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

import logging
import os
import subprocess
import time
from dataclasses import dataclass
from string import Template
from typing import (
    Any,
    Dict,
    Optional,
)

from typing_extensions import Protocol

from galaxy.util import (
    RWXR_XR_X,
    unicodify,
)
from galaxy.util.resources import resource_string

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

DEFAULT_JOB_FILE_TEMPLATE = Template(resource_string(__name__, "DEFAULT_JOB_FILE_TEMPLATE.sh"))

SLOTS_STATEMENT_CLUSTER_DEFAULT = resource_string(__name__, "CLUSTER_SLOTS_STATEMENT.sh")

MEMORY_STATEMENT_DEFAULT_TEMPLATE = Template(resource_string(__name__, "MEMORY_STATEMENT_TEMPLATE.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 = 0.25
REQUIRED_TEMPLATE_PARAMS = ["working_directory", "command"]
OPTIONAL_TEMPLATE_PARAMS: Dict[str, Any] = {
    "galaxy_lib": None,
    "galaxy_virtual_env": None,
    "headers": "",
    "env_setup_commands": [],
    "slots_statement": SLOTS_STATEMENT_CLUSTER_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 >>> '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) metadata_directory = kwds.get("metadata_directory", kwds["working_directory"]) if job_instrumenter: del kwds["job_instrumenter"] kwds["instrument_pre_commands"] = job_instrumenter.pre_execute_commands(metadata_directory) or "" kwds["instrument_post_commands"] = job_instrumenter.post_execute_commands(metadata_directory) or "" if "memory_statement" not in kwds: kwds["memory_statement"] = MEMORY_STATEMENT_DEFAULT_TEMPLATE.safe_substitute( metadata_directory=metadata_directory ) # Setup home directory var kwds["home_directory"] = kwds.get("home_directory", os.path.join(kwds["working_directory"], "home")) 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)
class DescribesScriptIntegrityChecks(Protocol): check_job_script_integrity: bool check_job_script_integrity_count: Optional[int] check_job_script_integrity_sleep: Optional[float] @dataclass class ScriptIntegrityChecks: """Minimal class implementing the DescribesScriptIntegrityChecks protocol""" check_job_script_integrity: bool check_job_script_integrity_count: Optional[int] = None check_job_script_integrity_sleep: Optional[float] = None
[docs]def write_script(path: str, contents, job_io: DescribesScriptIntegrityChecks, mode: int = RWXR_XR_X) -> None: 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) if job_io.check_job_script_integrity: assert job_io.check_job_script_integrity_count is not None assert job_io.check_job_script_integrity_sleep is not None _handle_script_integrity(path, job_io.check_job_script_integrity_count, job_io.check_job_script_integrity_sleep)
def _handle_script_integrity( path: str, check_job_script_integrity_count: int, check_job_script_integrity_sleep: float ) -> None: script_integrity_verified = False for _ in range(check_job_script_integrity_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(check_job_script_integrity_sleep) if not script_integrity_verified: raise Exception(f"Failed to write job script '{path}', could not verify job script integrity.") __all__ = ( "job_script", "write_script", "INTEGRITY_INJECTION", )