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Source code for galaxy.jobs.runners.util.job_script
import io
import logging
import os
import subprocess
import time
from string import Template
from pkg_resources import resource_string
from galaxy.util import 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"\\nexport GALAXY_SLOTS\\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=0o755):
dir = os.path.dirname(path)
if not os.path.exists(dir):
os.makedirs(dir)
with io.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 i 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',
)