Moved JSON classes to .....rest.model

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

@@ -16,59 +16,18 @@
 
 package org.genesys2.server.service;
 
-import java.text.MessageFormat;
 import java.util.List;
 import java.util.Map;
 
-import org.genesys2.server.model.impl.AccessionIdentifier3;
 import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson;
+import org.genesys2.server.servlet.controller.rest.model.AccessionJson;
 
 import com.fasterxml.jackson.databind.node.ObjectNode;
 
 public interface BatchRESTService {
 
-	boolean upsertAccessionData(FaoInstitute institute, Map<DataJson, ObjectNode> batch);
+	boolean upsertAccessionData(FaoInstitute institute, Map<AccessionJson, ObjectNode> batch);
 
-	void upsertAccessionNames(FaoInstitute institute, List<AcceNames> batch);
-
-	public static class DataJson implements AccessionIdentifier3 {
-		public String instCode;
-		public String acceNumb;
-		public String genus;
-
-		@Override
-		public String getHoldingInstitute() {
-			return instCode;
-		}
-
-		@Override
-		public String getAccessionName() {
-			return acceNumb;
-		}
-
-		@Override
-		public String getGenus() {
-			return genus;
-		}
-
-		@Override
-		public String toString() {
-			return MessageFormat.format("AID3 instCode={0} acceNumb={1} genus={2}", instCode, acceNumb, genus);
-		}
-	}
-
-	public static class AcceNames extends BatchRESTService.DataJson {
-		public List<AcceAlias> aliases;
-	}
-
-	public static class AcceAlias {
-		public String name;
-		public String instCode;
-		public int type = 0;
-
-		@Override
-		public String toString() {
-			return "" + name + "@" + instCode;
-		}
-	}
+	void upsertAccessionNames(FaoInstitute institute, List<AccessionNamesJson> batch);
 }

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

@@ -40,6 +40,9 @@ 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.model.AccessionAliasJson;
+import org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson;
+import org.genesys2.server.servlet.controller.rest.model.AccessionJson;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Service;
@@ -72,13 +75,13 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
-	public boolean upsertAccessionData(FaoInstitute institute, Map<BatchRESTService.DataJson, ObjectNode> batch) {
+	public boolean upsertAccessionData(FaoInstitute institute, Map<AccessionJson, ObjectNode> batch) {
 		LOG.info("Batch processing " + batch.size() + " entries for " + institute);
 		List<Accession> toSave = new ArrayList<Accession>();
 		List<AllAcqCollect> toSaveColl = new ArrayList<AllAcqCollect>();
 		List<AccessionGeo> toSaveGeo = new ArrayList<AccessionGeo>();
 
-		for (BatchRESTService.DataJson dataJson : batch.keySet()) {
+		for (AccessionJson dataJson : batch.keySet()) {
 			if (LOG.isDebugEnabled())
 				LOG.debug("Loading accession " + dataJson);
 
@@ -255,13 +258,13 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
-	public void upsertAccessionNames(FaoInstitute institute, List<AcceNames> batch) {
+	public void upsertAccessionNames(FaoInstitute institute, List<AccessionNamesJson> batch) {
 		LOG.info("Batch processing " + batch.size() + " entries for " + institute);
 
 		List<AccessionAlias> toSave = new ArrayList<AccessionAlias>();
 		List<AccessionAlias> toRemove = new ArrayList<AccessionAlias>();
 
-		for (AcceNames dataJson : batch) {
+		for (AccessionNamesJson dataJson : batch) {
 			Accession accession = genesysService.getAccession(institute.getCode(), dataJson.genus, dataJson.acceNumb);
 			if (accession == null) {
 				LOG.warn("No such accession " + dataJson);
@@ -272,9 +275,9 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			List<AccessionAlias> existingAliases = genesysService.listAccessionAliases(accession);
 			// Find aliases to remove
 			for (final AccessionAlias aa : existingAliases) {
-				if (null == CollectionUtils.find(dataJson.aliases, new Predicate<AcceAlias>() {
+				if (null == CollectionUtils.find(dataJson.aliases, new Predicate<AccessionAliasJson>() {
 					@Override
-					public boolean evaluate(AcceAlias alias) {
+					public boolean evaluate(AccessionAliasJson alias) {
 						return StringUtils.equals(alias.name, aa.getName());
 					}
 				})) {
@@ -282,7 +285,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				}
 			}
 			// Add or update
-			for (final AcceAlias aa : dataJson.aliases) {
+			for (final AccessionAliasJson aa : dataJson.aliases) {
 				AccessionAlias accessionAlias = CollectionUtils.find(existingAliases, new Predicate<AccessionAlias>() {
 					@Override
 					public boolean evaluate(AccessionAlias alias) {

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

@@ -28,6 +28,8 @@ 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.servlet.controller.rest.model.AccessionNamesJson;
+import org.genesys2.server.servlet.controller.rest.model.AccessionJson;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
@@ -100,18 +102,18 @@ public class AccessionController extends RestController {
 	JsonNode check(@PathVariable("instCode") String instCode, @RequestBody String content) throws JsonProcessingException, IOException {
 		// TODO Check user's permissions to update this WIEWS institute.
 		JsonNode json = mapper.readTree(content);
-		Map<BatchRESTService.DataJson, ObjectNode> batch = new HashMap<BatchRESTService.DataJson, ObjectNode>();
+		Map<AccessionJson, ObjectNode> batch = new HashMap<AccessionJson, ObjectNode>();
 
 		if (json.isArray()) {
 			for (JsonNode j : json) {
-				BatchRESTService.DataJson dataJson = readAid3(j);
+				AccessionJson dataJson = readAid3(j);
 				if (!instCode.equals(dataJson.instCode)) {
 					throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
 				}
 				batch.put(dataJson, (ObjectNode) j);
 			}
 		} else {
-			BatchRESTService.DataJson dataJson = readAid3(json);
+			AccessionJson dataJson = readAid3(json);
 			if (!instCode.equals(dataJson.instCode)) {
 				throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
 			}
@@ -121,7 +123,7 @@ public class AccessionController extends RestController {
 		LOG.info("Batch processing " + batch.size() + " entries");
 		ArrayNode rets = mapper.createArrayNode();
 
-		for (BatchRESTService.DataJson dataJson : batch.keySet()) {
+		for (AccessionJson dataJson : batch.keySet()) {
 			if (LOG.isDebugEnabled())
 				LOG.debug("Loading accession " + dataJson);
 
@@ -164,18 +166,18 @@ public class AccessionController extends RestController {
 		}
 
 		JsonNode json = mapper.readTree(content);
-		Map<BatchRESTService.DataJson, ObjectNode> batch = new HashMap<BatchRESTService.DataJson, ObjectNode>();
+		Map<AccessionJson, ObjectNode> batch = new HashMap<AccessionJson, ObjectNode>();
 
 		if (json.isArray()) {
 			for (JsonNode j : json) {
-				BatchRESTService.DataJson dataJson = readAid3(j);
+				AccessionJson dataJson = readAid3(j);
 				if (!instCode.equals(dataJson.instCode)) {
 					throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
 				}
 				batch.put(dataJson, (ObjectNode) j);
 			}
 		} else {
-			BatchRESTService.DataJson dataJson = readAid3(json);
+			AccessionJson dataJson = readAid3(json);
 			if (!instCode.equals(dataJson.instCode)) {
 				throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
 			}
@@ -195,7 +197,7 @@ public class AccessionController extends RestController {
 	 */
 	@RequestMapping(value = "/{instCode}/names", method = { RequestMethod.POST, RequestMethod.PUT }, consumes = { MediaType.APPLICATION_JSON_VALUE }, produces = { MediaType.APPLICATION_JSON_VALUE })
 	public @ResponseBody
-	String upsertAccessionNames(@PathVariable("instCode") String instCode, @RequestBody List<BatchRESTService.AcceNames> batch) {
+	String upsertAccessionNames(@PathVariable("instCode") String instCode, @RequestBody List<AccessionNamesJson> batch) {
 		// User's permission to WRITE to this WIEWS institute are checked in
 		// BatchRESTService.
 		FaoInstitute institute = instituteService.getInstitute(instCode);
@@ -207,8 +209,8 @@ public class AccessionController extends RestController {
 		return JSON_OK;
 	}
 
-	private BatchRESTService.DataJson readAid3(JsonNode json) {
-		BatchRESTService.DataJson dataJson = new BatchRESTService.DataJson();
+	private AccessionJson readAid3(JsonNode json) {
+		AccessionJson dataJson = new AccessionJson();
 
 		dataJson.instCode = json.has("instCode") ? json.get("instCode").textValue() : null;
 		dataJson.acceNumb = json.has("acceNumb") ? json.get("acceNumb").textValue() : null;

src/main/java/org/genesys2/server/servlet/controller/rest/model/AccessionAliasJson.java

+package org.genesys2.server.servlet.controller.rest.model;
+
+public class AccessionAliasJson {
+	public String name;
+	public String instCode;
+	public int type = 0;
+
+	@Override
+	public String toString() {
+		return "" + name + "@" + instCode;
+	}
+}
\ No newline at end of file

src/main/java/org/genesys2/server/servlet/controller/rest/model/AccessionJson.java

+package org.genesys2.server.servlet.controller.rest.model;
+
+import java.text.MessageFormat;
+
+import org.genesys2.server.model.impl.AccessionIdentifier3;
+
+public class AccessionJson implements AccessionIdentifier3 {
+	public String instCode;
+	public String acceNumb;
+	public String genus;
+
+	@Override
+	public String getHoldingInstitute() {
+		return instCode;
+	}
+
+	@Override
+	public String getAccessionName() {
+		return acceNumb;
+	}
+
+	@Override
+	public String getGenus() {
+		return genus;
+	}
+
+	@Override
+	public String toString() {
+		return MessageFormat.format("AID3 instCode={0} acceNumb={1} genus={2}", instCode, acceNumb, genus);
+	}
+}
\ No newline at end of file

src/main/java/org/genesys2/server/servlet/controller/rest/model/AccessionNamesJson.java

+package org.genesys2.server.servlet.controller.rest.model;
+
+import java.util.List;
+
+public class AccessionNamesJson extends AccessionJson {
+	public List<AccessionAliasJson> aliases;
+}
\ No newline at end of file