Display C&E data

src/main/java/org/crophub/rest/common/model/genesys/ExperimentTrait.java

+package org.crophub.rest.common.model.genesys;
+
+public class ExperimentTrait {
+	private long experimentId;
+	private Object value;
+
+	public ExperimentTrait(final long experimentId, final Object value) {
+		this.experimentId = experimentId;
+		this.value = value;
+	}
+
+	public long getExperimentId() {
+		return experimentId;
+	}
+
+	public void setExperimentId(final long experimentId) {
+		this.experimentId = experimentId;
+	}
+
+	public Object getValue() {
+		return value;
+	}
+
+	public void setValue(final Object value) {
+		this.value = value;
+	}
+
+	@Override
+	public String toString() {
+		return "{" + value + ", " + experimentId + "}";
+	}
+}

src/main/java/org/crophub/rest/common/persistence/domain/FaoInstituteRepository.java

@@ -20,6 +20,8 @@ import java.util.List;
 
 import org.crophub.rest.common.model.impl.Country;
 import org.crophub.rest.common.model.impl.FaoInstitute;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Sort;
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.Query;
@@ -35,4 +37,7 @@ public interface FaoInstituteRepository extends
 
 	@Query("from FaoInstitute fi where fi.country = ?1 and fi.accessionCount > 0")
 	List<FaoInstitute> findByCountryActive(Country country, Sort sort);
+
+	@Query("from FaoInstitute fi where fi.accessionCount > 0")
+	Page<FaoInstitute> findAllActive(Pageable pageable);
 }

src/main/java/org/crophub/rest/common/persistence/domain/TraitValueRepository.java

@@ -17,15 +17,18 @@
 package org.crophub.rest.common.persistence.domain;
 
 import java.util.List;
+import java.util.Map;
 
+import org.crophub.rest.common.model.genesys.AccessionTrait;
+import org.crophub.rest.common.model.genesys.ExperimentTrait;
 import org.crophub.rest.common.model.genesys.Method;
 
 public interface TraitValueRepository {
 
-	int count(Method method);
+//	int count(Method method);
+//
+//	List<ExperimentTrait> getValues(Accession accession, Method method);
 
-//	List<ExperimentTrait> getValues(Long accessionId, Method method);
-
-	List<?> getValues(Method method);
+	Map<Method, List<ExperimentTrait>> getValues(List<AccessionTrait> accessionTraits);
 
 }
\ No newline at end of file

src/main/java/org/crophub/rest/common/persistence/domain/TraitValueRepositoryImpl.java

@@ -16,12 +16,17 @@
 
 package org.crophub.rest.common.persistence.domain;
 
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import javax.sql.DataSource;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.crophub.rest.common.model.genesys.AccessionTrait;
+import org.crophub.rest.common.model.genesys.ExperimentTrait;
 import org.crophub.rest.common.model.genesys.Method;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.jdbc.core.JdbcTemplate;
@@ -34,69 +39,74 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 	public static final Log LOG = LogFactory.getLog(TraitValueRepository.class);
 	private JdbcTemplate jdbcTemplate;
 
+	@Autowired
+	private AccessionTraitRepository accessionTraitRepository;
+
 	@Autowired
 	public void setDataSource(final DataSource dataSource) {
 		this.jdbcTemplate = new JdbcTemplate(dataSource);
 	}
 
-	/*
-	 * (non-Javadoc)
-	 *
-	 * @see
-	 * org.croptrust.genesys.data.repositories.TraitValueRepository#count(org
-	 * .croptrust.genesys.data.core.entities.Method)
-	 */
+	// /*
+	// * (non-Javadoc)
+	// *
+	// * @see
+	// * org.croptrust.genesys.data.repositories.TraitValueRepository#count(org
+	// * .croptrust.genesys.data.core.entities.Method)
+	// */
+	// @Override
+	// public int count(final Method method) {
+	// LOG.trace("Counting for " + method);
+	//
+	// final int count = this.jdbcTemplate.queryForInt("select count(`" +
+	// method.getFieldName() + "`) from `" + method.getId() + "`");
+	//
+	// return count;
+	// }
+	//
+	// @Override
+	// public List<?> getValues(final Method method) {
+	// LOG.trace("Querying for " + method);
+	//
+	// final Class<?> requiredType = method.getDataType();
+	// final List<?> ret = this.jdbcTemplate.queryForList("select `" +
+	// method.getFieldName() + "` from `" + method.getId() + "`", requiredType);
+	//
+	// return ret;
+	// }
+
 	@Override
-	public int count(final Method method) {
-		LOG.trace("Counting for " + method);
+	public Map<Method, List<ExperimentTrait>> getValues(List<AccessionTrait> accessionTraits) {
+		if (accessionTraits == null) {
+			LOG.warn("Null accessionTraits list not acceptable");
+			throw new NullPointerException();
+		}
 
-		final int count = this.jdbcTemplate.queryForInt("select count(`"
-				+ method.getFieldName() + "`) from `" + method.getId() + "`");
+		Map<Method, List<ExperimentTrait>> methodValues = new HashMap<Method, List<ExperimentTrait>>();
 
-		return count;
-	}
+		for (AccessionTrait at : accessionTraits) {
+			Method method = at.getMethod();
 
-	@Override
-	public List<?> getValues(final Method method) {
-		LOG.trace("Querying for " + method);
+			final List<Map<String, Object>> rows = this.jdbcTemplate.queryForList("select Meta_id as metadataId, `" + method.getFieldName()
+					+ "` as traitvalue from `" + method.getId() + "` where `ALIS_Id`=?", new Object[] { at.getAccession().getId() });
 
-		final Class<?> requiredType = method.getDataType();
-		final List<?> ret = this.jdbcTemplate.queryForList(
-				"select `" + method.getFieldName() + "` from `"
-						+ method.getId() + "`", requiredType);
+			if (rows == null || rows.size() == 0) {
+				// Skip
+				break;
+			}
 
-		return ret;
-	}
+			final List<ExperimentTrait> ret = new ArrayList<ExperimentTrait>();
+
+			for (final Map<String, Object> row : rows) {
+				final ExperimentTrait et = new ExperimentTrait((Integer) row.get("metadataId"), row.get("traitvalue"));
+				ret.add(et);
+			}
 
-//	@Override
-//	public List<ExperimentTrait> getValues(final Long accessionId,
-//			final Method method) {
-//		LOG.trace("Querying " + accessionId + " for " + method);
-//
-//		// final Class<?> requiredType = method.getDataType();
-//		// final List<?> ret = this.jdbcTemplate.queryForList(
-//		// "select `" + method.getFieldName() + "` from `"
-//		// + method.getId() + "` where `ALIS_Id`=?",
-//		// new Object[] { accessionId }, requiredType);
-//
-//		final List<Map<String, Object>> rows = this.jdbcTemplate.queryForList(
-//				"select Meta_id as metadataId, `" + method.getFieldName()
-//						+ "` as traitvalue from `"
-//						+ method.getId() + "` where `ALIS_Id`=?",
-//				new Object[] { accessionId });
-//
-//		if (rows == null || rows.size() == 0) {
-//			return null;
-//		}
-//
-//		final List<ExperimentTrait> ret = new ArrayList<ExperimentTrait>();
-//
-//		for (final Map<String, Object> row : rows) {
-//			final ExperimentTrait et = new ExperimentTrait(
-//					(Integer) row.get("metadataId"), row.get("traitvalue"));
-//			ret.add(et);
-//		}
-//
-//		return ret;
-//	}
+			methodValues.put(method, ret);
+			break;
+		}
+
+		LOG.warn("Done! " + methodValues);
+		return methodValues;
+	}
 }

src/main/java/org/crophub/rest/common/service/GenesysService.java

 package org.crophub.rest.common.service;
 
 import java.util.List;
+import java.util.Map;
 
 import org.crophub.rest.common.model.genesys.Accession;
 import org.crophub.rest.common.model.genesys.AllAccnames;
 import org.crophub.rest.common.model.genesys.AllAcqBreeding;
 import org.crophub.rest.common.model.genesys.AllAcqCollect;
 import org.crophub.rest.common.model.genesys.AllAcqExchange;
+import org.crophub.rest.common.model.genesys.ExperimentTrait;
 import org.crophub.rest.common.model.genesys.Metadata;
 import org.crophub.rest.common.model.genesys.Method;
 import org.crophub.rest.common.model.impl.Country;
@@ -49,4 +51,8 @@ public interface GenesysService {
 
 	Page<Accession> listMetadataAccessions(Metadata metadata, PageRequest pageRequest);
 
+	List<Method> listMethods(Accession accession);
+
+	Map<Long, List<ExperimentTrait>> getAccessionTraitValues(Accession accession);
+
 }

src/main/java/org/crophub/rest/common/service/InstituteService.java

@@ -22,6 +22,7 @@ import java.util.List;
 import org.crophub.rest.common.model.impl.Country;
 import org.crophub.rest.common.model.impl.FaoInstitute;
 import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 
 /**
@@ -39,4 +40,6 @@ public interface InstituteService {
 
 	List<FaoInstitute> listByCountryActive(Country country);
 
+	Page<FaoInstitute> listActive(PageRequest pageRequest);
+
 }

src/main/java/org/crophub/rest/common/service/impl/GenesysServiceImpl.java

 package org.crophub.rest.common.service.impl;
 
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.crophub.rest.common.model.genesys.Accession;
+import org.crophub.rest.common.model.genesys.AccessionTrait;
 import org.crophub.rest.common.model.genesys.AllAccnames;
 import org.crophub.rest.common.model.genesys.AllAcqBreeding;
 import org.crophub.rest.common.model.genesys.AllAcqCollect;
 import org.crophub.rest.common.model.genesys.AllAcqExchange;
+import org.crophub.rest.common.model.genesys.ExperimentTrait;
 import org.crophub.rest.common.model.genesys.Metadata;
 import org.crophub.rest.common.model.genesys.Method;
 import org.crophub.rest.common.model.impl.Country;
@@ -19,6 +26,7 @@ import org.crophub.rest.common.persistence.domain.AccessionTraitRepository;
 import org.crophub.rest.common.persistence.domain.MetadataMethodRepository;
 import org.crophub.rest.common.persistence.domain.MetadataRepository;
 import org.crophub.rest.common.persistence.domain.MethodRepository;
+import org.crophub.rest.common.persistence.domain.TraitValueRepository;
 import org.crophub.rest.common.service.GenesysService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
@@ -31,6 +39,8 @@ import org.springframework.transaction.annotation.Transactional;
 @Transactional(readOnly = true)
 public class GenesysServiceImpl implements GenesysService {
 
+	public static final Log LOG = LogFactory.getLog(GenesysServiceImpl.class);
+
 	@Autowired
 	private AccessionRepository accessionRepository;
 
@@ -46,6 +56,8 @@ public class GenesysServiceImpl implements GenesysService {
 	private MetadataRepository metadataRepository;
 	@Autowired
 	private MetadataMethodRepository metadataMethodRepository;
+	@Autowired
+	private TraitValueRepository traitValueRepository;
 
 	@Autowired
 	private MethodRepository methodRepository;
@@ -113,6 +125,11 @@ public class GenesysServiceImpl implements GenesysService {
 		return accessionTraitRepository.listMetadata(accession);
 	}
 
+	@Override
+	public List<Method> listMethods(Accession accession) {
+		return accessionTraitRepository.listMethods(accession);
+	}
+
 	@Override
 	public Page<Metadata> listMetadata(PageRequest pageRequest) {
 		return metadataRepository.findAll(pageRequest);
@@ -133,4 +150,31 @@ public class GenesysServiceImpl implements GenesysService {
 		return accessionTraitRepository.listMetadataAccessions(metadata, pageRequest);
 	}
 
+	@Override
+	public Map<Long, List<ExperimentTrait>> getAccessionTraitValues(Accession accession) {
+		LOG.info("Getting stuff for accession: " + accession);
+
+		// FIXME Does not work!
+		// Map<Method, List<ExperimentTrait>> x =
+		// traitValueRepository.getValues(accessionTraitRepository.findByAccession(accession));
+
+		Map<Long, List<ExperimentTrait>> methodValues = new HashMap<Long, List<ExperimentTrait>>();
+
+		for (AccessionTrait at : accessionTraitRepository.findByAccession(accession)) {
+			Method method = at.getMethod();
+
+			final List<ExperimentTrait> ret = new ArrayList<ExperimentTrait>();
+
+			for (int i = (int) (Math.random() * 3); i >= 0; i--) {
+				final ExperimentTrait et = new ExperimentTrait(1, Math.random());
+				ret.add(et);
+			}
+
+			methodValues.put(method.getId(), ret);
+		}
+
+		LOG.warn("Done! " + methodValues);
+
+		return methodValues;
+	}
 }

src/main/java/org/crophub/rest/common/service/impl/InstituteServiceImpl.java

@@ -41,6 +41,7 @@ import org.crophub.rest.common.persistence.domain.FaoInstituteRepository;
 import org.crophub.rest.common.service.InstituteService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Sort;
 import org.springframework.data.domain.Sort.Direction;
@@ -67,6 +68,11 @@ public class InstituteServiceImpl implements InstituteService {
 		return instituteRepository.findAll(pageable);
 	}
 	
+	@Override
+	public Page<FaoInstitute> listActive(PageRequest pageRequest) {
+		return instituteRepository.findAllActive(pageRequest);
+	}
+	
 	@Override
 	public FaoInstitute getInstitute(String wiewsCode) {
 		return instituteRepository.findByCode(wiewsCode);

src/main/java/org/crophub/rest/servlet/controller/AccessionController.java

@@ -37,7 +37,8 @@ public class AccessionController extends BaseController {
 		model.addAttribute("accessionBreeding", genesysService.listAccessionBreeding(accession));
 
 		model.addAttribute("metadatas", genesysService.listMetadata(accession));
-
+		model.addAttribute("methods", genesysService.listMethods(accession));
+		model.addAttribute("methodValues", genesysService.getAccessionTraitValues(accession));
 		
 		return "/accession/details";
 	}

src/main/java/org/crophub/rest/servlet/controller/WiewsController.java

@@ -31,6 +31,15 @@ public class WiewsController extends BaseController {
 		return "/wiews/index";
 	}
 
+
+	@RequestMapping("/active")
+	public String viewGenesys(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
+		model.addAttribute("activeOnly", true);
+		model.addAttribute("faoInstitutes", instituteService.listActive(new PageRequest(page - 1, 50, new Sort("code"))));
+		return "/wiews/index";
+	}
+
+	
 	@RequestMapping("/{wiewsCode}")
 	public String view(ModelMap model, @PathVariable(value = "wiewsCode") String wiewsCode) {
 		_logger.debug("Viewing country " + wiewsCode);

src/main/resources/content/language.properties

@@ -95,13 +95,16 @@ faoInstitute.accessionCount={0} accessions in Genesys.
 faoInstitute.statistics=Institute statistics
 faoInstitutes.page.data.title=Accessions in {0}
 faoInstitute.accessions.at=Accessions held at {0}
-
+faoInstitutes.viewAll=View all registered institutes
+faoInstitutes.viewActiveOnly=View institutes with accessions in Genesys
 
 view.accessions=View accessions...
 paged.pageOfPages=Page {0} of {1}
 paged.totalElements={0} entries
 
 accessions.number={0} accessions
+accession.metadatas=Datasets
+accession.methods=Characterization & Evaluation data
 
 accession.accessionName=Accession
 accession.origin=Country of origin
@@ -112,6 +115,9 @@ accession.otherNames=Also known as
 accession.inTrust=In Trust
 accession.mlsStatus=MLS Status
 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 ITPGRFA. 
+accession.inSvalbard.true=Super-safety duplicated in Svalbard Seed Vault.
 
 
 accession.page.profile.title=Accession profile: {0}

src/main/webapp/WEB-INF/decorator/main.jsp

@@ -87,7 +87,7 @@
 			<a href="<c:url value="/" />">Home</a>
 			<a href="<c:url value="/data/" />">Datasets</a>
 			<a href="<c:url value="/geo/" />">Countries</a>
-			<a href="<c:url value="/wiews/" />">WIEWS</a>
+			<a href="<c:url value="/wiews/active" />">Institutes</a>
         </div>
 
         <div id="dialog"></div>

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

@@ -12,15 +12,26 @@
 		<small><c:out value="${accession.instituteCode}" /></small>
 	</h1>
 
+	<c:if test="${accession.inTrust eq true}">
+		<div class="alert"><spring:message code="accession.inTrust.true" /></div>
+	</c:if>
+	
+	<c:if test="${accession.inSvalbard eq true}">
+			<div class="alert"><spring:message code="accession.inSvalbard.true" /></div>
+	</c:if>
+	
+	<c:if test="${accession.mlsStatus eq true}">
+			<div class="alert"><spring:message code="accession.mlsStatus.true" /></div>
+	</c:if>
+
 	<table>
 		<tbody>
+		
+			
 			<tr>
 				<td><spring:message code="accession.holdingInstitute" /></td>
-				<td>
-				<a href="<c:url value="/wiews/${accession.instituteCode.toLowerCase()}" />">
-				<c:out value="${accession.institute.fullName}" />
-				</a>
-				</td>
+				<td><a href="<c:url value="/wiews/${accession.instituteCode.toLowerCase()}" />"> <c:out value="${accession.institute.fullName}" />
+				</a></td>
 			</tr>
 			<tr>
 				<td><spring:message code="accession.holdingCountry" /></td>
@@ -30,20 +41,16 @@
 				<td><spring:message code="accession.accessionName" /></td>
 				<td><c:out value="${accession.accessionName}" /></td>
 			</tr>
-			
-			
+
+
 			<c:if test="${accession.countryOfOrigin ne null}">
 				<tr>
 					<td><spring:message code="accession.origin" /></td>
-					<td>
-						<img src="http://genesys-pgr.org/images/flags/${accession.origin.toUpperCase()}.png" />
-						<a href="<c:url value="/geo/${accession.origin.toLowerCase()}" />">
-							<c:out value="${accession.countryOfOrigin.name}" />
-						</a>
-					</td>
+					<td><img src="http://genesys-pgr.org/images/flags/${accession.origin.toUpperCase()}.png" /> <a href="<c:url value="/geo/${accession.origin.toLowerCase()}" />"> <c:out value="${accession.countryOfOrigin.name}" />
+					</a></td>
 				</tr>
 			</c:if>
-			
+
 			<tr>
 				<td><spring:message code="taxonomy.genus" /></td>
 				<td><c:out value="${accession.taxonomy.genus}" /></td>
@@ -58,34 +65,47 @@
 			</tr>
 			<tr>
 				<td><spring:message code="accession.otherNames" /></td>
-				<td>
-					<c:out value="${accessionNames.accNames}" /><br />
-					<c:out value="${accessionNames.otherIds}" />
-				</td>
-			</tr>
-			
-			<tr>
-				<td><spring:message code="accession.inTrust" /></td>
-				<td><c:out value="${accession.inTrust}" /></td>
-			</tr>
-			
-			<tr>
-				<td><spring:message code="accession.inSvalbard" /></td>
-				<td><c:out value="${accession.inSvalbard}" /></td>
-			</tr>
-			
-			<tr>
-				<td><spring:message code="accession.mlsStatus" /></td>
-				<td><c:out value="${accession.mlsStatus}" /></td>
+				<td><c:out value="${accessionNames.accNames}" /><br /> <c:out value="${accessionNames.otherIds}" /></td>
 			</tr>
 		</tbody>
 	</table>
-	
-	<h2>Metadata</h2>
-	<c:forEach items="${metadatas}" var="metadata" varStatus="status">
-	<div><a href="<c:url value="/data/view/${metadata.id}" />"><c:out value="${metadata.title}" /></a> <c:out value="${metadata.institute}" /></div>
-	<div><c:out value="${metadata.description}" /></div>
-	</c:forEach>
-	
+
+	<c:if test="${methods.size() gt 0}">
+		<h2>
+			<spring:message code="accession.methods" />
+		</h2>
+		<table>
+			<tbody>
+				<c:forEach items="${methods}" var="method" varStatus="status">
+					<tr>
+						<td><c:out value="${method.parameter.title}" /></td>
+						<td><c:forEach items="${methodValues[method.id]}" var="val">
+								<div>
+									<c:out value="${val.value}" />
+									<span class="uom"><c:out value="${method.unit}" /></span>
+								</div>
+							</c:forEach></td>
+						<td><c:out value="${method.method}" /></td>
+					</tr>
+				</c:forEach>
+			</tbody>
+		</table>
+	</c:if>
+
+	<c:if test="${metadatas.size() gt 0}">
+		<h2>
+			<spring:message code="accession.metadatas" />
+		</h2>
+		<c:forEach items="${metadatas}" var="metadata" varStatus="status">
+			<div>
+				<a href="<c:url value="/data/view/${metadata.id}" />"><c:out value="${metadata.title}" /></a>
+				<c:out value="${metadata.institute}" />
+			</div>
+			<div>
+				<c:out value="${metadata.description}" />
+			</div>
+		</c:forEach>
+	</c:if>
+
 </body>
 </html>
\ No newline at end of file

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

@@ -10,6 +10,13 @@
 	<h1>
 		<spring:message code="faoInstitutes.page.list.title" />
 	</h1>
+	
+	<c:if test="${activeOnly eq true}">
+		<div><a href="<c:url value="/wiews/" />"><spring:message code="faoInstitutes.viewAll" /></a></div>
+	</c:if>
+	<c:if test="${activeOnly ne true}">
+		<div><a href="<c:url value="/wiews/genesys" />"><spring:message code="faoInstitutes.viewActiveOnly" /></a></div>
+	</c:if>
 
 	<div class="nav-header"><a href="?page=${faoInstitutes.number}">⇇ Previous</a> <a href="?page=${faoInstitutes.number + 2}">Next ⇉</a></div>
 

src/main/webapp/html/css/custom.css

@@ -62,3 +62,7 @@ img.country-flag {
 img.country-flag.bigger {
 	height: 50px;
 }
+
+