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.job_metrics.instrumenters.env
"""The module describes the ``env`` job metrics plugin."""
import logging
import re
from typing import (
List,
Optional,
)
from . import InstrumentPlugin
from ..formatting import JobMetricFormatter
from ..safety import Safety
log = logging.getLogger(__name__)
class EnvFormatter(JobMetricFormatter):
pass
[docs]class EnvPlugin(InstrumentPlugin):
"""Instrumentation plugin capable of recording all or specific environment
variables for a job at runtime.
"""
plugin_type = "env"
formatter = EnvFormatter()
variables: Optional[List[str]]
default_safety = Safety.UNSAFE
[docs] def __init__(self, **kwargs):
variables_str = kwargs.get("variables", None)
if isinstance(variables_str, list):
self.variables = variables_str
elif variables_str:
self.variables = [v.strip() for v in variables_str.split(",")]
else:
self.variables = None
[docs] def pre_execute_instrument(self, job_directory: str):
"""Use env to dump all environment variables to a file."""
return f"env > '{self.__env_file(job_directory)}'"
[docs] def job_properties(self, job_id, job_directory):
"""Recover environment variables dumped out on compute server and filter
out specific variables if needed.
"""
variables = self.variables
properties = {}
env_string = "".join(open(self.__env_file(job_directory)).readlines())
while env_string:
# Check if the next lines contain a shell function.
# We use '\n\}\n' as regex termination because shell
# functions can be nested.
# We use the non-greedy '.+?' because of re.DOTALL .
m = re.match(r"([^=]+)=(\(\) \{.+?\n\})\n", env_string, re.DOTALL)
if m is None:
m = re.match("([^=]+)=(.*)\n", env_string)
if m is None:
# Some problem recording or reading back env output.
message_template = "Problem parsing env metric output for job %s - properties will be incomplete"
message = message_template % job_id
log.debug(message)
break
(var, value) = m.groups()
if not variables or var in variables:
properties[var] = value
env_string = env_string[m.end() :]
return properties
def __env_file(self, job_directory):
return self._instrument_file_path(job_directory, "vars")
__all__ = ("EnvPlugin",)