diff --git a/backend/src/main/resources/application.yml b/backend/src/main/resources/application.yml
index 3b87c03f896f584172004ea031b0703edb5d653b..72884e5f8dcdc90cd8520ba2071eeeab1762dec3 100644
--- a/backend/src/main/resources/application.yml
+++ b/backend/src/main/resources/application.yml
@@ -21,18 +21,14 @@ logging.level:
gpds:
elasticsearch-alias-template:
- gnpis_{source}_{documentType}_5432_scratchy-group{groupId}
+ gnpis_{source}_{documentType}_5432_krusty-group{groupId}
elasticsearch-xref-index-name:
- urgi_xref
+ urgi_xref_dev
cropOntology-repository-url:
https://urgi.versailles.inra.fr/files/ephesis/trait-ontology/data_16.3/ontology-repository.json
- # TODO: Remove this and store at document generation directly (in BrAPI `observationVariable.documentationURL` field)
- cropOntology-portal-link:
- https://urgi.versailles.inra.fr/ephesis/ephesis/ontologyportal.do#termIdentifier=
-
# Provides access to user group WS used to query private data ES aliases
security-user-group-ws-url:
security-user-group-ws-token:
diff --git a/backend/src/main/resources/fr/inra/urgi/gpds/repository/file/datasources.jsonld b/backend/src/main/resources/fr/inra/urgi/gpds/repository/file/datasources.jsonld
index 8a860fa2469617a406b5e26976e448459e04354a..6b319a0137746dff7d0327143ee2aadc52623a76 100644
--- a/backend/src/main/resources/fr/inra/urgi/gpds/repository/file/datasources.jsonld
+++ b/backend/src/main/resources/fr/inra/urgi/gpds/repository/file/datasources.jsonld
@@ -40,7 +40,8 @@
"@id": "https://urgi.versailles.inra.fr",
"schema:identifier": "URGI",
"schema:name": "URGI GnpIS",
- "schema:url": "https://urgi.versailles.inra.fr"
+ "schema:url": "https://urgi.versailles.inra.fr/gnpis/",
+ "schema:image": "./logos/GnpIS.png"
},
{
"@type": "schema:DataCatalog",
diff --git a/backend/src/main/resources/fr/inra/urgi/gpds/repository/file/logos/GnpIS.png b/backend/src/main/resources/fr/inra/urgi/gpds/repository/file/logos/GnpIS.png
new file mode 100644
index 0000000000000000000000000000000000000000..1c682eaa80e2bb8de17bf9d545608a316dd89833
Binary files /dev/null and b/backend/src/main/resources/fr/inra/urgi/gpds/repository/file/logos/GnpIS.png differ
diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 098e7f6fe33e72a87a111ee4c56d26a97621c492..362fd3605dad3122e12b3c7a254afdf3b5fa9efe 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -1189,6 +1189,16 @@
"integrity": "sha1-SlKCrBZHKek2Gbz9OtFR+BfOkfU=",
"dev": true
},
+ "angular-coordinates": {
+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/angular-coordinates/-/angular-coordinates-1.0.0.tgz",
+ "integrity": "sha1-IcuYpv+PTV6LWLjOjvzBP7elnug="
+ },
+ "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 +1268,7 @@
"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 +2469,8 @@
"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 +2866,8 @@
"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 +3834,8 @@
"ansi-regex": {
"version": "2.1.1",
"bundled": true,
- "dev": true
+ "dev": true,
+ "optional": true
},
"aproba": {
"version": "1.2.0",
@@ -3842,12 +3856,14 @@
"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 +3878,20 @@
"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 +4008,8 @@
"inherits": {
"version": "2.0.3",
"bundled": true,
- "dev": true
+ "dev": true,
+ "optional": true
},
"ini": {
"version": "1.3.5",
@@ -4001,6 +4021,7 @@
"version": "1.0.0",
"bundled": true,
"dev": true,
+ "optional": true,
"requires": {
"number-is-nan": "^1.0.0"
}
@@ -4015,6 +4036,7 @@
"version": "3.0.4",
"bundled": true,
"dev": true,
+ "optional": true,
"requires": {
"brace-expansion": "^1.1.7"
}
@@ -4022,12 +4044,14 @@
"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 +4070,7 @@
"version": "0.5.1",
"bundled": true,
"dev": true,
+ "optional": true,
"requires": {
"minimist": "0.0.8"
}
@@ -4126,7 +4151,8 @@
"number-is-nan": {
"version": "1.0.1",
"bundled": true,
- "dev": true
+ "dev": true,
+ "optional": true
},
"object-assign": {
"version": "4.1.1",
@@ -4138,6 +4164,7 @@
"version": "1.4.0",
"bundled": true,
"dev": true,
+ "optional": true,
"requires": {
"wrappy": "1"
}
@@ -4223,7 +4250,8 @@
"safe-buffer": {
"version": "5.1.2",
"bundled": true,
- "dev": true
+ "dev": true,
+ "optional": true
},
"safer-buffer": {
"version": "2.1.2",
@@ -4259,6 +4287,7 @@
"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 +4307,7 @@
"version": "3.0.1",
"bundled": true,
"dev": true,
+ "optional": true,
"requires": {
"ansi-regex": "^2.0.0"
}
@@ -4321,12 +4351,14 @@
"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 +4367,7 @@
"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 +4380,7 @@
"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 +4418,8 @@
"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 +4599,8 @@
"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 +5320,8 @@
"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 +5964,7 @@
"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 +5977,8 @@
"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 +6253,8 @@
"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 +6902,7 @@
"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 +7909,7 @@
"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 +7921,7 @@
"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 +7932,8 @@
"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 +7942,7 @@
"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 +7953,7 @@
"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 +7964,7 @@
"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 +9239,7 @@
"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 +10596,7 @@
"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"
}
diff --git a/frontend/package.json b/frontend/package.json
index ecf1d222fecc1eacf6ed1e1ff8967b339829f9c4..20b0faab9a271c44b216f69db0b1f105dc16c904 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -24,6 +24,8 @@
"@ng-bootstrap/ng-bootstrap": "4.0.0",
"@types/leaflet": "1.2.14",
"@types/leaflet.markercluster": "1.0.3",
+ "angular-coordinates": "1.0.0",
+ "angular-mocks": "1.7.8",
"bootstrap": "4.1.3",
"core-js": "2.5.7",
"font-awesome": "4.7.0",
diff --git a/frontend/src/app/app-routing.module.ts b/frontend/src/app/app-routing.module.ts
index baefb2f81feef7dc3b34054582c20fd86b921c24..3833afd2b7e91c006e2a4ca16858050827862206 100644
--- a/frontend/src/app/app-routing.module.ts
+++ b/frontend/src/app/app-routing.module.ts
@@ -5,15 +5,15 @@ import { GermplasmCardComponent } from './germplasm-card/germplasm-card.componen
import { StudyCardComponent } from './study-card/study-card.component';
import { SiteCardComponent } from './site-card/site-card.component';
-const routes: Routes = [
- { path: 'germplasm', component: GermplasmCardComponent },
+export const routes: Routes = [
{ path: 'studies/:id', component: StudyCardComponent },
{ path: 'sites/:id', component: SiteCardComponent },
{ path: '', component: ResultPageComponent },
+ { path: 'germplasm', component: GermplasmCardComponent }
];
@NgModule({
- imports: [RouterModule.forRoot(routes)],
+ imports: [RouterModule.forRoot(routes, { onSameUrlNavigation: 'reload' })],
exports: [RouterModule]
})
export class AppRoutingModule {
diff --git a/frontend/src/app/app.component.html b/frontend/src/app/app.component.html
index feb91773f62d372bf293b41a03a4e1debf5076b5..1bdaa071a44e1fcc6bac0e097cdaccdbcd195b9d 100644
--- a/frontend/src/app/app.component.html
+++ b/frontend/src/app/app.component.html
@@ -1,4 +1,7 @@
<gpds-navbar></gpds-navbar>
+<div class="alert alert-warning text-center mb-4" role="alert">
+This is a <b>beta</b> application. Please <a href="mailto:urgi-contact@inra.fr" class="alert-link" style="text-decoration: underline">contact us</a> for any comments
+</div>
<div class="container">
<gpds-error></gpds-error>
<router-outlet></router-outlet>
diff --git a/frontend/src/app/app.module.ts b/frontend/src/app/app.module.ts
index 8a99e373a1ec2e6ba6f918f47c2dc62ff022cb28..a6a37d9da503c9e7116a23e4dabb5f8e008e8092 100644
--- a/frontend/src/app/app.module.ts
+++ b/frontend/src/app/app.module.ts
@@ -24,6 +24,7 @@ import { LoadingSpinnerComponent } from './loading-spinner/loading-spinner.compo
import { CardTableComponent } from './card-table/card-table.component';
import { MomentModule } from 'ngx-moment';
import { XrefsComponent } from './xrefs/xrefs.component';
+import { CoordinatesModule } from 'angular-coordinates';
@NgModule({
@@ -58,7 +59,8 @@ import { XrefsComponent } from './xrefs/xrefs.component';
NgbPopoverModule,
FormsModule,
ReactiveFormsModule,
- MomentModule
+ MomentModule,
+ CoordinatesModule
],
providers: [
{ provide: HTTP_INTERCEPTORS, useExisting: ErrorInterceptorService, multi: true }
diff --git a/frontend/src/app/brapi.service.spec.ts b/frontend/src/app/brapi.service.spec.ts
index aecbcbbe4287507d1d5241348d4dd127d88c7a0f..a83f8ef65fad2c060aa12c80739ee6b109e59f07 100644
--- a/frontend/src/app/brapi.service.spec.ts
+++ b/frontend/src/app/brapi.service.spec.ts
@@ -2,26 +2,22 @@ import { BrapiService } from './brapi.service';
import {
BrapiContacts,
BrapiGermplasm,
+ BrapiGermplasmAttributes,
+ BrapiGermplasmPedigree,
+ BrapiGermplasmProgeny,
BrapiLocation,
BrapiObservationVariable,
+ BrapiProgeny,
BrapiResult,
BrapiResults,
+ BrapiSibling,
BrapiStudy,
BrapiTrial
} from './models/brapi.model';
import { DataDiscoverySource } from './models/data-discovery.model';
-import {
- BrapiDescriptor,
- BrapiDonor,
- BrapiGermplasmAttributes,
- BrapiGermplasmPedigree,
- BrapiGermplasmProgeny,
- BrapiSet,
- BrapiSibling
-} from './models/brapi.germplasm.model';
-import { Germplasm, GermplasmData, GermplasmResult, Institute, Origin, Site } from './models/gnpis.germplasm.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';
describe('BrapiService', () => {
@@ -112,17 +108,49 @@ describe('BrapiService', () => {
data: [{
germplasmDbId: 'g1',
accessionNumber: 'G_10',
+ defaultDisplayName: null,
+ germplasmPUI: null,
+ pedigree: null,
+ seedSource: null,
+ synonyms: null,
+ commonCropName: null,
+ instituteCode: null,
+ instituteName: null,
+ biologicalStatusOfAccessionCode: null,
+ countryOfOriginCode: null,
+ typeOfGermplasmStorageCode: null,
+ taxonIds: null,
germplasmName: 'germplam1',
genus: 'Populus',
species: 'x generosa',
- subtaxa: ''
+ subtaxa: '',
+ speciesAuthority: null,
+ subtaxaAuthority: null,
+ donors: null,
+ acquisitionDate: null
}, {
germplasmDbId: 'g2',
accessionNumber: 'G_20',
germplasmName: 'germplam2',
genus: 'Triticum',
species: 'aestivum',
- subtaxa: 'subsp'
+ subtaxa: 'subsp',
+ defaultDisplayName: null,
+ germplasmPUI: null,
+ pedigree: null,
+ seedSource: null,
+ synonyms: null,
+ commonCropName: null,
+ instituteCode: null,
+ instituteName: null,
+ biologicalStatusOfAccessionCode: null,
+ countryOfOriginCode: null,
+ typeOfGermplasmStorageCode: null,
+ taxonIds: null,
+ speciesAuthority: null,
+ subtaxaAuthority: null,
+ donors: null,
+ acquisitionDate: null
}],
}
};
@@ -149,13 +177,14 @@ describe('BrapiService', () => {
defaultDisplayName: 'frere1'
};
- const brapiDescriptor: BrapiDescriptor = {
- name: 'caracteristique1',
- pui: '12',
- value: '32'
+ const brapiProgeny: BrapiProgeny = {
+ germplasmDbId: 'test',
+ defaultDisplayName: 'progeny1',
+ parentType: 'parent1'
};
- const brapiGermplasmPedigree: GermplasmResult<BrapiGermplasmPedigree> = {
+ const brapiGermplasmPedigree: BrapiResult<BrapiGermplasmPedigree> = {
+ metadata: null,
result: {
germplasmDbId: 'test',
defaultDisplayName: '12',
@@ -173,11 +202,12 @@ describe('BrapiService', () => {
}
};
- const brapiGermplasmProgeny: GermplasmResult<BrapiGermplasmProgeny> = {
+ const brapiGermplasmProgeny: BrapiResult<BrapiGermplasmProgeny> = {
+ metadata: null,
result: {
germplasmDbId: 'test',
defaultDisplayName: '11',
- progeny: [brapiSibling]
+ progeny: [brapiProgeny]
}
};
@@ -192,9 +222,9 @@ describe('BrapiService', () => {
address: '12',
logo: null
};
- const origin: Origin = {
+ const origin: GermplasmInstitute = {
+ ...institute,
institute: institute,
- germplasmPUI: '12',
accessionNumber: '12',
accessionCreationDate: '1993',
materialType: 'feuille',
@@ -204,14 +234,15 @@ describe('BrapiService', () => {
distributionStatus: null
};
- const brapiDonor: BrapiDonor = {
+ const brapiDonor: Donor = {
donorInstitute: institute,
- germplasmPUI: '12',
- accessionNumber: '12',
- donorInstituteCode: 'urgi'
+ donorGermplasmPUI: '12',
+ donorAccessionNumber: '12',
+ donorInstituteCode: 'urgi',
+ donationDate: null
};
- const brapiSet: BrapiSet = {
+ const germplasmSet: GermplasmSet = {
germplasmCount: 12,
germplasmRef: null,
id: 12,
@@ -219,18 +250,21 @@ describe('BrapiService', () => {
type: 'plan'
};
- const brapiGermplasmAttributes: GermplasmResult<GermplasmData<BrapiGermplasmAttributes[]>> = {
+ const brapiGermplasmAttributes: BrapiResult<BrapiGermplasmAttributes> = {
+ metadata: null,
result: {
+ germplasmDbId: 'test',
data: [{
+ attributeCode: 'att',
+ attributeDbId: 'attr2',
attributeName: 'longueur',
+ determinedDate: '2019',
value: '30'
}]
}
};
const germplasmTest: Germplasm = {
- url: 'www.cirad.fr',
- source: 'cirad',
germplasmDbId: 'test',
defaultDisplayName: 'test',
accessionNumber: 'test',
@@ -264,20 +298,15 @@ describe('BrapiService', () => {
holdingGenbank: institute,
presenceStatus: null,
children: null,
- descriptors: [brapiDescriptor],
originSite: null,
collectingSite: null,
evaluationSites: null,
collector: origin,
breeder: origin,
distributors: [origin],
- panel: [brapiSet],
- collection: [brapiSet],
- population: [brapiSet]
- };
-
- const germplasmResultTest = {
- result: germplasmTest
+ panel: [germplasmSet],
+ collection: [germplasmSet],
+ population: [germplasmSet]
};
let brapiService: BrapiService;
@@ -365,7 +394,7 @@ describe('BrapiService', () => {
it('should fetch the pedigree', () => {
- let fetchedGermplasmPedigree: GermplasmResult<BrapiGermplasmPedigree>;
+ let fetchedGermplasmPedigree: BrapiResult<BrapiGermplasmPedigree>;
const germplasmDbId: string = brapiGermplasmPedigree.result.germplasmDbId;
brapiService.germplasmPedigree(germplasmDbId).subscribe(response => {
fetchedGermplasmPedigree = response;
@@ -377,7 +406,8 @@ describe('BrapiService', () => {
});
- it('should fetch the germplasm progeny', () => {
+ // TODO test the progeny call when the information about parent will be added
+ /*it('should fetch the germplasm progeny', () => {
let fetchedGermplasmProgeny: GermplasmResult<BrapiGermplasmProgeny>;
const germplasmDbId: string = brapiGermplasmProgeny.result.germplasmDbId;
@@ -389,11 +419,11 @@ describe('BrapiService', () => {
expect(fetchedGermplasmProgeny).toEqual(brapiGermplasmProgeny);
- });
+ });*/
it('should fetch the germplasm attributes', () => {
- let fetchedGermplasmAttributes: GermplasmResult<GermplasmData<BrapiGermplasmAttributes[]>>;
+ let fetchedGermplasmAttributes: BrapiResult<BrapiGermplasmAttributes>;
const germplasmDbId: string = germplasmTest.germplasmDbId;
brapiService.germplasmAttributes(germplasmDbId).subscribe(response => {
fetchedGermplasmAttributes = response;
diff --git a/frontend/src/app/brapi.service.ts b/frontend/src/app/brapi.service.ts
index bed9d9a83435a0485e9454ff4c1e317d51f0f891..a32154a558e86966cdc2a69014343a7c2649e6fc 100644
--- a/frontend/src/app/brapi.service.ts
+++ b/frontend/src/app/brapi.service.ts
@@ -1,9 +1,10 @@
import { Injectable } from '@angular/core';
import { Observable } from 'rxjs';
import { HttpClient } from '@angular/common/http';
-import { Germplasm, GermplasmData, GermplasmResult } from './models/gnpis.germplasm.model';
import {
BrapiGermplasm,
+ BrapiGermplasmAttributes,
+ BrapiGermplasmPedigree,
BrapiLocation,
BrapiObservationVariable,
BrapiResult,
@@ -11,7 +12,7 @@ import {
BrapiStudy,
BrapiTrial
} from './models/brapi.model';
-import { BrapiGermplasmAttributes, BrapiGermplasmPedigree, BrapiGermplasmProgeny } from './models/brapi.germplasm.model';
+import { Germplasm } from './models/gnpis.model';
export const BASE_URL = 'brapi/v1';
@@ -28,18 +29,18 @@ export class BrapiService {
.get<Germplasm>(`${BASE_URL}/germplasm/${germplasmDbId}`);
}
- germplasmPedigree(germplasmDbId: string): Observable<GermplasmResult<BrapiGermplasmPedigree>> {
+ germplasmPedigree(germplasmDbId: string): Observable<BrapiResult<BrapiGermplasmPedigree>> {
return this.http
- .get<GermplasmResult<BrapiGermplasmPedigree>>(`${BASE_URL}/germplasm/${germplasmDbId}/pedigree`);
+ .get<BrapiResult<BrapiGermplasmPedigree>>(`${BASE_URL}/germplasm/${germplasmDbId}/pedigree`);
}
-
- germplasmProgeny(germplasmDbId: string): Observable<GermplasmResult<BrapiGermplasmProgeny>> {
+ // TODO use the progeny call when the information about parent will be added
+ /*germplasmProgeny(germplasmDbId: string): Observable<GermplasmResult<BrapiGermplasmProgeny>> {
return this.http.get<GermplasmResult<BrapiGermplasmProgeny>>(`${BASE_URL}/germplasm/${germplasmDbId}/progeny`);
- }
+ }*/
- germplasmAttributes(germplasmDbId: string): Observable<GermplasmResult<GermplasmData<BrapiGermplasmAttributes[]>>> {
+ germplasmAttributes(germplasmDbId: string): Observable<BrapiResult<BrapiGermplasmAttributes>> {
return this.http
- .get<GermplasmResult<GermplasmData<BrapiGermplasmAttributes[]>>>(`${BASE_URL}/germplasm/${germplasmDbId}/attributes`);
+ .get<BrapiResult<BrapiGermplasmAttributes>>(`${BASE_URL}/germplasm/${germplasmDbId}/attributes`);
}
study(studyDbId: string): Observable<BrapiResult<BrapiStudy>> {
diff --git a/frontend/src/app/card-row/card-row.component.html b/frontend/src/app/card-row/card-row.component.html
index e3d9f2587f5fe4f6857effbfb70828c6073eb35d..42301209673db46dd7a6c413ccd04b6bd375f749 100644
--- a/frontend/src/app/card-row/card-row.component.html
+++ b/frontend/src/app/card-row/card-row.component.html
@@ -1,4 +1,4 @@
-<ng-container *ngIf="test && (value === undefined || value)">
+<ng-container *ngIf="(test && value === undefined) || (value)">
<div class="row row-sep">
<div class="col-4 field my-2">
{{ label }}
diff --git a/frontend/src/app/card-row/card-row.component.scss b/frontend/src/app/card-row/card-row.component.scss
index 5f6ecd43d609ce9c88484a500fe32cc215501c3c..d5fab77cbcf99eb6409d67cec2b3906bb40d8186 100644
--- a/frontend/src/app/card-row/card-row.component.scss
+++ b/frontend/src/app/card-row/card-row.component.scss
@@ -1,7 +1,7 @@
-.row-sep {
- border-top: 0.01px solid #f0f0f0;
-}
+@import '../../styles.scss';
.field {
font-weight: bold;
+ overflow-wrap: normal;
}
+
diff --git a/frontend/src/app/card-section/card-section.component.html b/frontend/src/app/card-section/card-section.component.html
index ffaa0ba6b3a5afb787f18d12f65b042585dc4b8a..bcf4fd14571926df10dfd812722441942d0c646c 100644
--- a/frontend/src/app/card-section/card-section.component.html
+++ b/frontend/src/app/card-section/card-section.component.html
@@ -1,4 +1,4 @@
-<div class="card mb-3 mt-4" *ngIf="test">
+<div class="card mb-3" *ngIf="test">
<div class="card-header">
{{ header }}
</div>
diff --git a/frontend/src/app/card-section/card-section.component.scss b/frontend/src/app/card-section/card-section.component.scss
index 155466cf1b6c0b21bbf28661089d1da24001ad64..78b6d191061a3269423b24f33facc74d9a1b2343 100644
--- a/frontend/src/app/card-section/card-section.component.scss
+++ b/frontend/src/app/card-section/card-section.component.scss
@@ -1,15 +1,17 @@
+@import '../../styles.scss';
+
+a {
+ text-decoration: underline;
+}
+
.card {
- margin-top: 25px;
- margin-bottom: 10px;
- border-color: rgba(89, 89, 89, 0.33);
- border-width: 1.5px;
+ border: none;
}
.card-header {
font-size: large;
font-weight: bold;
- color: #0f6191;
- background-color: #eaeaea;
- border-color: rgba(29, 29, 29, 0.16);
- border-width: 2.5px;
+ color: #f5f5f5;
+ background-image:repeating-linear-gradient(#0f96cd, #0f6191, #0f76a5) ;
}
+
diff --git a/frontend/src/app/card-table/card-table.component.html b/frontend/src/app/card-table/card-table.component.html
index beb8c09450a0d12acbc7dfdd9ff074745d034690..93b0d733aa34a09284d88cec0f4626d25ff022d0 100644
--- a/frontend/src/app/card-table/card-table.component.html
+++ b/frontend/src/app/card-table/card-table.component.html
@@ -1,4 +1,4 @@
-<div class="table-responsive scroll-table">
+<div class="table-responsive scroll-table table-card-body">
<table class="table table-sm table-striped">
<thead *ngIf="headers">
<tr>
diff --git a/frontend/src/app/card-table/card-table.component.scss b/frontend/src/app/card-table/card-table.component.scss
index f721891f8501e63874515eb0119c44fcf7ce090a..85f3be7e4aa2bc69e5f668af489d1a1c9f8bbc85 100644
--- a/frontend/src/app/card-table/card-table.component.scss
+++ b/frontend/src/app/card-table/card-table.component.scss
@@ -3,9 +3,17 @@
max-height: 200px;
overflow-y: auto;
- thead {
+ thead th {
position: sticky;
top: 0;
background-color: white;
}
}
+
+.table-card-body {
+ padding: 0;
+ border: 2px solid rgb(195, 214, 226);
+ border-top-width: 0px;
+ border-bottom-left-radius: 0.25rem;
+ border-bottom-right-radius: 0.25rem;
+}
diff --git a/frontend/src/app/form/form.component.html b/frontend/src/app/form/form.component.html
index 3df3dbe20dcb972a632008200d563d2b1c63ada5..f0ffe68003cb3aa53f209e2d2dbaf9c583cfe4c2 100644
--- a/frontend/src/app/form/form.component.html
+++ b/frontend/src/app/form/form.component.html
@@ -10,7 +10,7 @@
<a tabindex="1"
class="nav-link {{ activeTab == 'Variable' ? 'active' : ''}}"
(click)="activeTab='Variable'">
- Variable
+ Trait
</a>
</li>
</ul>
diff --git a/frontend/src/app/germplasm-card/germplasm-card.component.html b/frontend/src/app/germplasm-card/germplasm-card.component.html
index 7ffb091702f715389456a2878f6eaeb898c777fc..7e3129e8ff3e41d6d0e74c53fb638fda16df5253 100644
--- a/frontend/src/app/germplasm-card/germplasm-card.component.html
+++ b/frontend/src/app/germplasm-card/germplasm-card.component.html
@@ -1,668 +1,860 @@
<gpds-loading-spinner [loading]="loading" class="float-right"></gpds-loading-spinner>
<ng-container *ngIf="germplasmGnpis">
- <h3>
+ <h3 class="mb-4">
+ <img *ngIf="germplasmGnpis.holdingGenbank && germplasmGnpis.holdingGenbank.instituteName"
+ [src]="IMAGES_BRC_URL"
+ align="right"/>
Germplasm: {{ germplasmGnpis.germplasmName }}
</h3>
- <div class="container-fluid">
- <div class="container">
- <div class="row">
- <div class="col-md-auto field" *ngIf="germplasmGnpis.photo && germplasmGnpis.photo.thumbnailFileName != null">
- <figure class="figure">
- <img
- src="{{ IMAGES_SIREGAL_URL }}/{{ germplasmGnpis.holdingGenbank.instituteCode }}/{{ germplasmGnpis.photo.thumbnailFileName }}"
- class="img-fluid">
- <figcaption class="figure-caption">
- <a class="btn popovers" data-boundary="window" placement="right" [ngbPopover]="imageTemplate"
- [popoverTitle]="Details" container="body">
- Click to see more details.
+ <!-- Display the map -->
+ <gpds-map [locations]="germplasmLocations"></gpds-map>
+
+ <div class="row align-items-center">
+
+ <!--Templates for gerplasm card-->
+ <ng-template #holdingInstituteTemplate>
+
+ <gpds-card-row
+ label=""
+ [test]="germplasmGnpis.holdingInstitute && germplasmGnpis.holdingInstitute.logo">
+ <ng-template>
+ <img
+ [src]="IMAGES_INSTITUTION_URL + germplasmGnpis.holdingInstitute.logo"/>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Code"
+ [value]="germplasmGnpis.holdingInstitute.instituteCode">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Acronym"
+ [value]="germplasmGnpis.holdingInstitute.acronym">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Organisation"
+ [value]="germplasmGnpis.holdingInstitute.organisation">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Type"
+ [value]="germplasmGnpis.holdingInstitute.instituteType">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Address"
+ [value]="germplasmGnpis.holdingInstitute.address">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Website"
+ [test]="germplasmGnpis.holdingInstitute.webSite">
+ <ng-template>
+ <a [href]="germplasmGnpis.breeder.institute.webSite" target="_blank">
+ {{ germplasmGnpis.holdingInstitute.webSite }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ </ng-template>
+
+
+ <ng-template #BreederInstituteTemplate>
+
+ <gpds-card-row
+ label=""
+ [test]="germplasmGnpis.breeder && germplasmGnpis.breeder.institute && germplasmGnpis.breeder.institute.logo">
+ <ng-template>
+ <img
+ [src]="IMAGES_INSTITUTION_URL + germplasmGnpis.breeder.institute.logo"/>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Code"
+ [value]="germplasmGnpis.breeder.institute.instituteCode">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Acronym"
+ [value]="germplasmGnpis.breeder.institute.acronym">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Organisation"
+ [value]="germplasmGnpis.breeder.institute.organisation">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Type"
+ [value]="germplasmGnpis.breeder.institute.instituteType">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Address"
+ [value]="germplasmGnpis.breeder.institute.address">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Website"
+ [test]="germplasmGnpis.breeder.institute.webSite">
+ <ng-template>
+ <a [href]="germplasmGnpis.breeder.institute.webSite" target="_blank">
+ {{ germplasmGnpis.breeder.institute.webSite }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ </ng-template>
+
+ <ng-template #CollectorInstituteTemplate>
+
+ <gpds-card-row
+ label=""
+ [test]="germplasmGnpis.collector && germplasmGnpis.collector.institute && germplasmGnpis.collector.institute.logo">
+ <ng-template>
+ <img
+ [src]="IMAGES_INSTITUTION_URL + germplasmGnpis.collector.institute.logo"/>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Code"
+ [value]="germplasmGnpis.collector.institute.instituteCode">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Acronym"
+ [value]="germplasmGnpis.collector.institute.acronym">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Organisation"
+ [value]="germplasmGnpis.collector.institute.organisation">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Address"
+ [value]="germplasmGnpis.collector.institute.address">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Website"
+ [test]="germplasmGnpis.collector.institute.webSite">
+ <ng-template>
+ <a [href]="germplasmGnpis.collector.institute.webSite" target="_blank">
+ {{ germplasmGnpis.collector.institute.webSite }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ </ng-template>
+
+
+ <!--Section for the image representing the germplasm and the details about this image-->
+ <div class="col-auto field" *ngIf="germplasmGnpis.photo && germplasmGnpis.photo.thumbnailFileName">
+ <a class="btn popovers" data-boundary="window" placement="right" [ngbPopover]="imageTemplate"
+ [popoverTitle]="germplasmGnpis.photo.photoName" container="body">
+ <img
+ [src]="IMAGES_ACCESSION_URL + germplasmGnpis.holdingGenbank.instituteCode + '/' + germplasmGnpis.photo.thumbnailFileName"
+ class="img-fluid">
+ <figcaption class="figure-caption">
+ Click to see more details
+ </figcaption>
+ </a>
+
+ <ng-template #imageTemplate>
+ <div class="card ngb-popover-window ">
+ <img class="card-img-top"
+ [src]="IMAGES_ACCESSION_URL + germplasmGnpis.holdingGenbank.instituteCode + '/' + germplasmGnpis.photo.fileName"
+ alt="" width="250px">
+ <div class="card-body">
+
+ <gpds-card-row
+ label="Accession name"
+ [value]="germplasmGnpis.germplasmName">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Photo name"
+ [value]="germplasmGnpis.photo.photoName">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Description"
+ [value]="germplasmGnpis.photo.description">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Copyright"
+ [value]="'© '+germplasmGnpis.photo.copyright">
+ </gpds-card-row>
+ </div>
+ </div>
+ </ng-template>
+ </div>
+
+ <!--Section for the information about the identification of the germplasm-->
+ <gpds-card-section
+ class="col-12 col-lg"
+ header="Identification">
+ <ng-template>
+ <div class="card-body card-section-body">
+
+ <gpds-card-row
+ label="Germplasm name"
+ [value]="germplasmGnpis.germplasmName">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Accession number"
+ [value]="germplasmGnpis.accessionNumber">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Permanent Unique Identifier"
+ [value]="germplasmGnpis.germplasmPUI">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Source"
+ [test]="germplasmSource">
+ <ng-template>
+ <a target="_blank"
+ [href]="germplasmSource['schema:url']">
+ <img [src]="germplasmSource['schema:image']" alt="Germplasm source image"/>
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Data source"
+ [test]="germplasmSource['schema:identifier'] && germplasmGnpis.documentationURL">
+ <ng-template>
+ <a target="_blank" [href]="germplasmGnpis.documentationURL">
+ Link to this study on {{ germplasmSource['schema:identifier'] }}
</a>
- </figcaption>
- </figure>
-
- <ng-template #imageTemplate>
- <div class="card ngb-popover-window ">
- <img class="card-img-top"
- src="{{ IMAGES_SIREGAL_URL }}/{{ germplasmGnpis.holdingGenbank.instituteCode }}/{{ germplasmGnpis.photo.fileName }}"
- alt="" width="500px">
- <div class="card-body">
- <table class="table">
- <tr *ngIf="germplasmGnpis.photo.photoName">
- <th class="fieldName">Name</th>
- <td class="field">{{ germplasmGnpis.photo.photoName }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.photo.description">
- <th class="fieldName">Description</th>
- <td class="field">{{ germplasmGnpis.photo.description }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.photo.copyright">
- <th class="fieldName">Copyright</th>
- <td class="field">{{ germplasmGnpis.photo.copyright }}</td>
- </tr>
- </table>
+ </ng-template>
+ </gpds-card-row>
+
+
+ <gpds-card-row
+ label="Accession synonyms"
+ [test]="germplasmGnpis.synonyms && germplasmGnpis.synonyms.length > 0">
+ <ng-template>
+ <div class="content-overflow">
+ {{ germplasmGnpis.synonyms.join(', ') }}
</div>
- </div>
- </ng-template>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Taxon"
+ [test]="germplasmGnpis.genus || germplasmGnpis.species || germplasmGnpis.subtaxa">
+ <ng-template>
+ <i>{{ germplasmGnpis.genus }} {{ germplasmGnpis.species }} {{ germplasmGnpis.subtaxa }}</i>
+ {{ germplasmGnpis.speciesAuthority ? '(' + germplasmGnpis.speciesAuthority + ')' : '' }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Taxon common names"
+ [test]="germplasmGnpis.taxonCommonNames && germplasmGnpis.taxonCommonNames.length > 0">
+ <ng-template>
+ <div class="content-overflow">
+ {{ germplasmGnpis.taxonCommonNames.join(', ') }}
+ </div>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Taxon synonyms"
+ [test]="germplasmGnpis.taxonSynonyms && germplasmGnpis.taxonSynonyms.length > 0">
+ <ng-template>
+ <div class="content-overflow">
+ <i>{{ germplasmGnpis.taxonSynonyms.join(', ') }}</i>
+ </div>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Biological status"
+ [value]="germplasmGnpis.biologicalStatusOfAccessionCode">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Genetic nature"
+ [value]="germplasmGnpis.geneticNature">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Seed source"
+ [value]="germplasmGnpis.seedSource">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Pedigree"
+ [value]="germplasmGnpis.pedigree">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Comments"
+ [value]="germplasmGnpis.comment">
+ </gpds-card-row>
</div>
- <div class="col">
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <thead class="text-white">
- <tr>
- <th class="headerTitle" scope="col" colspan="2">
- Identification
- </th>
- </tr>
- </thead>
- <tr *ngIf="germplasmGnpis.accessionNumber">
- <th class="fieldName" scope="row">Accession number</th>
- <td class="field">{{ germplasmGnpis.accessionNumber }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.acquisitionDate">
- <th class="fieldName" scope="row">Acquisition date</th>
- <td
- class="field">{{ germplasmGnpis.acquisitionDate | amParse:'YYYYMMDD' | amDateFormat:'YYYY-MM-DD' }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.germplasmName">
- <th class="fieldName" scope="row">Germplasm name</th>
- <td class="field">{{ germplasmGnpis.germplasmName }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.germplasmPUI">
- <th class="fieldName" scope="row">Permanent Unique Identifier</th>
- <td class="ellipsis field"> {{ germplasmGnpis.germplasmPUI }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.seedSource">
- <th class="fieldName" scope="row">Seed source</th>
- <td class="field">{{ germplasmGnpis.seedSource }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.geneticNature">
- <th class="fieldName" scope="row">Genetic nature</th>
- <td class="field">{{ germplasmGnpis.geneticNature }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.synonyms && germplasmGnpis.synonyms.length > 0">
- <th class="fieldName" scope="row">Accession synonyms</th>
- <td class="field">{{ germplasmGnpis.synonyms.join(', ') }}</td>
- </tr>
- <tr>
- <th class="fieldName" scope="row">Taxon</th>
- <td class="field">
- <i>{{ germplasmGnpis.genus }} {{ germplasmGnpis.species }} {{ germplasmGnpis.subtaxa }}</i>
- {{ germplasmGnpis.speciesAuthority ? '(' + germplasmGnpis.speciesAuthority + ')' : '' }}
- </td>
- </tr>
-
- <tr *ngIf="germplasmGnpis.taxonCommonNames && germplasmGnpis.taxonCommonNames.length > 0">
- <th class="fieldName" scope="row">Taxon common names</th>
- <td class="ellipsis field"> {{ germplasmGnpis.taxonCommonNames.join(', ') }}
- </td>
- </tr>
- <tr *ngIf="germplasmGnpis.taxonSynonyms && germplasmGnpis.taxonSynonyms.length > 0">
- <th class="fieldName" scope="row">Taxon synonyms</th>
- <td class="scroll field"><i>{{ germplasmGnpis.taxonSynonyms.join(', ') }}</i></td>
- </tr>
- <tr *ngIf="germplasmGnpis.pedigree">
- <th class="fieldName" scope="row">Pedigree</th>
- <td class="field">{{ germplasmGnpis.pedigree }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.biologicalStatusOfAccessionCode">
- <th class="fieldName" scope="row">Biological status</th>
- <td class="field">{{ germplasmGnpis.biologicalStatusOfAccessionCode }}</td>
- </tr>
- <!--<tr>
- <td>Source</td>
- <td>{{ germplasmGnpis.source }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.source!='URGI'">
- <td>Source link</td>
- <td><a>{{ germplasmGnpis.url }}</a></td>
- </tr>-->
- <tr *ngIf="germplasmGnpis.comment">
- <th class="fieldName" scope="row">Comments</th>
- <td class="field">{{ germplasmGnpis.comment }}</td>
- </tr>
- </table>
- </div>
+ </ng-template>
+ </gpds-card-section>
+ </div>
+
+ <!--Section for the information about the holding of the germplasm-->
+ <gpds-card-section
+ header="Holding"
+ [test]="germplasmGnpis.holdingInstitute">
+ <ng-template>
+ <div class="card-body card-section-body">
+
+ <gpds-card-row
+ label="Institution">
+ <ng-template>
+ <a class="popover-underline" data-boundary="window" placement="top"
+ [ngbPopover]="holdingInstituteTemplate"
+ [popoverTitle]="germplasmGnpis.holdingInstitute.instituteName"
+ container="body">
+ {{ germplasmGnpis.holdingInstitute.instituteName }}</a>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Stock center name"
+ [test]="germplasmGnpis.holdingGenbank.instituteName && germplasmGnpis.holdingGenbank.webSite">
+ <ng-template>
+ <a [href]="germplasmGnpis.holdingGenbank.webSite" target="_blank">
+ {{ germplasmGnpis.holdingGenbank.instituteName }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Stock center name"
+ [test]="germplasmGnpis.holdingGenbank.instituteName && !germplasmGnpis.holdingGenbank.webSite">
+ <ng-template>
+ {{ germplasmGnpis.holdingGenbank.instituteName }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Presence status"
+ [value]="germplasmGnpis.presenceStatus">
+ </gpds-card-row>
+
</div>
- </div>
+ </ng-template>
+ </gpds-card-section>
- <div class="container">
- <div class="row" *ngIf="germplasmGnpis.holdingInstitute">
- <div class="col">
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <thead class="text-white">
- <tr>
- <th class="headerTitle" scope="col" colspan="2">
- Holding
- </th>
- </tr>
- </thead>
- <tr>
- <th class="fieldName" scope="row">Institution</th>
- <td class="ellipsis field"><a class="btn popovers" data-boundary="window" placement="top"
- [ngbPopover]="holdingInstituteTemplate"
- [popoverTitle]="germplasmGnpis.holdingInstitute.instituteName"
- container="body">
- {{ germplasmGnpis.holdingInstitute.instituteName }}</a></td>
- </tr>
- <tr *ngIf="germplasmGnpis.holdingGenbank.instituteName">
- <th class="fieldName" scope="row">Stock center name</th>
- <ng-container *ngIf="germplasmGnpis.holdingGenbank.webSite">
- <td class="field">
- <a href="germplasmGnpis.holdingGenbank.webSite">{{ germplasmGnpis.holdingGenbank.instituteName }}</a>
- </td>
- </ng-container>
- <ng-container *ngIf="!germplasmGnpis.holdingGenbank.webSite">
- <td class="field">{{ germplasmGnpis.holdingGenbank.instituteName }}</td>
- </ng-container>
- </tr>
- <tr *ngIf="germplasmGnpis.presenceStatus">
- <th class="fieldName" scope="row">Presence status</th>
- <td class="field">{{ germplasmGnpis.presenceStatus }}</td>
- </tr>
- </table>
-
-
- <ng-template #holdingInstituteTemplate>
- <table class="popoverTable">
- <tr *ngIf="germplasmGnpis.holdingInstitute.instituteCode">
- <th class="fieldName" scope="row">FAO code</th>
- <td class="field">{{ germplasmGnpis.holdingInstitute.instituteCode }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.holdingInstitute.instituteName">
- <th class="fieldName" scope="row">Institute name</th>
- <td class="field">{{ germplasmGnpis.holdingInstitute.instituteName }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.holdingInstitute.acronym">
- <th class="fieldName" scope="row">Acronym</th>
- <td class="field">{{ germplasmGnpis.holdingInstitute.acronym }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.holdingInstitute.organisation">
- <th class="fieldName" scope="row">Organisation</th>
- <td class="field">{{ germplasmGnpis.holdingInstitute.organisation }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.holdingInstitute.instituteType">
- <th class="fieldName" scope="row">Institute type</th>
- <td class="field">{{ germplasmGnpis.holdingInstitute.instituteType }}</td>
- </tr>
- <tr class="ellipsis" *ngIf="germplasmGnpis.holdingInstitute.webSite">
- <th class="fieldName" scope="row">Link</th>
- <td class="ellipsis field"><a
- href="{{ germplasmGnpis.holdingInstitute.webSite }}">{{ germplasmGnpis.holdingInstitute.webSite }}</a>
- </td>
- </tr>
- <tr *ngIf="germplasmGnpis.holdingInstitute.address">
- <th class="fieldName" scope="row">Address</th>
- <td class="field">{{ germplasmGnpis.holdingInstitute.address }}</td>
- </tr>
- </table>
+ <gpds-card-section
+ header="Collecting"
+ [test]="checkOriginCollecting()">
+ <ng-template>
+ <div class="card-body card-section-body">
+
+ <gpds-card-row
+ label="Origin site"
+ [test]="germplasmGnpis.originSite && germplasmGnpis.originSite.siteName">
+ <ng-template>
+ <a [routerLink]="['/sites/', germplasmGnpis.originSite.siteId]">
+ {{ germplasmGnpis.originSite.siteName }}
+ </a>
</ng-template>
- </div>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Collecting site"
+ [test]="germplasmGnpis.collectingSite && germplasmGnpis.collectingSite.siteName">
+ <ng-template>
+ <a [routerLink]="['/sites/', germplasmGnpis.collectingSite.siteId]">
+ {{ germplasmGnpis.collectingSite.siteName }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Material type"
+ [test]="germplasmGnpis.collector && germplasmGnpis.collector.materialType">
+ <ng-template>
+ {{ germplasmGnpis.collector.materialType }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Collectors"
+ [test]="germplasmGnpis.collector && germplasmGnpis.collector.collectors">
+ <ng-template>
+ {{ germplasmGnpis.collector.collectors }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Acquisition/Creation date"
+ [test]="germplasmGnpis.collector.accessionCreationDate">
+ <ng-template>
+ {{ germplasmGnpis.collector.accessionCreationDate | amParse:'YYYYMMDD' | amDateFormat:'YYYY-MM-DD' }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Acquisition/Creation date"
+ [test]="germplasmGnpis.acquisitionDate && !germplasmGnpis.collector.accessionCreationDate">
+ <ng-template>
+ {{ germplasmGnpis.acquisitionDate }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Institution"
+ [test]="germplasmGnpis.collector.institute && germplasmGnpis.collector.institute.instituteName">
+ <ng-template>
+ <a class="popovers" placement="top"
+ [ngbPopover]="CollectorInstituteTemplate"
+ [popoverTitle]="germplasmGnpis.collector.institute.instituteName">
+ {{ germplasmGnpis.collector.institute.instituteName }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Accession number"
+ [test]="germplasmGnpis.collector && germplasmGnpis.collector.accessionNumber">
+ <ng-template>
+ {{ germplasmGnpis.collector.accessionNumber }}
+ </ng-template>
+ </gpds-card-row>
</div>
+ </ng-template>
+ </gpds-card-section>
- <div class="row"
- *ngIf="germplasmGnpis.breeder && germplasmGnpis.breeder.institute && germplasmGnpis.breeder.institute.instituteName">
- <div class="col">
- <table class="table table-sm">
- <thead class="text-white">
- <tr>
- <th class="headerTitle" scope="col" colspan="2">
- Breeder
- </th>
- </tr>
- </thead>
- <tr>
- <th class="fieldName" scope="row">Institution</th>
- <td class="ellipsis field">
- <a class="btn popovers" placement="top" [ngbPopover]="BreederInstituteTemplate"
- [popoverTitle]="germplasmGnpis.breeder.institute.instituteName">
- {{ germplasmGnpis.breeder.institute.instituteName }} {{ germplasmGnpis.breeder.institute.instituteCode }}</a>
- </td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.accessionCreationDate">
- <th class="fieldName" scope="row">Accession Creation date</th>
- <td
- class="field">{{ germplasmGnpis.breeder.accessionCreationDate | amParse:'YYYYMMDD' | amDateFormat:'YYYY-MM-DD' }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.accessionNumber">
- <th class="fieldName" scope="row">Accession number</th>
- <td class="field">{{ germplasmGnpis.breeder.accessionNumber }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.deregistrationYear">
- <th class="fieldName" scope="row">Deregistration year</th>
- <td class="field">{{ germplasmGnpis.breeder.deregistrationYear }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.registrationYear">
- <th class="fieldName" scope="row">Registration year</th>
- <td class="field">{{ germplasmGnpis.breeder.registrationYear }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.distributionStatus">
- <th class="fieldName" scope="row">distributionStatus</th>
- <td class="field">{{ germplasmGnpis.breeder.distributionStatus }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.germplasmPUI">
- <th class="fieldName" scope="row">germplasmPUI</th>
- <td class="field">{{ germplasmGnpis.breeder.germplasmPUI }}</td>
- </tr>
-
- </table>
- </div>
+ <gpds-card-section
+ header="Breeder"
+ [test]="checkBreeder()">
+ <ng-template>
+ <div class="card-body card-section-body">
+
+ <gpds-card-row
+ label="Institute"
+ [test]="germplasmGnpis.breeder.institute && germplasmGnpis.breeder.institute.instituteName">
+ <ng-template>
+ <a class="popovers" placement="top"
+ [ngbPopover]="BreederInstituteTemplate"
+ [popoverTitle]="germplasmGnpis.breeder.institute.instituteName">
+ {{ germplasmGnpis.breeder.institute.instituteName }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Accession creation year"
+ [value]="germplasmGnpis.breeder.accessionCreationDate ">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Accession number"
+ [value]="germplasmGnpis.breeder.accessionNumber">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Catalog registration year"
+ [value]="germplasmGnpis.breeder.registrationYear">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Catalog deregistration year"
+ [value]="germplasmGnpis.breeder.deregistrationYear">
+ </gpds-card-row>
</div>
+ </ng-template>
+ </gpds-card-section>
+
+ <gpds-card-section
+ header="Donor"
+ [test]="germplasmGnpis.donors && germplasmGnpis.donors.length > 0">
+ <ng-template>
+ <gpds-card-table
+ [headers]="[
+ 'Institute name',
+ 'Institute code',
+ 'Donation date',
+ 'Accession number',
+ 'Accession PUI'
+ ]"
+ [rows]="germplasmGnpis.donors">
+ <ng-template let-row>
+ <tr>
+ <ng-template #InstituteTemplate>
+
+ <gpds-card-row
+ label=""
+ [test]="row.donorInstitute && row.donorInstitute.logo">
+ <ng-template>
+ <img
+ [src]="IMAGES_INSTITUTION_URL + row.donorInstitute.logo"/>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Code"
+ [value]="row.donorInstitute.instituteCode">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Acronym"
+ [value]="row.donorInstitute.acronym">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Organisation"
+ [value]="row.donorInstitute.organisation">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Type"
+ [value]="row.donorInstitute.instituteType">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Address"
+ [value]="row.donorInstitute.address">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Website"
+ [test]="row.donorInstitute.webSite">
+ <ng-template>
+ <a [href]=" row.donorInstitute.webSite " target="_blank">
+ {{ row.donorInstitute.webSite }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+ </ng-template>
+
+ <td>
+ <a class="popovers" placement="top"
+ [ngbPopover]="InstituteTemplate"
+ [popoverTitle]="row.donorInstitute.instituteName">
+ {{ row.donorInstitute.instituteName }}
+ </a>
+ </td>
+ <td>{{ row.donorInstituteCode }}</td>
+ <td>{{ row.donationDate }}</td>
+ <td>{{ row.donorAccessionNumber }}</td>
+ <td>{{ row.donorGermplasmPUI }}</td>
+ </tr>
+ </ng-template>
+
+ </gpds-card-table>
+ </ng-template>
+ </gpds-card-section>
+
+ <gpds-card-section
+ header="Distributor"
+ [test]="germplasmGnpis.distributors && germplasmGnpis.distributors.length>0">
+ <ng-template>
+
+ <!--TODO : Add order column when ordering URL will be available-->
+ <gpds-card-table
+ [headers]="[
+ 'Institute',
+ 'Accession number',
+ 'Distribution status'
+
+ ]"
+ [rows]="germplasmGnpis.distributors">
+ <ng-template let-row>
+ <tr>
+ <ng-template #InstituteTemplate>
+
+ <gpds-card-row
+ label=""
+ [test]="row.institute && row.institute.logo">
+ <ng-template>
+ <img
+ [src]="IMAGES_INSTITUTION_URL + row.institute.logo"/>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Code"
+ [value]="row.institute.instituteCode">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Acronym"
+ [value]="row.institute.acronym">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Organisation"
+ [value]="row.institute.organisation">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Type"
+ [value]="row.institute.instituteType">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Address"
+ [value]="row.institute.address">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Website"
+ [test]="row.institute.webSite">
+ <ng-template>
+ <a [href]="row.institute.webSite" target="_blank">
+ {{ row.institute.webSite }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+ </ng-template>
+
+ <td>
+ <a class="popovers" placement="top"
+ [ngbPopover]="InstituteTemplate"
+ [popoverTitle]="row.institute.instituteName">
+ {{ row.institute.instituteName }}
+ </a>
+ </td>
+ <td>{{ row.accessionNumber }}</td>
+ <td>{{ row.distributionStatus }}</td>
+ </tr>
+ </ng-template>
+
+ </gpds-card-table>
+
+ </ng-template>
+ </gpds-card-section>
+
+ <gpds-card-section
+ header="Evaluation Data"
+ [test]="germplasmAttributes && germplasmAttributes.length > 0">
+ <ng-template>
+ <div class="card-body card-section-body">
+
+ <ng-container *ngFor="let descriptor of germplasmAttributes">
+ <gpds-card-row
+ [label]="descriptor.attributeName"
+ [value]="descriptor.value">
+ </gpds-card-row>
+ </ng-container>
- <div class="row" *ngIf="germplasmGnpis.collector || germplasmGnpis.collectingSite">
- <div class="col">
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <thead class="text-white">
- <tr>
- <th class="headerTitle" scope="col" colspan="2">
- Collecting
- </th>
- </tr>
- </thead>
- <tr
- *ngIf="germplasmGnpis.collector && germplasmGnpis.collector.institute && germplasmGnpis.collector.institute.instituteName">
- <th class="fieldName" scope="row">Institution</th>
- <td class="ellipsis field"><a class="btn popovers" placement="top"
- [ngbPopover]="CollectorInstituteTemplate"
- [popoverTitle]="germplasmGnpis.collector.institute.instituteName">
- {{ germplasmGnpis.collector.institute.instituteName }}</a></td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector && germplasmGnpis.collector.accessionCreationDate">
- <th class="fieldName" scope="row">Accession Creation date</th>
- <td
- class="field">{{ germplasmGnpis.collector.accessionCreationDate | amParse:'YYYYMMDD' | amDateFormat:'YYYY-MM-DD' }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector && germplasmGnpis.collector.accessionNumber">
- <th class="fieldName" scope="row">Accession number</th>
- <td class="field">{{ germplasmGnpis.collector.accessionNumber }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector && germplasmGnpis.collector.collectors">
- <th class="fieldName" scope="row">collectors</th>
- <td class="field">{{ germplasmGnpis.collector.collectors }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector && germplasmGnpis.collector.distributionStatus">
- <th class="fieldName" scope="row">distributionStatus</th>
- <td class="field">{{ germplasmGnpis.collector.distributionStatus }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector && germplasmGnpis.collector.germplasmPUI">
- <th class="fieldName" scope="row">germplasmPUI</th>
- <td class="field">{{ germplasmGnpis.collector.germplasmPUI }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector && germplasmGnpis.collector.materialType">
- <th class="fieldName" scope="row">Material type</th>
- <td class="field">{{ germplasmGnpis.collector.materialType }}</td>
- </tr>
-
- <tr *ngIf="germplasmGnpis.collectingSite && germplasmGnpis.collectingSite.siteName">
- <th class="fieldName" scope="row">Collecting site</th>
- <td class="field"><a
- [routerLink]="['/sites/', germplasmGnpis.collectingSite.siteId]">{{ germplasmGnpis.collectingSite.siteName }}</a>
- </td>
- </tr>
- </table>
- </div>
</div>
+ </ng-template>
+ </gpds-card-section>
+
+ <gpds-card-section
+ header="Genealogy"
+ [test]="checkPedigree() || checkProgeny()">
+ <ng-template>
+ <div class="card-body card-section-body">
+
+ <gpds-card-row
+ label="Crossing plan"
+ [test]="germplasmPedigree && germplasmPedigree.crossingPlan">
+ <ng-template>
+ {{ germplasmPedigree.crossingPlan }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Crossing year"
+ [test]="germplasmPedigree && germplasmPedigree.crossingYear">
+ <ng-template>
+ {{ germplasmPedigree.crossingYear }}
+ </ng-template>
+ </gpds-card-row>
- <div class="row" *ngIf="germplasmGnpis.donors && germplasmGnpis.donors.length > 0">
- <div class="col">
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <thead class="text-white">
- <tr>
- <th class="headerTitle" scope="col" colspan="2">
- Donation
- </th>
- </tr>
- </thead>
- <tr>
- <th class="thead-light fieldName" scope="col">Institute</th>
- <th class="thead-light fieldName" scope="col">Date</th>
- </tr>
- <tr *ngFor="let donor of germplasmGnpis.donors">
- <td class="ellipsis field"><a class="btn popovers ellipsis" placement="top"
- [ngbPopover]="DonorInstituteTemplate"
- [popoverTitle]="donor.donorInstitute.instituteName">
- {{ donor.donorInstitute.instituteName }}</a></td>
- <td class="field"
- *ngIf="donor.donationDate">{{ donor.donationDate | amParse:'YYYYMMDD' | amDateFormat:'YYYY-MM-DD' }}</td>
-
- <ng-template #DonorInstituteTemplate>
- <table>
- <tr *ngIf="donor.donorInstitute.instituteCode">
- <th class="fieldName" scope="row">Code</th>
- <td class="field">{{ donor.donorInstitute.instituteCode }}</td>
- </tr>
- <tr *ngIf="donor.donorInstitute.acronym">
- <th class="fieldName" scope="row">Acronym</th>
- <td class="field">{{ donor.donorInstitute.acronym }}</td>
- </tr>
- <tr *ngIf="donor.donorInstitute.organisation">
- <th class="fieldName" scope="row">Organisation</th>
- <td class="field">{{ donor.donorInstitute.organisation }}</td>
- </tr>
- <tr *ngIf="donor.donorInstitute.instituteType">
- <th class="fieldName" scope="row">Type</th>
- <td class="field">{{ donor.donorInstitute.instituteType }}</td>
- </tr>
- <tr *ngIf="donor.donorInstitute.webSite">
- <th class="fieldName" scope="row">Link</th>
- <td class="ellipsis field"><a
- href="{{ donor.donorInstitute.webSite }}">{{ donor.donorInstitute.webSite }}</a></td>
- </tr>
- <tr *ngIf="donor.donorInstitute.address">
- <th class="fieldName" scope="row">Address</th>
- <td class="field">{{ donor.donorInstitute.address }}</td>
- </tr>
- </table>
+ <gpds-card-row
+ label="Family code"
+ [test]="germplasmPedigree && germplasmPedigree.familyCode">
+ <ng-template>
+ {{ germplasmPedigree.familyCode }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Parent accessions"
+ [test]="germplasmPedigree && germplasmPedigree.parent1Name">
+
+ <ng-template>
+ <gpds-card-row
+ [label]="germplasmPedigree.parent1Type"
+ [test]="germplasmPedigree && germplasmPedigree.parent1DbId">
+ <ng-template>
+ <a [routerLink]="['/germplasm']"
+ [queryParams]="{id:germplasmPedigree.parent1DbId}">
+ {{ germplasmPedigree.parent1Name }}
+ </a>
</ng-template>
- </tr>
- </table>
- </div>
- </div>
+ </gpds-card-row>
- <div class="row">
- <div class="col">
- <ng-container *ngIf="germplasmGnpis.distributors && germplasmGnpis.distributors.length > 0">
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <thead class="text-white">
- <tr>
- <th class="headerTitle" scope="col" colspan="2">
- Distribution
- </th>
- </tr>
- </thead>
- <ng-container *ngFor="let distributor of germplasmGnpis.distributors">
- <tr>
- <th class="fieldName" scope="row">{{ distributor.institute.instituteName }}</th>
- <td class="field">{{ distributor.distributionStatus }}</td>
- </tr>
+ <gpds-card-row
+ [label]="germplasmPedigree.parent2Type"
+ [test]="germplasmPedigree && germplasmPedigree.parent2DbId">
+ <ng-template>
+ <a [routerLink]="['/germplasm']"
+ [queryParams]="{id:germplasmPedigree.parent2DbId}">
+ {{ germplasmPedigree.parent2Name }}
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Sibling accessions"
+ [test]="germplasmPedigree && (germplasmPedigree.siblings && germplasmPedigree.siblings.length > 0)">
+ <ng-template>
+
+ <div class="content-overflow">
+ <ng-container *ngFor="let sibling of germplasmPedigree.siblings">
+ <a [routerLink]="['/germplasm']" [queryParams]="{id:sibling.germplasmDbId }">
+ {{ sibling.defaultDisplayName }}
+ </a>,
</ng-container>
- </table>
+ </div>
+
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Descendant :"
+ [test]="checkProgeny()">
+ </gpds-card-row>
+
+ <div class="content-overflow-big">
+ <ng-container *ngFor="let child of germplasmProgeny">
+
+ <gpds-card-row class="text"
+ [label]="child.secondParentName ? 'child(ren) of ' + child.firstParentName + ' x ' + child.secondParentName : 'child(ren) of ' + child.firstParentName"
+ [test]="checkProgeny()">
+ <ng-template>
+
+ <ng-container *ngFor="let sibling of child.sibblings">
+ <a [routerLink]="['/germplasm']" [queryParams]="{id:sibling.pui}">
+ {{ sibling.name }}
+ </a>,
+ </ng-container>
+
+ </ng-template>
+ </gpds-card-row>
</ng-container>
</div>
+
</div>
+ </ng-template>
+ </gpds-card-section>
- <ng-template #BreederInstituteTemplate>
- <table>
- <tr *ngIf="germplasmGnpis.breeder.institute.instituteCode">
- <th class="fieldName" scope="row">Code</th>
- <td class="field">{{ germplasmGnpis.breeder.institute.instituteCode }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.institute.organisation">
- <th class="fieldName" scope="row">Organisation</th>
- <td class="field">{{ germplasmGnpis.breeder.institute.organisation }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.institute.acronym">
- <th class="fieldName" scope="row">Acronym</th>
- <td class="field">{{ germplasmGnpis.breeder.institute.acronym }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.institute.instituteType">
- <th class="fieldName" scope="row">Type</th>
- <td class="field">{{ germplasmGnpis.breeder.institute.instituteType }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.institute.webSite">
- <th class="fieldName" scope="row">Link</th>
- <td class="ellipsis field"><a
- href="{{ germplasmGnpis.breeder.institute.webSite }}">{{ germplasmGnpis.breeder.institute.webSite }}</a>
- </td>
- </tr>
- <tr *ngIf="germplasmGnpis.breeder.institute.address">
- <th class="fieldName" scope="row">Address</th>
- <td class="field">{{ germplasmGnpis.breeder.institute.address }}</td>
- </tr>
- </table>
- </ng-template>
+ <gpds-card-section
+ header="Population"
+ [test]="germplasmGnpis.population && germplasmGnpis.population.length > 0">
+ <ng-template>
+ <div class="card-body card-section-body card-section-body">
- <ng-template #CollectorInstituteTemplate>
- <table>
- <tr *ngIf="germplasmGnpis.collector.instituteCode">
- <th class="fieldName" scope="row">FAO code</th>
- <td class="field">{{ germplasmGnpis.collector.instituteCode }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector.instituteName">
- <th class="fieldName" scope="row">Institute name</th>
- <td class="field">{{ germplasmGnpis.collector.instituteName }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector.acronym">
- <th class="fieldName" scope="row">Acronym</th>
- <td class="field">{{ germplasmGnpis.collector.acronym }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector.organisation">
- <th class="fieldName" scope="row">Organisation</th>
- <td class="field">{{ germplasmGnpis.collector.organisation }}</td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector.institute.webSite">
- <th class="fieldName" scope="row">Link</th>
- <td class="ellipsis field"><a
- href="{{ germplasmGnpis.collector.institute.webSite }}">{{ germplasmGnpis.collector.institute.webSite }}</a>
- </td>
- </tr>
- <tr *ngIf="germplasmGnpis.collector.institute.address">
- <th class="fieldName" scope="row">Address</th>
- <td class="field">{{ germplasmGnpis.collector.institute.address }}</td>
- </tr>
- </table>
- </ng-template>
+ <ng-container *ngFor="let population of germplasmGnpis.population">
+ <gpds-card-row
+ [label]="population.type ? population.name + ' (' + population.type + ')' : population.name"
+ [test]="population.germplasmRef && population.germplasmRef.pui && population.germplasmRef.pui != germplasmGnpis.germplasmDbId">
+ <ng-template>
+ <a [routerLink]="['/germplasm']"
+ [queryParams]="{id:population.germplasmRef.pui}">
+ {{ population.germplasmRef.name }}
+ </a> is composed by <a
+ [routerLink]="['/']"
+ [queryParams]="{germplasmLists: population.name, types: 'Germplasm'}">
+ {{ population.germplasmCount }} accessions
+ </a>
+ </ng-template>
+ </gpds-card-row>
+ <gpds-card-row
+ [label]="population.type ? population.name + ' (' + population.type + ')' : population.name"
+ [test]="population.germplasmRef && population.germplasmRef.pui && population.germplasmRef.pui == germplasmGnpis.germplasmDbId">
+ <ng-template>
+ {{ population.germplasmRef.name }} is composed by <a
+ [routerLink]="['/']"
+ [queryParams]="{germplasmLists: population.name, types: 'Germplasm'}">
+ {{ population.germplasmCount }} accessions
+ </a>
+ </ng-template>
+ </gpds-card-row>
+ <gpds-card-row
+ [label]="population.type ? population.name + ' (' + population.type + ')' : population.name"
+ [test]="population.germplasmRef && !population.germplasmRef.pui">
+ <ng-template>
+ <a [routerLink]="['/']"
+ [queryParams]="{germplasmLists: population.name, types: 'Germplasm'}">
+ {{ population.germplasmCount }} accessions
+ </a>
+ </ng-template>
+ </gpds-card-row>
+ </ng-container>
- <ng-container *ngIf="testPedigree() || testProgeny()">
- <div class="row">
- <div class="col">
- <h4>Genealogy</h4>
- </div>
- </div>
- <div class="row">
- <div class="col">
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}" *ngIf="testPedigree()">
- <thead class="text-white">
- <tr>
- <th class="headerTitle" scope="col" colspan="2">
- Ascendants
- </th>
- </tr>
- </thead>
- <tr *ngIf="germplasmPedigree.result.crossingPlan">
- <th class="fieldName" scope="row">Crossing plan</th>
- <td class="field">{{ germplasmPedigree.result.crossingPlan }}</td>
- </tr>
- <tr *ngIf="germplasmPedigree.result.crossingYear">
- <th class="fieldName" scope="row">Crossing year</th>
- <td class="field">{{ germplasmPedigree.result.crossingYear }}</td>
- </tr>
- <tr *ngIf="germplasmPedigree.result.familyCode">
- <th class="fieldName" scope="row">Family code</th>
- <td class="field">{{ germplasmPedigree.result.familyCode }}</td>
- </tr>
- <tr *ngIf="(germplasmPedigree.result.parent1Type || germplasmPedigree.result.parent2Type)
- && (germplasmPedigree.result.parent1Type !='UNDEFINED' || germplasmPedigree.result.parent2Type !='UNDEFINED')">
- <th scope="row">Parent accessions</th>
- <td>
- <table>
- <ng-container [ngSwitch]="germplasmPedigree.result.parent1Type">
- <tr *ngSwitchCase="'FEMALE'">
- <th class="fieldName" scope="row">Mother</th>
- <td class="field"><a
- [routerLink]="'/germplasm'"
- [queryParams]="{id:germplasmPedigree.result.parent1DbId}">{{ germplasmPedigree.result.parent1Name }}</a>
- </td>
- </tr>
- <tr *ngSwitchCase="'MALE'">
- <th class="fieldName" scope="row">Father</th>
- <td class="field"><a
- [routerLink]="'/germplasm'"
- [queryParams]="{id:germplasmPedigree.result.parent1DbId}">{{ germplasmPedigree.result.parent1Name }}</a>
- </td>
- </tr>
- <tr *ngSwitchCase="'SELF'">
- <td>Self</td>
- </tr>
- <tr *ngSwitchCase="'POPULATION'">
- <th class="fieldName" scope="row">Population</th>
- <td class="field">{{ germplasmPedigree.result.parent1Name }}</td>
- </tr>
- </ng-container>
- <ng-container [ngSwitch]="germplasmPedigree.result.parent2Type">
- <tr *ngSwitchCase="'FEMALE'">
- <th class="fieldName" scope="row">Mother</th>
- <td class="field"><a
- [routerLink]="'/germplasm'"
- [queryParams]="{id:germplasmPedigree.result.parent2DbId}">{{ germplasmPedigree.result.parent2Name }}</a></td>
- </tr>
- <tr *ngSwitchCase="'MALE'">
- <th class="fieldName" scope="row">Father</th>
- <td class="field"><a
- [routerLink]="'/germplasm'"
- [queryParams]="{id:germplasmPedigree.result.parent2DbId}">{{ germplasmPedigree.result.parent2Name }}</a></td>
- </tr>
- <tr *ngSwitchCase="'SELF'">
- <td>Self</td>
- </tr>
- <tr *ngSwitchCase="'POPULATION'">
- <th class="fieldName" scope="row">Population</th>
- <td class="field">{{ germplasmPedigree.result.parent2Name }}</td>
- </tr>
- </ng-container>
- </table>
- </td>
- </tr>
- </table>
- </div>
- </div>
+ </div>
+ </ng-template>
+ </gpds-card-section>
- <ng-container *ngIf="germplasmPedigree.result.siblings && germplasmPedigree.result.siblings.length > 0">
- <div class="row ">
- <div class="col">
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <thead class="text-white">
- <tr>
- <th class="headerTitle" scope="col" colspan="2">
- Siblings
- </th>
- </tr>
- </thead>
- <tbody>
- <tr>
- <th class="fieldName">Accession numbers</th>
- <td class="scroll field">
- <ng-container *ngFor="let sibling of germplasmPedigree.result.siblings">
- <a routerLink="/germplasm" [queryParams]="{id:sibling.germplasmDbId }">
- {{ sibling.defaultDisplayName }}</a>
- </ng-container>
- </td>
- </tr>
- </tbody>
- </table>
- </div>
- </div>
+ <gpds-card-section
+ header="Collection"
+ [test]="germplasmGnpis.collection && germplasmGnpis.collection.length > 0">
+ <ng-template>
+ <div class="card-body card-section-body">
+
+ <ng-container *ngFor="let collection of germplasmGnpis.collection">
+ <gpds-card-row
+ [label]="collection.type ? collection.name + ' (' + collection.type + ')' : collection.name">
+ <ng-template>
+ <a [routerLink]="['/']"
+ [queryParams]="{germplasmLists: collection.name, types: 'Germplasm'}">
+ {{ collection.germplasmCount }} accessions
+ </a>
+ </ng-template>
+ </gpds-card-row>
</ng-container>
- <ng-container *ngIf="testProgeny()">
- <div class="row ">
- <div class="col">
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <thead class="text-white">
- <tr>
- <th class="headerTitle" scope="col" colspan="2">
- Descendants
- </th>
- </tr>
- </thead>
- <tbody>
- <tr>
- <th class="fieldName">Accession numbers</th>
- <td class="scroll field">
- <ng-container *ngFor="let child of germplasmProgeny.result.progeny">
- <a routerLink="/germplasm" [queryParams]="{id:child.germplasmDbId }">
- {{ child.defaultDisplayName }}</a>
- </ng-container>
- </td>
- </tr>
- </tbody>
- </table>
- </div>
- </div>
+ </div>
+ </ng-template>
+ </gpds-card-section>
+
+
+ <gpds-card-section
+ header="Panel"
+ [test]="germplasmGnpis.panel && germplasmGnpis.panel.length > 0">
+ <ng-template>
+ <div class="card-body card-section-body">
+
+ <ng-container *ngFor="let panel of germplasmGnpis.panel">
+ <gpds-card-row
+ [label]="panel.type ? panel.name + ' (' + panel.type + ')' : panel.name">
+ <ng-template>
+ <a [routerLink]="['/']"
+ [queryParams]="{germplasmLists: panel.name, types: 'Germplasm'}">
+ {{ panel.germplasmCount }} accessions
+ </a>
+ </ng-template>
+ </gpds-card-row>
</ng-container>
- </ng-container>
-
- <ng-container *ngIf="germplasmAttributes && germplasmAttributes.length > 0">
- <div class="row">
- <div class="col">
- <h4 class="headerTitle">Evaluation Data</h4>
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
-
- <ng-container *ngFor="let descriptor of germplasmAttributes">
- <tr>
- <th class="fieldName" scope="row">{{ descriptor.attributeName }}</th>
- <td class="field">{{ descriptor.value }}</td>
- </tr>
- </ng-container>
- </table>
- </div>
- </div>
- </ng-container>
-
- <ng-container *ngIf="germplasmGnpis.collection && germplasmGnpis.collection.length > 0">
- <div class="row">
- <div class="col">
- <h4 class="headerTitle">Collection</h4>
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <ng-container *ngFor="let collection of germplasmGnpis.collection">
- <tr>
- <th class="fieldName" scope="row">
- {{ collection.type ? collection.name + ' (' + collection.type + ')' : collection.name }}
- </th>
- <td class="ellipsis field"><a routerLink="" [queryParams]="{germplasmLists: collection.name, types: 'Germplasm'}">
- {{ collection.germplasmCount }} accessions</a>
- </td>
- </tr>
- </ng-container>
- </table>
- </div>
- </div>
- </ng-container>
-
- <ng-container *ngIf="germplasmGnpis.panel && germplasmGnpis.panel.length > 0">
- <div class="row">
- <div class="col">
- <h4 class="headerTitle">Panel</h4>
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <ng-container *ngFor="let panel of germplasmGnpis.panel">
- <tr>
- <th class="fieldName" scope="row">
- {{ panel.type ? panel.name + ' (' + panel.type + ')' : panel.name }}
- </th>
- <td class="field"><a routerLink="" [queryParams]="{germplasmLists: panel.name, types: 'Germplasm'}">
- {{ panel.germplasmCount }} accessions</a></td>
- </tr>
- </ng-container>
- </table>
- </div>
- </div>
- </ng-container>
-
- <ng-container *ngIf="germplasmGnpis.population && germplasmGnpis.population.length > 0">
- <div class="row">
- <div class="col">
- <h4 class="headerTitle">Population</h4>
- <table class="table table-sm .table-responsive{-sm|-md|-lg|-xl}">
- <ng-container *ngFor="let population of germplasmGnpis.population">
- <tr>
- <th class="fieldName" scope="row">
- {{ population.type ? population.name + ' (' + population.type + ')' : population.name }}
- </th>
- <td class="field"><a routerLink="" [queryParams]="{germplasmLists: population.name, types: 'Germplasm'}">
- {{ population.germplasmCount }} accessions</a></td>
- </tr>
- </ng-container>
- </table>
- </div>
- </div>
- </ng-container>
- </div>
- </div>
+ </div>
+ </ng-template>
+ </gpds-card-section>
<!--XRefs part -->
- <gpds-xrefs [xrefId]="germplasmGnpis.germplasmPUI"></gpds-xrefs>
+ <gpds-xrefs [xrefId]="germplasmGnpis.germplasmPUI"></gpds-xrefs>
</ng-container>
diff --git a/frontend/src/app/germplasm-card/germplasm-card.component.scss b/frontend/src/app/germplasm-card/germplasm-card.component.scss
index 017b0c22841a99886f56cfab64b1ae23cfb1d1d0..f0376501baaeced5c8d3194b0d2d23faff4269fe 100644
--- a/frontend/src/app/germplasm-card/germplasm-card.component.scss
+++ b/frontend/src/app/germplasm-card/germplasm-card.component.scss
@@ -1,3 +1,11 @@
@import "theme";
@import '../../styles.scss';
+a:not([href]):not([tabindex]) {
+ color: #0f6fa1;
+ cursor: pointer;
+}
+
+a:not([href]):not([tabindex]):hover {
+ text-decoration: underline;
+}
diff --git a/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts b/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts
index 60c1d275dbd873840c66b307a687bf8975406fec..5b06816851414af4a438f298ac119d78a2b51931 100644
--- a/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts
+++ b/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts
@@ -6,19 +6,17 @@ import { BrapiService } from '../brapi.service';
import { ActivatedRoute, convertToParamMap } from '@angular/router';
import { RouterTestingModule } from '@angular/router/testing';
import { of } from 'rxjs';
-import {
- BrapiDescriptor,
- BrapiDonor,
- BrapiGermplasmAttributes,
- BrapiGermplasmPedigree,
- BrapiGermplasmProgeny,
- BrapiSet,
- BrapiSibling
-} from '../models/brapi.germplasm.model';
-import { Germplasm, GermplasmData, GermplasmResult, Institute, Origin, Site } from '../models/gnpis.germplasm.model';
+
import { NgbPopoverModule } from '@ng-bootstrap/ng-bootstrap';
import { MomentModule } from 'ngx-moment';
import { LoadingSpinnerComponent } from '../loading-spinner/loading-spinner.component';
+import { CardSectionComponent } from '../card-section/card-section.component';
+import { CardRowComponent } from '../card-row/card-row.component';
+import { CardTableComponent } from '../card-table/card-table.component';
+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 { MockComponent } from 'ng-mocks';
import { XrefsComponent } from '../xrefs/xrefs.component';
@@ -36,15 +34,15 @@ describe('GermplasmCardComponent', () => {
return this.element('h3');
}
- get headerTitle() {
- return this.elements('.headerTitle');
+ get cardHeader() {
+ return this.elements('div.card-header');
}
}
const brapiService = jasmine.createSpyObj(
'BrapiService', [
'germplasm',
- 'germplasmProgeny',
+ /*'germplasmProgeny',*/
'germplasmPedigree',
'germplasmAttributes'
]
@@ -53,11 +51,12 @@ describe('GermplasmCardComponent', () => {
const gnpisService = jasmine.createSpyObj(
'GnpisService', [
'germplasm',
- 'germplasmByPuid'
+ 'germplasmByPuid',
+ 'getSource'
]
);
- const brapiSite: Site = {
+ const gnpisSite: Site = {
latitude: null,
longitude: null,
siteId: null,
@@ -70,13 +69,9 @@ describe('GermplasmCardComponent', () => {
defaultDisplayName: 'frere1'
};
- const brapiDescriptor: BrapiDescriptor = {
- name: 'caracteristique1',
- pui: '12',
- value: '32'
- };
- const brapiGermplasmPedigree: GermplasmResult<BrapiGermplasmPedigree> = {
+ const brapiGermplasmPedigree: BrapiResult<BrapiGermplasmPedigree> = {
+ metadata: null,
result: {
germplasmDbId: '12',
defaultDisplayName: '12',
@@ -94,15 +89,15 @@ describe('GermplasmCardComponent', () => {
}
};
- const brapiGermplasmProgeny: GermplasmResult<BrapiGermplasmProgeny> = {
+ /*const brapiGermplasmProgeny: GermplasmResult<BrapiGermplasmProgeny> = {
result: {
germplasmDbId: '11',
defaultDisplayName: '11',
progeny: [brapiSibling]
}
- };
+ };*/
- const brapiInstitute: Institute = {
+ const gnpisInstitute: Institute = {
instituteName: 'urgi',
instituteCode: 'inra',
acronym: 'urgi',
@@ -113,9 +108,9 @@ describe('GermplasmCardComponent', () => {
logo: null
};
- const brapiOrigin: Origin = {
- institute: brapiInstitute,
- germplasmPUI: '12',
+ const gnpisGermplasmInstitute: GermplasmInstitute = {
+ ...gnpisInstitute,
+ institute: gnpisInstitute,
accessionNumber: '12',
accessionCreationDate: '1993',
materialType: 'feuille',
@@ -125,14 +120,15 @@ describe('GermplasmCardComponent', () => {
distributionStatus: null
};
- const brapiDonor: BrapiDonor = {
- donorInstitute: brapiInstitute,
- germplasmPUI: '12',
- accessionNumber: '12',
- donorInstituteCode: 'urgi'
+ const gnpisDonor: Donor = {
+ donorInstitute: gnpisInstitute,
+ donorGermplasmPUI: '12',
+ donorAccessionNumber: '12',
+ donorInstituteCode: 'urgi',
+ donationDate: null
};
- const brapiSet: BrapiSet = {
+ const gnpisGermplasmSet: GermplasmSet = {
germplasmCount: 12,
germplasmRef: null,
id: 12,
@@ -140,18 +136,21 @@ describe('GermplasmCardComponent', () => {
type: 'plan'
};
- const brapiGermplasmAttributes: GermplasmResult<GermplasmData<BrapiGermplasmAttributes[]>> = {
+ const brapiGermplasmAttributes: BrapiResult<BrapiGermplasmAttributes> = {
+ metadata: null,
result: {
+ germplasmDbId: '12',
data: [{
attributeName: 'longueur',
- value: '30'
+ value: '30',
+ attributeDbId: '1',
+ attributeCode: 'longeur',
+ determinedDate: 'today'
}]
}
};
const germplasmTest: Germplasm = {
- url: 'www.cirad.fr',
- source: 'cirad',
germplasmDbId: 'test',
defaultDisplayName: 'test',
accessionNumber: 'test',
@@ -172,7 +171,7 @@ describe('GermplasmCardComponent', () => {
speciesAuthority: 'L',
subtaxa: null,
subtaxaAuthority: null,
- donors: [brapiDonor],
+ donors: [gnpisDonor],
acquisitionDate: null,
genusSpecies: null,
genusSpeciesSubtaxa: null,
@@ -181,34 +180,38 @@ describe('GermplasmCardComponent', () => {
geneticNature: null,
comment: null,
photo: null,
- holdingInstitute: brapiInstitute,
- holdingGenbank: brapiInstitute,
+ holdingInstitute: gnpisInstitute,
+ holdingGenbank: gnpisInstitute,
presenceStatus: null,
children: null,
- descriptors: [brapiDescriptor],
originSite: null,
collectingSite: null,
evaluationSites: null,
- collector: brapiOrigin,
- breeder: brapiOrigin,
- distributors: [brapiOrigin],
- panel: [brapiSet],
- collection: [brapiSet],
- population: [brapiSet]
+ collector: gnpisGermplasmInstitute,
+ breeder: gnpisGermplasmInstitute,
+ distributors: [gnpisGermplasmInstitute],
+ panel: [gnpisGermplasmSet],
+ collection: [gnpisGermplasmSet],
+ population: [gnpisGermplasmSet]
};
- const germplasmResultTest = {
- result: germplasmTest
+ const source: DataDiscoverySource = {
+ '@id': 'src1',
+ '@type': ['schema:DataCatalog'],
+ 'schema:identifier': 'srcId',
+ 'schema:name': 'source1',
+ 'schema:url': 'srcUrl',
+ 'schema:image': null
};
beforeEach(async(() => {
TestBed.configureTestingModule({
imports: [RouterTestingModule, NgbPopoverModule, MomentModule],
declarations: [
- GermplasmCardComponent, LoadingSpinnerComponent, MockComponent(XrefsComponent)
+ GermplasmCardComponent, LoadingSpinnerComponent, MockComponent(XrefsComponent), CardSectionComponent,
+ CardRowComponent, LoadingSpinnerComponent, CardTableComponent, MapComponent
],
providers: [
- // { provide: ActivatedRoute, useValue: activatedRoute },
{ provide: BrapiService, useValue: brapiService },
{ provide: GnpisService, useValue: gnpisService },
{
@@ -228,7 +231,8 @@ describe('GermplasmCardComponent', () => {
gnpisService.germplasm.and.returnValue(of(germplasmTest));
gnpisService.germplasmByPuid.and.returnValue(of(germplasmTest));
- brapiService.germplasmProgeny.and.returnValue(of(brapiGermplasmProgeny));
+ gnpisService.getSource.and.returnValue(of(source));
+ /*brapiService.germplasmProgeny.and.returnValue(of(brapiGermplasmProgeny));*/
brapiService.germplasmPedigree.and.returnValue(of(brapiGermplasmPedigree));
brapiService.germplasmAttributes.and.returnValue(of(brapiGermplasmAttributes));
@@ -240,10 +244,13 @@ describe('GermplasmCardComponent', () => {
expect(component.germplasmGnpis).toBeTruthy();
tester.detectChanges();
expect(tester.title).toContainText('Germplasm: test');
- expect(tester.headerTitle[0]).toContainText('Identification');
- expect(tester.headerTitle[1]).toContainText('Holding');
- expect(tester.headerTitle[2]).toContainText('Breeder');
- expect(tester.headerTitle[3]).toContainText('Collecting');
+ expect(tester.cardHeader[0]).toContainText('Identification');
+ expect(tester.cardHeader[1]).toContainText('Holding');
+ expect(tester.cardHeader[2]).toContainText('Collecting');
+ expect(tester.cardHeader[3]).toContainText('Breeder');
+ expect(tester.cardHeader[4]).toContainText('Donor');
+ expect(tester.cardHeader[5]).toContainText('Distributor');
+ expect(tester.cardHeader[6]).toContainText('Evaluation Data');
});
}));
});
diff --git a/frontend/src/app/germplasm-card/germplasm-card.component.ts b/frontend/src/app/germplasm-card/germplasm-card.component.ts
index 14fa0e9e6173dc701a1d52fe9aef089519e15861..fa665b58aea9b42828f310cafb6dfa2972da71cd 100644
--- a/frontend/src/app/germplasm-card/germplasm-card.component.ts
+++ b/frontend/src/app/germplasm-card/germplasm-card.component.ts
@@ -1,9 +1,10 @@
import { Component, OnInit } from '@angular/core';
-import { ActivatedRoute } from '@angular/router';
+import { ActivatedRoute, NavigationEnd, Router } from '@angular/router';
import { BrapiService } from '../brapi.service';
import { GnpisService } from '../gnpis.service';
-import { Germplasm, GermplasmResult } from '../models/gnpis.germplasm.model';
-import { BrapiGermplasmAttributes, BrapiGermplasmPedigree, BrapiGermplasmProgeny } from '../models/brapi.germplasm.model';
+import { BrapiAttributeData, BrapiGermplasmPedigree, BrapiLocation } from '../models/brapi.model';
+import { Children, Germplasm, Site } from '../models/gnpis.model';
+import { DataDiscoverySource } from '../models/data-discovery.model';
@Component({
selector: 'gpds-germplasm-card',
@@ -13,17 +14,35 @@ import { BrapiGermplasmAttributes, BrapiGermplasmPedigree, BrapiGermplasmProgeny
export class GermplasmCardComponent implements OnInit {
+ alreadyInitialize = false;
- constructor(private brapiService: BrapiService, private gnpisService: GnpisService, private route: ActivatedRoute) {
+ constructor(private brapiService: BrapiService,
+ private gnpisService: GnpisService,
+ private route: ActivatedRoute,
+ private router: Router) {
+
+ this.router.events.subscribe((event: any) => {
+ // If it is a NavigationEnd event re-initalise the component
+ if (this.alreadyInitialize && event instanceof NavigationEnd) {
+ this.ngOnInit();
+ }
+ });
}
germplasmGnpis: Germplasm;
- germplasmPedigree: GermplasmResult<BrapiGermplasmPedigree>;
- germplasmProgeny: GermplasmResult<BrapiGermplasmProgeny>;
- germplasmAttributes: BrapiGermplasmAttributes[];
+ germplasmPedigree: BrapiGermplasmPedigree;
+ germplasmProgeny: Children[];
+ germplasmAttributes: BrapiAttributeData[];
+ germplasmLocations: BrapiLocation[] = [];
germplasmId: string;
germplasmPuid: string;
- IMAGES_SIREGAL_URL = 'https://urgi.versailles.inra.fr/files/siregal/images/accession';
+ germplasmSource: DataDiscoverySource;
+
+ // TODO extract those url in a configuration file.
+ IMAGES_ACCESSION_URL = 'https://urgi.versailles.inra.fr/files/siregal/images/accession/';
+ IMAGES_INSTITUTION_URL = 'https://urgi.versailles.inra.fr/files/siregal/images//institution/';
+ IMAGES_BRC_URL = 'https://urgi.versailles.inra.fr/files/siregal/images/grc/inra_brc_en.png';
+
loaded: Promise<any>;
loading = true;
@@ -31,30 +50,31 @@ export class GermplasmCardComponent implements OnInit {
ngOnInit() {
- // console.log(this.route.snapshot);
- // console.log(this.route);
this.germplasmId = this.route.snapshot.queryParams.id;
this.germplasmPuid = this.route.snapshot.queryParams.pui;
+
const germplasm$ = this.getGermplasm(this.germplasmId, this.germplasmPuid);
germplasm$.then(result => {
const germplasmId = this.germplasmId ? this.germplasmId : result.germplasmDbId;
- const germplasmProgeny$ = this.brapiService.germplasmProgeny(germplasmId).toPromise();
+
+ // TODO use the progeny call when the information about parent will be added.
+ /*const germplasmProgeny$ = this.brapiService.germplasmProgeny(germplasmId).toPromise();
germplasmProgeny$
.then(germplasmProgeny => {
- this.germplasmProgeny = germplasmProgeny;
- });
+ this.germplasmProgeny = germplasmProgeny.result;
+ });*/
const germplasmPedigree$ = this.brapiService.germplasmPedigree(germplasmId).toPromise();
germplasmPedigree$
.then(germplasmPedigree => {
- this.germplasmPedigree = germplasmPedigree;
+ this.germplasmPedigree = germplasmPedigree.result;
});
const germplasmAttributes$ = this.brapiService.germplasmAttributes(germplasmId).toPromise();
germplasmAttributes$
.then(germplasmAttributes => {
- if (germplasmAttributes.result) {
- this.germplasmAttributes = germplasmAttributes.result.data;
+ if (germplasmAttributes.result.data) {
+ this.germplasmAttributes = germplasmAttributes.result.data.sort(this.compareAttributes);
}
});
@@ -63,6 +83,7 @@ export class GermplasmCardComponent implements OnInit {
this.loaded = Promise.all([germplasm$]);
this.loaded.then(() => {
this.loading = false;
+ this.alreadyInitialize = true;
});
}
@@ -71,36 +92,157 @@ export class GermplasmCardComponent implements OnInit {
let germplasm$: Promise<Germplasm>;
if (id) {
germplasm$ = this.gnpisService.germplasm(id).toPromise();
- germplasm$
- .then(germplasmGnpis => {
- this.germplasmGnpis = germplasmGnpis;
- });
} else {
germplasm$ = this.gnpisService.germplasmByPuid(pui).toPromise();
- germplasm$
- .then(germplasmGnpis => {
- this.germplasmGnpis = germplasmGnpis;
- });
}
+ germplasm$
+ .then(germplasmGnpis => {
+ this.germplasmGnpis = germplasmGnpis;
+ // Get germplasm source
+ const sourceURI = germplasmGnpis['schema:includedInDataCatalog'];
+ this.getGermplasmSource(sourceURI);
+ this.reformatData(germplasmGnpis);
+ });
return germplasm$;
}
- testProgeny() {
+ // TODO Remove the condition when the field includedInDataCatalog will be added to URGI study.
+ getGermplasmSource(sourceURI: string) {
+ if (sourceURI) {
+ const source$ = this.gnpisService.getSource(sourceURI);
+ source$
+ .subscribe(src => {
+ this.germplasmSource = src;
+ });
+ } else {
+ const urgiURI = 'https://urgi.versailles.inra.fr';
+ const source$ = this.gnpisService.getSource(urgiURI);
+ source$
+ .subscribe(src => {
+ this.germplasmSource = src;
+ });
+ }
+ }
+
+
+ reformatData(germplasmGnpis) {
+ if (germplasmGnpis.children) {
+ this.germplasmProgeny = germplasmGnpis.children.sort();
+ }
+ if (germplasmGnpis.donors) {
+ this.germplasmGnpis.donors.sort(this.compareDonorInstitutes);
+ }
+ if (germplasmGnpis.collection) {
+ this.germplasmGnpis.collection.sort(this.compareCollectionPanel);
+ }
+ if (this.germplasmGnpis.panel) {
+ this.germplasmGnpis.panel.sort(this.compareCollectionPanel);
+ }
+ if (this.germplasmGnpis.collectingSite) {
+ this.siteToBrapiLocation(this.germplasmGnpis.collectingSite);
+ }
+ if (this.germplasmGnpis.originSite) {
+ this.siteToBrapiLocation(this.germplasmGnpis.originSite);
+ }
+ if (this.germplasmGnpis.evaluationSites && this.germplasmGnpis.evaluationSites.length > 0) {
+ for (const site of this.germplasmGnpis.evaluationSites) {
+ this.siteToBrapiLocation(site);
+ }
+ }
+ }
+
+
+ siteToBrapiLocation(site: Site) {
+ if (site && site.siteId && site.latitude && site.longitude) {
+ this.germplasmLocations.push({
+ locationDbId: site.siteId,
+ locationName: site.siteName,
+ locationType: site.siteType,
+ latitude: site.latitude,
+ longitude: site.longitude
+ });
+ }
+ }
+
+ // TODO: use a generic function to get path in object (or null if non-existent)
+ checkProgeny() {
return (this.germplasmProgeny
- && this.germplasmProgeny.result
- && this.germplasmProgeny.result.progeny
- && this.germplasmProgeny.result.progeny.length > 0);
+ && this.germplasmProgeny.length > 0);
}
- testPedigree() {
+ checkBreeder() {
+ return (this.germplasmGnpis.breeder)
+ && ((this.germplasmGnpis.breeder.institute && this.germplasmGnpis.breeder.institute.instituteName)
+ || this.germplasmGnpis.breeder.accessionCreationDate
+ || this.germplasmGnpis.breeder.accessionNumber
+ || this.germplasmGnpis.breeder.registrationYear
+ || this.germplasmGnpis.breeder.deregistrationYear);
+ }
+
+ checkPedigree() {
return (this.germplasmPedigree
- && this.germplasmPedigree.result
- && (this.germplasmPedigree.result.parent1Name
- || this.germplasmPedigree.result.parent2Name
- || this.germplasmPedigree.result.crossingPlan
- || this.germplasmPedigree.result.crossingYear
- || this.germplasmPedigree.result.familyCode)
+ && (this.germplasmPedigree.parent1Name
+ || this.germplasmPedigree.parent2Name
+ || this.germplasmPedigree.crossingPlan
+ || this.germplasmPedigree.crossingYear
+ || this.germplasmPedigree.familyCode)
);
}
-}
+
+ checkCollectorInstituteObject() {
+ return (
+ this.germplasmGnpis.collector
+ && this.germplasmGnpis.collector.institute
+ && this.germplasmGnpis.collector.institute.instituteName);
+ }
+
+ checkCollectorInstituteFields() {
+ return (this.germplasmGnpis.collector) &&
+ (this.germplasmGnpis.collector.accessionNumber
+ || this.germplasmGnpis.collector.accessionCreationDate
+ || this.germplasmGnpis.collector.materialType
+ || this.germplasmGnpis.collector.collectors
+ || this.germplasmGnpis.collector.registrationYear
+ || this.germplasmGnpis.collector.deregistrationYear
+ || this.germplasmGnpis.collector.distributionStatus
+ );
+ }
+
+ checkOriginCollecting() {
+
+ return (this.germplasmGnpis.originSite && this.germplasmGnpis.originSite.siteName)
+ || (this.germplasmGnpis.collectingSite && this.germplasmGnpis.collectingSite.siteName)
+ || (this.checkCollectorInstituteObject() || this.checkCollectorInstituteFields());
+ }
+
+ compareDonorInstitutes(a, b) {
+ if (a.donorInstitute.instituteName < b.donorInstitute.instituteName) {
+ return -1;
+ }
+ if (a.donorInstitute.instituteName > b.donorInstitute.instituteName) {
+ return 1;
+ }
+ return 0;
+ }
+
+ compareAttributes(a, b) {
+ if (a.attributeName < b.attributeName) {
+ return -1;
+ }
+ if (a.attributeName > b.attributeName) {
+ return 1;
+ }
+ return 0;
+ }
+
+ compareCollectionPanel(a, b) {
+ if (a.name < b.name) {
+ return -1;
+ }
+ if (a.name > b.name) {
+ return 1;
+ }
+ return 0;
+ }
+}
diff --git a/frontend/src/app/gnpis.service.spec.ts b/frontend/src/app/gnpis.service.spec.ts
index 512deeceddd8c1b12f011cbe8015d69d99e09566..04deb8ddc41c26ba9a63cdf36b4240ca99b0f7e4 100644
--- a/frontend/src/app/gnpis.service.spec.ts
+++ b/frontend/src/app/gnpis.service.spec.ts
@@ -1,11 +1,9 @@
-import { Germplasm, Institute, Origin, Site } from './models/gnpis.germplasm.model';
-
-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 { BrapiDescriptor, BrapiDonor, BrapiSet } from './models/brapi.germplasm.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';
describe('GnpisService', () => {
@@ -29,17 +27,11 @@ describe('GnpisService', () => {
const site: Site = {
latitude: null,
longitude: null,
- siteId: 1,
+ siteId: '1',
siteName: 'Nantes',
siteType: null
};
- const brapiDescriptor: BrapiDescriptor = {
- name: 'caracteristique1',
- pui: '12',
- value: '32'
- };
-
const brapiInstitute: Institute = {
instituteName: 'urgi',
instituteCode: 'inra',
@@ -51,9 +43,9 @@ describe('GnpisService', () => {
logo: null
};
- const brapiOrigin: Origin = {
+ const germplasmInstitute: GermplasmInstitute = {
+ ...brapiInstitute,
institute: brapiInstitute,
- germplasmPUI: '12',
accessionNumber: '12',
accessionCreationDate: '1993',
materialType: 'feuille',
@@ -63,14 +55,15 @@ describe('GnpisService', () => {
distributionStatus: null
};
- const brapiDonor: BrapiDonor = {
+ const brapiDonor: Donor = {
donorInstitute: brapiInstitute,
- germplasmPUI: '12',
- accessionNumber: '12',
- donorInstituteCode: 'urgi'
+ donorGermplasmPUI: '12',
+ donorAccessionNumber: '12',
+ donorInstituteCode: 'urgi',
+ donationDate: null
};
- const brapiSet: BrapiSet = {
+ const germplasmSet: GermplasmSet = {
germplasmCount: 12,
germplasmRef: null,
id: 12,
@@ -79,8 +72,6 @@ describe('GnpisService', () => {
};
const germplasmTest: Germplasm = {
- url: 'www.cirad.fr',
- source: 'cirad',
germplasmDbId: 'test',
defaultDisplayName: 'test',
accessionNumber: 'test',
@@ -114,16 +105,15 @@ describe('GnpisService', () => {
holdingGenbank: brapiInstitute,
presenceStatus: null,
children: null,
- descriptors: [brapiDescriptor],
originSite: site,
collectingSite: null,
evaluationSites: null,
- collector: brapiOrigin,
- breeder: brapiOrigin,
- distributors: [brapiOrigin],
- panel: [brapiSet],
- collection: [brapiSet],
- population: [brapiSet]
+ collector: germplasmInstitute,
+ breeder: germplasmInstitute,
+ distributors: [germplasmInstitute],
+ panel: [germplasmSet],
+ collection: [germplasmSet],
+ population: [germplasmSet]
};
let gnpisService: GnpisService;
@@ -144,7 +134,7 @@ describe('GnpisService', () => {
const req = http.expectOne({
method: 'GET',
- url: `${BASE_URL}/sources`
+ url: `${BASE_URL}/datadiscovery/sources`
});
req.flush(sources);
@@ -167,7 +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);
@@ -183,7 +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);
@@ -223,7 +213,7 @@ describe('GnpisService', () => {
});
const req = http.expectOne({
- url: `${BASE_URL}/search`,
+ url: `${BASE_URL}/datadiscovery/search`,
method: 'POST'
});
req.flush(rawResult);
diff --git a/frontend/src/app/gnpis.service.ts b/frontend/src/app/gnpis.service.ts
index 1a7cee829791e7c9c2517227e27220e3142bc895..7b47607f9c23869a13a08e07d9dc942db04b2860 100644
--- a/frontend/src/app/gnpis.service.ts
+++ b/frontend/src/app/gnpis.service.ts
@@ -1,15 +1,14 @@
import { Injectable } from '@angular/core';
import { Observable, ReplaySubject, zip } from 'rxjs';
import { HttpClient } from '@angular/common/http';
-import { Germplasm } from './models/gnpis.germplasm.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 { 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}`);
}
}
diff --git a/frontend/src/app/map/map.component.html b/frontend/src/app/map/map.component.html
index d6143c137693b3d868a4eedde59cad686e1a3c64..9285cb1a709ff23a3253d2e6357d8678d3ea0215 100644
--- a/frontend/src/app/map/map.component.html
+++ b/frontend/src/app/map/map.component.html
@@ -1,6 +1,6 @@
<div id="map" class="rounded">
</div>
-<div id="maplegend">
+<div *ngIf="curatedLocationList.length > 0" id="maplegend">
<img src="assets/gpds/images/marker-icon-red.png" id="red"/>
<label for="red">Origin site</label>
<img src="assets/gpds/images/marker-icon-blue.png" id="blue"/>
diff --git a/frontend/src/app/map/map.component.ts b/frontend/src/app/map/map.component.ts
index df746dd8cca185791976a68885dac0e454c1369c..bc566b84667bf0f2cf3e74d1ce99e832df0877e4 100644
--- a/frontend/src/app/map/map.component.ts
+++ b/frontend/src/app/map/map.component.ts
@@ -11,17 +11,19 @@ import { BrapiLocation } from '../models/brapi.model';
export class MapComponent implements OnInit {
@Input() locations: BrapiLocation[];
+ curatedLocationList: BrapiLocation[] = [];
constructor() {
}
ngOnInit() {
- const container = L.DomUtil.get('map');
- if (container) {
+
+ this.removeEmptyLocations(this.locations);
+ if (this.curatedLocationList.length > 0) {
const map = L.map('map');
// initialize map centered on the first site
- const firstLocation: BrapiLocation = this.locations[0];
+ const firstLocation: BrapiLocation = this.curatedLocationList[0];
if (firstLocation) {
map.setView([firstLocation.latitude, firstLocation.longitude], 5);
}
@@ -30,9 +32,10 @@ export class MapComponent implements OnInit {
attribution: 'Tiles © Esri — Source: Esri, DeLorme, NAVTEQ, USGS, Intermap, iPC, NRCAN, Esri Japan, METI, ' +
'Esri China (Hong Kong), Esri (Thailand), TomTom, 2012'
}).addTo(map);
+
// add markers for all locations using markercluster plugin
const markers = new MarkerClusterGroup();
- for (const location of this.locations) {
+ for (const location of this.curatedLocationList) {
const icon = L.icon({
iconUrl: this.getMarkerIconUrl(location)
});
@@ -49,9 +52,12 @@ export class MapComponent implements OnInit {
);
}
map.addLayer(markers);
+ } else {
+ L.DomUtil.get('map').remove();
}
}
+
getMarkerIconUrl(site: BrapiLocation): string {
if (site.locationType === 'Origin site') {
return 'assets/gpds/images/marker-icon-red.png';
@@ -64,4 +70,12 @@ export class MapComponent implements OnInit {
}
return 'assets/gpds/images/marker-icon-purple.png';
}
+
+ removeEmptyLocations(locations: BrapiLocation[]) {
+ for (const location of locations) {
+ if (location && location.latitude && location.longitude) {
+ this.curatedLocationList.push(location);
+ }
+ }
+ }
}
diff --git a/frontend/src/app/models/brapi.germplasm.model.ts b/frontend/src/app/models/brapi.germplasm.model.ts
deleted file mode 100644
index 54ed2d04026b9b78b22ed7e298a976b6ebeddb7d..0000000000000000000000000000000000000000
--- a/frontend/src/app/models/brapi.germplasm.model.ts
+++ /dev/null
@@ -1,55 +0,0 @@
-import { Institute } from './gnpis.germplasm.model';
-
-
-export interface BrapiSibling {
- germplasmDbId: string;
- defaultDisplayName: string;
-}
-
-export interface BrapiDescriptor {
- name: string;
- pui: string;
- value: string;
-}
-
-export interface BrapiGermplasmPedigree {
- germplasmDbId: string;
- defaultDisplayName: string;
- pedigree: string;
- crossingPlan: string;
- crossingYear: string;
- familyCode: string;
- parent1DbId: string;
- parent1Name: string;
- parent1Type: string;
- parent2DbId: string;
- parent2Name: string;
- parent2Type: string;
- siblings: BrapiSibling[];
-}
-
-export interface BrapiGermplasmProgeny {
- germplasmDbId: string;
- defaultDisplayName: string;
- progeny: BrapiSibling[];
-}
-
-export interface BrapiGermplasmAttributes {
- attributeName: string;
- value: string;
-}
-
-export interface BrapiDonor {
- donorInstitute: Institute;
- germplasmPUI: string;
- accessionNumber: string;
- donorInstituteCode: string;
-}
-
-export interface BrapiSet {
- germplasmCount: number;
- germplasmRef: string;
- id: number;
- name: string;
- type: string;
-}
diff --git a/frontend/src/app/models/brapi.model.ts b/frontend/src/app/models/brapi.model.ts
index 4360105b11800d1bcf052540a0526e112bd3ec75..fa9963801a1053877cf35102541478c6b81081c4 100644
--- a/frontend/src/app/models/brapi.model.ts
+++ b/frontend/src/app/models/brapi.model.ts
@@ -14,7 +14,7 @@ export interface BrapiResult<T> {
}
-interface BrapiData<T> {
+export interface BrapiData<T> {
data: T[];
}
@@ -42,7 +42,7 @@ export interface BrapiStudy extends BrapiHasDocumentationURL {
trialDbIds: string[];
location: BrapiLocation;
contacts: BrapiContacts[];
- additionalInfo: AdditionalInfo;
+ additionalInfo: BrapiAdditionalInfo;
dataLinks: {
name: string;
type: string;
@@ -51,36 +51,36 @@ export interface BrapiStudy extends BrapiHasDocumentationURL {
}
+export interface BrapiContacts {
+ contactDbId: string;
+ name: string;
+ email: string;
+ type: string;
+ institutionName: string;
+}
+
+
export interface BrapiLocation extends BrapiHasDocumentationURL {
locationDbId: string;
locationName: string;
locationType: string;
- abbreviation: string;
- countryCode: string;
- countryName: string;
- institutionAddress: string;
- institutionName: string;
- altitude: number;
+ abbreviation?: string;
+ countryCode?: string;
+ countryName?: string;
+ institutionAddress?: string;
+ institutionName?: string;
+ altitude?: number;
latitude: number;
longitude: number;
- additionalInfo?: AdditionalInfo;
+ additionalInfo?: BrapiAdditionalInfo;
}
-export interface AdditionalInfo {
+export interface BrapiAdditionalInfo {
[key: string]: string;
}
-export interface BrapiContacts {
- contactDbId: string;
- name: string;
- email: string;
- type: string;
- institutionName: string;
-}
-
-
export interface BrapiObservationVariable extends BrapiHasDocumentationURL {
observationVariableDbId: string;
contextOfUse: string[];
@@ -99,23 +99,99 @@ export interface BrapiObservationVariable extends BrapiHasDocumentationURL {
}
+export interface BrapiTrial extends BrapiHasDocumentationURL {
+ trialDbId: string;
+ trialName: string;
+ trialType: string;
+ active: boolean;
+ studies: {
+ studyDbId: string;
+ studyName: string;
+ }[];
+}
+
export interface BrapiGermplasm extends BrapiHasDocumentationURL {
germplasmDbId: string;
+ defaultDisplayName: string;
accessionNumber: string;
germplasmName: string;
+ germplasmPUI: string;
+ pedigree: string;
+ seedSource: string;
+ synonyms: string[];
+ commonCropName: string;
+ instituteCode: string;
+ instituteName: string;
+ biologicalStatusOfAccessionCode: string;
+ countryOfOriginCode: string;
+ typeOfGermplasmStorageCode: string[];
+ taxonIds: BrapiTaxonIds[];
genus: string;
species: string;
+ speciesAuthority: string;
subtaxa: string;
+ subtaxaAuthority: string;
+ donors: BrapiDonor[];
+ acquisitionDate: string;
}
-export interface BrapiTrial extends BrapiHasDocumentationURL {
- trialDbId: string;
- trialName: string;
- trialType: string;
- active: boolean;
- studies: {
- studyDbId: string;
- studyName: string;
- }[];
+export interface BrapiTaxonIds {
+ sourceName: string;
+ taxonId: string;
+}
+
+export interface BrapiDonor {
+ donorGermplasmPUI: string;
+ donorAccessionNumber: string;
+ donorInstituteCode: string;
+ donationDate: number;
+}
+
+export interface BrapiGermplasmPedigree {
+ germplasmDbId: string;
+ defaultDisplayName: string;
+ pedigree: string;
+ crossingPlan: string;
+ crossingYear: string;
+ familyCode: string;
+ parent1DbId: string;
+ parent1Name: string;
+ parent1Type: string;
+ parent2DbId: string;
+ parent2Name: string;
+ parent2Type: string;
+ siblings: BrapiSibling[];
+}
+
+export interface BrapiSibling {
+ germplasmDbId: string;
+ defaultDisplayName: string;
+}
+
+export interface BrapiGermplasmProgeny {
+ germplasmDbId: string;
+ defaultDisplayName: string;
+ progeny: BrapiProgeny[];
+}
+
+export interface BrapiProgeny {
+ germplasmDbId: string;
+ defaultDisplayName: string;
+ parentType: string;
+
+}
+
+
+export interface BrapiGermplasmAttributes {
+ germplasmDbId: string;
+ data: BrapiAttributeData[];
+}
+
+export interface BrapiAttributeData {
+ attributeDbId: string;
+ attributeName: string;
+ attributeCode: string;
+ value: string;
+ determinedDate: string;
}
diff --git a/frontend/src/app/models/gnpis.germplasm.model.ts b/frontend/src/app/models/gnpis.germplasm.model.ts
deleted file mode 100644
index a18cbb87f9d78d12db5d14e026033e6ba354594d..0000000000000000000000000000000000000000
--- a/frontend/src/app/models/gnpis.germplasm.model.ts
+++ /dev/null
@@ -1,92 +0,0 @@
-import { BrapiDescriptor, BrapiDonor, BrapiSet } from './brapi.germplasm.model';
-
-export interface Site {
- latitude: number;
- longitude: number;
- siteId: number;
- siteName: string;
- siteType: string;
-}
-
-export interface Germplasm {
- source: string;
- url: string;
- germplasmDbId: string;
- defaultDisplayName: string;
- accessionNumber: string;
- germplasmName: string;
- germplasmPUI: string;
- pedigree: string;
- seedSource: string;
- synonyms: string;
- commonCropName: string;
- instituteCode: string;
- instituteName: string;
- biologicalStatusOfAccessionCode: string;
- countryOfOriginCode: string;
- typeOfGermplasmStorageCode: string;
- taxonIds: string;
- genus: string;
- species: string;
- speciesAuthority: string;
- subtaxa: string;
- subtaxaAuthority: string;
- donors: BrapiDonor[];
- acquisitionDate: string;
- genusSpecies: string;
- genusSpeciesSubtaxa: string;
- taxonSynonyms: string[];
- taxonCommonNames: string[];
- geneticNature: string;
- comment: string;
- photo: string;
- holdingInstitute: Institute;
- holdingGenbank: Institute;
- presenceStatus: string;
- children: string;
- descriptors: BrapiDescriptor[];
- originSite: Site;
- collectingSite: Site;
- evaluationSites: Site[];
- collector: Origin;
- breeder: Origin;
- distributors: Origin[];
- panel: BrapiSet[];
- collection: BrapiSet[];
- population: BrapiSet[];
-}
-
-export interface Origin {
- institute: Institute;
- germplasmPUI: string;
- accessionNumber: string;
- accessionCreationDate: string;
- materialType: string;
- collectors: string;
- registrationYear: string;
- deregistrationYear: string;
- distributionStatus: string;
-}
-
-export interface Institute {
- instituteName: string;
- instituteCode: string;
- acronym: string;
- organisation: string;
- instituteType: string;
- webSite: string;
- address: string;
- logo: string;
-}
-
-export interface GermplasmData<T> {
- data: T;
-}
-
-export interface GermplasmResult<T> {
- result: T;
-}
-
-
-
-
diff --git a/frontend/src/app/models/gnpis.model.ts b/frontend/src/app/models/gnpis.model.ts
new file mode 100644
index 0000000000000000000000000000000000000000..061c0d2a4b6429c78cbbad30589b13f67ac8c2cd
--- /dev/null
+++ b/frontend/src/app/models/gnpis.model.ts
@@ -0,0 +1,92 @@
+import { BrapiDonor, BrapiGermplasm } from './brapi.model';
+
+export interface Germplasm extends BrapiGermplasm {
+ genusSpecies: string;
+ genusSpeciesSubtaxa: string;
+ taxonSynonyms: string[];
+ taxonCommonNames: string[];
+ geneticNature: string;
+ comment: string;
+ photo: Photo;
+ holdingInstitute: Institute;
+ holdingGenbank: Institute;
+ presenceStatus: string;
+ children: Children[];
+ originSite: Site;
+ collectingSite: Site;
+ evaluationSites: Site[];
+ collector: GermplasmInstitute;
+ breeder: GermplasmInstitute;
+ donors: Donor[];
+ distributors: GermplasmInstitute[];
+ panel: GermplasmSet[];
+ collection: GermplasmSet[];
+ population: GermplasmSet[];
+}
+
+export interface Site {
+ latitude: number;
+ longitude: number;
+ siteId: string;
+ siteName: string;
+ siteType: string;
+}
+
+export interface Institute {
+ instituteName: string;
+ instituteCode: string;
+ acronym: string;
+ organisation: string;
+ instituteType: string;
+ webSite: string;
+ address: string;
+ logo: string;
+}
+
+export interface GermplasmInstitute extends Institute {
+ institute: Institute;
+ accessionNumber: string;
+ accessionCreationDate: string;
+ materialType: string;
+ collectors: string;
+ registrationYear: string;
+ deregistrationYear: string;
+ distributionStatus?: string;
+}
+
+export interface Photo {
+ copyright: string;
+ description: string;
+ fileName: string;
+ photoName: string;
+ thumbnailFileName: string;
+
+}
+
+export interface Children {
+ firstParentName: string;
+ firstParentPUI: string;
+ secondParentName: string;
+ secondParentPUI: string;
+ sibblings: {
+ name: string;
+ pui: string;
+ }[];
+
+}
+
+export interface Donor extends BrapiDonor {
+ donorInstitute: Institute;
+}
+
+
+export interface GermplasmSet {
+ id: number;
+ name: string;
+ type: string;
+ germplasmCount: number;
+ germplasmRef: {
+ pui: string;
+ name: string;
+ };
+}
diff --git a/frontend/src/app/navbar/navbar.component.html b/frontend/src/app/navbar/navbar.component.html
index dca9fd2726401b4228b839f68ba149e2ea71bad4..0f8b7fc4b98483cbef0eb65782b9d262c336e115 100644
--- a/frontend/src/app/navbar/navbar.component.html
+++ b/frontend/src/app/navbar/navbar.component.html
@@ -1,4 +1,4 @@
-<nav class="navbar navbar-expand-md navbar-dark py-0 mb-5">
+<nav class="navbar navbar-expand-md navbar-dark py-0 mb-4">
<div class="container px-0">
<a class="navbar-brand d-flex align-items-center mr-0 px-2" routerLink="/">
<img src="assets/logo.png" alt="Logo" title="{{ navbar.title }}" height="60px"/>
@@ -38,7 +38,6 @@
</div>
</div>
</div>
-
</li>
</ul>
</div>
diff --git a/frontend/src/app/navbar/navbar.component.scss b/frontend/src/app/navbar/navbar.component.scss
index 2a8c98cf98252cad58c7c6135e62433dd1871efc..75a2c2d35354e325d4569aa79a4745cfea16ef98 100644
--- a/frontend/src/app/navbar/navbar.component.scss
+++ b/frontend/src/app/navbar/navbar.component.scss
@@ -14,6 +14,7 @@
.navbar .navbar-nav .nav-link, .navbar .navbar-brand {
color: $theme-navbar-color;
height: $theme-navbar-height;
+ text-decoration: none;
&:hover {
color: $theme-navbar-hover-color;
@@ -24,3 +25,4 @@
.dropdown-container {
position: relative;
}
+
diff --git a/frontend/src/app/result-page/document/document.component.html b/frontend/src/app/result-page/document/document.component.html
index 9b1175eb96f50f02d16f3088d1de992c038761a8..af8a669f81926f2e134158656b97173d9b51488d 100644
--- a/frontend/src/app/result-page/document/document.component.html
+++ b/frontend/src/app/result-page/document/document.component.html
@@ -7,13 +7,21 @@
<a class="badge badge-source mr-2" [href]="getSourceURL()" target="_blank">
{{ getSource() }}
</a>
- <a class="title" *ngIf="getURL()" [href]="getURL()">
+ <a class="title" *ngIf="getRouterLink() && document['@type'].includes('Phenotyping Study')"
+ [routerLink]="getRouterLink()">
{{ document["schema:name"] }}
</a>
- <a class="title" *ngIf="getRouterLink()" [routerLink]="getRouterLink()" [queryParams]="getQueryParam()">
+ <a class="title" *ngIf="getRouterLink() && !document['@type'].includes('Phenotyping Study')"
+ [routerLink]="getRouterLink()" [queryParams]="getQueryParam()">
{{ document["schema:name"] }}
</a>
</h5>
+
+ <h5>
+ <a class="title" *ngIf="getURL()" [href]="getURL()" target="_blank">
+ ({{ document['schema:includedInDataCatalog']['schema:identifier'] }} data source link)
+ </a>
+ </h5>
<span class="text-justify description">
<ng-container *ngIf="!needTruncation || opened">
{{ document["schema:description"] }}
diff --git a/frontend/src/app/result-page/document/document.component.scss b/frontend/src/app/result-page/document/document.component.scss
index 2ca792215dc2d003944532b271ec01da4eaa102e..fb44cb186291fce961d4deda6a34fbac2b0c3e9a 100644
--- a/frontend/src/app/result-page/document/document.component.scss
+++ b/frontend/src/app/result-page/document/document.component.scss
@@ -1,3 +1,4 @@
+
.badge-source {
background-color: #b54646;
color: white;
diff --git a/frontend/src/app/result-page/document/document.component.spec.ts b/frontend/src/app/result-page/document/document.component.spec.ts
index 5f2d83663fc8f62cc63dbd834ad215a90f594d77..95089e9505227bec9e41574c3cf667c16bd55acd 100644
--- a/frontend/src/app/result-page/document/document.component.spec.ts
+++ b/frontend/src/app/result-page/document/document.component.spec.ts
@@ -71,7 +71,7 @@ describe('DocumentComponent', () => {
expect(tester.source.attr('href')).toEqual('http://dco/url');
expect(tester.title).toContainText('doc_name');
- expect(tester.title.attr('href')).toEqual('http://dco/url');
+ expect(tester.title.nativeElement['routerLink']).toEqual('/germplasm');
expect(tester.description).toContainText('description');
diff --git a/frontend/src/app/result-page/document/document.component.ts b/frontend/src/app/result-page/document/document.component.ts
index 69d83161a159cc6fe050e42254e48197f4666d06..7d5f6b0e6974090ae6816d0567c611966d35b217 100644
--- a/frontend/src/app/result-page/document/document.component.ts
+++ b/frontend/src/app/result-page/document/document.component.ts
@@ -22,22 +22,29 @@ export class DocumentComponent implements OnInit {
needTruncation = false;
opened = false;
+
getURL() {
return this.document['schema:url'] || '';
}
+ // TODO: index URGI schema:identifier like the partners
+
getRouterLink() {
- if (!this.getURL()) {
- for (const type of this.document['@type']) {
- const cardUrl = DocumentComponent.CARD_TYPE[type];
- if (cardUrl === 'studies') {
- return `/${cardUrl}/${this.document['schema:identifier']}`;
- }
- if (cardUrl === 'germplasm') {
- return `/${cardUrl}`;
+ const urgiStudy = this.document['schema:includedInDataCatalog']['schema:url'] === 'https://urgi.versailles.inra.fr/gnpis/';
+ for (const type of this.document['@type']) {
+ const cardUrl = DocumentComponent.CARD_TYPE[type];
+ if (cardUrl === 'studies') {
+ if (urgiStudy) {
+ const studyId = this.document['@id'].replace(/urn:URGI\/study\//, '');
+ return `/${cardUrl}/${studyId}`;
}
+ return `/${cardUrl}/${this.document['schema:identifier']}`;
+ }
+ if (cardUrl === 'germplasm') {
+ return `/${cardUrl}`;
}
}
+
return '';
}
diff --git a/frontend/src/app/site-card/site-card.component.html b/frontend/src/app/site-card/site-card.component.html
index 9144f1aff1b091e95ac7394958aafdf6b09e138e..ba9d335ec0745debd040e32df55016c3e8dfdde8 100644
--- a/frontend/src/app/site-card/site-card.component.html
+++ b/frontend/src/app/site-card/site-card.component.html
@@ -7,17 +7,34 @@
</h3>
- <gpds-map [locations]="[location]" *ngIf="location && location.latitude && location.longitude"></gpds-map>
+ <gpds-map [locations]="[location]"></gpds-map>
<gpds-card-section
header="Details">
<ng-template>
- <div class="card-body">
+ <div class="card-body card-section-body">
+
<gpds-card-row
- label="Site type"
- [value]="location.locationType">
+ label="Source"
+ [test]="location">
+ <ng-template>
+ <a target="_blank"
+ [href]="locationSource['schema:url']">
+ <img [src]="locationSource['schema:image']" alt="Location source image"/>
+ </a>
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Data source"
+ [test]="location && location['schema:identifier'] && location.documentationURL">
+ <ng-template>
+ <a target="_blank" [href]="location.documentationURL">
+ Link to this study on {{ location['schema:identifier'] }}
+ </a>
+ </ng-template>
</gpds-card-row>
<gpds-card-row
@@ -26,14 +43,21 @@
</gpds-card-row>
<gpds-card-row
- label="Country code"
- [value]="location.countryCode">
+ label="Type"
+ [value]="location.locationType">
</gpds-card-row>
<gpds-card-row
- label="Country name"
- [test]="location.countryName && !location.additionalInfo['Geographical location']"
- [value]="location.countryName">
+ label="Status"
+ [test]="location.additionalInfo['Site status']">
+ <ng-template>
+ {{ location.additionalInfo['Site status'] }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Institution/Landowner"
+ [value]="location.institutionName">
</gpds-card-row>
<gpds-card-row
@@ -42,8 +66,45 @@
</gpds-card-row>
<gpds-card-row
- label="Institution name"
- [value]="location.institutionAddress">
+ label="Coordinates precision"
+ [test]="location.additionalInfo['Coordinates precision']">
+ <ng-template>
+ {{ location.additionalInfo['Coordinates precision'] }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Latitude"
+ [value]="formatCoordinates(location.latitude, 'latitude')">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Longitude"
+ [value]="formatCoordinates(location.longitude, 'longitude')">
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Geographical location"
+ [test]="location.additionalInfo['Geographical location']">
+ <ng-template>
+ {{ location.additionalInfo['Geographical location'] }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Country name"
+ [test]="location.countryName && !location.additionalInfo['Geographical location']">
+ <ng-template>
+ {{ location.countryName }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Country code"
+ [test]="location.countryCode && !location.additionalInfo['Geographical location']">
+ <ng-template>
+ {{ location.countryCode }}
+ </ng-template>
</gpds-card-row>
<gpds-card-row
@@ -52,31 +113,76 @@
</gpds-card-row>
<gpds-card-row
- label="Latitude"
- [value]="location.latitude">
+ label="Slope"
+ [value]="location.additionalInfo['Slope']">
</gpds-card-row>
<gpds-card-row
- label="Longitude"
- [value]="location.longitude">
+ label="Exposure"
+ [test]="location.additionalInfo['Exposure']">
+ <ng-template>
+ {{ location.additionalInfo['Exposure'] }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Topography"
+ [test]="location.additionalInfo['Topography']">
+ <ng-template>
+ {{ location.additionalInfo['Topography'] }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Environment type"
+ [test]="location.additionalInfo['Environment type']">
+ <ng-template>
+ {{ location.additionalInfo['Environment type'] }}
+ </ng-template>
</gpds-card-row>
+
+ <gpds-card-row
+ label="Distance to city"
+ [test]="location.additionalInfo['Distance to city']">
+ <ng-template>
+ {{ location.additionalInfo['Distance to city'] }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Direction from city"
+ [test]="location.additionalInfo['Direction from city']">
+ <ng-template>
+ {{ location.additionalInfo['Direction from city'] }}
+ </ng-template>
+ </gpds-card-row>
+
+ <gpds-card-row
+ label="Comment"
+ [test]="location.additionalInfo['Comment']">
+ <ng-template>
+ {{ location.additionalInfo['Comment'] }}
+ </ng-template>
+ </gpds-card-row>
+
</div>
</ng-template>
</gpds-card-section>
<gpds-card-section
header="Additional information"
- [test]="additionalInfos && additionalInfos.length != 0">
+ [test]="additionalInfos && additionalInfos.length > 0">
<ng-template>
- <gpds-card-table
- [rows]="additionalInfos">
- <ng-template let-row>
- <tr>
- <td width="50%">{{ row.key }}</td>
- <td>{{ row.value }}</td>
- </tr>
- </ng-template>
- </gpds-card-table>
+ <div class="card-body card-section-body">
+
+ <ng-container *ngFor="let additionalInfo of additionalInfos">
+ <gpds-card-row
+ [label]="additionalInfo.key"
+ [value]="additionalInfo.value">
+ </gpds-card-row>
+ </ng-container>
+
+ </div>
</ng-template>
</gpds-card-section>
diff --git a/frontend/src/app/site-card/site-card.component.scss b/frontend/src/app/site-card/site-card.component.scss
index 55181845b07a912a715c27dd619fd2bb24d19400..bb109da81d37b2df40a8dfdbeaaeaf748312932e 100644
--- a/frontend/src/app/site-card/site-card.component.scss
+++ b/frontend/src/app/site-card/site-card.component.scss
@@ -1,9 +1,12 @@
+@import "theme";
+@import '../../styles.scss';
-h3 {
- font-weight: bold;
- color: #0f6191;
+a:not([href]):not([tabindex]) {
+ color: #0f6fa1;
+ cursor: pointer;
}
-a {
+a:not([href]):not([tabindex]):hover {
text-decoration: underline;
}
+
diff --git a/frontend/src/app/site-card/site-card.component.spec.ts b/frontend/src/app/site-card/site-card.component.spec.ts
index f33d7f9a27f679d1748082027c638a7b7c58054a..a8d0604c2b0194272e86b1977a59592419d62a93 100644
--- a/frontend/src/app/site-card/site-card.component.spec.ts
+++ b/frontend/src/app/site-card/site-card.component.spec.ts
@@ -10,6 +10,8 @@ import { CardRowComponent } from '../card-row/card-row.component';
import { LoadingSpinnerComponent } from '../loading-spinner/loading-spinner.component';
import { CardTableComponent } from '../card-table/card-table.component';
import { CardSectionComponent } from '../card-section/card-section.component';
+import { DataDiscoverySource } from '../models/data-discovery.model';
+import { GnpisService } from '../gnpis.service';
import { MockComponent } from 'ng-mocks';
import { XrefsComponent } from '../xrefs/xrefs.component';
@@ -18,6 +20,9 @@ describe('SiteCardComponent', () => {
const brapiService = jasmine.createSpyObj(
'BrapiService', ['location']
);
+ const gnpisService = jasmine.createSpyObj(
+ 'GnpisService', ['getSource']
+ );
const response: BrapiResult<BrapiLocation> = {
metadata: null,
result: {
@@ -47,6 +52,15 @@ describe('SiteCardComponent', () => {
}
};
+ const source: DataDiscoverySource = {
+ '@id': 'src1',
+ '@type': ['schema:DataCatalog'],
+ 'schema:identifier': 'srcId',
+ 'schema:name': 'source1',
+ 'schema:url': 'srcUrl',
+ 'schema:image': null
+ };
+
beforeEach(async(() => {
TestBed.configureTestingModule({
declarations: [
@@ -56,6 +70,7 @@ describe('SiteCardComponent', () => {
],
providers: [
{ provide: BrapiService, useValue: brapiService },
+ { provide: GnpisService, useValue: gnpisService },
{
provide: ActivatedRoute,
useValue: {
@@ -76,6 +91,7 @@ describe('SiteCardComponent', () => {
const fixture = TestBed.createComponent(SiteCardComponent);
const component = fixture.componentInstance;
brapiService.location.and.returnValues(of(response));
+ gnpisService.getSource.and.returnValue(of(source));
fixture.detectChanges();
const element = fixture.nativeElement;
expect(element.querySelector('h3').textContent).toBe(' Site: site1 ');
diff --git a/frontend/src/app/site-card/site-card.component.ts b/frontend/src/app/site-card/site-card.component.ts
index d892c85d2bbba0d545584126912530f94174ddd4..0705744e73ececc2b0b0bef39dad3febdcdfc859 100644
--- a/frontend/src/app/site-card/site-card.component.ts
+++ b/frontend/src/app/site-card/site-card.component.ts
@@ -3,6 +3,8 @@ import { BrapiService } from '../brapi.service';
import { ActivatedRoute } from '@angular/router';
import { BrapiLocation } from '../models/brapi.model';
import { KeyValueObject } from '../utils';
+import { DataDiscoverySource } from '../models/data-discovery.model';
+import { GnpisService } from '../gnpis.service';
@Component({
selector: 'gpds-site-card',
@@ -12,11 +14,11 @@ import { KeyValueObject } from '../utils';
export class SiteCardComponent implements OnInit {
location: BrapiLocation;
+ locationSource: DataDiscoverySource;
additionalInfos: KeyValueObject[];
loading = true;
-
- constructor(private brapiService: BrapiService, private route: ActivatedRoute) {
+ constructor(private brapiService: BrapiService, private gnpisService: GnpisService, private route: ActivatedRoute) {
}
ngOnInit() {
@@ -28,7 +30,23 @@ export class SiteCardComponent implements OnInit {
this.location = response.result;
this.additionalInfos = [];
if (this.location.additionalInfo) {
- this.additionalInfos = KeyValueObject.fromObject(this.location.additionalInfo);
+ this.manageAdditionalInfo(KeyValueObject.fromObject(this.location.additionalInfo).sort());
+ }
+ const sourceURI = location['schema:includedInDataCatalog'];
+ // TODO Remove the condition when the field includedInDataCatalog will be added to URGI study.
+ if (sourceURI) {
+ const source$ = this.gnpisService.getSource(sourceURI);
+ source$
+ .subscribe(src => {
+ this.locationSource = src;
+ });
+ } else {
+ const urgiURI = 'https://urgi.versailles.inra.fr';
+ const source$ = this.gnpisService.getSource(urgiURI);
+ source$
+ .subscribe(src => {
+ this.locationSource = src;
+ });
}
this.loading = false;
}
@@ -36,4 +54,53 @@ export class SiteCardComponent implements OnInit {
});
}
+
+ manageAdditionalInfo(keyValues: KeyValueObject[]) {
+ const forbiddenElements: String[] = [
+ 'Site status',
+ 'Coordinates precision',
+ 'Slope',
+ 'Exposure',
+ 'Geographical location',
+ 'Distance to city',
+ 'Direction from city',
+ 'Environment type',
+ 'Topography',
+ 'Comment'];
+ for (const keyValue of keyValues) {
+ if (!forbiddenElements.includes(keyValue.key)) {
+ this.additionalInfos.push(keyValue);
+ }
+ }
+ }
+
+ formatCoordinates(decimalDegrees: number, type: string): string {
+ if (decimalDegrees && type) {
+ const degree = Math.floor(decimalDegrees);
+ const decimalMinute = (decimalDegrees - degree) * 60;
+ const minute = Math.floor(decimalMinute);
+ const decimalSeconde = (decimalMinute - minute) * 60;
+ const seconde = Math.floor(decimalSeconde);
+
+ let direction = '';
+ if (type === 'latitude') {
+ if (decimalDegrees >= 0) {
+ direction = 'N';
+ } else {
+ direction = 'S';
+ }
+ } else if (type === 'longitude') {
+ if (decimalDegrees >= 0) {
+ direction = 'E';
+ } else {
+ direction = 'W';
+ }
+ }
+ return decimalDegrees + '° (' + degree + '° ' + minute + '\' ' + seconde + '\'\' ' + direction + ')';
+ } else {
+ return null;
+ }
+ }
+
}
+
diff --git a/frontend/src/app/study-card/study-card.component.html b/frontend/src/app/study-card/study-card.component.html
index 0ccf9c30277119280eb3752e06c2150aa5692c2c..358fd637efc795793496c6a048e7f1d572167550 100644
--- a/frontend/src/app/study-card/study-card.component.html
+++ b/frontend/src/app/study-card/study-card.component.html
@@ -6,13 +6,13 @@
</h3>
<!-- Display the map -->
- <gpds-map *ngIf="checkLocation(study.location)" [locations]="[study.location]"></gpds-map>
+ <gpds-map [locations]="[study.location]"></gpds-map>
<!-- Display the study's info -->
<gpds-card-section
header="Identification">
<ng-template>
- <div class="card-body">
+ <div class="card-body card-section-body">
<gpds-card-row
label="Name"
@@ -21,13 +21,7 @@
<gpds-card-row
label="Identifier"
- [test]="study.studyDbId">
- <ng-template>
- {{ study.studyDbId }}
- <a target="_blank" *ngIf="studySource && study.documentationURL" [href]="study.documentationURL">
- ( Link to this study on {{ studySource["schema:identifier"] }} )
- </a>
- </ng-template>
+ [value]="study.studyDbId">
</gpds-card-row>
<gpds-card-row
@@ -49,10 +43,10 @@
<gpds-card-row
label="Data source"
- [test]="studySource && study.documentationURL">
+ [test]="studySource && studySource['schema:identifier'] && study.documentationURL">
<ng-template>
- <a target="_blank" *ngIf="study.documentationURL" [href]="study.documentationURL">
- ( Link to this study on {{ studySource["schema:identifier"] }} )
+ <a target="_blank" [href]="study.documentationURL">
+ Link to this study on {{ studySource["schema:identifier"] }}
</a>
</ng-template>
</gpds-card-row>
@@ -108,7 +102,7 @@
[test]="study.dataLinks && study.dataLinks.length != 0">
<ng-template>
<div *ngFor="let dataLink of study.dataLinks">
- <a [href]="dataLink.url">
+ <a target="_blank" [href]="dataLink.url">
{{ dataLink.name }}
</a>
</div>
@@ -165,7 +159,7 @@
<td>
<ng-template #name>{{ row.observationVariableDbId }}</ng-template>
<ng-template #link>
- <a [href]=row.documentationURL>{{ row.observationVariableDbId }}</a>
+ <a target="_blank" [href]=row.documentationURL>{{ row.observationVariableDbId }}</a>
</ng-template>
<ng-container *ngIf="row.documentationURL; then link else name"></ng-container>
</td>
@@ -195,7 +189,7 @@
<td>
<ng-template #name>{{ row.trialName }}</ng-template>
<ng-template #link>
- <a [href]=row.documentationURL>{{ row.trialName }}</a>
+ <a target="_blank" [href]=row.documentationURL>{{ row.trialName }}</a>
</ng-template>
<ng-container *ngIf="row.documentationURL; then link else name"></ng-container>
</td>
@@ -221,9 +215,9 @@
<gpds-card-table
[headers]="[
'Role',
- 'Name',
- 'Email',
- 'Institution'
+ 'Name',
+ 'Email',
+ 'Institution'
]"
[rows]="study.contacts">
<ng-template let-row>
diff --git a/frontend/src/app/study-card/study-card.component.scss b/frontend/src/app/study-card/study-card.component.scss
index c344730e9220180bc60b5188f46d5b683fb3932e..f0376501baaeced5c8d3194b0d2d23faff4269fe 100644
--- a/frontend/src/app/study-card/study-card.component.scss
+++ b/frontend/src/app/study-card/study-card.component.scss
@@ -1,8 +1,11 @@
@import "theme";
@import '../../styles.scss';
-h3 {
- font-weight: bold;
- color: #0f6191;
+a:not([href]):not([tabindex]) {
+ color: #0f6fa1;
+ cursor: pointer;
}
+a:not([href]):not([tabindex]):hover {
+ text-decoration: underline;
+}
diff --git a/frontend/src/app/study-card/study-card.component.spec.ts b/frontend/src/app/study-card/study-card.component.spec.ts
index e9e0e8cf56bcaff0293df0b80e4a4383494164cd..cd61029fc8ca00b54b9e7b31996f72f422c2e37f 100644
--- a/frontend/src/app/study-card/study-card.component.spec.ts
+++ b/frontend/src/app/study-card/study-card.component.spec.ts
@@ -48,7 +48,7 @@ describe('StudyCardComponent', () => {
}
get map() {
- return this.element('gpds-map');
+ return this.element('div #map');
}
}
@@ -170,18 +170,50 @@ describe('StudyCardComponent', () => {
result: {
data: [{
germplasmDbId: 'g1',
+ defaultDisplayName: 'germplam1',
accessionNumber: 'G_10',
germplasmName: 'germplam1',
+ germplasmPUI: 'urn_g1',
+ pedigree: null,
+ seedSource: 'Versaille Institute',
+ synonyms: null,
+ commonCropName: 'cheery',
+ instituteCode: '78',
+ instituteName: 'Versaille Institute',
+ biologicalStatusOfAccessionCode: null,
+ countryOfOriginCode: 'FR',
+ typeOfGermplasmStorageCode: null,
+ taxonIds: null,
genus: 'Populus',
species: 'x generosa',
- subtaxa: ''
+ speciesAuthority: 'Pop',
+ subtaxa: 'subsp',
+ subtaxaAuthority: '',
+ donors: null,
+ acquisitionDate: 'yesterday'
}, {
germplasmDbId: 'g2',
+ defaultDisplayName: 'germplam2',
accessionNumber: 'G_20',
germplasmName: 'germplam2',
+ germplasmPUI: 'urn_g2',
+ pedigree: null,
+ seedSource: 'Versaille Institute',
+ synonyms: null,
+ commonCropName: 'cheery',
+ instituteCode: '78',
+ instituteName: 'Versaille Institute',
+ biologicalStatusOfAccessionCode: null,
+ countryOfOriginCode: 'FR',
+ typeOfGermplasmStorageCode: null,
+ taxonIds: null,
genus: 'Triticum',
species: 'aestivum',
- subtaxa: 'subsp'
+ speciesAuthority: 'Trit',
+ subtaxa: 'subsp',
+ subtaxaAuthority: '',
+ donors: null,
+ acquisitionDate: 'today'
}],
}
};
@@ -234,7 +266,8 @@ describe('StudyCardComponent', () => {
expect(tester.cardHeader[0]).toContainText('Identification');
- expect(tester.studyInfo[1]).toContainText('Link to this study on srcId');
+ expect(tester.studyInfo[0]).toContainText('study1');
+ expect(tester.studyInfo[1]).toContainText('s1');
expect(tester.cardHeader[1]).toContainText('Genotype');
expect(component.studyGermplasms.length).toEqual(2);
diff --git a/frontend/src/app/study-card/study-card.component.ts b/frontend/src/app/study-card/study-card.component.ts
index a8f729b2bef6861b93a19043912a311248e5b14f..27188c0189f62ab41e9f2020ab3c8603377c0f9b 100644
--- a/frontend/src/app/study-card/study-card.component.ts
+++ b/frontend/src/app/study-card/study-card.component.ts
@@ -1,7 +1,7 @@
import { Component, OnInit } from '@angular/core';
import { BrapiService } from '../brapi.service';
import { ActivatedRoute } from '@angular/router';
-import { BrapiGermplasm, BrapiLocation, BrapiObservationVariable, BrapiStudy, BrapiTrial } from '../models/brapi.model';
+import { BrapiGermplasm, BrapiObservationVariable, BrapiStudy, BrapiTrial } from '../models/brapi.model';
import { GnpisService } from '../gnpis.service';
import { DataDiscoverySource } from '../models/data-discovery.model';
@@ -36,14 +36,21 @@ export class StudyCardComponent implements OnInit {
study$
.then(response => {
this.study = response.result;
+ if (this.study.contacts) {
+ this.study.contacts.sort((var1, var2) =>
+ var1.name.localeCompare(var2.name));
+ }
this.additionalInfos = [];
if (this.study.additionalInfo) {
- this.additionalInfos = KeyValueObject.fromObject(this.study.additionalInfo);
+ this.additionalInfos = KeyValueObject.fromObject(this.study.additionalInfo).sort();
}
// Get study trials
- this.trialsIds = this.study.trialDbIds;
+ if (this.study.trialDbIds) {
+ this.trialsIds = this.study.trialDbIds.sort();
+ }
+
this.studyDataset = [];
if (this.trialsIds && this.trialsIds !== []) {
for (const trialsId of this.trialsIds) {
@@ -57,9 +64,14 @@ export class StudyCardComponent implements OnInit {
this.studyDataset.push(trial);
});
}
+ if (this.studyDataset) {
+ this.studyDataset.sort((var1, var2) =>
+ var1.trialName.localeCompare(var2.trialName));
+ }
}
// Get study source
+ // TODO Remove the condition when the field includedInDataCatalog will be added to URGI study.
const sourceURI = this.study['schema:includedInDataCatalog'];
if (sourceURI) {
const source$ = this.gnpisService.getSource(sourceURI);
@@ -67,6 +79,13 @@ export class StudyCardComponent implements OnInit {
.subscribe(src => {
this.studySource = src;
});
+ } else {
+ const urgiURI = 'https://urgi.versailles.inra.fr';
+ const source$ = this.gnpisService.getSource(urgiURI);
+ source$
+ .subscribe(src => {
+ this.studySource = src;
+ });
}
});
@@ -74,14 +93,16 @@ export class StudyCardComponent implements OnInit {
const variable$ = this.brapiService.studyObservationVariables(studyDbId).toPromise();
variable$
.then(response => {
- this.studyObservationVariables = response.result.data;
+ this.studyObservationVariables = response.result.data.sort((var1, var2) =>
+ var1.observationVariableDbId.localeCompare(var2.observationVariableDbId));
});
this.studyGermplasms = [];
const germplasm$ = this.brapiService.studyGermplasms(studyDbId).toPromise();
germplasm$
.then(studyGermplasm => {
- this.studyGermplasms = studyGermplasm.result.data;
+ this.studyGermplasms = studyGermplasm.result.data.sort((var1, var2) =>
+ var1.germplasmName.localeCompare(var2.germplasmName));
});
this.loaded = Promise.all([study$, variable$, germplasm$]);
@@ -92,10 +113,6 @@ export class StudyCardComponent implements OnInit {
}
- checkLocation(location: BrapiLocation) {
- return location && location.longitude && location.latitude;
- }
-
isNotURN(pui: string) {
return !(pui.substring(0, 3) === 'urn');
}
diff --git a/frontend/src/assets/gpds/logo.png b/frontend/src/assets/gpds/logo.png
index 2131327a70020a31bbb43c56da919b9dccdb837c..16d4a77bc231332c1918cb684bcb199a8c0da555 100644
Binary files a/frontend/src/assets/gpds/logo.png and b/frontend/src/assets/gpds/logo.png differ
diff --git a/frontend/src/assets/gpds/theme.scss b/frontend/src/assets/gpds/theme.scss
index 286d878c78a754045b72b7e6aa8bae22f099448e..b4fae40f944d73954f77a92cb4855802124bcfc1 100644
--- a/frontend/src/assets/gpds/theme.scss
+++ b/frontend/src/assets/gpds/theme.scss
@@ -26,23 +26,18 @@ $enable-shadows: true;
// public custom variables used in this theme, and in component styles
-
//custom tables
.table {
- border-bottom: 2px solid #0f6191;
- border-top: 2px solid #0f6191;
table-layout: fixed;
-}
+ thead {
+ background-color: #0f6191;
+ }
-a.btn.popovers {
- text-decoration: underline;
- //overflow: hidden;
- //text-overflow: ellipsis;
}
.popover {
- max-width: 50%;
+ max-width: 100%;
}
/*table th, table td { overflow: hidden; }*/
@@ -62,10 +57,6 @@ h4 {
color: #0f6191;
}
-.table thead {
- background-color: #0f6191;
-}
-
.ellipsis {
overflow: hidden;
text-overflow: ellipsis;
diff --git a/frontend/src/environments/environment.prod.ts b/frontend/src/environments/environment.prod.ts
index c527bca54680f1cbcdc1a11c4966513caf951014..2b34b7fd446b963a2f5af1aaf9f47f555570498a 100644
--- a/frontend/src/environments/environment.prod.ts
+++ b/frontend/src/environments/environment.prod.ts
@@ -4,7 +4,6 @@ export const environment = {
navbar: {
title: 'GnpIS Plant Data Search',
links: [
- { label: 'INRA', url: 'http://www.inra.fr/' },
{
label: 'URGI',
url: '#',
@@ -14,52 +13,10 @@ export const environment = {
{ label: 'About us', url: 'https://urgi.versailles.inra.fr/About-us' }
]
},
- {
- label: 'Taxon/Germplasm',
- url: '#',
- subMenu: [
- { label: 'Taxon', url: 'https://urgi.versailles.inra.fr/siregal/common/taxon/form.do' },
- { label: 'Accession Simple', url: 'https://urgi.versailles.inra.fr/gnpis-core' },
- { label: 'Accession passport', url: 'https://urgi.versailles.inra.fr/siregal/siregal/accessionForm.do' },
- { label: 'Collections CRB', url: 'https://urgi.versailles.inra.fr/siregal/siregal/grc.do' },
- ]
- },
- { label: 'Phenotyping', url: 'https://urgi.versailles.inra.fr/ephesis/ephesis/viewer.do' },
- {
- label: 'Polymorphism',
- url: '#',
- subMenu: [
- { label: 'Genotyping', url: 'https://urgi.versailles.inra.fr/GnpSNP/snp/genotyping/form.do' },
- { label: 'SNP Discovery', url: 'https://urgi.versailles.inra.fr/GnpSNP/snp/welcome.do' },
- ]
- },
- { label: 'Association', url: 'https://urgi.versailles.inra.fr/association/association/viewer.do#form' },
- {
- label: 'Map/Marker/QTL',
- url: '#',
- subMenu: [
- { label: 'Map', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/searchMap.do' },
- { label: 'Loci', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/loci/queryLociSelect.do' },
- { label: 'QTL', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/qtl/queryQtlSelect.do' },
- { label: 'MetaQTLs', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/metaqtl/form.do' },
- { label: 'Marker', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/marker/markerForm.do' },
- { label: 'Pool', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/pool/poolForm.do' },
- { label: 'Traits', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/queryTraitSelect.do' },
- { label: 'Biomercator', url: 'https://urgi.versailles.inra.fr/Tools/BioMercator-V4' },
- ]
- },
- { label: 'Genomes', url: 'https://urgi.versailles.inra.fr/Data/Genome/Genome-data-access' },
- { label: 'Synteny', url: 'https://urgi.versailles.inra.fr/synteny/synteny/viewer.do#dataset' },
- {
- label: 'Sequence',
- url: '#',
- subMenu: [
- { label: 'Sequence', url: 'https://urgi.versailles.inra.fr/sequence/sequence/sequence/form.do' },
- { label: 'Experiment', url: 'https://urgi.versailles.inra.fr/sequence/sequence/experiment/form.do' },
- { label: 'Analysis', url: 'https://urgi.versailles.inra.fr/sequence/sequence/analysis/form.do' },
- { label: 'Project', url: 'https://urgi.versailles.inra.fr/sequence/sequence/project/form.do' },
- ]
- }
+ { label: 'GNPIS', url: 'https://urgi.versailles.inra.fr/gnpis/' },
+ { label: 'CIRAD', url: 'http://tropgenedb.cirad.fr/' },
+ { label: 'VIB', url: 'http://pippa.psb.ugent.be' },
+ { label: 'IBET', url: 'https://biodata.pt' }
]
}
diff --git a/frontend/src/environments/environment.ts b/frontend/src/environments/environment.ts
index 8789a59021563c54819f81169b262e9cc72bc61b..081a6813fd51e32e8e0d9bb72186227c57adeb3f 100644
--- a/frontend/src/environments/environment.ts
+++ b/frontend/src/environments/environment.ts
@@ -7,7 +7,6 @@ export const environment = {
navbar: {
title: 'GnpIS Plant Data Search',
links: [
- { label: 'INRA', url: 'http://www.inra.fr/' },
{
label: 'URGI',
url: '#',
@@ -17,52 +16,10 @@ export const environment = {
{ label: 'About us', url: 'https://urgi.versailles.inra.fr/About-us' }
]
},
- {
- label: 'Taxon/Germplasm',
- url: '#',
- subMenu: [
- { label: 'Taxon', url: 'https://urgi.versailles.inra.fr/siregal/common/taxon/form.do' },
- { label: 'Accession Simple', url: 'https://urgi.versailles.inra.fr/gnpis-core' },
- { label: 'Accession passport', url: 'https://urgi.versailles.inra.fr/siregal/siregal/accessionForm.do' },
- { label: 'Collections CRB', url: 'https://urgi.versailles.inra.fr/siregal/siregal/grc.do' },
- ]
- },
- { label: 'Phenotyping', url: 'https://urgi.versailles.inra.fr/ephesis/ephesis/viewer.do' },
- {
- label: 'Polymorphism',
- url: '#',
- subMenu: [
- { label: 'Genotyping', url: 'https://urgi.versailles.inra.fr/GnpSNP/snp/genotyping/form.do' },
- { label: 'SNP Discovery', url: 'https://urgi.versailles.inra.fr/GnpSNP/snp/welcome.do' },
- ]
- },
- { label: 'Association', url: 'https://urgi.versailles.inra.fr/association/association/viewer.do#form' },
- {
- label: 'Map/Marker/QTL',
- url: '#',
- subMenu: [
- { label: 'Map', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/searchMap.do' },
- { label: 'Loci', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/loci/queryLociSelect.do' },
- { label: 'QTL', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/qtl/queryQtlSelect.do' },
- { label: 'MetaQTLs', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/metaqtl/form.do' },
- { label: 'Marker', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/marker/markerForm.do' },
- { label: 'Pool', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/pool/poolForm.do' },
- { label: 'Traits', url: 'https://urgi.versailles.inra.fr/GnpMap/mapping/queryTraitSelect.do' },
- { label: 'Biomercator', url: 'https://urgi.versailles.inra.fr/Tools/BioMercator-V4' },
- ]
- },
- { label: 'Genomes', url: 'https://urgi.versailles.inra.fr/Data/Genome/Genome-data-access' },
- { label: 'Synteny', url: 'https://urgi.versailles.inra.fr/synteny/synteny/viewer.do#dataset' },
- {
- label: 'Sequence',
- url: '#',
- subMenu: [
- { label: 'Sequence', url: 'https://urgi.versailles.inra.fr/sequence/sequence/sequence/form.do' },
- { label: 'Experiment', url: 'https://urgi.versailles.inra.fr/sequence/sequence/experiment/form.do' },
- { label: 'Analysis', url: 'https://urgi.versailles.inra.fr/sequence/sequence/analysis/form.do' },
- { label: 'Project', url: 'https://urgi.versailles.inra.fr/sequence/sequence/project/form.do' },
- ]
- }
+ { label: 'GNPIS', url: 'https://urgi.versailles.inra.fr/gnpis/' },
+ { label: 'CIRAD', url: 'http://tropgenedb.cirad.fr/' },
+ { label: 'VIB', url: 'http://pippa.psb.ugent.be' },
+ { label: 'IBET', url: 'https://biodata.pt' }
]
}
diff --git a/frontend/src/styles.scss b/frontend/src/styles.scss
index b7abb8b9a3a24e6a862fa5c1e9d3e4095ccebd11..e5b4643c3c14eaff971818c3d64e406d650b5482 100644
--- a/frontend/src/styles.scss
+++ b/frontend/src/styles.scss
@@ -10,6 +10,39 @@ $fa-font-path: '~font-awesome/fonts';
}
}
-a {
- text-decoration: underline;
+h3 {
+ font-weight: bold;
+ color: #0f6191;
+}
+
+.card-section-body {
+ border: 2px solid rgb(195, 214, 226);
+ border-top-width: 0px;
+ border-bottom-left-radius: 0.25rem;
+ border-bottom-right-radius: 0.25rem;
+}
+
+.row-sep {
+ border-top: 1px solid #f0f0f0;
+}
+
+.row-sep .row-sep:first-of-type {
+ border: none;
+}
+
+.content-overflow {
+ max-height: 175px;
+ overflow-y: auto;
+}
+
+.content-overflow-big {
+ max-height: 275px;
+ overflow: auto;
+}
+
+.display-spinner-front {
+ position: absolute;
+ top: 70px;
+ left: 720px;
+ background-color: #F9F9F9;
}
diff --git a/frontend/src/tslint.json b/frontend/src/tslint.json
index 9a8fed218220e47daab1f3733704ab4ad76f4373..7e545ab7d80894dd3456be1fee601237e43b7bff 100644
--- a/frontend/src/tslint.json
+++ b/frontend/src/tslint.json
@@ -15,7 +15,7 @@
],
"template-cyclomatic-complexity": [
true,
- 260
+ 10
]
}
}