Merge pull request #90 from EBISPOT/06/07/22_release

06/07/22 release

src/app/core/guards/auth.guard.ts

@@ -1,20 +1,21 @@
 import { Injectable } from '@angular/core';
 import { CanActivate, ActivatedRouteSnapshot, RouterStateSnapshot, Router } from '@angular/router';
 import { AuthService } from '../services/auth.service';
+import { TokenStorageService } from '../services/token-storage.service';
 
 @Injectable({
   providedIn: 'root'
 })
 export class AuthGuard implements CanActivate {
 
-  constructor(private authService: AuthService, private router: Router) {
+  constructor(private authService: AuthService, private tss: TokenStorageService) {
   }
 
   canActivate(route: ActivatedRouteSnapshot, state: RouterStateSnapshot): boolean {
     if (this.authService.loggedIn() && this.authService.isCurator()) {
       return true;
     } else {
-      this.router.navigateByUrl('/login').then();
+      this.tss.signOut(state.url);
       return false;
     }
   }

src/app/core/interceptors/auth.interceptor.ts

@@ -3,6 +3,10 @@ import { Injectable } from '@angular/core';
 import { HttpInterceptor, HttpHandler, HttpRequest } from '@angular/common/http';
 
 import { TokenStorageService } from '../services/token-storage.service';
+import { of } from 'rxjs';
+import { catchError } from 'rxjs/operators';
+import { Router } from '@angular/router';
+import { MatDialog } from '@angular/material/dialog';
 
 const TOKEN_HEADER_KEY = 'Authorization';
 
@@ -17,7 +21,17 @@ export class AuthInterceptor implements HttpInterceptor {
     if (token != null) {
       authReq = req.clone({headers: req.headers.set(TOKEN_HEADER_KEY, 'Bearer ' + token)});
     }
-    return next.handle(authReq);
+    return next.handle(authReq).pipe(
+      catchError(
+        (err, caught) => {
+          if (err.status === 401) {
+            this.tokenStorageService.signOut();
+            return of(err);
+          }
+          throw err;
+        }
+      )
+    );
   }
 }
 

src/app/core/models/sample.ts

@@ -0,0 +1,6 @@
+export interface Sample {
+  GCST: string;
+  initialSampleDescription: string;
+  replicateSampleDescription: string;
+  studyTag: string;
+}

src/app/core/models/study.ts

@@ -30,4 +30,8 @@ export interface Study {
   agreedToCc0: boolean;
   diseaseTrait: ReportedTrait;
   efoTraits: EfoTrait[];
-}
+  backgroundEfoTraits: EfoTrait[];
+  sumstats_flag: boolean;
+  pooled_flag: boolean;
+  gxe_flag: boolean;
+}

src/app/core/models/submission.ts

@@ -24,4 +24,6 @@ export interface Submission {
   editTemplate: Provenance;
   lockDetails: {lockedBy: Provenance, status: string};
   agreedToCc0: boolean;
+  opentargets_flag: boolean;
+  userrequested_flag: boolean;
 }

src/app/core/services/auth.service.ts

@@ -19,17 +19,14 @@ export class AuthService {
   }
 
   isCurator() {
-    return this.getDecodedToken().domains.indexOf('self.GWAS_Curator') > -1;
+    return this.getDecodedToken()?.domains?.indexOf('self.GWAS_Curator') > -1;
   }
 
   getDecodedToken() {
     const jwtToken = this.tokenStorageService.getToken();
-    let decoded = jwt_decode(jwtToken);
+    const decoded = jwt_decode(jwtToken);
     if (Date.now() > decoded.exp * 1000) {
-      decoded = 'SESSION TIMEOUT';
-      alert(decoded);
       this.tokenStorageService.signOut();
-      this.router.navigateByUrl('/login').then();
     }
     return decoded;
   }
@@ -82,6 +79,6 @@ export class AuthService {
   }
 
   logout() {
-    this.tokenStorageService.signOut();
+    window.localStorage.removeItem('id_token');
   }
 }

src/app/core/services/curation-http.service.ts

@@ -42,6 +42,14 @@ export class CurationHttpService {
     ).pipe(catchError(CurationHttpService.formatErrors));
   }
 
+  patch(path: string, body: any = {}, params: HttpParams = new HttpParams()): Observable<any> {
+    return this.http.patch(
+      `${environment.CURATION_API_URL}${path}`,
+      body,
+      {params}
+    ).pipe(catchError(CurationHttpService.formatErrors));
+  }
+
   download(path: string, params: HttpParams = new HttpParams()): Observable<any> {
     return this.http.get(`${environment.CURATION_API_URL}${path}`, {params, responseType: 'blob'})
       .pipe(catchError(CurationHttpService.formatErrors));

src/app/core/services/submission.service.ts

@@ -8,6 +8,7 @@ import { SubmissionHistory } from '../models/submissionHistory';
 import { CurationHttpService } from './curation-http.service';
 import { ReportedTrait } from '../models/reportedTrait';
 import { Study } from '../models/study';
+import { EfoTrait } from '../models/efoTrait';
 
 @Injectable({
   providedIn: 'root'
@@ -115,6 +116,11 @@ export class SubmissionService {
     return this.curationHttp.get('/submissions/' + submissionId + '/studies/' + studyId);
   }
 
+  downloadBulkStudyMultiTraitUploadTemplate() {
+
+    return this.curationHttp.download('/reported-traits/templates?file=study-multi-trait');
+  }
+
   downloadBulkStudyTraitUploadTemplate() {
 
     return this.curationHttp.download('/reported-traits/templates?file=study-trait');
@@ -125,14 +131,46 @@ export class SubmissionService {
     return this.curationHttp.download('/reported-traits/templates?file=study-efo-trait');
   }
 
+  downloadSamplesPrefilledTemplate(submissionId: string) {
+
+    return this.curationHttp.download('/submissions/' + submissionId + '/studies/sampledescription/files');
+  }
+
   editReportedTraits(trait: ReportedTrait, submissionId, study: Study) {
 
     return this.curationHttp.put('/submissions/' + submissionId + '/studies/' + study.studyId,
       {diseaseTrait: trait, study_tag: study.study_tag});
   }
 
+  editEfoTraits(efoTraits: EfoTrait[], submissionId, study: Study) {
+
+    return this.curationHttp.put('/submissions/' + submissionId + '/studies/' + study.studyId,
+      {efoTraits, study_tag: study.study_tag});
+  }
+
+  editBgEfoTraits(backgroundEfoTraits: EfoTrait[], submissionId, study: Study) {
+
+    return this.curationHttp.put('/submissions/' + submissionId + '/studies/' + study.studyId,
+      {backgroundEfoTraits, study_tag: study.study_tag});
+  }
+
   filterSubmissions(filtersString: string, size: number, page: number, sort: string, order: string) {
     const params = filtersString + '&size=' + String(size) + '&sort=' + sort + ',' + order;
     return this.curationHttp.get('/submissions?' + params);
   }
+
+  patchSubmission(submission: Submission) {
+
+    return this.curationHttp.patch('/submissions/' + submission.submissionId, submission);
+  }
+
+  getSubmissionSamples(size: number, page: number, sort: string, order: string, submissionId: string) {
+
+    let params: HttpParams = new HttpParams();
+    params = params
+      .set('size', String(size))
+      .set('page', String(page))
+      .set('sort', sort + ',' + order);
+    return this.curationHttp.get('/submissions/' + submissionId + '/studies/sampledescription', params);
+  }
 }

src/app/core/services/token-storage.service.ts

@@ -1,4 +1,6 @@
 import { Injectable } from '@angular/core';
+import { Router, RouterStateSnapshot } from '@angular/router';
+import { MatDialog } from '@angular/material/dialog';
 
 const TOKEN_KEY = 'id_token';
 
@@ -7,11 +9,14 @@ const TOKEN_KEY = 'id_token';
 })
 export class TokenStorageService {
 
-  constructor() {
+  constructor(private router: Router, private dialog: MatDialog) {
   }
 
-  signOut() {
-    window.localStorage.clear();
+  signOut(guardReturnUri?: string) {
+    setTimeout('alert("SESSION EXPIRED")', 1);
+    this.dialog.closeAll();
+    this.router.navigate(['/login'], {queryParams: {returnUrl: guardReturnUri ? guardReturnUri : 'home'}}).then();
+    window.localStorage.removeItem(TOKEN_KEY);
   }
 
   public saveToken(token: string) {

src/app/feature/authentication/pages/login/login.component.ts

@@ -1,6 +1,6 @@
 import { Component, HostListener, OnInit } from '@angular/core';
 import { AuthService } from '../../../../core/services/auth.service';
-import { Router } from '@angular/router';
+import { ActivatedRoute, Router } from '@angular/router';
 import { environment } from '../../../../../environments/environment';
 
 @Component({
@@ -11,11 +11,13 @@ import { environment } from '../../../../../environments/environment';
 export class LoginComponent implements OnInit {
   window: any;
   bgImage: string;
-  constructor(private authService: AuthService, private router: Router) {}
+  private returnUrl: string;
+  constructor(private authService: AuthService, private router: Router, private route: ActivatedRoute) {}
 
   ngOnInit(): void {
     if (this.authService.loggedIn()) { this.router.navigateByUrl('/').then(); }
     this.randomBgImage();
+    this.returnUrl = this.route.snapshot.queryParams.returnUrl || '/';
   }
 
   login() {
@@ -27,7 +29,7 @@ export class LoginComponent implements OnInit {
     if (event.origin === environment.AAPURL) {
       this.authService.saveToken(event.data);
       this.window.close();
-      this.router.navigateByUrl('/').then();
+      this.router.navigateByUrl(this.returnUrl).then();
     }
   }
 

src/app/feature/efo-trait/pages/efo-traits/efo-traits.component.html

@@ -119,6 +119,12 @@ <h3 class="hidden sm:block mt-2">OR</h3>
       <div class="flex justify-center" *ngIf="report">
         <button mat-raised-button color="warn" (click)="downloadBulkUploadReport()">Download report</button>
       </div>
+      <div class="flex justify-center" *ngIf="report && report.hasErrors == true">
+        <h4 class="color-warn">Report may contain errors, please download and have a look.</h4>
+      </div>
+      <div class="flex justify-center" *ngIf="uploadError">
+        <h4 class="color-warn">{{uploadError}}</h4>
+      </div>
       <div class="flex justify-center" *ngIf="traitUploader.queue.length > 0">
         <mat-progress-bar mode="determinate" [value]="traitUploader.progress"></mat-progress-bar>
       </div>
@@ -129,7 +135,7 @@ <h3 class="hidden sm:block mt-2">OR</h3>
           Upload
         </button>
         <button [disabled]="traitUploader.queue.length == 0" mat-raised-button color="primary"
-                (click)="traitUploader.isUploading ? traitUploader.cancelAll() : traitUploader.clearQueue(); fileInput.value = '';">
+                (click)="traitUploader.isUploading ? traitUploader.cancelAll() : traitUploader.clearQueue(); fileInput.value = ''; uploadError = null;">
           <span *ngIf="traitUploader.isUploading">Cancel</span>
           <span *ngIf="!traitUploader.isUploading">Reset</span>
         </button>

src/app/feature/efo-trait/pages/efo-traits/efo-traits.component.ts

@@ -55,6 +55,7 @@ export class EfoTraitsComponent implements OnInit, AfterViewInit {
   editFormInitialValue: any;
   isEditFormDirty = false;
   menuShow = false;
+  uploadError: any;
 
   constructor(private tokenService: TokenStorageService, private dialog: MatDialog,
               private snackBar: MatSnackBar, private efoTraitService: EfoTraitService) {
@@ -74,6 +75,7 @@ export class EfoTraitsComponent implements OnInit, AfterViewInit {
     });
 
     this.traitUploader.onAfterAddingFile = (file) => {
+      this.uploadError = null;
       file.withCredentials = false;
       this.report = null;
       if (this.traitUploader.queue.length > 1) {
@@ -82,13 +84,17 @@ export class EfoTraitsComponent implements OnInit, AfterViewInit {
       }
     };
     this.traitUploader.onSuccessItem = (item, response) => {
+      this.uploadError = null;
       this.snackBar.open('Traits file was uploaded successfully.', '', {duration: 2500});
-      this.report = response;
+      this.report = JSON.parse(response);
       this.traitUploader.clearQueue();
       this.fileInput.nativeElement.value = '';
       this.reloadTraits();
     };
-    this.traitUploader.onErrorItem = () => {
+    this.traitUploader.onErrorItem = (item, response) => {
+      const prefix = 'FileProcessingException:';
+      const message = JSON.parse(response).message;
+      this.uploadError = message.slice(message.indexOf(prefix) + prefix.length);
       this.snackBar.open('An unexpected error occurred while uploading traits.', '', {duration: 2500});
     };
   }
@@ -286,7 +292,7 @@ export class EfoTraitsComponent implements OnInit, AfterViewInit {
   downloadBulkUploadReport() {
 
     const link = document.createElement('a');
-    link.href = window.URL.createObjectURL(new Blob([this.report]));
+    link.href = window.URL.createObjectURL(new Blob([atob(this.report.uploadReport)]));
     link.setAttribute('download', 'efo-traits-bulk-report.tsv');
     document.body.appendChild(link);
     link.click();

src/app/feature/reported-trait/pages/reported-trait/reported-trait.component.html

@@ -105,6 +105,12 @@ <h3 class="hidden sm:block mt-2">OR</h3>
       <div class="flex justify-center" *ngIf="report">
         <button mat-raised-button color="warn" (click)="downloadBulkUploadReport()">Download report</button>
       </div>
+      <div class="flex justify-center" *ngIf="report && report.hasErrors == true">
+        <h4 class="color-warn">Report may contain errors, please download and have a look.</h4>
+      </div>
+      <div class="flex justify-center" *ngIf="uploadError">
+        <h4 class="color-warn">{{uploadError}}</h4>
+      </div>
       <div class="flex justify-center" *ngIf="traitUploader.queue.length > 0">
         <mat-progress-bar mode="determinate" [value]="traitUploader.progress"></mat-progress-bar>
       </div>
@@ -115,7 +121,7 @@ <h3 class="hidden sm:block mt-2">OR</h3>
           Upload
         </button>
         <button [disabled]="traitUploader.queue.length == 0" mat-raised-button color="primary"
-                (click)="traitUploader.isUploading ? traitUploader.cancelAll() : traitUploader.clearQueue(); fileInput.value = '';">
+                (click)="traitUploader.isUploading ? traitUploader.cancelAll() : traitUploader.clearQueue(); fileInput.value = ''; uploadError = false;">
           <span *ngIf="traitUploader.isUploading">Cancel</span>
           <span *ngIf="!traitUploader.isUploading">Reset</span>
         </button>

src/app/feature/reported-trait/pages/reported-trait/reported-trait.component.ts

@@ -15,7 +15,6 @@ import { MatSnackBar } from '@angular/material/snack-bar';
 import { FileUploader } from 'ng2-file-upload';
 import { environment } from '../../../../../environments/environment';
 import { TokenStorageService } from '../../../../core/services/token-storage.service';
-import { TraitUploadApiResponse } from '../../../../core/models/rest/api-responses/traitUploadApiResponse';
 
 @Component({
   selector: 'app-reported-trait',
@@ -50,6 +49,7 @@ export class ReportedTraitComponent implements OnInit, AfterViewInit {
   analysisId = '';
   menuShow = false;
   report: any;
+  uploadError: any;
 
   constructor(private reportedTraitService: ReportedTraitService, private tokenService: TokenStorageService,
               private dialog: MatDialog, private snackBar: MatSnackBar) {
@@ -75,13 +75,17 @@ export class ReportedTraitComponent implements OnInit, AfterViewInit {
       }
     };
     this.traitUploader.onSuccessItem = (item, response) => {
+      this.uploadError = null;
       this.snackBar.open('Traits file was uploaded successfully.', '', {duration: 2500});
-      this.report = response;
+      this.report = JSON.parse(response);
       this.traitUploader.clearQueue();
       this.fileInput.nativeElement.value = '';
       this.reloadTraits();
     };
-    this.traitUploader.onErrorItem = () => {
+    this.traitUploader.onErrorItem = (item, response) => {
+      const prefix = 'FileProcessingException:';
+      const message = JSON.parse(response).message;
+      this.uploadError = message.slice(message.indexOf(prefix) + prefix.length);
       this.snackBar.open('An unexpected error occurred while uploading traits.', '', {duration: 2500});
     };
 
@@ -283,13 +287,11 @@ export class ReportedTraitComponent implements OnInit, AfterViewInit {
         this.dataSource = new MatTableDataSource<ReportedTrait>(value?._embedded?.diseaseTraits ? value._embedded.diseaseTraits : null);
         this.resultsLength = value.page.totalElements;
       });
-
   }
 
   downloadBulkUploadReport() {
-
     const link = document.createElement('a');
-    link.href = window.URL.createObjectURL(new Blob([this.report]));
+    link.href = window.URL.createObjectURL(new Blob([atob(this.report.uploadReport)]));
     link.setAttribute('download', 'reported-traits-bulk-report.tsv');
     document.body.appendChild(link);
     link.click();