Metabolic pathways visualisation (#731): context menu navigation

epam · Jan 30, 2022 · 5c9f93d · 5c9f93d
1 parent 403c6c4
commit 5c9f93d
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Showing 5 changed files with 53 additions and 2 deletions.
diff --git a/...sTablePanel/ngbGenesTable/ngbGenesTableContextMenu/ngbGenesTableContextMenu.controller.js b/...sTablePanel/ngbGenesTable/ngbGenesTableContextMenu/ngbGenesTableContextMenu.controller.js
@@ -119,4 +119,20 @@ export default class NgbGenesTableContextMenuController extends BaseController {
         this.dispatcher.emitSimpleEvent('read:show:homologs', data);
         event.stopImmediatePropagation();
     }
+
+    pathwaysSearch() {
+        this.close();
+        const layoutChange = this.appLayout.Panels.pathways;
+        layoutChange.displayed = true;
+        this.dispatcher.emitSimpleEvent('layout:item:change', {layoutChange});
+        const readInfo = {
+            search: this.entity[`${this.ngbGenesTableService.defaultPrefix}featureName`]
+        };
+        const data = {
+            ...readInfo,
+            source: 'gene'
+        };
+        this.dispatcher.emitSimpleEvent('read:show:pathways', data);
+        event.stopImmediatePropagation();
+    }
 }
diff --git a/...sTablePanel/ngbGenesTable/ngbGenesTableContextMenu/ngbGenesTableContextMenu.template.html b/...sTablePanel/ngbGenesTable/ngbGenesTableContextMenu/ngbGenesTableContextMenu.template.html
@@ -30,5 +30,15 @@
                 </span>
             </md-button>
         </md-menu-item>
+        <md-menu-item>
+            <md-button ng-click="ctrl.isGene && ctrl.pathwaysSearch($event)"
+                       ng-disabled="!ctrl.isGene">
+                <span>Show pathways</span>
+                <span class="ngb-context-menu-warning" ng-if="!ctrl.isGene">
+                    <ng-md-icon class="ngb-context-menu-warning-icon" icon="warning" size="15"></ng-md-icon>
+                    Feature type is not Gene or Name is missing
+                </span>
+            </md-button>
+        </md-menu-item>
     </md-menu-content>
 </div>
diff --git a/client/client/app/components/ngbPathways/ngbPathways.service.js b/client/client/app/components/ngbPathways/ngbPathways.service.js
@@ -47,7 +47,7 @@ export default class ngbPathwaysService {
 
     initEvents() {
         this.dispatcher.on('read:show:pathways', data => {
-            this.currentSearch = data;
+            this.currentSearch = data ? data.search : null;
         });
     }
 }
diff --git a/client/client/app/components/ngbPathways/ngbPathwaysPanel.controller.js b/client/client/app/components/ngbPathways/ngbPathwaysPanel.controller.js
@@ -8,7 +8,8 @@ export default class ngbPathwaysPanelController extends baseController {
     searchRequest;
 
     events = {
-        'read:show:pathways': () => {
+        'read:show:pathways': data => {
+            this.searchRequest = data ? data.search : null;
             this.changeState('INTERNAL_PATHWAYS');
         }
     };

diff --git a/client/client/app/components/ngbTracksView/ngbTrack/ngbTrack.events.js b/client/client/app/components/ngbTracksView/ngbTrack/ngbTrack.events.js
@@ -217,6 +217,30 @@ export default class ngbTrackEvents {
                             : undefined,
                     });
                 }
+                if (data.feature.feature
+                    && data.feature.feature.toLowerCase() === 'gene'
+                    && data.feature.name) {
+                    const layoutChange = this.appLayout.Panels.pathways;
+                    layoutChange.displayed = true;
+                    menuData.push({
+                        events: [
+                            {
+                                data: {layoutChange},
+                                name: 'layout:item:change'
+                            },
+                            {
+                                data: {
+                                    search: data.feature.name
+                                },
+                                name: 'read:show:pathways'
+                            }],
+                        title: 'Show pathways',
+                        disabled: (data.feature.feature || '').toLowerCase() !== 'gene' || !data.feature.name,
+                        warning: (data.feature.feature || '').toLowerCase() !== 'gene' || !data.feature.name
+                            ? 'Feature type is not Gene or Name is missing'
+                            : undefined,
+                    });
+                }
                 if (menuData.length > 0) {
                     const childScope = this.$scope.$new(false);
                     childScope.menuData = menuData;