Traits & Extras

.settings/org.eclipse.core.resources.prefs

 eclipse.preferences.version=1
 encoding//src/main/resources=UTF-8
 encoding//src/main/resources/content/language.properties=UTF-8
+encoding//src/main/webapp/WEB-INF/jsp/descr/index.jsp=UTF-8
 encoding//src/main/webapp/WEB-INF/jsp/login.jsp=UTF-8
 encoding//src/main/webapp/WEB-INF/jsp/metadata/index.jsp=UTF-8
 encoding//src/main/webapp/WEB-INF/jsp/metadata/view.jsp=UTF-8

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

@@ -21,8 +21,12 @@ import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
+import org.crophub.rest.common.model.impl.Crop;
+
 @Entity
 @Table(name = "parameters")
 public class Parameter implements java.io.Serializable {
@@ -33,7 +37,7 @@ public class Parameter implements java.io.Serializable {
 	private static final long serialVersionUID = -4831244149317371274L;
 	private Long id;
 	// private Language language;
-	// private Crop crop;
+	private Crop crop;
 	// private Category category;
 	private String title;
 
@@ -60,17 +64,17 @@ public class Parameter implements java.io.Serializable {
 	// public void setLanguage(final Language language) {
 	// this.language = language;
 	// }
-	//
-	// @ManyToOne(cascade = {}, optional = false)
-	// @JoinColumn(name = "cropId")
-	// public Crop getCrop() {
-	// return this.crop;
-	// }
-	//
-	// public void setCrop(final Crop crop) {
-	// this.crop = crop;
-	// }
-	//
+	
+	@ManyToOne(cascade = {}, optional = false)
+	@JoinColumn(name = "Crop_Id")
+	public Crop getCrop() {
+		return this.crop;
+	}
+
+	public void setCrop(final Crop crop) {
+		this.crop = crop;
+	}
+
 	// @ManyToOne(cascade = {}, optional = false)
 	// @JoinColumn(name = "categoryId", nullable = false)
 	// public Category getCategory() {

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

@@ -33,4 +33,7 @@ public interface MetadataMethodRepository extends JpaRepository<MetadataMethod,
 	@Query("select distinct mm.method from MetadataMethod mm where mm.metadata = ?1")
 	List<Method> listMetadataMethods(Metadata metadata);
 
+	@Query("select distinct mm.metadata from MetadataMethod mm where mm.method = ?1")
+	List<Metadata> listMetadataByMethod(Method method);
+
 }

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

@@ -19,8 +19,13 @@ package org.crophub.rest.common.persistence.domain;
 import java.util.List;
 
 import org.crophub.rest.common.model.genesys.Method;
+import org.crophub.rest.common.model.genesys.Parameter;
 import org.springframework.data.jpa.repository.JpaRepository;
 
 public interface MethodRepository extends JpaRepository<Method, Long> {
 	List<Method> findByFieldType(int fieldType);
+
+	List<Method> findByParameter(Parameter parameter);
+
+	Method findByIdAndParameter(long id, Parameter findOne);
 }

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

+package org.crophub.rest.common.service;
+
+import java.util.List;
+
+import org.crophub.rest.common.model.genesys.Metadata;
+import org.crophub.rest.common.model.genesys.Method;
+import org.crophub.rest.common.model.genesys.Parameter;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+
+public interface TraitService {
+
+	Page<Parameter> listTraits(Pageable pageable);
+
+	Parameter getTrait(long traitId);
+
+	List<Method> getTraitMethods(Parameter trait);
+
+	Method getMethod(long traitId);
+
+	List<Metadata> listMetadataByMethod(Method method);
+
+}

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

@@ -31,6 +31,7 @@ import org.crophub.rest.common.model.genesys.AllEnvironment;
 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.genesys.Parameter;
 import org.crophub.rest.common.model.genesys.Taxonomy;
 import org.crophub.rest.common.model.impl.Country;
 import org.crophub.rest.common.model.impl.Crop;
@@ -46,8 +47,10 @@ import org.crophub.rest.common.persistence.domain.CropTaxonomyRepository;
 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.ParameterRepository;
 import org.crophub.rest.common.persistence.domain.TraitValueRepository;
 import org.crophub.rest.common.service.GenesysService;
+import org.crophub.rest.common.service.TraitService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
@@ -57,7 +60,7 @@ import org.springframework.transaction.annotation.Transactional;
 
 @Service
 @Transactional(readOnly = true)
-public class GenesysServiceImpl implements GenesysService {
+public class GenesysServiceImpl implements GenesysService, TraitService {
 
 	public static final Log LOG = LogFactory.getLog(GenesysServiceImpl.class);
 
@@ -89,6 +92,9 @@ public class GenesysServiceImpl implements GenesysService {
 	@Autowired
 	private MethodRepository methodRepository;
 
+	@Autowired
+	private ParameterRepository parameterRepository;
+
 	@Override
 	public long countByInstitute(FaoInstitute institute) {
 		return accessionRepository.countByInstitute(institute);
@@ -228,4 +234,29 @@ public class GenesysServiceImpl implements GenesysService {
 	public Page<Accession> listAccessionsByCrop(Crop crop, Pageable pageable) {
 		return accessionRepository.findByTaxonomy(cropTaxonomyRepository.findTaxonomiesByCrop(crop), pageable);
 	}
+
+	@Override
+	public Page<Parameter> listTraits(Pageable pageable) {
+		return parameterRepository.findAll(pageable);
+	}
+
+	@Override
+	public Parameter getTrait(long traitId) {
+		return parameterRepository.findOne(traitId);
+	}
+
+	@Override
+	public List<Method> getTraitMethods(Parameter trait) {
+		return methodRepository.findByParameter(trait);
+	}
+
+	@Override
+	public Method getMethod(long methodId) {
+		return methodRepository.findOne(methodId);
+	}
+
+	@Override
+	public List<Metadata> listMetadataByMethod(Method method) {
+		return metadataMethodRepository.listMetadataByMethod(method);
+	}
 }

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

@@ -16,15 +16,18 @@
 
 package org.crophub.rest.servlet.controller;
 
-import java.util.List;
-
-import org.crophub.rest.common.model.impl.Descriptor;
-import org.crophub.rest.common.service.DescriptorService;
+import org.crophub.rest.common.model.genesys.Method;
+import org.crophub.rest.common.model.genesys.Parameter;
+import org.crophub.rest.common.service.TraitService;
+import org.crophub.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Sort;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.ModelMap;
-import org.springframework.validation.Validator;
+import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
 
 /**
  * Controller which simply handles *.html requests
@@ -34,17 +37,46 @@ import org.springframework.web.bind.annotation.RequestMapping;
 public class DescriptorController extends BaseController {
 
 	@Autowired
-	private DescriptorService descriptorService;
-
-	@Autowired
-	private Validator validator;
+	private TraitService traitService;
 
 	@RequestMapping
-	public String index(ModelMap model) {
-		List<Descriptor> descriptors = descriptorService.list();
-		_logger.info("Got " + descriptors.size() + " descriptors");
-		model.addAttribute("descriptors", descriptors);
+	public String index(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
+		model.addAttribute("traits", traitService.listTraits(new PageRequest(page - 1, 50, new Sort("title"))));
+
 		return "/descr/index";
 	}
-	
+
+	@RequestMapping("/{id}")
+	public String view(ModelMap model, @PathVariable("id") long traitId) {
+		Parameter trait = traitService.getTrait(traitId);
+		if (trait == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		model.addAttribute("trait", trait);
+		model.addAttribute("traitMethods", traitService.getTraitMethods(trait));
+
+		return "/descr/details";
+	}
+
+	@RequestMapping("/{traitId}/{methodId}")
+	public String view(ModelMap model, @PathVariable("traitId") long traitId, @PathVariable("methodId") long methodId) {
+		Parameter trait = traitService.getTrait(traitId);
+		if (trait == null) {
+			throw new ResourceNotFoundException();
+		}
+		Method method = traitService.getMethod(methodId);
+		if (method == null) {
+			throw new ResourceNotFoundException();
+		}
+		if (!method.getParameter().getId().equals(trait.getId())) {
+			_logger.warn("Method does not belong to Param");
+		}
+
+		model.addAttribute("trait", trait);
+		model.addAttribute("method", method);
+		model.addAttribute("metadatas", traitService.listMetadataByMethod(method));
+
+		return "/descr/method";
+	}
 }

src/main/resources/content/language.properties

@@ -76,7 +76,8 @@ footer.copyright-statement=© 2013 Data Providers and GCDT
 
 menu.home=Home
 menu.browse=Browse
-menu.datasets=Datasets
+menu.datasets=C&E Data
+menu.descriptors=Descriptors
 menu.countries=Countries
 menu.institutes=Institutes
 menu.my-list=My List
@@ -97,6 +98,7 @@ user.create-new-account=Create an account
 
 crop.croplist=Crop list
 crop.page.profile.title={0} profile
+crop.taxonomy-rules=Taxonomic rules
 
 activity.recent-activity=Recent activity
 
@@ -125,7 +127,7 @@ paged.pageOfPages=Page {0} of {1}
 paged.totalElements={0} entries
 
 accessions.number={0} accessions
-accession.metadatas=Datasets
+accession.metadatas=C&E Data
 accession.methods=Characterization & Evaluation data
 
 accession.accessionName=Accession
@@ -160,6 +162,7 @@ accession.taxonomy-at-institute=View {0} at {1}
 taxonomy.genus=Genus
 taxonomy.species=Species
 taxonomy.taxonName=Taxonomy
+taxonomy-list=Taxonomy list
 
 selection.page.title=Selected accessions
 selection.add=Add {0} to list

src/main/resources/spring/spring-db.xml

@@ -30,6 +30,11 @@
 		<property name="driverClassName" value="${db.driverClassName}" />
 		<property name="username" value="${db.username}" />
 		<property name="password" value="${db.password}" />
+		<!-- 
+	 	<property name="timeBetweenEvictionRunsMillis" value="5000" />
+		<property name="minEvictableIdleTimeMillis" value="5000" />
+	 	<property name="minIdle" value="0" />
+	 -->
 	</bean>
 
 	<bean class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean" id="entityManagerFactory">

src/main/resources/spring/spring.properties

@@ -20,7 +20,7 @@
 #db.username = sa
 #db.password =
 
-db.url=jdbc:mysql://localhost/pgrsys_genesys?useUnicode=true&characterEncoding=UTF-8&useFastDateParsing=false
+db.url=jdbc:mysql://127.0.0.1/pgrsys_genesys?useUnicode=true&characterEncoding=UTF-8&useFastDateParsing=false
 db.driverClassName = com.mysql.jdbc.Driver
 db.username = root
 db.password = 

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

@@ -97,6 +97,7 @@
 				<li><a href="<c:url value="/" />"><spring:message code="menu.home" /></a></li>
 				<li><a href="<c:url value="/acn/" />"><spring:message code="menu.browse" /></a></li>
 				<li><a href="<c:url value="/data/" />"><spring:message code="menu.datasets" /></a></li>
+				<li><a href="<c:url value="/descriptors/" />"><spring:message code="menu.descriptors" /></a></li>
 				<li><a href="<c:url value="/geo/" />"><spring:message code="menu.countries" /></a></li>
 				<li><a href="<c:url value="/wiews/active" />"><spring:message code="menu.institutes" /></a></li>
 				<li><a href="<c:url value="/sel/" />"><spring:message code="menu.my-list" /><div id="selcounter">${selection.size() gt 0 ? selection.size() : ''}</div></a></li>

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

@@ -21,22 +21,25 @@
 		<c:out value="${crop.description}" />
 	</div>
 
+	<h4><spring:message code="crop.taxonomy-rules" /></h4>
 	<ul class="funny-list">
 		<c:forEach items="${crop.cropRules}" var="rule">
-			<li><c:out value="${rule.included}" /> <c:out value="${rule.genus}" /> <c:out value="${rule.species}" /></li>
+			<li class="${rule.included ? '' : 'excluded'}" /><b>${rule.included ? '+' : '-'}</b> <c:out value="${rule.genus}" /> <c:out value="${rule.species eq null ? '*' : rule.species}" /></li>
 		</c:forEach>
 	</ul>
 
-
+<%-- 
 	<div class="free-text">
 		<c:out value="${crop.language}" />
 	</div>
-
+ --%>
+ 
 	<a href="<c:url value="/c/${crop.shortName}/data" />"><spring:message code="view.accessions" /></a>
 
+	<h3><spring:message code="taxonomy-list" /></h3>
 	<ul class="funny-list">
 		<c:forEach items="${cropTaxonomies}" var="cropTaxonomy">
-			<li><c:out value="${cropTaxonomy.taxonomy.taxonName}" /></li>
+			<li><a href="<c:url value="/acn/t/${cropTaxonomy.taxonomy.genus}/${cropTaxonomy.taxonomy.species}" />"><c:out value="${cropTaxonomy.taxonomy.taxonName}" /></a></li>
 		</c:forEach>
 	</ul>
 

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

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="metadata.page.title" /></title>
+</head>
+<body>
+	<h1><c:out value="${trait.title}" /></h1>
+	<div><a href="<c:url value="/c/${trait.crop.shortName}" />">${trait.crop.name}</a> trait</div>
+	
+	<h4>Methods</h4>
+	<table>
+		<tbody>
+			<c:forEach items="${traitMethods}" var="method">
+				<tr>
+					<td><c:out value="${method.parameter.title}" /></td>
+					<td><a href="<c:url value="/descriptors/${trait.id}/${method.id}" />"><c:out value="${method.method}" /></a></td>
+					<td><c:out value="${method.fieldName}" /></td>
+					<td><c:out value="${method.unit}" /></td>
+				</tr>
+			</c:forEach>
+		</tbody>
+	</table>
+</body>
+</html>
\ No newline at end of file

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

 <!DOCTYPE html>
 
-<%@include file="../init.jsp"%>
+<%@include file="/WEB-INF/jsp/init.jsp"%>
 
 <html>
 <head>
-    <%@include file="../head-init.jsp"%>
-
-    <title><spring:message code="sample.message.index.title"/></title>
-
-    <link type="text/css" href="/html/css/jquery-ui.css" rel="stylesheet"/>
-    <link type="text/css" href="/html/css/jquery.dataTables.css" rel="stylesheet"/>
-
-    <%--Fallback for older browsers--%>
-    <script type="text/javascript" src="/html/js/json2.js"></script>
-
-    <script type="text/javascript" src="/html/js/globalize.js"></script>
-    <script type="text/javascript" src="/html/js/jquery-ui.min.js"></script>
-    <script type="text/javascript" src="/html/js/jquery.dataTables.js"></script>
-    <script type="text/javascript" src="/html/js/handlebars.js"></script>
-    <script type="text/javascript" src="/html/js/bootstrap.min.js"></script>
-    <script type="text/javascript" src="/html/js/main.js"></script>
-
+<title><spring:message code="metadata.page.title" /></title>
 </head>
 <body>
-    <div class="container">
-    <div id="header">
-        <div class="page-header clearfix">
-
-            <h4 class="pull-left"><spring:message code="sample.message.welcome"/></h4>
-
-            <div class="navbar pull-right">
-            <div class="nav-collapse">
-                <ul class="nav">
-                    <li class="dropdown">
-                        <a class="dropdown-toggle" data-toggle="dropdown" title="<spring:message code="sample.message.change.locale"/>">
-                            <spring:message code="sample.message.current.locale"/>
-                            <b class="caret"></b>
-                        </a>
-                        <ul class="dropdown-menu">
-                            <li><a href="?lang=en"><spring:message code="sample.message.locale.en"/></a></li>
-                            <li><a href="?lang=ru"><spring:message code="sample.message.locale.ru"/></a></li>
-                        </ul>
-                    </li>
-                </ul>
-            </div>
-            </div>
-        </div>
-    </div>
-
-    <div id="content">
-        <div class="page-header">
-            <a id="show-users" href="#" class="btn">Users</a>
-        </div>
-
-        <div id="dialog"></div>
-
-        <c:forEach items="${descriptors}" var="descriptor" varStatus="status">
-	        <h3><c:out value="${descriptor.name}" /></h3>
-	        <p><c:out value="${descriptor.description}" /></p>
-        </c:forEach>
 
-    </div>
-    </div>
+	<div class="nav-header">
+		<spring:message code="paged.totalElements" arguments="${traits.totalElements}" />
+		<br />
+		<spring:message code="paged.pageOfPages" arguments="${traits.number+1},${traits.totalPages}" />
+		<a href="?page=${traits.number}">⇇ Previous</a> <a href="?page=${traits.number + 2}">Next ⇉</a>
+	</div>
+
+	<table class="accessions">
+		<thead>
+			<tr>
+				<td class="idx-col" />
+				<td>Trait</td>
+				<td>Crop</td>
+			</tr>
+		</thead>
+		<tbody>
+			<c:forEach items="${traits.content}" var="trait" varStatus="status">
+				<tr class="${status.count % 2 == 0 ? 'even' : 'odd'}">
+					<td class="idx-col">${status.count + traits.size * traits.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.name}</a></td>
+				</tr>
+			</c:forEach>
+		</tbody>
+	</table>
 </body>
 </html>
\ No newline at end of file

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

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="metadata.page.title" /></title>
+</head>
+<body>
+	<h1>
+		<c:out value="${trait.title}" />
+	</h1>
+
+	<table>
+		<tbody>
+			<tr>
+				<td><a href="<c:url value="/descriptors/${trait.id}" />"><c:out value="${method.parameter.title}" /></a></td>
+				<td><a href="<c:url value="/descriptors/${trait.id}/${method.id}" />"><c:out value="${method.method}" /></a></td>
+				<td><c:out value="${method.fieldName}" /></td>
+				<td><c:out value="${method.unit}" /></td>
+			</tr>
+		</tbody>
+	</table>
+
+	<h3><spring:message code="accession.metadatas" /></h3>
+	
+	<ul class="funny-list">
+		<c:forEach items="${metadatas}" var="metadata">
+			<li><a href="/data/view/${metadata.id}"><c:out value="${metadata.title}" /></a> <c:out value="${metadata.institute}" /></li>
+		</c:forEach>
+	</ul>
+</body>
+</html>
\ No newline at end of file

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

@@ -16,8 +16,8 @@
 		<tbody>
 			<c:forEach items="${methods}" var="method">
 				<tr>
-					<td><c:out value="${method.parameter.title}" /></td>
-					<td><c:out value="${method.method}" /></td>
+					<td><a href="<c:url value="/descriptors/${method.parameter.id}" />"><c:out value="${method.parameter.title}" /></a></td>
+					<td><a href="<c:url value="/descriptors/${method.parameter.id}/${method.id}" />"><c:out value="${method.method}" /></a></td>
 					<td><c:out value="${method.fieldName}" /></td>
 					<td><c:out value="${method.unit}" /></td>
 				</tr>

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

@@ -58,13 +58,16 @@ td {
 	padding: 0.2em 0.5em;
 }
 
-td.idx-col {
+.idx-col {
 	font-size: 80%;
 	width: 4em;
 	/* background-color: #eaeaea; */
 	/* text-align: right; */
 	vertical-align: middle;
 }
+span.idx-col {
+	display: inline-block;
+}
 
 tr.odd td {
 	background-color: #f8f7f5;