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.metrics.instrumenters.env

"""The module describes the ``env`` job metrics plugin."""
import logging
import re

from . import InstrumentPlugin
from .. import formatting

log = logging.getLogger(__name__)


class EnvFormatter(formatting.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()
[docs] def __init__(self, **kwargs): variables_str = kwargs.get("variables", None) if variables_str: variables = [v.strip() for v in variables_str.split(",")] else: variables = None self.variables = variables
[docs] def pre_execute_instrument(self, job_directory): """ Use env to dump all environment variables to a file. """ return "env > '%s'" % self.__env_file(job_directory)
[docs] def post_execute_instrument(self, job_directory): return None
[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', )