Accession#remarks

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

+/**
+ * Copyright 2014 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.Lob;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.persistence.Version;
+
+import org.genesys2.server.model.BusinessModel;
+import org.hibernate.search.annotations.Field;
+import org.hibernate.search.annotations.Indexed;
+import org.hibernate.search.annotations.Store;
+
+/**
+ * Accession "alias"
+ */
+@Entity
+@Table(name = "accessionremark")
+@Indexed
+public class AccessionRemark extends BusinessModel {
+
+	@Version
+	private long version = 0;
+
+	@ManyToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
+	@JoinColumn(name = "accessionId", nullable = false, updatable = false)
+	private Accession accession;
+
+	@Lob
+	@Column(name = "remark")
+	@Field(name = "body", store = Store.NO)
+	private String remark;
+
+	@Column(length = 30)
+	private String fieldName;
+
+	public AccessionRemark() {
+	}
+
+	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 getRemark() {
+		return remark;
+	}
+
+	public void setRemark(String remark) {
+		this.remark = remark;
+	}
+
+	public String getFieldName() {
+		return fieldName;
+	}
+
+	public void setFieldName(String fieldName) {
+		this.fieldName = fieldName;
+	}
+
+}

src/main/java/org/genesys2/server/model/json/AccessionJson.java

@@ -27,6 +27,7 @@ public class AccessionJson {
 	private String donorName;
 	private CollectingJson coll;
 	private GeoJson geo;
+	private Remark[] remarks;
 
 	public long getVersion() {
 		return version;
@@ -228,4 +229,11 @@ public class AccessionJson {
 		this.geo = geo;
 	}
 
+	public Remark[] getRemarks() {
+		return remarks;
+	}
+	
+	public void setRemarks(Remark[] remarks) {
+		this.remarks = remarks;
+	}
 }

src/main/java/org/genesys2/server/model/json/GenesysJsonFactory.java

 package org.genesys2.server.model.json;
 
+import java.util.List;
+
 import org.apache.commons.lang3.StringUtils;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.genesys.AccessionRemark;
 import org.genesys2.server.model.genesys.Taxonomy2;
 
 public class GenesysJsonFactory {
@@ -107,4 +110,21 @@ public class GenesysJsonFactory {
 		return col;
 	}
 
+	public static Remark[] from(List<AccessionRemark> listAccessionRemarks) {
+		if (listAccessionRemarks == null)
+			return null;
+		Remark[] rs = new Remark[listAccessionRemarks.size()];
+		for (int i = 0; i < listAccessionRemarks.size(); i++) {
+			rs[i] = from(listAccessionRemarks.get(i));
+		}
+		return rs;
+	}
+
+	private static Remark from(AccessionRemark accessionRemark) {
+		Remark r = new Remark();
+		r.setFieldName(accessionRemark.getFieldName());
+		r.setRemark(accessionRemark.getRemark());
+		return r;
+	}
+
 }

src/main/java/org/genesys2/server/model/json/Remark.java

+package org.genesys2.server.model.json;
+
+public class Remark {
+	private String fieldName;
+	private String remark;
+
+	public String getFieldName() {
+		return fieldName;
+	}
+
+	public void setFieldName(String fieldName) {
+		this.fieldName = fieldName;
+	}
+
+	public String getRemark() {
+		return remark;
+	}
+
+	public void setRemark(String remark) {
+		this.remark = remark;
+	}
+
+}

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

+/**
+ * Copyright 2014 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.Collection;
+import java.util.List;
+
+import javax.persistence.OrderBy;
+
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionRemark;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+public interface AccessionRemarkRepository extends JpaRepository<AccessionRemark, Long> {
+
+	@OrderBy("fieldName")
+	List<AccessionRemark> findByAccession(Accession accession);
+
+	@Modifying
+	@Query("delete from AccessionRemark ar where ar.accession in (from Accession a where a.id in ( :ids ))")
+	void deleteForAccessions(@Param("ids") Collection<Long> accessionIds);
+}

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

@@ -29,6 +29,7 @@ import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AccessionExchange;
 import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.genesys.AccessionRemark;
 import org.genesys2.server.model.genesys.AllAccnames;
 import org.genesys2.server.model.genesys.ExperimentTrait;
 import org.genesys2.server.model.genesys.Metadata;
@@ -70,6 +71,8 @@ public interface GenesysService {
 
 	AccessionGeo listAccessionGeo(Accession accession);
 
+	List<AccessionRemark> listAccessionRemarks(Accession accession);
+
 	List<Metadata> listMetadata(Accession accession);
 
 	Page<Metadata> listMetadata(Pageable pageable);
@@ -167,7 +170,7 @@ public interface GenesysService {
 
 	/**
 	 * For institutes with {@link FaoInstitute#uniqueAcceNumbs}
-	 *
+	 * 
 	 * @param instCode
 	 * @param acceNumb
 	 * @return the 1 accession
@@ -179,4 +182,9 @@ public interface GenesysService {
 	Set<Long> listAccessions(FaoInstitute holdingInstitute, Set<Long> accessionIds);
 
 	int countAccessions(String jsonFilter);
+
+	void saveRemarks(List<AccessionRemark> toSaveRemarks);
+
+	void removeRemarks(List<AccessionRemark> toRemoveRemarks);
+
 }

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

@@ -20,6 +20,7 @@ import static org.genesys2.util.NumberUtils.areEqual;
 
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.UUID;
@@ -36,6 +37,7 @@ import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AccessionExchange;
 import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.genesys.AccessionRemark;
 import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
@@ -91,6 +93,8 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		final List<AccessionGeo> toSaveGeo = new ArrayList<AccessionGeo>();
 		final List<AccessionBreeding> toSaveBreed = new ArrayList<AccessionBreeding>();
 		final List<AccessionExchange> toSaveExch = new ArrayList<AccessionExchange>();
+		final List<AccessionRemark> toSaveRemarks = new ArrayList<AccessionRemark>();
+		final List<AccessionRemark> toRemoveRemarks = new ArrayList<AccessionRemark>();
 
 		final Map<Accession, ArrayNode> acceNames = new HashMap<Accession, ArrayNode>();
 		final Map<Accession, ArrayNode> otherNumbs = new HashMap<Accession, ArrayNode>();
@@ -142,6 +146,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			updated |= updateAcceNumb(accession, accnJson.get("newAcceNumb"));
 			updated |= updateOrgCty(accession, accnJson.get("orgCty"));
 			updated |= updateUuid(accession, accnJson.get("uuid"));
+			updated |= updateRemarks(accession, accnJson.get("remarks"), toSaveRemarks, toRemoveRemarks);
 
 			// TODO Move other setters to methods
 
@@ -402,6 +407,13 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			genesysService.saveExchange(toSaveExch);
 		}
 
+		if (toSaveRemarks.size() > 0) {
+			genesysService.saveRemarks(toSaveRemarks);
+		}
+		if (toRemoveRemarks.size() > 0) {
+			genesysService.removeRemarks(toRemoveRemarks);
+		}
+
 		updateAccessionAliases(acceNames, AliasType.ACCENAME);
 		updateAccessionAliases(otherNumbs, AliasType.OTHERNUMB);
 		updateAccessionAliases(donorNumbs, AliasType.DONORNUMB);
@@ -410,6 +422,72 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		return toSave.size() > 0 || toSaveColl.size() > 0 || toSaveGeo.size() > 0 || toSaveBreed.size() > 0 || toSaveExch.size() > 0;
 	}
 
+	private boolean updateRemarks(Accession accession, JsonNode jsonNode, List<AccessionRemark> toSaveRemarks, List<AccessionRemark> toRemoveRemarks)
+			throws RESTApiDataTypeException {
+		if (jsonNode == null || jsonNode.isNull()) {
+			return false;
+		}
+
+		if (!jsonNode.isArray()) {
+			throw new RESTApiDataTypeException("'remarks' must be an array");
+		}
+		ArrayNode arr = (ArrayNode) jsonNode;
+		Iterator<JsonNode> it = arr.elements();
+		List<AccessionRemark> existingRemarks = genesysService.listAccessionRemarks(accession);
+
+		if (existingRemarks != null)
+			toRemoveRemarks.addAll(existingRemarks);
+
+		while (it.hasNext()) {
+			JsonNode n = it.next();
+			if (n == null || n.isNull()) {
+				continue;
+			}
+
+			String remarkText = n.textValue();
+			if (StringUtils.isBlank(remarkText))
+				continue;
+
+			String[] mcpdRemark = remarkText.split(":", 2);
+			String fieldName = null, remark = null;
+			if (mcpdRemark.length == 2) {
+				fieldName = StringUtils.defaultIfBlank(mcpdRemark[0].trim(), null);
+				remark = StringUtils.defaultIfBlank(mcpdRemark[1].trim(), null);
+			} else {
+				remark = StringUtils.defaultIfBlank(mcpdRemark[0].trim(), null);
+			}
+
+			if (remark == null && fieldName == null) {
+				continue;
+			}
+
+			LOG.debug("fieldName=" + fieldName + " remark=" + remark);
+
+			AccessionRemark ar = findRemark(existingRemarks, fieldName, remark);
+			if (ar == null) {
+				ar = new AccessionRemark();
+				ar.setAccession(accession);
+				ar.setFieldName(fieldName);
+				ar.setRemark(remark);
+				toSaveRemarks.add(ar);
+			} else {
+				toRemoveRemarks.remove(ar);
+			}
+		}
+
+		return false;
+	}
+
+	private AccessionRemark findRemark(List<AccessionRemark> existingRemarks, String fieldName, String remark) {
+		if (existingRemarks == null)
+			return null;
+		for (AccessionRemark ar : existingRemarks) {
+			if (StringUtils.equals(ar.getFieldName(), fieldName) && StringUtils.equals(ar.getRemark(), remark))
+				return ar;
+		}
+		return null;
+	}
+
 	private boolean updateAcceNumb(Accession accession, JsonNode value) throws RESTApiDataTypeException, RESTApiValueException {
 		if (value != null) {
 			if (!value.isTextual()) {
@@ -474,10 +552,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 	/**
 	 * Inspect incoming JSON and change taxonomy if required
-	 *
+	 * 
 	 * @param accession
 	 * @param accnJson
-	 *
+	 * 
 	 * @return true if taxonomy was modified
 	 * @throws RESTApiException
 	 */
@@ -495,8 +573,8 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		current.setSubtaxa(stringIfProvided(accnJson.get("subtaxa"), current.getSubtaxa()));
 		current.setSubtAuthor(stringIfProvided(accnJson.get("subtauthor"), current.getSubtAuthor()));
 
-		final Taxonomy2 ensuredTaxonomy = taxonomyService.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
-				current.getSubtAuthor());
+		final Taxonomy2 ensuredTaxonomy = taxonomyService.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(),
+				current.getSubtaxa(), current.getSubtAuthor());
 
 		if (!ensuredTaxonomy.sameAs(taxonomy)) {
 
@@ -512,7 +590,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 	/**
 	 * Return
-	 *
+	 * 
 	 * @param jsonNode
 	 * @param currentValue
 	 * @return
@@ -553,7 +631,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 	/**
 	 * Converts textValue to JSON array node if required.
-	 *
+	 * 
 	 * @param accnJson
 	 * @param key
 	 * @return
@@ -582,7 +660,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 	/**
 	 * Convert to {@link AccessionAlias}
-	 *
+	 * 
 	 * @param acceNames
 	 */
 	private void updateAccessionAliases(Map<Accession, ArrayNode> acceNames, AliasType aliasType) {

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

@@ -47,6 +47,9 @@ public class GenesysRESTServiceImpl implements GenesysRESTService {
 
 		final AccessionGeo geo = genesysService.listAccessionGeo(accession);
 		aj.setGeo(GenesysJsonFactory.from(geo));
+		
+		aj.setRemarks(GenesysJsonFactory.from(genesysService.listAccessionRemarks(accession)));
+		
 		return aj;
 	}
 

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

@@ -46,6 +46,7 @@ import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AccessionExchange;
 import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.genesys.AccessionRemark;
 import org.genesys2.server.model.genesys.AccessionTrait;
 import org.genesys2.server.model.genesys.AllAccnames;
 import org.genesys2.server.model.genesys.ExperimentAccessionTrait;
@@ -68,6 +69,7 @@ import org.genesys2.server.persistence.domain.AccessionCollectRepository;
 import org.genesys2.server.persistence.domain.AccessionExchangeRepository;
 import org.genesys2.server.persistence.domain.AccessionGeoRepository;
 import org.genesys2.server.persistence.domain.AccessionNameRepository;
+import org.genesys2.server.persistence.domain.AccessionRemarkRepository;
 import org.genesys2.server.persistence.domain.AccessionRepository;
 import org.genesys2.server.persistence.domain.AccessionTraitRepository;
 import org.genesys2.server.persistence.domain.CropTaxonomyRepository;
@@ -160,6 +162,8 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	private HtmlSanitizer htmlSanitizer;
 	@Autowired
 	private AccessionAliasRepository accessionAliasRepository;
+	@Autowired
+	private AccessionRemarkRepository accessionRemarkRepository;
 
 	private final ObjectMapper mapper = new ObjectMapper();
 
@@ -306,6 +310,14 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		return accessionExchangeRepository.findByAccession(accession);
 	}
 
+	@Override
+	public List<AccessionRemark> listAccessionRemarks(Accession accession) {
+		if (accession == null || accession.getId() == null) {
+			return null;
+		}
+		return accessionRemarkRepository.findByAccession(accession);
+	}
+
 	@Override
 	public AllAccnames listAccessionNames(Accession accession) {
 		return accessionNamesRepository.findByAccession(accession);
@@ -589,6 +601,18 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	public void saveExchange(List<AccessionExchange> all) {
 		accessionExchangeRepository.save(all);
 	}
+	
+	@Override
+	@Transactional(readOnly = false)
+	public void saveRemarks(List<AccessionRemark> toSaveRemarks) {
+		accessionRemarkRepository.save(toSaveRemarks);
+	}
+	
+	@Override
+	@Transactional(readOnly = false)
+	public void removeRemarks(List<AccessionRemark> toRemoveRemarks) {
+		accessionRemarkRepository.delete(toRemoveRemarks);
+	}
 
 	@Override
 	public long countAvailable(Set<Long> accessionIds) {
@@ -695,12 +719,12 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		}
 
 		final Parameter parameter = parameterRepository.findByRdfUri(rdfUri); // assumes
-																		// that
-																		// crop
-																		// x
-																		// title
-																		// is
-																		// unique(?)
+		// that
+		// crop
+		// x
+		// title
+		// is
+		// unique(?)
 		return parameter;
 	}
 
@@ -709,12 +733,12 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	@Transactional(readOnly = true)
 	public Parameter getParameter(Crop crop, String title) {
 		final Parameter parameter = parameterRepository.findByCropAndTitle(crop, title); // assumes
-																					// that
-																					// crop
-																					// x
-																					// title
-																					// is
-																					// unique(?)
+		// that
+		// crop
+		// x
+		// title
+		// is
+		// unique(?)
 		return parameter;
 	}
 

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

@@ -65,6 +65,7 @@ public class AccessionController extends BaseController {
 		model.addAttribute("accessionBreeding", genesysService.listAccessionBreeding(accession));
 		model.addAttribute("accessionGeo", genesysService.listAccessionGeo(accession));
 		model.addAttribute("svalbardData", genesysService.getSvalbardData(accession));
+		model.addAttribute("accessionRemarks", genesysService.listAccessionRemarks(accession));
 
 		model.addAttribute("metadatas", genesysService.listMetadata(accession));
 		model.addAttribute("methods", genesysService.listMethods(accession));

src/main/resources/content/language.properties

@@ -301,6 +301,7 @@ accession.svalbard-data.taxonomy=Reported scientific name
 accession.svalbard-data.depositDate=Deposit date
 accession.svalbard-data.boxNumber=Box number
 accession.svalbard-data.quantity=Quantity
+accession.remarks=Remarks
 
 taxonomy.genus=Genus
 taxonomy.species=Species

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

@@ -72,81 +72,80 @@
 		</c:if>
 	</div>
 	
-	<table class="accessions crop-details">
-		<tbody>
-			<tr>
-				<td><spring:message code="accession.holdingInstitute" /></td>
-				<td><a property="dwc:instituteId" href="<c:url value="/wiews/${accession.instituteCode}" />"> <c:out value="${accession.institute.fullName}" />
-				</a></td>
-			</tr>
-			<tr>
-				<td><spring:message code="accession.holdingCountry" /></td>
-				<td><a href="<c:url value="/geo/${accession.institute.country.code3}" />"><c:out value="${accession.institute.country.getName(pageContext.response.locale)}" /></a></td>
-			</tr>
-			<tr>
-				<td><spring:message code="accession.accessionName" /></td>
-				<td><c:out value="${accession.accessionName}" /></td>
-			</tr>
+	<div class="crop-details">
+			<div class="row">
+				<div class="col-xs-4"><spring:message code="accession.holdingInstitute" /></div>
+				<div class="col-xs-8"><a property="dwc:instituteId" href="<c:url value="/wiews/${accession.instituteCode}" />"> <c:out value="${accession.institute.fullName}" />
+				</a></div>
+			</div>
+			<div class="row">
+				<div class="col-xs-4"><spring:message code="accession.holdingCountry" /></div>
+				<div class="col-xs-8"><a href="<c:url value="/geo/${accession.institute.country.code3}" />"><c:out value="${accession.institute.country.getName(pageContext.response.locale)}" /></a></div>
+			</div>
+			<div class="row">
+				<div class="col-xs-4"><spring:message code="accession.accessionName" /></div>
+				<div class="col-xs-8"><c:out value="${accession.accessionName}" /></div>
+			</div>
 			<c:if test="${accession.uuid ne null}">
-			<tr>
-				<td><spring:message code="accession.uuid" /></td>
-				<td><b><c:out value="${accession.uuid}" /></b></td>
-			</tr>
+			<div class="row">
+				<div class="col-xs-4"><spring:message code="accession.uuid" /></div>
+				<div class="col-xs-8"><b><c:out value="${accession.uuid}" /></b></div>
+			</div>
 			</c:if>
 
 			<c:if test="${crops ne null}">
-				<tr>
-					<td><spring:message code="accession.crop" /></td>
-					<td><c:forEach items="${crops}" var="crop">
+				<div class="row">
+					<div class="col-xs-4"><spring:message code="accession.crop" /></div>
+					<div class="col-xs-8"><c:forEach items="${crops}" var="crop">
 							<a href="<c:url value="/c/${crop.shortName}" />"><c:out value="${crop.getName(pageContext.response.locale)}" /></a>
-						</c:forEach></td>