Restored trait categories (+1 squashed commit)

Squashed commits:
[1b78b4d] Added support to filter on C&E

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

@@ -43,23 +43,16 @@ public class Parameter extends VersionedAuditedModel implements AclAwareModel {
 	@JoinColumn(name = "cropId")
 	private Crop crop;
 
-	// private Category category;
+	@ManyToOne(cascade = {}, optional = false)
+	@JoinColumn(name = "categoryId", nullable = false)
+	private ParameterCategory category;
+
 	@Column(nullable = false, length = 32)
 	private String title;
 
 	public Parameter() {
 	}
 
-	// @ManyToOne(cascade = {}, optional = false)
-	// @JoinColumn(name = "languageId")
-	// public Language getLanguage() {
-	// return this.language;
-	// }
-	//
-	// public void setLanguage(final Language language) {
-	// this.language = language;
-	// }
-
 	@PrePersist
 	void ensureUUID() {
 		if (this.uuid == null) {
@@ -75,15 +68,13 @@ public class Parameter extends VersionedAuditedModel implements AclAwareModel {
 		this.crop = crop;
 	}
 
-	// @ManyToOne(cascade = {}, optional = false)
-	// @JoinColumn(name = "categoryId", nullable = false)
-	// public Category getCategory() {
-	// return this.category;
-	// }
-	//
-	// public void setCategory(final Category category) {
-	// this.category = category;
-	// }
+	public ParameterCategory getCategory() {
+		return this.category;
+	}
+
+	public void setCategory(final ParameterCategory category) {
+		this.category = category;
+	}
 
 	public String getTitle() {
 		return this.title;

src/main/java/org/genesys2/server/model/genesys/ParameterCategory.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 java.io.IOException;
+import java.util.Locale;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.Lob;
+import javax.persistence.Transient;
+
+import org.genesys2.server.model.VersionedAuditedModel;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+@Entity(name = "parametercategory")
+public class ParameterCategory extends VersionedAuditedModel {
+	@Column(length = 100)
+	private String name;
+
+	@Lob
+	private String nameL;
+
+	@Transient
+	private JsonNode nameJ;
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public String getNameL() {
+		return nameL;
+	}
+
+	public void setNameL(String nameL) {
+		this.nameL = nameL;
+	}
+
+	public String getName(Locale locale) {
+		return getNameLocal(locale);
+	}
+
+	private synchronized String getNameLocal(Locale locale) {
+		if (this.nameJ == null && this.nameL != null) {
+			ObjectMapper mapper = new ObjectMapper();
+			try {
+				this.nameJ = mapper.readTree(nameL);
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}
+
+		return this.nameJ != null && this.nameJ.has(locale.getLanguage()) ? this.nameJ.get(locale.getLanguage()).textValue() : this.name;
+	}
+}

src/main/java/org/genesys2/server/persistence/domain/ParameterCategoryRepository.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 org.genesys2.server.model.genesys.ParameterCategory;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface ParameterCategoryRepository extends JpaRepository<ParameterCategory, Long> {
+
+}

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

@@ -43,4 +43,6 @@ public interface TraitValueRepository {
 	 */
 	List<Object> upsert(Metadata metadata, Accession accession, Method method, List<Object> list);
 
+	Map<String, Long> getStatistics(Method method);
+
 }
\ No newline at end of file

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

@@ -20,6 +20,7 @@ import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
+import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -340,4 +341,16 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 		return this.jdbcTemplate.queryForObject(String.format("SELECT COUNT(*) FROM `%s` WHERE metadataId=? AND accessionId=?", methodId), Integer.class,
 				metadataId, accessionId);
 	}
+	
+	@Override
+	public Map<String, Long> getStatistics(Method method) {
+		final HashMap<String, Long> stats=new HashMap<String, Long>();
+		this.jdbcTemplate.query(MessageFormat.format("SELECT `{0}`, COUNT(*) FROM `{1,number,#}` GROUP BY `{0}`", method.getFieldName(), method.getId()), new RowCallbackHandler() {
+			@Override
+			public void processRow(ResultSet rs) throws SQLException {
+				stats.put(rs.getString(1), rs.getLong(2));
+			}
+		});
+		return stats;
+	}
 }

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

@@ -17,6 +17,7 @@
 package org.genesys2.server.service;
 
 import java.util.List;
+import java.util.Map;
 
 import org.genesys2.server.model.genesys.Metadata;
 import org.genesys2.server.model.genesys.Method;
@@ -77,4 +78,6 @@ public interface TraitService {
 	 */
 	List<Method> listMyMethods();
 
+	Map<String, Long> getMethodStatistics(Method method);
+
 }

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

@@ -28,9 +28,11 @@ import org.apache.commons.lang.ArrayUtils;
 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.Method;
 import org.genesys2.server.persistence.domain.AccessionRepository;
 import org.genesys2.server.persistence.domain.TraitValueRepository;
 import org.genesys2.server.service.GenesysFilterService;
+import org.genesys2.server.service.TraitService;
 import org.genesys2.server.service.GenesysFilterService.GenesysFilter.FilterType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
@@ -59,6 +61,9 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 	@Autowired
 	private AccessionRepository accessionRepository;
 
+	@Autowired
+	private TraitService traitService;
+
 	// @PersistenceContext
 	// private EntityManager entityManager;
 
@@ -128,6 +133,26 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		createQuery(sbf, "geo.latitude", jsonTree.get("lat"), params);
 		createQuery(sbf, "geo.elevation", jsonTree.get("elevation"), params);
 		createQuery(sbf, "crop.shortName", jsonTree.get("crop"), params);
+
+		for (Iterator<String> it = jsonTree.fieldNames(); it.hasNext();) {
+			String fieldName = it.next();
+			if (fieldName.startsWith("gm:")) {
+				LOG.info("Filtering on C&E data, method=" + fieldName);
+				// Handle Genesys Method!
+				long methodId = Long.parseLong(fieldName.substring(3));
+				// Need to validate method
+				Method method = traitService.getMethod(methodId);
+				if (method != null) {
+					String alias = "gm" + methodId;
+					sb.append(" inner join `").append(methodId).append("` ").append(alias).append(" on ");
+					sb.append(alias).append(".accessionId=a.id");
+					createQuery(sbf, alias + ".`" + method.getFieldName() + "`", jsonTree.get(fieldName), params);
+				} else {
+					LOG.warn("No such method with id=" + methodId);
+				}
+			}
+		}
+
 		sb.append(sbf.toString());
 
 		LOG.info("Parameter count: " + params.size());

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

@@ -239,10 +239,11 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 			return null;
 		return accessionGeoRepository.findByAccession(accession);
 	}
-	
+
 	@Override
 	public List<AccessionGeo> listAccessionsGeo(Set<Long> copy) {
-		if (copy==null || copy.isEmpty()) return null;
+		if (copy == null || copy.isEmpty())
+			return null;
 		return accessionGeoRepository.findForAccessions(copy);
 	}
 
@@ -1124,4 +1125,12 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		for (Long id : toRemove)
 			this.accessionAliasRepository.delete(id);
 	}
+
+	@Override
+	public Map<String, Long> getMethodStatistics(Method method) {
+		if (method.isCoded()) {
+			return traitValueRepository.getStatistics(method);
+		} else
+			return null;
+	}
 }

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

@@ -16,8 +16,11 @@
 
 package org.genesys2.server.servlet.controller;
 
+import java.util.Map;
+
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.Parameter;
+import org.genesys2.server.model.genesys.TraitCode;
 import org.genesys2.server.service.TraitService;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -77,6 +80,13 @@ public class DescriptorController extends BaseController {
 		model.addAttribute("method", method);
 		model.addAttribute("metadatas", traitService.listMetadataByMethod(method));
 
+		if (method.isCoded()) {
+			Map<String, String> codeMap = TraitCode.parseCodeMap(method.getOptions());
+			model.addAttribute("codeMap", codeMap);
+			model.addAttribute("codeStatistics", traitService.getMethodStatistics(method));
+		}
+
+		
 		return "/descr/method";
 	}
 }

src/main/resources/content/language.properties

@@ -183,7 +183,7 @@ accession.duplSite=Safety duplication
 accession.inSvalbard=Svalbardized
 accession.inTrust.true=This accession is under Article 15 of the International Treaty on Plant Genetic Resources for Food and Agriculture.
 accession.mlsStatus.true=This accession is in the Multilateral System of the ITPGRFA. 
-accession.inSvalbard.true=Super-safety duplicated in Svalbard Seed Vault.
+accession.inSvalbard.true=Safety duplicated in Svalbard Seed Vault.
 accession.not-available-for-distribution=The accession is NOT available for distribution. 
 accession.available-for-distribution=The accession is available for distribution. 
 accession.elevation=Elevation
@@ -430,3 +430,6 @@ userprofile.email.send=Send email
 verification.invalid-key=Token key is not valid.
 verification.token-key=Validation key
 login.invalid-token=Invalid access token
+
+descriptor.category=Descriptor category
+method.coding-table=Coding table
\ No newline at end of file

src/main/resources/content/language_fr.properties

@@ -171,7 +171,7 @@ accession.mlsStatus=Statut MLS
 # accession.inSvalbard=Svalbardized
 accession.inTrust.true=L'accession est sous l'article 15 du traité international sur les ressources phytogénétiques pour l'alimentation et l'agriculture.
 accession.mlsStatus.true=Ce numéro se trouve dans le Système multilatéral du TIRPAA.
-accession.inSvalbard.true=Super-sécurité dupliquée dans la Réserve mondiale de semences du Svalbard.
+accession.inSvalbard.true=Sécurité dupliquée dans la Réserve mondiale de semences du Svalbard.
 # accession.not-available-for-distribution=The accession is NOT available for distribution.
 # accession.available-for-distribution=The accession is available for distribution.
 # accession.elevation=Elevation

src/main/resources/content/language_pt.properties

@@ -171,7 +171,7 @@ accession.mlsStatus=Estado MLS
 accession.inSvalbard=Svalbardizado
 accession.inTrust.true=Esta adesão está sob o Artigo 15 do Tratado Internacional de Recursos Genéticos Vegetais para Comida e Agricultura.
 accession.mlsStatus.true=Esta adesão pertence ao Sistema Multilateral do ITPGRFA.
-accession.inSvalbard.true=Super-segurança duplicada no Cofre de Sementes de Svalbard.
+accession.inSvalbard.true=Segurança duplicada no Cofre de Sementes de Svalbard.
 # accession.not-available-for-distribution=The accession is NOT available for distribution.
 # accession.available-for-distribution=The accession is available for distribution.
 # accession.elevation=Elevation

src/main/resources/spring/spring.properties

@@ -50,7 +50,7 @@ cdn.base=http://cdn.sandbox.genesys-pgr.org
 cdn.flags.url=${cdn.base}/flags
 
 # Content creation on startup
-auto.createContent=true
+auto.createContent=false
 
 # Mail properties
 mail.host=localhost

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

@@ -12,7 +12,10 @@
 		<small>${trait.crop.getName(pageContext.response.locale)}</small>
 	</h1>
 	<div>
-		<spring:message code="filter.crop" />: <b><a href="<c:url value="/c/${trait.crop.shortName}" />">${trait.crop.getName(pageContext.response.locale)}</a></b>
+		<spring:message code="filter.crop" />: <b><a href="<c:url value="/c/${trait.crop.shortName}/descriptors" />">${trait.crop.getName(pageContext.response.locale)}</a></b>
+	</div>
+	<div>
+		<spring:message code="descriptor.category" />: <c:out value="${trait.category.getName(pageContext.response.locale)}" />
 	</div>
 	<h4>
 		<spring:message code="ce.methods" />

src/main/webapp/WEB-INF/jsp/descr/index.jsp

@@ -11,17 +11,21 @@
 		<spring:message code="trait-list" />
 	</h1>
 
+	<div class="main-col-header clearfix">
+	<div class="nav-header pull-left">
+		<div class="results"><spring:message code="paged.totalElements" arguments="${pagedData.totalElements}" /></div>
+		<div class="pagination">
+			<spring:message code="paged.pageOfPages" arguments="${pagedData.number+1},${pagedData.totalPages}" />
+			<a class="${pagedData.number eq 0 ? 'disabled' :''}" href="?page=${pagedData.number eq 0 ? 1 : pagedData.number}"><spring:message code="pagination.previous-page" /></a> <a href="?page=${pagedData.number + 2}"><spring:message code="pagination.next-page" /></a>
+		</div>
+	</div>
+	</div>
+	
 	<c:if test="${crop ne null}">
-		<div>
+		<div class="applied-filters">
 			<spring:message code="filter.crop" />: <b><a href="<c:url value="/c/${crop.shortName}" />">${crop.getName(pageContext.response.locale)}</a></b>
 		</div>
 	</c:if>
-	<div class="nav-header">
-		<spring:message code="paged.totalElements" arguments="${pagedData.totalElements}" />
-		<br />
-		<spring:message code="paged.pageOfPages" arguments="${pagedData.number+1},${pagedData.totalPages}" />
-		<a class="${pagedData.number eq 0 ? 'disabled' :''}" href="?page=${pagedData.number eq 0 ? 1 : pagedData.number}"><spring:message code="pagination.previous-page" /></a> <a href="?page=${pagedData.number + 2}"><spring:message code="pagination.next-page" /></a>
-	</div>
 
 	<table class="accessions">
 		<thead>
@@ -29,6 +33,7 @@
 				<td class="idx-col" />
 				<td>Trait</td>
 				<td>Crop</td>
+				<td><spring:message code="descriptor.category" /></td>
 			</tr>
 		</thead>
 		<tbody>
@@ -37,6 +42,7 @@
 					<td class="idx-col">${status.count + pagedData.size * pagedData.number}</td>
 					<td><a href="<c:url value="/descriptors/${trait.id}" />">${trait.title}</a></td>
 					<td><a href="<c:url value="/c/${trait.crop.shortName}" />">${trait.crop.getName(pageContext.response.locale)}</a></td>
+					<td><c:out value="${trait.category.getName(pageContext.response.locale)}" /></td>
 				</tr>
 			</c:forEach>
 		</tbody>

src/main/webapp/WEB-INF/jsp/descr/method.jsp

@@ -10,7 +10,9 @@
 	<h1>
 		<c:out value="${trait.title}" />
 	</h1>
-
+	<div>
+		<spring:message code="filter.crop" />: <b><a href="<c:url value="/c/${trait.crop.shortName}/descriptors" />">${trait.crop.getName(pageContext.response.locale)}</a></b>
+	</div>
 	<table>
 		<tbody>
 			<tr>
@@ -21,16 +23,35 @@
 			</tr>
 		</tbody>
 	</table>
+	
+	<c:if test="${method.coded}">
+		<h3><spring:message code="method.coding-table" /></h3>
+		<ul class="funny-list">
+		<c:forEach items="${codeMap.keySet()}" var="key" varStatus="status">
+			<li class="${status.count % 2 == 0 ? 'even' : 'odd'}">
+				<span class="method-code"><c:out value="${key}" /></span>
+				<a title="<spring:message code="view.accessions" />" href="<c:url value="/acn/f"><c:param name="filter">{"gm:${method.id}":["${key}"]}</c:param></c:url>">
+					<c:out value="${codeMap[key]}" />
+				</a>
+				count=${codeStatistics[key]}
+			</li>
+		</c:forEach>
+		</ul>
+	</c:if>
 
 	<h3><spring:message code="accession.metadatas" /></h3>
 
 	<ul class="funny-list">
 		<c:forEach items="${metadatas}" var="metadata" varStatus="status">
-			<li class="clearfix ${status.count % 2 == 0 ? 'even' : 'odd'}"><a class="show pull-left" href="/data/view/${metadata.id}"><c:out value="${metadata.title}" /></a>
+			<li class="clearfix ${status.count % 2 == 0 ? 'even' : 'odd'}">
+				<a class="show pull-left" href="/data/view/${metadata.id}"><c:out value="${metadata.title}" /></a>
 				<div class="pull-right">
 					<c:out value="${metadata.instituteCode}" />
 				</div></li>
 		</c:forEach>
 	</ul>
+	<style>
+		span.method-code { font-weight: bold; font-size: 110%; margin-left: 2em; float: right; } 
+	</stlye>
 </body>
 </html>
\ No newline at end of file