Merge pull request #754 from IntegratedBreedingPlatform/IBP-5656-Flap…

…jackBytesIntegration

IBP-5656-FlapjackBytesIntegration

src/main/jhipster/package.json

@@ -27,6 +27,7 @@
     "core-js": "2.5.7",
     "d3": "^5.16.0",
     "d3-graphviz": "^2.6.1",
+    "flapjack-bytes": "git+https://github.com/cropgeeks/flapjack-bytes.git",
     "font-awesome": "4.7.0",
     "jquery": "3.2.1",
     "leaflet": "1.7.1",

src/main/jhipster/src/main/webapp/app/germplasm-details/genotyping/genotyping-pane.component.html

@@ -98,54 +98,12 @@
 			</form>
 			<hr>
 			<div class="row">
-				<div class="col-md-8">
-					<span *ngIf="isGenotypingCallsLoading" class="throbber"></span>
-					<div class="table-responsive">
-						<table class="table table-striped table-bordered table-curved" *ngIf="genotypingCalls && genotypingCalls.length else nodata">
-							<thead>
-							<tr>
-								<th jhiTranslate="genotyping.calls.table.marker.column">Marker</th>
-								<th jhiTranslate="genotyping.calls.table.genotype.call.column">Genotype Call</th>
-							</tr>
-							</thead>
-							<tbody>
-							<tr *ngFor="let item of genotypingCalls">
-								<td>{{item?.variantName}}</td>
-								<td>{{item?.genotype?.values[0]}}</td>
-							</tr>
-							</tbody>
-						</table>
-					</div>
-					<div *ngIf="genotypingCalls && genotypingCalls.length">
-						<div class="row">
-							<div class="col">
-								<div class="pagination-container">
-									<div class="pagination-box pagination-box-left"></div>
-									<div class="pagination-box">
-										<ngb-pagination [collectionSize]="totalCount" [(page)]="page" [pageSize]="pageSize" [disabled]="isGenotypingCallsLoading"
-														[maxSize]="5" [rotate]="true" (pageChange)="loadGenotypingCalls()"></ngb-pagination>
-									</div>
-									<div class="pagination-box pagination-box-right"></div>
-								</div>
-							</div>
-						</div>
-					</div>
+				<div class="col-md-12">
+					<span *ngIf="isExportingFlapjack" class="throbber"></span>
+					<div id="flapjack-div" ref="bytes"></div>
+					<br/>
 				</div>
 			</div>
 		</div>
 	</div>
 </div>
-<ng-template #nodata>
-	<table class="table table-striped table-bordered table-curved">
-		<thead>
-		<tr>
-			<th></th>
-		</tr>
-		</thead>
-		<tbody>
-		<tr>
-			<td jhiTranslate="no.data"></td>
-		</tr>
-		</tbody>
-	</table>
-</ng-template>

src/main/jhipster/src/main/webapp/app/germplasm-details/genotyping/genotyping-pane.component.ts

@@ -17,6 +17,8 @@ import { Sample } from '../../entities/sample';
 import { SearchGermplasmRequest } from '../../shared/brapi/model/germplasm/search-germplasm-request';
 import { JhiAlertService } from 'ng-jhipster';
 import { SearchSamplesRequest } from '../../shared/brapi/model/samples/search-samples-request';
+import { ExportFlapjackRequest } from '../../shared/brapi/model/export/export-flapjack-request';
+const flapjack = require('flapjack-bytes/src/flapjack-bytes');
 
 @Component({
     selector: 'jhi-genotyping-pane',
@@ -29,7 +31,7 @@ export class GenotypingPaneComponent implements OnInit {
     totalCount = 10;
     page = 1;
     pageSize = 10;
-    isGenotypingCallsLoading = false;
+    isExportingFlapjack = false;
     isStudyLoading = false;
     isVariantSetLoading = false;
     isSamplesLoading = false;
@@ -66,7 +68,8 @@ export class GenotypingPaneComponent implements OnInit {
     ngOnInit(): void {
         this.cropGenotypingParameterService.getByCropName(this.context.cropName).pipe(flatMap((result) => {
             this.cropGenotypingParameter = result;
-            this.genotypingBrapiService.baseUrl = this.cropGenotypingParameter.endpoint;
+            this.genotypingBrapiService.brapiEndpoint = this.cropGenotypingParameter.endpoint;
+            this.genotypingBrapiService.baseUrl = this.cropGenotypingParameter.baseUrl;
             return this.cropGenotypingParameterService.getToken(this.context.cropName);
         })).subscribe((accessToken) => {
             this.genotypingBrapiService.accessToken = accessToken;
@@ -80,7 +83,7 @@ export class GenotypingPaneComponent implements OnInit {
 
     isGenotypingParameterConfigured() {
         return this.cropGenotypingParameter && this.cropGenotypingParameter.cropName && this.cropGenotypingParameter.endpoint && this.cropGenotypingParameter.tokenEndpoint
-            && this.cropGenotypingParameter.userName && this.cropGenotypingParameter.password && this.cropGenotypingParameter.programId;
+            && this.cropGenotypingParameter.userName && this.cropGenotypingParameter.password && this.cropGenotypingParameter.programId && this.cropGenotypingParameter.baseUrl;
     }
 
     linkBySelectOnChange() {
@@ -169,32 +172,35 @@ export class GenotypingPaneComponent implements OnInit {
     }
 
     selectVariantsetOnChange() {
-        this.genotypingBrapiService.searchCallsets({
-            variantSetDbIds: [this.selectedVariantSet.variantSetDbId],
-            germplasmDbIds: [this.genotypingGermplasm.germplasmDbId]
-        }).subscribe((brapiResponse) => {
-            if (brapiResponse && brapiResponse.result.data.length) {
-                this.genotypingCallSet = brapiResponse.result.data[0];
-                this.loadGenotypingCalls();
-            } else {
-                this.alertService.error('genotyping.no.genotyping.callsets.found');
-            }
-        });
+        if (this.selectedVariantSet) {
+            this.isExportingFlapjack = true;
+            const exportFlapjackRequest = new ExportFlapjackRequest([], [], 'FLAPJACK', [this.genotypingGermplasm.germplasmName], true,
+                100, this.selectedVariantSet.referenceSetDbId);
+            this.genotypingBrapiService.exportFlapjack(exportFlapjackRequest).subscribe((response) => {
+                this.isExportingFlapjack = false;
+                let file = response.replace('.fjzip', '');
+                file = this.extractHostName(this.cropGenotypingParameter.baseUrl) + file;
+
+                const flapjackDiv = '#flapjack-div';
+                const renderer = flapjack.default();
+                renderer.renderGenotypesUrl({
+                    domParent: flapjackDiv,
+                    width: document.querySelector(flapjackDiv).getBoundingClientRect().width,
+                    height: 250,
+                    mapFileURL: file + '.map',
+                    genotypeFileURL: file + '.genotype',
+                    phenotypeFileURL: file + '.phenotype',
+                    overviewWidth: document.querySelector(flapjackDiv).getBoundingClientRect().width,
+                    overviewHeight: 25,
+                    dataSetId: this.cropGenotypingParameter.programId,
+                });
+            });
+        }
     }
 
-    loadGenotypingCalls() {
-        if (this.genotypingCallSet) {
-            this.isGenotypingCallsLoading = true;
-            this.genotypingBrapiService.searchCalls({
-                callSetDbIds: [this.genotypingCallSet.callSetDbId],
-                pageSize: this.pageSize,
-                pageToken: (this.page - 1).toString()
-            }).subscribe(((brapiResponse) => {
-                this.genotypingCalls = brapiResponse.result.data;
-                this.totalCount = brapiResponse.metadata.pagination.totalCount;
-                this.isGenotypingCallsLoading = false;
-            }));
-        }
+    extractHostName(baseUrl) {
+        const { hostname, protocol } = new URL(baseUrl);
+        return protocol + '//' + hostname;
     }
 
     resetForm() {

src/main/jhipster/src/main/webapp/app/shared/brapi/model/export/export-flapjack-request.ts

@@ -0,0 +1,11 @@
+export class ExportFlapjackRequest {
+    constructor(
+        public callSetIds: string[],
+        public callSetIds2: string[],
+        public exportFormat: string,
+        public exportedIndividuals: string[],
+        public keepExportOnServer: boolean, // Must be true, so that we can load the files from the server in flapjack-bytes
+        public pageSize: number,
+        public variantSetId: string) {
+    }
+};

src/main/jhipster/src/main/webapp/app/shared/brapi/service/genotyping-brapi.service.ts

@@ -14,38 +14,44 @@ import { CallSet } from '../model/callsets/callset';
 import { Call } from '../model/calls/call';
 import { SearchSamplesRequest } from '../model/samples/search-samples-request';
 import { Sample } from '../model/samples/sample';
+import { ExportFlapjackRequest } from '../model/export/export-flapjack-request';
 
 @Injectable()
 export class GenotypingBrapiService {
 
-    baseUrl: string;
+    brapiEndpoint: string;
     accessToken: string;
+    baseUrl: string;
 
     constructor(private http: HttpClient) {
     }
 
     searchStudies(searchStudiesRequest: SearchStudiesRequest): Observable<BrapiResponse<Study>> {
-        return this.http.post<BrapiResponse<Study>>(`${this.baseUrl}/search/studies`, searchStudiesRequest, { headers: this.createHeader() });
+        return this.http.post<BrapiResponse<Study>>(`${this.brapiEndpoint}/search/studies`, searchStudiesRequest, { headers: this.createHeader() });
     }
 
     searchGermplasm(searchGermplasmRequest: SearchGermplasmRequest): Observable<BrapiResponse<Germplasm>> {
-        return this.http.post<BrapiResponse<Germplasm>>(`${this.baseUrl}/search/germplasm`, searchGermplasmRequest, { headers: this.createHeader() });
+        return this.http.post<BrapiResponse<Germplasm>>(`${this.brapiEndpoint}/search/germplasm`, searchGermplasmRequest, { headers: this.createHeader() });
     }
 
     searchVariantsets(searchVariantsetRequest: SearchVariantsetRequest): Observable<BrapiResponse<VariantSet>> {
-        return this.http.post<BrapiResponse<VariantSet>>(`${this.baseUrl}/search/variantsets`, searchVariantsetRequest, { headers: this.createHeader() });
+        return this.http.post<BrapiResponse<VariantSet>>(`${this.brapiEndpoint}/search/variantsets`, searchVariantsetRequest, { headers: this.createHeader() });
     }
 
     searchCallsets(searchCallsetRequest: SearchCallsetsRequest): Observable<BrapiResponse<CallSet>> {
-        return this.http.post<BrapiResponse<CallSet>>(`${this.baseUrl}/search/callsets`, searchCallsetRequest, { headers: this.createHeader() });
+        return this.http.post<BrapiResponse<CallSet>>(`${this.brapiEndpoint}/search/callsets`, searchCallsetRequest, { headers: this.createHeader() });
     }
 
     searchCalls(searchCallsRequest: SearchCallsRequest): Observable<BrapiResponse<Call>> {
-        return this.http.post<BrapiResponse<Call>>(`${this.baseUrl}/search/calls`, searchCallsRequest, { headers: this.createHeader() });
+        return this.http.post<BrapiResponse<Call>>(`${this.brapiEndpoint}/search/calls`, searchCallsRequest, { headers: this.createHeader() });
     }
 
     searchSamples(searchSamplesRequest: SearchSamplesRequest): Observable<BrapiResponse<Sample>> {
-        return this.http.post<BrapiResponse<Germplasm>>(`${this.baseUrl}/search/samples`, searchSamplesRequest, { headers: this.createHeader() });
+        return this.http.post<BrapiResponse<Germplasm>>(`${this.brapiEndpoint}/search/samples`, searchSamplesRequest, { headers: this.createHeader() });
+    }
+
+    exportFlapjack(exportRequest: ExportFlapjackRequest): Observable<string> {
+        return this.http.post<string>(`${this.baseUrl}/rest/gigwa/exportData`, exportRequest, {headers: this.createHeader(), responseType: 'text' as 'json'});
     }
 
     // FIXME: Find a way to have a separate instance of HttpClient with its own HttpInterceptor

src/main/jhipster/src/main/webapp/app/shared/crop/model/crop-genotyping-parameter.ts

@@ -5,7 +5,8 @@ export class CropGenotypingParameter {
         public tokenEndpoint: string,
         public userName: string,
         public password: string,
-        public programId: string
+        public programId: string,
+        public baseUrl: string
     ) {
     }
 }

src/main/jhipster/yarn.lock

@@ -957,6 +957,13 @@ aws4@^1.2.1, aws4@^1.8.0:
   version "1.9.1"
   resolved "https://registry.yarnpkg.com/aws4/-/aws4-1.9.1.tgz#7e33d8f7d449b3f673cd72deb9abdc552dbe528e"
 
+axios@^0.19.0:
+  version "0.19.2"
+  resolved "https://registry.yarnpkg.com/axios/-/axios-0.19.2.tgz#3ea36c5d8818d0d5f8a8a97a6d36b86cdc00cb27"
+  integrity sha512-fjgm5MvRHLhx+osE2xoekY70AhARk3a6hkN+3Io1jc00jtquGvxYlKlsFUhmUET0V5te6CcZI7lcv2Ym61mjHA==
+  dependencies:
+    follow-redirects "1.5.10"
+
 axios@^0.21.1:
   version "0.21.1"
   resolved "https://registry.yarnpkg.com/axios/-/axios-0.21.1.tgz#22563481962f4d6bde9a76d516ef0e5d3c09b2b8"
@@ -3453,6 +3460,13 @@ debug@2.6.8:
   dependencies:
     ms "2.0.0"
 
+debug@=3.1.0:
+  version "3.1.0"
+  resolved "https://registry.yarnpkg.com/debug/-/debug-3.1.0.tgz#5bb5a0672628b64149566ba16819e61518c67261"
+  integrity sha512-OX8XqP7/1a9cqkxYw2yXss15f26NKWBpDXQd0/uK/KPqdQhxbPa994hnzjcE2VqQpDslf55723cKPUOGSmMY3g==
+  dependencies:
+    ms "2.0.0"
+
 debug@^3.0.0, debug@^3.1.0, debug@^3.1.1:
   version "3.2.6"
   resolved "https://registry.yarnpkg.com/debug/-/debug-3.2.6.tgz#e83d17de16d8a7efb7717edbe5fb10135eee629b"
@@ -4651,6 +4665,13 @@ first-chunk-stream@^2.0.0:
   dependencies:
     readable-stream "^2.0.2"
 
+"flapjack-bytes@git+https://github.com/cropgeeks/flapjack-bytes.git":
+  version "0.1.0"
+  resolved "git+https://github.com/cropgeeks/flapjack-bytes.git#0f0283c6118b2a03c28309aeb5e91fda1215ee05"
+  dependencies:
+    axios "^0.19.0"
+    node-interval-tree "^1.3.3"
+
 flatten@^1.0.2:
   version "1.0.3"
   resolved "https://registry.yarnpkg.com/flatten/-/flatten-1.0.3.tgz#c1283ac9f27b368abc1e36d1ff7b04501a30356b"
@@ -4667,6 +4688,13 @@ flush-write-stream@^1.0.0:
     inherits "^2.0.3"
     readable-stream "^2.3.6"
 
+follow-redirects@1.5.10:
+  version "1.5.10"
+  resolved "https://registry.yarnpkg.com/follow-redirects/-/follow-redirects-1.5.10.tgz#7b7a9f9aea2fdff36786a94ff643ed07f4ff5e2a"
+  integrity sha512-0V5l4Cizzvqt5D44aTXbFZz+FtyXV1vrDN6qrelxtfYQKW0KO0W2T/hkE8xvGa/540LkZlkaUjO4ailYTFtHVQ==
+  dependencies:
+    debug "=3.1.0"
+
 follow-redirects@^1.0.0:
   version "1.9.0"
   resolved "https://registry.yarnpkg.com/follow-redirects/-/follow-redirects-1.9.0.tgz#8d5bcdc65b7108fe1508649c79c12d732dcedb4f"
@@ -7617,6 +7645,13 @@ node-forge@0.9.0:
   version "0.9.0"
   resolved "https://registry.yarnpkg.com/node-forge/-/node-forge-0.9.0.tgz#d624050edbb44874adca12bb9a52ec63cb782579"
 
+node-interval-tree@^1.3.3:
+  version "1.3.3"
+  resolved "https://registry.yarnpkg.com/node-interval-tree/-/node-interval-tree-1.3.3.tgz#15ffb904cde08270214acace8dc7653e89ae32b7"
+  integrity sha512-K9vk96HdTK5fEipJwxSvIIqwTqr4e3HRJeJrNxBSeVMNSC/JWARRaX7etOLOuTmrRMeOI/K5TCJu3aWIwZiNTw==
+  dependencies:
+    shallowequal "^1.0.2"
+
 node-libs-browser@^2.0.0:
   version "2.2.1"
   resolved "https://registry.yarnpkg.com/node-libs-browser/-/node-libs-browser-2.2.1.tgz#b64f513d18338625f90346d27b0d235e631f6425"
@@ -9911,6 +9946,11 @@ shallow-clone@^3.0.0:
   dependencies:
     kind-of "^6.0.2"
 
+shallowequal@^1.0.2:
+  version "1.1.0"
+  resolved "https://registry.yarnpkg.com/shallowequal/-/shallowequal-1.1.0.tgz#188d521de95b9087404fd4dcb68b13df0ae4e7f8"
+  integrity sha512-y0m1JoUZSlPAjXVtPPW70aZWfIL/dSP7AFkRnniLCrK/8MDKog3TySTBmckD+RObVxH0v4Tox67+F14PdED2oQ==
+
 shebang-command@^1.2.0:
   version "1.2.0"
   resolved "https://registry.yarnpkg.com/shebang-command/-/shebang-command-1.2.0.tgz#44aac65b695b03398968c39f363fee5deafdf1ea"

src/main/web/yarn.lock

@@ -2599,9 +2599,9 @@ braces@~3.0.2:
   dependencies:
     fill-range "^7.0.1"
 
-"brapi-sync@git+ssh://git@github.com/IntegratedBreedingPlatform/brapi-sync.git#semver:1.4.0":
-  version "1.4.0"
-  resolved "git+ssh://git@github.com/IntegratedBreedingPlatform/brapi-sync.git#c8f7344c25678c2d3207c5422cadb00e42eb96bb"
+"brapi-sync@git+ssh://git@github.com/IntegratedBreedingPlatform/brapi-sync.git#semver:1.5.0":
+  version "1.5.0"
+  resolved "git+ssh://git@github.com/IntegratedBreedingPlatform/brapi-sync.git#662b33e223403df5459584612b7335903252163c"
   dependencies:
     "@angular/animations" "~11.2.4"
     "@angular/common" "~11.2.4"