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Commit 0def31cc authored by Jérémy Destin's avatar Jérémy Destin Committed by Célia Michotey
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refactor: Rebase from master to add xref. Minor fixes. GNP-5490

parent 9bf1df03
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frontend/package-lock.json
View file @ 0def31cc
......@@ -1189,6 +1189,11 @@
"integrity": "sha1-SlKCrBZHKek2Gbz9OtFR+BfOkfU=",
"dev": true
},
"angular-mocks": {
"version": "1.7.8",
"resolved": "https://registry.npmjs.org/angular-mocks/-/angular-mocks-1.7.8.tgz",
"integrity": "sha512-LB13ESBT0eJrhQhfPXyLR9qm4LI9g44hyBFwUqZKEHEA4DpfxVTu0ONipiNoN0zWtmEAezA8u2gjcoaO2TStig=="
},
"ansi-colors": {
"version": "3.2.3",
"resolved": "https://registry.npmjs.org/ansi-colors/-/ansi-colors-3.2.3.tgz",
......@@ -1258,6 +1263,7 @@
"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"
......@@ -2458,7 +2464,8 @@
"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",
......@@ -2854,7 +2861,8 @@
"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",
......@@ -3821,7 +3829,8 @@
"ansi-regex": {
"version": "2.1.1",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"aproba": {
"version": "1.2.0",
......@@ -3842,12 +3851,14 @@
"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"
......@@ -3862,17 +3873,20 @@
"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",
......@@ -3989,7 +4003,8 @@
"inherits": {
"version": "2.0.3",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"ini": {
"version": "1.3.5",
......@@ -4001,6 +4016,7 @@
"version": "1.0.0",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"number-is-nan": "^1.0.0"
}
......@@ -4015,6 +4031,7 @@
"version": "3.0.4",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"brace-expansion": "^1.1.7"
}
......@@ -4022,12 +4039,14 @@
"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"
......@@ -4046,6 +4065,7 @@
"version": "0.5.1",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"minimist": "0.0.8"
}
......@@ -4126,7 +4146,8 @@
"number-is-nan": {
"version": "1.0.1",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"object-assign": {
"version": "4.1.1",
......@@ -4138,6 +4159,7 @@
"version": "1.4.0",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"wrappy": "1"
}
......@@ -4223,7 +4245,8 @@
"safe-buffer": {
"version": "5.1.2",
"bundled": true,
"dev": true
"dev": true,
"optional": true
},
"safer-buffer": {
"version": "2.1.2",
......@@ -4259,6 +4282,7 @@
"version": "1.0.2",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"code-point-at": "^1.0.0",
"is-fullwidth-code-point": "^1.0.0",
......@@ -4278,6 +4302,7 @@
"version": "3.0.1",
"bundled": true,
"dev": true,
"optional": true,
"requires": {
"ansi-regex": "^2.0.0"
}
......@@ -4321,12 +4346,14 @@
"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
}
}
},
......@@ -4335,6 +4362,7 @@
"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",
......@@ -4347,6 +4375,7 @@
"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",
......@@ -4384,7 +4413,8 @@
"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",
......@@ -4564,7 +4594,8 @@
"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",
......@@ -5284,7 +5315,8 @@
"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",
......@@ -5927,6 +5959,7 @@
"resolved": "https://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",
......@@ -5939,7 +5972,8 @@
"version": "2.3.0",
"resolved": "https://registry.npmjs.org/pify/-/pify-2.3.0.tgz",
"integrity": "sha1-7RQaasBDqEnqWISY59yosVMw6Qw=",
"dev": true
"dev": true,
"optional": true
}
}
},
......@@ -6214,7 +6248,8 @@
"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",
......@@ -6862,6 +6897,7 @@
"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",
......@@ -7868,6 +7904,7 @@
"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",
......@@ -7879,6 +7916,7 @@
"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",
......@@ -7889,7 +7927,8 @@
"version": "2.3.0",
"resolved": "https://registry.npmjs.org/pify/-/pify-2.3.0.tgz",
"integrity": "sha1-7RQaasBDqEnqWISY59yosVMw6Qw=",
"dev": true
"dev": true,
"optional": true
}
}
},
......@@ -7898,6 +7937,7 @@
"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"
......@@ -7908,6 +7948,7 @@
"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"
......@@ -7918,6 +7959,7 @@
"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"
}
......@@ -9192,6 +9234,7 @@
"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"
}
......@@ -10548,6 +10591,7 @@
"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 @ 0def31cc
......@@ -24,6 +24,7 @@
"@ng-bootstrap/ng-bootstrap": "4.0.0",
"@types/leaflet": "1.2.14",
"@types/leaflet.markercluster": "1.0.3",
"angular-mocks": "1.7.8",
"bootstrap": "4.1.3",
"core-js": "2.5.7",
"font-awesome": "4.7.0",
......
frontend/src/app/card-section/card-section.component.scss
View file @ 0def31cc
......@@ -12,6 +12,6 @@ a {
font-size: large;
font-weight: bold;
color: #f5f5f5;
background-color: #0f6191;
background-image:repeating-linear-gradient(#0f96cd, #0f6191, #0f76a5) ;
}
frontend/src/app/germplasm-card/germplasm-card.component.html
View file @ 0def31cc
......@@ -849,10 +849,6 @@
</ng-template>
</gpds-card-section>
</div>
<!--XRefs part -->
<gpds-xrefs [xrefId]="germplasmGnpis.germplasmPUI"></gpds-xrefs>
</ng-container>
......
frontend/src/app/germplasm-card/germplasm-card.component.spec.ts
View file @ 0def31cc
......@@ -17,13 +17,6 @@ import { MapComponent } from '../map/map.component';
import { BrapiGermplasmAttributes, BrapiGermplasmPedigree, BrapiResult, BrapiSibling } from '../models/brapi.model';
import { Donor, Germplasm, GermplasmInstitute, GermplasmSet, Institute, Site } from '../models/gnpis.model';
import { DataDiscoverySource } from '../models/data-discovery.model';
import {
BrapiGermplasmAttributes,
BrapiGermplasmPedigree,
BrapiResult,
BrapiSibling
} from "../models/brapi.model";
import {Donor, Germplasm, GermplasmInstitute, GermplasmSet, Institute, Site} from "../models/gnpis.model";
import { MockComponent } from 'ng-mocks';
import { XrefsComponent } from '../xrefs/xrefs.component';
......@@ -215,8 +208,7 @@ describe('GermplasmCardComponent', () => {
TestBed.configureTestingModule({
imports: [RouterTestingModule, NgbPopoverModule, MomentModule],
declarations: [
GermplasmCardComponent, LoadingSpinnerComponent, MockComponent(XrefsComponent)
GermplasmCardComponent, CardSectionComponent,
GermplasmCardComponent, LoadingSpinnerComponent, MockComponent(XrefsComponent), CardSectionComponent,
CardRowComponent, LoadingSpinnerComponent, CardTableComponent, MapComponent
],
providers: [
......
frontend/src/app/gnpis.service.spec.ts
View file @ 0def31cc
import { BASE_URL, BASE_URL_GERMPLASM, GnpisService } from './gnpis.service';
import { BASE_URL, GnpisService } from './gnpis.service';
import { BrapiMetaData, BrapiResults } from './models/brapi.model';
import { DataDiscoveryCriteria, DataDiscoverySource } from './models/data-discovery.model';
import { HttpClientTestingModule, HttpTestingController } from '@angular/common/http/testing';
......@@ -134,7 +134,7 @@ describe('GnpisService', () => {
const req = http.expectOne({
method: 'GET',
url: `${BASE_URL}/sources`
url: `${BASE_URL}/datadiscovery/sources`
});
req.flush(sources);
......@@ -157,7 +157,7 @@ describe('GnpisService', () => {
});
const req = http.expectOne({
url: `${BASE_URL}/suggest?field=${field}&text=${text}&fetchSize=${fetchSize}`,
url: `${BASE_URL}/datadiscovery/suggest?field=${field}&text=${text}&fetchSize=${fetchSize}`,
method: 'POST'
});
req.flush(expectedSuggestions);
......@@ -173,7 +173,7 @@ describe('GnpisService', () => {
gnpisService.germplasm(germplasmDbId).subscribe(response => {
fetchedGermplasm = response;
});
http.expectOne(`${BASE_URL_GERMPLASM}/germplasm?id=${germplasmDbId}`)
http.expectOne(`${BASE_URL}/germplasm?id=${germplasmDbId}`)
.flush(germplasmTest);
expect(fetchedGermplasm).toEqual(germplasmTest);
......@@ -213,7 +213,7 @@ describe('GnpisService', () => {
});
const req = http.expectOne({
url: `${BASE_URL}/search`,
url: `${BASE_URL}/datadiscovery/search`,
method: 'POST'
});
req.flush(rawResult);
......
frontend/src/app/gnpis.service.ts
View file @ 0def31cc
......@@ -8,8 +8,7 @@ import { Germplasm } from './models/gnpis.model';
import { XrefResponse } from './models/xref.model';
export const BASE_URL = 'gnpis/v1/datadiscovery';
export const BASE_URL_GERMPLASM = 'gnpis/v1';
export const BASE_URL = 'gnpis/v1';
@Injectable({
providedIn: 'root'
......@@ -22,7 +21,7 @@ export class GnpisService {
}
private fetchSources(): void {
this.http.get(`${BASE_URL}/sources`).subscribe(
this.http.get(`${BASE_URL}/datadiscovery/sources`).subscribe(
(response: BrapiResults<DataDiscoverySource>) => {
const sourceByURI = {};
for (const source of response.result.data) {
......@@ -49,7 +48,7 @@ export class GnpisService {
): Observable<string[]> {
const params = { field, text, fetchSize: fetchSize.toString() };
return this.http.post<string[]>(
`${BASE_URL}/suggest`, criteria, { params }
`${BASE_URL}/datadiscovery/suggest`, criteria, { params }
);
}
......@@ -65,7 +64,7 @@ export class GnpisService {
// Get source by URI
this.sourceByURI$,
// Get documents by criteria
this.http.post<any>(`${BASE_URL}/search`, criteria)
this.http.post<any>(`${BASE_URL}/datadiscovery/search`, criteria)
).pipe(map(([sourceByURI, response]) => {
// Extract BrAPI documents from result
const documents = response.result.data;
......@@ -94,11 +93,11 @@ export class GnpisService {
}
germplasm(germplasmDbId: string): Observable<Germplasm> {
return this.http.get<Germplasm>(`${BASE_URL_GERMPLASM}/germplasm?id=${germplasmDbId}`);
return this.http.get<Germplasm>(`${BASE_URL}/germplasm?id=${germplasmDbId}`);
}
germplasmByPuid(pui: string): Observable<Germplasm> {
return this.http.get<Germplasm>(`${BASE_URL_GERMPLASM}/germplasm?pui=${pui}`);
return this.http.get<Germplasm>(`${BASE_URL}/germplasm?pui=${pui}`);
}
/**
......@@ -109,7 +108,7 @@ export class GnpisService {
}
xref(xrefId: string): Observable<XrefResponse> {
return this.http.get<XrefResponse>(`gnpis/v1/xref/documentbyfulltextid?linkedRessourcesID=${xrefId}`);
return this.http.get<XrefResponse>(`${BASE_URL}/xref/documentbyfulltextid?linkedRessourcesID=${xrefId}`);
}
}
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