def setUp(self):
self.logger = create_logger(__name__, 'ERROR')
self.pathway = rpPathway.from_rpSBML(
infile=self.rpsbml_path,
logger=self.logger
)
def setUp(self):
self.logger = create_logger(__name__, 'ERROR')
# Create persistent temp folder
# to deflate compressed data file so that
# it remains reachable outside of this method.
# Has to remove manually it in tearDown() method
self.temp_d = mkdtemp()
self.rpsbml = rpSBML(inFile=self.e_coli_model_path, logger=self.logger)
def setUp(self):
self.logger = create_logger(__name__, 'ERROR')
self.rxn_1 = rpReaction(
id='rxn_1',
reactants={
'MNXM188': 1,
'MNXM4': 1,
'MNXM6': 1,
'MNXM1': 3
},
products={
'CMPD_0000000004': 1,
'CMPD_0000000003': 1,
'MNXM13': 1,
'MNXM15': 3,
'MNXM5': 1
},
)
self.rxn_2 = rpReaction(
id='rxn_2',
reactants={
'MNXM4': 1,
'CMPD_0000000003': 2
},
products={
'MNXM1': 1,
'TARGET_0000000001': 1
},
)
self.rxn_3 = rpReaction(
id='rxn_3',
reactants={
'CMPD_0000000004': 3,
'MNXM4': 1,
'MNXM6': 1
},
products={
'MNXM13': 1,
'MNXM5': 1
},
)
self.reactions = [self.rxn_1, self.rxn_2, self.rxn_3]
self.sto_mat_1 = [[-3.0, 1.0, 0.0], [-1.0, -1.0, -1.0],
[1.0, 0.0, 1.0], [3.0, 0.0, 0.0], [1.0, 0.0, -3.0],
[1.0, 0.0, 1.0], [0.0, 1.0, 0.0], [1.0, -2.0, 0.0],
[-1.0, 0.0, 0.0], [-1.0, 0.0, -1.0]]
def _cli():
parser = build_args_parser()
args = parse_and_check_args(parser)
if args.log.lower() in ['silent', 'quiet'] or args.silent:
args.log = 'CRITICAL'
# Store KNIME vars into a dictionary
kvars = set_vars(args.kexec, args.kver, args.kpkg_install, args.kwf)
# Print out configuration
if not args.silent and args.log.lower() not in ['critical', 'error']:
print_conf(kvars, prog=parser.prog)
# Create logger
logger = create_logger(parser.prog, args.log)
logger.debug('args: ' + str(args))
logger.debug('kvars: ' + str(kvars))
r_code, result_files = retropath2(sink_file=args.sink_file,
source_file=args.source_file,
rules_file=args.rules_file,
outdir=args.outdir,
kvars=kvars,
max_steps=args.max_steps,
topx=args.topx,
dmin=args.dmin,
dmax=args.dmax,
mwmax_source=args.mwmax_source,
mwmax_cof=args.mwmax_cof,
timeout=args.timeout,
logger=logger)
if r_code == 'OK' or r_code == 'TimeLimit':
logger.info('{attr1}Results{attr2}'.format(attr1=attr('bold'),
attr2=attr('reset')))
logger.info(' |- Checking... ')
r_code = check_results(result_files, logger)
logger.info(' |--path: ' + args.outdir)
else:
logger.error('Exiting...')
return __ERROR_CODES__[r_code]
def init(parser: ArgumentParser, args: Namespace) -> Logger:
from brs_utils import create_logger
from rptools._version import __version__
if args.log.lower() in ['silent', 'quiet'] or args.silent:
args.log = 'CRITICAL'
# Create logger
logger = create_logger(parser.prog, args.log)
logger.info(
'{color}{typo}rptools {version}{rst}{color} ({prog}){rst}\n'.format(
prog=logger.name,
version=__version__,
color=fg('white'),
typo=attr('bold'),
rst=attr('reset')))
logger.debug(args)
return logger
def init(parser: 'ArgumentParser', args: 'Namespace') -> Logger:
from brs_utils import create_logger
from rr_cache._version import __version__
if args.log.lower() in ['silent', 'quiet'] or args.silent:
args.log = 'CRITICAL'
if args.log.lower() in ['silent', 'quiet', 'def_info'] or args.silent:
disable_rdkit_logging()
# # Disable RDKIT logging
# from rdkit import RDLogger
# RDLogger.DisableLog('rdApp.*')
# Create logger
logger = create_logger(parser.prog, args.log)
logger.info('{color}{typo}rr_cache {version}{rst}{color}{rst}\n'.format(
version=__version__,
color=fg('white'),
typo=attr('bold'),
rst=attr('reset')))
logger.debug(args)
return logger
def setUp(self):
self.logger = create_logger(__name__, 'ERROR')
def test_call(self):
logger = create_logger('TEST', 'INFO')
self.assertTrue(True)
def setUp(self, logger: Logger = None):
if logger is None:
self.logger = create_logger(__name__, 'ERROR')
else:
self.logger = logger