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)
