def setup(self, app_args):
# basic arguments for every node
basic_args = [Argument(Keys.INPUT, KeyHelp.INPUT, default=''),
Argument(Keys.OUTPUT, KeyHelp.OUTPUT, default=''),
Argument(Keys.MODULE, KeyHelp.MODULE, default=''),
Argument(Keys.LOG_LEVEL, KeyHelp.LOG_LEVEL, default="DEBUG")]
# Fixme: Prettify WORKDIR creation system
# WORKDIR: if WORKDIR is defined add related args
for i, arg in enumerate(app_args):
if arg.name == Keys.WORKDIR:
app_args.insert(i + 1, Argument(Keys.BASEDIR, KeyHelp.BASEDIR, default='.'))
app_args.insert(i + 2, Argument(Keys.JOB_ID, KeyHelp.JOB_ID, default=''))
app_args.insert(i + 3, Argument(Keys.SUBJOBLIST, KeyHelp.SUBJOBLIST, default=''))
app_args.insert(i + 4, Argument(Keys.NAME, KeyHelp.NAME, default=self.__class__.__name__))
break
defaults, cliargs = parse_sysargs(basic_args + app_args)
# construct info from defaults < info < commandlineargs
ih = get_handler(cliargs.get(Keys.INPUT, None))
fileinfo = ih.read(cliargs.get(Keys.INPUT, None))
info = dicts.merge(cliargs, dicts.merge(fileinfo, defaults))
# setup logging
log = Logger.create(info[Keys.LOG_LEVEL])
# request by malars: show dataset prominent in logger
if Keys.DATASET_CODE in info:
if not isinstance(info[Keys.DATASET_CODE], list):
if Keys.MZXML in info and not isinstance(info[Keys.MZXML], list):
log.info("Dataset is %s (%s)" % (info[Keys.DATASET_CODE], os.path.basename(info[Keys.MZXML])))
else:
log.info("Dataset is %s" % info[Keys.DATASET_CODE])
else:
log.debug("Datasets are %s" % info[Keys.DATASET_CODE])
# WORKDIR: create WORKDIR (only after mk log)
info = dirs.create_workdir(log, info)
# filter to requested args
if Keys.ALL_ARGS in info:
# if ALL_ARGS is set give whole info to app...
req_info = info
else:
req_info = {}
# ...otherwise copy only explicitly requested args to app
for key in [arg.name for arg in basic_args + app_args]:
if key in info:
req_info[key] = info[key]
log.debug("info for app: %s" % req_info)
return log, req_info, info
def test1_arg_priority(self):
"""Test the argument priorities. Disabled."""
sys.argv = ['--INPUT', 'fcuk.ini', '--OUTPUT', 'kufc.ini']
# basic arguments for every node
basic_args = [
Argument(Keys.INPUT, KeyHelp.INPUT, default=''),
Argument(Keys.OUTPUT, KeyHelp.OUTPUT, default=''),
Argument(Keys.MODULE, KeyHelp.MODULE, default=''),
Argument(Keys.LOG_LEVEL, KeyHelp.LOG_LEVEL, default="DEBUG")
]
# WORKDIR: if WORKDIR is defined add related args
app_args = []
for i, arg in enumerate(app_args):
if arg.name == Keys.WORKDIR:
app_args.insert(
i + 1, Argument(Keys.BASEDIR, KeyHelp.BASEDIR,
default='.'))
app_args.insert(
i + 2, Argument(Keys.JOB_ID, KeyHelp.JOB_ID, default=''))
app_args.insert(
i + 3,
Argument(Keys.SUBJOBLIST, KeyHelp.SUBJOBLIST, default=''))
app_args.insert(
i + 4,
Argument(Keys.NAME,
KeyHelp.NAME,
default=self.__class__.__name__))
break
blub = basic_args + app_args
defaults, cliargs = parse_sysargs(blub)
# construct info from defaults < info < commandlineargs
inifile = cliargs.get(Keys.INPUT, None)
info_fh = get_handler(inifile)
fileinfo = info_fh.read(inifile)
info = dicts.merge(cliargs, dicts.merge(fileinfo, defaults))
# request by malars: show dataset prominent in logger
if Keys.DATASET_CODE in info:
if not isinstance(info[Keys.DATASET_CODE], list):
if Keys.MZXML in info and not isinstance(
info[Keys.MZXML], list):
logging.info("Dataset is %s (%s)", info[Keys.DATASET_CODE],
os.path.basename(info[Keys.MZXML]))
else:
logging.info("Dataset is %s", info[Keys.DATASET_CODE])
else:
logging.debug("Datasets are %s", info[Keys.DATASET_CODE])
def test1_arg_priority(self):
return
sys.argv = [ '--INPUT', 'fcuk.ini', '--OUTPUT', 'kufc.ini']
# basic arguments for every node
basic_args = [Argument(Keys.INPUT, KeyHelp.INPUT, default=''),
Argument(Keys.OUTPUT, KeyHelp.OUTPUT, default=''),
Argument(Keys.MODULE, KeyHelp.MODULE, default=''),
Argument(Keys.LOG_LEVEL, KeyHelp.LOG_LEVEL, default="DEBUG")]
# Fixme: Prettify WORKDIR creation system
# WORKDIR: if WORKDIR is defined add related args
app_args = []
for i, arg in enumerate(app_args):
if arg.name == Keys.WORKDIR:
app_args.insert(i + 1, Argument(Keys.BASEDIR, KeyHelp.BASEDIR, default='.'))
app_args.insert(i + 2, Argument(Keys.JOB_ID, KeyHelp.JOB_ID, default=''))
app_args.insert(i + 3, Argument(Keys.SUBJOBLIST, KeyHelp.SUBJOBLIST, default=''))
app_args.insert(i + 4, Argument(Keys.NAME, KeyHelp.NAME, default=self.__class__.__name__))
break
blub = basic_args + app_args
defaults, cliargs = parse_sysargs(blub)
# construct info from defaults < info < commandlineargs
inifile = cliargs.get(Keys.INPUT, None)
ih = get_handler(inifile)
fileinfo = ih.read(inifile)
info = dicts.merge(cliargs, dicts.merge(fileinfo, defaults))
# setup logging
log = Logger.create(info[Keys.LOG_LEVEL])
# request by malars: show dataset prominent in logger
if Keys.DATASET_CODE in info:
if not isinstance(info[Keys.DATASET_CODE], list):
if Keys.MZXML in info and not isinstance(info[Keys.MZXML], list):
log.info("Dataset is %s (%s)" % (info[Keys.DATASET_CODE], os.path.basename(info[Keys.MZXML])))
else:
log.info("Dataset is %s" % info[Keys.DATASET_CODE])
else:
log.debug("Datasets are %s" % info[Keys.DATASET_CODE])
def setup(self, app_args):
# basic arguments for every node
basic_args = [
Argument(Keys.INPUT, KeyHelp.INPUT, default=''),
Argument(Keys.OUTPUT, KeyHelp.OUTPUT, default=''),
Argument(Keys.MODULE, KeyHelp.MODULE, default=''),
Argument(Keys.LOG_LEVEL, KeyHelp.LOG_LEVEL, default="INFO")
]
# WORKDIR: if WORKDIR is defined add related args
for i, arg in enumerate(app_args):
if arg.name == Keys.WORKDIR:
app_args.insert(
i + 1, Argument(Keys.BASEDIR, KeyHelp.BASEDIR,
default='.'))
app_args.insert(
i + 2, Argument(Keys.JOB_ID, KeyHelp.JOB_ID, default=''))
app_args.insert(
i + 3,
Argument(Keys.SUBJOBLIST, KeyHelp.SUBJOBLIST, default=''))
app_args.insert(
i + 4,
Argument(Keys.NAME,
KeyHelp.NAME,
default=self.__class__.__name__))
break
defaults, cliargs = parse_sysargs(basic_args + app_args)
# construct info from defaults < info < commandlineargs
infh = get_handler(cliargs.get(Keys.INPUT, None))
fileinfo = infh.read(cliargs.get(Keys.INPUT, None))
info = dicts.merge(cliargs, dicts.merge(fileinfo, defaults))
# request by malars: show dataset prominent in logger
if Keys.DATASET_CODE in info:
if not isinstance(info[Keys.DATASET_CODE], list):
if Keys.MZXML in info and not isinstance(
info[Keys.MZXML], list):
logging.info("Dataset is %s (%s)", info[Keys.DATASET_CODE],
os.path.basename(info[Keys.MZXML]))
else:
logging.info("Dataset is %s", info[Keys.DATASET_CODE])
else:
logging.debug("Datasets are %s", info[Keys.DATASET_CODE])
# WORKDIR: create WORKDIR (only after mk)
info = dirs.create_workdir(info)
# filter to requested args
if Keys.ALL_ARGS in info:
# if ALL_ARGS is set give whole info to app...
req_info = info
else:
req_info = {}
# ...otherwise copy only explicitly requested args to app
for key in [arg.name for arg in basic_args + app_args]:
if key in info:
req_info[key] = info[key]
logging.debug("info for app: %s", req_info)
return req_info, info
def test_parse_args(cls):
"""Test to parse arguments."""
sys.argv = ['--INPUT', 'fcuk.ini', '--OUTPUT', 'kufc.ini']
defaults, cliargs = parse_sysargs([])
print(defaults)
print(cliargs)
def test_parseArgs(self):
sys.argv = [ '--INPUT', 'fcuk.ini', '--OUTPUT', 'kufc.ini']
defaults, cliargs = parse_sysargs([])
print cliargs;