Fix container recording for pulsar

And re-use abstractions for determining file path.
galaxyproject · Jul 26, 2024 · 9b772f1 · 9b772f1
1 parent 5a27e70
commit 9b772f1
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Showing 3 changed files with 18 additions and 11 deletions.
diff --git a/lib/galaxy/job_metrics/instrumenters/core.py b/lib/galaxy/job_metrics/instrumenters/core.py
@@ -2,7 +2,6 @@
 
 import json
 import logging
-import os
 import time
 from typing import (
     Any,
@@ -25,7 +24,6 @@
 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"
 
@@ -89,9 +87,12 @@ def job_properties(self, job_id, job_directory: str) -> Dict[str, Any]:
             properties[RUNTIME_SECONDS_KEY] = end - start
         return properties
 
+    def get_container_file_path(self, job_directory):
+        return self._instrument_file_path(job_directory, "container")
+
     def __read_container_details(self, job_directory) -> Dict[str, str]:
         try:
-            with open(os.path.join(job_directory, CONTAINER_FILE)) as fh:
+            with open(self.get_container_file_path(job_directory)) as fh:
                 return json.load(fh)
         except FileNotFoundError:
             return {}

diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
@@ -1,7 +1,10 @@
 import json
 import typing
 from logging import getLogger
-from os import getcwd
+from os import (
+    getcwd,
+    makedirs,
+)
 from os.path import (
     abspath,
     join,
@@ -81,8 +84,16 @@ def build_command(
         __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)
 
     __handle_task_splitting(commands_builder, job_wrapper)
-
     for_pulsar = "pulsar_version" in remote_command_params
+    if container:
+        if core_job_metric_plugin := runner.app.job_metrics.default_job_instrumenter.get_configured_plugin("core"):
+            directory = join(job_wrapper.working_directory, "metadata") if for_pulsar else job_wrapper.working_directory
+            makedirs(directory, exist_ok=True)
+            container_file_path = core_job_metric_plugin.get_container_file_path(directory)
+            with open(container_file_path, "w") as container_file:
+                container_file.write(
+                    json.dumps({"container_id": container.container_id, "container_type": container.container_type})
+                )
     if (container and modify_command_for_container) or job_wrapper.commands_in_new_shell:
         if container and modify_command_for_container:
             # Many Docker containers do not have /bin/bash.
@@ -181,10 +192,6 @@ 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,

diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
@@ -36,8 +36,7 @@ def _run_and_get_contents(self, tool_id: str, history_id: str):
         run_response = self.dataset_populator.run_tool(tool_id, {}, history_id)
         job_id = run_response["jobs"][0]["id"]
         self.dataset_populator.wait_for_job(job_id=job_id, assert_ok=True, timeout=EXTENDED_TIMEOUT)
-        job_details = self.dataset_populator.get_job_details(job_id=job_id, full=True).json()
-        job_metrics = job_details["job_metrics"]
+        job_metrics = self.dataset_populator._get(f"/api/jobs/{job_id}/metrics").json()
         # would be nice if it wasn't just a list of unpredictable order ...
         container_id = None
         container_type = None