Source code for luigi.contrib.lsf_runner

# -*- coding: utf-8 -*-

"""
.. Copyright 2012-2015 Spotify AB
   Copyright 2018
   Copyright 2018 EMBL-European Bioinformatics Institute

   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.
"""

import os
import sys
try:
    # Dill is used for handling pickling and unpickling if there is a deference
    # in server setups between the LSF submission node and the nodes in the
    # cluster
    import dill as pickle
except ImportError:
    import pickle
import logging
from luigi.safe_extractor import SafeExtractor




def do_work_on_compute_node(work_dir):
    # Extract the necessary dependencies
    extract_packages_archive(work_dir)

    # Open up the pickle file with the work to be done
    os.chdir(work_dir)
    with open("job-instance.pickle", "r") as pickle_file_handle:
        job = pickle.load(pickle_file_handle)

    # Do the work contained
    job.work()





def extract_packages_archive(work_dir):
    package_file = os.path.join(work_dir, "packages.tar")
    if not os.path.exists(package_file):
        return

    curdir = os.path.abspath(os.curdir)

    os.chdir(work_dir)
    extractor = SafeExtractor(work_dir)
    extractor.safe_extract(package_file)
    if '' not in sys.path:
        sys.path.insert(0, '')

    os.chdir(curdir)





def main(args=sys.argv):
    """Run the work() method from the class instance in the file "job-instance.pickle".
    """
    try:
        # Set up logging.
        logging.basicConfig(level=logging.WARN)
        work_dir = args[1]
        assert os.path.exists(work_dir), "First argument to lsf_runner.py must be a directory that exists"
        do_work_on_compute_node(work_dir)
    except Exception as exc:
        # Dump encoded data that we will try to fetch using mechanize
        print(exc)
        raise



if __name__ == '__main__':
    main()