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 8d7ff171dee8f6c5a6348270bb51dc3484c6f317..4e1cb28e8895f1d23f26ea4d39cace0a6aace908 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -1459,26 +1459,26 @@ public class ProjectService implements IProjectService {
userService.updateUser(dbUser);
user.setAnnotationSchema(annotationSchema);
}
-
+
@Override
public List<UserAnnotatorsParam> getAnnotatorsParams(User user) {
- User dbUser = userDao.getById(user.getId());
- UserAnnotationSchema annotationSchema = dbUser.getAnnotationSchema();
- if (annotationSchema == null) {
- annotationSchema = new UserAnnotationSchema();
- dbUser.setAnnotationSchema(annotationSchema);
- }
-
- /*
- * Hibernate lazy loads collections so each element needs to be accessed
- * to be loaded now or otherwise the data might not be available
- * when accessed because the session might not be available at that time.
- */
- List<UserAnnotatorsParam> aps = new ArrayList<>();
- for (UserAnnotatorsParam ap: annotationSchema.getAnnotatorsParams()){
- aps.add(ap);
- }
- return aps;
+ User dbUser = userDao.getById(user.getId());
+ UserAnnotationSchema annotationSchema = dbUser.getAnnotationSchema();
+ if (annotationSchema == null) {
+ annotationSchema = new UserAnnotationSchema();
+ dbUser.setAnnotationSchema(annotationSchema);
+ }
+
+ /*
+ * Hibernate lazy loads collections so each element needs to be accessed to be
+ * loaded now or otherwise the data might not be available when accessed because
+ * the session might not be available at that time.
+ */
+ List<UserAnnotatorsParam> aps = new ArrayList<>();
+ for (UserAnnotatorsParam ap : annotationSchema.getAnnotatorsParams()) {
+ aps.add(ap);
+ }
+ return aps;
}
/**
@@ -1627,4 +1627,9 @@ public class ProjectService implements IProjectService {
this.taxonomyBackend = taxonomyBackend;
}
+ @Override
+ public List<Project> getAllProjects() {
+ return projectDao.getAll();
+ }
+
}
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 9d504bffe34a272052035caa6d0d4d04fdee4830..b802cfe8897af65cc9a6d99b1b2af672d19c5806 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
@@ -22,180 +22,184 @@ import lcsb.mapviewer.services.view.ProjectView;
*/
public interface IProjectService {
- /**
- * Returns a project with a give {@link Project#projectId project identifier}.
- *
- * @param projectId
- * {@link Project#projectId project identifier}
- * @return project with an identifier given as parameter. Null if such project
- * doesn't exist.
- */
- Project getProjectByProjectId(String projectId, AuthenticationToken token) throws UserAccessException;
-
- /**
- * Checks if project with a given {@link Project#projectId identifier} exists.
- *
- * @param projectId
- * {@link Project#projectId project identifier}
- * @return <code>true</code> if the project with the given name exists,
- * <code>false</code> otherwise
- */
- boolean projectExists(String projectId);
-
- /**
- * Returns list of all projects.
- *
- * @return list of all projects.
- */
- 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(AuthenticationToken token);
-
- /**
- * Updates project.
- *
- * @param projectView
- * project view with the data to update
- */
- void updateProject(ProjectView projectView);
-
- /**
- * Removes project from the system.
- *
- * @param homeDir
- * directory where the system is deployed
- *
- * @param projectView
- * information about project to remove
- * @param async
- * should the operation be done asynchronously
- * @throws UserAccessException
- */
- void removeProject(ProjectView projectView, String homeDir, boolean async, AuthenticationToken token) throws UserAccessException;
-
- /**
- * Removes project from the system.
- *
- * @param homeDir
- * directory where the system is deployed
- * @param project
- * object to remove
- * @param async
- * should the operation be done asynchronously
- * @throws UserAccessException
- */
- void removeProject(Project project, String homeDir, boolean async, AuthenticationToken token) throws UserAccessException;
-
- /**
- * Gets view of the project by the {@link Project#projectId project
- * identifier}.
- *
- * @param projectId
- * {@link Project#projectId project identifier}
- * @return view of the project
- * @throws UserAccessException
- */
- ProjectView getProjectViewByProjectId(String projectId, AuthenticationToken token) throws UserAccessException;
-
- /**
- * Adds project to the system.
- *
- * @param project
- * object to add
- */
- void addProject(Project project);
-
- /**
- * Return the view of the project identified by database identifier.
- *
- * @param id
- * database identifier of the project
- * @return project view
- * @throws UserAccessException
- */
- ProjectView getProjectViewById(Integer id, AuthenticationToken token) throws UserAccessException;
-
- /**
- * Creates project using give parameters. See {@link CreateProjectParams}.
- *
- * @param params
- * information about project to create
- * @throws SecurityException
- */
- void createProject(CreateProjectParams params) throws SecurityException;
-
- /**
- * Creates empty {@link ProjectView}.
- *
- * @return empty {@link ProjectView}
- */
- ProjectView createEmpty();
-
- /**
- * Creates {@link TreeNode} that contains information about all classes that
- * can be annotated and associate set of
- * {@link lcsb.mapviewer.annotation.services.annotators.ElementAnnotator
- * ElementAnnotator} valid for these classes.
- *
- * @param user
- * for which information should be retrieved
- * @return {@link TreeNode} that contains information about all classes that
- * can be annotated
- */
- TreeNode createClassAnnotatorTree(User user);
-
- /**
- * Update default set of annotators, lists of required/valid annotations for a
- * given user and default params used when creating project.
- *
- * @param user
- * user for which we updte information
- * @param sbgnFormat
- * new
- * {@link lcsb.mapviewer.model.user.UserAnnotationSchema#sbgnFormat}
- * value
- * @param networkLayoutAsDefault
- * new
- * {@link lcsb.mapviewer.model.user.UserAnnotationSchema#networkLayoutAsDefault}
- * value
- * @param annotatorsTree
- * {@link TreeNode} that contains information about all classes that
- * can be annotated
- */
- void updateClassAnnotatorTreeForUser(User user, TreeNode annotatorsTree, boolean sbgnFormat, boolean networkLayoutAsDefault);
-
- /**
- * Method that updates information about raw {@link Project} object.
- *
- * @param project
- * project to update
- */
- void updateProject(Project project);
-
- /**
- * Returns content of the file that was used to create project given in the
- * parameter.
- *
- * @param projectView
- * view of the {@link Project} for which we are looking for an
- * original source file
- * @return content of the file that was used to create project given in the
- * parameter
- */
- byte[] getInputDataForProject(ProjectView projectView);
-
- UserAnnotationSchema prepareUserAnnotationSchema(User user);
-
- /**
- * Retrieves list of annotators {@link UserAnnotatorsParam parameters}
- * @return
- * list of annotators parameters
- */
- List<UserAnnotatorsParam> getAnnotatorsParams(User user);
+ /**
+ * Returns a project with a give {@link Project#projectId project identifier}.
+ *
+ * @param projectId
+ * {@link Project#projectId project identifier}
+ * @return project with an identifier given as parameter. Null if such project
+ * doesn't exist.
+ */
+ Project getProjectByProjectId(String projectId, AuthenticationToken token) throws UserAccessException;
+
+ /**
+ * Checks if project with a given {@link Project#projectId identifier} exists.
+ *
+ * @param projectId
+ * {@link Project#projectId project identifier}
+ * @return <code>true</code> if the project with the given name exists,
+ * <code>false</code> otherwise
+ */
+ boolean projectExists(String projectId);
+
+ /**
+ * Returns list of all projects.
+ *
+ * @return list of all projects.
+ */
+ 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(AuthenticationToken token);
+
+ /**
+ * Updates project.
+ *
+ * @param projectView
+ * project view with the data to update
+ */
+ void updateProject(ProjectView projectView);
+
+ /**
+ * Removes project from the system.
+ *
+ * @param homeDir
+ * directory where the system is deployed
+ *
+ * @param projectView
+ * information about project to remove
+ * @param async
+ * should the operation be done asynchronously
+ * @throws UserAccessException
+ */
+ void removeProject(ProjectView projectView, String homeDir, boolean async, AuthenticationToken token)
+ throws UserAccessException;
+
+ /**
+ * Removes project from the system.
+ *
+ * @param homeDir
+ * directory where the system is deployed
+ * @param project
+ * object to remove
+ * @param async
+ * should the operation be done asynchronously
+ * @throws UserAccessException
+ */
+ void removeProject(Project project, String homeDir, boolean async, AuthenticationToken token)
+ throws UserAccessException;
+
+ /**
+ * Gets view of the project by the {@link Project#projectId project identifier}.
+ *
+ * @param projectId
+ * {@link Project#projectId project identifier}
+ * @return view of the project
+ * @throws UserAccessException
+ */
+ ProjectView getProjectViewByProjectId(String projectId, AuthenticationToken token) throws UserAccessException;
+
+ /**
+ * Adds project to the system.
+ *
+ * @param project
+ * object to add
+ */
+ void addProject(Project project);
+
+ /**
+ * Return the view of the project identified by database identifier.
+ *
+ * @param id
+ * database identifier of the project
+ * @return project view
+ * @throws UserAccessException
+ */
+ ProjectView getProjectViewById(Integer id, AuthenticationToken token) throws UserAccessException;
+
+ /**
+ * Creates project using give parameters. See {@link CreateProjectParams}.
+ *
+ * @param params
+ * information about project to create
+ * @throws SecurityException
+ */
+ void createProject(CreateProjectParams params) throws SecurityException;
+
+ /**
+ * Creates empty {@link ProjectView}.
+ *
+ * @return empty {@link ProjectView}
+ */
+ ProjectView createEmpty();
+
+ /**
+ * Creates {@link TreeNode} that contains information about all classes that can
+ * be annotated and associate set of
+ * {@link lcsb.mapviewer.annotation.services.annotators.ElementAnnotator
+ * ElementAnnotator} valid for these classes.
+ *
+ * @param user
+ * for which information should be retrieved
+ * @return {@link TreeNode} that contains information about all classes that can
+ * be annotated
+ */
+ TreeNode createClassAnnotatorTree(User user);
+
+ /**
+ * Update default set of annotators, lists of required/valid annotations for a
+ * given user and default params used when creating project.
+ *
+ * @param user
+ * user for which we updte information
+ * @param sbgnFormat
+ * new
+ * {@link lcsb.mapviewer.model.user.UserAnnotationSchema#sbgnFormat}
+ * value
+ * @param networkLayoutAsDefault
+ * new
+ * {@link lcsb.mapviewer.model.user.UserAnnotationSchema#networkLayoutAsDefault}
+ * value
+ * @param annotatorsTree
+ * {@link TreeNode} that contains information about all classes that
+ * can be annotated
+ */
+ void updateClassAnnotatorTreeForUser(User user, TreeNode annotatorsTree, boolean sbgnFormat,
+ boolean networkLayoutAsDefault);
+
+ /**
+ * Method that updates information about raw {@link Project} object.
+ *
+ * @param project
+ * project to update
+ */
+ void updateProject(Project project);
+
+ /**
+ * Returns content of the file that was used to create project given in the
+ * parameter.
+ *
+ * @param projectView
+ * view of the {@link Project} for which we are looking for an original
+ * source file
+ * @return content of the file that was used to create project given in the
+ * parameter
+ */
+ byte[] getInputDataForProject(ProjectView projectView);
+
+ UserAnnotationSchema prepareUserAnnotationSchema(User user);
+
+ /**
+ * Retrieves list of annotators {@link UserAnnotatorsParam parameters}
+ *
+ * @return list of annotators parameters
+ */
+ List<UserAnnotatorsParam> getAnnotatorsParams(User user);
+
+ List<Project> getAllProjects();
}
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 27d28c8d53f74fe1064a7edf21ae6852d5fbb540..20dad609ea8eccaf77c5e4527fd8ef37ba478f65 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java
@@ -31,137 +31,144 @@ import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
@ApplicationScoped
public class StartupBean {
- /**
- * Default class logger.
- */
- private final transient Logger logger = Logger.getLogger(StartupBean.class);
-
- /**
- * Dao used to access information about projects.
- *
- */
- @ManagedProperty(value = "#{ProjectDao}")
- private transient ProjectDao projectDao;
-
- /**
- * Service used to access configuration params from db.
- *
- * @see IProjectService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- /**
- * Service used to access information about reference genomes.
- *
- * @see IReferenceGenomeService
- */
- @ManagedProperty(value = "#{ReferenceGenomeService}")
- private transient IReferenceGenomeService referenceGenomeService;
-
- /**
- * Method that process initial script of application.
- */
- @PostConstruct
- public void init() {
- logger.debug("Application startup script starts");
- try {
- setInterruptedProjectsStatuses();
- Configuration.setxFrameDomain(configurationService.getConfigurationValue(ConfigurationElementType.X_FRAME_DOMAIN));
-
- removeInterruptedReferenceGenomeDownloads();
- } catch (Exception e) {
- logger.error("Problem running init script...", e);
- }
- logger.debug("Application startup script ends");
- }
-
- /**
- * Removes downloads of reference genomes that were interrupted by tomcat
- * restart.
- */
- private void removeInterruptedReferenceGenomeDownloads() {
- for (ReferenceGenome genome : referenceGenomeService.getDownloadedGenomes()) {
- if (genome.getDownloadProgress() < IProgressUpdater.MAX_PROGRESS) {
- logger.warn("Removing genome that was interrupted: " + genome);
- try {
- referenceGenomeService.removeGenome(genome);
- } catch (IOException e) {
- logger.error("Problem with removing genome: " + genome);
- }
- }
- }
- }
-
- /**
- * Set {@link ProjectStatus#FAIL} statuses to projects that were uploading
- * when application was shutdown.
- */
- private void setInterruptedProjectsStatuses() {
- 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()) {
- errors = "";
- } else {
- errors = errors.trim() + "\n";
- }
- errors += "Project uploading was interrupted by application restart (at the stage: " + project.getStatus() + ").";
- project.setStatus(ProjectStatus.FAIL);
- project.setErrors(errors);
- projectDao.update(project);
- logger.info("Status of project: " + project.getProjectId() + " changed to fail. Errors: " + errors);
- }
- }
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the referenceGenomeService
- * @see #referenceGenomeService
- */
- public IReferenceGenomeService getReferenceGenomeService() {
- return referenceGenomeService;
- }
-
- /**
- * @param referenceGenomeService
- * the referenceGenomeService to set
- * @see #referenceGenomeService
- */
- 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;
- }
+ /**
+ * Default class logger.
+ */
+ private final transient Logger logger = Logger.getLogger(StartupBean.class);
+
+ /**
+ * Dao used to access information about projects.
+ *
+ */
+ @ManagedProperty(value = "#{ProjectService}")
+ private transient IProjectService projectService;
+
+ /**
+ * Service used to access configuration params from db.
+ *
+ * @see IProjectService
+ */
+ @ManagedProperty(value = "#{ConfigurationService}")
+ private transient IConfigurationService configurationService;
+
+ /**
+ * Service used to access information about reference genomes.
+ *
+ * @see IReferenceGenomeService
+ */
+ @ManagedProperty(value = "#{ReferenceGenomeService}")
+ private transient IReferenceGenomeService referenceGenomeService;
+
+ /**
+ * Method that process initial script of application.
+ */
+ @PostConstruct
+ public void init() {
+ logger.debug("Application startup script starts");
+ setInterruptedProjectsStatuses();
+ modifyXFrameDomain();
+ removeInterruptedReferenceGenomeDownloads();
+ logger.debug("Application startup script ends");
+ }
+
+ private void modifyXFrameDomain() {
+ try {
+ Configuration
+ .setxFrameDomain(configurationService.getConfigurationValue(ConfigurationElementType.X_FRAME_DOMAIN));
+ } catch (Exception e) {
+ logger.error("Problem with modyfing x frame domain...", e);
+ }
+ }
+
+ /**
+ * Removes downloads of reference genomes that were interrupted by tomcat
+ * restart.
+ */
+ private void removeInterruptedReferenceGenomeDownloads() {
+ try {
+ for (ReferenceGenome genome : referenceGenomeService.getDownloadedGenomes()) {
+ if (genome.getDownloadProgress() < IProgressUpdater.MAX_PROGRESS) {
+ logger.warn("Removing genome that was interrupted: " + genome);
+ try {
+ referenceGenomeService.removeGenome(genome);
+ } catch (IOException e) {
+ logger.error("Problem with removing genome: " + genome);
+ }
+ }
+ }
+ } catch (Exception e) {
+ logger.error("Problem with removing interrupted downloads...", e);
+ }
+
+ }
+
+ /**
+ * Set {@link ProjectStatus#FAIL} statuses to projects that were uploading when
+ * application was shutdown.
+ */
+ private void setInterruptedProjectsStatuses() {
+ try {
+ for (Project project : projectService.getAllProjects()) {
+ if (!ProjectStatus.DONE.equals(project.getStatus()) && !ProjectStatus.FAIL.equals(project.getStatus())) {
+ String errors = project.getErrors();
+ if (errors == null || errors.trim().isEmpty()) {
+ errors = "";
+ } else {
+ errors = errors.trim() + "\n";
+ }
+ errors += "Project uploading was interrupted by application restart (at the stage: " + project.getStatus()
+ + ").";
+ project.setStatus(ProjectStatus.FAIL);
+ project.setErrors(errors);
+ projectService.updateProject(project);
+ logger.info("Status of project: " + project.getProjectId() + " changed to fail. Errors: " + errors);
+ }
+ }
+ } catch (Exception e) {
+ logger.error("Problem with changing project status ...", e);
+ }
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ /**
+ * @return the referenceGenomeService
+ * @see #referenceGenomeService
+ */
+ public IReferenceGenomeService getReferenceGenomeService() {
+ return referenceGenomeService;
+ }
+
+ /**
+ * @param referenceGenomeService
+ * the referenceGenomeService to set
+ * @see #referenceGenomeService
+ */
+ public void setReferenceGenomeService(IReferenceGenomeService referenceGenomeService) {
+ this.referenceGenomeService = referenceGenomeService;
+ }
+
+ public IProjectService getProjectService() {
+ return projectService;
+ }
+
+ public void setProjectService(IProjectService projectService) {
+ this.projectService = projectService;
+ }
+
}