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Source code for galaxy.jobs.metrics.instrumenters.env

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

from ..instrumenters import InstrumentPlugin
from ...metrics 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( '([^=]+)=(\(\) \{.+?\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', )