REST: upsert API call returns update result per accession

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

@@ -28,7 +28,7 @@ import com.fasterxml.jackson.databind.node.ObjectNode;
 
 public interface BatchRESTService {
 
-	boolean upsertAccessionData(FaoInstitute institute, Map<AccessionHeaderJson, ObjectNode> batch) throws RESTApiException;
+	List<UpsertResponse> upsertAccessionData(FaoInstitute institute, Map<AccessionHeaderJson, ObjectNode> batch) throws RESTApiException;
 
 	void upsertAccessionNames(FaoInstitute institute, List<AccessionNamesJson> batch)throws RESTApiException;
 

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

+/**
+ * Copyright 2015 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
+package org.genesys2.server.service;
+
+import java.io.Serializable;
+import java.util.UUID;
+
+/**
+ * Upsert response
+ */
+public class UpsertResponse implements Serializable {
+	private static final long serialVersionUID = 3266359129838078166L;
+
+	private String instCode;
+	private String acceNumb;
+	private String genus;
+	private String error;
+	private UpsertResult result;
+
+	public static class UpsertResult {
+		private Type action = Type.NOOP;
+		private UUID uuid;
+
+		public static enum Type {
+			NOOP, INSERT, UPDATE, DELETE
+		}
+
+		/**
+		 * @param action
+		 *            UPSERT or INSERT or DELETE
+		 */
+		public UpsertResult(Type action) {
+			this.action = action;
+		}
+
+		public Type getAction() {
+			return action;
+		}
+
+		public void setAction(Type action) {
+			this.action = action;
+		}
+
+		public UUID getUuid() {
+			return uuid;
+		}
+
+		public void setUUID(UUID uuid) {
+			this.uuid = uuid;
+		}
+	}
+
+	public UpsertResponse(String instCode, String acceNumb, String genus) {
+		this.instCode = instCode;
+		this.acceNumb = acceNumb;
+		this.genus = genus;
+	}
+
+	public String getInstCode() {
+		return instCode;
+	}
+
+	public String getAcceNumb() {
+		return acceNumb;
+	}
+
+	public String getGenus() {
+		return genus;
+	}
+
+	public String getError() {
+		return error;
+	}
+
+	public UpsertResult getResult() {
+		return result;
+	}
+
+	public void setResult(UpsertResult result) {
+		this.result = result;
+	}
+
+	public void setError(String error) {
+		this.error = error;
+	}
+}

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

@@ -50,7 +50,8 @@ import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.OrganizationService;
 import org.genesys2.server.service.TaxonomyService;
-import org.genesys2.server.servlet.controller.rest.PleaseRetryException;
+import org.genesys2.server.service.UpsertResponse;
+import org.genesys2.server.service.UpsertResponse.UpsertResult;
 import org.genesys2.server.servlet.controller.rest.model.AccessionAliasJson;
 import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
 import org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson;
@@ -137,11 +138,13 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
-	public boolean upsertAccessionData(FaoInstitute institute, Map<AccessionHeaderJson, ObjectNode> batch) throws RESTApiException {
+	public List<UpsertResponse> upsertAccessionData(FaoInstitute institute, Map<AccessionHeaderJson, ObjectNode> batch) throws RESTApiException {
 		LOG.info("Batch processing " + batch.size() + " entries for " + institute.getCode());
 
 		final boolean useUniqueAcceNumbs = institute.hasUniqueAcceNumbs();
 
+		final List<UpsertResponse> upsertResponses = new ArrayList<UpsertResponse>();
+
 		final List<Accession> toSave = new ArrayList<Accession>();
 		final List<AccessionCollect> toSaveColl = new ArrayList<AccessionCollect>();
 		final List<AccessionCollect> toRemoveColl = new ArrayList<AccessionCollect>();
@@ -180,20 +183,18 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				LOG.debug("Loading accession " + dataJson);
 			}
 
+			UpsertResponse upsertResponse = new UpsertResponse(dataJson.instCode, dataJson.acceNumb, dataJson.genus);
+			upsertResponses.add(upsertResponse);
+			UpsertResult upsertResult = null;
+
 			if (!institute.getCode().equals(dataJson.instCode)) {
-				throw new RuntimeException("Accession does not belong to instCode=" + institute.getCode() + " acn=" + dataJson);
+				throw new RESTApiException("Accession does not belong to instCode=" + institute.getCode() + " acn=" + dataJson);
 			}
 
-			Accession accession = CollectionUtils.find(loaded, new Predicate<Accession>() {
-				@Override
-				public boolean evaluate(Accession a) {
-					if (useUniqueAcceNumbs) {
-						return a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb);
-					} else {
-						return a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb) && a.getTaxonomy().getGenus().equalsIgnoreCase(dataJson.genus);
-					}
-				}
-			});
+			Accession accession = loaded.stream()
+					.filter(a -> useUniqueAcceNumbs ? (a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb))
+							: (a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb) && a.getTaxonomy().getGenus().equalsIgnoreCase(dataJson.genus)))
+					.findFirst().orElse(null);
 
 			boolean updated = false;
 
@@ -214,9 +215,14 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				}
 
 				updated = true;
+				upsertResult = new UpsertResult(UpsertResult.Type.INSERT);
+
 			} else {
 				if (LOG.isTraceEnabled())
 					LOG.trace("*** Updating accession " + dataJson);
+
+				upsertResult = new UpsertResult(UpsertResult.Type.UPDATE);
+				upsertResult.setUUID(accession.getUuid());
 			}
 
 			if (accession.getAccessionId().getId() == null || useUniqueAcceNumbs && accnJson.get(Api1Constants.Accession.GENUS) != null
@@ -321,7 +327,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 					updated = true;
 				}
 			}
-			
+
 			value = accnJson.get(Api1Constants.Accession.ACCEURL);
 			if (value != null) {
 				if (!value.isNull() && !value.isTextual()) {
@@ -500,11 +506,34 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			if (updated) {
 				toSave.add(accession);
 			}
+
+			// Set upsert result
+			upsertResponse.setResult(upsertResult);
 		}
 
 		if (toSave.size() > 0) {
 			LOG.info("Storing " + toSave.size() + " accessions.");
-			genesysService.saveAccessions(institute, toSave);
+			List<Accession> savedData = genesysService.saveAccessions(institute, toSave);
+
+			// Iterate savedData to extract UUIDs
+			upsertResponses.stream().forEach(response -> {
+				Accession accession = savedData.stream()
+						.filter(a -> useUniqueAcceNumbs ? (a.getAccessionName()
+								.equalsIgnoreCase(response.getAcceNumb()))
+								: (a.getAccessionName().equalsIgnoreCase(response.getAcceNumb())
+										&& a.getTaxonomy().getGenus().equalsIgnoreCase(response.getGenus())))
+						.findFirst().orElse(null);
+
+				UpsertResult result = response.getResult();
+				if (accession != null) {
+					if (result.getUuid() == null) {
+						result.setAction(UpsertResult.Type.INSERT);
+					} else {
+						result.setAction(UpsertResult.Type.UPDATE);
+					}
+					result.setUUID(accession.getUuid());
+				}
+			});
 		}
 
 		if (toSaveColl.size() > 0) {
@@ -548,7 +577,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		updateAccessionAliases(collNumbs, AliasType.COLLNUMB, false);
 
 		LOG.info("Done saving data");
-		return toSave.size() > 0 || toSaveColl.size() > 0 || toSaveGeo.size() > 0 || toSaveBreed.size() > 0 || toSaveExch.size() > 0;
+		return upsertResponses;
 	}
 
 	private boolean updateStorage(AccessionData accession, ObjectNode accnJson) throws RESTApiDataTypeException {
@@ -736,7 +765,12 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	 * @throws RESTApiException
 	 */
 	private boolean updateTaxonomy(AccessionData accession, JsonNode accnJson) throws RESTApiException {
-		boolean updated = false;
+		if (accession.getTaxonomy() != null && (!accnJson.has(Api1Constants.Accession.GENUS_NEW) && !accnJson.has(Api1Constants.Accession.SPECIES))) {
+			if (LOG.isWarnEnabled())
+				LOG.warn("Not updating taxonomy without newGenus or species data");
+
+			return false;
+		}
 
 		// Do not persist this one, temporary use
 		final Taxonomy2 taxonomy = accession.getTaxonomy();
@@ -761,15 +795,17 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 		if (ensuredTaxonomy == null) {
 			LOG.warn("Could not find taxonomy for upsert " + current);
-			throw new PleaseRetryException("Could not find taxonomy " + current.getTaxonName());
+			// throw new PleaseRetryException("Could not find taxonomy " +
+			// current.getTaxonName());
+			throw new RESTApiException("Could not find taxonomy. Provide GENUS, SPECIES, SPAUTHOR, SUBTAXA and SUBTAUTHOR fields");
 		}
 
-		if (!ensuredTaxonomy.sameAs(taxonomy)) {
+		if (!ensuredTaxonomy.sameAs(accession.getTaxonomy())) {
 			accession.setTaxonomy(ensuredTaxonomy);
-			updated = true;
+			return true;
+		} else {
+			return false;
 		}
-
-		return updated;
 	}
 
 	/**
@@ -880,7 +916,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		}
 
 		if (toSave.size() > 0) {
-			// LOG.info("Saving aliases  count=" + toSave.size());
+			// LOG.info("Saving aliases count=" + toSave.size());
 			genesysService.saveAliases(toSave);
 		}
 		if (toRemove.size() > 0) {
@@ -916,7 +952,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				LOG.warn("No such accession " + dataJson);
 				continue;
 			}
-			// LOG.info("Updating  " + dataJson + " with=" + dataJson.aliases);
+			// LOG.info("Updating " + dataJson + " with=" + dataJson.aliases);
 
 			final List<AccessionAliasJson> aliases = dataJson.aliases;
 			final List<AccessionAlias> existingAliases = genesysService.listAccessionAliases(accession.getAccessionId());

src/main/java/org/genesys2/server/servlet/controller/rest/AccessionController.java

@@ -30,7 +30,6 @@ import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.json.AccessionJson;
 import org.genesys2.server.model.json.Api1Constants;
 import org.genesys2.server.service.BatchRESTService;
-import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.ElasticService;
 import org.genesys2.server.service.FilterConstants;
 import org.genesys2.server.service.GenesysFilterService;
@@ -39,6 +38,7 @@ import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TaxonomyService;
+import org.genesys2.server.service.UpsertResponse;
 import org.genesys2.server.service.impl.FilterHandler;
 import org.genesys2.server.service.impl.FilterHandler.AppliedFilter;
 import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
@@ -84,9 +84,6 @@ public class AccessionController extends RestController {
 	@Autowired
 	private GenesysFilterService filterService;
 
-	@Autowired
-	private CropService cropService;
-
 	@Autowired
 	BatchRESTService batchRESTService;
 
@@ -198,8 +195,9 @@ public class AccessionController extends RestController {
 	 * @throws RESTApiException
 	 */
 	@RequestMapping(value = "/{instCode}/upsert", method = { RequestMethod.POST, RequestMethod.PUT }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody String upsertInstituteAccession(@PathVariable("instCode") String instCode, @RequestBody String content)
+	public @ResponseBody Object upsertInstituteAccession(@PathVariable("instCode") String instCode, @RequestBody String content)
 			throws JsonProcessingException, IOException, RESTApiException {
+
 		// User's permission to WRITE to this WIEWS institute are checked in
 		// BatchRESTService.
 		final FaoInstitute institute = instituteService.getInstitute(instCode);
@@ -234,11 +232,17 @@ public class AccessionController extends RestController {
 				// persisted
 				batchRESTService.ensureTaxonomies(institute, batch);
 				// Step 2: Upsert data
-				batchRESTService.upsertAccessionData(institute, batch);
+				List<UpsertResponse> response = null;
+				try {
+					response = batchRESTService.upsertAccessionData(institute, batch);
+				} catch (RESTApiException e) {
+					LOG.info("Retrying upsert one by one due to " + e.getMessage());
+					response = upsertAccessionData1by1(institute, batch);
+				}
 				// Force update institute#accessionCount (outside previous
 				// transaction)
 				genesysService.updateAccessionCount(institute);
-				return JSON_OK;
+				return response;
 			} catch (PleaseRetryException | HibernateOptimisticLockingFailureException
 					| org.springframework.orm.hibernate3.HibernateOptimisticLockingFailureException e) {
 				LOG.info("Will retry upsert. Error: " + e.getMessage());
@@ -246,7 +250,34 @@ public class AccessionController extends RestController {
 			}
 		}
 
-		throw new RESTApiException("Could not upsert accession data.", cause);
+		throw new RESTApiException("Could not upsert accession data. " + cause.getMessage(), cause);
+	}
+
+	private List<UpsertResponse> upsertAccessionData1by1(FaoInstitute institute, Map<AccessionHeaderJson, ObjectNode> batch) {
+		LOG.info("Attempting insert 1 by 1");
+
+		final Map<AccessionHeaderJson, ObjectNode> batchOfOne = new HashMap<AccessionHeaderJson, ObjectNode>();
+		List<UpsertResponse> response = new ArrayList<UpsertResponse>();
+		for (AccessionHeaderJson acceJ : batch.keySet()) {
+
+			try {
+			
+				batchOfOne.clear();
+				batchOfOne.put(acceJ, batch.get(acceJ));
+				UpsertResponse accessionResponse = batchRESTService.upsertAccessionData(institute, batchOfOne).get(0);
+				response.add(accessionResponse);
+				
+			} catch (RESTApiException e) {
+				if (LOG.isInfoEnabled()) {
+					LOG.info("Error upserting " + acceJ.instCode + ": " + e.getMessage());
+				}
+
+				UpsertResponse accessionResponse = new UpsertResponse(acceJ.instCode, acceJ.acceNumb, acceJ.genus);
+				accessionResponse.setError(e.getMessage());
+				response.add(accessionResponse);
+			}
+		}
+		return response;
 	}
 
 	/**