Browse by taxonomy

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

@@ -20,6 +20,7 @@ import java.util.Collection;
 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.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
@@ -36,6 +37,12 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 
 	@Query("select count(a) from Accession a where a.institute = ?1")
 	long countByInstitute(FaoInstitute institute);
+	
+	@Query("select t.genus, count(a) as x from Accession a inner join a.taxonomy t where a.institute = ?1 group by t.genus order by x desc")
+	List<Object[]> statisticsGenusInInstitute(FaoInstitute institute);
+
+	@Query("select taxonomy, count(a) as x from Accession a where a.institute = ?1 group by a.taxonomy order by x desc")
+	List<Object[]> statisticsTaxonomyInInstitute(FaoInstitute institute);
 
 	@Query("select count(a) from Accession a where a.origin = ?1")
 	long countByOrigin(String isoCode3);
@@ -66,4 +73,6 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 
 	@Query("from Accession a where a.id in ( ?1 )")
 	Page<Accession> findById(Collection<Long> accessionIds, Pageable pageable);
+
+	Page<Accession> findByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable);
 }

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

+/**
+ * Copyright 2013 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
+package org.crophub.rest.common.persistence.domain;
+
+import org.crophub.rest.common.model.genesys.Taxonomy;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface TaxonomyRepository extends JpaRepository<Taxonomy, Long> {
+	Taxonomy getByGenusAndSpecies(String genus, String species);
+}

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

@@ -12,6 +12,7 @@ import org.crophub.rest.common.model.genesys.AllAcqExchange;
 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.Taxonomy;
 import org.crophub.rest.common.model.impl.Country;
 import org.crophub.rest.common.model.impl.FaoInstitute;
 import org.springframework.data.domain.Page;
@@ -60,4 +61,10 @@ public interface GenesysService {
 
 	Page<Accession> listAccessions(Collection<Long> accessionIds, Pageable pageable);
 
+	List<Object[]> statisticsGenusByInstitute(FaoInstitute faoInstitute);
+
+	List<Object[]> statisticsTaxonomyByInstitute(FaoInstitute faoInstitute);
+
+	Page<Accession> listAccessionsByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable);
+
 }

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

+package org.crophub.rest.common.service;
+
+import org.crophub.rest.common.model.genesys.Taxonomy;
+
+public interface TaxonomyService {
+
+	Taxonomy get(String genus, String species);
+
+}

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

@@ -14,6 +14,7 @@ import org.crophub.rest.common.model.genesys.AllAcqExchange;
 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.Taxonomy;
 import org.crophub.rest.common.model.impl.Country;
 import org.crophub.rest.common.model.impl.FaoInstitute;
 import org.crophub.rest.common.persistence.domain.AccessionBreedingRepository;
@@ -167,4 +168,19 @@ public class GenesysServiceImpl implements GenesysService {
 		List<Method> methods = metadataMethodRepository.listMetadataMethods(metadata);
 		return traitValueRepository.getValues(metadata, methods, accessions);
 	}
+	
+	@Override
+	public List<Object[]> statisticsGenusByInstitute(FaoInstitute institute) {
+		return accessionRepository.statisticsGenusInInstitute(institute);
+	}
+
+	@Override
+	public List<Object[]> statisticsTaxonomyByInstitute(FaoInstitute institute) {
+		return accessionRepository.statisticsTaxonomyInInstitute(institute);
+	}
+	
+	@Override
+	public Page<Accession> listAccessionsByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable) {
+		return accessionRepository.findByInstituteAndTaxonomy(institute, taxonomy, pageable);
+	}
 }

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

+package org.crophub.rest.common.service.impl;
+
+import org.crophub.rest.common.model.genesys.Taxonomy;
+import org.crophub.rest.common.persistence.domain.TaxonomyRepository;
+import org.crophub.rest.common.service.TaxonomyService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+@Service
+@Transactional(readOnly = true)
+public class TaxonomyServiceImpl implements TaxonomyService {
+
+	@Autowired
+	private TaxonomyRepository taxonomyRepository;
+
+	@Override
+	public Taxonomy get(String genus, String species) {
+		return taxonomyRepository.getByGenusAndSpecies(genus, species);
+	}
+
+}

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

 package org.crophub.rest.servlet.controller;
 
+import java.util.HashMap;
+
 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;
@@ -21,17 +25,19 @@ public class WiewsController extends BaseController {
 
 	@Autowired
 	private InstituteService instituteService;
-	
+
 	@Autowired
 	private GenesysService genesysService;
 
+	@Autowired
+	private TaxonomyService taxonomyService;
+
 	@RequestMapping("/")
 	public String view(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
 		model.addAttribute("faoInstitutes", instituteService.list(new PageRequest(page - 1, 50, new Sort("code"))));
 		return "/wiews/index";
 	}
 
-
 	@RequestMapping("/active")
 	public String viewGenesys(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
 		model.addAttribute("activeOnly", true);
@@ -39,7 +45,6 @@ public class WiewsController extends BaseController {
 		return "/wiews/index";
 	}
 
-	
 	@RequestMapping("/{wiewsCode}")
 	public String view(ModelMap model, @PathVariable(value = "wiewsCode") String wiewsCode) {
 		_logger.debug("Viewing country " + wiewsCode);
@@ -48,16 +53,17 @@ public class WiewsController extends BaseController {
 			throw new ResourceNotFoundException();
 		}
 		model.addAttribute("faoInstitute", faoInstitute);
-		
+
 		model.addAttribute("countByInstitute", genesysService.countByInstitute(faoInstitute));
-		
+		model.addAttribute("statisticsGenus", genesysService.statisticsGenusByInstitute(faoInstitute));
+		model.addAttribute("statisticsTaxonomy", genesysService.statisticsTaxonomyByInstitute(faoInstitute));
+
 		return "/wiews/details";
 	}
 
-
-
 	@RequestMapping("/{wiewsCode}/data")
-	public String viewData(ModelMap model, @PathVariable(value = "wiewsCode") String wiewsCode, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
+	public String viewData(ModelMap model, @PathVariable(value = "wiewsCode") String wiewsCode,
+			@RequestParam(value = "page", required = false, defaultValue = "1") int page) {
 		_logger.debug("Viewing country " + wiewsCode);
 		FaoInstitute faoInstitute = instituteService.getInstitute(wiewsCode);
 		if (faoInstitute == null) {
@@ -72,4 +78,32 @@ public class WiewsController extends BaseController {
 
 		return "/wiews/data";
 	}
+
+	@RequestMapping("/{wiewsCode}/t/{genus}/{species}")
+	public String viewDataByGenusSpecies(ModelMap model, @PathVariable(value = "wiewsCode") String wiewsCode, @PathVariable(value = "genus") String genus,
+			@PathVariable(value = "species") String species, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
+		_logger.debug("Viewing country " + wiewsCode);
+		FaoInstitute faoInstitute = instituteService.getInstitute(wiewsCode);
+		if (faoInstitute == null) {
+			throw new ResourceNotFoundException();
+		}
+		model.addAttribute("faoInstitute", faoInstitute);
+
+		// 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);
+		
+		_logger.warn("Searching accessions of: " + faoInstitute);
+		Page<Accession> accessions = genesysService.listAccessionsByInstituteAndTaxonomy(faoInstitute, taxonomy, new PageRequest(page - 1, 50, new Sort("accessionName")));
+		_logger.info("Got: " + accessions);
+		model.addAttribute("accessions", accessions);
+
+		return "/wiews/data";
+	}
+
 }

src/main/resources/content/language.properties

@@ -95,7 +95,7 @@ country.page.profile.title=Country profile: {0}
 country.page.list.title=Country list
 country.page.not-current=This is a historic entry.
 country.page.faoInstitutes={0} institutes registered in WIEWS
-country.stat.countByLocation={0} accessions held by institutes in this country
+country.stat.countByLocation={0} accessions at institutes in this country
 country.stat.countByOrigin={0} accessions registered in Genesys come from this country.
 country.statistics=Country statistics
 country.accessions.from=Accessions collected in {0}
@@ -106,7 +106,7 @@ faoInstitutes.stat.accessionCount=Accessions in Genesys: {0}.
 faoInstitute.accessionCount={0} accessions in Genesys.
 faoInstitute.statistics=Institute statistics
 faoInstitutes.page.data.title=Accessions in {0}
-faoInstitute.accessions.at=Accessions held at {0}
+faoInstitute.accessions.at=Accessions at {0}
 faoInstitutes.viewAll=View all registered institutes
 faoInstitutes.viewActiveOnly=View institutes with accessions in Genesys
 faoInstitute.no-accessions-registered=Please get in touch with us if you can facilitate in providing data from this institiute.
@@ -149,3 +149,6 @@ 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.
+
+filter.taxonomy=Taxonomy
+

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

@@ -15,6 +15,13 @@
 		<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 />

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

@@ -8,19 +8,21 @@
 </head>
 <body>
 	<h1>
-		<img class="country-flag bigger" src="http://genesys-pgr.org/images/flags/${faoInstitute.country.code3.toUpperCase()}.png" />	
+		<img class="country-flag bigger" src="http://genesys-pgr.org/images/flags/${faoInstitute.country.code3.toUpperCase()}.png" />
 		<c:out value="${faoInstitute.fullName}" />
-			<small><c:out value="${faoInstitute.code}" /></small>
+		<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>
+		<div class="alert">
+			<spring:message code="faoInstitute.no-accessions-registered" />
+		</div>
 	</c:if>
 
 	<%-- <c:if test="${not faoInstitutes.current}">
 		<div class="alert"><spring:message code="faoInstitutes.page.not-current"/></div>
 	</c:if> --%>
-	
+
 	<div>
 		<%-- <img src="http://genesys-pgr.org/images/flags/${faoInstitute.country.code3.toUpperCase()}.png" /> --%>
 		<a href="<c:url value="/geo/${faoInstitute.country.code3.toLowerCase()}" />"><c:out value="${faoInstitute.country.name}" /></a>
@@ -41,9 +43,11 @@
 	<div>
 		<a href="<c:out value="${faoInstitute.url}" />"><c:out value="${faoInstitute.url}" /></a>
 	</div>
-	
 
-	<h3><spring:message code="faoInstitute.statistics" /></h3>
+
+	<h3>
+		<spring:message code="faoInstitute.statistics" />
+	</h3>
 	<div>
 		<spring:message code="faoInstitutes.stat.accessionCount" arguments="${countByInstitute}" />
 		<c:if test="${countByInstitute gt 0}">
@@ -51,5 +55,26 @@
 		</c:if>
 	</div>
 
+	<div class="clearfix" style="margin-top: 2em;">
+		<div class="pull-left" style="margin-right: 3em;">
+			<h4>By Genus</h4>
+			<ul class="funny-list statistics">
+				<c:forEach items="${statisticsGenus}" var="stat" varStatus="status">
+					<li><span class="stats-number"><fmt:formatNumber value="${stat[1]}" /></span> <c:out value="${stat[0]}" /></li>
+				</c:forEach>
+			</ul>
+		</div>
+
+		<div class="pull-left" style="margin-right: 3em;">
+			<h4>By Species</h4>
+			<ul class="funny-list statistics">
+				<c:forEach items="${statisticsTaxonomy}" var="stat" varStatus="status">
+					<li><span class="stats-number"><fmt:formatNumber value="${stat[1]}" /></span> <a href="<c:url value="/wiews/${faoInstitute.code.toLowerCase()}/t/${stat[0].genus}/${stat[0].species}" />"><c:out value="${stat[0].taxonName}" /></a></li>
+				</c:forEach>
+			</ul>
+		</div>
+	</div>
+
+
 </body>
 </html>
\ No newline at end of file

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

@@ -214,4 +214,13 @@ body {
 
 .dropdown-menu {
 	background-color: #303030;
+}
+
+
+ul.statistics .stats-number {
+	display: inline-block;
+	text-align: right;
+	margin-left: 2em;
+	width: 4em;
+	float: right;
 }
\ No newline at end of file