Wide format for dataset observations

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

@@ -19,8 +19,11 @@ package org.crophub.rest.common.persistence.domain;
 import java.util.List;
 import java.util.Map;
 
+import org.crophub.rest.common.model.genesys.Accession;
 import org.crophub.rest.common.model.genesys.AccessionTrait;
 import org.crophub.rest.common.model.genesys.ExperimentTrait;
+import org.crophub.rest.common.model.genesys.Metadata;
+import org.crophub.rest.common.model.genesys.Method;
 
 public interface TraitValueRepository {
 
@@ -30,4 +33,6 @@ public interface TraitValueRepository {
 
 	Map<Long, List<ExperimentTrait>> getValues(List<AccessionTrait> accessionTraits);
 
+	Map<Long, Map<Long, Object>> getValues(Metadata metadata, List<Method> methods, List<Accession> accessions);
+
 }
\ No newline at end of file

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

@@ -25,8 +25,10 @@ import javax.sql.DataSource;
 
 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.ExperimentTrait;
+import org.crophub.rest.common.model.genesys.Metadata;
 import org.crophub.rest.common.model.genesys.Method;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.jdbc.core.JdbcTemplate;
@@ -108,4 +110,42 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 		LOG.warn("Done! " + methodValues);
 		return methodValues;
 	}
+
+	@Override
+	public Map<Long, Map<Long, Object>> getValues(Metadata metadata, List<Method> methods, List<Accession> accessions) {
+		Map<Long, Map<Long, Object>> accessionMetadataValues = new HashMap<Long, Map<Long, Object>>();
+
+		for (Accession accession : accessions) {
+			// create lists
+			accessionMetadataValues.put(accession.getId(), new HashMap<Long, Object>());
+		}
+
+		for (Method method : methods) {
+			
+			
+			// FIXME We're loading all entries for metadata, should limit only to the accessions in the list!
+			final List<Map<String, Object>> rows = this.jdbcTemplate.queryForList("select `ALIS_Id` as accessionId, `" + method.getFieldName()
+					+ "` as traitvalue from `" + method.getId() + "` where `Meta_Id`=?", new Object[] { metadata.getId() });
+
+			if (rows == null || rows.size() == 0) {
+				// Skip
+				continue;
+			}
+
+			for (final Map<String, Object> row : rows) {
+				long accessionId = (Integer) row.get("accessionId");
+				Object value = row.get("traitvalue");
+
+				if (value!=null) {
+					Map<Long, Object> accessionValues = accessionMetadataValues.get(accessionId);
+					if (accessionValues!=null)
+						accessionValues.put(method.getId(), value);
+				}
+			}
+		}
+
+		LOG.warn("Done! ");
+		return accessionMetadataValues;
+	}
+
 }

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

@@ -55,4 +55,6 @@ public interface GenesysService {
 
 	Map<Long, List<ExperimentTrait>> getAccessionTraitValues(Accession accession);
 
+	Map<Long, Map<Long, Object>> getMetadataTraitValues(Metadata metadata, List<Accession> content);
+
 }

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

@@ -152,4 +152,10 @@ public class GenesysServiceImpl implements GenesysService {
 		LOG.debug("Getting trait values for accession: " + accession);
 		return traitValueRepository.getValues(accessionTraitRepository.findByAccession(accession));
 	}
+
+	@Override
+	public Map<Long, Map<Long, Object>> getMetadataTraitValues(Metadata metadata, List<Accession> accessions) {
+		List<Method> methods = metadataMethodRepository.listMetadataMethods(metadata);
+		return traitValueRepository.getValues(metadata, methods, accessions);
+	}
 }

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

@@ -16,10 +16,12 @@
 
 package org.crophub.rest.servlet.controller;
 
+import org.crophub.rest.common.model.genesys.Accession;
 import org.crophub.rest.common.model.genesys.Metadata;
 import org.crophub.rest.common.service.GenesysService;
 import org.crophub.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.ModelMap;
@@ -56,7 +58,12 @@ public class DatasetController extends BaseController {
 		}
 		model.addAttribute("metadata", metadata);
 		model.addAttribute("methods", genesysService.listMethods(metadata));
-		model.addAttribute("accessions", genesysService.listMetadataAccessions(metadata, new PageRequest(page - 1, 50)));
+
+		Page<Accession> accessions = genesysService.listMetadataAccessions(metadata, new PageRequest(page - 1, 50));
+		model.addAttribute("accessions", accessions);
+
+		// Map[accession.id][method.id]
+		model.addAttribute("accessionMethods", genesysService.getMetadataTraitValues(metadata, accessions.getContent()));
 
 		return "/metadata/view";
 	}

src/main/webapp/WEB-INF/jsp/metadata/view.jsp

@@ -52,21 +52,39 @@
 		<thead>
 			<tr>
 				<td><spring:message code="accession.accessionName" /></td>
-				<td><spring:message code="accession.origin" /></td>
-				<td><spring:message code="accession.taxonomy" /></td>
-				<td><spring:message code="accession.holdingInstitute" /></td>
+		<%-- 		<td><spring:message code="accession.origin" /></td>
+		 --%>		<td><spring:message code="accession.taxonomy" /></td>
+	<%-- 			<td><spring:message code="accession.holdingInstitute" /></td>
 				<td><spring:message code="accession.holdingCountry" /></td>
-			</tr>
+	 --%>	
+				 <c:forEach items="${methods}" var="method">
+				 	<td>
+				 		<c:out value="${method.fieldName}" />
+				 		<c:if test="${method.unit ne ''}">[<c:out value="${method.unit}" />]</c:if>
+				 	</td>
+				 </c:forEach>
+	 	
+	 
+	 
+	 		</tr>
 		</thead>
 		<tbody>
 			<c:forEach items="${accessions.content}" var="accession" varStatus="status">
 				<tr>
 					<td><a href="<c:url value="/acn/id/${accession.id}" />"><b><c:out value="${accession.accessionName}" /></b></a></td>
-					<td><a href="<c:url value="/geo/${accession.origin.toLowerCase()}" />"><c:out value="${accession.countryOfOrigin.name}" /></a></td>
-					<td><c:out value="${accession.taxonomy.taxonName}" /></td>
-					<td><a href="<c:url value="/wiews/${accession.institute.code.toLowerCase()}" />"><c:out value="${accession.institute.code}" /></a></td>
+			<%-- 		<td><a href="<c:url value="/geo/${accession.origin.toLowerCase()}" />"><c:out value="${accession.countryOfOrigin.name}" /></a></td>
+			 --%>		<td><c:out value="${accession.taxonomy.taxonName}" /></td>
+				<%-- 	<td><a href="<c:url value="/wiews/${accession.institute.code.toLowerCase()}" />"><c:out value="${accession.institute.code}" /></a></td>
 					<td><a href="<c:url value="/geo/${accession.institute.country.code3.toLowerCase()}" />"><c:out value="${accession.institute.country.name}" /></a></td>
-				</tr>
+				 --%>
+				 
+				 <c:set value="${accessionMethods[accession.id]}" var="methodValues" />
+				 <c:forEach items="${methods}" var="method">
+				 	<td>
+				 		<c:out value="${method.decode(methodValues[method.id])}" />
+				 	</td>
+				 </c:forEach>
+				 </tr>
 			</c:forEach>
 		</tbody>
 	</table>