AccessionId#uuid added, initial resolver code implemented

src/main/java/org/genesys2/server/model/IdUUID.java

+package org.genesys2.server.model;
+
+import java.util.UUID;
+
+public interface IdUUID {
+	UUID getUuid();
+}

src/main/java/org/genesys2/server/model/elastic/AccessionDetails.java

@@ -5,6 +5,7 @@ import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.UUID;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
@@ -37,7 +38,7 @@ public class AccessionDetails {
 	private Long id;
 
 	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
-	private String uuid;
+	private UUID uuid;
 	@Field(type = FieldType.String)
 	private String acceNumb;
 	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
@@ -185,11 +186,11 @@ public class AccessionDetails {
 		this.id = id;
 	}
 
-	public String getUuid() {
+	public UUID getUuid() {
 		return uuid;
 	}
-
-	public void setUuid(String uuid) {
+	
+	public void setUuid(UUID uuid) {
 		this.uuid = uuid;
 	}
 

src/main/java/org/genesys2/server/model/genesys/AccessionData.java

@@ -40,17 +40,6 @@ public abstract class AccessionData extends AccessionId {
 
 	public static final List<AccessionData> EMPTY_LIST = Collections.unmodifiableList(new ArrayList<AccessionData>());
 
-	@Column(length = 36)
-	private String uuid;
-
-	public String getUuid() {
-		return uuid;
-	}
-
-	public void setUuid(String uuid) {
-		this.uuid = uuid;
-	}
-
 	@Column(name = "instCode", length = 10, nullable = false)
 	private String instituteCode;
 

src/main/java/org/genesys2/server/model/genesys/AccessionId.java

@@ -16,11 +16,16 @@
 
 package org.genesys2.server.model.genesys;
 
+import java.util.UUID;
+
+import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.Inheritance;
 import javax.persistence.InheritanceType;
+import javax.persistence.PrePersist;
 import javax.persistence.Table;
 
+import org.genesys2.server.model.IdUUID;
 import org.genesys2.server.model.VersionedAuditedModel;
 
 /**
@@ -30,6 +35,24 @@ import org.genesys2.server.model.VersionedAuditedModel;
 @Entity
 @Inheritance(strategy = InheritanceType.JOINED)
 @Table(name = "acce")
-public class AccessionId extends VersionedAuditedModel {
+public class AccessionId extends VersionedAuditedModel implements IdUUID {
+
+	@Column(columnDefinition = "binary(16)", updatable = false)
+	protected UUID uuid;
+
+	@PrePersist
+	private void prepersist() {
+		if (uuid == null) {
+			uuid = UUID.randomUUID();
+		}
+	}
+
+	@Override
+	public UUID getUuid() {
+		return this.uuid;
+	}
 
+	public void setUuid(UUID uuid) {
+		this.uuid = uuid;
+	}
 }

src/main/java/org/genesys2/server/model/json/AccessionJson.java

@@ -16,6 +16,8 @@
 
 package org.genesys2.server.model.json;
 
+import java.util.UUID;
+
 import org.genesys2.server.model.json.Api1Constants.Accession;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
@@ -39,7 +41,7 @@ public class AccessionJson {
 	@JsonProperty(value = Accession.SUBTAUTHOR)
 	private String subtauthor;
 	@JsonProperty(value = Accession.UUID)
-	private String uuid;
+	private UUID uuid;
 	@JsonProperty(value = Accession.ORIGCTY)
 	private String orgCty;
 	@JsonProperty(value = Accession.ACQDATE)
@@ -147,11 +149,11 @@ public class AccessionJson {
 		this.subtauthor = subtauthor;
 	}
 
-	public String getUuid() {
+	public UUID getUuid() {
 		return uuid;
 	}
 
-	public void setUuid(String uuid) {
+	public void setUuid(UUID uuid) {
 		this.uuid = uuid;
 	}
 

src/main/java/org/genesys2/server/persistence/domain/AccessionHistoricRepository.java

@@ -16,10 +16,20 @@
 
 package org.genesys2.server.persistence.domain;
 
+import java.util.List;
+import java.util.UUID;
+
 import org.genesys2.server.model.genesys.AccessionHistoric;
+import org.genesys2.server.model.impl.FaoInstitute;
 import org.springframework.data.jpa.repository.JpaRepository;
 
 public interface AccessionHistoricRepository extends JpaRepository<AccessionHistoric, Long> {
 
+	AccessionHistoric findOneByUuid(UUID uuid);
+
+	List<AccessionHistoric> findByInstituteAndAccessionName(FaoInstitute faoInstitute, String acceNumb);
+
+	List<AccessionHistoric> findByAccessionName(String acceNumb);
+
 
 }

src/main/java/org/genesys2/server/persistence/domain/AccessionRepository.java

@@ -19,6 +19,7 @@ package org.genesys2.server.persistence.domain;
 import java.util.Collection;
 import java.util.List;
 import java.util.Set;
+import java.util.UUID;
 
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Taxonomy2;
@@ -108,4 +109,8 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Modifying
 	@Query(nativeQuery=true, value="delete from accession where id = ?1")
 	public void deleteActive(long id);
+
+	public Accession findOneByUuid(UUID uuid);
+
+	public List<Accession> findByAccessionName(String acceNumb);
 }

src/main/java/org/genesys2/server/service/ResolverService.java

+package org.genesys2.server.service;
+
+import java.util.List;
+import java.util.UUID;
+
+import org.genesys2.server.model.IdUUID;
+import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.impl.FaoInstitute;
+
+public interface ResolverService {
+
+	IdUUID forward(UUID uuid);
+
+	List<AccessionId> findMatches(FaoInstitute faoInstitute, String acceNumb);
+
+}

src/main/java/org/genesys2/server/service/impl/BatchRESTServiceImpl.java

@@ -701,16 +701,9 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 	private boolean updateUuid(AccessionData accession, JsonNode value) throws RESTApiValueException {
 		if (value != null) {
-			final String uuid = value.isNull() ? null : value.textValue();
-			if (!StringUtils.equals(uuid, accession.getUuid())) {
-				if (uuid != null) {
-					try {
-						// Throws a runtime exception if format is invalid
-						UUID.fromString(uuid);
-					} catch (final RuntimeException e) {
-						throw new RESTApiValueException("UUID " + uuid + " is not in valid format: " + e.getMessage());
-					}
-				}
+			final UUID uuid = value.isNull() ? null : UUID.fromString(value.textValue());
+
+			if (accession.getUuid() == null && uuid != null) {
 				accession.setUuid(uuid);
 				return true;
 			}

src/main/java/org/genesys2/server/service/impl/ResolverServiceImpl.java

+package org.genesys2.server.service.impl;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+
+import org.genesys2.server.model.IdUUID;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionHistoric;
+import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.persistence.domain.AccessionHistoricRepository;
+import org.genesys2.server.persistence.domain.AccessionRepository;
+import org.genesys2.server.service.ResolverService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+@Service
+@Transactional(readOnly = true)
+public class ResolverServiceImpl implements ResolverService {
+
+	@Autowired
+	private AccessionRepository repoAccession;
+
+	@Autowired
+	private AccessionHistoricRepository repoAccessionHistoric;
+
+	@Override
+	public IdUUID forward(UUID uuid) {
+		Accession accession = repoAccession.findOneByUuid(uuid);
+		if (accession != null) {
+			return accession;
+		}
+
+		AccessionHistoric accessionHistoric = repoAccessionHistoric.findOneByUuid(uuid);
+		if (accessionHistoric != null) {
+			return accessionHistoric;
+		}
+
+		return null;
+	}
+
+	@Override
+	public List<AccessionId> findMatches(FaoInstitute faoInstitute, String acceNumb) {
+		List<AccessionId> matches = new ArrayList<AccessionId>();
+		if (faoInstitute != null) {
+			matches.addAll(repoAccession.findByInstituteAndAccessionName(faoInstitute, acceNumb));
+			matches.addAll(repoAccessionHistoric.findByInstituteAndAccessionName(faoInstitute, acceNumb));
+		} else {
+			matches.addAll(repoAccession.findByAccessionName(acceNumb));
+			matches.addAll(repoAccessionHistoric.findByAccessionName(acceNumb));
+		}
+		return matches;
+	}
+
+}

src/main/java/org/genesys2/server/servlet/controller/ResolverController.java

+/**
+ * Copyright 2015 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.genesys2.server.servlet.controller;
+
+import java.util.List;
+import java.util.UUID;
+
+import org.genesys2.server.model.IdUUID;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionHistoric;
+import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.service.InstituteService;
+import org.genesys2.server.service.ResolverService;
+import org.genesys2.spring.ResourceNotFoundException;
+import org.springframework.beans.factory.annotation.Autowired;
+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
+@RequestMapping(value = "/resolver")
+public class ResolverController {
+
+	@Autowired
+	private ResolverService resolverService;
+
+	@Autowired
+	private InstituteService instituteService;
+
+	@RequestMapping(value = "")
+	public String form() {
+		return "/resolver/index";
+	}
+
+	@RequestMapping(value = "/reverse", method = RequestMethod.POST, params = { "acceNumb" })
+	public String reverse(ModelMap model, @RequestParam(required = true, value = "acceNumb") String acceNumb,
+			@RequestParam(required = false, value = "instCode") String instCode) {
+
+		FaoInstitute faoInstitute = instituteService.findInstitute(instCode);
+		List<AccessionId> accessions = resolverService.findMatches(faoInstitute, acceNumb);
+		model.addAttribute("accessions", accessions);
+		return "/resolver/reverse";
+	}
+
+	@RequestMapping(value = "/forward", method = RequestMethod.POST, params = { "uuid" })
+	public String forwardGui(ModelMap model, @RequestParam(required = true, value = "uuid") UUID uuid) {
+		return forwardUuid(model, uuid);
+	}
+
+	@RequestMapping(value = "/{uuid:.{36}}", method = RequestMethod.GET)
+	public String forwardUuid(ModelMap model, @PathVariable(value = "uuid") UUID uuid) {
+
+		final IdUUID resolved = resolverService.forward(uuid);
+
+		if (resolved == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		if (resolved instanceof Accession) {
+			return "redirect:/acn/id/" + ((Accession) resolved).getId();
+		}
+
+		if (resolved instanceof AccessionHistoric) {
+			return "redirect:/history/acn/id/" + resolved.getUuid();
+		}
+
+		throw new ResourceNotFoundException("We don't have an object with UUID " + uuid);
+	}
+}

src/main/resources/content/language.properties

@@ -603,3 +603,13 @@ worldclim.other-climate=Other climatic data
 
 download.page.title=Before you download
 download.download-now=Start download, I will wait.
+
+resolver.page.index.title=Find permanent identifier
+resolver.acceNumb=Accession Number
+resolver.instCode=Holding institute code
+resolver.lookup=Find identifier
+resolver.uuid=UUID
+resolver.resolve=Resolve
+
+resolver.page.reverse.title=Resolution results
+accession.purl=Permanent URL

src/main/sourceapp/styles/bootstrap.scss

@@ -89,3 +89,8 @@ html[dir="rtl"] {
 .navbar-right {
   margin-right: 0;
 }
+
+
+.text-clip {
+	@include text-overflow;
+}

src/main/sourceapp/styles/genesys.scss

@@ -1254,27 +1254,31 @@ table.accessions tr.not-available>td, table tr.expired>td {
 
 .crop-details {
   font-size: 14px;
-}
-
-.crop-details>div.row {
-  background-color: #f8f7f5;
-  margin: 5px 0 5px 0;
-}
-
-.crop-details>div.row>div {
-  padding: 10px;
-}
-
-.crop-details h4 {
-  color: #2b2924;
-  font-size: 22px;
-  font-weight: bold;
-  margin: 0;
-  padding: 20px 0 5px;
-}
 
-.crop-details h2, .crop-details>div:nth-of-type(even) {
-  background-color: #f3f2ee;
+  > div.row {
+    background-color: #f8f7f5;
+    margin: 5px 0 5px 0;
+  
+    >div {
+      padding: 10px;
+    }
+  }
+  
+  h4 {
+    color: #2b2924;
+    font-size: 22px;
+    font-weight: bold;
+    margin: 0;
+    padding: 20px 0 5px;
+  }
+  
+  .header {
+    font-weight: bold;
+  }
+  
+  h2, >div:nth-of-type(even) {
+    background-color: #f3f2ee;
+  }
 }
 
 table.crop-details h4 {

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

@@ -103,6 +103,16 @@
 	</div>
 	
 	<div class="crop-details">
+            <c:if test="${accession.uuid ne null}">
+              <div class="row text-muted">
+                <div class="col-xs-4"><spring:message code="accession.uuid" /></div>
+                <div class="col-xs-8"><c:out value="${accession.uuid}" /></div>
+              </div>
+              <div class="row">
+                <div class="col-xs-4"><spring:message code="accession.purl" /></div>
+                <div class="col-xs-8"><a href="https://purl.org/germplasm/id/${accession.uuid}"><c:out value="https://purl.org/germplasm/id/${accession.uuid}" /></a></div>
+              </div>
+            </c:if>
 			<div class="row">
 				<div class="col-xs-4"><spring:message code="accession.holdingInstitute" /></div>
 				<div class="col-xs-8"><a property="dwc:institutionCode" href="<c:url value="/wiews/${accession.instituteCode}" />"> <c:out value="${accession.institute.fullName}" />
@@ -116,12 +126,6 @@
 				<div class="col-xs-4"><spring:message code="accession.accessionName" /></div>
 				<div class="col-xs-8"><c:out value="${accession.accessionName}" /></div>
 			</div>
-			<c:if test="${accession.uuid ne null}">
-			<div class="row">
-				<div class="col-xs-4"><spring:message code="accession.uuid" /></div>
-				<div class="col-xs-8"><b><c:out value="${accession.uuid}" /></b></div>
-			</div>
-			</c:if>
 
 			<c:if test="${crops ne null}">
 				<div class="row">

src/main/webapp/WEB-INF/jsp/accession/explore-es.jsp

@@ -259,7 +259,7 @@
 					<td class="sel" x-aid="${accession.id}"></td>
 					<td><a href="<c:url value="/acn/id/${accession.id}" />"><b><c:out value="${accession.acceNumb}" /></b></a></td>
 					<%-- <td><a href="<c:url value="/acn/t/${accession.taxonomy.genus}/${accession.taxonomy.species}" />"><c:out value="${accession.taxonomy.sciName}" /></a></td> --%>
-					<td><c:out value="${accession.taxonomy.sciName}" /></td>
+					<td><span dir="ltr" class="sci-name"><c:out value="${accession.taxonomy.sciName}" /></span></td>
 					<%-- <td class="notimportant"><a href="<c:url value="/geo/${accession.orgCty.iso3}" />"><c:out value="${accession.orgCty.name}" /></a></td> --%>
 					<td class="notimportant"><c:out value="${jspHelper.getCountry(accession.orgCty.iso3).getName(pageContext.response.locale)}" /></td>
 					<td class="notimportant"><spring:message code="accession.sampleStatus.${accession.sampStat}" /></td>

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

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="resolver.page.index.title" /></title>
+</head>
+<body>
+  <h1>
+    <spring:message code="resolver.page.index.title" />
+  </h1>
+
+  <form class="form-horizontal" method="post" role="form" action="<c:url value="/resolver/reverse" />">
+    <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
+    <div class="form-group">
+      <label class="control-label col-sm-4"><spring:message code="resolver.acceNumb" /></label>
+      <div class="col-sm-8">
+        <input type="text" class="form-control" name="acceNumb" />
+      </div>
+    </div>
+    <div class="form-group">
+      <label class="control-label col-sm-4"><spring:message code="resolver.instCode" /></label>
+      <div class="col-sm-8">
+        <input type="text" class="form-control" name="instCode" />
+      </div>
+    </div>
+    <div class="form-group">
+      <div class="col-sm-offset-4 col-sm-8">
+        <button class="btn btn-primary" type="submit">
+          <spring:message code="resolver.lookup" />
+        </button>
+      </div>
+    </div>
+  </form>
+
+
+  <form class="form-horizontal" method="post" role="form" action="<c:url value="/resolver/forward" />">
+    <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
+    <div class="form-group">
+      <label class="control-label col-sm-4"><spring:message code="resolver.uuid" /></label>
+      <div class="col-sm-8">
+        <input type="text" class="form-control" name="uuid" />
+      </div>
+    </div>
+    <div class="form-group">
+      <div class="col-sm-offset-4 col-sm-8">
+        <button class="btn btn-primary" type="submit">
+          <spring:message code="resolver.resolve" />
+        </button>
+      </div>
+    </div>
+  </form>
+
+
+</body>
+</html>
\ No newline at end of file

src/main/webapp/WEB-INF/jsp/resolver/reverse.jsp

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="resolver.page.reverse.title" /></title>
+</head>
+<body>
+  <h1>
+    <spring:message code="resolver.page.reverse.title" />
+  </h1>
+
+  <div class="crop-details">
+    <div class="row header not-important">
+      <div class="col-sm-2">
+        <spring:message code="accession.holdingInstitute" />
+      </div>
+      <div class="col-sm-2">
+        <spring:message code="accession.accessionName" />
+      </div>
+      <div class="col-sm-4">
+        <spring:message code="accession.taxonomy" />
+      </div>
+    </div>
+    <c:forEach items="${accessions}" var="accession" varStatus="status">
+      <div class="row ${accession.getClass().simpleName=='AccessionHistoric' ? 'text-muted' : ''}">
+        <div class="col-sm-2">
+          <a href="<c:url value="/wiews/${accession.institute.code}" />"><c:out value="${accession.institute.code}" /></a>
+        </div>
+        <div class="col-sm-2">
+          <c:choose>
+            <c:when test="${accession.getClass().simpleName=='AccessionHistoric'}">
+              <a href="<c:url value="/archive/acn/${accession.uuid}" />"><c:out value="${accession.accessionName}" /></a>
+            </c:when>
+            <c:otherwise>
+              <a href="<c:url value="/acn/id/${accession.id}" />"><c:out value="${accession.accessionName}" /></a>
+            </c:otherwise>
+          </c:choose>
+        </div>
+        <div class="col-sm-4">
+          <span dir="ltr" class="sci-name text-clip"><c:out value="${accession.taxonomy.taxonName}" /></span>
+        </div>
+        <div class="col-sm-4">
+          <a href="https://purl.org/germplasm/id/${accession.uuid}"><c:out value="${accession.uuid}" /></a>
+        </div>
+      </div>
+    </c:forEach>
+  </div>
+</body>
+</html>
\ No newline at end of file