Unverified Commit e7c5543c authored Apr 07, 2023 by mvdbeek

Fix pulsar error when when home_target is pwd

Fixes:
```
ERROR    galaxy.jobs.runners.pulsar:pulsar.py:531 failure running job 533
Traceback (most recent call last):
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 484, in __prepare_job
    job_wrapper.prepare(**prepare_kwds)
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/__init__.py", line 1253, in prepare
    ) = tool_evaluator.build()
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 560, in build
    global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables")
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 90, in global_tool_logs
    raise e
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 86, in global_tool_logs
    return func()
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 664, in _build_environment_variables
    home_dir = self.compute_environment.home_directory()
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 1163, in home_directory
    return self._target_to_directory(self.job_wrapper.home_target)
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 1179, in _target_to_directory
    raise Exception(f"Unknown target type [{target}]")
Exception: Unknown target type [pwd]
```

parent f4143b0b

lib/galaxy/jobs/runners/pulsar.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -1139,6 +1139,8 @@ class PulsarComputeEnvironment(ComputeEnvironment):
		return self._shared_home_dir
		elif target == "job_home":
		return "$_GALAXY_JOB_HOME_DIR"
		elif target == "pwd":
		os.path.join(self.working_directory(), "working")
		else:
		raise Exception(f"Unknown target type [{target}]")

test/integration/test_pulsar_embedded.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -33,5 +33,6 @@ test_tools = integration_util.integration_tool_runner(
		"multi_output_assign_primary_ext_dbkey",
		"strict_shell",
		"tool_provided_metadata_9",
		"simple_constructs_y",
		]
		)