fix: Fix PathwayBrowser navigation and event hierarchy tree

projects/pathway-browser/src/app/details/tabs/result-tab/result-tab.component.ts

@@ -277,7 +277,7 @@ export class ResultTabComponent {
   visitPathway(pathway: Analysis.Pathway) {
     this.data.selectedPathwayStId.set(pathway.stId)
     console.log("Navigating to " + pathway.stId)
-    this.router.navigate([pathway.stId], {queryParamsHandling: 'preserve', preserveFragment: true})
+    this.state.navigateTo(pathway.stId, {queryParamsHandling: 'preserve', preserveFragment: true})
   }
 
 

projects/pathway-browser/src/app/diagram/diagram.component.ts

@@ -397,12 +397,12 @@ export class DiagramComponent implements AfterViewInit, OnDestroy {
         this.cy.on('zoom', () => this.controlZoom.set(this.zoomToControlTransform(this.cy.zoom())));
 
         this.reactomeStyle.clearCache();
-        this.cy.on('dblclick', '.SUB.Pathway', (e) => this.router.navigate([e.target.data('graph.stId')], {
+        this.cy.on('dblclick', '.SUB.Pathway', (e) => this.state.navigateTo(e.target.data('graph.stId'), {
           queryParamsHandling: "preserve",
           preserveFragment: true
         }))
 
-        this.cy.on('dblclick', '.Interacting.Pathway', (e) => this.router.navigate([e.target.data('graph.stId')], {
+        this.cy.on('dblclick', '.Interacting.Pathway', (e) => this.state.navigateTo(e.target.data('graph.stId'), {
           queryParams: {select: this.pathwayId()},
           queryParamsHandling: "merge",
           preserveFragment: true

projects/pathway-browser/src/app/event-hierarchy/event-hierarchy.component.ts

@@ -3,7 +3,7 @@ import {Event} from "../model/graph/event/event.model";
 import {EventService, SelectableObject} from "../services/event.service";
 import {SpeciesService} from "../services/species.service";
 import {combineLatest, combineLatestWith, filter, fromEvent, map, Observable, of, switchMap, take, tap} from "rxjs";
-import {MatTree, MatTreeNestedDataSource, MatTreeNodeDef} from "@angular/material/tree";
+import {MatTree, MatTreeNestedDataSource, MatTreeNodeDef, MatTreeNodeOutlet, MatTreeNodeToggle} from "@angular/material/tree";
 import {UrlStateService} from "../services/url-state.service";
 import {SplitComponent} from "angular-split";
 import {UntilDestroy, untilDestroyed} from "@ngneat/until-destroy";
@@ -35,6 +35,8 @@ import {PassiveDirective} from "../utils/passive.directive";
     MatTree,
     MatNestedTreeNode,
     MatTreeNodeDef,
+    MatTreeNodeToggle,
+    MatTreeNodeOutlet,
     MatButton,
     MatIconButton,
     NgClass,
@@ -168,11 +170,15 @@ export class EventHierarchyComponent implements AfterViewInit, OnDestroy {
     }, 100);
 
     this.eventService.treeData$.pipe(untilDestroyed(this)).subscribe(events => {
+      // Save expanded node stIds before resetting the data source
+      const expandedIds = this.collectExpandedIds(this.treeDataSource.data);
       // @ts-ignore
       // Mat tree has a bug causing children to not be rendered in the UI without first setting the data to null
       // This is a workaround to add child data to tree and update the view. see details: https://github.com/angular/components/issues/11381
       this.treeDataSource.data = []; //todo: check performance issue
       this.treeDataSource.data = events as Event[];
+      // Restore expansion state
+      this.restoreExpandedIds(events as Event[], expandedIds);
       this.adjustWidths();
     });
 
@@ -393,20 +399,16 @@ export class EventHierarchyComponent implements AfterViewInit, OnDestroy {
     const selectedEventId = isPathway(treeEvent) && treeEvent.hasDiagram ? null : treeEvent.stId;
     this._ignore = true;
     // this.speciesService.setIgnore(true);
-    this.router.navigate([diagramId], {
+    this.state.navigateTo(diagramId ?? null, {
       queryParamsHandling: "preserve" // Keep existing query params
     }).then(() => {
       this.state.select.set(selectedEventId);
       this.eventService.setCurrentTreeEvent(treeEvent);
-      // Listen for NavigationEnd event to reset _ignore
-      this.router.events.pipe(
-        filter(routerEvent => routerEvent instanceof NavigationEnd),
-        take(1) // Take the first NavigationEnd event and unsubscribe automatically
-      ).subscribe(() => {
-        this._ignore = false;
-        // this.speciesService.setIgnore(false);
-      });
-
+      // Reset _ignore after setting state. The .then() callback fires after
+      // NavigationEnd has already been emitted, so waiting for a future
+      // NavigationEnd would leave _ignore stuck at true if no further
+      // navigation occurs.
+      this._ignore = false;
     }).catch(err => {
       throw new Error('Navigation error:', err);
     });
@@ -530,4 +532,35 @@ export class EventHierarchyComponent implements AfterViewInit, OnDestroy {
     labelSpan.classList.remove('add-overflowX');
     el.classList.remove('no-transition');
   }
+
+  private collectExpandedIds(nodes: Event[]): Set<string> {
+    const expanded = new Set<string>();
+    const traverse = (items: Event[]) => {
+      for (const node of items) {
+        if (this.tree?.isExpanded(node)) {
+          expanded.add(node.stId);
+        }
+        if (isPathway(node) && node.events) {
+          traverse(node.events.map(e => e.element));
+        }
+      }
+    };
+    traverse(nodes);
+    return expanded;
+  }
+
+  private restoreExpandedIds(nodes: Event[], expandedIds: Set<string>): void {
+    if (expandedIds.size === 0) return;
+    const traverse = (items: Event[]) => {
+      for (const node of items) {
+        if (expandedIds.has(node.stId)) {
+          this.tree?.expand(node);
+        }
+        if (isPathway(node) && node.events) {
+          traverse(node.events.map(e => e.element));
+        }
+      }
+    };
+    traverse(nodes);
+  }
 }

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

@@ -108,7 +108,7 @@ export class ReacfoamComponent implements OnDestroy {
 
     onGroupDoubleClick: (event: any) => {
       event.preventDefault();
-      this.router.navigate([event.group.stId], {queryParamsHandling: 'preserve', preserveFragment: true})
+      this.state.navigateTo(event.group.stId, {queryParamsHandling: 'preserve', preserveFragment: true})
     },
 
     onGroupClick: (event: any) => {

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

@@ -121,7 +121,7 @@ export class SpeciesService {
       else params[key] = JSON.parse(newValue);
     }
 
-    this.router.navigate([pathwayId].filter(isDefined), {
+    this.state.navigateTo(pathwayId ?? null, {
       queryParams: params,
       preserveFragment: true
     });

projects/pathway-browser/src/app/services/url-state.service.ts

@@ -1,5 +1,5 @@
 import {effect, inject, Injectable, signal, WritableSignal} from '@angular/core';
-import {ActivatedRoute, NavigationEnd, Params, Router} from "@angular/router";
+import {ActivatedRoute, NavigationEnd, NavigationExtras, Params, Router} from "@angular/router";
 import {catchError, filter, firstValueFrom, map, of, switchMap} from "rxjs";
 import {isArray, isNumber} from "lodash";
 import {HttpClient} from "@angular/common/http";
@@ -112,7 +112,11 @@ export class UrlStateService implements State {
   constructor() {
     this.router.events.pipe(
       filter(event => event instanceof NavigationEnd),
-      switchMap(() => this.router.routerState.root.firstChild?.params || of()),
+      switchMap(() => {
+        let route = this.router.routerState.root;
+        while (route.firstChild) route = route.firstChild;
+        return route.params;
+      }),
       map(params => params['pathwayId'])
     ).subscribe((id) => {
       this.pathwayId.set(id)
@@ -127,7 +131,7 @@ export class UrlStateService implements State {
         return;
       }
 
-      this.router.navigate(this.pathwayId() ? [this.pathwayId()] : [], {
+      this.navigateTo(this.pathwayId() ?? null, {
         queryParamsHandling: 'preserve',
         preserveFragment: true
       });
@@ -153,7 +157,7 @@ export class UrlStateService implements State {
           }
         }
 
-        this.router.navigate(id ? [id] : [], {
+        this.navigateTo(id ?? null, {
           queryParamsHandling: 'merge',
           fragment: fragment.replace(FRAGMENT_PATTERN, ''),
           preserveFragment: false,
@@ -215,7 +219,21 @@ export class UrlStateService implements State {
         console.log('In content or search route, not navigating on state change');
         return;
       }
-      this.router.navigate(this.pathwayId() ? [this.pathwayId()] : [], {queryParams, preserveFragment: true});
+      this.navigateTo(this.pathwayId() ?? null, {queryParams, preserveFragment: true});
+    });
+  }
+
+  /**
+   * Navigate to a pathway within the PathwayBrowser route context.
+   * Resolves the correct base path whether running standalone or inside the umbrella app.
+   */
+  navigateTo(pathwayId: string | null, extras: NavigationExtras = {}): Promise<boolean> {
+    let route = this.router.routerState.root;
+    while (route.firstChild) route = route.firstChild;
+    const segments = pathwayId ? [pathwayId] : [];
+    return this.router.navigate(segments, {
+      relativeTo: route.parent,
+      ...extras
     });
   }