Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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

from re import search

EXTERNAL_ID_TYPE_ANY = None

EXTERNAL_ID_PATTERNS = [
    ('condor', r'submitted to cluster (\d+)\.'),
    ('slurm', r'Submitted batch job (\w+)'),
    ('torque', r'(.+)'),  # Default 'pattern' assumed by Galaxy code circa August 2013.
]


def parse_external_id(output, type=EXTERNAL_ID_TYPE_ANY):
    """
    Attempt to parse the output of job submission commands for an external id.__doc__

    >>> parse_external_id("12345.pbsmanager")
    '12345.pbsmanager'
    >>> parse_external_id('Submitted batch job 185')
    '185'
    >>> parse_external_id('Submitted batch job 185', type='torque')
    'Submitted batch job 185'
    >>> parse_external_id('submitted to cluster 125.')
    '125'
    >>> parse_external_id('submitted to cluster 125.', type='slurm')
    >>>
    """
    external_id = None
    for pattern_type, pattern in EXTERNAL_ID_PATTERNS:
        if type != EXTERNAL_ID_TYPE_ANY and type != pattern_type:
            continue

        match = search(pattern, output)
        if match:
            external_id = match.group(1)
            break

    return external_id