public void deleteUser(String userId) throws CatalogIOException { URI userUri = getUserUri(userId); checkUriExists(userUri); deleteDirectory(userUri); }
public void renameProject(String userId, String oldProjectId, String newProjectId) throws CatalogIOException { URI oldFolder = getProjectUri(userId, oldProjectId); URI newFolder = getProjectUri(userId, newProjectId); rename(oldFolder, newFolder); }
public URI createStudy(String userId, String projectId, String studyId) throws CatalogIOException { checkParam(studyId); URI projectUri = getProjectUri(userId, projectId); checkDirectoryUri(projectUri, true); URI studyUri = getStudyUri(userId, projectId, studyId); return createStudy(studyUri); }
public URI createProject(String userId, String projectId) throws CatalogIOException { checkParam(projectId); URI projectUri = getProjectUri(userId, projectId); try { if (!exists(projectUri)) { projectUri = createDirectory(projectUri, true); } } catch (CatalogIOException e) { throw new CatalogIOException("createProject(): could not create the project folder", e); } return projectUri; }
public URI createStudy(URI studyUri) throws CatalogIOException { checkUriScheme(studyUri); try { if (!exists(studyUri)) { studyUri = createDirectory(studyUri); } } catch (CatalogIOException e) { throw new CatalogIOException("createStudy method: could not create the study folder: " + e.toString(), e); } return studyUri; }
public CatalogIOManager getDefault() throws CatalogIOException { return get(defaultCatalogScheme); }
public void deleteProject(String userId, String projectId) throws CatalogIOException { URI projectUri = getProjectUri(userId, projectId); checkUriExists(projectUri); deleteDirectory(projectUri); }
public void deleteStudy(URI studyUri) throws CatalogIOException { checkUriScheme(studyUri); checkUriExists(studyUri); deleteDirectory(studyUri); }
public DataInputStream getFileObject(URI studyUri, String objectId, int start, int limit) throws CatalogIOException { URI fileUri = getFileUri(studyUri, objectId); return getFileObject(fileUri, start, limit); }
public boolean existProject(String userId, String projectId) throws CatalogIOException { return exists(getProjectUri(userId, projectId)); }
public URI createDirectory(URI uri) throws CatalogIOException { return createDirectory(uri, false); }
public abstract void createFile(URI fileUri, InputStream inputStream) throws CatalogIOException;
public abstract DataInputStream getGrepFileObject(URI fileUri, String pattern, boolean ignoreCase, boolean multi) throws CatalogIOException;
public abstract DataInputStream getFileObject(URI fileUri, int start, int limit) throws CatalogIOException;
public CatalogIOManager(Configuration configuration) throws CatalogIOException { this(); this.configuration = configuration; setup(); }
public URI getJobsUri(String userId) throws CatalogIOException { checkParam(userId); return jobsDir; }
private void configureIOManager(Configuration properties) throws CatalogIOException { catalogIOManagerFactory = new CatalogIOManagerFactory(properties); }
public URI getProjectsUri(String userId) throws CatalogIOException { return getUserUri(userId).resolve(USER_PROJECTS_FOLDER); }
public ExecutionOutputRecorder(CatalogManager catalogManager, String sessionId) throws CatalogIOException { this.catalogManager = catalogManager; this.ioManager = catalogManager.getCatalogIOManagerFactory().get("file"); this.sessionId = sessionId; }
@Deprecated public CatalogIOManager(Properties properties) throws CatalogIOException { this(); this.properties = properties; setup(); }