Source code for galaxy.job_metrics.instrumenters.core

"""The module describes the ``core`` job metrics plugin."""
import logging
import time

from . import InstrumentPlugin
from .. import formatting

log = logging.getLogger(__name__)

GALAXY_SLOTS_KEY = "galaxy_slots"
GALAXY_MEMORY_MB_KEY = "galaxy_memory_mb"
START_EPOCH_KEY = "start_epoch"
END_EPOCH_KEY = "end_epoch"
RUNTIME_SECONDS_KEY = "runtime_seconds"


class CorePluginFormatter(formatting.JobMetricFormatter):

    def format(self, key, value):
        value = int(value)
        if key == GALAXY_SLOTS_KEY:
            return ("Cores Allocated", "%d" % value)
        elif key == GALAXY_MEMORY_MB_KEY:
            return ("Memory Allocated (MB)", "%d" % value)
        elif key == RUNTIME_SECONDS_KEY:
            return ("Job Runtime (Wall Clock)", formatting.seconds_to_str(value))
        else:
            # TODO: Use localized version of this from galaxy.ini
            title = "Job Start Time" if key == START_EPOCH_KEY else "Job End Time"
            return (title, time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(value)))


[docs]class CorePlugin(InstrumentPlugin):
    """ Simple plugin that collects data without external dependencies. In
    particular it currently collects value set for Galaxy slots.
    """
    plugin_type = "core"
    formatter = CorePluginFormatter()

[docs]    def __init__(self, **kwargs):
        pass

[docs]    def pre_execute_instrument(self, job_directory):
        commands = []
        commands.append(self.__record_galaxy_slots_command(job_directory))
        commands.append(self.__record_galaxy_memory_mb_command(job_directory))
        commands.append(self.__record_seconds_since_epoch_to_file(job_directory, "start"))
        return commands

[docs]    def post_execute_instrument(self, job_directory):
        commands = []
        commands.append(self.__record_seconds_since_epoch_to_file(job_directory, "end"))
        return commands

[docs]    def job_properties(self, job_id, job_directory):
        galaxy_slots_file = self.__galaxy_slots_file(job_directory)
        galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory)

        properties = {}
        properties[GALAXY_SLOTS_KEY] = self.__read_integer(galaxy_slots_file)
        properties[GALAXY_MEMORY_MB_KEY] = self.__read_integer(galaxy_memory_mb_file)
        start = self.__read_seconds_since_epoch(job_directory, "start")
        end = self.__read_seconds_since_epoch(job_directory, "end")
        if start is not None and end is not None:
            properties[START_EPOCH_KEY] = start
            properties[END_EPOCH_KEY] = end
            properties[RUNTIME_SECONDS_KEY] = end - start
        return properties

    def __record_galaxy_slots_command(self, job_directory):
        galaxy_slots_file = self.__galaxy_slots_file(job_directory)
        return '''echo "$GALAXY_SLOTS" > '%s' ''' % galaxy_slots_file

    def __record_galaxy_memory_mb_command(self, job_directory):
        galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory)
        return '''echo "$GALAXY_MEMORY_MB" > '%s' ''' % galaxy_memory_mb_file

    def __record_seconds_since_epoch_to_file(self, job_directory, name):
        path = self._instrument_file_path(job_directory, "epoch_%s" % name)
        return 'date +"%s" > ' + path

    def __read_seconds_since_epoch(self, job_directory, name):
        path = self._instrument_file_path(job_directory, "epoch_%s" % name)
        return self.__read_integer(path)

    def __galaxy_slots_file(self, job_directory):
        return self._instrument_file_path(job_directory, "galaxy_slots")

    def __galaxy_memory_mb_file(self, job_directory):
        return self._instrument_file_path(job_directory, "galaxy_memory_mb")

    def __read_integer(self, path):
        value = None
        try:
            value = int(open(path, "r").read())
        except Exception:
            pass
        return value


__all__ = ('CorePlugin', )