Improved support for Accession 'other' names

pom.xml

@@ -101,11 +101,6 @@
 			<version>${commons.beanutils.version}</version>
 		</dependency>
 
-		<dependency>
-			<groupId>commons-collections</groupId>
-			<artifactId>commons-collections</artifactId>
-			<version>${commons.collections.version}</version>
-		</dependency>
 
 		<dependency>
 			<groupId>commons-fileupload</groupId>
@@ -352,6 +347,11 @@
 			<artifactId>spring-aspects</artifactId>
 			<version>3.2.5.RELEASE</version>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-collections4</artifactId>
+			<version>4.0</version>
+		</dependency>
 	</dependencies>
 
 	<build>

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

+/**
+ * Copyright 2013 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.model.genesys;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.persistence.Version;
+
+import org.genesys2.server.model.BusinessModel;
+
+/**
+ * Accession "alias"
+ */
+@Entity
+@Table(name = "accessionalias")
+public class AccessionAlias extends BusinessModel {
+
+	public static enum AliasType {
+		GENERIC(0), DONORNAME(1), BREEDERNAME(2), DATABASEID(3), LOCALNAME(4);
+
+		private int id;
+
+		private AliasType(int id) {
+			this.id = id;
+		}
+
+		public static AliasType getType(Integer id) {
+			if (id == null) {
+				return null;
+			}
+
+			for (AliasType aliasType : AliasType.values()) {
+				if (id.equals(aliasType.getId())) {
+					return aliasType;
+				}
+			}
+
+			throw new IllegalArgumentException("No matching type for id " + id);
+		}
+
+		public int getId() {
+			return id;
+		}
+	}
+
+	@Version
+	private long version = 0;
+
+	@ManyToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
+	@JoinColumn(name = "accessionId", nullable = false, updatable = false)
+	private Accession accession;
+
+	@Column(name = "name", length = 150)
+	private String name;
+
+	@Column(length = 7)
+	private String instCode;
+
+	@Column
+	private int aliasType = AliasType.GENERIC.id;
+
+	@Column(length = 2)
+	private String lang;
+
+	public AccessionAlias() {
+	}
+
+	public long getVersion() {
+		return version;
+	}
+
+	public void setVersion(long version) {
+		this.version = version;
+	}
+
+	public Accession getAccession() {
+		return accession;
+	}
+
+	public void setAccession(Accession accession) {
+		this.accession = accession;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public String getInstCode() {
+		return instCode;
+	}
+
+	public void setInstCode(String instCode) {
+		this.instCode = instCode;
+	}
+
+	public AliasType getAliasType() {
+		return AliasType.getType(this.aliasType);
+	}
+
+	public void setAliasType(AliasType aliasType) {
+		this.aliasType = aliasType.getId();
+	}
+	
+	public String getLang() {
+		return lang;
+	}
+	
+	public void setLang(String lang) {
+		this.lang = lang;
+	}
+}

src/main/java/org/genesys2/server/persistence/domain/AccessionAliasRepository.java

+/**
+ * Copyright 2013 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.persistence.domain;
+
+import java.util.List;
+
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionAlias;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface AccessionAliasRepository extends JpaRepository<AccessionAlias, Long> {
+
+	List<AccessionAlias> findByAccession(Accession accession);
+
+}

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

@@ -17,6 +17,7 @@
 package org.genesys2.server.service;
 
 import java.text.MessageFormat;
+import java.util.List;
 import java.util.Map;
 
 import org.genesys2.server.model.impl.AccessionIdentifier3;
@@ -28,6 +29,8 @@ public interface BatchRESTService {
 
 	boolean upsertAccessionData(FaoInstitute institute, Map<DataJson, ObjectNode> batch);
 
+	void upsertAccessionNames(FaoInstitute institute, List<AcceNames> batch);
+
 	public static class DataJson implements AccessionIdentifier3 {
 		public String instCode;
 		public String acceNumb;
@@ -54,4 +57,18 @@ public interface BatchRESTService {
 		}
 	}
 
+	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;
+		}
+	}
 }

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

@@ -24,6 +24,7 @@ import java.util.Map;
 import java.util.Set;
 
 import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AllAccnames;
 import org.genesys2.server.model.genesys.AllAcqBreeding;
@@ -60,6 +61,8 @@ public interface GenesysService {
 
 	AllAccnames listAccessionNames(Accession accession);
 
+	List<AccessionAlias> listAccessionAliases(Accession accession);
+
 	AllAcqExchange listAccessionExchange(Accession accession);
 
 	AllAcqCollect listAccessionCollect(Accession accession);
@@ -138,4 +141,8 @@ public interface GenesysService {
 
 	void writeAccessions(FaoInstitute faoInstitute, OutputStream outputStream) throws IOException;
 
+	void saveAliases(List<AccessionAlias> aliases);
+
+	void removeAliases(List<AccessionAlias> aliases);
+
 }

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

@@ -21,13 +21,17 @@ import java.util.List;
 import java.util.Map;
 import java.util.UUID;
 
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.collections4.Predicate;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AllAcqCollect;
 import org.genesys2.server.model.genesys.Taxonomy;
+import org.genesys2.server.model.genesys.AccessionAlias.AliasType;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.BatchRESTService;
@@ -248,4 +252,65 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		return toSave.size() > 0 || toSaveColl.size() > 0 || toSaveGeo.size() > 0;
 	}
 
+	@Override
+	@Transactional
+	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
+	public void upsertAccessionNames(FaoInstitute institute, List<AcceNames> 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) {
+			Accession accession = genesysService.getAccession(institute.getCode(), dataJson.genus, dataJson.acceNumb);
+			if (accession == null) {
+				LOG.warn("No such accession " + dataJson);
+				continue;
+			}
+			// LOG.info("Updating  " + dataJson + " with=" + dataJson.aliases);
+
+			List<AccessionAlias> existingAliases = genesysService.listAccessionAliases(accession);
+			// Find aliases to remove
+			for (final AccessionAlias aa : existingAliases) {
+				if (null == CollectionUtils.find(dataJson.aliases, new Predicate<AcceAlias>() {
+					@Override
+					public boolean evaluate(AcceAlias alias) {
+						return StringUtils.equals(alias.name, aa.getName());
+					}
+				})) {
+					toRemove.add(aa);
+				}
+			}
+			// Add or update
+			for (final AcceAlias aa : dataJson.aliases) {
+				AccessionAlias accessionAlias = CollectionUtils.find(existingAliases, new Predicate<AccessionAlias>() {
+					@Override
+					public boolean evaluate(AccessionAlias alias) {
+						return StringUtils.equals(alias.getName(), aa.name);
+					}
+				});
+
+				if (accessionAlias == null) {
+					accessionAlias = new AccessionAlias();
+					accessionAlias.setAccession(accession);
+				}
+
+				accessionAlias.setName(aa.name);
+				accessionAlias.setInstCode(aa.instCode);
+				accessionAlias.setAliasType(AliasType.getType(aa.type));
+
+				toSave.add(accessionAlias);
+			}
+		}
+
+		if (toSave.size() > 0) {
+			LOG.info("Saving aliases for instCode=" + institute.getCode() + " count=" + toSave.size());
+			genesysService.saveAliases(toSave);
+		}
+		if (toRemove.size() > 0) {
+			LOG.info("Removing aliases for instCode=" + institute.getCode() + " count=" + toRemove.size());
+			genesysService.removeAliases(toRemove);
+		}
+
+	}
 }

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

@@ -35,6 +35,7 @@ import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AccessionTrait;
 import org.genesys2.server.model.genesys.AllAccnames;
@@ -54,6 +55,7 @@ import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.Organization;
+import org.genesys2.server.persistence.domain.AccessionAliasRepository;
 import org.genesys2.server.persistence.domain.AccessionBreedingRepository;
 import org.genesys2.server.persistence.domain.AccessionCollectRepository;
 import org.genesys2.server.persistence.domain.AccessionExchangeRepository;
@@ -146,6 +148,10 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	@Autowired
 	private HtmlSanitizer htmlSanitizer;
 
+	@Autowired
+	private AccessionAliasRepository accessionAliasRepository;
+	
+
 	@Override
 	public long countByInstitute(FaoInstitute institute) {
 		return accessionRepository.countByInstitute(institute);
@@ -256,6 +262,11 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	public AllAccnames listAccessionNames(Accession accession) {
 		return accessionNamesRepository.findByAccession(accession);
 	}
+	
+	@Override
+	public List<AccessionAlias> listAccessionAliases(Accession accession) {
+		return accessionAliasRepository.findByAccession(accession);
+	}
 
 	@Override
 	public List<Metadata> listMetadata(Accession accession) {
@@ -800,4 +811,16 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	public void refreshMetadataMethods() {
 		genesysLowlevelRepository.refreshMetadataMethods();
 	}
+	
+	@Override
+	@Transactional
+	public void saveAliases(List<AccessionAlias> aliases) {
+		accessionAliasRepository.save(aliases);
+	}
+	
+	@Override
+	@Transactional
+	public void removeAliases(List<AccessionAlias> aliases) {
+		accessionAliasRepository.delete(aliases);		
+	}
 }

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

@@ -22,7 +22,7 @@ import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 
-import org.apache.commons.collections.ListUtils;
+import org.apache.commons.collections4.ListUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -54,7 +54,6 @@ public class InstituteServiceImpl implements InstituteService {
 
 	public static final Log LOG = LogFactory.getLog(InstituteServiceImpl.class);
 
-	@SuppressWarnings("unchecked")
 	private static final List<FaoInstitute> EMPTY_LIST = ListUtils.unmodifiableList(new ArrayList<FaoInstitute>());
 
 	@Autowired

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

@@ -68,6 +68,7 @@ public class AccessionController extends BaseController {
 		model.addAttribute("accession", accession);
 		model.addAttribute("faoInstitute", instituteService.getInstitute(accession.getInstituteCode()));
 		model.addAttribute("accessionNames", genesysService.listAccessionNames(accession));
+		model.addAttribute("accessionAliases", genesysService.listAccessionAliases(accession));
 		model.addAttribute("accessionExchange", genesysService.listAccessionExchange(accession));
 		model.addAttribute("accessionCollect", genesysService.listAccessionCollect(accession));
 		model.addAttribute("accessionBreeding", genesysService.listAccessionBreeding(accession));

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

@@ -18,6 +18,7 @@ package org.genesys2.server.servlet.controller.rest;
 
 import java.io.IOException;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 import org.genesys2.server.model.genesys.Accession;
@@ -185,6 +186,27 @@ public class AccessionController extends RestController {
 		return JSON_OK;
 	}
 
+	/**
+	 * Update accessions in the system
+	 * 
+	 * @return
+	 * @throws IOException
+	 * @throws JsonProcessingException
+	 */
+	@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) {
+		// User's permission to WRITE to this WIEWS institute are checked in
+		// BatchRESTService.
+		FaoInstitute institute = instituteService.getInstitute(instCode);
+		if (institute == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		batchRESTService.upsertAccessionNames(institute, batch);
+		return JSON_OK;
+	}
+
 	private BatchRESTService.DataJson readAid3(JsonNode json) {
 		BatchRESTService.DataJson dataJson = new BatchRESTService.DataJson();
 

src/main/resources/content/language.properties

@@ -201,6 +201,11 @@ accession.sampleStatus.420=Mutant/genetic stock
 accession.sampleStatus.500=Advanced/improved cultivar
 accession.sampleStatus.999=Other
 accession.availability=Availability
+accession.aliasType.GENERIC=
+accession.aliasType.DONORNAME=(Donor accession name)
+accession.aliasType.BREEDERNAME=(Used by breeders)
+accession.aliasType.DATABASEID=(Database ID)
+accession.aliasType.LOCALNAME=(Local name)
 
 accession.availability.=Unknown
 accession.availability.true=Available

src/main/webapp/WEB-INF/jsp/accession/details.jsp

@@ -109,10 +109,24 @@
 				<td><spring:message code="accession.availability.${accession.availability}" /></td>
 			</tr>
 			
-			
 			<tr>
 				<td><spring:message code="accession.otherNames" /></td>
-				<td><c:out value="${accessionNames.accNames}" /><br /> <c:out value="${accessionNames.otherIds}" /></td>
+				<td>
+				<c:forEach items="${accessionAliases}" var="accessionAlias">
+					<div>
+						<c:out value="${accessionAlias.name}" />
+						<c:if test="${accessionAlias.instCode != ''}">
+							<a href="<c:url value="/wiews/${accessionAlias.instCode.toLowerCase()}" />">
+							${accessionAlias.instCode}
+							</a>
+						</c:if>
+						<c:if test="${accessionAlias.lang != ''}">
+							<c:out value="${accessionAlias.lang}" />
+						</c:if>
+						<spring:message code="accession.aliasType.${accessionAlias.aliasType}" />
+					</div>			
+				</c:forEach>
+				</td>
 			</tr>
 			
 			<tr>