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Commit 4c11f518 authored by Jérémy Destin's avatar Jérémy Destin
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feat: Add plantMaterial export button on germplasm card. GNP-5540.

parent 332e5ced
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Showing with 169 additions and 30 deletions
backend/src/main/java/fr/inra/urgi/faidare/api/gnpis/v1/GnpISGermplasmController.java
View file @ 4c11f518
......@@ -12,16 +12,14 @@ import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.io.FileSystemResource;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
import org.springframework.web.bind.annotation.*;
import javax.servlet.http.HttpServletResponse;
import javax.validation.Valid;
import java.io.File;
import java.util.Collections;
import static org.springframework.web.bind.annotation.RequestMethod.GET;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(tags = {"GnpIS API"}, description = "Extended GnpIS API")
@RestController
......@@ -89,8 +87,8 @@ public class GnpISGermplasmController {
* resp.setContentType("application/zip");
* </pre>
*/
@RequestMapping(value = "/csv", method = GET, produces = "text/csv")
public FileSystemResource export(GermplasmPOSTSearchCriteria criteria, HttpServletResponse response) {
@PostMapping(value = "/csv", produces = "text/csv", consumes = APPLICATION_JSON_VALUE)
public FileSystemResource export(@RequestBody @Valid GermplasmPOSTSearchCriteria criteria, HttpServletResponse response) {
try {
File exportFile = germplasmService.exportCSV(criteria);
response.setHeader("Content-Disposition", "attachment; filename=germplasm.gnpis.csv");
......
frontend/package-lock.json
View file @ 4c11f518
......@@ -821,6 +821,12 @@
}
}
},
"@types/file-saver": {
"version": "2.0.1",
"resolved": "https://registry.npmjs.org/@types/file-saver/-/file-saver-2.0.1.tgz",
"integrity": "sha512-g1QUuhYVVAamfCifK7oB7G3aIl4BbOyzDOqVyUfEr4tfBKrXfeH+M+Tg7HKCXSrbzxYdhyCP7z9WbKo0R2hBCw==",
"dev": true
},
"@types/geojson": {
"version": "7946.0.6",
"resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.6.tgz",
......@@ -1273,6 +1279,7 @@
"resolved": "https://registry.npmjs.org/are-we-there-yet/-/are-we-there-yet-1.1.5.tgz",
"integrity": "sha512-5hYdAkZlcG8tOLujVDTgCT+uPX0VnpAH28gWsLfzpXYm7wP6mp5Q/gYyR7YQ0cKVJcXJnl3j2kpBan13PtQf6w==",
"dev": true,
"optional": true,
"requires": {
"delegates": "^1.0.0",
"readable-stream": "^2.0.6"
......@@ -2484,7 +2491,8 @@
"version": "1.1.0",
"resolved": "https://registry.npmjs.org/console-control-strings/-/console-control-strings-1.1.0.tgz",
"integrity": "sha1-PXz0Rk22RG6mRL9LOVB/mFEAjo4=",
"dev": true
"dev": true,
"optional": true
},
"constants-browserify": {
"version": "1.0.0",
......@@ -2886,7 +2894,8 @@
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/delegates/-/delegates-1.0.0.tgz",
"integrity": "sha1-hMbhWbgZBP3KWaDvRM2HDTElD5o=",
"dev": true
"dev": true,
"optional": true
},
"depd": {
"version": "1.1.2",
......@@ -3608,6 +3617,11 @@
"schema-utils": "^1.0.0"
}
},
"file-saver": {
"version": "2.0.2",
"resolved": "https://registry.npmjs.org/file-saver/-/file-saver-2.0.2.tgz",
"integrity": "sha512-Wz3c3XQ5xroCxd1G8b7yL0Ehkf0TC9oYC6buPFkNnU9EnaPlifeAFCyCh+iewXTyFRcg0a6j3J7FmJsIhlhBdw=="
},
"fileset": {
"version": "2.0.3",
"resolved": "https://registry.npmjs.org/fileset/-/fileset-2.0.3.tgz",
......@@ -3853,7 +3867,8 @@
"ansi-regex": {
"version": "2.1.1",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"aproba": {
"version": "1.2.0",
......@@ -3874,12 +3889,14 @@
"balanced-match": {
"version": "1.0.0",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"brace-expansion": {
"version": "1.1.11",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"balanced-match": "^1.0.0",
"concat-map": "0.0.1"
......@@ -3894,17 +3911,20 @@
"code-point-at": {
"version": "1.1.0",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"concat-map": {
"version": "0.0.1",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"console-control-strings": {
"version": "1.1.0",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"core-util-is": {
"version": "1.0.2",
......@@ -4021,7 +4041,8 @@
"inherits": {
"version": "2.0.3",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"ini": {
"version": "1.3.5",
......@@ -4033,6 +4054,7 @@
"version": "1.0.0",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"number-is-nan": "^1.0.0"
}
......@@ -4047,6 +4069,7 @@
"version": "3.0.4",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"brace-expansion": "^1.1.7"
}
......@@ -4054,12 +4077,14 @@
"minimist": {
"version": "0.0.8",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"minipass": {
"version": "2.3.5",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"safe-buffer": "^5.1.2",
"yallist": "^3.0.0"
......@@ -4078,6 +4103,7 @@
"version": "0.5.1",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"minimist": "0.0.8"
}
......@@ -4158,7 +4184,8 @@
"number-is-nan": {
"version": "1.0.1",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"object-assign": {
"version": "4.1.1",
......@@ -4170,6 +4197,7 @@
"version": "1.4.0",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"wrappy": "1"
}
......@@ -4255,7 +4283,8 @@
"safe-buffer": {
"version": "5.1.2",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"safer-buffer": {
"version": "2.1.2",
......@@ -4291,6 +4320,7 @@
"version": "1.0.2",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"code-point-at": "^1.0.0",
"is-fullwidth-code-point": "^1.0.0",
......@@ -4310,6 +4340,7 @@
"version": "3.0.1",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"ansi-regex": "^2.0.0"
}
......@@ -4353,12 +4384,14 @@
"wrappy": {
"version": "1.0.2",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"yallist": {
"version": "3.0.3",
"bundled": true,
"dev": true
"dev": true,
"optional": true
}
}
},
......@@ -4367,6 +4400,7 @@
"resolved": "https://registry.npmjs.org/fstream/-/fstream-1.0.11.tgz",
"integrity": "sha1-XB+x8RdHcRTwYyoOtLcbPLD9MXE=",
"dev": true,
"optional": true,
"requires": {
"graceful-fs": "^4.1.2",
"inherits": "~2.0.0",
......@@ -4379,6 +4413,7 @@
"resolved": "https://registry.npmjs.org/gauge/-/gauge-2.7.4.tgz",
"integrity": "sha1-LANAXHU4w51+s3sxcCLjJfsBi/c=",
"dev": true,
"optional": true,
"requires": {
"aproba": "^1.0.3",
"console-control-strings": "^1.0.0",
......@@ -4416,7 +4451,8 @@
"version": "4.0.1",
"resolved": "https://registry.npmjs.org/get-stdin/-/get-stdin-4.0.1.tgz",
"integrity": "sha1-uWjGsKBDhDJJAui/Gl3zJXmkUP4=",
"dev": true
"dev": true,
"optional": true
},
"get-stream": {
"version": "3.0.0",
......@@ -4605,7 +4641,8 @@
"version": "2.0.1",
"resolved": "https://registry.npmjs.org/has-unicode/-/has-unicode-2.0.1.tgz",
"integrity": "sha1-4Ob+aijPUROIVeCG0Wkedx3iqLk=",
"dev": true
"dev": true,
"optional": true
},
"has-value": {
"version": "1.0.0",
......@@ -5325,7 +5362,8 @@
"version": "0.2.1",
"resolved": "https://registry.npmjs.org/is-utf8/-/is-utf8-0.2.1.tgz",
"integrity": "sha1-Sw2hRCEE0bM2NA6AeX6GXPOffXI=",
"dev": true
"dev": true,
"optional": true
},
"is-windows": {
"version": "1.0.2",
......@@ -5968,6 +6006,7 @@
"resolved": "http://registry.npmjs.org/load-json-file/-/load-json-file-1.1.0.tgz",
"integrity": "sha1-lWkFcI1YtLq0wiYbBPWfMcmTdMA=",
"dev": true,
"optional": true,
"requires": {
"graceful-fs": "^4.1.2",
"parse-json": "^2.2.0",
......@@ -5980,7 +6019,8 @@
"version": "2.3.0",
"resolved": "http://registry.npmjs.org/pify/-/pify-2.3.0.tgz",
"integrity": "sha1-7RQaasBDqEnqWISY59yosVMw6Qw=",
"dev": true
"dev": true,
"optional": true
}
}
},
......@@ -6255,7 +6295,8 @@
"version": "1.0.1",
"resolved": "https://registry.npmjs.org/map-obj/-/map-obj-1.0.1.tgz",
"integrity": "sha1-2TPOuSBdgr3PSIb2dCvcK03qFG0=",
"dev": true
"dev": true,
"optional": true
},
"map-visit": {
"version": "1.0.0",
......@@ -6919,6 +6960,7 @@
"resolved": "https://registry.npmjs.org/npmlog/-/npmlog-4.1.2.tgz",
"integrity": "sha512-2uUqazuKlTaSI/dC8AzicUck7+IrEaOnN/e0jd3Xtt1KcGpwx30v50mL7oPyr/h9bL3E4aZccVwpwP+5W9Vjkg==",
"dev": true,
"optional": true,
"requires": {
"are-we-there-yet": "~1.1.2",
"console-control-strings": "~1.1.0",
......@@ -7933,6 +7975,7 @@
"resolved": "https://registry.npmjs.org/read-pkg/-/read-pkg-1.1.0.tgz",
"integrity": "sha1-9f+qXs0pyzHAR0vKfXVra7KePyg=",
"dev": true,
"optional": true,
"requires": {
"load-json-file": "^1.0.0",
"normalize-package-data": "^2.3.2",
......@@ -7944,6 +7987,7 @@
"resolved": "https://registry.npmjs.org/path-type/-/path-type-1.1.0.tgz",
"integrity": "sha1-WcRPfuSR2nBNpBXaWkBwuk+P5EE=",
"dev": true,
"optional": true,
"requires": {
"graceful-fs": "^4.1.2",
"pify": "^2.0.0",
......@@ -7954,7 +7998,8 @@
"version": "2.3.0",
"resolved": "http://registry.npmjs.org/pify/-/pify-2.3.0.tgz",
"integrity": "sha1-7RQaasBDqEnqWISY59yosVMw6Qw=",
"dev": true
"dev": true,
"optional": true
}
}
},
......@@ -7963,6 +8008,7 @@
"resolved": "https://registry.npmjs.org/read-pkg-up/-/read-pkg-up-1.0.1.tgz",
"integrity": "sha1-nWPBMnbAZZGNV/ACpX9AobZD+wI=",
"dev": true,
"optional": true,
"requires": {
"find-up": "^1.0.0",
"read-pkg": "^1.0.0"
......@@ -7973,6 +8019,7 @@
"resolved": "https://registry.npmjs.org/find-up/-/find-up-1.1.2.tgz",
"integrity": "sha1-ay6YIrGizgpgq2TWEOzK1TyyTQ8=",
"dev": true,
"optional": true,
"requires": {
"path-exists": "^2.0.0",
"pinkie-promise": "^2.0.0"
......@@ -7983,6 +8030,7 @@
"resolved": "https://registry.npmjs.org/path-exists/-/path-exists-2.1.0.tgz",
"integrity": "sha1-D+tsZPD8UY2adU3V77YscCJ2H0s=",
"dev": true,
"optional": true,
"requires": {
"pinkie-promise": "^2.0.0"
}
......@@ -9263,6 +9311,7 @@
"resolved": "https://registry.npmjs.org/strip-bom/-/strip-bom-2.0.0.tgz",
"integrity": "sha1-YhmoVhZSBJHzV4i9vxRHqZx+aw4=",
"dev": true,
"optional": true,
"requires": {
"is-utf8": "^0.2.0"
}
......@@ -10625,6 +10674,7 @@
"resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.3.tgz",
"integrity": "sha512-QGkOQc8XL6Bt5PwnsExKBPuMKBxnGxWWW3fU55Xt4feHozMUhdUMaBCk290qpm/wG5u/RSKzwdAC4i51YigihA==",
"dev": true,
"optional": true,
"requires": {
"string-width": "^1.0.2 || 2"
}
......
frontend/package.json
View file @ 4c11f518
......@@ -28,6 +28,7 @@
"angular-mocks": "1.7.8",
"bootstrap": "4.1.3",
"core-js": "2.5.7",
"file-saver": "2.0.2",
"font-awesome": "4.7.0",
"leaflet": "1.3.4",
"leaflet.markercluster": "1.4.1",
......@@ -46,6 +47,7 @@
"@angular/cli": "7.3.4",
"@angular/compiler-cli": "7.2.7",
"@angular/language-service": "7.2.7",
"@types/file-saver": "2.0.1",
"@types/jasmine": "2.8.12",
"@types/jasminewd2": "2.0.6",
"@types/node": "8.9.5",
......
frontend/src/app/germplasm-card/germplasm-card.component.html
View file @ 4c11f518
......@@ -13,6 +13,8 @@
<div class="row align-items-center justify-content-center">
<button (click)="exportPlantMaterial(germplasmGnpis)">Export</button>
<!--Templates for gerplasm card-->
<ng-template #taxonTemplate>
......
frontend/src/app/germplasm-card/germplasm-card.component.ts
View file @ 4c11f518
......@@ -3,8 +3,9 @@ import { ActivatedRoute } from '@angular/router';
import { BrapiService } from '../brapi.service';
import { GnpisService } from '../gnpis.service';
import { BrapiAttributeData, BrapiGermplasmPedigree, BrapiLocation, BrapiTaxonIds } from '../models/brapi.model';
import { Children, Germplasm, Site } from '../models/gnpis.model';
import { Children, Germplasm, GermplasmExportCriteria, Site } from '../models/gnpis.model';
import { environment } from '../../environments/environment';
import { saveAs } from 'file-saver';
@Component({
selector: 'faidare-germplasm-card',
......@@ -231,4 +232,23 @@ export class GermplasmCardComponent implements OnInit {
}
return 0;
}
exportPlantMaterial(germplasm: Germplasm) {
const germplasmExportCriteria: GermplasmExportCriteria = {
accessionNumbers: [germplasm.accessionNumber],
germplasmDbIds: [],
germplasmGenus: [],
germplasmNames: [],
germplasmPUIs: [germplasm.germplasmPUI],
germplasmSpecies: []
};
this.gnpisService.plantMaterialExport(germplasmExportCriteria).subscribe(
result => {
const blob = new Blob([result], { type: 'text/plain;charset=utf-8' });
saveAs(blob, 'germplasm.gnpis.csv');
},
error => {
console.log(error);
});
}
}
frontend/src/app/gnpis.service.spec.ts
View file @ 4c11f518
......@@ -3,7 +3,15 @@ import { BrapiMetaData, BrapiResults } from './models/brapi.model';
import { DataDiscoveryCriteria, DataDiscoverySource } from './models/data-discovery.model';
import { HttpClientTestingModule, HttpTestingController } from '@angular/common/http/testing';
import { TestBed } from '@angular/core/testing';
import { Donor, Germplasm, GermplasmInstitute, GermplasmSet, Institute, Site } from './models/gnpis.model';
import {
Donor,
Germplasm,
GermplasmExportCriteria,
GermplasmInstitute,
GermplasmSet,
Institute,
Site
} from './models/gnpis.model';
describe('GnpisService', () => {
......@@ -115,6 +123,25 @@ describe('GnpisService', () => {
population: [germplasmSet]
};
const germplasmExportCriteria: GermplasmExportCriteria = {
accessionNumbers: ['VCR010'],
germplasmDbIds: [],
germplasmGenus: [],
germplasmNames: [],
germplasmPUIs: [],
germplasmSpecies: []
};
const exportFile: string = '"DOI";"AccessionNumber";' +
'"AccessionName";"TaxonGroup";' +
'"HoldingInstitution";"LotName";' +
'"LotSynonym";' +
'"CollectionName";' +
'"CollectionType";' +
'"PanelName";' +
'"PanelSize"\n' +
'"https://germplasmdoi";"germplasm01";GermplasmTest;Pea;INRA-URGI;;;;;;';
let gnpisService: GnpisService;
let http: HttpTestingController;
beforeEach(() => {
......@@ -228,5 +255,18 @@ describe('GnpisService', () => {
});
});
});
it('should export germplasm as PlantMaterial', () => {
gnpisService.plantMaterialExport(germplasmExportCriteria).subscribe(
plantMaterialExport => {
expect(plantMaterialExport).toEqual(exportFile);
}
);
const req = http.expectOne({
url: `${BASE_URL}/germplasm/csv`,
method: 'POST'
});
req.flush(exportFile);
});
})
;
frontend/src/app/gnpis.service.ts
View file @ 4c11f518
import { Injectable } from '@angular/core';
import { Observable, ReplaySubject, zip } from 'rxjs';
import { HttpClient } from '@angular/common/http';
import { DataDiscoveryCriteria, DataDiscoveryFacet, DataDiscoveryResults, DataDiscoverySource } from './models/data-discovery.model';
import {
DataDiscoveryCriteria,
DataDiscoveryFacet,
DataDiscoveryResults,
DataDiscoverySource
} from './models/data-discovery.model';
import { BrapiResults } from './models/brapi.model';
import { map } from 'rxjs/operators';
import { Germplasm } from './models/gnpis.model';
import { Germplasm, GermplasmExportCriteria } from './models/gnpis.model';
import { XrefResponse } from './models/xref.model';
import { removeNullUndefined } from './utils';
......@@ -118,4 +123,17 @@ export class GnpisService {
return this.http.get<XrefResponse>(`${BASE_URL}/xref/documentbyfulltextid?linkedRessourcesID=${xrefId}`);
}
// TODO Change return type
plantMaterialExport(criteria: GermplasmExportCriteria): Observable<any> {
const requestOptions: Object = {
/* other options here */
responseType: 'text'
};
return this.http.post<any>(
`${BASE_URL}/germplasm/csv`,
criteria,
requestOptions
);
}
}
frontend/src/app/models/gnpis.model.ts
View file @ 4c11f518
import { BrapiDonor, BrapiGermplasm } from './brapi.model';
export interface GermplasmExportCriteria {
accessionNumbers: string[];
germplasmDbIds: string[];
germplasmGenus: string[];
germplasmNames: string[];
germplasmPUIs: string[];
germplasmSpecies: string[];
}
export interface Germplasm extends BrapiGermplasm {
genusSpecies: string;
genusSpeciesSubtaxa: string;
......
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