Spring 3.2.4 fixes issue with JdbcTemplate and closing connections

Decode coded values

pom.xml

@@ -41,7 +41,7 @@
 		<log4j.version>1.2.17</log4j.version>
 
 		<aspectj.version>1.7.2</aspectj.version>
-		<spring.framework.version>3.2.2.RELEASE</spring.framework.version>
+		<spring.framework.version>3.2.4.RELEASE</spring.framework.version>
 		<spring.security.version>3.1.4.RELEASE</spring.security.version>
 		<spring.data.core.version>1.5.1.RELEASE</spring.data.core.version>
 		<spring.data.jpa.version>1.3.2.RELEASE</spring.data.jpa.version>

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

@@ -157,6 +157,11 @@ public class Method implements java.io.Serializable {
 	public boolean isCoded() {
 		return this.fieldType == 0;
 	}
+	
+	// FIXME String?
+	public Object decode(Object value) {
+		return isCoded() && value!=null ? TraitCode.decode(this.options, value.toString()) : value;
+	}
 
 	/**
 	 * Get list of codes for a coded descriptor.

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

+package org.crophub.rest.common.model.genesys;
+
+import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.commons.lang.StringUtils;
+
+/**
+ * Class representing one coded trait descriptor value.
+ *
+ * @author mobreza
+ */
+public class TraitCode {
+	final static Pattern p = Pattern.compile("([^,]+),([^;$]*)(;|$)");
+	private final String code;
+	private final String value;
+
+	public TraitCode(final String code, final String value) {
+		this.code = code;
+		this.value = value;
+	}
+
+	public String getCode() {
+		return code;
+	}
+
+	public String getValue() {
+		return value;
+	}
+
+	@Override
+	public String toString() {
+		return MessageFormat.format("Coded code={0} value={1}", code,
+				value);
+	}
+
+	public static String decode(final String options, final String value) {
+		if (StringUtils.isNotBlank(options)) {
+			final Matcher m = p.matcher(options);
+			while (m.find()) {
+				if (m.group(1).equalsIgnoreCase(value)) {
+					return m.group(2);
+				}
+			}
+		}
+		return value;
+	}
+	
+	public static List<TraitCode> parseOptions(final String options) {
+		final List<TraitCode> codes = new ArrayList<TraitCode>();
+		if (StringUtils.isNotBlank(options)) {
+			final Matcher m = p.matcher(options);
+			while (m.find()) {
+				codes.add(new TraitCode(m.group(1), m
+						.group(2)));
+			}
+		}
+		return codes;
+	}
+
+	public static Map<String, TraitCode> parseOptionsMap(final String options) {
+		final Map<String, TraitCode> map = new HashMap<String, TraitCode>();
+		for (final TraitCode code : parseOptions(options)) {
+			map.put(code.getCode(), code);
+		}
+		return map;
+	}
+}

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

@@ -21,7 +21,6 @@ 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 {
 
@@ -29,6 +28,6 @@ public interface TraitValueRepository {
 //
 //	List<ExperimentTrait> getValues(Accession accession, Method method);
 
-	Map<Method, List<ExperimentTrait>> getValues(List<AccessionTrait> accessionTraits);
+	Map<Long, List<ExperimentTrait>> getValues(List<AccessionTrait> accessionTraits);
 
 }
\ No newline at end of file

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

@@ -76,13 +76,13 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 	// }
 
 	@Override
-	public Map<Method, List<ExperimentTrait>> getValues(List<AccessionTrait> accessionTraits) {
+	public Map<Long, List<ExperimentTrait>> getValues(List<AccessionTrait> accessionTraits) {
 		if (accessionTraits == null) {
 			LOG.warn("Null accessionTraits list not acceptable");
 			throw new NullPointerException();
 		}
 
-		Map<Method, List<ExperimentTrait>> methodValues = new HashMap<Method, List<ExperimentTrait>>();
+		Map<Long, List<ExperimentTrait>> methodValues = new HashMap<Long, List<ExperimentTrait>>();
 
 		for (AccessionTrait at : accessionTraits) {
 			Method method = at.getMethod();
@@ -92,7 +92,7 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 
 			if (rows == null || rows.size() == 0) {
 				// Skip
-				break;
+				continue;
 			}
 
 			final List<ExperimentTrait> ret = new ArrayList<ExperimentTrait>();
@@ -102,8 +102,7 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 				ret.add(et);
 			}
 
-			methodValues.put(method, ret);
-			break;
+			methodValues.put(method.getId(), ret);
 		}
 
 		LOG.warn("Done! " + methodValues);

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;
@@ -152,29 +149,7 @@ public class GenesysServiceImpl implements GenesysService {
 
 	@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;
+		LOG.debug("Getting trait values for accession: " + accession);
+		return traitValueRepository.getValues(accessionTraitRepository.findByAccession(accession));
 	}
 }

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

@@ -81,7 +81,7 @@
 						<td><c:out value="${method.parameter.title}" /></td>
 						<td><c:forEach items="${methodValues[method.id]}" var="val">
 								<div>
-									<c:out value="${val.value}" />
+									<c:out value="${method.decode(val.value)}" />
 									<span class="uom"><c:out value="${method.unit}" /></span>
 								</div>
 							</c:forEach></td>