Metabolic pathways visualisation (#731): get species for filtering fr…

…om track
epam · Mar 30, 2022 · ea1bf20 · ea1bf20
1 parent 7363f6e
commit ea1bf20
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Showing 6 changed files with 25 additions and 10 deletions.
diff --git a/...sTablePanel/ngbGenesTable/ngbGenesTableContextMenu/ngbGenesTableContextMenu.controller.js b/...sTablePanel/ngbGenesTable/ngbGenesTableContextMenu/ngbGenesTableContextMenu.controller.js
@@ -126,7 +126,9 @@ export default class NgbGenesTableContextMenuController extends BaseController {
         layoutChange.displayed = true;
         this.dispatcher.emitSimpleEvent('layout:item:change', {layoutChange});
         const readInfo = {
-            search: this.entity[`${this.ngbGenesTableService.defaultPrefix}featureName`]
+            search: this.entity[`${this.ngbGenesTableService.defaultPrefix}featureName`],
+            speciesList: [],
+            rewriteSpecies: true
         };
         const data = {
             ...readInfo,

diff --git a/...t/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.service.js b/...t/app/components/ngbPathways/ngbInternalPathwaysTable/ngbInternalPathwaysTable.service.js
@@ -33,6 +33,7 @@ export default class ngbInternalPathwaysTableService extends ClientPaginationSer
         this.genomeDataService = genomeDataService;
         this.loadSpeciesList();
     }
+
     _internalPathways;
 
     get internalPathways() {
@@ -113,13 +114,18 @@ export default class ngbInternalPathwaysTableService extends ClientPaginationSer
     }
 
     async loadInternalPathways(currentSearch) {
+        if (currentSearch.rewriteSpecies) {
+            this.internalPathwaysFilter.organisms = currentSearch.speciesList;
+            currentSearch.speciesList = [];
+            currentSearch.rewriteSpecies = false;
+        }
         const filter = {
             pagingInfo: {
                 pageSize: this.pageSize,
                 pageNum: this.currentPage
             },
             sortInfo: this.orderBy ? this.orderBy[0] : null,
-            term: currentSearch || '',
+            term: currentSearch.search || '',
             taxIds: this.internalPathwaysFilter.organisms || []
         };
 

diff --git a/...waysTableFilter/ngbInternalPathwaysFilterList/ngbInternalPathwaysFilterList.controller.js b/...waysTableFilter/ngbInternalPathwaysFilterList/ngbInternalPathwaysFilterList.controller.js
@@ -27,7 +27,7 @@ export default class ngbInternalPathwaysFilterListController {
                 if (this.ngbInternalPathwaysTableService.internalPathwaysFilter.organisms) {
                     this.selectedItems = this.ngbInternalPathwaysTableService.speciesList
                         .filter(organism => this.ngbInternalPathwaysTableService.internalPathwaysFilter.organisms.indexOf(organism.taxId) >= 0)
-                        .map(organism => organism.speciesName);
+                        .map(organism => organism.taxId);
                     this.displayText = [...this.selectedItems].join(', ');
                 }
                 break;
@@ -146,10 +146,7 @@ export default class ngbInternalPathwaysFilterListController {
                 prevValue.sort();
                 const prevValueStr = JSON.stringify(prevValue).toUpperCase();
                 const currValue = this.ngbInternalPathwaysTableService.speciesList
-                    .filter(organism => organism.speciesName
-                        ? selectedItemsLowerCase.indexOf(organism.speciesName.toLowerCase()) >= 0
-                        : selectedItemsLowerCase.indexOf(organism.taxId.toString()) >= 0
-                    )
+                    .filter(organism => selectedItemsLowerCase.indexOf(organism.taxId.toString()) >= 0)
                     .map(organism => organism.taxId);
                 currValue.sort();
                 const currValueStr = JSON.stringify(currValue).toUpperCase();

diff --git a/client/client/app/components/ngbPathways/ngbPathways.service.js b/client/client/app/components/ngbPathways/ngbPathways.service.js
@@ -82,7 +82,7 @@ export default class ngbPathwaysService {
 
     initEvents() {
         this.dispatcher.on('read:show:pathways', data => {
-            this.currentSearch = data ? data.search : null;
+            this.currentSearch = data || null;
         });
     }
 

diff --git a/client/client/app/components/ngbPathways/ngbPathwaysPanel.controller.js b/client/client/app/components/ngbPathways/ngbPathwaysPanel.controller.js
@@ -48,7 +48,11 @@ export default class ngbPathwaysPanelController extends baseController {
     }
 
     searchPathway() {
-        this.ngbPathwaysService.currentSearch = this.searchRequest;
+        this.ngbPathwaysService.currentSearch = {
+            search: this.searchRequest,
+            speciesList: [],
+            rewriteSpecies: true
+        };
         this.dispatcher.emitSimpleEvent('pathways:internalPathways:search');
         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
@@ -220,6 +220,10 @@ export default class ngbTrackEvents {
                 if (data.feature.feature && data.feature.name) {
                     const layoutChange = this.appLayout.Panels.pathways;
                     layoutChange.displayed = true;
+                    const [reference] = this.projectContext.references.filter(ref => ref.id === track.referenceId);
+                    const speciesList = reference && reference.species
+                        ? [reference.species.taxId]
+                        : null;
                     menuData.push({
                         events: [
                             {
@@ -228,7 +232,9 @@ export default class ngbTrackEvents {
                             },
                             {
                                 data: {
-                                    search: data.feature.name
+                                    speciesList,
+                                    search: data.feature.name,
+                                    rewriteSpecies: true
                                 },
                                 name: 'read:show:pathways'
                             }],