Merge branch 'fix-taxonomy-update' into 'master'

Fix: Taxonomy should not be updated when only "genus" is provided

See merge request genesys-pgr/genesys-server!285

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

@@ -33,6 +33,7 @@ import javax.persistence.UniqueConstraint;
 import org.apache.commons.lang3.StringUtils;
 import org.genesys2.server.model.GlobalVersionedAuditedModel;
 import org.genesys2.server.model.impl.CropTaxonomy;
+import org.genesys2.server.model.json.Api1Constants;
 import org.hibernate.annotations.Type;
 import org.springframework.data.elasticsearch.annotations.Field;
 import org.springframework.data.elasticsearch.annotations.FieldIndex;
@@ -40,6 +41,7 @@ import org.springframework.data.elasticsearch.annotations.FieldIndex;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
 
 @Cacheable
 @Entity
@@ -51,18 +53,23 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 	private static final long serialVersionUID = 8881324404490162933L;
 
 	@Column(nullable = false, length = 100)
+	@JsonProperty(value = Api1Constants.Accession.GENUS)
 	private String genus;
 
 	@Column(nullable = false, length = 100)
+	@JsonProperty(value = Api1Constants.Accession.SPECIES)
 	private String species;
 
 	@Column(nullable = false, length = 100)
+	@JsonProperty(value = Api1Constants.Accession.SPAUTHOR)
 	private String spAuthor;
 
 	@Column(nullable = false, length = 100)
+	@JsonProperty(value = Api1Constants.Accession.SUBTAXA)
 	private String subtaxa;
 
 	@Column(nullable = false, length = 100)
+	@JsonProperty(value = Api1Constants.Accession.SUBTAUTHOR)
 	private String subtAuthor;
 
 	@Column(nullable = false)

src/main/java/org/genesys2/server/service/worker/AccessionUploader.java

@@ -44,6 +44,7 @@ import org.genesys2.server.model.genesys.PDCI;
 import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.model.json.Api1Constants;
 import org.genesys2.server.persistence.AccessionRepository;
 import org.genesys2.server.persistence.FaoInstituteRepository;
 import org.genesys2.server.service.CropService;
@@ -429,9 +430,36 @@ public class AccessionUploader implements InitializingBean {
 		} else if (taxonomy.equalTo(source)) {
 			// NOOP
 		} else {
-			LOG.trace("Ensuring taxonomy {}", jsonNode);
-			taxonomy = taxonomyService.ensureTaxonomy(source);
-			accession.setTaxonomy(taxonomy);
+			LOG.trace("Updating taxonomy of {} with {}", accession.getAccessionNumber(), jsonNode);
+			if (jsonNode.has(Api1Constants.Accession.GENUS) && jsonNode.has(Api1Constants.Accession.SPECIES)) {
+				Taxonomy2 updated = new Taxonomy2(taxonomy);
+				
+				updated.setGenus(source.getGenus());
+				updated.setSpecies(source.getSpecies());
+
+				if (jsonNode.has(Api1Constants.Accession.SPAUTHOR)) {
+					updated.setSpAuthor(source.getSpAuthor());
+				} else {
+					updated.setSpAuthor(null);
+				}
+				if (jsonNode.has(Api1Constants.Accession.SUBTAXA)) {
+					updated.setSubtaxa(source.getSubtaxa());
+					if (jsonNode.has(Api1Constants.Accession.SUBTAUTHOR)) {
+						updated.setSubtAuthor(source.getSubtAuthor());
+					} else {
+						updated.setSubtAuthor(null);
+					}
+				} else {
+					updated.setSubtaxa(null);
+					updated.setSubtAuthor(null);
+				}
+
+				if (! updated.equalTo(taxonomy)) { 
+					LOG.trace("Ensuring taxonomy {}", updated);
+					updated = taxonomyService.ensureTaxonomy(updated);
+					accession.setTaxonomy(updated);
+				}
+			}
 		}
 	}
 

src/test/java/org/genesys/test/server/services/AccessionUploaderTest.java

@@ -22,6 +22,7 @@ import java.util.List;
 
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.model.json.Api1Constants;
 import org.genesys2.server.persistence.AccessionIdRepository;
 import org.genesys2.server.persistence.AccessionRepository;
 import org.genesys2.server.persistence.FaoInstituteRepository;
@@ -243,9 +244,33 @@ public class AccessionUploaderTest extends AbstractServicesTest {
 		Accession a2 = accessionRepository.findByDoi(DOI_1);
 		assertThat(a2.getId(), equalTo(a1.getId()));
 		assertThat(a2.getUuid(), equalTo(a1.getUuid()));
-		assertThat(a2.getGenus(), is(GENUS_2));
+		// Genus not updated, missing species
+		assertThat(a2.getGenus(), is(GENUS_1));
 		assertThat(a2.getAccessionNumber(), is(ACCENUMB_2));
 	}
+
+	/**
+	 * Updating accession number and taxonomy must work with DOI only.
+	 */
+	@Test
+	public void testUpdateTaxonomysUsingDOI() {
+		accessionUploader.upsertAccessions(institute, upsertAccession(institute.getCode(), ACCENUMB_1, GENUS_1, DOI_1));
+
+		// update taxonomy
+		ArrayNode json = upsertAccession(institute.getCode(), ACCENUMB_1, GENUS_1, DOI_1);
+		ObjectNode taxa = (ObjectNode) json.get(0).get("taxonomy");
+		taxa.put(Api1Constants.Accession.GENUS, GENUS_2);
+		taxa.put(Api1Constants.Accession.SPECIES, "species");
+		taxa.put(Api1Constants.Accession.SPAUTHOR, "M.");
+
+		accessionUploader.upsertAccessions(institute, json);
+		assertThat(accessionRepository.count(), is(1l));
+		Accession a2 = accessionRepository.findByDoi(DOI_1);
+		assertThat(a2.getGenus(), is(GENUS_2));
+		assertThat(a2.getTaxonomy().getSpecies(), is("species"));
+		assertThat(a2.getTaxonomy().getSpAuthor(), is("M."));
+		assertThat(a2.getTaxonomy().getSubtAuthor(), is(""));
+	}
 	
 
 	/**
@@ -261,6 +286,26 @@ public class AccessionUploaderTest extends AbstractServicesTest {
 		assertThat(op.get(0).getError(), is("Accession does not belong to institute " + institute2.getCode()));
 	}
 
+	@Test
+	public void testTaxonomyNotModified() {
+		// upload accesion with species
+		ArrayNode json = upsertAccession(institute.getCode(), ACCENUMB_1, GENUS_1, DOI_1);
+		ObjectNode taxa = (ObjectNode) json.get(0).get("taxonomy");
+		taxa.put(Api1Constants.Accession.SPECIES, "species");
+		taxa.put(Api1Constants.Accession.SPAUTHOR, "M.");
+		accessionUploader.upsertAccessions(institute, json);
+
+		Accession a1 = accessionRepository.findOne(institute, null, ACCENUMB_1, GENUS_1);
+		assertThat(a1.getTaxonomy().getSpecies(), equalTo("species"));
+		assertThat(a1.getTaxonomy().getSpAuthor(), equalTo("M."));
+		
+		// Update without providing taxonomy details
+		accessionUploader.upsertAccessions(institute, upsertAccession(institute.getCode(), ACCENUMB_1, GENUS_1, DOI_1));
+		Accession a1a = accessionRepository.findOne(institute, DOI_1, ACCENUMB_1, GENUS_1);
+		
+		assertThat(a1a.getTaxonomy().getSpecies(), equalTo("species"));
+		assertThat(a1a.getTaxonomy().getSpAuthor(), equalTo("M."));
+	}
 
 	/**
 	 * Report invalid field in JSON