Correct test bugs after rebase. Linting corrections.

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

@@ -4,8 +4,8 @@ import { ResultPageComponent } from './result-page/result-page.component';
 import { GermplasmCardComponent } from './germplasm-card/germplasm-card.component';
 import { StudyCardComponent } from './study-card/study-card.component';
 import { SiteCardComponent } from './site-card/site-card.component';
-import { MarkdownPageComponent } from "./markdown-page/markdown-page.component";
-import { environment } from "../environments/environment";
+import { MarkdownPageComponent } from './markdown-page/markdown-page.component';
+import { environment } from '../environments/environment';
 
 export const routes: Routes = [
     { path: 'studies/:id', component: StudyCardComponent },

frontend/src/app/app.module.ts

@@ -26,8 +26,8 @@ import { MomentModule } from 'ngx-moment';
 import { XrefsComponent } from './xrefs/xrefs.component';
 import { CoordinatesModule } from 'angular-coordinates';
 import { CardGenericDocumentComponent } from './card-generic-document/card-generic-document.component';
-import { MarkdownModule, MarkedOptions, MarkedRenderer } from "ngx-markdown";
-import { MarkdownPageComponent } from "./markdown-page/markdown-page.component";
+import { MarkdownModule, MarkedOptions, MarkedRenderer } from 'ngx-markdown';
+import { MarkdownPageComponent } from './markdown-page/markdown-page.component';
 
 @NgModule({
     declarations: [

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

@@ -4,7 +4,7 @@ import { BrapiService } from '../brapi.service';
 import { GnpisService } from '../gnpis.service';
 import { BrapiAttributeData, BrapiGermplasmPedigree, BrapiLocation, BrapiTaxonIds } from '../models/brapi.model';
 import { Children, Germplasm, Site } from '../models/gnpis.model';
-import { environment } from "../../environments/environment";
+import { environment } from '../../environments/environment';
 
 @Component({
     selector: 'faidare-germplasm-card',
@@ -21,7 +21,7 @@ export class GermplasmCardComponent implements OnInit {
                 private route: ActivatedRoute) {
     }
 
-   taxonIdsWithURL: BrapiTaxonIds[] = [];
+    taxonIdsWithURL: BrapiTaxonIds[] = [];
     germplasmGnpis: Germplasm;
     germplasmPedigree: BrapiGermplasmPedigree;
     germplasmProgeny: Children[];
@@ -141,9 +141,9 @@ export class GermplasmCardComponent implements OnInit {
     addRefURL(taxonIds: BrapiTaxonIds[]) {
         for (const taxonId of taxonIds) {
             if (environment.taxaLinks[taxonId.sourceName]) {
-                 taxonId.url = environment.taxaLinks[taxonId.sourceName] + taxonId.taxonId;
+                taxonId.url = environment.taxaLinks[taxonId.sourceName] + taxonId.taxonId;
             } else {
-                 taxonId.url = null;
+                taxonId.url = null;
             }
             this.taxonIdsWithURL.push(taxonId);
         }

frontend/src/app/markdown-page/markdown-page.component.spec.ts

@@ -2,9 +2,9 @@ import { async, ComponentFixture, TestBed } from '@angular/core/testing';
 import { NO_ERRORS_SCHEMA } from '@angular/core';
 
 import { MarkdownPageComponent } from './markdown-page.component';
-import { ActivatedRoute } from "@angular/router";
-import { environment } from "../../environments/environment";
-import { of } from "rxjs";
+import { ActivatedRoute } from '@angular/router';
+import { environment } from '../../environments/environment';
+import { of } from 'rxjs';
 
 describe('MarkdownPageComponent', () => {
     let component: MarkdownPageComponent;

frontend/src/app/markdown-page/markdown-page.component.ts

 import { Component, OnInit } from '@angular/core';
-import {ActivatedRoute} from "@angular/router";
+import { ActivatedRoute } from '@angular/router';
 
 @Component({
-  selector: 'dd-about',
-  templateUrl: './markdown-page.component.html',
-  styleUrls: ['./markdown-page.component.scss']
+    selector: 'faidare-markdown',
+    templateUrl: './markdown-page.component.html',
+    styleUrls: ['./markdown-page.component.scss']
 })
 export class MarkdownPageComponent implements OnInit {
 
-  mdFile: string = "";
+    mdFile = '';
 
-  constructor(private route: ActivatedRoute) {
-  }
+    constructor(private route: ActivatedRoute) {
+    }
 
-  ngOnInit() {
-      this.route.data.subscribe(
-          value => this.mdFile = value.mdFile);
-  }
+    ngOnInit() {
+        this.route.data.subscribe(
+            value => this.mdFile = value.mdFile);
+    }
 
-  onLoad(e: any) {
-    // console.log('Into onLoad');
-    // console.log(e);
-  }
+    onLoad(e: any) {
+        // console.log('Into onLoad');
+        // console.log(e);
+    }
 
-  onError(e: any) {
-    console.log('Got error', e);
-  }
+    onError(e: any) {
+        console.log('Got error', e);
+    }
 
 }

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

@@ -39,9 +39,7 @@
             <a class="nav-link d-flex align-items-center dropdown-toggle" ngbDropdownToggle
                role="button"
                aria-haspopup="true"
-               aria-expanded="false">
-              More ...
-            </a>
+               aria-expanded="false">More...</a>
             <div class="dropdown-menu" ngbDropdownMenu>
               <!-- About link -->
               <a class="dropdown-item" routerLink="/about" routerLinkActive="true" title="About">About</a>
@@ -58,7 +56,7 @@
     </div>
     <a class="navbar-brand d-flex align-items-center"
        [href]="navbar.contributor.url" target="_blank">
-      <img src="{{ navbar.contributor.logo }}" alt="{{ navbar.contributor.name }} logo" height="60px"/>
+      <img src="{{ navbar.contributor.logo }}" alt="{{ navbar.contributor.name }} logo" title="{{ navbar.contributor.name }}" height="60px"/>
     </a>
     <div>
       <!--<a *ngIf="displayBackButton"

frontend/src/app/navbar/navbar.component.spec.ts

@@ -27,32 +27,62 @@ class NavbarComponentTester extends ComponentTester<NavbarComponent> {
         return this.element('li').element('a');
     }
 
-    get firstLinkSubLinks() {
-        return this.element('li').elements('a');
+    get providerLinks() {
+        return this.links[1].elements('a');
     }
 
-    get logo() {
-        return this.element('img');
+    get logos() {
+        return this.elements('img');
     }
 }
 
 describe('NavbarComponent', () => {
 
-    beforeEach(() => TestBed.configureTestingModule({
-        declarations: [NavbarComponent]
-    }));
+    const dataSource1: DataDiscoverySource = {
+        '@id': 'urn:source1',
+        '@type': ['schema:DataCatalog'],
+        'schema:name': 'Example source1',
+        'schema:url': 'http://example1.com',
+        'schema:image': 'http://example1.com/logo.png'
+    };
+
+    const dataSource2: DataDiscoverySource = {
+        '@id': 'urn:source2',
+        '@type': ['schema:DataCatalog'],
+        'schema:name': 'Example source2',
+        'schema:url': 'http://example2.com',
+        'schema:image': 'http://example2.com/logo.png'
+    };
+
+    let gnpisService;
+
+    beforeEach(() => {
+        gnpisService = jasmine.createSpyObj(
+            'GnpisService', [
+                'getSource',
+                'suggest'
+            ]
+        );
+        gnpisService.suggest.and.returnValue(of([dataSource1['@id'], dataSource2['@id']]));
+        gnpisService.getSource.withArgs(dataSource1['@id']).and.returnValue(of(dataSource1));
+        gnpisService.getSource.withArgs(dataSource2['@id']).and.returnValue(of(dataSource2));
+
+        TestBed.configureTestingModule({
+            declarations: [NavbarComponent],
+            providers: [
+                { provide: GnpisService, useValue: gnpisService }
+            ]
+        }).compileComponents();
+    });
 
     it('should toggle the class on click', () => {
         const tester = new NavbarComponentTester();
 
         tester.detectChanges();
-
         expect(tester.navBar.classes).toContain('collapse');
 
         tester.toggler.click();
-
         tester.detectChanges();
-
         expect(tester.navBar.classes).not.toContain('collapse');
     });
 
@@ -65,14 +95,7 @@ describe('NavbarComponent', () => {
             title: 'FAIR Data-finder for Agronomic REsearch',
             logo: 'assets/applicationLogo.png',
             links: [
-                {
-                    label: 'Data providers',
-                    url: '#',
-                    subMenu: [
-                        { label: 'GNPIS', url: 'https://urgi.versailles.inra.fr/gnpis/' },
-                        { label: 'URGI', url: 'https://urgi.versailles.inra.fr/' }
-                    ]
-                }
+                { label: 'URGI', url: 'https://urgi.versailles.inra.fr/' }
             ],
             contributor: {
                 name: 'Elixir',
@@ -85,19 +108,29 @@ describe('NavbarComponent', () => {
         expect(gnpisService.suggest).toHaveBeenCalledTimes(1);
         expect(gnpisService.getSource).toHaveBeenCalledTimes(2);
 
-        expect(tester.logo.attr('title')).toBe('FAIR Data-finder for Agronomic REsearch');
+        expect(tester.logos.length).toBe(2);
+        expect(tester.logos.shift().attr('title')).toBe('FAIR Data-finder for Agronomic REsearch');
+        expect(tester.logos.pop().attr('title')).toBe('Elixir');
+
+        expect(tester.links.length).toBe(3);
+        // 'More...' section (containing Help, About, Join and Legal links) added automatically
+        // 'Data providers' section (containing data sources) fetch and added automatically
 
-        expect(tester.links.length - 1).toBe(1);
-        // minus 1 because of More section (containing Help, About, Join and Legal links) added automatically
-        // Two static links + two dynamic links (fetched data sources)
-        //expect(tester.links.length).toBe(4);
+        expect(tester.firstLink.textContent).toBe('URGI');
+        expect(tester.firstLink.attr('href')).toBe('https://urgi.versailles.inra.fr/');
+        expect(tester.firstLink.attr('target')).toBe('_blank');
 
-        expect(tester.firstLink.textContent).toBe('Data providers');
-        expect(tester.firstLinkSubLinks.length -1).toBe(2);
+        expect(tester.providerLinks.length - 1).toBe(2);
         // minus 1 because of the dropdown link
+        expect(tester.providerLinks.shift().textContent).toBe('Data providers');
+        expect(tester.providerLinks.pop().textContent).toBe('Example source2');
+        expect(tester.providerLinks.pop().attr('href')).toBe('http://example2.com');
+        expect(tester.providerLinks.pop().attr('target')).toBe('_blank');
 
-        expect(tester.firstLinkSubLinks.pop().attr('href')).toBe('https://urgi.versailles.inra.fr/');
-        expect(tester.firstLinkSubLinks.pop().textContent).toBe('URGI');
-        expect(tester.firstLinkSubLinks.pop().attr('target')).toBe('_blank');
-    });
-});
+        expect(tester.links[2].element('a').textContent).toBe('More...');
+
+    }));
+
+})
+
+;

frontend/src/app/navbar/navbar.component.ts

@@ -53,6 +53,12 @@ export class NavbarComponent implements OnInit {
     navbar: NavBar = environment.navbar;
     navbarCollapsed = true;
 
+    dataProvider: Link = {
+        label: 'Data providers',
+        url: '#',
+        subMenu: []
+    };
+
     constructor(private gnpisService: GnpisService) {
     }
 
@@ -66,12 +72,13 @@ export class NavbarComponent implements OnInit {
                 flatMap(dataSourceURI => this.gnpisService.getSource(dataSourceURI)),
             )
             .subscribe(dataSource => {
-                // Add each data source to the nav bar links
-                this.navbar.links.push({
+                // Add each data source to the nav bar, under 'Data providers'
+                this.dataProvider.subMenu.push({
                     label: dataSource['schema:name'],
                     url: dataSource['schema:url']
                 });
             });
+        this.navbar.links.push(this.dataProvider);
     }
 
     toggleNavbar() {

frontend/src/environments/environment.prod.ts

@@ -14,16 +14,6 @@ export const environment = {
                     { label: 'News', url: 'https://urgi.versailles.inra.fr/About-us/News' },
                     { label: 'About us', url: 'https://urgi.versailles.inra.fr/About-us' }
                 ]
-            },
-            {
-                label: 'Data providers',
-                url: '#',
-                subMenu: [
-                    { label: 'GNPIS', url: 'https://urgi.versailles.inra.fr/gnpis/' },
-                    { label: 'CIRAD TropGENE', url: 'http://tropgenedb.cirad.fr/' },
-                    { label: 'VIB Pippa', url: 'http://pippa.psb.ugent.be' },
-                    { label: 'IBET BioData', url: 'https://biodata.pt' }
-                ]
             }
         ],
         contributor: {
@@ -38,8 +28,8 @@ export const environment = {
     legalMentionsMdFile: 'assets/legal.md',
     taxaLinks: {
         NCBI: 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=',
-        ThePlantList:'http://www.theplantlist.org/tpl1.1/record/',
+        ThePlantList: 'http://www.theplantlist.org/tpl1.1/record/',
         TAXREF: 'https://inpn.mnhn.fr/espece/cd_nom/',
-        CatalogueOfLife:'http://www.catalogueoflife.org/col/details/species/id/'
+        CatalogueOfLife: 'http://www.catalogueoflife.org/col/details/species/id/'
     }
 };

frontend/src/environments/environment.ts

@@ -17,16 +17,6 @@ export const environment = {
                     { label: 'News', url: 'https://urgi.versailles.inra.fr/About-us/News' },
                     { label: 'About us', url: 'https://urgi.versailles.inra.fr/About-us' }
                 ]
-            },
-            {
-                label: 'Data providers',
-                url: '#',
-                subMenu: [
-                    { label: 'GNPIS', url: 'https://urgi.versailles.inra.fr/gnpis/' },
-                    { label: 'CIRAD TropGENE', url: 'http://tropgenedb.cirad.fr/' },
-                    { label: 'VIB Pippa', url: 'http://pippa.psb.ugent.be' },
-                    { label: 'IBET BioData', url: 'https://biodata.pt' }
-                ]
             }
         ],
         contributor: {
@@ -41,9 +31,9 @@ export const environment = {
     legalMentionsMdFile: 'assets/legal.md',
     taxaLinks: {
         NCBI: 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=',
-        ThePlantList:'http://www.theplantlist.org/tpl1.1/record/',
+        ThePlantList: 'http://www.theplantlist.org/tpl1.1/record/',
         TAXREF: 'https://inpn.mnhn.fr/espece/cd_nom/',
-        CatalogueOfLife:'http://www.catalogueoflife.org/col/details/species/id/'
+        CatalogueOfLife: 'http://www.catalogueoflife.org/col/details/species/id/'
     }
 };