FIX Taxonomy also updated when only sub-elements are provided for update

(e.g. only spauthor)

src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java

@@ -66,6 +66,19 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "taxonomy")
 	private List<CropTaxonomy> cropTaxonomies;
 
+	public Taxonomy2() {
+	}
+
+	public Taxonomy2(Taxonomy2 taxonomy) {
+		if (taxonomy != null) {
+			this.genus = taxonomy.genus;
+			this.species = taxonomy.species;
+			this.spAuthor = taxonomy.spAuthor;
+			this.subtaxa = taxonomy.subtaxa;
+			this.subtAuthor = taxonomy.subtAuthor;
+		}
+	}
+
 	@PrePersist
 	private void prePersist() {
 		this.taxonName = getTaxonName();
@@ -166,7 +179,8 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 
 	@Override
 	public String toString() {
-		return MessageFormat.format("Tax id={0} taxonName={1} genus={2} sp={3} spauthor={4} subtaxa={5} subtauthor={6}", id, getTaxonName(), genus, species, spAuthor, subtaxa, subtAuthor);
+		return MessageFormat.format("Tax id={0} taxonName={1} genus={2} sp={3} spauthor={4} subtaxa={5} subtauthor={6}", id, getTaxonName(), genus, species,
+				spAuthor, subtaxa, subtAuthor);
 	}
 
 }

src/main/java/org/genesys2/server/model/json/GenesysJsonFactory.java

@@ -21,12 +21,17 @@ public class GenesysJsonFactory {
 		aj.setUuid(accession.getUuid());
 
 		Taxonomy2 tax = accession.getTaxonomy();
-		aj.setGenus(tax.getGenus());
-		aj.setSpecies(tax.getSpecies());
-		aj.setSpauthor(tax.getSpAuthor());
-		aj.setSubtaxa(tax.getSubtaxa());
-		aj.setSubtauthor(tax.getSubtAuthor());
-		aj.setOrgCty(accession.getCountryOfOrigin().getCode3());
+		if (tax != null) {
+			aj.setGenus(tax.getGenus());
+			aj.setSpecies(tax.getSpecies());
+			aj.setSpauthor(tax.getSpAuthor());
+			aj.setSubtaxa(tax.getSubtaxa());
+			aj.setSubtauthor(tax.getSubtAuthor());
+		}
+		if (accession.getCountryOfOrigin() != null) {
+			aj.setOrgCty(accession.getCountryOfOrigin().getCode3());
+		}
+
 		aj.setAcqDate(accession.getAcquisitionDate());
 		aj.setMlsStat(accession.getMlsStatus());
 		aj.setInTrust(accession.getInTrust());

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

@@ -444,11 +444,9 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		boolean updated = false;
 
 		// Do not persist this one, temporary use
-		Taxonomy2 current = new Taxonomy2();
 		Taxonomy2 taxonomy = accession.getTaxonomy();
+		Taxonomy2 current = new Taxonomy2(taxonomy);
 		// Load JSON values into "current"
-		if (taxonomy!=null)
-			current.setId(taxonomy.getId());
 		current.setGenus(stringIfProvided(accnJson.get("genus"), current.getGenus()));
 		current.setGenus(stringIfProvided(accnJson.get("newGenus"), current.getGenus()));
 		current.setSpecies(stringIfProvided(accnJson.get("species"), current.getSpecies()));
@@ -459,7 +457,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		Taxonomy2 ensuredTaxonomy = taxonomyService.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(),
 				current.getSubtaxa(), current.getSubtAuthor());
 		
-		if (!(ensuredTaxonomy.sameAs(current))) {
+		if (!(ensuredTaxonomy.sameAs(taxonomy))) {
 
 			accession.setTaxonomy(ensuredTaxonomy);
 			accession.setTaxGenus(ensuredTaxonomy.getTaxGenus());
@@ -485,6 +483,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				// We expect a String node
 				throw new RESTApiDataTypeException("Not a String");
 			}
+			if (jsonNode.isNull()) return null;
 			return StringUtils.defaultIfBlank(jsonNode.textValue(), currentValue);
 		}
 		return currentValue;