Projects

src/main/java/org/genesys2/server/model/impl/AccessionList.java

@@ -45,7 +45,7 @@ public class AccessionList extends VersionedAuditedModel implements AclAwareMode
 	protected UUID uuid;
 
 	@ManyToMany(cascade = {}, fetch = FetchType.LAZY)
-	@JoinTable(name = "accelistitems", joinColumns = @JoinColumn(name = "listid"), inverseJoinColumns = @JoinColumn(name="acceid"))
+	@JoinTable(name = "accelistitems", joinColumns = @JoinColumn(name = "listid") , inverseJoinColumns = @JoinColumn(name = "acceid") )
 	private Set<AccessionId> accessionIds;
 
 	@Column(name = "title", nullable = false)
@@ -54,6 +54,9 @@ public class AccessionList extends VersionedAuditedModel implements AclAwareMode
 	@Column(name = "description", nullable = true)
 	private String description;
 
+	@Column
+	private boolean shared;
+
 	public UUID getUuid() {
 		return uuid;
 	}
@@ -95,5 +98,17 @@ public class AccessionList extends VersionedAuditedModel implements AclAwareMode
 	public void setTitle(String title) {
 		this.title = title;
 	}
+	
+	public void setShared(boolean shared) {
+		this.shared = shared;
+	}
+
+	public boolean isShared() {
+		return shared;
+	}
+	
+	public boolean getShared() {
+		return shared;
+	}
 
 }
\ No newline at end of file

src/main/java/org/genesys2/server/model/impl/Project.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.model.impl;
 
 import org.genesys2.server.model.AclAwareModel;
@@ -11,47 +27,51 @@ import java.util.UUID;
 @Table(name = "project")
 public class Project extends VersionedAuditedModel implements AclAwareModel {
 
-    @Column(length=200, nullable=false)
-    private String name;
+	private static final long serialVersionUID = -2262512202111475334L;
+
+	@Column(length = 200, nullable = false)
+	private String name;
 
-    @Column(length=200, nullable=true)
-    private String url;
+	@Column(length = 200, nullable = true)
+	private String url;
 
-    @Column(length=50, nullable=false, unique=true)
-    private String code;
+	@Column(length = 50, nullable = false, unique = true)
+	private String code;
 
-    @OneToMany(fetch = FetchType.LAZY, targetEntity = AccessionList.class)
-    private List<UUID> accessionLists;
+	@Column(name = "uuid", nullable = false)
+	@ElementCollection(fetch = FetchType.LAZY)
+	@CollectionTable(name = "project_accelist", joinColumns = @JoinColumn(name = "projectId", referencedColumnName = "id"))
+	private List<UUID> accessionLists;
 
-    public String getName() {
-        return name;
-    }
+	public String getName() {
+		return name;
+	}
 
-    public void setName(String name) {
-        this.name = name;
-    }
+	public void setName(String name) {
+		this.name = name;
+	}
 
-    public String getUrl() {
-        return url;
-    }
+	public String getUrl() {
+		return url;
+	}
 
-    public void setUrl(String url) {
-        this.url = url;
-    }
+	public void setUrl(String url) {
+		this.url = url;
+	}
 
-    public String getCode() {
-        return code;
-    }
+	public String getCode() {
+		return code;
+	}
 
-    public void setCode(String code) {
-        this.code = code;
-    }
+	public void setCode(String code) {
+		this.code = code;
+	}
 
-    public List<UUID> getAccessionLists() {
-        return accessionLists;
-    }
+	public List<UUID> getAccessionLists() {
+		return accessionLists;
+	}
 
-    public void setAccessionLists(List<UUID> accessionLists) {
-        this.accessionLists = accessionLists;
-    }
+	public void setAccessionLists(List<UUID> accessionLists) {
+		this.accessionLists = accessionLists;
+	}
 }

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

@@ -36,6 +36,9 @@ public interface AccessionListRepository extends JpaRepository<AccessionList, Lo
 
 	AccessionList findByUuid(UUID uuid);
 
+	@Query("from AccessionList al where al.uuid in (?1)")
+	List<AccessionList> findByUuids(List<UUID> uuid);
+
 	@Query(nativeQuery = true, value = "insert into accelistitems (listid, acceid) values (?1, ?2)")
 	@Modifying
 	void addOne(AccessionList list, AccessionId accession);
@@ -47,4 +50,5 @@ public interface AccessionListRepository extends JpaRepository<AccessionList, Lo
 	@Query(nativeQuery=true, value="select count(acceid) from accelistitems where listid = ?1")
 	int sizeOf(AccessionList list);
 
+
 }

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

-package org.genesys2.server.persistence.domain;
+/**
+ * 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.persistence.domain;
 
 import org.genesys2.server.model.impl.Project;
 import org.springframework.data.jpa.repository.JpaRepository;

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

@@ -40,6 +40,7 @@ public interface AccessionListService {
 	Set<Long> getAccessionIds(AccessionList loaded);
 
 	AccessionList getList(UUID uuid);
+	List<AccessionList> getLists(List<UUID> uuid);
 
 	void removeAll(AccessionList accessionList);
 
@@ -50,4 +51,5 @@ public interface AccessionListService {
 	void addToList(AccessionList loaded, AppliedFilters filters);
 
 	int sizeOf(AccessionList loaded);
+
 }
\ No newline at end of file

src/main/java/org/genesys2/server/service/ProjectService.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.service;
 
 import org.genesys2.server.model.impl.Project;

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

@@ -21,6 +21,7 @@ import java.util.List;
 import java.util.Set;
 import java.util.UUID;
 
+import org.apache.commons.collections.ListUtils;
 import org.apache.log4j.Logger;
 import org.genesys2.server.model.genesys.AccessionData;
 import org.genesys2.server.model.impl.AccessionList;
@@ -34,6 +35,7 @@ import org.genesys2.server.service.impl.FilterHandler.LiteralValueFilter;
 import org.genesys2.spring.SecurityContextUtil;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.access.prepost.PostAuthorize;
+import org.springframework.security.access.prepost.PostFilter;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
@@ -53,11 +55,18 @@ public class AccessionListServiceImpl implements AccessionListService {
 	}
 
 	@Override
-	@PostAuthorize("hasRole('ADMINISTRATOR') or hasPermission(returnObject, 'READ')")
+	@PostAuthorize("hasRole('ADMINISTRATOR') or hasPermission(returnObject, 'READ') or returnObject.shared == true")
 	public AccessionList getList(UUID uuid) {
 		return accessionListRepository.findByUuid(uuid);
 	}
 
+	@SuppressWarnings("unchecked")
+	@Override
+	@PostFilter("hasRole('ADMINISTRATOR') or hasPermission(filterObject, 'READ') or filterObject.shared == true")
+	public List<AccessionList> getLists(List<UUID> uuids) {
+		return uuids == null || uuids.isEmpty() ? ListUtils.EMPTY_LIST : accessionListRepository.findByUuids(uuids);
+	}
+
 	@Override
 	@PreAuthorize("isAuthenticated() and (#accessionList.id==null or hasRole('ADMINISTRATOR') or hasPermission(#accessionList, 'WRITE'))")
 	@Transactional

src/main/java/org/genesys2/server/service/impl/ProjectServiceImpl.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.service.impl;
 
 import org.genesys2.server.model.impl.Project;
@@ -15,54 +31,60 @@ import java.util.List;
 import java.util.Locale;
 
 @Service
-@Transactional
-public class ProjectServiceImpl implements ProjectService{
+@Transactional(readOnly = true)
+public class ProjectServiceImpl implements ProjectService {
 
-    @Autowired
-    ProjectRepository projectRepository;
+	@Autowired
+	ProjectRepository projectRepository;
 
-    @Autowired
-    ContentService contentService;
+	@Autowired
+	ContentService contentService;
 
-    @Override
-    public Page<Project> list(Pageable p) {
-        return projectRepository.findAll(p);
-    }
+	@Override
+	public Page<Project> list(Pageable p) {
+		return projectRepository.findAll(p);
+	}
 
-    @Override
-    public Project getProjectById(Long id) {
-        return projectRepository.findOne(id);
-    }
+	@Override
+	public Project getProjectById(Long id) {
+		return projectRepository.findOne(id);
+	}
 
-    @Override
-    public Project getProjectByCode(String code) {
-        return projectRepository.findByCode(code);
-    }
+	@Override
+	public Project getProjectByCode(String code) {
+		Project project = projectRepository.findByCode(code);
+		project.getAccessionLists().size();
+		return project;
+	}
 
-    @Override
-    public List<Project> getAllProjects() {
-        return projectRepository.findAll();
-    }
+	@Override
+	public List<Project> getAllProjects() {
+		return projectRepository.findAll();
+	}
 
-    @Override
-    public List<Project> getProjectsByName(String name) {
-        return projectRepository.findByName(name);
-    }
+	@Override
+	public List<Project> getProjectsByName(String name) {
+		return projectRepository.findByName(name);
+	}
 
-    @Override
-    public void saveProject(Project project) {
-        projectRepository.save(project);
-    }
+	@Override
+	@PreAuthorize("#project.id==null or hasRole('ADMINISTRATOR') or hasRole('CONTENTMANAGER') or hasPermission(#project, 'ADMINISTRATION')")
+	@Transactional
+	public void saveProject(Project project) {
+		projectRepository.save(project);
+	}
 
-    @Override
-    public void deleteProject(Project project) {
-        projectRepository.delete(project);
-    }
+	@Override
+	@PreAuthorize("hasRole('ADMINISTRATOR') or hasRole('CONTENTMANAGER') or hasPermission(#project, 'ADMINISTRATION')")
+	@Transactional
+	public void deleteProject(Project project) {
+		projectRepository.delete(project);
+	}
 
-    @Override
-    @PreAuthorize("hasRole('ADMINISTRATOR') or hasRole('CONTENTMANAGER') or hasPermission(#crop, 'ADMINISTRATION')")
-    @Transactional(readOnly = false)
-    public void updateBlurp(Project project, String textBody, String summary, Locale locale) {
-        contentService.updateArticle(project, "blurp", null, textBody, summary, locale);
-    }
+	@Override
+	@PreAuthorize("hasRole('ADMINISTRATOR') or hasRole('CONTENTMANAGER') or hasPermission(#project, 'ADMINISTRATION')")
+	@Transactional
+	public void updateBlurp(Project project, String textBody, String summary, Locale locale) {
+		contentService.updateArticle(project, "blurp", null, textBody, summary, locale);
+	}
 }

src/main/java/org/genesys2/server/servlet/controller/ProjectController.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.Locale;
+
 import org.genesys2.server.model.impl.Project;
+import org.genesys2.server.service.AccessionListService;
 import org.genesys2.server.service.ContentService;
 import org.genesys2.server.service.ProjectService;
 import org.genesys2.spring.ResourceNotFoundException;
@@ -11,67 +30,90 @@ 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.ModelAttribute;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
 
-import java.util.Locale;
-
 @Controller
 @RequestMapping("/project")
-public class ProjectController extends BaseController{
+public class ProjectController extends BaseController {
+
+	@Autowired
+	private ProjectService projectService;
+
+	@Autowired
+	private AccessionListService accessionListService;
+
+	@Autowired
+	ContentService contentService;
+
+	@RequestMapping({ "/", "" })
+	public String projects() {
+		return "redirect:/project/list";
+	}
+
+	@RequestMapping("/list")
+	public String listProjects(ModelMap modelMap, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
 
-    @Autowired
-    private ProjectService projectService;
+		Page<Project> projects = projectService.list(new PageRequest(page - 1, 20, new Sort("name")));
 
-    @Autowired
-    ContentService contentService;
+		modelMap.addAttribute("pagedData", projects);
 
-    @RequestMapping({"/", ""})
-    public String projects(){
-        return "redirect:/project/list";
-    }
+		return "/project/index";
+	}
 
-    @RequestMapping("/list")
-    public String listProjects(ModelMap modelMap, @RequestParam(value = "page", required = false, defaultValue = "1") int page){
+	@RequestMapping("/{code}")
+	public String viewProject(ModelMap modelMap, @PathVariable(value = "code") String code) {
+		Project project = projectService.getProjectByCode(code);
+		if (project != null) {
+			modelMap.addAttribute("project", project);
+			modelMap.addAttribute("accessionLists", accessionListService.getLists(project.getAccessionLists()));
+			modelMap.addAttribute("blurp", contentService.getArticle(project, "blurp", getLocale()));
+		} else {
+			throw new ResourceNotFoundException("No project with code " + code);
+		}
+		return "/project/view";
+	}
 
-        Page<Project> projects = projectService.list(new PageRequest(page - 1, 20, new Sort("name")));
+	@RequestMapping("/add-project")
+	public String addProject(ModelMap modelMap) {
+		modelMap.addAttribute("project", new Project());
+		return "/project/edit";
+	}
 
-        modelMap.addAttribute("pagedData", projects);
+	@RequestMapping("/{code}/edit")
+	public String editProject(ModelMap modelMap, @PathVariable(value = "code") String code) {
+		viewProject(modelMap, code);
+		return "/project/edit";
+	}
 
-        return "/project/index";
-    }
+	@RequestMapping("/update-project")
+	public String update(ModelMap modelMap, @ModelAttribute("project") Project p, @RequestParam("blurp") String aboutBody,
+			@RequestParam(value = "summary", required = false) String summary) {
 
-    @RequestMapping("/{code}")
-    public String viewProject(ModelMap modelMap, @PathVariable(value = "code")String code){
-        Project project = projectService.getProjectByCode(code);
-        modelMap.addAttribute("blurp", contentService.getArticle(project, "blurp", getLocale()));
-        modelMap.addAttribute("project", project);
-        return "/project/view";
-    }
+		_logger.debug("Updating project " + p.getCode());
+		Project project = null;
 
-    @RequestMapping("/edit/{code}")
-    public String editProject(ModelMap modelMap, @PathVariable(value = "code") String code){
-        viewProject(modelMap, code);
-        return "/project/edit";
-    }
+		if (p.getId() != null)
+			project = projectService.getProjectById(p.getId());
 
-    @RequestMapping("/{code}/update")
-    public String update(ModelMap modelMap, @PathVariable(value = "code")String code, @RequestParam("blurp") String aboutBody,
-                         @RequestParam(value = "summary", required = false) String summary){
+		if (project == null) {
+			project = new Project();
+		}
 
-        _logger.debug("Updating project " + code);
-        final Project project = projectService.getProjectByCode(code);
-        if (project == null) {
-            throw new ResourceNotFoundException();
-        }
+		project.setCode(p.getCode());
+		project.setUrl(p.getUrl());
+		project.setName(p.getName());
+		project.setAccessionLists(p.getAccessionLists());
 
-        projectService.updateBlurp(project, aboutBody, summary, getLocale());
+		projectService.saveProject(project);
+		projectService.updateBlurp(project, aboutBody, summary, getLocale());
 
-        return "redirect:/project/" + code;
-    }
+		return "redirect:/project/" + p.getCode();
+	}
 
-    protected Locale getLocale() {
-        return LocaleContextHolder.getLocale();
-    }
+	protected Locale getLocale() {
+		return LocaleContextHolder.getLocale();
+	}
 }

src/main/resources/content/language.properties

@@ -156,9 +156,14 @@ country.replaced-by=Country code is replaced by: {0}
 country.is-itpgrfa-contractingParty={0} is party to the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA).
 select-country=Select country
 
-project.page.list.title=WIEWS Projects
-project.page.profile.title=WIEWS {0}
+project.page.list.title=Projects
+project.page.profile.title={0}
+project.code=Project Code
+project.name=Project Name
+project.url=Project website
 project.summary=Summary (HTML metadata)
+project.accessionLists=Accession Lists
+
 
 faoInstitutes.page.list.title=WIEWS Institutes
 faoInstitutes.page.profile.title=WIEWS {0}
@@ -737,3 +742,4 @@ region.page.show.world = Show all world regions
 region.countries-in-region=List of countries in {0}
 region.regions-in-region=FAO Regions in {0}
 region.show-all-regions=List all FAO regions
+

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

@@ -58,6 +58,7 @@
 							<li><a href="<c:url value="/team" />"><spring:message code="user.pulldown.teams" /></a></li>
 							<li><a href="<c:url value="/management/" />"><spring:message code="user.pulldown.oauth-clients" /></a></li>
 							<li><a href="<c:url value="/content" />"><spring:message code="user.pulldown.manage-content" /></a></li>
+							<li><a href="<c:url value="/project" />"><spring:message code="project.page.list.title" /></a></li>
                             </security:authorize>
                             <li><a href="<c:url value="/profile/${user.username}" />"><spring:message code="user.pulldown.profile"/></a></li>
                             <li><a id="logout1" href="#" onclick="document.getElementById('logoutForm').submit();"  ><spring:message code="user.pulldown.logout"/></a>

src/main/webapp/WEB-INF/jsp/project/edit.jsp

 <!DOCTYPE html>
 
-<%@include file="/WEB-INF/jsp/init.jsp" %>
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+<%@ taglib prefix="sf" uri="http://www.springframework.org/tags/form"%>
 
 <html>
 <head>
-    <title><spring:message code="project.page.profile.title" arguments="${project.name}" argumentSeparator="|" /></title>
+<title><spring:message code="project.page.profile.title" arguments="${project.name}" argumentSeparator="|" /></title>
 </head>
 <body>
+	<h1>
+		${project.name}
+		<small>
+			<c:out value="${project.code}" />
+		</small>
+	</h1>