diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
index ca0c72a1213ceb9a5309643f95ef843e61b1a0b2..8ee4e0cefaf44bb525d71dd1923407e8230debfe 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.api.projects;
import java.io.IOException;
+import java.util.List;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
@@ -37,6 +38,13 @@ public class ProjectController extends BaseController {
return projectController.getMetaData(projectId, token);
}
+ @RequestMapping(value = "/projects/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<ProjectMetaData> getProjects(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return projectController.getProjects(token);
+ }
+
@RequestMapping(value = "/projects/{projectId}/statistics", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
public Object getStatistics(//
@PathVariable(value = "projectId") String projectId, //
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 529e8792c63d95a2a1c58797e75bc9da6c4cc8a9..da81928faa1673a509ebedaa2607403d142f9158 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -94,17 +94,11 @@ public class ProjectRestImpl extends BaseRestImpl {
if (project == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
- ProjectMetaData result = createData(project, authenticationToken);
- if (project.getOrganism() != null) {
- result.setOrganism(createAnnotation(project.getOrganism()));
- }
- if (project.getDisease() != null) {
- result.setDisease(createAnnotation(project.getDisease()));
- }
+ ProjectMetaData result = createData(project);
return result;
}
- private ProjectMetaData createData(Project project, AuthenticationToken token) {
+ private ProjectMetaData createData(Project project) {
ProjectMetaData result = new ProjectMetaData();
result.setName(project.getName());
@@ -130,6 +124,13 @@ public class ProjectRestImpl extends BaseRestImpl {
result.setTopOverviewImage(factory.create(project.getOverviewImages().get(0)));
}
+ if (project.getOrganism() != null) {
+ result.setOrganism(createAnnotation(project.getOrganism()));
+ }
+ if (project.getDisease() != null) {
+ result.setDisease(createAnnotation(project.getDisease()));
+ }
+
return result;
}
@@ -383,4 +384,14 @@ public class ProjectRestImpl extends BaseRestImpl {
return result;
}
+ public List<ProjectMetaData> getProjects(String token) throws SecurityException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ List<Project> projects = getProjectService().getAllProjects(authenticationToken);
+ List<ProjectMetaData> result = new ArrayList<>();
+ for (Project project : projects) {
+ result.add(createData(project));
+ }
+ return result;
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index ec6bb96897cb4a0c4b6f3a8223ea59bc6be51813..4d008c74dc9ecfaaadda2c0750045acc84547236 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
@@ -28,8 +28,6 @@ import lcsb.mapviewer.persist.dao.map.LayoutDao;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.layout.FullLayoutAliasView;
import lcsb.mapviewer.services.search.layout.FullLayoutReactionView;
@@ -45,8 +43,7 @@ public class OverlayRestImpl extends BaseRestImpl {
/**
* Default class logger.
*/
- private Logger logger = Logger.getLogger(OverlayRestImpl.class);
-
+ private Logger logger = Logger.getLogger(OverlayRestImpl.class);
@Autowired
private ILayoutService layoutService;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
index 8340abe87ecc4061b61e2ab7a6dcd37e9a994217..75b04a6d071ab987dc60926aabe7429ff1e5f819 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
@@ -5,7 +5,6 @@ import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
import java.util.List;
-import java.util.Map;
import org.junit.After;
import org.junit.AfterClass;
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index ee67364eb830c52470c347b423fffacb13bf2eed..604b1f3da3158fa9ae3749ff2d88893e06a91c17 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -284,15 +284,24 @@ public class ProjectService implements IProjectService {
}
@Override
- public List<Project> getAllProjects() {
- List<Project> result = projectDao.getAll();
+ public List<Project> getAllProjects(AuthenticationToken token) {
+ List<Project> projects = projectDao.getAll();
+ if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
+ return projects;
+ }
+ List<Project> result = new ArrayList<>();
+ for (Project project : projects) {
+ if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, result)) {
+ result.add(project);
+ }
+ }
return result;
}
@Override
- public List<ProjectView> getAllProjectViews() {
- List<ProjectView> result = new ArrayList<ProjectView>();
- List<Project> projects = getAllProjects();
+ public List<ProjectView> getAllProjectViews(AuthenticationToken token) {
+ List<ProjectView> result = new ArrayList<>();
+ List<Project> projects = getAllProjects(token);
for (Project project : projects) {
result.add(projectViewFactory.create(project));
}
@@ -661,8 +670,6 @@ public class ProjectService implements IProjectService {
* params used to create model
* @param dbProject
* project where the model should be placed
- * @return model loaded from the input and updated by PostLoadModification
- * (from CreateProjectParams)
* @throws InvalidInputDataExecption
* thrown when there is a problem with input file
*/
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
index 5175441f3ffc840f43b4f81e3e35b02430dea2b9..36035412c901ef307dde799f32f2a241d1641237 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
@@ -44,14 +44,14 @@ public interface IProjectService {
*
* @return list of all projects.
*/
- List<Project> getAllProjects();
+ List<Project> getAllProjects(AuthenticationToken token);
/**
* Returns a list of Project views for all projects.
*
* @return list of Project views for all projects
*/
- List<ProjectView> getAllProjectViews();
+ List<ProjectView> getAllProjectViews(AuthenticationToken token);
/**
* Updates project.
@@ -184,4 +184,5 @@ public interface IProjectService {
* parameter
*/
byte[] getInputDataForProject(ProjectView projectView);
+
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index 101892cd487cc00c34ea5f1c8678aeaa2d734e82..f2d08ea6cc581e3b68b5b7eb0f3d0157503f3671 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -85,14 +85,14 @@ public class ProjectServiceTest extends ServiceTestFunctions {
@Test
public void test() {
try {
- List<Project> projects = projectService.getAllProjects();
+ List<Project> projects = projectService.getAllProjects(adminToken);
Project project = new Project();
project.setProjectId(projectId);
projectDao.add(project);
projectDao.evict(project);
- List<Project> projects2 = projectService.getAllProjects();
+ List<Project> projects2 = projectService.getAllProjects(adminToken);
assertEquals(projects.size() + 1, projects2.size());
@@ -124,7 +124,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
project.setProjectId(project_id);
projectDao.add(project);
- List<ProjectView> projects2 = projectService.getAllProjectViews();
+ List<ProjectView> projects2 = projectService.getAllProjectViews(adminToken);
ProjectView row = null;
for (ProjectView projectRow : projects2) {
if (projectRow.getIdObject() == project.getId()) {
@@ -174,7 +174,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
project.setProjectId(projectId);
projectDao.add(project);
- List<ProjectView> projects2 = projectService.getAllProjectViews();
+ List<ProjectView> projects2 = projectService.getAllProjectViews(adminToken);
ProjectView row = null;
for (ProjectView projectRow : projects2) {
if (projectRow.getIdObject() == project.getId()) {
@@ -315,9 +315,9 @@ public class ProjectServiceTest extends ServiceTestFunctions {
// and now check layouts (check if every submodel have them, and point
// into different directory)
- //there are 2 levels
+ // there are 2 levels
int semanticOverlays = 2;
- //-1 is due to pathways and compartments that is not there
+ // -1 is due to pathways and compartments that is not there
int overlays = BuildInLayout.values().length + semanticOverlays - 1;
assertEquals(overlays, model.getLayouts().size());
assertEquals(overlays, s1Model.getLayouts().size());
@@ -719,7 +719,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
assertEquals("Cannot find overview images the model", 2, project.getOverviewImages().size());
- assertEquals("Number of layouts doesn't match", BuildInLayout.values().length-1, model.getLayouts().size());
+ assertEquals("Number of layouts doesn't match", BuildInLayout.values().length - 1, model.getLayouts().size());
assertEquals(BuildInLayout.NESTED.getTitle(), model.getLayouts().get(0).getTitle());
assertEquals(BuildInLayout.NORMAL.getTitle(), model.getLayouts().get(1).getTitle());
projectService.removeProject(project, null, false, adminToken);
@@ -763,7 +763,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
assertEquals("Cannot find overview images the model", 2, project.getOverviewImages().size());
- assertEquals("Number of layouts doesn't match", BuildInLayout.values().length-1, model.getLayouts().size());
+ assertEquals("Number of layouts doesn't match", BuildInLayout.values().length - 1, model.getLayouts().size());
assertEquals(BuildInLayout.NESTED.getTitle(), model.getLayouts().get(1).getTitle());
assertEquals(BuildInLayout.NORMAL.getTitle(), model.getLayouts().get(0).getTitle());
projectService.removeProject(project, null, false, adminToken);
@@ -814,7 +814,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
- assertEquals("Number of layouts doesn't match", BuildInLayout.values().length-1, model.getLayouts().size());
+ assertEquals("Number of layouts doesn't match", BuildInLayout.values().length - 1, model.getLayouts().size());
projectService.removeProject(project, null, false, adminToken);
} catch (Exception e) {
e.printStackTrace();
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
index 0e08e4a105f21283040a4609fe99c885458f1cfb..d023d64bf743dad4d9ecf3b64e5d6cfd7d7d7a3b 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
@@ -587,7 +587,7 @@ public class ProjectBean extends AbstractManagedBean implements Serializable {
projects = new ArrayList<>();
}
projects.clear();
- List<ProjectView> localProjectList = projectService.getAllProjectViews();
+ List<ProjectView> localProjectList = projectService.getAllProjectViews(userBean.getAuthenticationToken());
for (ProjectView projectRow : localProjectList) {
projects.add(projectRow);
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java b/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java
index bbdc0f5f8702c77af9f9ce6c16849ff958b606bf..27d28c8d53f74fe1064a7edf21ae6852d5fbb540 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java
@@ -15,6 +15,7 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
@@ -33,15 +34,14 @@ public class StartupBean {
/**
* Default class logger.
*/
- private final transient Logger logger = Logger.getLogger(StartupBean.class);
+ private final transient Logger logger = Logger.getLogger(StartupBean.class);
/**
- * Service used to access information about projects.
+ * Dao used to access information about projects.
*
- * @see IProjectService
*/
- @ManagedProperty(value = "#{ProjectService}")
- private transient IProjectService projectService;
+ @ManagedProperty(value = "#{ProjectDao}")
+ private transient ProjectDao projectDao;
/**
* Service used to access configuration params from db.
@@ -49,7 +49,7 @@ public class StartupBean {
* @see IProjectService
*/
@ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
+ private transient IConfigurationService configurationService;
/**
* Service used to access information about reference genomes.
@@ -98,7 +98,7 @@ public class StartupBean {
* when application was shutdown.
*/
private void setInterruptedProjectsStatuses() {
- for (Project project : projectService.getAllProjects()) {
+ for (Project project : projectDao.getAll()) {
if (!ProjectStatus.DONE.equals(project.getStatus()) && !ProjectStatus.FAIL.equals(project.getStatus())) {
String errors = project.getErrors();
if (errors == null || errors.trim().isEmpty()) {
@@ -109,29 +109,12 @@ public class StartupBean {
errors += "Project uploading was interrupted by application restart (at the stage: " + project.getStatus() + ").";
project.setStatus(ProjectStatus.FAIL);
project.setErrors(errors);
- projectService.updateProject(project);
+ projectDao.update(project);
logger.info("Status of project: " + project.getProjectId() + " changed to fail. Errors: " + errors);
}
}
}
- /**
- * @return the projectService
- * @see #projectService
- */
- public IProjectService getProjectService() {
- return projectService;
- }
-
- /**
- * @param projectService
- * the projectService to set
- * @see #projectService
- */
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
/**
* @return the configurationService
* @see #configurationService
@@ -165,4 +148,20 @@ public class StartupBean {
public void setReferenceGenomeService(IReferenceGenomeService referenceGenomeService) {
this.referenceGenomeService = referenceGenomeService;
}
+
+ /**
+ * @return the projectDao
+ * @see #projectDao
+ */
+ public ProjectDao getProjectDao() {
+ return projectDao;
+ }
+
+ /**
+ * @param projectDao the projectDao to set
+ * @see #projectDao
+ */
+ public void setProjectDao(ProjectDao projectDao) {
+ this.projectDao = projectDao;
+ }
}