Browse all by taxonomy

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

@@ -75,4 +75,6 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	Page<Accession> findById(Collection<Long> accessionIds, Pageable pageable);
 
 	Page<Accession> findByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable);
+
+	Page<Accession> findByTaxonomy(Taxonomy taxonomy, Pageable pageable);
 }

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

@@ -67,4 +67,6 @@ public interface GenesysService {
 
 	Page<Accession> listAccessionsByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable);
 
+	Page<Accession> listAccessionsByTaxonomy(Taxonomy taxonomy, Pageable pageable);
+
 }

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

@@ -183,4 +183,9 @@ public class GenesysServiceImpl implements GenesysService {
 	public Page<Accession> listAccessionsByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable) {
 		return accessionRepository.findByInstituteAndTaxonomy(institute, taxonomy, pageable);
 	}
+	
+	@Override
+	public Page<Accession> listAccessionsByTaxonomy(Taxonomy taxonomy, Pageable pageable) {
+		return accessionRepository.findByTaxonomy(taxonomy, pageable);
+	}
 }

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

 package org.crophub.rest.servlet.controller;
 
+import java.util.HashMap;
 import java.util.List;
 
 import org.crophub.rest.common.model.genesys.Accession;
+import org.crophub.rest.common.model.genesys.Taxonomy;
 import org.crophub.rest.common.model.impl.FaoInstitute;
 import org.crophub.rest.common.service.GenesysService;
 import org.crophub.rest.common.service.InstituteService;
+import org.crophub.rest.common.service.TaxonomyService;
 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.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.RequestParam;
 
 @Controller
 @RequestMapping("/acn")
@@ -23,11 +30,15 @@ public class AccessionController extends BaseController {
 	@Autowired
 	private GenesysService genesysService;
 
+	@Autowired
+	private TaxonomyService taxonomyService;
+	
+	
 	@RequestMapping("/id/{accessionId}")
 	public String view(ModelMap model, @PathVariable(value = "accessionId") long accessionId) {
 		_logger.debug("Viewing ACN " + accessionId);
-		Accession accession=genesysService.getAccession(accessionId);
-		if (accession==null) {
+		Accession accession = genesysService.getAccession(accessionId);
+		if (accession == null) {
 			throw new ResourceNotFoundException();
 		}
 		model.addAttribute("accession", accession);
@@ -39,22 +50,23 @@ public class AccessionController extends BaseController {
 		model.addAttribute("metadatas", genesysService.listMetadata(accession));
 		model.addAttribute("methods", genesysService.listMethods(accession));
 		model.addAttribute("methodValues", genesysService.getAccessionTraitValues(accession));
-		
+
 		return "/accession/details";
 	}
-	
+
 	@RequestMapping("/{holdingInstitute}/{accessionName}")
-	public String viewInstituteAccession(ModelMap model, @PathVariable(value = "holdingInstitute") String holdingInstitute,  @PathVariable(value = "accessionName") String accessionName) {
+	public String viewInstituteAccession(ModelMap model, @PathVariable(value = "holdingInstitute") String holdingInstitute,
+			@PathVariable(value = "accessionName") String accessionName) {
 		_logger.debug("Viewing ACN " + accessionName);
 		FaoInstitute faoInstitute = instituteService.getInstitute(holdingInstitute);
-		if (faoInstitute==null) {
+		if (faoInstitute == null) {
 			throw new ResourceNotFoundException();
 		}
-		List<Accession> accessions=genesysService.listAccessions(faoInstitute, accessionName);
-		if (accessions.size()==0) {
+		List<Accession> accessions = genesysService.listAccessions(faoInstitute, accessionName);
+		if (accessions.size() == 0) {
 			throw new ResourceNotFoundException();
 		}
-		if (accessions.size()==1) {
+		if (accessions.size() == 1) {
 			return "redirect:/acn/id/" + accessions.get(0).getId();
 		}
 
@@ -63,4 +75,36 @@ public class AccessionController extends BaseController {
 
 		return "/accession/resolve";
 	}
+
+	/**
+	 * View by Taxonomy
+	 * 
+	 * @param model
+	 * @param wiewsCode
+	 * @param genus
+	 * @param species
+	 * @param page
+	 * @return
+	 */
+	@RequestMapping("/t/{genus}/{species}")
+	public String viewDataByGenusSpecies(ModelMap model, @PathVariable(value = "genus") String genus,
+			@PathVariable(value = "species") String species, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
+
+		// Taxonomy
+		Taxonomy taxonomy = taxonomyService.get(genus, species);
+		_logger.debug("Got " + taxonomy);
+
+		HashMap<Object, Object> filters = new HashMap<Object, Object>();
+		filters.put("filter.taxonomy", taxonomy);
+
+		model.addAttribute("filters", filters);
+
+		Page<Accession> accessions = genesysService.listAccessionsByTaxonomy(taxonomy, new PageRequest(page - 1, 50, new Sort(
+				"accessionName")));
+		_logger.info("Got: " + accessions);
+		model.addAttribute("accessions", accessions);
+
+		return "/accession/data";
+	}
+
 }

src/main/resources/content/language.properties

@@ -136,6 +136,7 @@ accession.inSvalbard.true=Super-safety duplicated in Svalbard Seed Vault.
 accession.page.profile.title=Accession profile: {0}
 accession.page.resolve.title=Multiple accessions found
 accession.resolve=Multiple accessions with the name ''{0}'' found in Genesys. Select one from the list. 
+accession.page.data.title=Accession browser
 
 
 taxonomy.genus=Genus

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

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="accession.page.data.title" /></title>
+</head>
+<body>
+	<h1>
+		<spring:message code="accession.page.data.title" />
+	</h1>
+	
+<%-- 	<div>
+		<a href="<c:url value="/geo/${faoInstitute.country.code3.toLowerCase()}" />"><c:out value="${faoInstitute.country.name}" /></a>
+	</div> --%>
+	
+	<c:if test="${filters ne null}">
+		<c:forEach items="${filters.keySet()}" var="by">
+			<div><spring:message code="${by}" />: <b>${filters[by].taxonName}</b></div>
+		</c:forEach>
+	</c:if>
+	
+	
+	<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=${accessions.number + 2}">Next ⇉</a>
+	</div>
+
+	<table>
+		<thead>
+			<tr>
+				<td class="idx-col"></td>
+				<td><spring:message code="accession.accessionName" /></td>
+				<td><spring:message code="accession.origin" /></td>
+				<td><spring:message code="accession.taxonomy" /></td>
+				<td><spring:message code="accession.holdingInstitute" /></td>
+				<td><spring:message code="accession.holdingCountry" /></td>
+			</tr>
+		</thead>
+		<tbody>
+			<c:forEach items="${accessions.content}" var="accession" varStatus="status">
+				<tr class="${status.count % 2 == 0 ? 'even' : 'odd'}">
+					<td class="idx-col">${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><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="${accession.institute.country.name}" /></a></td>
+				</tr>
+			</c:forEach>
+		</tbody>
+	</table>
+
+	<div class="nav-header">
+		<a href="?page=${accessions.number}">⇇ Previous</a> <a href="?page=${accessions.number + 2}">Next ⇉</a>
+	</div>
+
+</body>
+</html>
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