added docker

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})
   }
 

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)
     }
   })

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

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]);
         }
       }

projects/pathway-browser/src/app/reacfoam/reacfoam.service.ts

@@ -115,13 +115,13 @@ export class ReacfoamService {
 
   fetchEventsHierarchy(species: Species, params: Partial<EventsHierarchy.QueryParams>): Observable<EventsHierarchy.Data[]> {
     cleanObject(params)
-    console.log('fetch events hierarchy')
+    //console.log('fetch events hierarchy')
     return this.http.get<EventsHierarchy.Data[]>(`${CONTENT_SERVICE}/data/eventsHierarchy/${species.taxId}`, {params})
   }
 
 
   fetchTLPLayoutMap(): Observable<Map<string, Layout.Data>> {
-    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

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<PaletteGroup> = new Set();
       if (result.summary.type === 'GSA_REGULATION') {

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
     });

projects/pathway-browser/src/app/services/diagram.service.ts

@@ -202,18 +202,18 @@ export class DiagramService {
       diagram: this.http.get<Diagram>(`${this.general.download()}/diagram/${id}.json`),
       graph: this.http.get<Graph.Data>(`${this.general.download()}/diagram/${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(
             switchMap(normalPathwayId => forkJoin({
               normalDiagram: this.http.get<Diagram>(`${this.general.download()}/diagram/${normalPathwayId}.json`),
               normalGraph: this.http.get<Graph.Data>(`${this.general.download()}/diagram/${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<string, Promise<string | undefined>> = 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<number, Edge>(diagram.edges.map(edge => [edge.id, edge]));
     const idToNodes = new Map<number, Node>(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]

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[]]);

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);
     }

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});

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())
   }
 
 

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();
     }
   }

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,

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({
@@ -487,7 +487,9 @@ export namespace Search {
       isDisease: boolean;
       hasEHLD?: boolean;
       hasReferenceEntity: boolean;
-      disease: boolean
+      disease: boolean;
+      deleted: boolean;
+      date: number;
     }
 
     export interface EntryResult {

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();

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'))
       })

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'),

projects/website-angular/src/app/article/article/article.component.scss

@@ -11,6 +11,7 @@
 
 .article-title {
   margin: 0 0 1rem 0;
+  line-height: 32px;
   color: var(--primary);
 }