From 31d52c26843d535e20a7ec06df563a425497b6cc Mon Sep 17 00:00:00 2001
From: jnizet <jb@ninja-squad.com>
Date: Thu, 26 Aug 2021 15:34:25 +0200
Subject: [PATCH 1/2] feat: germplasm card
---
.../web/germplasm/GermplasmController.java | 392 ++++++++++++++++
.../faidare/web/germplasm/GermplasmModel.java | 139 ++++++
.../urgi/faidare/web/site/SiteController.java | 2 +-
.../faidare/web/study/StudyController.java | 2 +-
.../faidare/web/thymeleaf/FaidareDialect.java | 25 ++
.../thymeleaf/FaidareExpressionFactory.java | 33 ++
.../web/thymeleaf/FaidareExpressions.java | 65 +++
.../main/resources/static/assets/style.css | 4 +
.../templates/fragments/institute.html | 34 ++
.../resources/templates/fragments/link.html | 20 +
.../resources/templates/fragments/row.html | 31 +-
.../resources/templates/fragments/source.html | 35 ++
.../resources/templates/fragments/xrefs.html | 5 +
.../main/resources/templates/germplasm.html | 418 ++++++++++++++++++
.../main/resources/templates/layout/main.html | 22 +
.../src/main/resources/templates/site.html | 17 +-
.../src/main/resources/templates/study.html | 16 +-
17 files changed, 1226 insertions(+), 34 deletions(-)
create mode 100644 backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
create mode 100644 backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java
create mode 100644 backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareDialect.java
create mode 100644 backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressionFactory.java
create mode 100644 backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressions.java
create mode 100644 backend/src/main/resources/templates/fragments/institute.html
create mode 100644 backend/src/main/resources/templates/fragments/link.html
create mode 100644 backend/src/main/resources/templates/fragments/source.html
create mode 100644 backend/src/main/resources/templates/germplasm.html
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
new file mode 100644
index 00000000..cf343049
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
@@ -0,0 +1,392 @@
+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;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java
new file mode 100644
index 00000000..8acdf78f
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java
@@ -0,0 +1,139 @@
+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()));
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java
index 1ed29438..151da527 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java
+++ b/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(
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
index 35767b09..ff6aee3b 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
+++ b/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(
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareDialect.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareDialect.java
new file mode 100644
index 00000000..2a02a842
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareDialect.java
@@ -0,0 +1,25 @@
+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
+public class FaidareDialect extends AbstractDialect implements IExpressionObjectDialect {
+
+ private final IExpressionObjectFactory FAIDARE_EXPRESSION_OBJECTS_FACTORY = new FaidareExpressionFactory();
+
+ protected FaidareDialect() {
+ super("faidare");
+ }
+
+ @Override
+ public IExpressionObjectFactory getExpressionObjectFactory() {
+ return FAIDARE_EXPRESSION_OBJECTS_FACTORY;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressionFactory.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressionFactory.java
new file mode 100644
index 00000000..e873375c
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressionFactory.java
@@ -0,0 +1,33 @@
+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import java.util.Collections;
+import java.util.Set;
+
+import org.thymeleaf.context.IExpressionContext;
+import org.thymeleaf.expression.IExpressionObjectFactory;
+
+/**
+ * The object factory for the {@link FaidareDialect}
+ * @author JB Nizet
+ */
+public class FaidareExpressionFactory implements IExpressionObjectFactory {
+ private static final String FAIDARE_EVALUATION_VARIABLE_NAME = "faidare";
+
+ private static final Set<String> ALL_EXPRESSION_OBJECT_NAMES =
+ Collections.singleton(FAIDARE_EVALUATION_VARIABLE_NAME);
+
+ @Override
+ public Set<String> getAllExpressionObjectNames() {
+ return ALL_EXPRESSION_OBJECT_NAMES;
+ }
+
+ @Override
+ public Object buildObject(IExpressionContext context, String expressionObjectName) {
+ return new FaidareExpressions(context.getLocale());
+ }
+
+ @Override
+ public boolean isCacheable(String expressionObjectName) {
+ return true;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressions.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressions.java
new file mode 100644
index 00000000..a9f699de
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressions.java
@@ -0,0 +1,65 @@
+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import java.nio.charset.StandardCharsets;
+import java.text.DecimalFormat;
+import java.util.Base64;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Locale;
+import java.util.Map;
+import java.util.function.Function;
+
+import fr.inra.urgi.faidare.domain.data.germplasm.CollPopVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.TaxonSourceVO;
+import org.apache.logging.log4j.util.Strings;
+
+/**
+ * The actual object offering Faidare helper methods to thymeleaf
+ * @author JB Nizet
+ */
+public class FaidareExpressions {
+
+ private static final Map<String, Function<String, String>> TAXON_ID_URL_FACTORIES_BY_SOURCE_NAME =
+ createTaxonIdUrlFactories();
+
+ private static Map<String, Function<String, String>> createTaxonIdUrlFactories() {
+ Map<String, Function<String, String>> result = new HashMap<>();
+ result.put("NCBI", s -> "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + s);
+ result.put("ThePlantList", s -> "http://www.theplantlist.org/tpl1.1/record/" + s);
+ result.put("TAXREF", s -> "https://inpn.mnhn.fr/espece/cd_nom/" + s);
+ result.put("CatalogueOfLife", s -> "http://www.catalogueoflife.org/col/details/species/id/" + s);
+ return Collections.unmodifiableMap(result);
+ }
+
+ private final Locale locale;
+
+ public FaidareExpressions(Locale locale) {
+ this.locale = locale;
+ }
+
+ public String toSiteParam(String siteId) {
+ return Base64.getUrlEncoder().encodeToString(("urn:URGI/location/" + siteId).getBytes(StandardCharsets.US_ASCII));
+ }
+
+ public String collPopTitle(CollPopVO collPopVO) {
+ return collPopTitle(collPopVO, Function.identity());
+ }
+
+ public String collPopTitleWithoutUnderscores(CollPopVO collPopVO) {
+ return collPopTitle(collPopVO, s -> s.replace('_', ' '));
+ }
+
+ public String taxonIdUrl(TaxonSourceVO taxonSource) {
+ Function<String, String> urlFactory =
+ TAXON_ID_URL_FACTORIES_BY_SOURCE_NAME.get(taxonSource.getSourceName());
+ return urlFactory != null ? urlFactory.apply(taxonSource.getTaxonId()) : null;
+ }
+
+ private String collPopTitle(CollPopVO collPopVO, Function<String, String> nameTransformer) {
+ if (Strings.isBlank(collPopVO.getType())) {
+ return nameTransformer.apply(collPopVO.getName());
+ } else {
+ return nameTransformer.apply(collPopVO.getName()) + " (" + collPopVO.getType() + ")";
+ }
+ }
+}
diff --git a/backend/src/main/resources/static/assets/style.css b/backend/src/main/resources/static/assets/style.css
index 59bcd117..340b22ea 100644
--- a/backend/src/main/resources/static/assets/style.css
+++ b/backend/src/main/resources/static/assets/style.css
@@ -1,3 +1,7 @@
.label {
font-weight: 500;
}
+
+.popover {
+ max-width: min(80vw, 600px);
+}
diff --git a/backend/src/main/resources/templates/fragments/institute.html b/backend/src/main/resources/templates/fragments/institute.html
new file mode 100644
index 00000000..0efa76dd
--- /dev/null
+++ b/backend/src/main/resources/templates/fragments/institute.html
@@ -0,0 +1,34 @@
+<!DOCTYPE html>
+
+<html xmlns:th="http://www.thymeleaf.org">
+
+<body>
+
+<!--
+Reusable fragment displaying the content of an institute popover.
+Its unique argument (institute) is an InstituteVO
+-->
+
+<th:block th:fragment="institute(institute)">
+ <div class="text-center py-2" th:if="${institute.logo}">
+ <img th:src="${institute.logo}" />
+ </div>
+ <div th:replace="fragments/row::text-row(label='Code', text=${institute.instituteCode})"></div>
+ <div th:replace="fragments/row::text-row(label='Acronym', text=${institute.acronym})"></div>
+ <div th:replace="fragments/row::text-row(label='Organization', text=${institute.organisation})"></div>
+ <div th:replace="fragments/row::text-row(label='Type', text=${institute.instituteType})"></div>
+ <div th:replace="fragments/row::text-row(label='Address', text=${institute.address})"></div>
+
+ <th:block th:if="${institute.webSite}">
+ <div th:replace="fragments/row::row(label='Website', content=~{::.institute-website})">
+ <a class="institute-website"
+ target="_blank"
+ th:href="${institute.webSite}"
+ th:text="${#strings.abbreviate(institute.webSite, 25)}"></a>
+ </div>
+ </th:block>
+</th:block>
+
+</body>
+
+</html>
diff --git a/backend/src/main/resources/templates/fragments/link.html b/backend/src/main/resources/templates/fragments/link.html
new file mode 100644
index 00000000..d7c43bbd
--- /dev/null
+++ b/backend/src/main/resources/templates/fragments/link.html
@@ -0,0 +1,20 @@
+<!DOCTYPE html>
+
+<html xmlns:th="http://www.thymeleaf.org">
+
+<body>
+<!--
+Reusable fragment displaying a link with a label if the provided url is not
+empty, or a span with the label if the provided url is empty.
+Both arguments are strings.
+-->
+<th:block th:fragment="link(label, url)">
+ <a th:unless="${#strings.isEmpty(url)}"
+ th:href="${url}"
+ th:text="${label}"></a>
+ <span th:if="${#strings.isEmpty(url)}" th:text="${label}"></span>
+</th:block>
+
+</body>
+
+</html>
diff --git a/backend/src/main/resources/templates/fragments/row.html b/backend/src/main/resources/templates/fragments/row.html
index 5b523cef..e5eb9e7f 100644
--- a/backend/src/main/resources/templates/fragments/row.html
+++ b/backend/src/main/resources/templates/fragments/row.html
@@ -4,6 +4,21 @@
<body>
+<!--
+Reusable fragment displaying a responsive row containing a label and a content.
+The label argument is a string.
+The content argument is a fragment which is displayed at the right of the label.
+
+Note that `th:if` is not evaluated when th:replace is used. So if this row must
+be displayed only if some condition is true, the fragment should be enclosed
+into a block with the condition:
+ <th:block th:if="${someCondition}">
+ <div th:replace="fragments/row::row(label='Some label', content=~{::#some-content-id})">
+ <span id="some-content-id">the content here</span>
+ </div>
+ </th:block>
+-->
+
<div th:fragment="row(label, content)" class="row py-2">
<div class="col-md-4 label pb-1 pb-md-0" th:text="${label}"></div>
<div class="col">
@@ -11,7 +26,21 @@
</div>
</div>
-<div th:fragment="text-row(label, text)" th:if="${!#strings.isEmpty(text)}" class="row py-2">
+<!--
+Reusable fragment displaying a responsive row containing a label and a textual content.
+The label argument is a string.
+The text argument is a string which is displayed at the right of the label.
+The whole row is omitted if the textual content is empty, so the caller does not
+need to test that condition.
+
+Note that `th:if` is not evaluated when th:replace is used. So if this row must
+be displayed only if some other condition is true, the fragment should be enclosed
+into a block with the condition:
+ <th:block th:if="${someCondition}">
+ <div th:replace="fragments/row::text-row(label='Some label', text=${someTextExpression})"></div>
+ </th:block>
+-->
+<div th:fragment="text-row(label, text)" th:unless="${#strings.isEmpty(text)}" class="row py-2">
<div class="col-md-4 label pb-1 pb-md-0" th:text="${label}"></div>
<div class="col" th:text="${text}"></div>
</div>
diff --git a/backend/src/main/resources/templates/fragments/source.html b/backend/src/main/resources/templates/fragments/source.html
new file mode 100644
index 00000000..795717ca
--- /dev/null
+++ b/backend/src/main/resources/templates/fragments/source.html
@@ -0,0 +1,35 @@
+<!DOCTYPE html>
+
+<html xmlns:th="http://www.thymeleaf.org">
+
+<body>
+
+<!--
+Reusable fragment displaying the source and the data links of an entity (site, study or germplasm).
+The source argument is a DataSource.
+The url argument is a string, which is the URL of the entity.
+The entityType argument is a string, which is used in the message
+"Link to this <entityType>".
+-->
+
+<th:block th:fragment="source(source, url, entityType)">
+ <th:block th:if="${source != null}">
+ <div th:replace="fragments/row::row(label='Source', content=~{::.source})">
+ <a class="source" target="_blank" th:href="${source.url}">
+ <img style="max-height: 60px;" th:src="${source.image}" th:alt="${source.name} + ' logo'" />
+ </a>
+ </div>
+ </th:block>
+
+ <th:block th:if="${url != null && source != null}">
+ <div th:replace="fragments/row::row(label='Data link', content=~{::.source-url})">
+ <a class="source-url" target="_blank" th:href="${url}">
+ Link to this <span th:text="${entityType}"></span> on <th:block th:text="${source.name}" />
+ </a>
+ </div>
+ </th:block>
+</th:block>
+
+</body>
+
+</html>
diff --git a/backend/src/main/resources/templates/fragments/xrefs.html b/backend/src/main/resources/templates/fragments/xrefs.html
index d51f1186..508b8923 100644
--- a/backend/src/main/resources/templates/fragments/xrefs.html
+++ b/backend/src/main/resources/templates/fragments/xrefs.html
@@ -4,6 +4,11 @@
<body>
+<!--
+Reusable fragment displaying a cross references section, with its title.
+The unique argument (crossReferences) is a List<XRefDocumentVO>
+-->
+
<div th:fragment="xrefs(crossReferences)" th:if="${!#lists.isEmpty(crossReferences)}">
<h2>Cross references</h2>
diff --git a/backend/src/main/resources/templates/germplasm.html b/backend/src/main/resources/templates/germplasm.html
new file mode 100644
index 00000000..840b0d44
--- /dev/null
+++ b/backend/src/main/resources/templates/germplasm.html
@@ -0,0 +1,418 @@
+<!DOCTYPE html>
+
+<html
+ xmlns:th="http://www.thymeleaf.org"
+ th:replace="~{layout/main :: layout(title=~{::title}, content=~{::main})}"
+>
+<head>
+ <title>Germplasm: <th:block th:text="${model.germplasm.germplasmName}" /></title>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+</head>
+
+<body>
+<main>
+ <div class="d-flex">
+ <h1 class="flex-grow-1">Germplasm: <th:block th:text="${model.germplasm.germplasmName}" /></h1>
+ <div th:if="${model.germplasm.holdingGenbank != null && model.germplasm.holdingGenbank.logo != null}">
+ <img th:src="${model.germplasm.holdingGenbank.logo}" th:alt="${model.germplasm.holdingGenbank.instituteName}" />
+ </div>
+ </div>
+
+ <div class="row align-items-center justify-content-center">
+ <div class="col-auto field" th:if="${model.germplasm.photo != null && model.germplasm.photo.thumbnailFile != null}">
+ <template id="photo-popover">
+ <div class="card">
+ <img th:src="${model.germplasm.photo.file}" class="card-img-top" alt="">
+ <div class="card-body">
+ <div th:replace="fragments/row::text-row(label='Accession name', text=${model.germplasm.germplasmName})"></div>
+ <div th:replace="fragments/row::text-row(label='Photo name', text=${model.germplasm.photo.photoName})"></div>
+ <div th:replace="fragments/row::text-row(label='Description', text=${model.germplasm.photo.description})"></div>
+ <div th:replace="fragments/row::text-row(label='Copyright', text=${model.germplasm.photo.copyright})"></div>
+ </div>
+ </div>
+ </template>
+
+ <button class="btn btn-link p-0"
+ data-bs-toggle="popover"
+ th:data-bs-title="${model.germplasm.photo.photoName}"
+ data-bs-element="#photo-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus">
+ <img th:src="${model.germplasm.photo.thumbnailFile}" class="img-fluid" />
+
+ <figcaption class="figure-caption">
+ © <span th:text="${model.germplasm.photo.copyright}"></span>
+ </figcaption>
+ </button>
+ </div>
+
+
+ <div class="col-12 col-lg">
+ <h2>Identification</h2>
+
+ <div th:replace="fragments/row::text-row(label='Germplasm name', text=${model.germplasm.germplasmName})"></div>
+ <div th:replace="fragments/row::text-row(label='Accession number', text=${model.germplasm.accessionNumber})"></div>
+
+ <div th:replace="fragments/source::source(source=${model.source}, url=${model.germplasm.url}, entityType='germplasm')"></div>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.synonyms)}">
+ <div th:replace="fragments/row::row(label='Accession synonyms', content=~{::#accession-synonyms})">
+ <div id="accession-synonyms" class="content-overflow" th:text="${#strings.listJoin(model.germplasm.synonyms, ', ')}"></div>
+ </div>
+ </th:block>
+
+ <th:block th:unless="${#strings.isEmpty(model.taxon)}">
+ <div th:replace="fragments/row::row(label='Taxon', content=~{::#taxon})">
+ <div id="taxon">
+ <template id="taxon-popover">
+ <th:block th:unless="${#strings.isEmpty(model.germplasm.genus)}">
+ <div th:replace="fragments/row::row(label='Genus', content=~{::#taxon-genus})">
+ <em id="taxon-genus" th:text="${model.germplasm.genus}"></em>
+ </div>
+ </th:block>
+ <th:block th:unless="${#strings.isEmpty(model.germplasm.species)}">
+ <div th:replace="fragments/row::row(label='Species', content=~{::#taxon-species})">
+ <span id="taxon-species">
+ <em th:text="${model.germplasm.species}"></em>
+ <span th:unless="${#strings.isEmpty(model.germplasm.speciesAuthority)}"
+ th:text="${'(' + model.germplasm.speciesAuthority + ')'}"></span>
+ </span>
+ </div>
+ </th:block>
+ <th:block th:unless="${#strings.isEmpty(model.germplasm.subtaxa)}">
+ <div th:replace="fragments/row::row(label='Subtaxa', content=~{::#taxon-subtaxa})">
+ <span id="taxon-subtaxa">
+ <em th:text="${model.germplasm.subtaxa}"></em>
+ <span th:unless="${#strings.isEmpty(model.germplasm.subtaxaAuthority)}"
+ th:text="${'(' + model.germplasm.subtaxaAuthority + ')'}"></span>
+ </span>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Authority', text=${model.taxonAuthor})"></div>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.taxonIds)}">
+ <div th:replace="fragments/row::row(label='Taxon IDs', content=~{::#taxon-ids})">
+ <div id="taxon-ids">
+ <div th:each="taxonId : ${model.germplasm.taxonIds}" class="row">
+ <div class="col-6 text-nowrap" th:text="${taxonId.sourceName}"></div>
+ <div class="col-6">
+ <span class="taxon-id"
+ th:replace="fragments/link::link(label=${taxonId.taxonId}, url=${#faidare.taxonIdUrl(taxonId)})"></span>
+ </div>
+ </div>
+ </div>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Comment', text=${model.germplasm.taxonComment})"></div>
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.taxonCommonNames)}">
+ <div th:replace="fragments/row::row(label='Taxon common names', content=~{::#taxon-common-names})">
+ <div id="taxon-common-names" class="content-overflow" th:text="${#strings.listJoin(model.germplasm.taxonCommonNames, ', ')}"></div>
+ </div>
+ </th:block>
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.taxonSynonyms)}">
+ <div th:replace="fragments/row::row(label='Taxon common names', content=~{::#taxon-synonyms})">
+ <div id="taxon-synonyms" class="content-overflow" th:text="${#strings.listJoin(model.germplasm.taxonSynonyms, ', ')}"></div>
+ </div>
+ </th:block>
+ </template>
+ <button class="btn btn-link p-0"
+ data-bs-toggle="popover"
+ th:data-bs-title="${model.taxon}"
+ data-bs-element="#taxon-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus">
+ <em th:text="${model.taxon}"></em>
+ <th:block th:unless="${#strings.isEmpty(model.taxonAuthor)}">(<span th:text="${model.taxonAuthor}"></span>)</th:block>
+ </button>
+ </div>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Biological status', text=${model.germplasm.biologicalStatusOfAccessionCode})"></div>
+ <div th:replace="fragments/row::text-row(label='Genetic nature', text=${model.germplasm.geneticNature})"></div>
+ <div th:replace="fragments/row::text-row(label='Seed source', text=${model.germplasm.seedSource})"></div>
+ <div th:replace="fragments/row::text-row(label='Pedigree', text=${model.germplasm.pedigree})"></div>
+ <div th:replace="fragments/row::text-row(label='Comments', text=${model.germplasm.comment})"></div>
+
+ <th:block th:if="${model.germplasm.originSite != null && !#strings.isEmpty(model.germplasm.originSite.siteName)}">
+ <div th:replace="fragments/row::row(label='Origin site', content=~{::#origin-site})">
+ <a id="origin-site" th:href="@{/sites/{siteId}(siteId=${#faidare.toSiteParam(model.germplasm.originSite.siteId)})}" th:text="${model.germplasm.originSite.siteName}"></a>
+ </div>
+ </th:block>
+ </div>
+ </div>
+
+ <th:block th:if="${model.germplasm.holdingInstitute}">
+ <h2>Depositary</h2>
+ <template id="holding-institute-popover">
+ <div th:replace="fragments/institute::institute(institute=${model.germplasm.holdingInstitute})"></div>
+ </template>
+ <div th:replace="fragments/row::row(label='Institution', content=~{::#institution})">
+ <button id="institution"
+ data-bs-toggle="popover"
+ th:data-bs-title="${model.germplasm.holdingInstitute.instituteName}"
+ data-bs-element="#holding-institute-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ class="btn btn-link p-0"
+ th:text="${model.germplasm.holdingInstitute.instituteName}"></button>
+ </div>
+
+ <th:block th:if="${model.germplasm.holdingGenbank != null && !#strings.isEmpty(model.germplasm.holdingGenbank.instituteName) && !#strings.isEmpty(model.germplasm.holdingGenbank.webSite)}">
+ <div th:replace="fragments/row::row(label='Stock center name', content=~{::#stock-center-name})">
+ <a id="stock-center-name"
+ target="_blank"
+ th:href="${model.germplasm.holdingGenbank.webSite}"
+ th:text="${model.germplasm.holdingGenbank.instituteName}"></a>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Presence status', text=${model.germplasm.presenceStatus})"></div>
+ </th:block>
+
+ <th:block th:if="${model.collecting}">
+ <h2>Collector</h2>
+ <th:block th:if="${model.germplasm.collectingSite != null && !#strings.isEmpty(model.germplasm.collectingSite.siteName)}">
+ <div th:replace="fragments/row::row(label='Collecting site', content=~{::#collecting-site})">
+ <a id="collecting-site"
+ th:href="@{/sites/{siteId}(siteId=${#faidare.toSiteParam(model.germplasm.collectingSite.siteId)})}"
+ th:text="${model.germplasm.collectingSite.siteName}"
+ ></a>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Material type', text=${model.germplasm.collector.materialType})"></div>
+ <div th:replace="fragments/row::text-row(label='Collectors', text=${model.germplasm.collector.collectors})"></div>
+
+ <th:block th:if="${!#strings.isEmpty(model.germplasm.acquisitionDate) && model.germplasm.collector.accessionCreationDate == null}">
+ <div th:replace="fragments/row::text-row(label='Acquisition / Creation date', text=${model.germplasm.acquisitionDate})"></div>
+ </th:block>
+
+ <th:block th:if="${model.germplasm.collector.institute != null && !#strings.isEmpty(model.germplasm.collector.institute.instituteName)}">
+ <template id="collector-institute-popover">
+ <div th:replace="fragments/institute::institute(institute=${model.germplasm.collector.institute})"></div>
+ </template>
+ <div th:replace="fragments/row::row(label='Institution', content=~{::#collecting-institution})">
+ <button id="collecting-institution"
+ data-bs-toggle="popover"
+ th:data-bs-title="${model.germplasm.collector.institute.instituteName}"
+ data-bs-element="#collector-institute-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ class="btn btn-link p-0"
+ th:text="${model.germplasm.collector.institute.instituteName}"></button>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Accession number', text=${model.germplasm.collector.accessionNumber})"></div>
+ </th:block>
+
+ <th:block th:if="${model.breeding}">
+ <h2>Breeder</h2>
+ <th:block th:if="${model.germplasm.breeder.institute != null && !#strings.isEmpty(model.germplasm.breeder.institute.instituteName)}">
+ <template id="breeder-institute-popover">
+ <div th:replace="fragments/institute::institute(institute=${model.germplasm.breeder.institute})"></div>
+ </template>
+ <div th:replace="fragments/row::row(label='Institute', content=~{::#breeding-institution})">
+ <button id="breeding-institution"
+ data-bs-toggle="popover"
+ th:data-bs-title="${model.germplasm.breeder.institute.instituteName}"
+ data-bs-element="#breeder-institute-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ class="btn btn-link p-0"
+ th:text="${model.germplasm.breeder.institute.instituteName}"></button>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Accession creation year', text=${model.germplasm.breeder.accessionCreationDate})"></div>
+ <div th:replace="fragments/row::text-row(label='Accession number', text=${model.germplasm.breeder.accessionNumber})"></div>
+ <div th:replace="fragments/row::text-row(label='Catalog registration year', text=${model.germplasm.breeder.registrationYear})"></div>
+ <div th:replace="fragments/row::text-row(label='Catalog deregistration year', text=${model.germplasm.breeder.deregistrationYear})"></div>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.donors)}">
+ <h2>Donors</h2>
+ <div class="table-responsive scroll-table table-card-body">
+ <div class="card">
+ <table class="table table-sm table-striped">
+ <thead>
+ <tr>
+ <th scope="col">Institute name</th>
+ <th scope="col">Institute code</th>
+ <th scope="col">Donation date</th>
+ <th scope="col">Accession number</th>
+ <th scope="col">Accession PUI</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="row, donorIterStat : ${model.germplasm.donors}">
+ <td>
+ <template th:id="${'donor-institute-popover-' + donorIterStat.index}">
+ <div th:replace="fragments/institute::institute(institute=${row.donorInstitute})"></div>
+ </template>
+ <button data-bs-toggle="popover"
+ th:data-bs-title="${row.donorInstitute.instituteName}"
+ th:data-bs-element="${'#donor-institute-popover-' + donorIterStat.index}"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ class="btn btn-link p-0"
+ th:text="${row.donorInstitute.instituteName}"></button>
+ </td>
+ <td th:text="${row.donorInstituteCode}"></td>
+ <td th:text="${row.donationDate}"></td>
+ <td th:text="${row.donorAccessionNumber}"></td>
+ <td th:text="${row.donorGermplasmPUI}"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.distributors)}">
+ <h2>Donors</h2>
+ <div class="table-responsive scroll-table table-card-body">
+ <div class="card">
+ <table class="table table-sm table-striped">
+ <thead>
+ <tr>
+ <th scope="col">Institute</th>
+ <th scope="col">Accession number</th>
+ <th scope="col">Distribution status</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="row, distributorIterStat : ${model.germplasm.distributors}">
+ <td>
+ <template th:id="${'distributor-institute-popover-' + distributorIterStat.index}">
+ <div th:replace="fragments/institute::institute(institute=${row.institute})"></div>
+ </template>
+ <button data-bs-toggle="popover"
+ th:data-bs-title="${row.institute.instituteName}"
+ th:data-bs-element="${'#distributor-institute-popover-' + distributorIterStat.index}"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ class="btn btn-link p-0"
+ th:text="${row.institute.instituteName}"></button>
+ </td>
+ <td th:text="${row.accessionNumber}"></td>
+ <td th:text="${row.distributionStatus}"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.attributes)}">
+ <h2>Evaluation Data</h2>
+ <th:block th:each="descriptor : ${model.attributes}">
+ <div th:replace="fragments/row::text-row(label=${descriptor.attributeName}, text=${descriptor.value})"></div>
+ </th:block>
+ </th:block>
+
+ <th:block th:if="${model.genealogyPresent}">
+ <h2>Genealogy</h2>
+
+ <th:block th:if="${model.pedigree != null}">
+ <div th:replace="fragments/row::text-row(label='Crossing plan', text=${model.pedigree.crossingPlan})"></div>
+ <div th:replace="fragments/row::text-row(label='Crossing year', text=${model.pedigree.crossingYear})"></div>
+ <div th:replace="fragments/row::text-row(label='Family code', text=${model.pedigree.familyCode})"></div>
+ <th:block th:unless="${#strings.isEmpty(model.pedigree.parent1Name)}">
+ <div th:replace="fragments/row::row(label='Parent accessions', content=~{::#parent-accessions})">
+ <div id="parent-accessions">
+ <th:block th:if="${model.pedigree.parent1DbId}">
+ <div th:replace="fragments/row::row(label=${model.pedigree.parent1Type}, content=~{::#parent1-link})">
+ <a id="parent1-link" th:href="@{/germplasms/{germplasmId}(germplasmId=${model.pedigree.parent1DbId})}" th:text="${model.pedigree.parent1Name}"></a>
+ </div>
+ </th:block>
+
+ <th:block th:if="${model.pedigree.parent2DbId}">
+ <div th:replace="fragments/row::row(label=${model.pedigree.parent2Type}, content=~{::#parent2-link})">
+ <a id="parent2-link" th:href="@{/germplasms/{germplasmId}(germplasmId=${model.pedigree.parent2DbId})}" th:text="${model.pedigree.parent2Name}"></a>
+ </div>
+ </th:block>
+ </div>
+ </div>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.pedigree.siblings)}">
+ <div th:replace="fragments/row::row(label='Sibling accessions', content=~{::#sibling-accessions})">
+ <div id="sibling-accessions" class="content-overflow">
+ <a th:each="sibling : ${model.pedigree.siblings}"
+ th:href="@{/germplasms/{germplasmId}(germplasmId=${sibling.germplasmDbId})}"
+ th:text="${sibling.defaultDisplayName}"></a>
+ </div>
+ </div>
+ </th:block>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.children)}">
+ <div th:replace="fragments/row::row(label='Descendants', content=~{::#descendants})">
+ <div id="descendants" class="content-overflow-big">
+ <th:block th:each="child : ${model.germplasm.children}">
+ <div th:replace="fragments/row::row(label=${#strings.isEmpty(child.secondParentName) ? ('children of ' + child.firstParentName) : ('children of ' + child.firstParentName + ' x ' + child.secondParentName) }, content=~{::.descendant-child})">
+ <div class="descendant-child">
+ <th:block th:each="sibling, siblingIterStat : ${child.sibblings}">
+ <a th:href="@{/germplasms(pui=${sibling.pui})}"
+ th:text="${sibling.name}"></a><th:block th:unless="${siblingIterStat.last}">, </th:block>
+ </th:block>
+ </div>
+ </div>
+ </th:block>
+ </div>
+ </div>
+ </th:block>
+
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.population)}">
+ <h2>Population</h2>
+ <th:block th:each="population : ${model.germplasm.population}">
+
+ <th:block th:if="${population.germplasmRef != null}">
+ <th:block th:unless="${#strings.isEmpty(population.germplasmRef.pui)}">
+ <div th:replace="fragments/row::row(label=${#faidare.collPopTitle(population)}, content=~{::.population-1})">
+ <div class="population-1">
+ <a th:if="${population.germplasmRef.pui != model.germplasm.germplasmPUI}"
+ th:href="@{/germplasms(pui=${population.germplasmRef.pui})}"
+ th:text="${population.germplasmRef.name}"></a>
+ <span th:if="${population.germplasmRef.pui == model.germplasm.germplasmPUI}"
+ th:text="${population.germplasmRef.name}"></span>
+ is composed by <span th:text="${population.germplasmCount}"></span> accession(s)
+ <!-- TODO there was a link pointing at a search here -->
+ </div>
+ </div>
+ </th:block>
+ </th:block>
+
+ <th:block th:if="${population.germplasmRef == null}">
+ <div th:replace="fragments/row::text-row(label=${#faidare.collPopTitle(population)}, text=${population.germplasmCount + ' accession(s)'})"></div>
+ <!-- TODO there was a link pointing at a search here -->
+ </th:block>
+ </th:block>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.collection)}">
+ <h2>Collection</h2>
+ <th:block th:each="collection : ${model.germplasm.collection}">
+ <div th:replace="fragments/row::text-row(label=${#faidare.collPopTitle(collection)}, text=${collection.germplasmCount + ' accession(s)'})"></div>
+ <!-- TODO there was a link pointing at a search here -->
+ </th:block>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.panel)}">
+ <h2>Panel</h2>
+ <th:block th:each="panel : ${model.germplasm.panel}">
+ <div th:replace="fragments/row::text-row(label=${#faidare.collPopTitleWithoutUnderscores(panel)}, text=${panel.germplasmCount + ' accession(s)'})"></div>
+ <!-- TODO there was a link pointing at a search here -->
+ </th:block>
+ </th:block>
+
+ <div th:replace="fragments/xrefs::xrefs(crossReferences=${model.crossReferences})"></div>
+</main>
+</body>
+</html>
diff --git a/backend/src/main/resources/templates/layout/main.html b/backend/src/main/resources/templates/layout/main.html
index 22bcdfd5..4cd33f70 100644
--- a/backend/src/main/resources/templates/layout/main.html
+++ b/backend/src/main/resources/templates/layout/main.html
@@ -26,5 +26,27 @@
common footer
</footer>
</div>
+ <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.0/dist/js/bootstrap.bundle.min.js" integrity="sha384-U1DAWAznBHeqEIlVSCgzq+c9gqGAJn5c/t99JyeKa9xxaYpSvHU5awsuZVVFIhvj" crossorigin="anonymous"></script>
+ <script type="text/javascript">
+ const popoverTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="popover"]'))
+ popoverTriggerList.forEach(popoverTriggerEl => {
+ const options = {};
+ const contentSelector = popoverTriggerEl.dataset.bsElement;
+ if (contentSelector) {
+ const content = document.querySelector(contentSelector);
+ if (content) {
+ options.content = () => {
+ const element = document.createElement('div');
+ element.innerHTML = content.innerHTML;
+ return element;
+ };
+ options.html = true;
+ } else {
+ throw new Error('element with selector ' + contentSelector + ' not found');
+ }
+ }
+ return new bootstrap.Popover(popoverTriggerEl, options);
+ });
+ </script>
</body>
</html>
diff --git a/backend/src/main/resources/templates/site.html b/backend/src/main/resources/templates/site.html
index ad6affc4..d5d65e5c 100644
--- a/backend/src/main/resources/templates/site.html
+++ b/backend/src/main/resources/templates/site.html
@@ -17,22 +17,7 @@
<div th:replace="fragments/row::text-row(label='Permanent unique identifier', text=${model.site.uri})"></div>
</th:block>
- <th:block th:if="${model.source != null}">
- <div th:replace="fragments/row::row(label='Source', content=~{::#source})">
- <a id="source" target="_blank" th:href="${model.source.url}">
- <img style="max-height: 60px;" th:src="${model.source.image}" th:alt="${model.source.name} + ' logo'" />
- </a>
- </div>
- </th:block>
-
- <th:block th:if="${model.site.url != null && model.source != null}">
- <div
- th:replace="fragments/row::row(label='Data link', content=~{::#url})">
- <a id="url" target="_blank" th:href="${model.site.url}">
- Link to this site on <th:block th:text="${model.source.name}" />
- </a>
- </div>
- </th:block>
+ <div th:replace="fragments/source::source(source=${model.source}, url=${model.site.url}, entityType='site')"></div>
<div th:replace="fragments/row::text-row(label='Abbreviation', text=${model.site.abbreviation})"></div>
<div th:replace="fragments/row::text-row(label='Type', text=${model.site.locationType})"></div>
diff --git a/backend/src/main/resources/templates/study.html b/backend/src/main/resources/templates/study.html
index a1cafc65..7bd5bbbd 100644
--- a/backend/src/main/resources/templates/study.html
+++ b/backend/src/main/resources/templates/study.html
@@ -18,21 +18,7 @@
<div th:replace="fragments/row::text-row(label='Name', text=${model.study.studyName})"></div>
<div th:replace="fragments/row::text-row(label='Identifier', text=${model.study.studyDbId})"></div>
- <th:block th:if="${model.source != null}">
- <div th:replace="fragments/row::row(label='Source', content=~{::#source}, text='')">
- <a id="source" target="_blank" th:href="${model.source.url}">
- <img style="max-height: 60px;" th:src="${model.source.image}" th:alt="${model.source.name} + ' logo'" />
- </a>
- </div>
- </th:block>
-
- <th:block th:if="${model.study.url != null && model.source != null}">
- <div th:replace="fragments/row::row(label='Data link', content=~{::#url}, text='')">
- <a id="url" target="_blank" th:href="${model.study.url}">
- Link to this study on <th:block th:text="${model.source.name}" />
- </a>
- </div>
- </th:block>
+ <div th:replace="fragments/source::source(source=${model.source}, url=${model.study.url}, entityType='study')"></div>
<div th:replace="fragments/row::text-row(label='Project name', text=${model.study.programName})"></div>
<div th:replace="fragments/row::text-row(label='Description', text=${model.study.studyDescription})"></div>
--
GitLab
From 951b746fe76e342e912269cb6895539c5f1296e3 Mon Sep 17 00:00:00 2001
From: cexbrayat <cedric@ninja-squad.com>
Date: Wed, 1 Sep 2021 16:25:20 +0200
Subject: [PATCH 2/2] fix: typos and missing alt attribute
---
backend/src/main/resources/templates/fragments/institute.html | 2 +-
backend/src/main/resources/templates/germplasm.html | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/backend/src/main/resources/templates/fragments/institute.html b/backend/src/main/resources/templates/fragments/institute.html
index 0efa76dd..7e603095 100644
--- a/backend/src/main/resources/templates/fragments/institute.html
+++ b/backend/src/main/resources/templates/fragments/institute.html
@@ -11,7 +11,7 @@ Its unique argument (institute) is an InstituteVO
<th:block th:fragment="institute(institute)">
<div class="text-center py-2" th:if="${institute.logo}">
- <img th:src="${institute.logo}" />
+ <img th:src="${institute.logo}" th:alt="${institute.instituteName}"/>
</div>
<div th:replace="fragments/row::text-row(label='Code', text=${institute.instituteCode})"></div>
<div th:replace="fragments/row::text-row(label='Acronym', text=${institute.acronym})"></div>
diff --git a/backend/src/main/resources/templates/germplasm.html b/backend/src/main/resources/templates/germplasm.html
index 840b0d44..1c51d438 100644
--- a/backend/src/main/resources/templates/germplasm.html
+++ b/backend/src/main/resources/templates/germplasm.html
@@ -112,7 +112,7 @@
</div>
</th:block>
<th:block th:unless="${#lists.isEmpty(model.germplasm.taxonSynonyms)}">
- <div th:replace="fragments/row::row(label='Taxon common names', content=~{::#taxon-synonyms})">
+ <div th:replace="fragments/row::row(label='Taxon synonyms', content=~{::#taxon-synonyms})">
<div id="taxon-synonyms" class="content-overflow" th:text="${#strings.listJoin(model.germplasm.taxonSynonyms, ', ')}"></div>
</div>
</th:block>
--
GitLab