def prepare_run(self, info):
info = create_workdir(info)
outfile = os.path.join(info[Keys.WORKDIR],
os.path.basename(info['FILE']))
command = "%s %s %s" % (info['EXECUTABLE'], info["FILE"], outfile)
info['FILE'] = outfile
return info, command
def run(self, log, info):
info = create_workdir(log, info)
info['TEMPLATEFILE'] = os.path.join(info[Keys.WORKDIR], "template_out.tpl")
templates.read_mod_write(info, templates.get_tpl_of_class(self), info['TEMPLATEFILE'])
log.debug("Templatefile sucessfully written. Contents are [%s]" % open(info['TEMPLATEFILE']).read())
return info
def prepare_run(self, log, info):
info = create_workdir(log, info)
numflag=""
if info['NUMERIC'] == "true":
numflag="-n "
outfile = os.path.join(info[Keys.WORKDIR], os.path.basename(info['FILE']))
command = "%s %s %s" % (info['EXECUTABLE'], info["FILE"], outfile)
info['FILE'] = outfile
return info, command
def run(self, info):
info = create_workdir(info)
info['TEMPLATEFILE'] = os.path.join(info[Keys.WORKDIR],
"template_out.tpl")
templates.read_mod_write(info, templates.get_tpl_of_class(self),
info['TEMPLATEFILE'])
logging.debug("Templatefile sucessfully written. Contents are [%s]", \
open(info['TEMPLATEFILE']).read())
return info
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 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 prepare_run(self, log, info):
info = create_workdir(log, info)
info["COPY"] = os.path.join(info[Keys.WORKDIR], os.path.basename(info["FILE"]))
command = "%s %s %s" % (info["EXECUTABLE"], info["FILE"], info["COPY"])
return info, command
