Merge branch 'master' into 'selection'

# Conflicts:
#   src/app/pages/explorer-page/explorer-page.component.ts

.gitlab-ci.yml

@@ -14,15 +14,6 @@ setup:
   script:
     - npm install
 
-check:audit:
-  image: trion/ng-cli-karma
-  stage: check
-  script:
-    - npm install
-    - npm audit --production
-  dependencies:
-    - setup
-
 check:lint:
   image: trion/ng-cli-karma
   stage: check
@@ -51,7 +42,6 @@ build:
     - npm install
     - npm run build
   dependencies:
-    - check:audit
     - check:lint
     - check:test
 

angular.json

@@ -129,4 +129,4 @@
   "cli": {
     "analytics": "bb00cc29-2ec5-4bd5-9235-62ac2e9e51b5"
   }
-}
+}
\ No newline at end of file

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

@@ -74,7 +74,7 @@
               <label class="checkbox">
                 <input type="checkbox" class="checkbox" [ngModel]="bait.checked"
                        (ngModelChange)="bait.checked = $event; filterNodes()">
-                Bait {{ bait.data.effectId }}
+                {{ bait.data.effectName }}
               </label>
             </div>
           </div>
@@ -174,7 +174,7 @@
           <button class="button is-primary" *ngIf="!inSelection(currentProteinAc)"
                   (click)="addToSelection(currentProteinAc)">Select for analysis
           </button>
-          <button class="button is-primary" *ngIf="inSelection(currentProteinAc)"
+          <button class="button is-danger" *ngIf="inSelection(currentProteinAc)"
                   (click)="removeFromSelection(currentProteinAc)">Remove from analysis
           </button>
         </div>

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

@@ -186,11 +186,19 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
     this.proteinData.linkNodes();
 
     // Populate baits
+    const effectNames = [];
+    this.proteinData.effects.sort((a, b) => {
+      return a.effectName.localeCompare(b.effectName);
+    });
     this.proteinData.effects.forEach((effect) => {
-      this.viralProteinCheckboxes.push({
-        checked: false,
-        data: effect,
-      });
+      const effectName = effect.effectName;
+      if (effectNames.indexOf(effectName) === -1) {
+        effectNames.push(effectName);
+        this.viralProteinCheckboxes.push({
+          checked: false,
+          data: effect,
+        });
+      }
     });
 
     const {nodes, edges} = this.mapDataToNodes(this.proteinData);
@@ -217,10 +225,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
     this.network.on('click', (properties) => {
       const id: Array<string> = properties.nodes;
       // TODO use groupID
-      console.log(id);
-      console.log(this.watcher);
       if (id.length > 0) {
-        console.log('clicked node:', id);
         if (id[0].startsWith('pg_')) {
           const protein = this.proteinData.getProtein(id[0].substr(3));
           this.openSummary(protein, false);
@@ -242,6 +247,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
 
     if (this.dumpPositions) {
       this.network.on('stabilizationIterationsDone', () => {
+        // tslint:disable-next-line:no-console
         console.log(JSON.stringify(this.network.getPositions()));
       });
       this.network.stabilize();
@@ -264,26 +270,32 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
     const addNodes = new Map<string, Node>();
 
     const showAll = !this.viralProteinCheckboxes.find((eff) => eff.checked);
-    console.log(showAll);
-
     const connectedProteinAcs = new Set<string>();
 
-    this.viralProteinCheckboxes.forEach((bait) => {
-      const nodeId = `eff_${bait.data.effectId}`;
-      const found = visibleIds.has(nodeId);
-      if ((bait.checked || showAll) && !found) {
-        const node = this.mapEffectToNode(bait.data);
-        // this.nodeData.nodes.add(node);
-        addNodes.set(node.id, node);
-      } else if ((!showAll && !bait.checked) && found) {
-        // this.nodeData.nodes.remove(nodeId);
-        removeIds.add(nodeId);
-      }
-      if (bait.checked || showAll) {
-        bait.data.proteins.forEach((pg) => {
-          connectedProteinAcs.add(pg.proteinAc);
-        });
-      }
+    this.viralProteinCheckboxes.forEach((cb) => {
+      const effects = [];
+      this.proteinData.effects.forEach((effect) => {
+        if (effect.effectName === cb.data.effectName) {
+          effects.push(effect);
+        }
+       });
+      effects.forEach((effect) => {
+        const nodeId = `eff_${effect.effectId}`;
+        const found = visibleIds.has(nodeId);
+        if ((cb.checked || showAll) && !found) {
+          const node = this.mapEffectToNode(effect);
+          // this.nodeData.nodes.add(node);
+          addNodes.set(node.id, node);
+        } else if ((!showAll && !cb.checked) && found) {
+          // this.nodeData.nodes.remove(nodeId);
+          removeIds.add(nodeId);
+        }
+        if (cb.checked || showAll) {
+          effect.proteins.forEach((pg) => {
+            connectedProteinAcs.add(pg.proteinAc);
+          });
+        }
+     });
     });
     this.filteredProteins = [];
     for (const protein of this.proteinData.proteins) {
@@ -296,7 +308,6 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
       if (contains && !found) {
         const node = this.mapProteinToNode(protein);
         // this.nodeData.nodes.add(node);
-
         addNodes.set(node.id, node);
       } else if (!contains && found) {
         // this.nodeData.nodes.remove(nodeId);
@@ -304,11 +315,10 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
       }
     }
 
-
     this.nodeData.nodes.remove(Array.from(removeIds.values()));
     this.nodeData.nodes.add(Array.from(addNodes.values()));
     this.fillQueryItems();
-  }
+ }
 
 
   public updatePhysicsEnabled() {

src/main.ts

@@ -12,4 +12,5 @@ if (environment.production) {
 }
 
 platformBrowserDynamic().bootstrapModule(AppModule)
+  // tslint:disable-next-line:no-console
   .catch(err => console.error(err));

tslint.json

@@ -44,14 +44,7 @@
       }
     ],
     "no-consecutive-blank-lines": false,
-    "no-console": [
-      true,
-      "debug",
-      "info",
-      "time",
-      "timeEnd",
-      "trace"
-    ],
+    "no-console": true,
     "no-empty": false,
     "no-inferrable-types": [
       true,
@@ -88,4 +81,4 @@
   "rulesDirectory": [
     "codelyzer"
   ]
-}
+}
\ No newline at end of file