Metabolic pathways visualisation (#731): load pathway from url

epam · Apr 4, 2022 · 30a1988 · 30a1988
1 parent 06d35f0
commit 30a1988
Show file tree

Hide file tree

Showing 7 changed files with 53 additions and 13 deletions.
diff --git a/client/client/app/app.controller.js b/client/client/app/app.controller.js
@@ -17,6 +17,7 @@ export default class ngbAppController extends baseController {
                 projectContext,
                 miewContext,
                 heatmapContext,
+                ngbPathwaysService,
                 eventHotkey,
                 $stateParams,
                 $rootScope,
@@ -41,6 +42,7 @@ export default class ngbAppController extends baseController {
             projectContext,
             miewContext,
             heatmapContext,
+            ngbPathwaysService,
             projectDataService,
             utilsDataService,
             apiService,
@@ -213,7 +215,8 @@ export default class ngbAppController extends baseController {
             filterByGenome,
             collapsedTrackHeaders,
             miew,
-            heatmap
+            heatmap,
+            pathway
         } = params;
         const position = start
             ? {end, start}
@@ -226,6 +229,7 @@ export default class ngbAppController extends baseController {
         }
         this.miewContext.routeInfo = miew;
         this.heatmapContext.routeInfo = heatmap;
+        this.ngbPathwaysService.routeInfo = pathway;
         const tracksState = tracks
             ? this.projectContext
                 .convertTracksStateFromJson(tracks)
@@ -318,6 +322,7 @@ export default class ngbAppController extends baseController {
         }
         state.miew = this.miewContext.routeInfo;
         state.heatmap = this.heatmapContext.routeInfo;
+        state.pathway = this.ngbPathwaysService.routeInfo;
         this.$state.go(this.$state.current.name, state, options);
     }
 

diff --git a/client/client/app/app.js b/client/client/app/app.js
@@ -24,6 +24,9 @@ import routes from './app.routes';
 import './app.scss';
 import angularMaterial from './compat/angularMaterial';
 import components from './components';
+import PathwaysService from './components/ngbPathways/ngbPathways.service.js';
+import AppearanceContext from './shared/appearanceContext';
+import BamCoverageContext from './shared/bamCoverageContext';
 import BLASTContext from './shared/blastContext';
 import browserDetect from './shared/browserDetect';
 import sharedComponents from './shared/components';
@@ -33,10 +36,8 @@ import HeatmapContext from './shared/heatmapContext';
 import './shared/hotkeys';
 import lastActionRepeater from './shared/lastActionRepeater';
 import MiewContext from './shared/miewContext';
-import NotificationsContext from './shared/notificationsContext';
-import AppearanceContext from './shared/appearanceContext';
 import MotifsContext from './shared/motifsContext';
-import BamCoverageContext from './shared/bamCoverageContext';
+import NotificationsContext from './shared/notificationsContext';
 
 // Import internal modules
 import projectContext from './shared/projectContext';
@@ -79,4 +80,5 @@ export default angular.module('NGB', [
     .service('appearanceContext', AppearanceContext.instance)
     .service('motifsContext', MotifsContext.instance)
     .service('bamCoverageContext', BamCoverageContext.instance)
+    .service('ngbPathwaysService', PathwaysService.instance)
     .name;
diff --git a/client/client/app/app.routes.js b/client/client/app/app.routes.js
@@ -23,6 +23,7 @@ export default function routes($urlRouterProvider, $httpProvider, $stateProvider
                 collapsedTrackHeaders: null,
                 miew: null,
                 heatmap: null,
+                pathway: null,
                 embedded: null,
                 controls: null
             },
@@ -31,7 +32,7 @@ export default function routes($urlRouterProvider, $httpProvider, $stateProvider
             },
             reloadOnSearch: false,
             template: require('./app.tpl.html'),
-            url: '/:referenceId/:chromosome/:start/:end?rewrite&bookmark&screenshot&toolbar&layout&tracks&filterByGenome&collapsedTrackHeaders&miew&heatmap&embedded&controls'
+            url: '/:referenceId/:chromosome/:start/:end?rewrite&bookmark&screenshot&toolbar&layout&tracks&filterByGenome&collapsedTrackHeaders&miew&heatmap&embedded&controls&pathway'
         });
 
 }
diff --git a/client/client/app/components/ngbPathways/index.js b/client/client/app/components/ngbPathways/index.js
@@ -4,7 +4,6 @@ import cytoscapePathwayComponent from './ngbCytoscapePathway';
 // Import components
 import ngbInternalPathwaysResult from './ngbInternalPathwaysResult';
 import ngbInternalPathwaysTable from './ngbInternalPathwaysTable';
-import service from './ngbPathways.service';
 import ngbPathwaysAnnotation from './ngbPathwaysAnnotation';
 import ngbPathwaysColorSchemePreference from './ngbPathwaysColorSchemePreference';
 
@@ -26,7 +25,6 @@ export default angular
         ngbPathwaysColorSchemePreference,
         ngbPathwaysAnnotation
     ])
-    .service('ngbPathwaysService', service.instance)
     .component('ngbPathwaysPanel', ngbPathwaysPanel)
     .controller(controller.UID, controller)
     .name;
diff --git a/...t/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.service.js b/...t/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.service.js
@@ -114,7 +114,7 @@ export default class ngbInternalPathwaysTableService extends ClientPaginationSer
     }
 
     async loadInternalPathways(currentSearch) {
-        if (currentSearch.rewriteSpecies) {
+        if (currentSearch && currentSearch.rewriteSpecies) {
             this.internalPathwaysFilter.organisms = currentSearch.speciesList;
             currentSearch.speciesList = [];
             currentSearch.rewriteSpecies = false;
@@ -125,7 +125,7 @@ export default class ngbInternalPathwaysTableService extends ClientPaginationSer
                 pageNum: this.currentPage
             },
             sortInfo: this.orderBy ? this.orderBy[0] : null,
-            term: currentSearch.search || '',
+            term: currentSearch && currentSearch.search || '',
             taxIds: this.internalPathwaysFilter.organisms || []
         };
 

diff --git a/client/client/app/components/ngbPathways/ngbPathways.service.js b/client/client/app/components/ngbPathways/ngbPathways.service.js
@@ -55,6 +55,7 @@ export default class ngbPathwaysService {
             ...loadedState,
             internalPathway: this._currentInternalPathway
         }));
+        this.report();
     }
 
     _currentState;
@@ -72,6 +73,30 @@ export default class ngbPathwaysService {
         }));
     }
 
+    get routeInfo() {
+        if (this.currentInternalPathway) {
+            return JSON.stringify(this.currentInternalPathway);
+        }
+        return null;
+    }
+
+    set routeInfo(routeInfo) {
+        try {
+            if (routeInfo) {
+                const internalPathway = JSON.parse(routeInfo);
+                const state = {
+                    internalPathway,
+                    state: this.pathwaysStates.INTERNAL_PATHWAYS_RESULT
+                };
+                this.initState(state);
+                this.dispatcher.emit('load:pathways', state);
+            }
+        } catch (_) {
+            this.currentState = this.pathwaysStates.INTERNAL_PATHWAYS;
+        }
+    }
+
+
     static instance(dispatcher, projectContext,
         ngbInternalPathwaysTableService, ngbInternalPathwaysResultService,
         ngbPathwaysAnnotationService) {
@@ -92,14 +117,14 @@ export default class ngbPathwaysService {
             ...loadedState
         };
         this._currentState = loadedState.state;
-        this._currentInternalPathway = loadedState.internalPathway;
+        this.currentInternalPathway = loadedState.internalPathway;
     }
 
     recoverLocalState(state) {
         if (state) {
             this.initState(state.layout);
             this.ngbPathwaysAnnotationService.initState(state.annotations);
-            this.dispatcher.emit('session:load:pathways', state.layout);
+            this.dispatcher.emit('load:pathways', state.layout);
         }
     }
 
@@ -110,4 +135,9 @@ export default class ngbPathwaysService {
         };
     }
 
+    report() {
+        this.dispatcher.emitGlobalEvent('route:change');
+    }
+
+
 }
diff --git a/client/client/app/components/ngbPathways/ngbPathwaysPanel.controller.js b/client/client/app/components/ngbPathways/ngbPathwaysPanel.controller.js
@@ -12,7 +12,7 @@ export default class ngbPathwaysPanelController extends baseController {
             this.searchRequest = data ? data.search : null;
             this.changeState('INTERNAL_PATHWAYS');
         },
-        'session:load:pathways': data => {
+        'load:pathways': data => {
             if (data && data.state) {
                 this.changeState(data.state);
             }
@@ -44,7 +44,11 @@ export default class ngbPathwaysPanelController extends baseController {
             this.currentPathwaysState = this.pathwaysStates[state];
             this.service = this.ngbPathwaysService.pathwaysServiceMap[this.currentPathwaysState];
             switch (state) {
-                case this.pathwaysStates.INTERNAL_PATHWAYS:
+                case this.pathwaysStates.INTERNAL_PATHWAYS: {
+                    this.ngbPathwaysService.currentInternalPathway = undefined;
+                    this.tabSelected = this.pathwaysStates.INTERNAL_PATHWAYS;
+                    break;
+                }
                 case this.pathwaysStates.INTERNAL_PATHWAYS_RESULT: {
                     this.tabSelected = this.pathwaysStates.INTERNAL_PATHWAYS;
                     break;