params) - console.log('fetch events hierarchy') + //console.log('fetch events hierarchy') return this.http.get(`${CONTENT_SERVICE}/data/eventsHierarchy/${species.taxId}`, {params}) } fetchTLPLayoutMap(): Observable> { - console.log('fetch tlp layout') + //console.log('fetch tlp layout') return this.http.get(LAYOUT_URL, {responseType: "text"}).pipe( map((text) => new Map( text.split("\n") // Split lines diff --git a/projects/pathway-browser/src/app/services/analysis.service.ts b/projects/pathway-browser/src/app/services/analysis.service.ts index b8c8eea..892c08c 100644 --- a/projects/pathway-browser/src/app/services/analysis.service.ts +++ b/projects/pathway-browser/src/app/services/analysis.service.ts @@ -245,7 +245,7 @@ export class AnalysisService { species: this.state.speciesFilter() }), loader: ({request, previous}) => { - console.log("Loading ", request, previous) + //console.log("Loading ", request, previous) return request.token ? this.loadAnalysis(request.token, { resource: request.resource || undefined, @@ -323,7 +323,7 @@ export class AnalysisService { effect(() => { const result = this.result(); - console.log('Result updated', result) + //console.log('Result updated', result) if (!result) return const validGroups: Set = new Set(); if (result.summary.type === 'GSA_REGULATION') { diff --git a/projects/pathway-browser/src/app/services/data-state.service.ts b/projects/pathway-browser/src/app/services/data-state.service.ts index 427d6da..ca7c50b 100644 --- a/projects/pathway-browser/src/app/services/data-state.service.ts +++ b/projects/pathway-browser/src/app/services/data-state.service.ts @@ -96,7 +96,7 @@ export class DataStateService { diagram: this.state.pathwayId(), species: this.species.currentSpecies().displayName, }) - console.log('updating request', params); + // console.log('updating request', params); return params; }) @@ -155,8 +155,8 @@ export class DataStateService { constructor(private state: UrlStateService, private http: HttpClient, private species: SpeciesService) { - effect(() => console.log('Flagging', this.flagIdentifiers())); - effect(() => console.log('Flagging error', this.flagResource.error())); + // effect(() => console.log('Flagging', this.flagIdentifiers())); + // effect(() => console.log('Flagging error', this.flagResource.error())); effect(() => { if (this._selectedElement.error()) this.state.select.set(null); // If selection doesn't exist (wrong id), we remove selection }); diff --git a/projects/pathway-browser/src/app/services/diagram.service.ts b/projects/pathway-browser/src/app/services/diagram.service.ts index a3e6ecb..c9a15e1 100644 --- a/projects/pathway-browser/src/app/services/diagram.service.ts +++ b/projects/pathway-browser/src/app/services/diagram.service.ts @@ -202,7 +202,7 @@ export class DiagramService { diagram: this.http.get(`${this.general.download()}/diagram/${id}.json`), graph: this.http.get(`${this.general.download()}/diagram/${id}.graph.json`) }).pipe( - tap(({diagram, graph}) => console.log('Original diagram:', diagram, 'Original graph', graph)), + // tap(({diagram, graph}) => console.log('Original diagram:', diagram, 'Original graph', graph)), switchMap(({diagram, graph}) => { if (diagram.forNormalDraw !== undefined && !diagram.forNormalDraw) { return this.getNormalPathway(diagram.stableId).pipe( @@ -210,10 +210,10 @@ export class DiagramService { normalDiagram: this.http.get(`${this.general.download()}/diagram/${normalPathwayId}.json`), normalGraph: this.http.get(`${this.general.download()}/diagram/${normalPathwayId}.graph.json`) })), - tap(({ - normalGraph, - normalDiagram - }) => console.log('Normal diagram:', normalGraph, 'Normal graph', normalDiagram)), + // tap(({ + // normalGraph, + // normalDiagram + // }) => console.log('Normal diagram:', normalGraph, 'Normal graph', normalDiagram)), map(({normalGraph, normalDiagram}) => { graph.nodes.push(...normalGraph.nodes); graph.edges.push(...normalGraph.edges); @@ -233,7 +233,7 @@ export class DiagramService { return of({diagram, graph}); } }), - tap((mergedResponse) => console.log('All responses:', mergedResponse)), + // tap((mergedResponse) => console.log('All responses:', mergedResponse)), map(mergedResponse => ({ ...mergedResponse, chebiMapping: this.getCHEBIStructure( @@ -244,7 +244,7 @@ export class DiagramService { ) })), map(({diagram, graph, chebiMapping}) => this.diagramFromData(diagram, graph, id, chebiMapping)), - tap((output) => console.log('Output:', output)), + // tap((output) => console.log('Output:', output)), ) } @@ -255,11 +255,11 @@ export class DiagramService { id: number | string = '', chebiMapping: Map> = new Map() ): cytoscape.ElementsDefinition { - console.log("edge.reactionType", new Set(diagram.edges.flatMap(edge => edge.reactionType))) - console.log("node.connectors.types", new Set(diagram.nodes.flatMap(node => node.connectors.flatMap(con => con.type)))) - console.log("node.renderableClass", new Set(diagram.nodes.flatMap(node => node.renderableClass))) - console.log("links.renderableClass", new Set(diagram.links.flatMap(link => link.renderableClass))) - console.log("shadow.renderableClass", new Set(diagram.shadows.flatMap(shadow => shadow.renderableClass))) + // console.log("edge.reactionType", new Set(diagram.edges.flatMap(edge => edge.reactionType))) + // console.log("node.connectors.types", new Set(diagram.nodes.flatMap(node => node.connectors.flatMap(con => con.type)))) + // console.log("node.renderableClass", new Set(diagram.nodes.flatMap(node => node.renderableClass))) + // console.log("links.renderableClass", new Set(diagram.links.flatMap(link => link.renderableClass))) + // console.log("shadow.renderableClass", new Set(diagram.shadows.flatMap(shadow => shadow.renderableClass))) const idToEdges = new Map(diagram.edges.map(edge => [edge.id, edge])); const idToNodes = new Map(diagram.nodes.map(node => [node.id, node])); @@ -673,7 +673,7 @@ export class DiagramService { } ) - console.log('All data created') + // console.log('All data created') return { nodes: [...compartmentNodes, ...reactionNodes, ...entityNodes, ...shadowNodes], edges: [...edges, ...linkEdges] diff --git a/projects/pathway-browser/src/app/services/event.service.ts b/projects/pathway-browser/src/app/services/event.service.ts index 49522a7..c353120 100644 --- a/projects/pathway-browser/src/app/services/event.service.ts +++ b/projects/pathway-browser/src/app/services/event.service.ts @@ -360,7 +360,7 @@ export class EventService { : object.stId; this.dboService.setCurrentObj(object); - console.log('Build tree with selected event', idToBuild); + // console.log('Build tree with selected event', idToBuild); const ancestors = idToBuild ? this.fetchEventAncestors(idToBuild).pipe(map(ancestors => this.getFinalAncestor(ancestors, diagramId ? [diagramId] : undefined))) : from([[] as Event[]]); diff --git a/projects/pathway-browser/src/app/services/species.service.ts b/projects/pathway-browser/src/app/services/species.service.ts index 440b062..e735376 100644 --- a/projects/pathway-browser/src/app/services/species.service.ts +++ b/projects/pathway-browser/src/app/services/species.service.ts @@ -116,7 +116,7 @@ export class SpeciesService { newValue = newValue.replaceAll(initial, replacement || ''); } newValue = newValue.replaceAll(',""', '').replaceAll('""', '').trim() // Remove trailing commas and quotes from lists - console.log(value, " => ", newValue); + // console.log(value, " => ", newValue); if (newValue.length === 0) delete params[key]; else params[key] = JSON.parse(newValue); } diff --git a/projects/pathway-browser/src/app/services/url-state.service.ts b/projects/pathway-browser/src/app/services/url-state.service.ts index 238bcd4..aa98b5c 100644 --- a/projects/pathway-browser/src/app/services/url-state.service.ts +++ b/projects/pathway-browser/src/app/services/url-state.service.ts @@ -123,11 +123,11 @@ export class UrlStateService implements State { }); effect(() => { - console.log('Updating patwhayId to ', this.pathwayId()) + // console.log('Updating patwhayId to ', this.pathwayId()) //If in content/search do not navigate if (this.router.url.includes('content') || this.router.url.includes('query')) { - console.log('In content or search route, not navigating on pathwayId change'); + // console.log('In content or search route, not navigating on pathwayId change'); return; } @@ -214,9 +214,9 @@ export class UrlStateService implements State { if (typeof paramValue === 'string') paramValue = paramValue.replaceAll(' ', '__') queryParams[key] = isArray(paramValue) ? paramValue.join(';') : paramValue; } - console.log('Updating URL from state', queryParams) + // console.log('Updating URL from state', queryParams) if (this.router.url.includes('content') || this.router.url.includes('query')) { - console.log('In content or search route, not navigating on state change'); + // console.log('In content or search route, not navigating on state change'); return; } this.navigateTo(this.pathwayId() ?? null, {queryParams, preserveFragment: true}); diff --git a/projects/pathway-browser/src/app/shared/logger/logger.component.ts b/projects/pathway-browser/src/app/shared/logger/logger.component.ts index 396533e..3f9973a 100644 --- a/projects/pathway-browser/src/app/shared/logger/logger.component.ts +++ b/projects/pathway-browser/src/app/shared/logger/logger.component.ts @@ -11,7 +11,7 @@ export class LoggerComponent implements OnInit{ } ngOnInit(): void { - console.log('Building ', this.toLog()) + // console.log('Building ', this.toLog()) } diff --git a/projects/pathway-browser/src/app/utils/expandable-virtual-scroll/expandable-virtual-scroll.strategy.ts b/projects/pathway-browser/src/app/utils/expandable-virtual-scroll/expandable-virtual-scroll.strategy.ts index c8633db..61eb84e 100644 --- a/projects/pathway-browser/src/app/utils/expandable-virtual-scroll/expandable-virtual-scroll.strategy.ts +++ b/projects/pathway-browser/src/app/utils/expandable-virtual-scroll/expandable-virtual-scroll.strategy.ts @@ -11,14 +11,14 @@ export class ExpandableVirtualScrollStrategy extends FixedSizeVirtualScrollStrat private maxBufferPx: number = 200; constructor() { - console.log('Expandable Virtual Scroll Strategy.'); + // console.log('Expandable Virtual Scroll Strategy.'); super(28, 100, 200); } override attach(viewport: CdkVirtualScrollViewport): void { // super.attach(viewport); this.viewport = viewport; - console.log('Attempting to attach', viewport); + // console.log('Attempting to attach', viewport); } setItemHeight(index: number, height: number) { @@ -28,7 +28,7 @@ export class ExpandableVirtualScrollStrategy extends FixedSizeVirtualScrollStrat } else { this._indexToHeight.set(index, height); } - console.log(index, height); + // console.log(index, height); this._updateViewport(); } } diff --git a/projects/pathway-browser/src/app/viewport/analysis-form/qualitative-analysis/qualitative-analysis.component.ts b/projects/pathway-browser/src/app/viewport/analysis-form/qualitative-analysis/qualitative-analysis.component.ts index 955ab9c..c63f4d3 100644 --- a/projects/pathway-browser/src/app/viewport/analysis-form/qualitative-analysis/qualitative-analysis.component.ts +++ b/projects/pathway-browser/src/app/viewport/analysis-form/qualitative-analysis/qualitative-analysis.component.ts @@ -103,7 +103,7 @@ export class QualitativeAnalysisComponent implements AfterViewInit { }); effect(async () => { if (!this.lottieCanvas() || this.lottieEnd !== undefined) return; - console.log('Building lottie') + // console.log('Building lottie') this.lottieEnd = await this.lottieService.buildLottie({ renderConfig: { autoResize: true, diff --git a/projects/pathway-browser/src/app/viewport/search/search.component.ts b/projects/pathway-browser/src/app/viewport/search/search.component.ts index d9185f4..c8ae515 100644 --- a/projects/pathway-browser/src/app/viewport/search/search.component.ts +++ b/projects/pathway-browser/src/app/viewport/search/search.component.ts @@ -193,7 +193,7 @@ export class SearchComponent { this.searchText.set(searchText); if (event) event.preventDefault(); this.collapsed.set('opened') - console.log('searching', searchText); + // console.log('searching', searchText); this.typeFilter.set([]) this.selectedResult.set(undefined) this.searchParams.set({ diff --git a/projects/pathway-browser/src/app/viewport/viewport.component.ts b/projects/pathway-browser/src/app/viewport/viewport.component.ts index 038ac9b..69e6d74 100644 --- a/projects/pathway-browser/src/app/viewport/viewport.component.ts +++ b/projects/pathway-browser/src/app/viewport/viewport.component.ts @@ -245,7 +245,7 @@ export class ViewportComponent implements AfterViewInit { playSpeed = model(2); updateSpeed = effect(() => { - console.log('Update play speed', this.playSpeed()); + // console.log('Update play speed', this.playSpeed()); if (this.interval) { this.pause(); this.play(); diff --git a/projects/reactome-cytoscape-style/src/lib/interactivity.ts b/projects/reactome-cytoscape-style/src/lib/interactivity.ts index 1a09382..f9edc2a 100644 --- a/projects/reactome-cytoscape-style/src/lib/interactivity.ts +++ b/projects/reactome-cytoscape-style/src/lib/interactivity.ts @@ -15,7 +15,7 @@ export class Interactivity { isMobile = 'ontouchstart' in document || navigator.maxTouchPoints > 0; constructor(private cy: cytoscape.Core, private properties: Properties) { - console.log('is mobile', this.isMobile) + // console.log('is mobile', this.isMobile) // @ts-ignore cy.elements().ungrabify().panify(); this.initHover(cy); @@ -102,7 +102,7 @@ export class Interactivity { .on('mouseover', 'edge', e => { const mapped = mapper(e.target); - if (mapped !== e.target) console.log(mapped, mapped.connectedNodes('.reaction')) + // if (mapped !== e.target) console.log(mapped, mapped.connectedNodes('.reaction')) hoverReaction(mapped.connectedNodes('.reaction')) }) diff --git a/projects/reactome-cytoscape-style/src/lib/style.ts b/projects/reactome-cytoscape-style/src/lib/style.ts index dc34449..515cfa6 100644 --- a/projects/reactome-cytoscape-style/src/lib/style.ts +++ b/projects/reactome-cytoscape-style/src/lib/style.ts @@ -198,7 +198,7 @@ export class Style { css: { "background-color": (node) => { const exp = node.data('exp') as number[]; - console.log(node.data(), exp) + // console.log(node.data(), exp) return exp !== undefined ? this.currentPalette(exp[0]).hex() : this.pm('analysis', 'notFound', c => c)() }, "border-width": this.p('global', 'thickness'), diff --git a/projects/website-angular/src/scripts/generate-index.ts b/projects/website-angular/src/scripts/generate-index.ts index 40a3268..bbdc40e 100644 --- a/projects/website-angular/src/scripts/generate-index.ts +++ b/projects/website-angular/src/scripts/generate-index.ts @@ -150,9 +150,9 @@ function generateSiteSearchIndex(): void { const outputPath = path.join(outputDir, 'site-search-index.json'); fs.writeFileSync(outputPath, JSON.stringify(items)); - console.log( - `Site search index generated: ${items.length} entries → ${outputPath}` - ); + // console.log( + // `Site search index generated: ${items.length} entries → ${outputPath}` + // ); } function loadNewsArticlesFromDir(dir: string): ArticleIndexItem[] { diff --git a/projects/website-angular/src/server.ts b/projects/website-angular/src/server.ts index cf38c8c..695e5a1 100644 --- a/projects/website-angular/src/server.ts +++ b/projects/website-angular/src/server.ts @@ -75,7 +75,7 @@ function run(): void { // Start up the Node server const server = app(); server.listen(port, () => { - console.log(`Node Express server listening on http://localhost:${port}`); + // console.log(`Node Express server listening on http://localhost:${port}`); }); }