Accession data of countries and institutes

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

 eclipse.preferences.version=1
 encoding//src/main/resources=UTF-8
+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/wiews/data.jsp=UTF-8
 encoding//src/main/webapp/WEB-INF/jsp/wiews/index.jsp=UTF-8
 encoding//src/test/resources=UTF-8
 encoding/<project>=UTF-8

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

@@ -36,7 +36,7 @@ import org.crophub.rest.common.model.impl.FaoInstitute;
 public class Accession implements java.io.Serializable {
 	private static final long serialVersionUID = -7630113633534038876L;
 	private Long id;
-//	private String instituteCode;
+	private String instituteCode;
 	private FaoInstitute institute;
 	private String accNumbHi;
 	private Taxonomy taxonomy;
@@ -68,7 +68,7 @@ public class Accession implements java.io.Serializable {
 	}
 
 	@ManyToOne(cascade = {}, optional = false)
-	@JoinColumn(name = "Institute", referencedColumnName="code", nullable = false)
+	@JoinColumn(name = "instituteId", nullable = false)
 	public FaoInstitute getInstitute() {
 		return this.institute;
 	}
@@ -77,14 +77,14 @@ public class Accession implements java.io.Serializable {
 		this.institute = institute;
 	}
 
-//	@Column(name = "Institute", length = 6)
-//	public String getInstituteCode() {
-//		return instituteCode;
-//	}
-//
-//	public void setInstituteCode(final String instituteCode) {
-//		this.instituteCode = instituteCode;
-//	}
+	@Column(name = "Institute", length = 6)
+	public String getInstituteCode() {
+		return instituteCode;
+	}
+
+	public void setInstituteCode(final String instituteCode) {
+		this.instituteCode = instituteCode;
+	}
 
 	@Column(name = "ACC_Numb_HI", nullable = false, length = 128)
 	public String getAccessionName() {

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

@@ -26,7 +26,7 @@ import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
 @Entity
-@Table(name = "taxonomy", uniqueConstraints = { @UniqueConstraint(columnNames = {
+@Table(name = "all_taxonomy", uniqueConstraints = { @UniqueConstraint(columnNames = {
 		"genus", "species" }) })
 public class Taxonomy implements java.io.Serializable {
 
@@ -49,7 +49,7 @@ public class Taxonomy implements java.io.Serializable {
 
 	@Id
 	@GeneratedValue
-	@Column(unique = true, nullable = false)
+	@Column(name="Taxon_Code", unique = true, nullable = false)
 	public Long getId() {
 		return this.id;
 	}
@@ -76,7 +76,7 @@ public class Taxonomy implements java.io.Serializable {
 		this.species = species;
 	}
 
-	@Column(nullable = false, length = 128)
+	@Column(name="Taxon_Name", nullable = false, length = 128)
 	public String getTaxonName() {
 		return this.taxonName;
 	}

src/main/java/org/crophub/rest/common/model/impl/FaoInstitute.java

@@ -47,19 +47,18 @@ public class FaoInstitute extends GeoEntity implements java.io.Serializable {
 	private String email;
 	private String acronym;
 	private Country country;
+	private long accessionCount;
 
 	public FaoInstitute() {
 	}
 
-	public FaoInstitute(final String institute, final String fullName,
-			final String email) {
+	public FaoInstitute(final String institute, final String fullName, final String email) {
 		this.code = institute;
 		this.fullName = fullName;
 		this.email = email;
 	}
 
-	public FaoInstitute(final String institute, final String fullName,
-			final String type, final String url, final String email) {
+	public FaoInstitute(final String institute, final String fullName, final String type, final String url, final String email) {
 		this.code = institute;
 		this.fullName = fullName;
 		this.type = type;
@@ -124,9 +123,7 @@ public class FaoInstitute extends GeoEntity implements java.io.Serializable {
 
 	@Override
 	public String toString() {
-		return MessageFormat.format(
-				"FaoInst id={0,number,#} code={1} fullName={2}", id, code,
-				fullName);
+		return MessageFormat.format("FaoInst id={0,number,#} code={1} fullName={2}", id, code, fullName);
 	}
 
 	@Column(length = 50)
@@ -147,4 +144,13 @@ public class FaoInstitute extends GeoEntity implements java.io.Serializable {
 	public void setCountry(final Country country) {
 		this.country = country;
 	}
+
+	public long getAccessionCount() {
+		return accessionCount;
+	}
+
+	public void setAccessionCount(long accessionCount) {
+		this.accessionCount = accessionCount;
+	}
+
 }

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

@@ -58,5 +58,7 @@ 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);
 }

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

@@ -32,4 +32,7 @@ public interface FaoInstituteRepository extends
 	List<String> findTypes();
 
 	List<FaoInstitute> findByCountry(Country country, Sort sort);
+
+	@Query("from FaoInstitute fi where fi.country = ?1 and fi.accessionCount > 0")
+	List<FaoInstitute> findByCountryActive(Country country, Sort sort);
 }

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

 package org.crophub.rest.common.service;
 
+import org.crophub.rest.common.model.genesys.Accession;
+import org.crophub.rest.common.model.impl.Country;
 import org.crophub.rest.common.model.impl.FaoInstitute;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
 
 public interface GenesysService {
 
@@ -10,4 +14,8 @@ public interface GenesysService {
 
 	long countByLocation(String isoCode3);
 
+	Page<Accession> listAccessionsByOrigin(Country country, Pageable pageable);
+
+	Page<Accession> listAccessionsByInstitute(FaoInstitute faoInstitute, Pageable pageable);
+
 }

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

@@ -37,4 +37,6 @@ public interface InstituteService {
 
 	List<FaoInstitute> listByCountry(Country country);
 
+	List<FaoInstitute> listByCountryActive(Country country);
+
 }

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

 package org.crophub.rest.common.service.impl;
 
+import org.crophub.rest.common.model.genesys.Accession;
+import org.crophub.rest.common.model.impl.Country;
 import org.crophub.rest.common.model.impl.FaoInstitute;
 import org.crophub.rest.common.persistence.domain.AccessionRepository;
 import org.crophub.rest.common.persistence.domain.MethodRepository;
 import org.crophub.rest.common.service.GenesysService;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
@@ -36,4 +40,14 @@ public class GenesysServiceImpl implements GenesysService {
 	public long countByLocation(String isoCode3) {
 		return accessionRepository.countByLocation(isoCode3);
 	}
+	
+	@Override
+	public Page<Accession> listAccessionsByOrigin(Country country, Pageable pageable) {
+		return accessionRepository.findByOrigin(country.getCode3(), pageable);
+	}
+	
+	@Override
+	public Page<Accession> listAccessionsByInstitute(FaoInstitute faoInstitute, Pageable pageable) {
+		return accessionRepository.findByInstitute(faoInstitute, pageable);
+	}
 }

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

@@ -43,6 +43,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Sort;
+import org.springframework.data.domain.Sort.Direction;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
@@ -76,6 +77,12 @@ public class InstituteServiceImpl implements InstituteService {
 		return instituteRepository.findByCountry(country, new Sort("code"));
 	}
 	
+
+	@Override
+	public List<FaoInstitute> listByCountryActive(Country country) {
+		return instituteRepository.findByCountryActive(country, new Sort(Direction.DESC, "accessionCount", "code"));
+	}
+	
 	/**
 	 * Update local FaoInstitute with data from WIEWS database
 	 *

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

@@ -6,10 +6,13 @@ import org.crophub.rest.common.service.GeoService;
 import org.crophub.rest.common.service.InstituteService;
 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.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
 
 @Controller
 @RequestMapping("/geo")
@@ -23,8 +26,7 @@ public class CountryController extends BaseController {
 
 	@Autowired
 	private GenesysService genesysService;
-	
-	
+
 	@RequestMapping
 	public String view(ModelMap model) {
 		model.addAttribute("countries", geoService.listAll());
@@ -40,12 +42,29 @@ public class CountryController extends BaseController {
 			throw new ResourceNotFoundException();
 		}
 		model.addAttribute("country", country);
+
+		// All institutes
 		model.addAttribute("faoInstitutes", instituteService.listByCountry(country));
-		
+		// Active ones
+		model.addAttribute("genesysInstitutes", instituteService.listByCountryActive(country));
+
 		model.addAttribute("countByOrigin", genesysService.countByOrigin(country.getCode3()));
 		model.addAttribute("countByLocation", genesysService.countByLocation(country.getCode3()));
 		
 		return "/country/details";
 	}
 
+
+	@RequestMapping("/{country}/data")
+	public String viewData(ModelMap model, @PathVariable(value = "country") String countryStr, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
+		_logger.debug("Viewing country " + countryStr);
+		Country country = geoService.getCountry(countryStr);
+		if (country==null) {
+			throw new ResourceNotFoundException();
+		}
+		model.addAttribute("country", country);
+		model.addAttribute("accessions", genesysService.listAccessionsByOrigin(country, new PageRequest(page - 1, 50, new Sort("accessionName"))));
+
+		return "/country/data";
+	}
 }

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

 package org.crophub.rest.servlet.controller;
 
+import org.crophub.rest.common.model.genesys.Accession;
 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.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;
@@ -43,4 +45,22 @@ public class WiewsController extends BaseController {
 		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) {
+		_logger.debug("Viewing country " + wiewsCode);
+		FaoInstitute faoInstitute = instituteService.getInstitute(wiewsCode);
+		if (faoInstitute == null) {
+			throw new ResourceNotFoundException();
+		}
+		model.addAttribute("faoInstitute", faoInstitute);
+		
+		_logger.warn("Searching accessions of: " + faoInstitute);
+		Page<Accession> accessions = genesysService.listAccessionsByInstitute(faoInstitute, 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

@@ -83,10 +83,31 @@ 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=Organizations registered in WIEWS
-country.stat.countByLocation={0} accessions held by institutes in this country.
+country.stat.countByLocation={0} accessions held by 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}
 
 faoInstitutes.page.list.title=WIEWS Institutes
 faoInstitutes.page.profile.title=WIEWS {0}
 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}
+
+
+view.accessions=View accessions...
+paged.pageOfPages=Page {0} of {1}
+
+accessions.number={0} accessions
+
+accession.accessionName=Accession
+accession.origin=Country of origin
+accession.holdingInstitute=Holding institute
+accession.holdingCountry=Location
+accession.taxonomy=Taxonomy
+
+
+
+

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

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="country.page.profile.title" arguments="${country.name}" argumentSeparator="|" /></title>
+</head>
+<body>
+	<c:if test="${country eq null}">
+		<div class="alert alert-error">
+			<spring:message code="data.error.404" />
+		</div>
+	</c:if>
+
+	<h1>
+		<spring:message code="country.accessions.from" arguments="${country.name}" />
+	</h1>
+	
+	<a href="<c:url value="/geo/${country.code3.toLowerCase()}" />"><c:out value="${country.name}" /></a>
+
+	<div class="nav-header">
+		<spring:message code="accessions.number" arguments="${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><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="${accessions.content}" var="accession" varStatus="status">
+				<tr>
+					<td><a href="<c:url value="/acn/id/${accession.id}" />"><b><c:out value="${accession.accessionName}" /></b></a></td>
+					<td><c:out value="${country.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="${accession.institute.country.name}" /></a></td>
+				</tr>
+			</c:forEach>
+		</tbody>
+	</table>
+	<div class="nav-header">
+		<a href="?page=${accessions.number}">⇇ Previous</a> <a href="?page=${accessions.number + 2}">Next ⇉</a>
+	</div>
+
+</body>
+</html>
\ No newline at end of file

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

@@ -24,13 +24,22 @@
 		<c:out value="${country.code2}" />
 	</div>
 	
-	<h2><spring:message code="country.statistics" /></h2>
-	<div><spring:message code="country.stat.countByOrigin" arguments="${countByOrigin}" /></div>
-	<div><spring:message code="country.stat.countByLocation" arguments="${countByLocation}" /></div>
-	
-	<h3>
+	<h3><spring:message code="country.statistics" /></h3>
+	<div>
+		<spring:message code="country.stat.countByOrigin" arguments="${countByOrigin}" />
+		<a href="<c:url value="/geo/${country.code3.toLowerCase()}/data" />"><spring:message code="view.accessions" /></a>
+	</div>
+
+	<h3><spring:message code="country.stat.countByLocation" arguments="${countByLocation}" /></h3>
+	<ul>
+		<c:forEach items="${genesysInstitutes}" var="faoInstitute" varStatus="status">
+			<li><a href="<c:url value="/wiews/${faoInstitute.code.toLowerCase()}" />"><b><c:out value="${faoInstitute.code}" /></b> <c:out value="${faoInstitute.fullName}" /></a> <spring:message code="faoInstitute.accessionCount" arguments="${faoInstitute.accessionCount}" /></li>
+		</c:forEach>
+	</ul>
+		
+	<h4>
 		<spring:message code="country.page.faoInstitutes" />
-	</h3>
+	</h4>
 
 	<ul>
 		<c:forEach items="${faoInstitutes}" var="faoInstitute" varStatus="status">

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

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="faoInstitutes.page.data.title" arguments="${faoInstitute.code}" argumentSeparator="|" /></title>
+</head>
+<body>
+	<h1>
+		<spring:message code="faoInstitute.accessions.at" arguments="${faoInstitute.fullName}" argumentSeparator="||," />
+	</h1>
+	<div>
+		<spring:message code="accessions.number" arguments="${accessions.totalElements}" />
+	</div>
+	<div>
+		<a href="<c:url value="/geo/${faoInstitute.country.code3.toLowerCase()}" />"><c:out value="${faoInstitute.country.name}" /></a>
+	</div>
+	
+	<div class="nav-header">
+		<spring:message code="paged.pageOfPages" arguments="${accessions.number+1},${accessions.totalPages}" />
+		<a href="?page=${accessions.number}">⇇ Previous</a>
+		<a href="?page=${accessions.number + 2}">Next ⇉</a>
+	</div>
+
+	<table>
+		<thead>
+			<tr>
+				<td><spring:message code="accession.accessionName" /></td>
+				<td><spring:message code="accession.origin" /></td>
+				<td><spring:message code="accession.taxonomy" /></td>
+				<td><spring:message code="accession.holdingInstitute" /></td>
+				<td><spring:message code="accession.holdingCountry" /></td>
+			</tr>
+		</thead>
+		<tbody>
+			<c:forEach items="${accessions.content}" var="accession" varStatus="status">
+				<tr>
+					<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.origin}" /></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>
\ No newline at end of file

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

@@ -32,7 +32,12 @@
 		<a href="<c:out value="${faoInstitute.url}" />"><c:out value="${faoInstitute.url}" /></a>
 	</div>
 	
-	<h2>Statistics</h2>
-	<div><spring:message code="faoInstitutes.stat.accessionCount" arguments="${countByInstitute}" /></div>
+
+	<h3><spring:message code="faoInstitute.statistics" /></h3>
+	<div>
+		<spring:message code="faoInstitutes.stat.accessionCount" arguments="${countByInstitute}" />
+		<a href="<c:url value="/wiews/${faoInstitute.code.toLowerCase()}/data" />"><spring:message code="view.accessions" /></a>
+	</div>
+
 </body>
 </html>
\ No newline at end of file

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

@@ -21,9 +21,16 @@
 }
 
 table {
+	width: 100%;
 	font-size: 12px;
 }
 
+table thead td {
+	font-size: 15px;
+	font-weight: normal;
+	padding: 0.5em 0.2em;
+}
+
 h1, h2, h3, h4 {
 }