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
index ec4ed09ba66253fc5662fbd9a60076c6c0153694..bfe7d484cb1b5afaed7e17f239db0c29ec5e8153 100644
--- 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
@@ -1,6 +1,5 @@
package fr.inra.urgi.faidare.web.germplasm;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
@@ -11,24 +10,14 @@ 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.GermplasmMcpdVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmSitemapVO;
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.SiteVO;
-import fr.inra.urgi.faidare.domain.data.germplasm.TaxonSourceVO;
+import fr.inra.urgi.faidare.domain.xref.XRefDocumentSearchCriteria;
import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
import fr.inra.urgi.faidare.repository.es.GermplasmAttributeRepository;
import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
@@ -82,11 +71,6 @@ public class GermplasmController {
throw new NotFoundException("Germplasm with ID " + germplasmId + " not found");
}
- // TODO remove this, which is used to display all the sections on a specific germplasm
- if (germplasm.getGermplasmDbId().equals("dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUwxOFJJTDJ3YXlfX185Ng==")) {
- germplasm = createGermplasm();
- }
-
return toModelAndView(germplasm);
}
@@ -137,19 +121,8 @@ public class GermplasmController {
List<BrapiGermplasmAttributeValue> attributes = getAttributes(germplasm);
PedigreeVO pedigree = getPedigree(germplasm);
- // TODO remove this
- if (germplasm.getGermplasmDbId().equals("dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUwxOFJJTDJ3YXlfX185Ng==")) {
- attributes = Arrays.asList(createAttribute());
- pedigree = createPedigree();
- }
-
- // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
- // XRefDocumentSearchCriteria.forXRefId(germplasm.getGermplasmDbId())
- // );
- // TODO replace this block by the above commented one
- List<XRefDocumentVO> crossReferences = Arrays.asList(
- createXref("foobar"),
- createXref("bazbing")
+ List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
+ XRefDocumentSearchCriteria.forXRefId(germplasm.getGermplasmDbId())
);
sortDonors(germplasm);
@@ -219,243 +192,6 @@ public class GermplasmController {
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.setGermplasmDbId("dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUwxOFJJTDJ3YXlfX185Ng==");
- 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");
- originSite.setSiteType("Origin site");
- originSite.setLatitude(47.0F);
- originSite.setLongitude(12.0F);
- result.setOriginSite(originSite);
-
- List<SiteVO> evaluationSites = new ArrayList<>();
- for (int i = 0; i < 5; i++) {
- SiteVO evaluationSite = new SiteVO();
- evaluationSite.setSiteId(Integer.toString(12347 + i));
- evaluationSite.setSiteType("Evaluation site");
- evaluationSite.setSiteName("Site " + i);
- evaluationSite.setLatitude(46.0F + i);
- evaluationSite.setLongitude(13.0F + i);
- evaluationSites.add(evaluationSite);
- }
- result.setEvaluationSites(evaluationSites);
-
- 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);
-
- SiteVO collectingSite = new SiteVO();
- collectingSite.setSiteId("1235");
- collectingSite.setSiteName("St Just");
- collectingSite.setSiteType("Collecting site");
- collectingSite.setLatitude(48.0F);
- collectingSite.setLongitude(13.0F);
- result.setCollectingSite(collectingSite);
- 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;
- }
-
private List<GermplasmExportableField> getFieldsToExport(GermplasmExportCommand command) {
List<GermplasmExportableField> fields = command.getFields();
if (fields.isEmpty()) {
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 cf17c73ddddca7b2d20e9ac263c93edc3c59beef..645b8fbf84d678e49f1586d32fcc389fba0f5ba3 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
@@ -1,14 +1,10 @@
package fr.inra.urgi.faidare.web.site;
-import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
-import javax.servlet.http.HttpServletRequest;
-
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.config.FaidareProperties;
-import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiAdditionalInfo;
import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
import fr.inra.urgi.faidare.domain.data.LocationVO;
import fr.inra.urgi.faidare.domain.xref.XRefDocumentSearchCriteria;
@@ -54,12 +50,8 @@ public class SiteController {
throw new NotFoundException("Site with ID " + siteId + " not found");
}
- // TODO uncomment this and remove the hard-coded xrefs
- // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
- // XRefDocumentSearchCriteria.forXRefId(site.getLocationDbId()));
- List<XRefDocumentVO> crossReferences = Arrays.asList(
- createXref("foobar"),
- createXref("bazbing")
+ List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
+ XRefDocumentSearchCriteria.forXRefId(site.getLocationDbId())
);
return new ModelAndView("site",
@@ -90,14 +82,4 @@ public class SiteController {
};
return ResponseEntity.ok().contentType(MediaType.TEXT_PLAIN).body(body);
}
-
- 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/study/StudyController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
index 626df842e50b8fe1eaab7f6492e70fb064da9b3d..de6875c2ade487535b5f9d59b0f87190436ec6a4 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
@@ -1,6 +1,5 @@
package fr.inra.urgi.faidare.web.study;
-import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.Iterator;
@@ -79,12 +78,8 @@ public class StudyController {
throw new NotFoundException("Study with ID " + studyId + " not found");
}
- // TODO uncomment this
- // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
- // XRefDocumentSearchCriteria.forXRefId(study.getStudyDbId()));
- List<XRefDocumentVO> crossReferences = Arrays.asList(
- createXref("foobar"),
- createXref("bazbing")
+ List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
+ XRefDocumentSearchCriteria.forXRefId(study.getStudyDbId())
);
List<GermplasmVO> germplasms = getGermplasms(study);
@@ -166,14 +161,4 @@ public class StudyController {
}
-
- 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;
- }
}