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Strip unicode null from tool stdio
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Fixes #18437.

On the non-pulsar side we strip nulls in set_meta.
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mvdbeek committed Jul 10, 2024
1 parent b4af9b3 commit 2b2a4f8
Showing 1 changed file with 3 additions and 2 deletions.
5 changes: 3 additions & 2 deletions lib/galaxy/jobs/runners/pulsar.py
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@
galaxy_directory,
specs,
string_as_bool_or_none,
unicodify,
)

log = logging.getLogger(__name__)
Expand Down Expand Up @@ -649,8 +650,8 @@ def finish_job(self, job_state: JobState):
client = self.get_client_from_state(job_state)
run_results = client.full_status()
remote_metadata_directory = run_results.get("metadata_directory", None)
tool_stdout = run_results.get("stdout", "")
tool_stderr = run_results.get("stderr", "")
tool_stdout = unicodify(run_results.get("stdout", ""), strip_null=True)
tool_stderr = unicodify(run_results.get("stderr", ""), strip_null=True)
job_stdout = run_results.get("job_stdout")
job_stderr = run_results.get("job_stderr")
exit_code = run_results.get("returncode")
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