REST API updated for bredCode, ancest

src/main/java/org/genesys2/server/model/genesys/AllAcqBreeding.java → src/main/java/org/genesys2/server/model/genesys/AccessionBreeding.java

@@ -32,7 +32,7 @@ import org.genesys2.server.model.BusinessModel;
  */
 @Entity
 @Table(name = "accessionbreeding")
-public class AllAcqBreeding extends BusinessModel{
+public class AccessionBreeding extends BusinessModel{
 
 	@Version
 	private long version = 0;
@@ -48,7 +48,7 @@ public class AllAcqBreeding extends BusinessModel{
 	@Lob
 	private String pedigree;
 
-	public AllAcqBreeding() {
+	public AccessionBreeding() {
 	}
 
 	public long getVersion() {

src/main/java/org/genesys2/server/persistence/domain/AccessionBreedingRepository.java

@@ -17,11 +17,11 @@
 package org.genesys2.server.persistence.domain;
 
 import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.model.genesys.AllAcqBreeding;
+import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.springframework.data.jpa.repository.JpaRepository;
 
-public interface AccessionBreedingRepository extends JpaRepository<AllAcqBreeding, Long> {
+public interface AccessionBreedingRepository extends JpaRepository<AccessionBreeding, Long> {
 
-	AllAcqBreeding findByAccession(Accession accession);
+	AccessionBreeding findByAccession(Accession accession);
 
 }

src/main/java/org/genesys2/server/service/GenesysService.java

@@ -27,7 +27,7 @@ import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AllAccnames;
-import org.genesys2.server.model.genesys.AllAcqBreeding;
+import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AllAcqExchange;
 import org.genesys2.server.model.genesys.ExperimentTrait;
@@ -67,7 +67,7 @@ public interface GenesysService {
 
 	AccessionCollect listAccessionCollect(Accession accession);
 
-	AllAcqBreeding listAccessionBreeding(Accession accession);
+	AccessionBreeding listAccessionBreeding(Accession accession);
 
 	AccessionGeo listAccessionGeo(Accession accession);
 
@@ -132,8 +132,8 @@ public interface GenesysService {
 	SvalbardData getSvalbardData(Accession accession);
 
 	void saveCollecting(List<AccessionCollect> all);
-
 	void saveGeo(List<AccessionGeo> all);
+	void saveBreeding(List<AccessionBreeding> all);
 
 	void refreshMetadataMethods();
 
@@ -145,4 +145,5 @@ public interface GenesysService {
 
 	void removeAliases(List<AccessionAlias> aliases);
 
+
 }

src/main/java/org/genesys2/server/service/impl/BatchRESTServiceImpl.java

@@ -30,6 +30,7 @@ import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AccessionCollect;
+import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.Taxonomy;
 import org.genesys2.server.model.genesys.AccessionAlias.AliasType;
 import org.genesys2.server.model.impl.Country;
@@ -80,6 +81,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		List<Accession> toSave = new ArrayList<Accession>();
 		List<AccessionCollect> toSaveColl = new ArrayList<AccessionCollect>();
 		List<AccessionGeo> toSaveGeo = new ArrayList<AccessionGeo>();
+		List<AccessionBreeding> toSaveBreed = new ArrayList<AccessionBreeding>();
 
 		for (AccessionJson dataJson : batch.keySet()) {
 			if (LOG.isDebugEnabled())
@@ -127,7 +129,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 					updated = true;
 				}
 			}
-			
+
 			/* Allow updating Genus */
 			value = accnJson.get("newGenus");
 			if (value != null) {
@@ -306,6 +308,23 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				toSaveGeo.add(accnGeo);
 			}
 
+			if (accnJson.has("bredCode") || accnJson.has("ancest")) {
+				AccessionBreeding accnBred = genesysService.listAccessionBreeding(accession);
+				if (accnBred == null) {
+					accnBred = new AccessionBreeding();
+					accnBred.setAccession(accession);
+				}
+				value = accnJson.get("bredCode");
+				if (value != null) {
+					accnBred.setBreederCode(value.isTextual() ? value.asText() : null);
+				}
+				value = accnJson.get("ancest");
+				if (value != null) {
+					accnBred.setPedigree(value.isTextual() ? value.asText() : null);
+				}
+				toSaveBreed.add(accnBred);
+			}
+
 			if (updated) {
 				toSave.add(accession);
 			}
@@ -325,7 +344,11 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			genesysService.saveGeo(toSaveGeo);
 		}
 
-		return toSave.size() > 0 || toSaveColl.size() > 0 || toSaveGeo.size() > 0;
+		if (toSaveBreed.size() > 0) {
+			genesysService.saveBreeding(toSaveBreed);
+		}
+
+		return toSave.size() > 0 || toSaveColl.size() > 0 || toSaveGeo.size() > 0 || toSaveBreed.size() > 0;
 	}
 
 	@Override

src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java

@@ -39,7 +39,7 @@ import org.genesys2.server.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AccessionTrait;
 import org.genesys2.server.model.genesys.AllAccnames;
-import org.genesys2.server.model.genesys.AllAcqBreeding;
+import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AllAcqExchange;
 import org.genesys2.server.model.genesys.ExperimentAccessionTrait;
@@ -225,7 +225,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	}
 
 	@Override
-	public AllAcqBreeding listAccessionBreeding(Accession accession) {
+	public AccessionBreeding listAccessionBreeding(Accession accession) {
 		if (accession == null || accession.getId() == null)
 			return null;
 		return accessionBreedingRepository.findByAccession(accession);
@@ -470,6 +470,12 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	public void saveGeo(List<AccessionGeo> all) {
 		accessionGeoRepository.save(all);
 	}
+	
+	@Override
+	@Transactional(readOnly = false)
+	public void saveBreeding(List<AccessionBreeding> all) {
+		accessionBreedingRepository.save(all);
+	}
 
 	@Override
 	public long countAvailable(Set<Long> accessionIds) {