Merge pull request #13642 from nsoranzo/release_22.01_fix_13637 (055a6428) · Commits · NDIP / Galaxy

lib/galaxy/jobs/command_factory.py

+6 −2

Original line number	Diff line number	Diff line
		@@ -39,6 +39,7 @@ def build_command(
		create_tool_working_directory=True,
		remote_command_params=None,
		remote_job_directory=None,
		stream_stdout_stderr=False,
		):
		"""
		Compose the sequence of commands necessary to execute a job. This will
		@@ -94,7 +95,7 @@ def build_command(

		for_pulsar = 'script_directory' in remote_command_params
		if not for_pulsar:
		commands_builder.capture_stdout_stderr('../outputs/tool_stdout', '../outputs/tool_stderr')
		commands_builder.capture_stdout_stderr('../outputs/tool_stdout', '../outputs/tool_stderr', stream_stdout_stderr=stream_stdout_stderr)

		# Don't need to create a separate tool working directory for Pulsar
		# jobs - that is handled by Pulsar.
		@@ -277,7 +278,10 @@ class CommandsBuilder:
		def append_commands(self, commands):
		self.append_command("; ".join(c for c in commands if c))

		def capture_stdout_stderr(self, stdout_file, stderr_file):
		def capture_stdout_stderr(self, stdout_file, stderr_file, stream_stdout_stderr=False):
		if not stream_stdout_stderr:
		self.append_command(f"> '{stdout_file}' 2> '{stderr_file}'", sep="")
		return
		trap_command = """trap 'rm -f "$__out" "$__err"' EXIT"""
		if TRAP_KILL_CONTAINER in self.commands:
		# We need to replace the container kill trap with one that removes the named pipes and kills the container

lib/galaxy/jobs/runners/init.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -224,6 +224,7 @@ class BaseJobRunner:
		include_metadata=False,
		include_work_dir_outputs=True,
		modify_command_for_container=True,
		stream_stdout_stderr=False,
		):
		"""Some sanity checks that all runners' queue_job() methods are likely to want to do"""
		job_id = job_wrapper.get_id_tag()
		@@ -250,6 +251,7 @@ class BaseJobRunner:
		include_metadata=include_metadata,
		include_work_dir_outputs=include_work_dir_outputs,
		modify_command_for_container=modify_command_for_container,
		stream_stdout_stderr=stream_stdout_stderr,
		)
		except Exception as e:
		log.exception("(%s) Failure preparing job", job_id)
		@@ -277,6 +279,7 @@ class BaseJobRunner:
		include_metadata=False,
		include_work_dir_outputs=True,
		modify_command_for_container=True,
		stream_stdout_stderr=False,
		):
		container = self._find_container(job_wrapper)
		if not container and job_wrapper.requires_containerization:
		@@ -288,6 +291,7 @@ class BaseJobRunner:
		include_work_dir_outputs=include_work_dir_outputs,
		modify_command_for_container=modify_command_for_container,
		container=container,
		stream_stdout_stderr=stream_stdout_stderr,
		)

		def get_work_dir_outputs(self, job_wrapper, job_working_directory=None, tool_working_directory=None):

lib/galaxy/jobs/runners/kubernetes.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -149,6 +149,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
		job_wrapper,
		include_metadata=False,
		modify_command_for_container=False,
		stream_stdout_stderr=True,
		):
		return

lib/galaxy_test/api/test_jobs.py

+34 −9

Original line number	Diff line number	Diff line
		@@ -205,25 +205,50 @@ steps:

		@uses_test_history(require_new=True)
		def test_show(self, history_id):
		# Create HDA to ensure at least one job exists...
		self.__history_with_new_dataset(history_id)

		jobs_response = self._get("jobs")
		first_job = jobs_response.json()[0]
		job_properties_tool_run = self.dataset_populator.run_tool(
		tool_id="job_properties",
		inputs={},
		history_id=history_id,
		)
		first_job = self.__jobs_index()[0]
		self._assert_has_key(first_job, 'id', 'state', 'exit_code', 'update_time', 'create_time')

		job_id = first_job["id"]
		show_jobs_response = self._get(f"jobs/{job_id}")
		job_id = job_properties_tool_run["jobs"][0]["id"]
		show_jobs_response = self.dataset_populator.get_job_details(job_id)
		self._assert_status_code_is(show_jobs_response, 200)

		job_details = show_jobs_response.json()
		self._assert_has_key(job_details, 'id', 'state', 'exit_code', 'update_time', 'create_time')

		show_jobs_response = self._get(f"jobs/{job_id}", {"full": True})
		show_jobs_response = self.dataset_populator.get_job_details(job_id, full=True)
		self._assert_status_code_is(show_jobs_response, 200)

		job_details = show_jobs_response.json()
		self._assert_has_key(job_details, 'id', 'state', 'exit_code', 'update_time', 'create_time', 'stdout', 'stderr', 'job_messages')
		self._assert_has_key(
		job_details,
		"create_time",
		"exit_code",
		"id",
		"job_messages",
		"job_stderr",
		"job_stdout",
		"state",
		"stderr",
		"stdout",
		"tool_stderr",
		"tool_stdout",
		"update_time",
		)

		self.dataset_populator.wait_for_job(job_id, assert_ok=True)
		show_jobs_response = self.dataset_populator.get_job_details(job_id, full=True)
		job_details = show_jobs_response.json()
		assert "The bool is not true\n" not in job_details["job_stdout"]
		assert "The bool is very not true\n" not in job_details["job_stderr"]
		assert job_details["tool_stdout"] == "The bool is not true\n"
		assert job_details["tool_stderr"] == "The bool is very not true\n"
		assert "The bool is not true\n" in job_details["stdout"]
		assert "The bool is very not true\n" in job_details["stderr"]

		@uses_test_history(require_new=True)
		def test_show_security(self, history_id):

lib/galaxy_test/base/populators.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -557,7 +557,7 @@ class BaseDatasetPopulator(BasePopulator):
		return wait_on_state(lambda: self.get_job_details(job_id, full=True), desc="job state", assert_ok=assert_ok, timeout=timeout)

		def get_job_details(self, job_id: str, full: bool = False) -> Response:
		return self._get(f"jobs/{job_id}?full={full}")
		return self._get(f"jobs/{job_id}", {"full": full})

		def cancel_history_jobs(self, history_id: str, wait=True) -> None:
		active_jobs = self.active_history_jobs(history_id)