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Source code for galaxy.job_metrics.instrumenters.core

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

from . import InstrumentPlugin
from ..formatting import (
from ..safety import Safety

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(JobMetricFormatter):
    def format(self, key: str, value: Any) -> FormattedMetric:
        value = int(value)
        if key == GALAXY_SLOTS_KEY:
            return FormattedMetric("Cores Allocated", "%d" % value)
        elif key == GALAXY_MEMORY_MB_KEY:
            return FormattedMetric("Memory Allocated (MB)", "%d" % value)
        elif key == RUNTIME_SECONDS_KEY:
            return FormattedMetric("Job Runtime (Wall Clock)", seconds_to_str(value))
            # TODO: Use localized version of this from galaxy.ini
            title = "Job Start Time" if key == START_EPOCH_KEY else "Job End Time"
            return FormattedMetric(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() default_safety = Safety.SAFE
[docs] def __init__(self, **kwargs): pass
[docs] def pre_execute_instrument(self, job_directory: str) -> List[str]: 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: str) -> List[str]: commands = [] commands.append(self.__record_seconds_since_epoch_to_file(job_directory, "end")) return commands
[docs] def job_properties(self, job_id, job_directory: str) -> Dict[str, Any]: 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 f"""echo "$GALAXY_SLOTS" > '{galaxy_slots_file}' """ def __record_galaxy_memory_mb_command(self, job_directory): galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory) return f"""echo "$GALAXY_MEMORY_MB" > '{galaxy_memory_mb_file}' """ def __record_seconds_since_epoch_to_file(self, job_directory, name): path = self._instrument_file_path(job_directory, f"epoch_{name}") return f'date +"%s" > {path}' def __read_seconds_since_epoch(self, job_directory, name): path = self._instrument_file_path(job_directory, f"epoch_{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).read()) except Exception: pass return value
__all__ = ("CorePlugin",)