def import_cancer_type(jvm_args, data_filename): args = jvm_args.split(' ') args.append(IMPORT_CANCER_TYPE_CLASS) args.append(data_filename) args.append("false") # don't clobber existing table args.append("--noprogress") # don't report memory usage and % progress run_java(*args)
def update_study_status(jvm_args, study_id): args = jvm_args.split(' ') args.append(UPDATE_STUDY_STATUS_CLASS) args.append(study_id) args.append("AVAILABLE") args.append("--noprogress") # don't report memory usage and % progress run_java(*args)
def add_global_case_list(jvm_args, study_id): args = jvm_args.split(' ') args.append(ADD_CASE_LIST_CLASS) args.append(study_id) args.append("all") args.append("--noprogress") # don't report memory usage and % progress run_java(*args)
def import_study_data(jvm_args, meta_filename, data_filename): args = jvm_args.split(' ') meta_file_dict, meta_file_type = cbioportal_common.parse_metadata_file( meta_filename, logger=LOGGER) if meta_file_type is None: # invalid file, skip return if not data_filename.endswith(meta_file_dict['data_filename']): print >> ERROR_FILE, ("'data_filename' in meta file contradicts " "data filename in command, skipping file") return importer = IMPORTER_CLASSNAME_BY_META_TYPE[meta_file_type] args.append(importer) if IMPORTER_REQUIRES_METADATA[importer]: args.append("--meta") args.append(meta_filename) args.append("--loadMode") args.append("bulkload") if importer in ("org.mskcc.cbio.portal.scripts.ImportMutSigData", "org.mskcc.cbio.portal.scripts.ImportGisticData"): args.append("--data") args.append(data_filename) args.append("--study") args.append(meta_file_dict['cancer_study_identifier']) else: args.append("--data") args.append(data_filename) args.append("--noprogress") # don't report memory usage and % progress run_java(*args)
def check_version(jvm_args): args = jvm_args.split(' ') args.append(VERSION_UTIL_CLASS) try: run_java(*args) except: print >> OUTPUT_FILE, 'Error, probably due to this version of the portal being out of sync with the database. Run the database migration script located at PORTAL_HOME/core/src/main/scripts/migrate_db.py before continuing.' raise
def remove_study(jvm_args, meta_filename): args = jvm_args.split(" ") args.append(REMOVE_STUDY_CLASS) meta_dict, meta_type = cbioportal_common.parse_metadata_file(meta_filename, logger=LOGGER) if meta_type != MetaFileTypes.STUDY: # invalid file, skip print >> ERROR_FILE, "Not a study meta file: " + meta_filename return args.append(meta_dict["cancer_study_identifier"]) args.append("--noprogress") # don't report memory usage and % progress run_java(*args)
def remove_study(jvm_args, meta_filename): args = jvm_args.split(' ') args.append(REMOVE_STUDY_CLASS) meta_dictionary = cbioportal_common.parse_metadata_file(meta_filename, logger=LOGGER) if meta_dictionary['meta_file_type'] != MetaFileTypes.STUDY: # invalid file, skip print >> ERROR_FILE, 'Not a study meta file: ' + meta_filename return args.append(meta_dictionary['cancer_study_identifier']) args.append("--noprogress") # don't report memory usage and % progress run_java(*args)
def import_study_data(jvm_args, meta_filename, data_filename, meta_file_dictionary=None): args = jvm_args.split(' ') # In case the meta file is already parsed in a previous function, it is not # necessary to parse it again if meta_file_dictionary is None: meta_file_dictionary = cbioportal_common.parse_metadata_file( meta_filename, logger=LOGGER) # Retrieve meta file type meta_file_type = meta_file_dictionary['meta_file_type'] # invalid file, skip if meta_file_type is None: print >> ERROR_FILE, ( "Unrecognized meta file type '%s', skipping file" % (meta_file_type)) return if not data_filename.endswith(meta_file_dictionary['data_filename']): print >> ERROR_FILE, ("'data_filename' in meta file contradicts " "data filename in command, skipping file") return importer = IMPORTER_CLASSNAME_BY_META_TYPE[meta_file_type] args.append(importer) if IMPORTER_REQUIRES_METADATA[importer]: args.append("--meta") args.append(meta_filename) args.append("--loadMode") args.append("bulkload") if importer in ("org.mskcc.cbio.portal.scripts.ImportMutSigData", "org.mskcc.cbio.portal.scripts.ImportGisticData"): args.append("--data") args.append(data_filename) args.append("--study") args.append(meta_file_dictionary['cancer_study_identifier']) elif importer == "org.mskcc.cbio.portal.scripts.ImportGenePanelProfileMap": args.append("--meta") args.append(meta_filename) args.append("--data") args.append(data_filename) else: args.append("--data") args.append(data_filename) args.append("--noprogress") # don't report memory usage and % progress run_java(*args)
def import_study_data(jvm_args, meta_filename, data_filename, meta_file_dictionary = None): args = jvm_args.split(' ') # In case the meta file is already parsed in a previous function, it is not # necessary to parse it again if meta_file_dictionary is None: meta_file_dictionary = cbioportal_common.parse_metadata_file( meta_filename, logger=LOGGER) # Retrieve meta file type meta_file_type = meta_file_dictionary['meta_file_type'] # invalid file, skip if meta_file_type is None: print >> ERROR_FILE, ("Unrecognized meta file type '%s', skipping file" % (meta_file_type)) return if not data_filename.endswith(meta_file_dictionary['data_filename']): print >> ERROR_FILE, ("'data_filename' in meta file contradicts " "data filename in command, skipping file") return importer = IMPORTER_CLASSNAME_BY_META_TYPE[meta_file_type] args.append(importer) if IMPORTER_REQUIRES_METADATA[importer]: args.append("--meta") args.append(meta_filename) args.append("--loadMode") args.append("bulkload") if importer in ("org.mskcc.cbio.portal.scripts.ImportMutSigData", "org.mskcc.cbio.portal.scripts.ImportGisticData"): args.append("--data") args.append(data_filename) args.append("--study") args.append(meta_file_dictionary['cancer_study_identifier']) elif importer == "org.mskcc.cbio.portal.scripts.ImportGenePanelProfileMap": args.append("--meta") args.append(meta_filename) args.append("--data") args.append(data_filename) else: args.append("--data") args.append(data_filename) args.append("--noprogress") # don't report memory usage and % progress run_java(*args)
def import_case_list(jvm_args, meta_filename): args = jvm_args.split(' ') args.append(IMPORT_CASE_LIST_CLASS) args.append(meta_filename) args.append("--noprogress") # don't report memory usage and % progress run_java(*args)
def import_study(jvm_args, meta_filename): args = jvm_args.split(' ') args.append(IMPORT_STUDY_CLASS) args.append(meta_filename) args.append("--noprogress") # don't report memory usage and % progress run_java(*args)