feat: germplasm card

backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java

+package fr.inra.urgi.faidare.web.germplasm;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import fr.inra.urgi.faidare.api.NotFoundException;
+import fr.inra.urgi.faidare.config.FaidareProperties;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmAttributeValue;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiSibling;
+import fr.inra.urgi.faidare.domain.criteria.GermplasmAttributeCriteria;
+import fr.inra.urgi.faidare.domain.criteria.GermplasmGETSearchCriteria;
+import fr.inra.urgi.faidare.domain.data.germplasm.CollPopVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.DonorVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GenealogyVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmAttributeValueVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmInstituteVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.InstituteVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.PhotoVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.PuiNameValueVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.SiblingVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.SimpleVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.SiteVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.TaxonSourceVO;
+import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
+import fr.inra.urgi.faidare.repository.es.GermplasmAttributeRepository;
+import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
+import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.servlet.ModelAndView;
+
+/**
+ * Controller used to display a germplasm card based on its ID.
+ * @author JB Nizet
+ */
+@Controller("webGermplasmController")
+@RequestMapping("/germplasms")
+public class GermplasmController {
+
+    private final GermplasmRepository germplasmRepository;
+    private final FaidareProperties faidareProperties;
+    private final XRefDocumentRepository xRefDocumentRepository;
+    private GermplasmAttributeRepository germplasmAttributeRepository;
+
+    public GermplasmController(GermplasmRepository germplasmRepository,
+                               FaidareProperties faidareProperties,
+                               XRefDocumentRepository xRefDocumentRepository,
+                               GermplasmAttributeRepository germplasmAttributeRepository) {
+        this.germplasmRepository = germplasmRepository;
+        this.faidareProperties = faidareProperties;
+        this.xRefDocumentRepository = xRefDocumentRepository;
+        this.germplasmAttributeRepository = germplasmAttributeRepository;
+    }
+
+    @GetMapping("/{germplasmId}")
+    public ModelAndView get(@PathVariable("germplasmId") String germplasmId) {
+        // GermplasmVO germplasm = germplasmRepository.getById(germplasmId);
+
+        // TODO replace this block by the above commented one
+        GermplasmVO germplasm = createGermplasm();
+
+        if (germplasm == null) {
+            throw new NotFoundException("Germplasm with ID " + germplasmId + " not found");
+        }
+
+        return toModelAndView(germplasm);
+    }
+
+    @GetMapping(params = "pui")
+    public ModelAndView getByPui(@RequestParam("pui") String pui) {
+        GermplasmGETSearchCriteria criteria = new GermplasmGETSearchCriteria();
+        criteria.setGermplasmPUI(Collections.singletonList(pui));
+        List<GermplasmVO> germplasms = germplasmRepository.find(criteria);
+        if (germplasms.size() != 1) {
+            throw new NotFoundException("Germplasm with PUI " + pui + " not found");
+        }
+
+        return toModelAndView(germplasms.get(0));
+    }
+
+    private ModelAndView toModelAndView(GermplasmVO germplasm) {
+        // List<BrapiGermplasmAttributeValue> attributes = getAttributes(germplasm);
+        // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
+        //     XRefDocumentSearchCriteria.forXRefId(site.getLocationDbId()));
+        // PedigreeVO pedigree = getPedigree(germplasm);
+        // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
+        //     XRefDocumentSearchCriteria.forXRefId(germplasm.getGermplasmDbId())
+        // );
+
+        // TODO replace this block by the above commented one
+        List<BrapiGermplasmAttributeValue> attributes = Arrays.asList(
+            createAttribute()
+        );
+        PedigreeVO pedigree = createPedigree();
+        List<XRefDocumentVO> crossReferences = Arrays.asList(
+            createXref("foobar"),
+            createXref("bazbing")
+        );
+
+
+        sortDonors(germplasm);
+        sortPopulations(germplasm);
+        sortCollections(germplasm);
+        sortPanels(germplasm);
+        return new ModelAndView("germplasm",
+                                "model",
+                                new GermplasmModel(
+                                    germplasm,
+                                    faidareProperties.getByUri(germplasm.getSourceUri()),
+                                    attributes,
+                                    pedigree,
+                                    crossReferences
+                                )
+        );
+    }
+
+    private void sortPopulations(GermplasmVO germplasm) {
+        if (germplasm.getPopulation() != null) {
+            germplasm.setPopulation(germplasm.getPopulation()
+                                             .stream()
+                                             .sorted(Comparator.comparing(
+                                                 CollPopVO::getName))
+                                             .collect(Collectors.toList()));
+        }
+    }
+
+    private void sortCollections(GermplasmVO germplasm) {
+        if (germplasm.getCollection() != null) {
+            germplasm.setCollection(germplasm.getCollection()
+                                             .stream()
+                                             .sorted(Comparator.comparing(CollPopVO::getName))
+                                             .collect(Collectors.toList()));
+        }
+    }
+
+    private void sortPanels(GermplasmVO germplasm) {
+        if (germplasm.getPanel() != null) {
+            germplasm.setPanel(germplasm.getPanel()
+                                        .stream()
+                                        .sorted(Comparator.comparing(CollPopVO::getName))
+                                        .collect(Collectors.toList()));
+        }
+    }
+
+    private void sortDonors(GermplasmVO germplasm) {
+        if (germplasm.getDonors() != null) {
+            germplasm.setDonors(germplasm.getDonors()
+                                         .stream()
+                                         .sorted(Comparator.comparing(donor -> donor.getDonorInstitute()
+                                                                                    .getInstituteName()))
+                                         .collect(Collectors.toList()));
+        }
+    }
+
+    private List<BrapiGermplasmAttributeValue> getAttributes(GermplasmVO germplasm) {
+        GermplasmAttributeCriteria criteria = new GermplasmAttributeCriteria();
+        criteria.setGermplasmDbId(germplasm.getGermplasmDbId());
+        return germplasmAttributeRepository.find(criteria)
+            .stream()
+            .flatMap(vo -> vo.getData().stream())
+            .sorted(Comparator.comparing(BrapiGermplasmAttributeValue::getAttributeName))
+            .collect(Collectors.toList());
+    }
+
+    private PedigreeVO getPedigree(GermplasmVO germplasm) {
+        return germplasmRepository.findPedigree(germplasm.getGermplasmDbId());
+    }
+
+    private BrapiGermplasmAttributeValue createAttribute() {
+        GermplasmAttributeValueVO result = new GermplasmAttributeValueVO();
+        result.setAttributeName("A1");
+        result.setValue("V1");
+        return result;
+    }
+
+    private GermplasmVO createGermplasm() {
+        GermplasmVO result = new GermplasmVO();
+
+        result.setGermplasmName("BLE BARBU DU ROUSSILLON");
+        result.setAccessionNumber("1408");
+        result.setSynonyms(Arrays.asList("BLE DU ROUSSILLON", "FRA051:1699", "ROUSSILLON"));
+        PhotoVO photo = new PhotoVO();
+        photo.setPhotoName("Blé du roussillon");
+        photo.setCopyright("INRA, Emmanuelle BOULAT/Lionel BARDY 2012");
+        photo.setThumbnailFile("https://urgi.versailles.inrae.fr/files/siregal/images/accession/CEREALS/thumbnails/thumb_1408_R09_S.jpg");
+        photo.setFile("https://urgi.versailles.inrae.fr/files/siregal/images/accession/CEREALS/1408_R09_S.jpg");
+        result.setPhoto(photo);
+
+        InstituteVO holdingGenBank = new InstituteVO();
+        holdingGenBank.setLogo("https://urgi.versailles.inra.fr/files/siregal/images/grc/inra_brc_en.png");
+        holdingGenBank.setInstituteName("INRA BRC");
+        holdingGenBank.setWebSite("http://google.fr");
+        result.setHoldingGenbank(holdingGenBank);
+
+        result.setBiologicalStatusOfAccessionCode("Traditional cultivar/landrace ");
+        result.setPedigree("LV");
+        SiteVO originSite = new SiteVO();
+        originSite.setSiteId("1234");
+        originSite.setSiteName("Le Moulon");
+        result.setOriginSite(originSite);
+
+        result.setGenus("Genus 1");
+        result.setSpecies("Species 1");
+        result.setSpeciesAuthority("Species Auth");
+        result.setSourceUri("https://urgi.versailles.inrae.fr/gnpis");
+        result.setSubtaxa("Subtaxa 1");
+        result.setGenusSpeciesSubtaxa("Triticum aestivum subsp. aestivum");
+        result.setSubtaxaAuthority("INRAE");
+        result.setTaxonIds(Arrays.asList(createTaxonId(), createTaxonId()));
+        result.setTaxonComment("C'est bon le blé");
+        result.setTaxonCommonNames(Arrays.asList("Blé tendre", "Bread wheat", "Soft wheat"));
+        result.setTaxonSynonyms(Arrays.asList("Blé tendre1", "Bread wheat1", "Soft wheat1"));
+
+        InstituteVO holdingInstitute = new InstituteVO();
+        holdingInstitute.setInstituteName("GDEC - UMR Génétique, Diversité et Ecophysiologie des Céréales");
+        holdingInstitute.setLogo("https://urgi.versailles.inra.fr/files/siregal/images/grc/inra_brc_en.png");
+        holdingInstitute.setWebSite("https://google.fr/q=qsdqsdqsdslqlsdnqlsdqlsdlqskdlqdqlsdqsdqsdqd");
+        holdingInstitute.setInstituteCode("GDEC");
+        holdingInstitute.setInstituteType("Type1");
+        holdingInstitute.setAcronym("G.D.E.C");
+        holdingInstitute.setAddress("Lyon");
+        holdingInstitute.setOrganisation("SAS");
+        result.setHoldingInstitute(holdingInstitute);
+
+        result.setPresenceStatus("Maintained");
+
+        GermplasmInstituteVO collector = new GermplasmInstituteVO();
+        collector.setMaterialType("Fork");
+        collector.setCollectors("Joe, Jack, William, Averell");
+        InstituteVO collectingInstitute = new InstituteVO();
+        collectingInstitute.setInstituteName("Ninja Squad");
+        collector.setInstitute(collectingInstitute);
+        collector.setAccessionNumber("567");
+        result.setCollector(collector);
+
+        result.setCollectingSite(originSite);
+        result.setAcquisitionDate("In the summer");
+
+        GermplasmInstituteVO breeder = new GermplasmInstituteVO();
+        InstituteVO breedingInstitute = new InstituteVO();
+        breedingInstitute.setInstituteName("Microsoft");
+        breeder.setInstitute(breedingInstitute);
+        breeder.setAccessionCreationDate(2015);
+        breeder.setAccessionNumber("678");
+        breeder.setRegistrationYear(2016);
+        breeder.setDeregistrationYear(2019);
+        result.setBreeder(breeder);
+
+        result.setDonors(Arrays.asList(
+            createDonor()
+        ));
+
+        result.setDistributors(Arrays.asList(
+            createDistributor()
+        ));
+
+        result.setChildren(Arrays.asList(createChild(), createChild()));
+
+        result.setGermplasmPUI("germplasmPUI");
+        result.setPopulation(Arrays.asList(createPopulation1(), createPopulation2(), createPopulation3()));
+
+        result.setCollection(Arrays.asList(createCollection()));
+
+        result.setPanel(Arrays.asList(createPanel()));
+
+        return result;
+    }
+
+    private DonorVO createDonor() {
+        DonorVO result = new DonorVO();
+        result.setDonorGermplasmPUI("PUI1");
+        result.setDonationDate(2017);
+        result.setDonorAccessionNumber("3456");
+        result.setDonorInstituteCode("GD46U");
+        InstituteVO institute = new InstituteVO();
+        institute.setInstituteName("Hello");
+        result.setDonorInstitute(institute);
+        return result;
+    }
+
+    private GermplasmInstituteVO createDistributor() {
+        GermplasmInstituteVO result = new GermplasmInstituteVO();
+        InstituteVO institute = new InstituteVO();
+        institute.setInstituteName("Microsoft");
+        result.setInstitute(institute);
+        result.setAccessionNumber("678");
+        result.setDistributionStatus("OK");
+        return result;
+    }
+
+    private PedigreeVO createPedigree() {
+        PedigreeVO result = new PedigreeVO();
+        result.setPedigree("Pedigree 1");
+        result.setParent1DbId("12345");
+        result.setParent1Name("Parent 1");
+        result.setParent1Type("P1");
+        result.setParent2DbId("12346");
+        result.setParent2Name("Parent 2");
+        result.setParent2Type("P2");
+        result.setCrossingPlan("crossing plan 1");
+        result.setCrossingYear("2012");
+        result.setSiblings(Arrays.asList(createBrapiSibling()));
+        return result;
+    }
+
+    private BrapiSibling createBrapiSibling() {
+        SiblingVO sibling = new SiblingVO();
+        sibling.setGermplasmDbId("5678");
+        sibling.setDefaultDisplayName("Sibling 5678");
+        return sibling;
+    }
+
+    private GenealogyVO createChild() {
+        GenealogyVO result = new GenealogyVO();
+        result.setFirstParentName("CP1");
+        result.setSecondParentName("CP2");
+        result.setSibblings(Arrays.asList(createPuiNameValueVO(), createPuiNameValueVO()));
+        return result;
+    }
+
+    private PuiNameValueVO createPuiNameValueVO() {
+        PuiNameValueVO result = new PuiNameValueVO();
+        result.setName("Child 1");
+        result.setPui("pui1");
+        return result;
+    }
+
+    private CollPopVO createPopulation1() {
+        CollPopVO result = new CollPopVO();
+        result.setName("Population 1");
+        result.setType("Pop Type 1");
+        result.setGermplasmCount(3);
+        result.setGermplasmRef(createPuiNameValueVO());
+        return result;
+    }
+
+    private CollPopVO createPopulation2() {
+        CollPopVO result = new CollPopVO();
+        result.setName("Population 2");
+        result.setGermplasmCount(3);
+        PuiNameValueVO puiNameValueVO = createPuiNameValueVO();
+        puiNameValueVO.setPui("germplasmPUI");
+        result.setGermplasmRef(puiNameValueVO);
+        return result;
+    }
+
+    private CollPopVO createPopulation3() {
+        CollPopVO result = new CollPopVO();
+        result.setName("Population 3");
+        result.setGermplasmCount(5);
+        return result;
+    }
+
+    private CollPopVO createCollection() {
+        CollPopVO result = new CollPopVO();
+        result.setName("Collection 1");
+        result.setGermplasmCount(7);
+        return result;
+    }
+
+    private CollPopVO createPanel() {
+        CollPopVO result = new CollPopVO();
+        result.setName("The_panel_1");
+        result.setGermplasmCount(2);
+        return result;
+    }
+
+    private TaxonSourceVO createTaxonId() {
+        TaxonSourceVO result = new TaxonSourceVO();
+        result.setTaxonId("taxon1");
+        result.setSourceName("ThePlantList");
+        return result;
+    }
+
+    private XRefDocumentVO createXref(String name) {
+        XRefDocumentVO xref = new XRefDocumentVO();
+        xref.setName(name);
+        xref.setDescription("A very large description for the xref " + name + " which has way more than 120 characters bla bla bla bla bla bla bla bla bla bla bla bla");
+        xref.setDatabaseName("db_" + name);
+        xref.setUrl("https://google.com");
+        xref.setEntryType("type " + name);
+        return xref;
+    }
+}

backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java

+package fr.inra.urgi.faidare.web.germplasm;
+
+import java.util.List;
+
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmAttributeValue;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmInstituteVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.data.DataSource;
+import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
+import org.apache.logging.log4j.util.Strings;
+
+/**
+ * The model used by the germplasm page
+ * @author JB Nizet
+ */
+public final class GermplasmModel {
+    private final GermplasmVO germplasm;
+    private final DataSource source;
+    private final List<BrapiGermplasmAttributeValue> attributes;
+    private final PedigreeVO pedigree;
+    private final List<XRefDocumentVO> crossReferences;
+
+    public GermplasmModel(GermplasmVO germplasm,
+                          DataSource source,
+                          List<BrapiGermplasmAttributeValue> attributes,
+                          PedigreeVO pedigree,
+                          List<XRefDocumentVO> crossReferences) {
+        this.germplasm = germplasm;
+        this.source = source;
+        this.attributes = attributes;
+        this.pedigree = pedigree;
+        this.crossReferences = crossReferences;
+    }
+
+    public GermplasmVO getGermplasm() {
+        return germplasm;
+    }
+
+    public DataSource getSource() {
+        return source;
+    }
+
+    public List<BrapiGermplasmAttributeValue> getAttributes() {
+        return attributes;
+    }
+
+    public PedigreeVO getPedigree() {
+        return pedigree;
+    }
+
+    public List<XRefDocumentVO> getCrossReferences() {
+        return crossReferences;
+    }
+
+    public String getTaxon() {
+        if (Strings.isNotBlank(this.germplasm.getGenusSpeciesSubtaxa())) {
+            return this.germplasm.getGenusSpeciesSubtaxa();
+        } else if (Strings.isNotBlank(this.germplasm.getGenusSpecies())) {
+            return this.germplasm.getGenusSpecies();
+        } else if (Strings.isNotBlank(this.germplasm.getSubtaxa())) {
+            return this.germplasm.getGenus() + " " + this.germplasm.getSpecies() + " " + this.germplasm.getSubtaxa();
+        } else if (Strings.isNotBlank(this.germplasm.getSpecies())) {
+            return this.germplasm.getGenus() + " " + this.germplasm.getSpecies();
+        } else {
+            return this.germplasm.getGenus();
+        }
+    }
+
+    public String getTaxonAuthor() {
+        if (Strings.isNotBlank(this.germplasm.getGenusSpeciesSubtaxa())) {
+            return this.germplasm.getSubtaxaAuthority();
+        } else if (Strings.isNotBlank(this.germplasm.getGenusSpecies())) {
+            return this.germplasm.getSpeciesAuthority();
+        } else if (Strings.isNotBlank(this.germplasm.getSubtaxa())) {
+            return this.germplasm.getSubtaxaAuthority();
+        } else if (Strings.isNotBlank(this.germplasm.getSpecies())) {
+            return this.germplasm.getSpeciesAuthority();
+        } else {
+            return null;
+        }
+    }
+
+    public boolean isCollecting() {
+        return this.isCollectingSitePresent()
+            || this.isCollectorInstitutePresent()
+            || this.isCollectorIntituteFieldPresent();
+    }
+
+    private boolean isCollectingSitePresent() {
+        return this.germplasm.getCollectingSite() != null && Strings.isNotBlank(this.germplasm.getCollectingSite().getSiteName());
+    }
+
+    private boolean isCollectorInstitutePresent() {
+        return this.germplasm.getCollector() != null &&
+            this.germplasm.getCollector().getInstitute() != null &&
+            Strings.isNotBlank(this.germplasm.getCollector().getInstitute().getInstituteName());
+    }
+
+    private boolean isCollectorIntituteFieldPresent() {
+        GermplasmInstituteVO collector = this.germplasm.getCollector();
+        return (collector != null) &&
+            (Strings.isNotBlank(collector.getAccessionNumber())
+                || collector.getAccessionCreationDate() != null
+                || Strings.isNotBlank(collector.getMaterialType())
+                || Strings.isNotBlank(collector.getCollectors())
+                || collector.getRegistrationYear() != null
+                || collector.getDeregistrationYear() != null
+                || Strings.isNotBlank(collector.getDistributionStatus())
+            );
+    }
+
+    public boolean isBreeding() {
+        GermplasmInstituteVO breeder = this.germplasm.getBreeder();
+        return breeder != null &&
+            ((breeder.getInstitute() != null && Strings.isNotBlank(breeder.getInstitute().getInstituteName())) ||
+                breeder.getAccessionCreationDate() != null ||
+                Strings.isNotBlank(breeder.getAccessionNumber()) ||
+                breeder.getRegistrationYear() != null ||
+                breeder.getDeregistrationYear() != null);
+    }
+
+    public boolean isGenealogyPresent() {
+        return isPedigreePresent() || isProgenyPresent();
+    }
+
+    private boolean isProgenyPresent() {
+        return germplasm.getChildren() != null && !germplasm.getChildren().isEmpty();
+    }
+
+    private boolean isPedigreePresent() {
+        return this.pedigree != null &&
+            (Strings.isNotBlank(this.pedigree.getParent1Name())
+            || Strings.isNotBlank(this.pedigree.getParent2Name())
+            || Strings.isNotBlank(this.pedigree.getCrossingPlan())
+            || Strings.isNotBlank(this.pedigree.getCrossingYear())
+            || Strings.isNotBlank(this.pedigree.getFamilyCode()));
+    }
+}

backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java

@@ -37,7 +37,7 @@ public class SiteController {
     }
 
     @GetMapping("/{siteId}")
-    public ModelAndView site(@PathVariable("siteId") String siteId) {
+    public ModelAndView get(@PathVariable("siteId") String siteId) {
         LocationVO site = locationRepository.getById(siteId);
 
         // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(

backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java

@@ -58,7 +58,7 @@ public class StudyController {
     }
 
     @GetMapping("/{studyId}")
-    public ModelAndView site(@PathVariable("studyId") String studyId) {
+    public ModelAndView get(@PathVariable("studyId") String studyId) {
         StudyDetailVO study = studyRepository.getById(studyId);
 
         // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(

backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareDialect.java

+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import org.springframework.stereotype.Component;
+import org.thymeleaf.dialect.AbstractDialect;
+import org.thymeleaf.dialect.IExpressionObjectDialect;
+import org.thymeleaf.expression.IExpressionObjectFactory;
+
+/**
+ * A thymeleaf dialect allowing to perform various tasks in the template related to Faidare
+ * @author JB Nizet
+ */
+@Component