Merge branch 'add-all-proteins-from-current-network-only' into 'master'

Add all proteins from current network only

See merge request covid-19/frontend!62

src/app/analysis.service.ts

@@ -60,6 +60,38 @@ export class AnalysisService {
     }
   }
 
+  public addAllHostProteins(nodes, proteins) {
+    const visibleIds = new Set<string>(nodes.getIds());
+    for (const protein of proteins) {
+      const nodeId = protein.proteinAc;
+      const found = visibleIds.has(nodeId) || visibleIds.has('p_' + nodeId);
+      if (found && !this.inSelection(protein.name)) {
+        this.addItem({
+          name: protein.proteinAc,
+          type: 'Host Protein',
+          data: protein
+        });
+      }
+    }
+  }
+
+  public addAllViralProteins(nodes, effects) {
+    const visibleIds = new Set<string>(nodes.getIds());
+    for (const effect of effects) {
+      const nodeId = effect.effectId;
+      const found = visibleIds.has(nodeId) || visibleIds.has('eff_' + effect.effectName + '_' +
+        effect.datasetName + '_' + effect.virusName);
+      if (found && !this.inSelection(effect.effectName + '_' +
+        effect.datasetName + '_' + effect.virusName)) {
+        this.addItem({
+          name: effect.effectId,
+          type: 'Viral Protein',
+          data: effect
+        });
+      }
+    }
+  }
+
   resetSelection() {
     const oldSelection = this.selectedItems.values();
     for (const item of oldSelection) {
@@ -110,14 +142,14 @@ export class AnalysisService {
     // const finishedDate = new Date(task.info.finishedAt);
     if (status === 'DONE') {
       toastMessage = 'Computation finished succesfully.';
-              // \n- Algorithm: ${task.info.algorithm}
-              // \n- Started At: ${startDate.getHours()}:${startDate.getMinutes()}
-              // \n- Finished At: ${finishedDate.getHours()}:${finishedDate.getMinutes()}`;
+      // \n- Algorithm: ${task.info.algorithm}
+      // \n- Started At: ${startDate.getHours()}:${startDate.getMinutes()}
+      // \n- Finished At: ${finishedDate.getHours()}:${finishedDate.getMinutes()}`;
       toastType = 'is-success';
     } else if (status === 'FAILED') {
       toastMessage = 'Computation failed.';
-              // \n- Algorithm: ${task.info.algorithm}
-              // \n- Started At: ${startDate.getHours()}:${startDate.getMinutes()}`;
+      // \n- Algorithm: ${task.info.algorithm}
+      // \n- Started At: ${startDate.getHours()}:${startDate.getMinutes()}`;
       toastType = 'is-danger';
     }
 
@@ -128,7 +160,7 @@ export class AnalysisService {
       pauseOnHover: true,
       type: toastType,
       position: 'top-center',
-      animate: { in: 'fadeIn', out: 'fadeOut' }
+      animate: {in: 'fadeIn', out: 'fadeOut'}
     });
   }
 

src/app/components/analysis-window/analysis-window.component.ts

@@ -29,6 +29,9 @@ interface Scored {
 })
 export class AnalysisWindowComponent implements OnInit, OnChanges {
 
+  constructor(private http: HttpClient, public analysis: AnalysisService) {
+  }
+
   @Input() token: string | null = null;
 
   @Output() tokenChange = new EventEmitter<string | null>();
@@ -47,14 +50,17 @@ export class AnalysisWindowComponent implements OnInit, OnChanges {
   public showDrugs = false;
   public tab = 'network';
 
+
+  private proteins: any;
+  public effects: any;
+
   public tableDrugs: Array<Drug & Scored> = [];
   public tableProteins: Array<Protein & Scored> = [];
   public tableViralProteins: Array<ViralProtein & Scored> = [];
   public tableNormalize = false;
   public tableHasScores = false;
 
-  constructor(private http: HttpClient, public analysis: AnalysisService) {
-  }
+  @Output() visibleItems: EventEmitter<any> = new EventEmitter();
 
   async ngOnInit() {
   }
@@ -186,6 +192,15 @@ export class AnalysisWindowComponent implements OnInit, OnChanges {
         });
       }
     }
+    this.emitVisibleItems(true);
+  }
+
+  public emitVisibleItems(on: boolean) {
+    if (on) {
+      this.visibleItems.emit([this.nodeData.nodes, [this.proteins, this.effects]]);
+    } else {
+      this.visibleItems.emit(null);
+    }
   }
 
   private async getTask(token: string): Promise<any> {
@@ -195,6 +210,7 @@ export class AnalysisWindowComponent implements OnInit, OnChanges {
   close() {
     this.token = null;
     this.tokenChange.emit(this.token);
+    this.emitVisibleItems(false);
   }
 
   discard() {
@@ -256,6 +272,8 @@ export class AnalysisWindowComponent implements OnInit, OnChanges {
 
     const nodeAttributes = result.nodeAttributes || [];
 
+    this.proteins = [];
+    this.effects = [];
     for (let i = 0; i < result.networks.length; i++) {
       const network = result.networks[i];
 
@@ -264,9 +282,12 @@ export class AnalysisWindowComponent implements OnInit, OnChanges {
       const isSeed = attributes.isSeed || {};
       const scores = attributes.scores || {};
       const details = attributes.details || {};
-
-
       for (const node of network.nodes) {
+        if (nodeTypes[node] === 'host') {
+          this.proteins.push(details[node]);
+        } else if (nodeTypes[node] === 'virus') {
+          this.effects.push(details[node]);
+        }
         nodes.push(this.mapNode(node, nodeTypes[node] || this.inferNodeType(node), isSeed[node], scores[node], details[node]));
       }
 

src/app/pages/explorer-page/explorer-page.component.html

@@ -187,7 +187,9 @@
 
     <div class="analysis-view" *ngIf="selectedAnalysisToken">
       <app-analysis-window [(token)]="selectedAnalysisToken"
-                           (showDetailsChange)="showDetails = $event[0]; changeInfo($event[1])"></app-analysis-window>
+                           (showDetailsChange)="showDetails = $event[0]; changeInfo($event[1])"
+                           (visibleItems)="analysisWindowChanged($event)"
+      ></app-analysis-window>
     </div>
   </div>
 
@@ -398,7 +400,7 @@
           </i>
         </div>
         <footer class="card-footer">
-          <a (click)="addAllHostProteins()" class="card-footer-item has-text-success">
+          <a (click)="analysis.addAllHostProteins(currentViewNodes, currentViewProteins)" class="card-footer-item has-text-success">
           <span class="icon">
             <i class="fa fa-plus"></i>
           </span>
@@ -406,7 +408,7 @@
             Host Proteins
           </span>
           </a>
-          <a (click)="addAllViralProteins()" class="card-footer-item has-text-success">
+          <a (click)="analysis.addAllViralProteins(currentViewNodes, currentViewEffects)" class="card-footer-item has-text-success">
           <span class="icon">
             <i class="fa fa-plus"></i>
           </span>

src/app/pages/explorer-page/explorer-page.component.ts

@@ -47,7 +47,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
   public edges: any;
 
   private network: any;
-  private nodeData: { nodes: any, edges: any } = {nodes: null, edges: null};
+  public nodeData: { nodes: any, edges: any } = {nodes: null, edges: null};
 
   private dumpPositions = false;
   public physicsEnabled = false;
@@ -61,6 +61,10 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
   public currentDataset = [];
   private screenshotArray = [0];
 
+  public currentViewProteins: Protein[];
+  public currentViewEffects: ViralProtein[];
+  public currentViewNodes: Node[];
+
   public datasetItems: Array<{ id: string, label: string, datasets: string, data: Array<[string, string]> }> = [
     {
       id: 'All (TUM & Krogan)',
@@ -321,6 +325,10 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
         data: effect
       });
     });
+
+    this.currentViewNodes = this.nodeData.nodes;
+    this.currentViewProteins = this.proteins;
+    this.currentViewEffects = this.effects;
   }
 
   public async filterNodes() {
@@ -457,32 +465,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
     };
   }
 
-  public addAllHostProteins() {
-    const visibleIds = new Set<string>(this.nodeData.nodes.getIds());
-    for (const protein of this.proteinData.proteins) {
-      const nodeId = `p_${protein.proteinAc}`;
-      const found = visibleIds.has(nodeId);
-      if (found && !this.analysis.inSelection(protein.name)) {
-        this.analysis.addItem({name: protein.proteinAc, type: 'Host Protein', data: protein});
-      }
-    }
-  }
-
-  public addAllViralProteins() {
-    const visibleIds = new Set<string>(this.nodeData.nodes.getIds());
-    for (const effect of this.proteinData.effects) {
-      const nodeId = `eff_${effect.effectName + '_' + effect.datasetName + '_' + effect.virusName}`;
-      const found = visibleIds.has(nodeId);
-      if (found && !this.analysis.inSelection(effect.effectName + '_' + effect.datasetName + '_' + effect.virusName)) {
-        this.analysis.addItem({
-          name: effect.effectId,
-          type: 'Viral Protein',
-          data: effect
-        });
-      }
-    }
-  }
-
   public toCanvas() {
     this.screenshotArray.forEach((key, index) => {
       const elem = document.getElementById(index.toString());
@@ -496,4 +478,15 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
     });
   }
 
+  analysisWindowChanged($event: any) {
+    if ($event) {
+      this.currentViewNodes = $event[0];
+      this.currentViewProteins = $event[1][0];
+      this.currentViewEffects = $event[1][1];
+    } else {
+      this.currentViewNodes = this.nodeData.nodes;
+      this.currentViewProteins = this.proteins;
+      this.currentViewEffects = this.effects;
+    }
+  }
 }