def execute(args):
task_family = None
# try to infer the task module from the passed task family and import it
parts = args.task_family.rsplit(".", 1)
if len(parts) == 2:
modid, cls_name = parts
try:
mod = __import__(modid, globals(), locals(), [cls_name])
if hasattr(mod, cls_name):
task_cls = getattr(mod, cls_name)
if not issubclass(task_cls, Task):
abort("object '{}' is not a Task".format(args.task_family))
task_family = task_cls.task_family
except ImportError as e:
logger.debug("import error in module {}: {}".format(modid, e))
# read task info from the db file and import it
if task_family is None:
info = read_task_from_db(args.task_family)
if not info:
abort("task family '{}' not found in db".format(args.task_family))
modid, task_family, _ = info
try:
__import__(modid, globals(), locals())
except ImportError:
abort("could not import module '{}'".format(modid))
# import the module and run luigi
luigi_run([task_family] + sys.argv[3:])
def run_and_expect(self,
joined_params,
retcode,
extra_args=['--local-scheduler', '--no-lock']):
with self.assertRaises(SystemExit) as cm:
luigi_run((joined_params.split(' ') + extra_args))
self.assertEqual(cm.exception.code, retcode)
def execute(args, argv):
"""
Executes the *run* subprogram with parsed commandline *args*.
"""
task_family = None
error = None
# try to infer the task module from the passed task family and import it
parts = args.task_family.rsplit(".", 1)
if len(parts) == 2:
modid, cls_name = parts
try:
mod = __import__(modid, globals(), locals(), [cls_name])
task_cls = getattr(mod, cls_name, None)
if task_cls is not None:
if not issubclass(task_cls, Task):
abort("object '{}' is not a Task".format(args.task_family))
task_family = task_cls.get_task_family()
except ImportError as e:
# distinguish import errors resulting from an unknown modid from all other cases
modid_unknown = str(e) == "No module named {}".format(modid)
if modid_unknown:
# keep the error in case the task family cannot be inferred from the index file
error = e
else:
raise
# read task info from the index file and import it
if task_family is None:
cfg = Config.instance()
index_file = cfg.get_expanded("core", "index_file")
if os.path.exists(index_file):
info = read_task_from_index(args.task_family, index_file)
if not info:
abort("task family '{}' not found in index".format(
args.task_family))
modid, task_family, _ = info
__import__(modid, globals(), locals())
# complain when no task could be found
if task_family is None:
if error:
raise error
else:
abort("task '{}' not found".format(args.task_family))
# run luigi
sys.argv[0] += " run"
luigi_run([task_family] + argv[3:])
def execute(args):
# read the module id for that task family from the db file
dbfile = Config.instance().get("core", "db_file")
with open(dbfile, "r") as f:
for line in f.readlines():
line = line.strip()
try:
mid, fam, params = line.split(":", 2)
except ValueError:
pass
if fam == args.task_family:
break
else:
abort("task family '%s' not found" % args.task_family)
# import the module and run luigi
__import__(mid, globals(), locals())
luigi_run([args.task_family] + sys.argv[3:])
def execute(args):
"""
Executes the *run* subprogram with parsed commandline *args*.
"""
task_family = None
error = None
# try to infer the task module from the passed task family and import it
parts = args.task_family.rsplit(".", 1)
if len(parts) == 2:
modid, cls_name = parts
try:
mod = __import__(modid, globals(), locals(), [cls_name])
if hasattr(mod, cls_name):
task_cls = getattr(mod, cls_name)
if not issubclass(task_cls, Task):
abort("object '{}' is not a Task".format(args.task_family))
task_family = task_cls.task_family
except ImportError as e:
logger.debug("import error in module {}: {}".format(modid, e))
error = e
# read task info from the db file and import it
if task_family is None:
db_file = Config.instance().get_expanded("core", "db_file")
if os.path.exists(db_file):
info = read_task_from_db(args.task_family, db_file)
if not info:
abort("task family '{}' not found in db".format(
args.task_family))
modid, task_family, _ = info
__import__(modid, globals(), locals())
# complain when no task could be found
if task_family is None:
if error:
raise error
else:
abort("task '{}' not found".format(args.task_family))
# import the module and run luigi
luigi_run([task_family] + sys.argv[3:])
def run_and_expect(self, joined_params, retcode, extra_args=['--local-scheduler', '--no-lock']):
with self.assertRaises(SystemExit) as cm:
luigi_run((joined_params.split(' ') + extra_args))
self.assertEqual(cm.exception.code, retcode)
def sciluigi_run(argv=sys.argv[1:]):
setup_logging()
luigi_run(argv)
# -*- coding: utf-8 -*-
from luigi.cmdline import luigi_run
if __name__ == '__main__':
luigi_run()
# -*- coding: utf-8 -*-
#
# Copyright 2012-2016 Spotify AB
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
from luigi.cmdline import luigi_run
if __name__ == '__main__':
luigi_run()
sys.path.append(os.path.abspath(sys.argv[0]))
sys.path.append(os.path.dirname(__file__) + '/luigi_pipelines/')
if bip:
scheduler_str = '--scheduler-host {bip}'.format(bip=bip)
else:
scheduler_str = '--local-scheduler'
if analyze_way == 'somatic':
RUN_COMMAND = raw_input(
"""%s\n\n If you sure, please input Y/y.""" %
formatter_output(parse_args.split(',')[0]))
if RUN_COMMAND.upper() == 'Y':
cmd_str = "--module SomaticPipelines workflow --x {args} {sch} --workers {worker}".format(
args=parse_args, worker=str(worker), sch=scheduler_str)
luigi_run(cmd_str.split(' '))
else:
print 'Exit now.'
exit()
elif analyze_way == 'germline':
RUN_COMMAND = raw_input(
"""%s\n\n If you sure, please input Y/y.""" %
formatter_output(parse_args.split(',')[0]))
if RUN_COMMAND.upper() == 'Y':
cmd_str = '--module GermlinePipelines workflow --x {args} {sch} --workers {worker}'.format(
args=parse_args, worker=str(worker), sch=scheduler_str)
luigi_run(cmd_str.split(' '))
else:
print 'Exit now.'
exit()
def run(args):
"""A wrapper around luigi CLI."""
luigi_run(args)
