Merge pull request #103 from EBISPOT/develop

release v1.1.0

Author: ala-ebi

src/app/app-routing.module.ts

@@ -14,6 +14,10 @@ const routes: Routes = [
     path: 'efo-traits',
     loadChildren: () => import('./feature/efo-trait/efo-trait.module').then(m => m.EfoTraitModule)
   },
+  {
+    path: 'studies',
+    loadChildren: () => import('./feature/study/study.module').then(m => m.StudyModule)
+  },
   {
     path: 'login',
     loadChildren: () => import('./feature/authentication/authentication.module').then(m => m.AuthenticationModule)

src/app/core/components/header/header.component.html

@@ -18,6 +18,7 @@
             <a routerLink="submissions" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white px-2 py-2 rounded-md text-sm font-medium">Submissions</a>
             <a routerLink="reported-traits" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white px-2 py-2 rounded-md text-sm font-medium">Reported traits</a>
             <a routerLink="efo-traits" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white px-2 py-2 rounded-md text-sm font-medium">EFO traits</a>
+            <a routerLink="studies" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white px-2 py-2 rounded-md text-sm font-medium">Studies</a>
           </div>
         </div>
       </div>

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

@@ -0,0 +1,9 @@
+import { ApiResponse } from './apiResponse';
+import { StudySolr } from '../../studySolr';
+
+export interface StudySearchApiResponse extends ApiResponse {
+
+  _embedded: {
+    studySolrDToes: StudySolr[];
+  };
+}

src/app/core/models/studySolr.ts

@@ -0,0 +1,11 @@
+export interface StudySolr {
+  reportedTrait: string;
+  efoTraits: string[];
+  pmid: string;
+  submissionId: string;
+  publicationDate: string;
+  firstAuthor: string;
+  title: string;
+  accessionId: string;
+  notes: string[];
+}

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

@@ -0,0 +1,16 @@
+import { TestBed } from '@angular/core/testing';
+
+import { StudyService } from './study.service';
+
+describe('StudyService', () => {
+  let service: StudyService;
+
+  beforeEach(() => {
+    TestBed.configureTestingModule({});
+    service = TestBed.inject(StudyService);
+  });
+
+  it('should be created', () => {
+    expect(service).toBeTruthy();
+  });
+});

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

@@ -0,0 +1,45 @@
+import { Injectable } from '@angular/core';
+import { CurationHttpService } from './curation-http.service';
+import { HttpParams } from '@angular/common/http';
+
+@Injectable({
+  providedIn: 'root'
+})
+export class StudyService {
+
+  constructor(private http: CurationHttpService) {}
+
+  search(size: number, page: number, sort: string, order: string, efoTrait: string, reportedTrait: string, note: string,
+         sumstatsFlag: string, pooledFlag: string, gxeFlag: string) {
+    let params: HttpParams = new HttpParams();
+    if (size) {
+      params = params.set('size', String(size));
+    }
+    if (page) {
+      params = params.set('page', String(page));
+    }
+    if (sort) {
+      params = params.set('sort', sort + ',' + order);
+    }
+    if (efoTrait){
+      params = params.set('efoTrait', efoTrait);
+    }
+    if (reportedTrait) {
+      params = params.set('reportedTrait', reportedTrait);
+    }
+    if (note) {
+      params = params.set('note', note);
+    }
+    if (sumstatsFlag !== 'any' && sumstatsFlag != null) {
+      params = params.set('sumstatsFlag', String(sumstatsFlag));
+    }
+    if (gxeFlag !== 'any' && gxeFlag != null) {
+      params = params.set('gxeFlag', String(gxeFlag));
+    }
+    if (pooledFlag !== 'any' && pooledFlag != null) {
+      params = params.set('pooledFlag', String(pooledFlag));
+    }
+
+    return this.http.get('/studies', params);
+  }
+}

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

@@ -173,4 +173,20 @@ export class SubmissionService {
       .set('sort', sort + ',' + order);
     return this.curationHttp.get('/submissions/' + submissionId + '/studies/sampledescription', params);
   }
+
+  getSnpStatus(submissionId: string) {
+    return this.curationHttp.get('/submissions/' + submissionId + '/associations/snp-status');
+  }
+
+  approveSnps(submissionId: string) {
+    return this.curationHttp.put('/submissions/' + submissionId + '/associations/approve-snps');
+  }
+
+  downloadSnpValidationReport(submissionId: string) {
+    return this.curationHttp.download('/submissions/' + submissionId + '/associations/snp-validation-report');
+  }
+
+  retriggerSnpValidation(submissionId: string) {
+    return this.http.get('/submissions/' + submissionId + '/validate-snps');
+  }
 }

src/app/feature/study/pages/study-search/study-search.component.css

@@ -0,0 +1,82 @@
+.mat-cell {
+  padding: 0 4px;
+}
+
+th {
+  color: black;
+  font-weight: bold;
+}
+.table-container {
+  position: relative;
+  overflow: auto;
+  width: 100%;
+}
+
+table {
+  width: 100%;
+  min-height: 300px;
+}
+
+th, td {
+    white-space: pre-wrap;
+    text-overflow:ellipsis;
+    overflow: hidden;
+}
+
+.loading-shade {
+  position: absolute;
+  top: 0;
+  left: 0;
+  bottom: 0;
+  right: 0;
+  background: rgba(0, 0, 0, 0.15);
+  z-index: 4;
+  display: flex;
+  align-items: center;
+  justify-content: center;
+}
+
+.filters-button {
+  width: 120px;
+}
+
+
+tr.example-detail-row {
+  height: 0;
+}
+
+tr.example-element-row:not(.example-expanded-row):active {
+  background: #efefef;
+}
+
+.example-element-row td {
+  border-bottom-width: 0;
+}
+
+.element-detail {
+  overflow: hidden;
+  display: flex;
+}
+
+.element-description {
+  padding: 16px;
+}
+
+.mat-row {
+  background-color: white;
+}
+
+.mat-row:nth-child(4n-1), .mat-row:nth-child(4n) {
+  background-color: #eee;
+}
+
+.ellipsis-col {
+  overflow: hidden;
+  max-width: 200px;
+  text-overflow: ellipsis;
+  white-space: nowrap;
+}
+
+::ng-deep .cdk-overlay-pane {
+  width: auto !important;
+}