refactor: Change the navbar logo to URGI logo. Change the links on the navbar....

refactor: Change the navbar logo to URGI logo. Change the links on the navbar. Add logo on germplasm and site cards and use GnpIS logo for GnpIS source.  Minor fixes. GNP-5490

backend/src/main/resources/application.yml

@@ -21,17 +21,19 @@ 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=
+  gnpis-legacy-url:
+    https://urgi.versailles.inra.fr/
+
+  siregal-files-url:
+    /files/siregal/images/
 
   # Provides access to user group WS used to query private data ES aliases
   security-user-group-ws-url:

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",
+      "schema:image": "./logos/GnpIS.png"
     },
     {
       "@type": "schema:DataCatalog",

frontend/src/app/app-routing.module.ts

@@ -9,11 +9,7 @@ export const routes: Routes = [
     { path: 'studies/:id', component: StudyCardComponent },
     { path: 'sites/:id', component: SiteCardComponent },
     { path: '', component: ResultPageComponent },
-    {
-        path: 'germplasm',
-        component: GermplasmCardComponent,
-        runGuardsAndResolvers: 'paramsOrQueryParamsChange'
-    }
+    { path: 'germplasm', component: GermplasmCardComponent }
 ];
 
 @NgModule({

frontend/src/app/app.component.html

 <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>

frontend/src/app/card-row/card-row.component.html

-<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 }}

frontend/src/app/form/form.component.scss

@@ -6,10 +6,6 @@ label {
   }
 }
 
-.nav-link {
-  text-decoration: none;
-}
-
 .nav-tabs {
   .nav-link.active {
     font-weight: bold;

frontend/src/app/germplasm-card/germplasm-card.component.html

@@ -220,6 +220,29 @@
             [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]="germplasmGnpis.documentationURL">
+            <ng-template>
+              <a target="_blank" [href]="germplasmGnpis.documentationURL">
+                Link to this study on source
+              </a>
+            </ng-template>
+          </gpds-card-row>
+
+
+
           <gpds-card-row
             label="Accession synonyms"
             [test]="germplasmGnpis.synonyms && germplasmGnpis.synonyms.length > 0">
@@ -452,7 +475,7 @@
   </gpds-card-section>
 
   <gpds-card-section
-    header="Donation"
+    header="Donor"
     [test]="germplasmGnpis.donors && germplasmGnpis.donors.length > 0">
     <ng-template>
       <gpds-card-table
@@ -532,7 +555,7 @@
   </gpds-card-section>
 
   <gpds-card-section
-    header="Distribution"
+    header="Distributor"
     [test]="germplasmGnpis.distributors && germplasmGnpis.distributors.length>0">
     <ng-template>
 

frontend/src/app/germplasm-card/germplasm-card.component.spec.ts

@@ -16,6 +16,7 @@ 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 {
     BrapiGermplasmAttributes,
     BrapiGermplasmPedigree,
@@ -57,7 +58,8 @@ describe('GermplasmCardComponent', () => {
     const gnpisService = jasmine.createSpyObj(
         'GnpisService', [
             'germplasm',
-            'germplasmByPuid'
+            'germplasmByPuid',
+            'getSource'
         ]
     );
 
@@ -200,6 +202,15 @@ describe('GermplasmCardComponent', () => {
         population: [gnpisGermplasmSet]
     };
 
+    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],
@@ -228,6 +239,7 @@ describe('GermplasmCardComponent', () => {
 
     gnpisService.germplasm.and.returnValue(of(germplasmTest));
     gnpisService.germplasmByPuid.and.returnValue(of(germplasmTest));
+    gnpisService.getSource.and.returnValue(of(source));
     /*brapiService.germplasmProgeny.and.returnValue(of(brapiGermplasmProgeny));*/
     brapiService.germplasmPedigree.and.returnValue(of(brapiGermplasmPedigree));
     brapiService.germplasmAttributes.and.returnValue(of(brapiGermplasmAttributes));
@@ -244,8 +256,8 @@ describe('GermplasmCardComponent', () => {
             expect(tester.cardHeader[1]).toContainText('Holding');
             expect(tester.cardHeader[2]).toContainText('Collecting');
             expect(tester.cardHeader[3]).toContainText('Breeder');
-            expect(tester.cardHeader[4]).toContainText('Donation');
-            expect(tester.cardHeader[5]).toContainText('Distribution');
+            expect(tester.cardHeader[4]).toContainText('Donor');
+            expect(tester.cardHeader[5]).toContainText('Distributor');
             expect(tester.cardHeader[6]).toContainText('Evaluation Data');
         });
     }));

frontend/src/app/germplasm-card/germplasm-card.component.ts

@@ -4,6 +4,7 @@ import { BrapiService } from '../brapi.service';
 import { GnpisService } from '../gnpis.service';
 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',
@@ -35,6 +36,7 @@ export class GermplasmCardComponent implements OnInit {
     germplasmLocations: BrapiLocation[] = [];
     germplasmId: string;
     germplasmPuid: string;
+    germplasmSource: DataDiscoverySource;
     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';
@@ -90,36 +92,73 @@ export class GermplasmCardComponent implements OnInit {
             germplasm$
                 .then(germplasmGnpis => {
                     this.germplasmGnpis = 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);
-                    }
-                    this.siteToBrapiLocation(this.germplasmGnpis.collectingSite);
-                    this.siteToBrapiLocation(this.germplasmGnpis.originSite);
-                    for (const site of this.germplasmGnpis.evaluationSites) {
-                        this.siteToBrapiLocation(site);
-                    }
+                    // Get germplasm source
+                    const sourceURI = germplasmGnpis['schema:includedInDataCatalog'];
+                    this.getGermplasmSource(sourceURI);
+                    this.reformatData(germplasmGnpis);
                 });
         } else {
             germplasm$ = this.gnpisService.germplasmByPuid(pui).toPromise();
             germplasm$
                 .then(germplasmGnpis => {
                     this.germplasmGnpis = germplasmGnpis;
+                    // Get germplasm source
+                    const sourceURI = germplasmGnpis['schema:includedInDataCatalog'];
+                    this.getGermplasmSource(sourceURI);
+                    this.reformatData(germplasmGnpis);
                 });
         }
         return germplasm$;
     }
 
+    // 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.siteId && site.latitude && site.longitude) {
+        if (site && site.siteId && site.latitude && site.longitude) {
             this.germplasmLocations.push({
                 locationDbId: site.siteId,
                 locationName: site.siteName,

frontend/src/app/map/map.component.ts

@@ -20,7 +20,6 @@ export class MapComponent implements OnInit {
 
         this.removeEmptyLocations(this.locations);
         if (this.curatedLocationList.length > 0) {
-            const container = L.DomUtil.get('map');
             const map = L.map('map');
 
             // initialize map centered on the first site

frontend/src/app/navbar/navbar.component.html

-<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"/>

frontend/src/app/site-card/site-card.component.html

@@ -16,6 +16,27 @@
     <ng-template>
       <div class="card-body card-section-body">
 
+        <gpds-card-row
+          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.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
           label="Abbreviation"
           [value]="location.abbreviation">

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 ');

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() {
@@ -30,6 +32,22 @@ export class SiteCardComponent implements OnInit {
                     if (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;
                 }
             );

frontend/src/app/study-card/study-card.component.html

@@ -45,7 +45,7 @@
           label="Data source"
           [test]="studySource && study.documentationURL">
           <ng-template>
-            <a target="_blank" *ngIf="study.documentationURL" [href]="study.documentationURL">
+            <a target="_blank" [href]="study.documentationURL">
               Link to this study on {{ studySource["schema:identifier"] }}
             </a>
           </ng-template>
@@ -102,7 +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>
@@ -159,7 +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>
@@ -189,7 +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>

frontend/src/app/study-card/study-card.component.ts

@@ -37,7 +37,8 @@ export class StudyCardComponent implements OnInit {
                 .then(response => {
                     this.study = response.result;
                     if (this.study.contacts) {
-                        this.study.contacts.sort(this.compareContacts);
+                        this.study.contacts.sort((var1, var2) =>
+                            var1.name.localeCompare(var2.name));
                     }
 
                     this.additionalInfos = [];
@@ -64,17 +65,25 @@ export class StudyCardComponent implements OnInit {
                                 });
                         }
                         if (this.studyDataset) {
-                            this.studyDataset.sort(this.compareTrials);
+                            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);
                         source$
                             .subscribe(src => {
-                                console.log(src);
+                                this.studySource = src;
+                            });
+                    } else {
+                        const urgiURI = 'https://urgi.versailles.inra.fr';
+                        const source$ = this.gnpisService.getSource(urgiURI);
+                        source$
+                            .subscribe(src => {
                                 this.studySource = src;
                             });
                     }
@@ -84,14 +93,16 @@ export class StudyCardComponent implements OnInit {
             const variable$ = this.brapiService.studyObservationVariables(studyDbId).toPromise();
             variable$
                 .then(response => {
-                    this.studyObservationVariables = response.result.data.sort(this.compareVariables);
+                    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.sort(this.compareStudyGermplasm);
+                    this.studyGermplasms = studyGermplasm.result.data.sort((var1, var2) =>
+                        var1.germplasmName.localeCompare(var2.germplasmName));
                 });
 
             this.loaded = Promise.all([study$, variable$, germplasm$]);
@@ -105,44 +116,4 @@ export class StudyCardComponent implements OnInit {
     isNotURN(pui: string) {
         return !(pui.substring(0, 3) === 'urn');
     }
-
-    compareTrials(a, b) {
-        if (a.trialName < b.trialName) {
-            return -1;
-        }
-        if (a.trialName > b.trialName) {
-            return 1;
-        }
-        return 0;
-    }
-
-    compareStudyGermplasm(a, b) {
-        if (a.germplasmName < b.germplasmName) {
-            return -1;
-        }
-        if (a.germplasmName > b.germplasmName) {
-            return 1;
-        }
-        return 0;
-    }
-
-    compareVariables(a, b) {
-        if (a.observationVariableDbId < b.observationVariableDbId) {
-            return -1;
-        }
-        if (a.observationVariableDbId > b.observationVariableDbId) {
-            return 1;
-        }
-        return 0;
-    }
-
-    compareContacts(a, b) {
-        if (a.name < b.name) {
-            return -1;
-        }
-        if (a.name > b.name) {
-            return 1;
-        }
-        return 0;
-    }
 }

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: '#',
@@ -17,34 +16,10 @@ export const environment = {
                     { label: 'About us', url: 'https://urgi.versailles.inra.fr/About-us' }
                 ]
             },
-            {
-                label: 'Genomes & Synteny',
-                url: '#',
-                subMenu: [
-                    { 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' }
-                ]
-            },