def get_meid(mvid): ''' Given a model_version_id, return its modelable_entity_id. Uses ENVIRONMENT_NAME environment variable to determine which database to read from''' sett = load_settings() eng = db.get_engine(conn_def='epi', env=sett['env_variables']['ENVIRONMENT_NAME']) meid = pd.read_sql( """ SELECT modelable_entity_id FROM epi.model_version WHERE model_version_id = %s""" % mvid, eng) return meid.values[0][0]
def get_meid(mvid): ''' Given a model_version_id, return its modelable_entity_id. Uses ENVIRONMENT_NAME environment variable to determine which database to read from''' sett = load_settings() eng = db.get_engine(conn_def='epi', env=sett['env_variables']['ENVIRONMENT_NAME']) meid = pd.read_sql(""" SELECT modelable_entity_id FROM epi.model_version WHERE model_version_id = %s""" % mvid, eng) try: return meid.values[0][0] except IndexError: raise RuntimeError(f"No meid for {mvid} in environment " f"{sett['env_variables']['ENVIRONMENT_NAME']} " f"to host {eng.host}")
import sqlalchemy from sqlalchemy.sql import text from cascade_ode.settings import load as load_settings from cascade_ode.demographics import Demographics from cascade_ode import db # Set default file mask to readable-for all users os.umask(0o0002) # Path to this file this_path = os.path.dirname(os.path.abspath(__file__)) # Get configuration options settings = load_settings() RUNNING = -1 FAILED = 7 def skip_if_uploaded(func): def decorated(*args, **kwargs): try: return func(*args, **kwargs) except sqlalchemy.exc.IntegrityError: log = logging.getLogger(__name__) log.debug( 'Skipping file since already uploaded: {}'.format(args)) return decorated
import os from functools import lru_cache import pandas as pd from cascade_ode.argument_parser import cascade_parser, inverse_parser from cascade_ode.patch_io import setup_io_patches from cascade_ode.settings import load as load_settings from cascade_ode import db from cascade_ode.setup_logger import setup_logger from cascade_ode import sge # Set default file mask to readable-for all users os.umask(0o0002) # Load settings from file settings = load_settings(check_for_custom_conda=True) @lru_cache() def prepare_directories(mvid, create_directories=True): """Defines, creates, and returns directories for cascade outputs and logs Args: mvid (int): model_version_id associated with given cascade model run. Used to create directory paths. create_directories (bool): boolean to specify weather or not to create given directories. Specify 'False' to only return directory strings. """ logdir = '%s/%s' % (settings['log_dir'], mvid) root_dir = '%s/%s' % (settings['cascade_ode_out_dir'], mvid)