Subsets with #accessionRefs instead of #accessions

- Follows Datasets model

src/main/java/org/genesys2/server/model/impl/Subset.java

@@ -92,14 +92,14 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 	@JsonView({ JsonViews.Public.class })
 	private FaoInstitute institute;
 
-	/** The accessions. */
+	/** The accessionRefs. */
 	@ElementCollection(fetch = FetchType.LAZY)
 	@CollectionTable(name = "subset_accessions", joinColumns = @JoinColumn(name = "subsetId"),
 			// index
 			indexes = { @Index(columnList = "subsetId, instCode, acceNumb"), @Index(columnList = "subsetId, genus") })
 	@Field(type = FieldType.Object)
 	@JsonView({ JsonViews.Public.class })
-	private List<AccessionRef> accessions;
+	private List<AccessionRef> accessionRefs;
 
 	/** The accession count. */
 	@Column(name = "accession_count", nullable = false)
@@ -115,11 +115,9 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 	@JsonView({ JsonViews.Public.class })
 	private List<SubsetCreator> creators;
 
-
 	/** The crops. */
 	@ElementCollection(fetch = FetchType.EAGER)
-	@CollectionTable(name = "subset_crops", joinColumns = @JoinColumn(name = "subsetId"),
-			indexes = { @Index(columnList = "subsetId, crop") })
+	@CollectionTable(name = "subset_crops", joinColumns = @JoinColumn(name = "subsetId"), indexes = { @Index(columnList = "subsetId, crop") })
 	@Column(name = "crop", nullable = false, length = Crop.CROP_SHORTNAME_LENGTH)
 	@JsonView({ JsonViews.Minimal.class })
 	private Set<String> crops;
@@ -141,13 +139,14 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 		trimStringsToNull();
 
 		this.wiewsCode = this.institute.getCode();
-		
-		if (this.getAccessions() != null) {
-			this.accessionCount=this.getAccessions().size();
+
+		if (this.getAccessionRefs() != null) {
+			this.accessionCount = this.getAccessionRefs().size();
 		}
 	}
-	
-	/* (non-Javadoc)
+
+	/*
+	 * (non-Javadoc)
 	 * @see org.genesys.blocks.security.model.AclAwareModel#aclParentObject()
 	 */
 	@Override
@@ -273,21 +272,21 @@ public class Subset extends UuidModel implements AclAwareModel, SelfCleaning {
 	}
 
 	/**
-	 * Gets the accessions.
+	 * Gets the accessionRefs.
 	 *
-	 * @return the accessions
+	 * @return the accessionRefs
 	 */
-	public List<AccessionRef> getAccessions() {
-		return accessions;
+	public List<AccessionRef> getAccessionRefs() {
+		return accessionRefs;
 	}
-	
+
 	/**
-	 * Sets the accessions.
+	 * Sets the accessionRefs.
 	 *
-	 * @param accessions the new accessions
+	 * @param accessionRefs the new accessionRefs
 	 */
-	public void setAccessions(List<AccessionRef> accessions) {
-		this.accessions = accessions;
+	public void setAccessionRefs(List<AccessionRef> accessions) {
+		this.accessionRefs = accessions;
 	}
 
 	/**

src/main/java/org/genesys2/server/mvc/SubsetController.java

@@ -90,7 +90,7 @@ public class SubsetController extends BaseController {
 			throw new ResourceNotFoundException(e.getMessage());
 		}
 
-		final List<UUID> accessionUuids = subset.getAccessions().stream().skip((page - 1) * 50).limit(50).map(AccessionRef::getAccession).map(AccessionData::getUuid).collect(Collectors.toList());
+		final List<UUID> accessionUuids = subset.getAccessionRefs().stream().skip((page - 1) * 50).limit(50).map(AccessionRef::getAccession).map(AccessionData::getUuid).collect(Collectors.toList());
 		List<AccessionData> content = genesysService.listActiveAndHistoric(accessionUuids);
 		PageImpl<AccessionData> accessions = new PageImpl<>(content, new PageRequest(page - 1, 50), subset.getAccessionCount());
 

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

@@ -134,7 +134,7 @@ public class SubsetServiceImpl implements SubsetService {
 		}
 		final Subset subset = new Subset();
 		copyValues(subset, source);
-		copyAccessions(subset, source.getAccessions());
+		copyAccessions(subset, source.getAccessionRefs());
 		subset.setState(PublishState.DRAFT);
 		return deepLoad(subsetRepository.save(subset));
 	}
@@ -147,16 +147,16 @@ public class SubsetServiceImpl implements SubsetService {
 	 */
 	private void copyAccessions(final Subset target, final List<AccessionRef> list) {
 		if ((list == null) || (list.size() == 0)) {
-			if (target.getAccessions() != null)
-				target.getAccessions().clear();
+			if (target.getAccessionRefs() != null)
+				target.getAccessionRefs().clear();
 			return;
 		}
 
-		if (target.getAccessions() != null && !target.getAccessions().isEmpty()) {
-			target.getAccessions().clear();
-			target.getAccessions().addAll(list.stream().distinct().collect(Collectors.toList()));
+		if (target.getAccessionRefs() != null && !target.getAccessionRefs().isEmpty()) {
+			target.getAccessionRefs().clear();
+			target.getAccessionRefs().addAll(list.stream().distinct().collect(Collectors.toList()));
 		} else {
-			target.setAccessions(list.stream().distinct().collect(Collectors.toList()));
+			target.setAccessionRefs(list.stream().distinct().collect(Collectors.toList()));
 		}
 
 	}
@@ -201,8 +201,8 @@ public class SubsetServiceImpl implements SubsetService {
 		subset.getInstitute().getId();
 		if (subset.getCrops() != null)
 		    subset.getCrops().size();
-		if (subset.getAccessions() != null)
-			subset.getAccessions().size();
+		if (subset.getAccessionRefs() != null)
+			subset.getAccessionRefs().size();
 		if (subset.getCreators() != null)
 			subset.getCreators().size();
 
@@ -258,8 +258,8 @@ public class SubsetServiceImpl implements SubsetService {
 		LOG.info("Update Subset.");
 		final Subset subset = loadSubset(source);
 
-		subset.getAccessions().clear();
-		copyAccessions(subset, source.getAccessions());
+		subset.getAccessionRefs().clear();
+		copyAccessions(subset, source.getAccessionRefs());
 		copyValues(subset, source);
 
 		return deepLoad(subsetRepository.save(subset));
@@ -293,7 +293,7 @@ public class SubsetServiceImpl implements SubsetService {
 		final Set<UUID> uuidsToRemove = accessions.stream().map(AccessionData::getUuid).collect(Collectors.toSet());
 
 		// Keep accessions that are not in the list
-		subset.setAccessions(subset.getAccessions().stream().filter(accessionId -> !uuidsToRemove.contains(accessionId.getAccession().getUuid())).collect(Collectors.toList()));
+		subset.setAccessionRefs(subset.getAccessionRefs().stream().filter(accessionId -> !uuidsToRemove.contains(accessionId.getAccession().getUuid())).collect(Collectors.toList()));
 
 		subset.setState(PublishState.DRAFT);
 
@@ -312,13 +312,13 @@ public class SubsetServiceImpl implements SubsetService {
 
 		final List<AccessionData> accessions = accessionRepository.findActiveAndHistoric(accessionsUuids);
 
-		final Set<UUID> currentAccessions = subset.getAccessions().stream().map(AccessionRef::getAccession).map(Accession::getUuid).collect(Collectors.toSet());
+		final Set<UUID> currentAccessions = subset.getAccessionRefs().stream().map(AccessionRef::getAccession).map(Accession::getUuid).collect(Collectors.toSet());
 
 		for (AccessionData accession : accessions) {
 			if (currentAccessions.contains(accession.getUuid())) {
 				LOG.warn("Current Subset already contains accession, ignoring");
 			} else {
-				subset.getAccessions().add(accession.toAccessionRef());
+				subset.getAccessionRefs().add(accession.toAccessionRef());
 				currentAccessions.add(accession.getUuid());
 			}
 		}
@@ -396,7 +396,7 @@ public class SubsetServiceImpl implements SubsetService {
 
 	@Override
 	public List<Subset> listByAccession(Accession accession) {
-		return (List<Subset>) subsetRepository.findAll(QSubset.subset.accessions.any().accession.eq(accession));
+		return (List<Subset>) subsetRepository.findAll(QSubset.subset.accessionRefs.any().accession.eq(accession));
 	}
 
 	@Transactional

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

@@ -74,9 +74,9 @@ public class AccessionRefAspect {
 	}
 
 	private void subsetsDereference(Accession accession) {
-		List<Subset> subsets = (List<Subset>) subsetRepository.findAll(QSubset.subset.accessions.any().accession.eq(accession));
+		List<Subset> subsets = (List<Subset>) subsetRepository.findAll(QSubset.subset.accessionRefs.any().accession.eq(accession));
 		for (Subset subset : subsets) {
-			subset.getAccessions().stream().filter(accessionRef -> accessionRef.getAccession().equals(accession)).forEach(accessionRef -> accessionRef.setAccession(null));
+			subset.getAccessionRefs().stream().filter(accessionRef -> accessionRef.getAccession().equals(accession)).forEach(accessionRef -> accessionRef.setAccession(null));
 			subsetRepository.save(subset);
 		}
 	}
@@ -109,10 +109,10 @@ public class AccessionRefAspect {
 	}
 
 	private void updateSubsets(Accession accession) {
-		List<Subset> subsets = (List<Subset>) subsetRepository.findAll(QSubset.subset.accessions.any().acceNumb.eq(accession.getAccessionNumber()).and(QSubset.subset.accessions
-			.any().genus.eq(accession.getTaxonomy().getGenus())).and(QSubset.subset.accessions.any().instCode.eq(accession.getInstitute().getCode())));
+		List<Subset> subsets = (List<Subset>) subsetRepository.findAll(QSubset.subset.accessionRefs.any().acceNumb.eq(accession.getAccessionNumber()).and(QSubset.subset.accessionRefs
+			.any().genus.eq(accession.getTaxonomy().getGenus())).and(QSubset.subset.accessionRefs.any().instCode.eq(accession.getInstitute().getCode())));
 		for (Subset subset : subsets) {
-			for (AccessionRef accRef : subset.getAccessions()) {
+			for (AccessionRef accRef : subset.getAccessionRefs()) {
 				accRef.setAccession(accession);
 				LOG.debug("Setting accessionRef.id of {accRef} to {acceId} for  subset: {subset}", accRef.toString(), subset.toString());
 			}

src/test/java/org/genesys/test/server/api/v1/SubsetRestControllerTest.java

@@ -121,7 +121,7 @@ public class SubsetRestControllerTest extends AbstractApiTest {
 	@Transactional
 	public void cleanup() throws Exception {
 		for (Subset subset : subsetRepository.findAll()) {
-			subset.setAccessions(new ArrayList<>());
+			subset.setAccessionRefs(new ArrayList<>());
 			subsetRepository.save(subset);
 		}
 		subsetRepository.deleteAll();
@@ -162,7 +162,7 @@ public class SubsetRestControllerTest extends AbstractApiTest {
                 .andExpect(jsonPath("$.publisher", is(PUBLISHER)))
                 .andExpect(jsonPath("$.dateCreated", is(DATE_CREATED)))
                 .andExpect(jsonPath("$.rights", is(RIGHTS)))
-                .andExpect(jsonPath("$.accessions", hasSize(2)));
+                .andExpect(jsonPath("$.accessionRefs", hasSize(2)));
 		/*@formatter:on*/
 	}
 
@@ -172,15 +172,15 @@ public class SubsetRestControllerTest extends AbstractApiTest {
 		storedSubset.setTitle(TITLE_2);
 		storedSubset.setDescription(DESCRIPTION_2);
 
-		assertThat(storedSubset.getAccessions().size(), is(2));
+		assertThat(storedSubset.getAccessionRefs().size(), is(2));
 
-		final AccessionRef accessionRef = storedSubset.getAccessions().stream().findFirst().get();
+		final AccessionRef accessionRef = storedSubset.getAccessionRefs().stream().findFirst().get();
 
-		storedSubset.getAccessions().clear();
-		assertThat(storedSubset.getAccessions().size(), is(0));
+		storedSubset.getAccessionRefs().clear();
+		assertThat(storedSubset.getAccessionRefs().size(), is(0));
 
-		storedSubset.getAccessions().add(accessionRef);
-		assertThat(storedSubset.getAccessions().size(), is(1));
+		storedSubset.getAccessionRefs().add(accessionRef);
+		assertThat(storedSubset.getAccessionRefs().size(), is(1));
 
 		storedSubset.getInstitute().setSettings(null);
 		storedSubset.getInstitute().setNetworks(null);
@@ -197,7 +197,7 @@ public class SubsetRestControllerTest extends AbstractApiTest {
                 .andExpect(jsonPath("$", not(nullValue())))
                 .andExpect(jsonPath("$.title", is(TITLE_2)))
                 .andExpect(jsonPath("$.description", is(DESCRIPTION_2)))
-                .andExpect(jsonPath("$.accessions", hasSize(1)));
+                .andExpect(jsonPath("$.accessionRefs", hasSize(1)));
 		/*@formatter:on*/
 	}
 
@@ -258,9 +258,9 @@ public class SubsetRestControllerTest extends AbstractApiTest {
 	@Test
 	public void removeAccessionsFromSubsetTest() throws Exception {
 		final Subset subset = subsetService.create(institute, setUpSubset());
-		assertThat(subset.getAccessions().size(), is(2));
+		assertThat(subset.getAccessionRefs().size(), is(2));
 
-		final Set<UUID> accessionsUuid = subset.getAccessions().stream().map(AccessionRef::getAccession).map(Accession::getUuid).collect(Collectors.toSet());
+		final Set<UUID> accessionsUuid = subset.getAccessionRefs().stream().map(AccessionRef::getAccession).map(Accession::getUuid).collect(Collectors.toSet());
 
 		/*@formatter:off*/
         mockMvc.perform(post(SubsetController.API_BASE.concat("/remove-accessions/{UUID},{version}"), subset.getUuid(), subset.getVersion())
@@ -272,13 +272,13 @@ public class SubsetRestControllerTest extends AbstractApiTest {
 		/*@formatter:on*/
 
 		final Subset updated = subsetService.get(subset.getUuid());
-		assertThat(updated.getAccessions().size(), is(0));
+		assertThat(updated.getAccessionRefs().size(), is(0));
 	}
 
 	@Test
 	public void addAccessionsToSubsetTest() throws Exception {
 		final Subset subset = subsetService.create(institute, setUpSubset());
-		assertThat(subset.getAccessions().size(), is(2));
+		assertThat(subset.getAccessionRefs().size(), is(2));
 
 		List<AccessionRef> newAccessions = setUpAccessions();
 		final Set<UUID> accessionsUuid = newAccessions.stream().map(AccessionRef::getAccession).map(Accession::getUuid).collect(Collectors.toSet());
@@ -293,7 +293,7 @@ public class SubsetRestControllerTest extends AbstractApiTest {
 		/*@formatter:on*/
 
 		final Subset updated = subsetService.get(subset.getUuid());
-		assertThat(updated.getAccessions().size(), is(4));
+		assertThat(updated.getAccessionRefs().size(), is(4));
 	}
 
 	@Test
@@ -364,7 +364,7 @@ public class SubsetRestControllerTest extends AbstractApiTest {
 		subset.setPublisher(PUBLISHER);
 		subset.setDateCreated(DATE_CREATED);
 		subset.setRights(RIGHTS);
-		subset.setAccessions(setUpAccessions());
+		subset.setAccessionRefs(setUpAccessions());
 
 
 		return subset;