def main(): if len(sys.argv) != 1 or sys.argv[1] == "-h" or sys.argv[1] == "--help": usage(sys.argv[0]) sys.exit() ini_file = sys.argv.pop(1) conf_parser = configparser.ConfigParser({'here': os.getcwd()}) conf_parser.read(ini_file) configuration = {} for key, value in conf_parser.items("app:main"): configuration[key] = value app = galaxy.app.UniverseApplication(global_conf=ini_file, **configuration) # Step through Datasets, determining size on disk for each. print("Determining the size of each dataset...") for row in app.model.Dataset.table.select().execute(): purged = app.model.Dataset.get(row.id).purged file_size = app.model.Dataset.get(row.id).file_size if file_size is None and not purged: size_on_disk = app.model.Dataset.get(row.id).get_size() print("Updating Dataset.%d with file_size: %d" % (row.id, size_on_disk)) app.model.Dataset.table.update( app.model.Dataset.table.c.id == row.id).execute( file_size=size_on_disk) app.shutdown() sys.exit(0)
def main(): if len(sys.argv) != 2 or sys.argv[1] == "-h" or sys.argv[1] == "--help" : usage(sys.argv[0]) sys.exit() ini_file = sys.argv.pop(1) conf_parser = ConfigParser.ConfigParser({'here': os.getcwd()}) conf_parser.read(ini_file) configuration = {} for key, value in conf_parser.items("app:main"): configuration[key] = value app = galaxy.app.UniverseApplication( global_conf=ini_file, **configuration ) # Search out tabular datatypes (and subclasses) and initialize metadata print "Seeking out tabular based files and initializing metadata" for row in app.model.Dataset.table.select().execute(): data = app.model.Dataset.get(row.id) if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('tabular'))): print row.id, data.extension # Call meta_data for all tabular files # special case interval type where we do not want to overwrite chr, start, end, etc assignments if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('interval'))): galaxy.datatypes.tabular.Tabular().set_meta(data) else: data.set_meta() app.model.context.add( data ) app.model.context.flush() app.shutdown() sys.exit(0)
def main(): ini_file = sys.argv.pop(1) conf_parser = ConfigParser.ConfigParser({'here':os.getcwd()}) conf_parser.read(ini_file) configuration = {} for key, value in conf_parser.items("app:main"): configuration[key] = value app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration ) #Step through Database, turning metadata bunches into dictionaries. #print "Changing metadata bunches to dictionaries." #for row in app.model.Dataset.table.select().execute(): # if isinstance (row.metadata, Bunch): # print row.id # app.model.Dataset.table.update(app.model.Dataset.table.c.id == row.id).execute( _metadata = row.metadata.__dict__ ) #Make sure all metadata is jsonified #print "Rewriting all metadata to database, setting metadata dbkey, to ensure JSONified storage." #for row in app.model.Dataset.table.select().execute(): # print row.id # data = app.model.Dataset.get(row.id) # dbkey = data.old_dbkey # if not dbkey or data.metadata.dbkey not in ["?", ["?"], None, []]: # dbkey = data.metadata.dbkey # if not dbkey: dbkey = "?" # #change dbkey then flush, then change to real value and flush, ensures that metadata is rewritten to database # data.dbkey="~" # data.flush() # data.dbkey=dbkey # data.flush() #Search out tabular datatypes (and subclasses) and initialize metadata print "Seeking out tabular based files and initializing metadata" for row in app.model.Dataset.table.select().execute(): data = app.model.Dataset.get(row.id) if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('tabular'))): print row.id, data.extension #Call meta_data for all tabular files #special case interval type where we do not want to overwrite chr, start, end, etc assignments if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('interval'))): galaxy.datatypes.tabular.Tabular().set_meta(data) else: data.set_meta() app.model.context.add( data ) app.model.context.flush() #Search out maf datatypes and make sure that available species is set. #print "Seeking out maf files and setting available species." #for row in app.model.Dataset.table.select(app.model.Dataset.table.c.extension == 'maf').execute(): # print row.id # sys.stdout.flush() # data = app.model.Dataset.get(row.id) # if data.missing_meta: # data.set_meta() #Call maf set metadata method, setting available species # data.flush() app.shutdown() sys.exit(0)
def main(): ini_file = sys.argv.pop(1) conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} ) conf_parser.read( ini_file ) configuration = {} for key, value in conf_parser.items( "app:main" ): configuration[key] = value app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration ) #Step through Datasets, determining size on disk for each. print "Determining the size of each dataset..." for row in app.model.Dataset.table.select().execute(): purged = app.model.Dataset.get( row.id ).purged file_size = app.model.Dataset.get( row.id ).file_size if file_size is None and not purged: size_on_disk = app.model.Dataset.get( row.id ).get_size() print "Updating Dataset.%d with file_size: %d" %( row.id, size_on_disk ) app.model.Dataset.table.update( app.model.Dataset.table.c.id == row.id ).execute( file_size=size_on_disk ) app.shutdown() sys.exit(0)
def main(): if len(sys.argv) != 2 or sys.argv[1] == "-h" or sys.argv[1] == "--help": usage(sys.argv[0]) sys.exit() ini_file = sys.argv.pop(1) conf_parser = configparser.ConfigParser({'here': os.getcwd()}) conf_parser.read(ini_file) configuration = {} for key, value in conf_parser.items("app:main"): configuration[key] = value app = galaxy.app.UniverseApplication(global_conf=ini_file, **configuration) # Search out tabular datatypes (and subclasses) and initialize metadata print("Seeking out tabular based files and initializing metadata") for row in app.model.Dataset.table.select().execute(): data = app.model.Dataset.get(row.id) if issubclass( type(data.datatype), type( app.datatypes_registry.get_datatype_by_extension( 'tabular'))): print(row.id, data.extension) # Call meta_data for all tabular files # special case interval type where we do not want to overwrite chr, start, end, etc assignments if issubclass( type(data.datatype), type( app.datatypes_registry.get_datatype_by_extension( 'interval'))): galaxy.datatypes.tabular.Tabular().set_meta(data) else: data.set_meta() app.model.context.add(data) app.model.context.flush() app.shutdown() sys.exit(0)
if galaxy_test_file_dir: os.environ['GALAXY_TEST_FILE_DIR'] = galaxy_test_file_dir success = _run_functional_test() except: log.exception("Failure running tests") log.info("Shutting down") # ---- Tear down ----------------------------------------------------------- if server: log.info("Shutting down embedded web server") server.server_close() server = None log.info("Embedded web server stopped") if app: log.info("Shutting down app") app.shutdown() app = None log.info("Embedded Universe application stopped") try: if os.path.exists( tempdir) and 'GALAXY_TEST_NO_CLEANUP' not in os.environ: log.info("Cleaning up temporary files in %s" % tempdir) shutil.rmtree(tempdir) else: log.info("GALAXY_TEST_NO_CLEANUP is on. Temporary files in %s" % tempdir) except: pass if success: return 0 else:
if galaxy_test_file_dir: os.environ[ 'GALAXY_TEST_FILE_DIR' ] = galaxy_test_file_dir success = _run_functional_test( ) except: log.exception( "Failure running tests" ) log.info( "Shutting down" ) # ---- Tear down ----------------------------------------------------------- if server: log.info( "Shutting down embedded web server" ) server.server_close() server = None log.info( "Embedded web server stopped" ) if app: log.info( "Shutting down app" ) app.shutdown() app = None log.info( "Embedded Universe application stopped" ) try: if os.path.exists( tempdir ) and 'GALAXY_TEST_NO_CLEANUP' not in os.environ: log.info( "Cleaning up temporary files in %s" % tempdir ) shutil.rmtree( tempdir ) else: log.info( "GALAXY_TEST_NO_CLEANUP is on. Temporary files in %s" % tempdir ) except: pass if psu_production and 'GALAXY_TEST_NO_CLEANUP' not in os.environ: for dir in ( file_path, new_file_path ): try: if os.path.exists( dir ): log.info( 'Cleaning up temporary files in %s' % dir )