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Source code for galaxy.jobs.runners.util.condor

"""
Condor helper utilities.
"""
from subprocess import (
    CalledProcessError,
    check_call,
    PIPE,
    Popen,
    STDOUT
)

from ..external import parse_external_id

DEFAULT_QUERY_CLASSAD = dict(
    universe='vanilla',
    getenv='true',
    notification='NEVER',
)

PROBLEM_RUNNING_CONDOR_SUBMIT = \
    "Problem encountered while running condor_submit."
PROBLEM_PARSING_EXTERNAL_ID = \
    "Failed to find job id from condor_submit"

SUBMIT_PARAM_PREFIX = "submit_"


[docs]def submission_params(prefix=SUBMIT_PARAM_PREFIX, **kwds): submission_params = {} for key in kwds: value = kwds[key] key = key.lower() if key.startswith(prefix): condor_key = key[len(prefix):] submission_params[condor_key] = value return submission_params
[docs]def build_submit_description(executable, output, error, user_log, query_params): """ Build up the contents of a condor submit description file. >>> submit_args = dict(executable='/path/to/script', output='o', error='e', user_log='ul') >>> submit_args['query_params'] = dict() >>> default_description = build_submit_description(**submit_args) >>> assert 'executable = /path/to/script' in default_description >>> assert 'output = o' in default_description >>> assert 'error = e' in default_description >>> assert 'queue' in default_description >>> assert 'universe = vanilla' in default_description >>> assert 'universe = standard' not in default_description >>> submit_args['query_params'] = dict(universe='standard') >>> std_description = build_submit_description(**submit_args) >>> assert 'universe = vanilla' not in std_description >>> assert 'universe = standard' in std_description """ all_query_params = DEFAULT_QUERY_CLASSAD.copy() all_query_params.update(query_params) submit_description = [] for key, value in all_query_params.items(): submit_description.append('%s = %s' % (key, value)) submit_description.append('executable = ' + executable) submit_description.append('output = ' + output) submit_description.append('error = ' + error) submit_description.append('log = ' + user_log) submit_description.append('queue') return '\n'.join(submit_description)
[docs]def condor_submit(submit_file): """ Submit a condor job described by the given file. Parse an external id for the submission or return None and a reason for the failure. """ external_id = None try: submit = Popen(('condor_submit', submit_file), stdout=PIPE, stderr=STDOUT) message, _ = submit.communicate() if submit.returncode == 0: external_id = parse_external_id(message, type='condor') else: message = PROBLEM_PARSING_EXTERNAL_ID except Exception as e: message = str(e) return external_id, message
[docs]def condor_stop(external_id): """ Stop running condor job and return a failure_message if this fails. """ failure_message = None try: check_call(('condor_rm', external_id)) except CalledProcessError: failure_message = "condor_rm failed" except Exception as e: "error encountered calling condor_rm: %s" % e return failure_message
[docs]def summarize_condor_log(log_file, external_id): """ """ log_job_id = external_id.zfill(3) s1 = s4 = s7 = s5 = s9 = False with open(log_file, 'r') as log_handle: for line in log_handle: if '001 (' + log_job_id + '.' in line: s1 = True if '004 (' + log_job_id + '.' in line: s4 = True if '007 (' + log_job_id + '.' in line: s7 = True if '005 (' + log_job_id + '.' in line: s5 = True if '009 (' + log_job_id + '.' in line: s9 = True file_size = log_handle.tell() return s1, s4, s7, s5, s9, file_size