Merge pull request #127 from EBISPOT/develop

Publication import and Submission linking

src/app/core/models/curationStatus.ts

@@ -0,0 +1,4 @@
+export interface CurationStatus {
+  curationStatusId: string;
+  status: string;
+}

src/app/core/models/curator.ts

@@ -0,0 +1,8 @@
+export interface Curator {
+  curatorId: string;
+  firstName: string;
+  lastName: string;
+  email: string;
+  // this is added in the front-end
+  fullName: string;
+}

src/app/core/models/publication.ts

@@ -1,3 +1,6 @@
+import { Curator } from './curator';
+import { CurationStatus } from './curationStatus';
+
 export interface Publication {
    publicationId: string;
    pmid: string;
@@ -10,4 +13,6 @@ export interface Publication {
      email: string;
    };
    status: string;
+   curationStatus: CurationStatus;
+   curator: Curator;
 }

src/app/core/models/rest/api-responses/curationStatusListApiResponse.ts

@@ -0,0 +1,8 @@
+import { ApiResponse } from './apiResponse';
+import { CurationStatus } from '../../curationStatus';
+
+export interface CurationStatusListApiResponse extends ApiResponse {
+  _embedded: {
+    curationStatusDToes: CurationStatus[];
+  };
+}

src/app/core/models/rest/api-responses/curatorListApiResponse.ts

@@ -0,0 +1,8 @@
+import { ApiResponse } from './apiResponse';
+import { Curator } from '../../curator';
+
+export interface CuratorListApiResponse extends ApiResponse {
+  _embedded: {
+    curatorDToes: Curator[];
+  };
+}

src/app/core/models/rest/api-responses/efoTraitsListApiResponse.ts

@@ -2,7 +2,6 @@ import { EfoTrait } from '../../efoTrait';
 import { ApiResponse } from './apiResponse';
 
 export interface EfoTraitsListApiResponse extends ApiResponse {
-
   _embedded: {
     efoTraits: EfoTrait[];
   };

src/app/core/models/rest/api-responses/epmcImportResult.ts

@@ -0,0 +1,7 @@
+import { Publication } from '../../publication';
+
+export interface EpmcImportResult {
+  publicationDto: Publication;
+  pmid: string;
+  status: string;
+}

src/app/core/models/rest/api-responses/publicationListApiResponse.ts

@@ -3,6 +3,6 @@ import { Publication } from '../../publication';
 
 export interface PublicationListApiResponse extends ApiResponse {
   _embedded: {
-    solrPublicationDToes: Publication[]
+    publications: Publication[]
   };
 }

src/app/core/models/submissionMatchingReport.ts

@@ -0,0 +1,9 @@
+export interface SubmissionMatchingReport {
+  submissionID: string;
+  pubMedID: string;
+  author: string;
+  doi: string;
+  cosScore: string;
+  levDistance: string;
+  jwScore: string;
+}

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

@@ -19,6 +19,9 @@ export class AuthService {
   }
 
   isCurator() {
+    if (environment.WHITELISTED_CURATORS.indexOf(this.getDecodedToken()?.email) > -1) {
+      return true;
+    }
     return this.getDecodedToken()?.domains?.indexOf('self.GWAS_Curator') > -1;
   }
 

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

@@ -11,7 +11,8 @@ export class PublicationService {
 
   constructor(private http: CurationHttpService) { }
 
-  getPublications(size: number, page: number, sort: string, order: string, pmid: string, title: string, curator: string): Observable<PublicationListApiResponse> {
+  getPublications(size: number, page: number, sort: string, order: string, pmid: string, title: string, curator: string,
+                  curationStatus: string, submitter: string): Observable<PublicationListApiResponse> {
     let params: HttpParams = new HttpParams();
     params = params
       .set('size', String(size))
@@ -28,6 +29,48 @@ export class PublicationService {
     if (curator) {
       params = params.set('curator', curator);
     }
+    if (curationStatus) {
+      params = params.set('curationStatus', curationStatus);
+    }
+    if (submitter) {
+      params = params.set('submitter', submitter);
+    }
     return this.http.get('/publications', params);
   }
+
+  getCurators() {
+    let params: HttpParams = new HttpParams();
+    params = params
+      .set('size', String(50))
+      .set('page', String(0));
+    return this.http.get('/curators', params);
+  }
+
+  getCurationStatuses() {
+    let params: HttpParams = new HttpParams();
+    params = params
+      .set('size', String(50))
+      .set('page', String(0));
+    return this.http.get('/curation-status', params);
+  }
+
+  updatePublicationCurationDetails(pmid: string, publicationCurationPatchDto: any) {
+    return this.http.patch('/publications/' + pmid + '/curation', publicationCurationPatchDto);
+  }
+
+  importPublicationsFromEpmc(pmids: string[]) {
+    return this.http.post('/publications/' + pmids.join(','));
+  }
+
+  getSubmissionMatchingReport(pmid: string) {
+    let params: HttpParams = new HttpParams();
+    params = params
+      .set('size', String(50))
+      .set('page', String(1));
+    return this.http.get('/publications/' + pmid + '/linked-submissions', params);
+  }
+
+  linkSubmission(pmid: string, submissionId: string) {
+    return this.http.put('/publications/' + pmid + '/link-submission', new HttpParams().set('submissionId', submissionId));
+  }
 }

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

@@ -9,7 +9,7 @@ export class StudyService {
 
   constructor(private http: CurationHttpService) {}
 
-  search(size: number, page: number, sort: string, order: string, efoTrait: string, reportedTrait: string, note: string,
+  search(size: number, page: number, sort: string, order: string, efoTrait: string, reportedTrait: string, note: string, gcst: string,
          sumstatsFlag: string, pooledFlag: string, gxeFlag: string) {
     let params: HttpParams = new HttpParams();
     if (size) {
@@ -30,6 +30,9 @@ export class StudyService {
     if (note) {
       params = params.set('note', note);
     }
+    if (gcst) {
+      params = params.set('accessionId', gcst);
+    }
     if (sumstatsFlag !== 'any' && sumstatsFlag != null) {
       params = params.set('sumstatsFlag', String(sumstatsFlag));
     }

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

@@ -34,7 +34,7 @@
           </li>
         </ul>
       </label>
-      <button mat-raised-button color="primary" style="font-size:12px; margin-right: -10px;" class="gwas-elevation" (click)="downloadEfoTraitsExport()">
+      <button mat-raised-button color="primary" (click)="downloadEfoTraitsExport()">
         <mat-icon>share</mat-icon>
         Export Data
       </button>

src/app/feature/publication/components/check-submission-dialog/check-submission-dialog.component.css

@@ -0,0 +1,24 @@
+.ellipsis-col {
+  overflow: hidden;
+  max-width: 200px;
+  text-overflow: ellipsis;
+  white-space: nowrap;
+}
+
+td, th {
+  padding: 7px !important;
+  text-align: left;;
+}
+
+.loading-shade {
+  position: absolute;
+  top: 0;
+  left: 0;
+  bottom: 0;
+  right: 0;
+  background: rgba(0, 0, 0, 0.15);
+  z-index: 1;
+  display: flex;
+  align-items: center;
+  justify-content: center;
+}

src/app/feature/publication/components/check-submission-dialog/check-submission-dialog.component.html

@@ -0,0 +1,62 @@
+<h2 mat-dialog-title>Potential matches for PMID {{pmid}}</h2>
+<h4 *ngIf="author">{{author}}</h4>
+<h4 *ngIf="title">{{title}}</h4>
+<mat-dialog-content class="mat-typography">
+  <div class="relative">
+    <div *ngIf="loadingInProgress" class="loading-shade">
+      <mat-spinner></mat-spinner>
+    </div>
+    <mat-checkbox class="mt-2" (change)="filter($event)">Include submissions having PMID</mat-checkbox>
+    <table mat-table [dataSource]="dataSource" class="w-full" matSort>
+      <ng-container matColumnDef="pubMedID">
+        <th mat-header-cell *matHeaderCellDef>PMID</th>
+        <td mat-cell *matCellDef="let row">{{row.pubMedID || 'NA'}}</td>
+      </ng-container>
+      <ng-container matColumnDef="submissionId">
+        <th mat-header-cell *matHeaderCellDef>SubmissionId</th>
+        <td mat-cell *matCellDef="let row">{{row.submissionID}}</td>
+      </ng-container>
+      <ng-container matColumnDef="author">
+        <th mat-header-cell *matHeaderCellDef mat-sort-header>Author</th>
+        <td mat-cell *matCellDef="let row">{{row.author}}</td>
+      </ng-container>
+      <ng-container matColumnDef="title">
+        <th mat-header-cell *matHeaderCellDef>Title</th>
+        <td mat-cell *matCellDef="let row" class="ellipsis-col">
+          <span matTooltip="{{row.title}}" matTooltipClass="mat-tooltip">{{row.title || 'NA'}}</span>
+        </td>
+      </ng-container>
+      <ng-container matColumnDef="doi">
+        <th mat-header-cell *matHeaderCellDef>DOI</th>
+        <td mat-cell *matCellDef="let row">
+          <a *ngIf="row.doi" mat-button [href]="row.doi" target="_blank">
+            Open DOI <mat-icon color="primary" style="font-size: 20px">open_in_new</mat-icon>
+          </a>
+        </td>
+      </ng-container>
+      <ng-container matColumnDef="cosineScore">
+        <th mat-header-cell *matHeaderCellDef>Cosine Score</th>
+        <td mat-cell *matCellDef="let row">{{row.cosScore}}</td>
+      </ng-container>
+      <ng-container matColumnDef="linkSubmission">
+        <th mat-header-cell *matHeaderCellDef></th>
+        <td mat-cell *matCellDef="let row">
+          <button mat-raised-button color="primary" [disabled]="row.pubMedID != null" (click)="linkSubmission(row.submissionID, row.author)">
+            Link submission
+          </button>
+        </td>
+      </ng-container>
+      <tr mat-header-row *matHeaderRowDef="displayedColumns"></tr>
+      <tr mat-row *matRowDef="let row; columns: displayedColumns;"></tr>
+      <tr class="mat-row" *matNoDataRow>
+        <td class="mat-cell text-center" colspan="9999">
+          <h3>No submissions found for PMID</h3>
+        </td>
+      </tr>
+    </table>
+    <mat-paginator [length]="resultsLength" [pageSizeOptions]="[5, 10, 20]" showFirstLastButtons></mat-paginator>
+  </div>
+</mat-dialog-content>
+<div mat-dialog-actions>
+  <button mat-button mat-dialog-close>Close</button>
+</div>

src/app/feature/publication/components/check-submission-dialog/check-submission-dialog.component.spec.ts

@@ -0,0 +1,25 @@
+import { ComponentFixture, TestBed } from '@angular/core/testing';
+
+import { CheckSubmissionDialogComponent } from './check-submission-dialog.component';
+
+describe('CheckSubmissionDialogComponent', () => {
+  let component: CheckSubmissionDialogComponent;
+  let fixture: ComponentFixture<CheckSubmissionDialogComponent>;
+
+  beforeEach(async () => {
+    await TestBed.configureTestingModule({
+      declarations: [ CheckSubmissionDialogComponent ]
+    })
+    .compileComponents();
+  });
+
+  beforeEach(() => {
+    fixture = TestBed.createComponent(CheckSubmissionDialogComponent);
+    component = fixture.componentInstance;
+    fixture.detectChanges();
+  });
+
+  it('should create', () => {
+    expect(component).toBeTruthy();
+  });
+});