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

import logging
import os
import subprocess
import time
from string import Template

from pkg_resources import resource_string

from galaxy.util import (
    RWXR_XR_X,
    unicodify,
)

log = logging.getLogger(__name__)
DEFAULT_SHELL = '/bin/bash'

DEFAULT_JOB_FILE_TEMPLATE = Template(
    unicodify(resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh'))
)

SLOTS_STATEMENT_CLUSTER_DEFAULT = \
    unicodify(resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh'))

MEMORY_STATEMENT_DEFAULT = \
    unicodify(resource_string(__name__, 'MEMORY_STATEMENT.sh'))

SLOTS_STATEMENT_SINGLE = """
GALAXY_SLOTS="1"
"""

INTEGRITY_INJECTION = """
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
    exit 42
fi
"""

INTEGRITY_SYNC_COMMAND = "/bin/sync"
DEFAULT_INTEGRITY_CHECK = True
DEFAULT_INTEGRITY_COUNT = 35
DEFAULT_INTEGRITY_SLEEP = .25
REQUIRED_TEMPLATE_PARAMS = ['working_directory', 'command', 'exit_code_path']
OPTIONAL_TEMPLATE_PARAMS = {
    'galaxy_lib': None,
    'galaxy_virtual_env': None,
    'headers': '',
    'env_setup_commands': [],
    'slots_statement': SLOTS_STATEMENT_CLUSTER_DEFAULT,
    'memory_statement': MEMORY_STATEMENT_DEFAULT,
    'instrument_pre_commands': '',
    'instrument_post_commands': '',
    'integrity_injection': INTEGRITY_INJECTION,
    'shell': DEFAULT_SHELL,
    'preserve_python_environment': True,
    'tmp_dir_creation_statement': '""',
}


[docs]def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
    """

    >>> has_exception = False
    >>> try: job_script()
    ... except Exception as e: has_exception = True
    >>> has_exception
    True
    >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec')
    >>> '\\nuptime\\n' in script
    True
    >>> 'echo $? > ec' in script
    True
    >>> 'GALAXY_LIB="None"' in script
    True
    >>> script.startswith('#!/bin/sh\\n#PBS -test\\n')
    False
    >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', headers='#PBS -test')
    >>> script.startswith('#!/bin/bash\\n\\n#PBS -test\\n')
    True
    >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', slots_statement='GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"')
    >>> script.find('GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"\\n') > 0
    True
    >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', memory_statement='GALAXY_MEMORY_MB="32768"')
    >>> script.find('GALAXY_MEMORY_MB="32768"\\n') > 0
    True
    """
    if any([param not in kwds for param in REQUIRED_TEMPLATE_PARAMS]):
        raise Exception("Failed to create job_script, a required parameter is missing.")
    job_instrumenter = kwds.get("job_instrumenter", None)
    if job_instrumenter:
        del kwds["job_instrumenter"]
        working_directory = kwds.get("metadata_directory", kwds["working_directory"])
        kwds["instrument_pre_commands"] = job_instrumenter.pre_execute_commands(working_directory) or ''
        kwds["instrument_post_commands"] = job_instrumenter.post_execute_commands(working_directory) or ''

    template_params = OPTIONAL_TEMPLATE_PARAMS.copy()
    template_params.update(**kwds)
    env_setup_commands_str = "\n".join(template_params["env_setup_commands"])
    template_params["env_setup_commands"] = env_setup_commands_str
    for key, value in template_params.items():
        template_params[key] = unicodify(value)
    if not isinstance(template, Template):
        template = Template(template)
    return template.safe_substitute(template_params)


[docs]def check_script_integrity(config):
    return getattr(config, "check_job_script_integrity", DEFAULT_INTEGRITY_CHECK)


[docs]def write_script(path, contents, config, mode=RWXR_XR_X):
    dir = os.path.dirname(path)
    if not os.path.exists(dir):
        os.makedirs(dir)

    with open(path, 'w', encoding='utf-8') as f:
        f.write(unicodify(contents))
    os.chmod(path, mode)
    _handle_script_integrity(path, config)


def _handle_script_integrity(path, config):
    if not check_script_integrity(config):
        return

    script_integrity_verified = False
    count = getattr(config, "check_job_script_integrity_count", DEFAULT_INTEGRITY_COUNT)
    sleep_amt = getattr(config, "check_job_script_integrity_sleep", DEFAULT_INTEGRITY_SLEEP)
    for _ in range(count):
        try:
            returncode = subprocess.call([path], env={"ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ": "1"})
            if returncode == 42:
                script_integrity_verified = True
                break

            log.debug("Script integrity error for file '%s': returncode was %d", path, returncode)

            # Else we will sync and wait to see if the script becomes
            # executable.
            try:
                # sync file system to avoid "Text file busy" problems.
                # These have occurred both in Docker containers and on EC2 clusters
                # under high load.
                subprocess.check_call(INTEGRITY_SYNC_COMMAND)
            except Exception as e:
                log.debug("Error syncing the filesystem: %s", unicodify(e))

        except Exception as exc:
            log.debug("Script not available yet: %s", unicodify(exc))

        time.sleep(sleep_amt)

    if not script_integrity_verified:
        raise Exception("Failed to write job script '%s', could not verify job script integrity." % path)


__all__ = (
    'check_script_integrity',
    'job_script',
    'write_script',
    'INTEGRITY_INJECTION',
)