Accession selection

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

@@ -4,6 +4,7 @@ encoding//src/main/webapp/WEB-INF/jsp/country/data.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
+encoding//src/main/webapp/WEB-INF/jsp/selection/index.jsp=UTF-8
 encoding//src/main/webapp/WEB-INF/jsp/wiews/data.jsp=UTF-8
 encoding//src/main/webapp/WEB-INF/jsp/wiews/index.jsp=UTF-8
 encoding//src/test/resources=UTF-8

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

@@ -16,6 +16,7 @@
 
 package org.crophub.rest.common.persistence.domain;
 
+import java.util.Collection;
 import java.util.List;
 
 import org.crophub.rest.common.model.genesys.Accession;
@@ -35,7 +36,7 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 
 	@Query("select count(a) from Accession a where a.institute = ?1")
 	long countByInstitute(FaoInstitute institute);
-	
+
 	@Query("select count(a) from Accession a where a.origin = ?1")
 	long countByOrigin(String isoCode3);
 
@@ -43,8 +44,7 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	long countByLocation(String isoCode3);
 
 	@Query("select a from Accession a where a.institute in ( ?1 )")
-	Page<Accession> findByInstitute(List<FaoInstitute> institutes,
-			Pageable pageable);
+	Page<Accession> findByInstitute(List<FaoInstitute> institutes, Pageable pageable);
 
 	@Query("select a from Accession a where a.genus in ( ?1 )")
 	Page<Accession> findByGenus(List<String> genus, Pageable pageable);
@@ -58,9 +58,12 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query("select a.taxonomy, count(a) as total from Accession a where a.genus in ( ?1 ) group by a.taxonomy order by total desc")
 	List<Object[]> statisticsTaxonomy(List<String> genus);
 
-//	List<Accession> findByOrigin(String origin);
+	// List<Accession> findByOrigin(String origin);
 
 	Page<Accession> findByOrigin(String isoCode3, Pageable pageable);
 
 	List<Accession> findByInstituteAndAccessionName(FaoInstitute faoInstitute, String accessionName);
+
+	@Query("from Accession a where a.id in ( ?1 )")
+	Page<Accession> findById(Collection<Long> accessionIds, Pageable pageable);
 }

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

 package org.crophub.rest.common.service;
 
+import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 
@@ -57,4 +58,6 @@ public interface GenesysService {
 
 	Map<Long, Map<Long, Object>> getMetadataTraitValues(Metadata metadata, List<Accession> content);
 
+	Page<Accession> listAccessions(Collection<Long> accessionIds, Pageable pageable);
+
 }

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

 package org.crophub.rest.common.service.impl;
 
+import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 
@@ -84,6 +85,14 @@ public class GenesysServiceImpl implements GenesysService {
 		return accessionRepository.findByInstitute(faoInstitute, pageable);
 	}
 
+	@Override
+	public Page<Accession> listAccessions(Collection<Long> accessionIds, Pageable pageable) {
+		if (accessionIds == null || accessionIds.size() == 0) {
+			return null;
+		}
+		return accessionRepository.findById(accessionIds, pageable);
+	}
+
 	@Override
 	public Accession getAccession(long accessionId) {
 		return accessionRepository.findOne(accessionId);

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

+package org.crophub.rest.servlet.controller;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.crophub.rest.common.model.genesys.Accession;
+import org.springframework.context.annotation.Scope;
+import org.springframework.stereotype.Component;
+
+@Component
+@Scope("session")
+public class SelectionBean {
+	private Set<Long> accessionIds = new HashSet<Long>();
+
+	public Set<Long> getAccessionIds() {
+		return accessionIds;
+	}
+
+	public void add(long id) {
+		accessionIds.add(id);
+	}
+
+	public void remove(long id) {
+		accessionIds.remove(id);
+	}
+
+	public void clear() {
+		accessionIds.clear();
+	}
+
+	public boolean contains(Accession accession) {
+		return accessionIds.contains(accession.getId());
+	}
+
+	public Set<Long> copy() {
+		return new HashSet<>(accessionIds);
+	}
+}

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

+package org.crophub.rest.servlet.controller;
+
+import org.crophub.rest.common.model.genesys.Accession;
+import org.crophub.rest.common.service.GenesysService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Scope;
+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.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+
+@Controller
+@Scope("request")
+@RequestMapping("/sel/")
+public class SelectionController extends BaseController {
+
+	@Autowired
+	private SelectionBean selectionBean;
+
+	@Autowired
+	private GenesysService genesysService;
+
+	@RequestMapping
+	public String view(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
+
+		model.addAttribute("accessions", genesysService.listAccessions(selectionBean.copy(), new PageRequest(page - 1, 50, new Sort("accessionName"))));
+
+		return "/selection/index";
+	}
+
+	@RequestMapping("add/{id}")
+	public String add(ModelMap model, @PathVariable("id") long accessionId) {
+		selectionBean.add(accessionId);
+		return "redirect:/sel/#a" + accessionId;
+	}
+
+	@RequestMapping(method = RequestMethod.POST, value = "add-many")
+	public String add(ModelMap model, @RequestParam(required = true, value = "accessionIds") String accessionIds) {
+		String[] splits = accessionIds.split("\\s");
+		for (String s : splits) {
+			try {
+				long accessionId = Long.parseLong(s);
+				Accession accession = genesysService.getAccession(accessionId);
+				if (accession != null) {
+					selectionBean.add(accessionId);
+				}
+			} catch (NumberFormatException e) {
+
+			}
+		}
+		return "redirect:/sel/";
+	}
+
+	@RequestMapping("remove/{id}")
+	public String remove(ModelMap model, @PathVariable("id") long accessionId) {
+		selectionBean.remove(accessionId);
+		return "redirect:/sel/";
+	}
+
+	@RequestMapping("clear")
+	public String remove(ModelMap model) {
+		selectionBean.clear();
+		return "redirect:/sel/";
+	}
+
+}

src/main/resources/content/language.properties

@@ -142,3 +142,10 @@ taxonomy.genus=Genus
 taxonomy.species=Species
 taxonomy.taxonName=Taxonomy
 
+selection.page.title=Selected accessions
+selection.add=Add {0} to list
+selection.remove=Remove {0} from list
+selection.clear=Clear the list
+selection.empty-list-warning=You have not added any accessions to the list.
+selection.add-many=Check and add
+selection.add-many.accessionIds=List accession IDs as used in Genesys separated by space or new line.

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

@@ -87,6 +87,7 @@
 				<li><a href="<c:url value="/data/" />">Datasets</a></li>
 				<li><a href="<c:url value="/geo/" />">Countries</a></li>
 				<li><a href="<c:url value="/wiews/active" />">Institutes</a></li>
+				<li><a href="<c:url value="/sel/" />">My List</a></li>
 			</ul>
 		</div>
 		

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

@@ -11,6 +11,10 @@
 		<c:out value="${accession.accessionName}" />
 		<small><c:out value="${accession.instituteCode}" /></small>
 	</h1>
+	
+	<div class="page-header">
+		<a href="<c:url value="/sel/add/${accession.id}" />"><spring:message code="selection.add" arguments="${accession.accessionName}" /></a>
+	</div>
 
 	<c:if test="${accession.inTrust eq true}">
 		<div class="alert"><spring:message code="accession.inTrust.true" /></div>

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

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="selection.page.title" /></title>
+</head>
+<body>
+	<h1>
+		<spring:message code="selection.page.title" />
+	</h1>
+
+	<c:if test="${accessions == null}">
+		<div class="alert">
+			<spring:message code="selection.empty-list-warning" />
+		</div>
+	</c:if>
+
+	<c:if test="${accessions != null}">
+		<div class="page-header">
+			<a href="<c:url value="/sel/clear" />">Clear list</a>
+		</div>
+
+		<div class="nav-header">
+			<spring:message code="accessions.number" arguments="${accessions.totalElements}" />
+			<br />
+			<spring:message code="paged.pageOfPages" arguments="${accessions.number+1},${accessions.totalPages}" />
+			<a href="?page=${accessions.number}">⇇ Previous</a> <a href="?page=${accessions.number + 2}">Next ⇉</a>
+		</div>
+
+		<table>
+			<thead>
+				<tr>
+					<td class="idx-col"></td>
+					<td><spring:message code="accession.accessionName" /></td>
+					<td><spring:message code="accession.origin" /></td>
+					<td><spring:message code="accession.taxonomy" /></td>
+					<td><spring:message code="accession.holdingInstitute" /></td>
+					<td><spring:message code="accession.holdingCountry" /></td>
+					<td></td>
+				</tr>
+			</thead>
+			<tbody>
+				<c:forEach items="${accessions.content}" var="accession" varStatus="status">
+					<tr id="a${accession.id}" class="targeted ${status.count % 2 == 0 ? 'even' : 'odd'}">
+						<td class="idx-col">${status.count + accessions.size * accessions.number}</td>
+						<td><a href="<c:url value="/acn/id/${accession.id}" />"><b><c:out value="${accession.accessionName}" /></b></a></td>
+						<td><c:out value="${accession.countryOfOrigin.name}" /></td>
+						<td><c:out value="${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>
+						<td class="idx-col"><a href="<c:url value="/sel/remove/${accession.id}" />">Remove</a></td>
+					</tr>
+				</c:forEach>
+			</tbody>
+		</table>
+
+	</c:if>
+
+
+	<c:if test="${accessions eq null or accessions.number eq 0}">
+		<h4 style="margin-top: 3em">Add multiple accessions</h4>
+		<form method="post" action="<c:url value="/sel/add-many" />" class="form-horizontal">
+			<div class="control-group">
+				<label for="accessionIds" class="control-label"><spring:message code="selection.add-many.accessionIds" /></label>
+				<div class="controls">
+					<textarea class="form-control" placeholder="12345 123545 423231" name="accessionIds"></textarea>
+				</div>
+			</div>
+			<div class="form-actions clearfix">
+				<input type="submit" value="<spring:message code="selection.add-many" />" />
+			</div>
+		</form>
+	</c:if>
+
+
+	<script type="text/javascript">
+	/*  jQuery(document).ready(function(){
+		if(document.location.hash != '') {
+			setTimeout(function() { document.location.hash=''; }, 2000);
+		} 
+	 }); */
+	</script>
+</body>
+</html>
\ No newline at end of file

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

@@ -7,7 +7,11 @@
 <title><spring:message code="faoInstitutes.page.profile.title" arguments="${faoInstitute.fullName}" argumentSeparator="|" /></title>
 </head>
 <body>
-	<h1><c:out value="${faoInstitute.fullName}" /></h1>
+	<h1>
+		<img class="country-flag bigger" src="http://genesys-pgr.org/images/flags/${faoInstitute.country.code3.toUpperCase()}.png" />	
+		<c:out value="${faoInstitute.fullName}" />
+			<small><c:out value="${faoInstitute.code}" /></small>
+	</h1>
 
 	<c:if test="${countByInstitute eq 0}">
 		<div class="alert"><spring:message code="faoInstitute.no-accessions-registered" /></div>
@@ -18,7 +22,7 @@
 	</c:if> --%>
 	
 	<div>
-		<img src="http://genesys-pgr.org/images/flags/${faoInstitute.country.code3.toUpperCase()}.png" />
+		<%-- <img src="http://genesys-pgr.org/images/flags/${faoInstitute.country.code3.toUpperCase()}.png" /> --%>
 		<a href="<c:url value="/geo/${faoInstitute.country.code3.toLowerCase()}" />"><c:out value="${faoInstitute.country.name}" /></a>
 	</div>
 

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

@@ -12,10 +12,10 @@
 	</h1>
 	
 	<c:if test="${activeOnly eq true}">
-		<div><a href="<c:url value="/wiews/" />"><spring:message code="faoInstitutes.viewAll" /></a></div>
+		<div class="page-header"><a href="<c:url value="/wiews/" />"><spring:message code="faoInstitutes.viewAll" /></a></div>
 	</c:if>
 	<c:if test="${activeOnly ne true}">
-		<div><a href="<c:url value="/wiews/active" />"><spring:message code="faoInstitutes.viewActiveOnly" /></a></div>
+		<div class="page-header"><a href="<c:url value="/wiews/active" />"><spring:message code="faoInstitutes.viewActiveOnly" /></a></div>
 	</c:if>
 
 	<div class="nav-header">

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

@@ -16,6 +16,10 @@
     font-size: 15px;
 }
 
+.form-actions {
+	padding: 1em 1em;
+}
+
 .nav-header {
 	padding: 1em 0;
 }
@@ -112,7 +116,7 @@ li.hoofdleter small {
 	margin-left: 1em;
 }
 
-div.targeted:target {
+.targeted:target {
 	background-color: #dfd0c0;
 }