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Commit 0dbd7728 authored by Piotr Gawron's avatar Piotr Gawron
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transaction was not available during loading war file in tomcat

parent 6959d58e
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service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
View file @ 0dbd7728
......@@ -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();
}
}
service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
View file @ 0dbd7728
......@@ -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();
}
web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java
View file @ 0dbd7728
......@@ -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