Merge branch 'feat/taxon_ids' into 'master'

Create popup for taxon information. Remove static URL. Refactor institutes popups. GNP-5096

See merge request urgi-is/gpds!19

backend/src/main/java/fr/inra/urgi/gpds/domain/data/germplasm/ExtendedGermplasm.java

@@ -20,6 +20,9 @@ public interface ExtendedGermplasm extends BrapiGermplasm, GnpISInternal {
     @JsonView(JSONView.GnpISFields.class)
     List<String> getTaxonCommonNames();
 
+    @JsonView(JSONView.GnpISFields.class)
+    String getTaxonComment();
+
     @JsonView(JSONView.GnpISFields.class)
     String getGeneticNature();
 

backend/src/main/java/fr/inra/urgi/gpds/domain/data/germplasm/GermplasmVO.java

@@ -55,6 +55,7 @@ public class GermplasmVO
 
     private List<String> taxonSynonyms;
     private List<String> taxonCommonNames;
+    private String taxonComment;
     private String geneticNature;
     private String comment;
     private PhotoVO photo;
@@ -354,6 +355,15 @@ public class GermplasmVO
         this.taxonCommonNames = taxonCommonNames;
     }
 
+    @Override
+    public String getTaxonComment() {
+        return taxonComment;
+    }
+
+    public void setTaxonComment(String taxonComment) {
+        this.taxonComment = taxonComment;
+    }
+
     @Override
     public String getGeneticNature() {
         return geneticNature;

backend/src/main/java/fr/inra/urgi/gpds/domain/data/germplasm/Photo.java

@@ -8,10 +8,10 @@ import fr.inra.urgi.gpds.domain.JSONView;
  */
 public interface Photo {
     @JsonView(JSONView.GnpISFields.class)
-    String getFileName();
+    String getFile();
 
     @JsonView(JSONView.GnpISFields.class)
-    String getThumbnailFileName();
+    String getThumbnailFile();
 
     @JsonView(JSONView.GnpISFields.class)
     String getPhotoName();

backend/src/main/java/fr/inra/urgi/gpds/domain/data/germplasm/PhotoVO.java

@@ -6,28 +6,28 @@ public class PhotoVO implements Serializable, Photo {
 
     private static final long serialVersionUID = -4993890419772211643L;
 
-    private String fileName;
-    private String thumbnailFileName;
+    private String file;
+    private String thumbnailFile;
     private String photoName;
     private String description;
     private String copyright;
 
     @Override
-    public String getFileName() {
-        return fileName;
+    public String getFile() {
+        return file;
     }
 
-    public void setFileName(String fileName) {
-        this.fileName = fileName;
+    public void setFile(String file) {
+        this.file = file;
     }
 
     @Override
-    public String getThumbnailFileName() {
-        return thumbnailFileName;
+    public String getThumbnailFile() {
+        return thumbnailFile;
     }
 
-    public void setThumbnailFileName(String thumbnailFileName) {
-        this.thumbnailFileName = thumbnailFileName;
+    public void setThumbnailFile(String thumbnailFile) {
+        this.thumbnailFile = thumbnailFile;
     }
 
     @Override

frontend/src/app/brapi.service.spec.ts

@@ -291,6 +291,7 @@ describe('BrapiService', () => {
         genusSpeciesSubtaxa: null,
         taxonSynonyms: ['pomme', 'api'],
         taxonCommonNames: ['pomme', 'api'],
+        taxonComment: null,
         geneticNature: null,
         comment: null,
         photo: null,

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

@@ -177,6 +177,7 @@ describe('GermplasmCardComponent', () => {
         genusSpeciesSubtaxa: null,
         taxonSynonyms: ['pomme', 'api'],
         taxonCommonNames: ['pomme', 'api'],
+        taxonComment: null,
         geneticNature: null,
         comment: null,
         photo: null,

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

@@ -2,7 +2,7 @@ import { Component, OnInit } from '@angular/core';
 import { ActivatedRoute, NavigationEnd, Router } from '@angular/router';
 import { BrapiService } from '../brapi.service';
 import { GnpisService } from '../gnpis.service';
-import { BrapiAttributeData, BrapiGermplasmPedigree, BrapiLocation } from '../models/brapi.model';
+import { BrapiAttributeData, BrapiGermplasmPedigree, BrapiLocation, BrapiTaxonIds } from '../models/brapi.model';
 import { Children, Germplasm, Site } from '../models/gnpis.model';
 import { DataDiscoverySource } from '../models/data-discovery.model';
 
@@ -29,6 +29,12 @@ export class GermplasmCardComponent implements OnInit {
         });
     }
 
+    NCBI_URL = 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=';
+    THEPLANTLIST_URL = 'http://www.theplantlist.org/tpl1.1/record/';
+    TAXREF_URL = 'https://inpn.mnhn.fr/espece/cd_nom/';
+    CATALOGUEOFLIFE_URL = 'http://www.catalogueoflife.org/col/details/species/id/';
+    taxonIdsWithURL: BrapiTaxonIds[] = [];
+
     germplasmGnpis: Germplasm;
     germplasmPedigree: BrapiGermplasmPedigree;
     germplasmProgeny: Children[];
@@ -36,20 +42,14 @@ export class GermplasmCardComponent implements OnInit {
     germplasmLocations: BrapiLocation[] = [];
     germplasmId: string;
     germplasmPuid: string;
+    germplasmTaxon: string;
+    germplasmTaxonAuthor: string;
     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;
 
-
     ngOnInit() {
-
         this.germplasmId = this.route.snapshot.queryParams.id;
         this.germplasmPuid = this.route.snapshot.queryParams.pui;
 
@@ -101,6 +101,7 @@ export class GermplasmCardComponent implements OnInit {
                 // Get germplasm source
                 const sourceURI = germplasmGnpis['schema:includedInDataCatalog'];
                 this.getGermplasmSource(sourceURI);
+                this.getTaxon(germplasmGnpis);
                 this.reformatData(germplasmGnpis);
             });
         return germplasm$;
@@ -124,6 +125,24 @@ export class GermplasmCardComponent implements OnInit {
         }
     }
 
+    getTaxon(germplasmGnpis) {
+        if (germplasmGnpis.genusSpeciesSubtaxa) {
+            this.germplasmTaxon = germplasmGnpis.genusSpeciesSubtaxa;
+            this.germplasmTaxonAuthor = germplasmGnpis.subtaxaAuthority;
+        } else if (germplasmGnpis.genusSpecies) {
+            this.germplasmTaxon = germplasmGnpis.genusSpecies;
+            this.germplasmTaxonAuthor = germplasmGnpis.speciesAuthority;
+        } else if (germplasmGnpis.subtaxa) {
+            this.germplasmTaxon = germplasmGnpis.genus + ' ' + germplasmGnpis.species + ' ' + germplasmGnpis.subtaxa;
+            this.germplasmTaxonAuthor = germplasmGnpis.subtaxaAuthority;
+        } else if (germplasmGnpis.species) {
+            this.germplasmTaxon = germplasmGnpis.genus + ' ' + germplasmGnpis.species;
+            this.germplasmTaxonAuthor = germplasmGnpis.speciesAuthority;
+        } else {
+            this.germplasmTaxon = germplasmGnpis.genus;
+            this.germplasmTaxonAuthor = '';
+        }
+    }
 
     reformatData(germplasmGnpis) {
         if (germplasmGnpis.children) {
@@ -133,10 +152,13 @@ export class GermplasmCardComponent implements OnInit {
             this.germplasmGnpis.donors.sort(this.compareDonorInstitutes);
         }
         if (germplasmGnpis.collection) {
-            this.germplasmGnpis.collection.sort(this.compareCollectionPanel);
+            this.germplasmGnpis.collection.sort(this.compareCollectionPopulationPanel);
+        }
+        if (germplasmGnpis.population) {
+            this.germplasmGnpis.population.sort(this.compareCollectionPopulationPanel);
         }
         if (this.germplasmGnpis.panel) {
-            this.germplasmGnpis.panel.sort(this.compareCollectionPanel);
+            this.germplasmGnpis.panel.sort(this.compareCollectionPopulationPanel);
         }
         if (this.germplasmGnpis.collectingSite) {
             this.siteToBrapiLocation(this.germplasmGnpis.collectingSite);
@@ -149,9 +171,11 @@ export class GermplasmCardComponent implements OnInit {
                 this.siteToBrapiLocation(site);
             }
         }
+        if (this.germplasmGnpis.taxonIds && this.germplasmGnpis.taxonIds.length > 0) {
+            this.addRefURL(this.germplasmGnpis.taxonIds);
+        }
     }
 
-
     siteToBrapiLocation(site: Site) {
         if (site && site.siteId && site.latitude && site.longitude) {
             this.germplasmLocations.push({
@@ -164,6 +188,23 @@ export class GermplasmCardComponent implements OnInit {
         }
     }
 
+    addRefURL(taxonIds: BrapiTaxonIds[]) {
+        for (const taxonId of taxonIds) {
+            if (taxonId.sourceName === 'NCBI') {
+                taxonId.url = this.NCBI_URL + taxonId.taxonId;
+            } else if (taxonId.sourceName === 'ThePlantList') {
+                taxonId.url = this.THEPLANTLIST_URL + taxonId.taxonId;
+            } else if (taxonId.sourceName === 'TAXREF') {
+                taxonId.url = this.TAXREF_URL + taxonId.taxonId;
+            } else if (taxonId.sourceName === 'CatalogueOfLife') {
+                taxonId.url = this.CATALOGUEOFLIFE_URL + taxonId.taxonId;
+            } else {
+                taxonId.url = null;
+            }
+            this.taxonIdsWithURL.push(taxonId);
+        }
+    }
+
     // TODO: use a generic function to get path in object (or null if non-existent)
     checkProgeny() {
         return (this.germplasmProgeny
@@ -189,7 +230,6 @@ export class GermplasmCardComponent implements OnInit {
         );
     }
 
-
     checkCollectorInstituteObject() {
         return (
             this.germplasmGnpis.collector
@@ -209,10 +249,8 @@ export class GermplasmCardComponent implements OnInit {
             );
     }
 
-    checkOriginCollecting() {
-
-        return (this.germplasmGnpis.originSite && this.germplasmGnpis.originSite.siteName)
-            || (this.germplasmGnpis.collectingSite && this.germplasmGnpis.collectingSite.siteName)
+    checkCollecting() {
+        return (this.germplasmGnpis.collectingSite && this.germplasmGnpis.collectingSite.siteName)
             || (this.checkCollectorInstituteObject() || this.checkCollectorInstituteFields());
     }
 
@@ -236,7 +274,7 @@ export class GermplasmCardComponent implements OnInit {
         return 0;
     }
 
-    compareCollectionPanel(a, b) {
+    compareCollectionPopulationPanel(a, b) {
         if (a.name < b.name) {
             return -1;
         }

frontend/src/app/gnpis.service.spec.ts

@@ -98,6 +98,7 @@ describe('GnpisService', () => {
         genusSpeciesSubtaxa: null,
         taxonSynonyms: ['pomme', 'api'],
         taxonCommonNames: ['pomme', 'api'],
+        taxonComment: null,
         geneticNature: null,
         comment: null,
         photo: null,

frontend/src/app/models/brapi.model.ts

@@ -139,6 +139,7 @@ export interface BrapiGermplasm extends BrapiHasDocumentationURL {
 export interface BrapiTaxonIds {
     sourceName: string;
     taxonId: string;
+    url: string;
 }
 
 export interface BrapiDonor {

frontend/src/app/models/gnpis.model.ts

@@ -5,6 +5,7 @@ export interface Germplasm extends BrapiGermplasm {
     genusSpeciesSubtaxa: string;
     taxonSynonyms: string[];
     taxonCommonNames: string[];
+    taxonComment: string;
     geneticNature: string;
     comment: string;
     photo: Photo;
@@ -57,9 +58,9 @@ export interface GermplasmInstitute extends Institute {
 export interface Photo {
     copyright: string;
     description: string;
-    fileName: string;
+    file: string;
     photoName: string;
-    thumbnailFileName: string;
+    thumbnailFile: string;
 
 }
 

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

@@ -248,7 +248,6 @@
     </ng-template>
   </gpds-card-section>
 
-
   <!--XRefs part -->
   <gpds-xrefs [xrefId]="study.studyDbId"></gpds-xrefs>
 </ng-container>

frontend/src/tslint.json

@@ -15,7 +15,7 @@
     ],
     "template-cyclomatic-complexity": [
       true,
-      10
+      11
     ]
   }
 }

frontend/tslint.json

@@ -159,7 +159,7 @@
     "template-conditional-complexity": true,
     "template-cyclomatic-complexity": [
       true,
-      10
+      11
     ],
     "templates-no-negated-async": true,
     "use-host-property-decorator": true,