Merge pull request #114 from tsheils/development

Development
ncats · Sep 19, 2023 · 3fe7689 · 3fe7689
2 parents 4825140 + cc3fb63
commit 3fe7689
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Showing 18 changed files with 15,541 additions and 35,158 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -1,6 +1,6 @@
 language: node_js
 node_js:
-  - '16'
+  - '18'
 
 addons:
   chrome: stable

diff --git a/apps/ramp-client/src/app/app.component.ts b/apps/ramp-client/src/app/app.component.ts
@@ -1,12 +1,11 @@
 import {
   ChangeDetectionStrategy,
   ChangeDetectorRef,
-  Component, ElementRef,
-  OnInit, ViewChild,
+  Component,
+  OnInit,
   ViewEncapsulation
 } from "@angular/core";
 import { MatDialog } from '@angular/material/dialog';
-import { ErrorDialogComponent } from '@ramp/shared/ui/error-dialog';
 import { LinkTemplateProperty } from '@ramp/shared/ui/header-template';
 import { RampFacade } from '@ramp/stores/ramp-store';
 
@@ -103,7 +102,7 @@ export class AppComponent implements OnInit {
   ngOnInit() {
     this.rampFacade.error$.subscribe((error) => {
       if (error) {
-        console.log(error);
+       // console.log(error);
         /* this.dialog.open(ErrorDialogComponent, {
           data: {
             error: error,

diff --git a/...atures/ramp/pathway-enrichment/src/lib/pathway-enrichment/pathway-enrichment.component.ts b/...atures/ramp/pathway-enrichment/src/lib/pathway-enrichment/pathway-enrichment.component.ts
@@ -162,6 +162,7 @@ export class PathwayEnrichmentComponent
       .subscribe(
       (res: any | undefined) => {
         if (res && res.data) {
+          if (res.data.length) {
             this.dataAsDataProperty = res.data.map((enrichment: FisherResult) => {
               const newObj: { [key: string]: DataProperty } = {};
               Object.entries(enrichment).map((value: any, index: any) => {
@@ -173,12 +174,23 @@ export class PathwayEnrichmentComponent
               });
               return newObj;
             });
-          this.enrichmentLoading = false;
+            this.enrichmentLoading = false;
 
 
-          this.allDataAsDataProperty = this.dataAsDataProperty;
-          this.imageLoading = false;
-          this.ref.markForCheck();
+            this.allDataAsDataProperty = this.dataAsDataProperty;
+            this.imageLoading = false;
+            this.ref.markForCheck();
+          } else {
+            const ref: MatDialogRef<CompleteDialogComponent> = this.dialog.open(CompleteDialogComponent, {
+              data: {
+                title: 'Pathway',
+                message: "No enriched pathways found.",
+                tabs: [ 'Pathways' ]
+
+              }
+            })
+
+          }
         }
         if (res && res.query) {
       this.query = res.query;
@@ -244,6 +256,7 @@ export class PathwayEnrichmentComponent
 
   fetchEnrichment(event: string[]): void {
     this.inputList = event.map(item => item.toLocaleLowerCase());
+    this.image = null;
     this.rampFacade.dispatch(fetchPathwaysFromAnalytes({ analytes: event }));
     this.pathwaysLoading = true;
     this.enrichmentLoading = true;

diff --git a/...-metabolites/src/lib/properties-from-metabolites/properties-from-metabolites.component.ts b/...-metabolites/src/lib/properties-from-metabolites/properties-from-metabolites.component.ts
@@ -123,15 +123,9 @@ export class PropertiesFromMetabolitesComponent
           value: value[1],
         });
       });
-
-      console.log(obj.iso_smiles)
       newObj.imageUrl.url = `${
         this.route.snapshot.data.renderUrl
       }(${encodeURIComponent(obj.iso_smiles)})?size=150`;
-      console.log(newObj.imageUrl.url)
-      console.log(`${
-        this.route.snapshot.data.renderUrl
-      }(${encodeURI(obj.iso_smiles)})?size=150`)
       newObj.imageUrl.label = newObj.common_name.value;
       return newObj;
     });

diff --git a/libs/features/ramp/ramp-header/src/lib/ramp-header/ramp-header.component.html b/libs/features/ramp/ramp-header/src/lib/ramp-header/ramp-header.component.html
@@ -1,4 +1,4 @@
-<ncats-frontend-library-header-template class="ramp-header" [links]="links">
+<ncats-frontend-library-header-template class="header" [links]="links">
   <div class="left-options">
     <a href="/" title="RaMP home page">
       <img

diff --git a/libs/shared/ncats/ncats-footer/src/lib/ncats-footer/ncats-footer.component.spec.ts b/libs/shared/ncats/ncats-footer/src/lib/ncats-footer/ncats-footer.component.spec.ts
@@ -1,5 +1,6 @@
 import { ComponentFixture, TestBed } from '@angular/core/testing';
 import { FlexLayoutModule } from "@angular/flex-layout";
+import { MatIconModule } from "@angular/material/icon";
 import { BrowserAnimationsModule } from "@angular/platform-browser/animations";
 import { RouterTestingModule } from "@angular/router/testing";
 
@@ -15,7 +16,8 @@ describe('NcatsFooterComponent', () => {
       imports: [
         RouterTestingModule,
         BrowserAnimationsModule,
-        FlexLayoutModule
+        FlexLayoutModule,
+        MatIconModule
       ]
     })
     .compileComponents();

diff --git a/libs/shared/ncats/ncats-header/src/lib/ncats-header/ncats-header.component.ts b/libs/shared/ncats/ncats-header/src/lib/ncats-header/ncats-header.component.ts
@@ -1,9 +1,10 @@
-import { Component } from '@angular/core';
+import { Component, ViewEncapsulation } from "@angular/core";
 
 @Component({
   selector: 'ncats-frontend-library-ncats-header',
   templateUrl: './ncats-header.component.html',
   styleUrls: ['./ncats-header.component.scss'],
+  encapsulation: ViewEncapsulation.None
 })
 export class NcatsHeaderComponent {
 }
diff --git a/libs/shared/ui/complete-dialog/src/lib/complete-dialog/complete-dialog.component.html b/libs/shared/ui/complete-dialog/src/lib/complete-dialog/complete-dialog.component.html
@@ -2,7 +2,8 @@
   <span mat-dialog-title>Analysis Complete</span> <mat-icon matRipple (click)="close()" class="close-button">close</mat-icon>
 </div>
 <div mat-dialog-content>
-  <p>{{data.title}} analysis is now complete. Click on the tabs or below buttons to view the data.</p>
+  <p *ngIf="!data.message">{{data.title}} analysis is now complete. Click on the tabs or below buttons to view the data.</p>
+  <p *ngIf="data.message">{{data.message}}</p>
   <br>
   <br>
 

diff --git a/libs/shared/ui/complete-dialog/src/lib/complete-dialog/complete-dialog.component.spec.ts b/libs/shared/ui/complete-dialog/src/lib/complete-dialog/complete-dialog.component.spec.ts
@@ -3,6 +3,7 @@ import { ComponentFixture, TestBed } from '@angular/core/testing';
 import { FlexLayoutModule } from "@angular/flex-layout";
 import { MatButtonModule } from "@angular/material/button";
 import { MAT_DIALOG_DATA, MatDialogModule, MatDialogRef } from "@angular/material/dialog";
+import { MatIconModule } from "@angular/material/icon";
 
 import { CompleteDialogComponent } from './complete-dialog.component';
 
@@ -16,7 +17,8 @@ describe('CompleteDialogComponent', () => {
       imports: [
         MatDialogModule,
         FlexLayoutModule,
-        MatButtonModule
+        MatButtonModule,
+        MatIconModule
       ],
       declarations: [CompleteDialogComponent],
       providers: [{ provide: MatDialogRef, useValue: {} }, { provide: MAT_DIALOG_DATA, useValue: "dfgdfg"  }]

diff --git a/libs/shared/ui/error-dialog/src/lib/error-dialog/error-dialog.component.spec.ts b/libs/shared/ui/error-dialog/src/lib/error-dialog/error-dialog.component.spec.ts
@@ -1,5 +1,8 @@
 import { ComponentFixture, TestBed } from '@angular/core/testing';
-import { MAT_DIALOG_DATA } from '@angular/material/dialog';
+import { FlexLayoutModule } from "@angular/flex-layout";
+import { MatButtonModule } from "@angular/material/button";
+import { MAT_DIALOG_DATA, MatDialogModule } from "@angular/material/dialog";
+import { MatIconModule } from "@angular/material/icon";
 
 import { ErrorDialogComponent } from './error-dialog.component';
 
@@ -10,7 +13,12 @@ describe('ErrorDialogComponent', () => {
   beforeEach(async () => {
     await TestBed.configureTestingModule({
       declarations: [ErrorDialogComponent],
-      imports: [],
+      imports: [
+        MatDialogModule,
+        FlexLayoutModule,
+        MatButtonModule,
+        MatIconModule
+      ],
       providers: [{ provide: MAT_DIALOG_DATA, useValue: {} }],
     }).compileComponents();
   });

diff --git a/libs/shared/ui/header-template/src/lib/header-template/header-template.component.html b/libs/shared/ui/header-template/src/lib/header-template/header-template.component.html
@@ -1,4 +1,4 @@
-<mat-sidenav-container class="mobile-menu-container">
+<mat-sidenav-container class="mobile-menu-container header">
   <nav>
     <mat-toolbar class="toolbar-template" [@slideInOut]="animationState">
       <ng-content select=".left-options"></ng-content>

diff --git a/libs/shared/ui/header-template/src/lib/header-template/header-template.theme.scss b/libs/shared/ui/header-template/src/lib/header-template/header-template.theme.scss
@@ -12,7 +12,7 @@
     .toolbar-template {
       position: fixed;
       margin-bottom: 60px;
-      background-color: mat.get-color-from-palette($primary);
+      background-color: mat.get-color-from-palette($accent) !important;
     }
   }
 }
diff --git a/libs/stores/ramp-store/src/lib/+state/ramp-store/ramp.effects.ts b/libs/stores/ramp-store/src/lib/+state/ramp-store/ramp.effects.ts
@@ -93,7 +93,7 @@ export class RampEffects {
             }
           ),
           catchError((error: ErrorEvent) => {
-            console.log(error);
+         //   console.log(error);
             return of(RampActions.fetchPathwaysFromAnalytesFailure({ error }));
           })
         )

diff --git a/libs/stores/ramp-store/src/lib/+state/ramp-store/ramp.reducer.ts b/libs/stores/ramp-store/src/lib/+state/ramp-store/ramp.reducer.ts
@@ -294,7 +294,7 @@ on(
     RampActions.fetchPropertiesFromMetabolitesFailure,
     filterEnrichmentFromMetabolitesFailure,
     (state, { error }) => {
-      console.log(error);
+     // console.log(error);
       return {
         ...state,
         loading: false,

diff --git a/libs/stores/ramp-store/src/lib/+state/ramp.service.ts b/libs/stores/ramp-store/src/lib/+state/ramp.service.ts
@@ -500,7 +500,7 @@ export class RampService {
     min_pathway_tocluster?: number,
     perc_pathway_overlap?: number
   ){
-    if(!dataframe.fishresults || dataframe.fishresults.length >= 10) {
+    if(!dataframe.fishresults || dataframe.fishresults.length >= 100) {
       return ""
     } else {
       const body = {
@@ -553,7 +553,7 @@ export class RampService {
       console.error(error); // log to console instead
 
       // TODO: better job of transforming error for user consumption
-      console.log(`${operation} failed: ${error.message}`);
+     // console.log(`${operation} failed: ${error.message}`);
 
       // Let the app keep running by returning an empty result.
       return of(result as T);

diff --git a/nx.json b/nx.json
@@ -8,7 +8,7 @@
   },
   "tasksRunnerOptions": {
     "default": {
-      "runner": "@nrwl/workspace/tasks-runners/default",
+      "runner": "nx/tasks-runners/default",
       "options": {
         "cacheableOperations": ["build", "lint", "test", "e2e"]
       }