diff --git a/lib/galaxy/job_metrics/instrumenters/core.py b/lib/galaxy/job_metrics/instrumenters/core.py index a08ad8f8de5e..a78cf6147a6b 100644 --- a/lib/galaxy/job_metrics/instrumenters/core.py +++ b/lib/galaxy/job_metrics/instrumenters/core.py @@ -1,11 +1,14 @@ """The module describes the ``core`` job metrics plugin.""" +import json import logging +import os import time from typing import ( Any, Dict, List, + Optional, ) from . import InstrumentPlugin @@ -23,10 +26,17 @@ START_EPOCH_KEY = "start_epoch" END_EPOCH_KEY = "end_epoch" RUNTIME_SECONDS_KEY = "runtime_seconds" +CONTAINER_FILE = "__container.json" +CONTAINER_ID = "container_id" +CONTAINER_TYPE = "container_type" class CorePluginFormatter(JobMetricFormatter): def format(self, key: str, value: Any) -> FormattedMetric: + if key == CONTAINER_ID: + return FormattedMetric("Container ID", value) + if key == CONTAINER_TYPE: + return FormattedMetric("Container Type", value) value = int(value) if key == GALAXY_SLOTS_KEY: return FormattedMetric("Cores Allocated", "%d" % value) @@ -73,12 +83,20 @@ def job_properties(self, job_id, job_directory: str) -> Dict[str, Any]: 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") + properties.update(self.__read_container_details(job_directory)) 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 __read_container_details(self, job_directory) -> Dict[str, str]: + try: + with open(os.path.join(job_directory, CONTAINER_FILE)) as fh: + return json.load(fh) + except FileNotFoundError: + return {} + 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}' """ diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py index 68f27efc7493..0b7e19904307 100644 --- a/lib/galaxy/jobs/command_factory.py +++ b/lib/galaxy/jobs/command_factory.py @@ -181,6 +181,10 @@ def __externalize_commands( source_command = "" if container: source_command = container.source_environment + with open(join(job_wrapper.working_directory, "__container.json"), "w") as container_file: + container_file.write( + json.dumps({"container_id": container.container_id, "container_type": container.container_type}) + ) script_contents = f"#!{shell}\n{integrity_injection}{set_e}{source_command}{tool_commands}" write_script( local_container_script,