Merge branch 'integrate-2-more-datasets' into 'master'

Integrate 2 more datasets

See merge request covid-19/frontend!83

src/app/analysis.service.ts

@@ -142,7 +142,7 @@ export class AnalysisService {
     });
   }
 
-  async startQuickAnalysis() {
+  async startQuickAnalysis(dataset: string) {
     if (!this.canLaunchTask()) {
       toast({
         message: `You can only run ${MAX_TASKS} tasks at once. Please wait for one of them to finish or delete it from the task list.`,
@@ -162,6 +162,7 @@ export class AnalysisService {
       algorithm: 'quick',
       target: 'drug',
       parameters: {
+        strain: dataset,
         seeds: this.getSelection().map((i) => i.backendId),
       },
     }).toPromise();

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

@@ -255,7 +255,7 @@ export class AnalysisWindowComponent implements OnInit, OnChanges {
     const isSeed = attributes.isSeed || {};
     const scores = attributes.scores || {};
     const details = attributes.details || {};
-    const wrappers: {[key: string]: Wrapper}  = {};
+    const wrappers: { [key: string]: Wrapper } = {};
     for (const node of network.nodes) {
       if (nodeTypes[node] === 'host') {
         this.proteins.push(details[node]);
@@ -286,6 +286,7 @@ export class AnalysisWindowComponent implements OnInit, OnChanges {
   private mapNode(nodeType: WrapperType, details: Protein | ViralProtein | Drug, isSeed?: boolean, score?: number): any {
     let nodeLabel;
     let wrapper: Wrapper;
+    let drugType;
     if (nodeType === 'host') {
       const protein = details as Protein;
       wrapper = getWrapperFromProtein(protein);
@@ -296,14 +297,19 @@ export class AnalysisWindowComponent implements OnInit, OnChanges {
     } else if (nodeType === 'drug') {
       const drug = details as Drug;
       wrapper = getWrapperFromDrug(drug);
-      nodeLabel = drug.name;
+      drugType = drug.status;
+      if (drugType === 'approved') {
+        nodeLabel = drug.name;
+      } else {
+        nodeLabel = drug.drugId;
+      }
     } else if (nodeType === 'virus') {
       const viralProtein = details as ViralProtein;
       wrapper = getWrapperFromViralProtein(viralProtein);
       nodeLabel = viralProtein.effectName;
     }
 
-    const node = NetworkSettings.getNodeStyle(nodeType, isSeed, this.analysis.inSelection(wrapper));
+    const node = NetworkSettings.getNodeStyle(nodeType, isSeed, this.analysis.inSelection(wrapper), drugType);
     node.id = wrapper.nodeId;
     node.label = nodeLabel;
     node.nodeType = nodeType;
@@ -313,7 +319,7 @@ export class AnalysisWindowComponent implements OnInit, OnChanges {
     return node;
   }
 
-  private mapEdge(edge: any, type: 'protein-protein' | 'to-drug', wrappers?: {[key: string]: Wrapper}): any {
+  private mapEdge(edge: any, type: 'protein-protein' | 'to-drug', wrappers?: { [key: string]: Wrapper }): any {
     let edgeColor;
     if (type === 'protein-protein') {
       edgeColor = {

src/app/components/info-box/info-box.component.html

@@ -33,8 +33,8 @@
       <b>DrugBank ID:</b>
       <a href="https://www.drugbank.ca/drugs/{{ wrapper.data.drugId }}" target="_blank"> {{ wrapper.data.drugId }}</a>
     </p>
-    <p *ngIf="wrapper.data.status === 'investigational' ">
-      <b>Status:</b> Investigational
+    <p *ngIf="wrapper.data.status === 'unapproved' ">
+      <b>Status:</b> Unapproved
       <span class="icon is-small"><i class="fas fa-search investigational"></i></span>
     <p *ngIf="wrapper.data.status === 'approved' ">
       <b>Status:</b> Approved

src/app/components/launch-analysis/launch-analysis.component.html

@@ -111,16 +111,6 @@
       </div>
 
       <div *ngIf="algorithm==='multisteiner'">
-        <div class="field">
-          <label class="label" for="multisteiner-strain">Virus Strain</label>
-          <div  class="control">
-            <div class="select">
-              <select id="multisteiner-strain" [(ngModel)]="multisteinerStrain">
-                <option [ngValue]="'SARS_CoV2'">SARS Coronavirus 2</option>
-              </select>
-            </div>
-          </div>
-        </div>
         <div class="field">
           <label class="label" for="multisteiner-numtrees">Number of Steiner trees to return</label>
           <div  class="control">

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

@@ -21,6 +21,8 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
   public show = false;
   @Input()
   public target: 'drug' | 'drug-target';
+  @Input()
+  public dataset;
   @Output()
   public showChange = new EventEmitter<boolean>();
 
@@ -29,20 +31,17 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
   public algorithms: Array<Algorithm> = [];
 
   // Trustrank Parameters
-  public trustrankStrain = 'SARS_CoV2';
   public trustrankIncludeIndirectDrugs = false;
   public trustrankIncludeNonApprovedDrugs = false;
   public trustrankDampingFactor = 0.85;
   public trustrankResultSize = 20;
 
   // Closeness Parameters
-  public closenessStrain = 'SARS_CoV2';
   public closenessIncludeIndirectDrugs = false;
   public closenessIncludeNonApprovedDrugs = false;
   public closenessResultSize = 20;
 
   // Degree Parameters
-  public degreeStrain = 'SARS_CoV2';
   public degreeIncludeNonApprovedDrugs = false;
   public degreeResultSize = 20;
 
@@ -50,7 +49,6 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
   public keypathwayminerK = 1;
 
   // Multisteiner Parameters
-  public multisteinerStrain = 'SARS_CoV2';
   public multisteinerNumTrees = 5;
 
   public hasBaits;
@@ -71,15 +69,9 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
     if (this.target === 'drug-target') {
       this.algorithms = [MULTISTEINER, KEYPATHWAYMINER, TRUSTRANK, CLOSENESS_CENTRALITY, DEGREE_CENTRALITY];
       this.algorithm = MULTISTEINER.slug;
-      this.trustrankStrain = 'SARS_CoV2';  // TODO: Change once we have multiple datasets
-      this.closenessStrain = 'SARS_CoV2';  // TODO: Change once we have multiple datasets
-      this.degreeStrain = 'SARS_CoV2';  // TODO: Change once we have multiple datasets
     } else if (this.target === 'drug') {
       this.algorithms = [TRUSTRANK, CLOSENESS_CENTRALITY, DEGREE_CENTRALITY];
       this.algorithm = TRUSTRANK.slug;
-      this.trustrankStrain = 'drugs';
-      this.closenessStrain = 'drugs';
-      this.degreeStrain = 'drugs';
     }
   }
 
@@ -94,25 +86,25 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
     };
 
     if (this.algorithm === 'trustrank') {
-      parameters.strain_or_drugs = this.trustrankStrain;
+      parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
       parameters.damping_factor = this.trustrankDampingFactor;
       parameters.include_indirect_drugs = this.trustrankIncludeIndirectDrugs;
       parameters.include_non_approved_drugs = this.trustrankIncludeNonApprovedDrugs;
       parameters.result_size = this.trustrankResultSize;
     } else if (this.algorithm === 'closeness') {
-      parameters.strain_or_drugs = this.closenessStrain;
+      parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
       parameters.include_indirect_drugs = this.closenessIncludeIndirectDrugs;
       parameters.include_non_approved_drugs = this.closenessIncludeNonApprovedDrugs;
       parameters.result_size = this.closenessResultSize;
     } else if (this.algorithm === 'degree') {
-      parameters.strain_or_drugs = this.degreeStrain;
+      parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
       parameters.include_indirect_drugs = this.closenessIncludeIndirectDrugs;
       parameters.include_non_approved_drugs = this.closenessIncludeNonApprovedDrugs;
       parameters.result_size = this.closenessResultSize;
     } else if (this.algorithm === 'keypathwayminer') {
       parameters.k = this.keypathwayminerK;
     } else if (this.algorithm === 'multisteiner') {
-      parameters.strain = this.multisteinerStrain;
+      parameters.strain = this.dataset;
       parameters.num_trees = this.multisteinerNumTrees;
     }
 

src/app/components/select-dataset/select-dataset.component.html

 <div class="content">
-  <ng-select disabled="true" [items]="datasetItems" bindLabel="id" [virtualScroll]="true" class="custom"
+  <ng-select [items]="datasetItems" bindLabel="label" [virtualScroll]="true" class="custom"
              placeholder="Select..." [ngModel]="selectedDataset" (ngModelChange)="select($event)">
     <ng-template ng-option-tmp let-item="item">
-      {{item.label}} <br/>
-      <small>{{item.datasets}}</small>
+      {{item.strains}} <br/>
+      <small>{{item.datasetNames}}</small>
     </ng-template>
   </ng-select>
+
+  <div class="info" *ngIf="selectedDataset && selectedDataset.label === 'CoV2 (Gordon et al., 2020)'">
+    <p>Virus: <b>SARS-CoV-2</b></p>
+    <p>Host/target: <b>Human</b>, HEK-293T kidney cells</p>
+    <p>Method: <b>AP-MS</b></p>
+    <p>Source:<a href="https://www.biorxiv.org/content/10.1101/2020.03.22.002386v3" target="_blank"> <b> Gordon et al., 2020</b></a></p>
+  </div>
+
+  <div class="info" *ngIf="selectedDataset && selectedDataset.label === 'CoV1 (Pfefferle)'">
+    TODO: Put CoV1 (Pfefferle)
+  </div>
+
+  <div class="info" *ngIf="selectedDataset && selectedDataset.label === 'CoV1 (VirHostNet)'">
+    TODO: Put CoV1 (VirHostNet)
+  </div>
 </div>

src/app/components/select-dataset/select-dataset.component.scss

+.info {
+  margin-top: 5px;
+
+  font-size: 12px;
+
+  p {
+    padding: 0;
+    margin: 0;
+  }
+}

src/app/components/select-dataset/select-dataset.component.ts

 import {Component, EventEmitter, Input, Output} from '@angular/core';
+import {Dataset} from '../../interfaces';
 
 @Component({
   selector: 'app-select-dataset',
@@ -11,7 +12,7 @@ export class SelectDatasetComponent {
   @Input() selectedDataset;
   @Output() selectedDatasetChange: EventEmitter<any> = new EventEmitter();
 
-  @Input() datasetItems: Array<{label: string, datasets: string, data: Array<[string, string]>}>;
+  @Input() datasetItems: Dataset[];
 
   public select(selectionItem) {
     this.selectedDataset = selectionItem;

src/app/interfaces.ts

@@ -75,7 +75,7 @@ export function getNodeIdsFromPVI(pvi: ProteinViralInteraction) {
   };
 }
 
-export function getNodeIdsFromPPI(edge: NetworkEdge, wrappers: {[key: string]: Wrapper}) {
+export function getNodeIdsFromPPI(edge: NetworkEdge, wrappers: { [key: string]: Wrapper }) {
   return {
     from: wrappers[edge.from].nodeId,
     to: wrappers[edge.to].nodeId,
@@ -154,3 +154,11 @@ export interface Drug {
   name: string;
   status: 'approved' | 'investigational';
 }
+
+export interface Dataset {
+  label: string;
+  strains: string;
+  datasetNames: string;
+  backendId: string;
+  data: Array<[string, string]>;
+}

src/app/main-network.ts

 import {HttpClient} from '@angular/common/http';
-import {ProteinViralInteraction, ViralProtein, Protein} from './interfaces';
+import {ProteinViralInteraction, ViralProtein, Protein, getProteinNodeId, getViralProteinNodeId} from './interfaces';
 
 export function getDatasetFilename(dataset: Array<[string, string]>): string {
   return `network-${JSON.stringify(dataset).replace(/[\[\]\",]/g, '')}.json`;
@@ -13,14 +13,14 @@ export class ProteinNetwork {
   public async loadPositions(http: HttpClient, dataset: Array<[string, string]>) {
     const nodePositions = await http.get(`assets/positions/${getDatasetFilename(dataset)}`).toPromise();
     this.proteins.forEach((node) => {
-      const nodePosition = nodePositions[`p_${node.proteinAc}`];
+      const nodePosition = nodePositions[getProteinNodeId(node)];
       if (nodePosition) {
         node.x = nodePosition.x;
         node.y = nodePosition.y;
       }
     });
     this.effects.forEach((node) => {
-      const nodePosition = nodePositions[`eff_${node.effectName}_${node.datasetName}_${node.virusName}`];
+      const nodePosition = nodePositions[getViralProteinNodeId(node)];
       if (nodePosition) {
         node.x = nodePosition.x;
         node.y = nodePosition.y;

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

-<app-launch-analysis [(show)]="showAnalysisDialog" [target]="analysisDialogTarget"></app-launch-analysis>
+<app-launch-analysis [(show)]="showAnalysisDialog"
+                     [target]="analysisDialogTarget"
+                     [dataset]="selectedDataset.backendId">
+</app-launch-analysis>
 
 <div class="covex explorer">
 
@@ -26,19 +29,7 @@
             <div class="card-content">
               <app-select-dataset [datasetItems]="datasetItems" [selectedDataset]="selectedDataset"
                                   (selectedDatasetChange)="selectedDataset = $event; createNetwork($event.data)">
-
               </app-select-dataset>
-              <div>
-                <br>
-                <font size="2">
-                  <p><span>Virus: <b>SARS-CoV-2</b></span>
-                  <p><span>Host/target: <b>Human</b>, HEK-293T kidney cells</span>
-                  <p><span>Method: <b>AP-MS</b></span>
-                  <p><span>Source:<a href="https://www.biorxiv.org/content/10.1101/2020.03.22.002386v3" target="_blank"> <b> Gordon et al., 2020</b></a></span>
-                </font>
-
-              </div>
-
             </div>
           </div>
         </div>
@@ -251,7 +242,8 @@
               <div class="tile notification is-info">
                 <div class="align-vmiddle">
                   <div class="digit">2</div>
-                  <button (click)="analysis.startQuickAnalysis()" [disabled]="analysis.getCount() === 0 || analysis.isLaunchingQuick()"
+                  <button (click)="analysis.startQuickAnalysis(selectedDataset.backendId)"
+                          [disabled]="analysis.getCount() === 0 || analysis.isLaunchingQuick()"
                           class="button is-white is-rounded">
                     <span class="icon">
                       <i class="fa fa-capsules" *ngIf="!analysis.isLaunchingQuick()"></i>

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

@@ -10,7 +10,7 @@ import {
   ViralProtein,
   Protein,
   Wrapper,
-  getWrapperFromViralProtein, getWrapperFromProtein, getNodeIdsFromPVI, getViralProteinNodeId, getProteinNodeId
+  getWrapperFromViralProtein, getWrapperFromProtein, getNodeIdsFromPVI, getViralProteinNodeId, getProteinNodeId, Dataset
 } from '../../interfaces';
 import {ProteinNetwork, getDatasetFilename} from '../../main-network';
 import {HttpClient, HttpParams} from '@angular/common/http';
@@ -69,8 +69,28 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
   public currentViewEffects: ViralProtein[];
   public currentViewNodes: Node[];
 
-  public datasetItems: Array<{ id: string, label: string, datasets: string, data: Array<[string, string]> }> = [
-    {id: 'CoV2 (Gordon et al., 2020)', label: 'CoV2', datasets: 'Gordon et al., 2020', data: [['Krogan', 'SARS-CoV2']]},
+  public datasetItems: Dataset[] = [
+    {
+      label: 'CoV2 (Gordon et al., 2020)',
+      strains: 'CoV2',
+      datasetNames: 'Gordon et al., 2020',
+      backendId: 'SARS_CoV2',
+      data: [['Krogan', 'SARS-CoV2']]
+    },
+    {
+      label: 'CoV1 (Pfefferle)',
+      strains: 'CoV1',
+      datasetNames: 'Pfefferle',
+      backendId: 'SARS_CoV1',
+      data: [['Pfefferle', 'SARS-CoV1']]
+    },
+    {
+      label: 'CoV1 (VirHostNet)',
+      strains: 'CoV1',
+      datasetNames: 'VirHostNet',
+      backendId: 'SARS_CoV1',
+      data: [['VirHostNet', 'SARS-CoV1']]
+    },
   ];
 
   public selectedDataset = this.datasetItems[0];
@@ -162,6 +182,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
   }
 
   public async createNetwork(dataset: Array<[string, string]>) {
+    this.analysis.resetSelection();
     await this.getNetwork(dataset);
     this.proteinData = new ProteinNetwork(this.proteins, this.effects, this.edges);
     if (!this.dumpPositions) {

src/assets/positions/network-PfefferleSARS-CoV1.json

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src/assets/positions/network-TUMHCoV.json

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