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Strip unicode null from tool stdio

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Fixes https://github.com/galaxyproject/galaxy/issues/18437.

On the non-pulsar side we strip nulls in set_meta.
This commit is contained in:
mvdbeek
2024-07-10 16:53:29 +02:00
parent b4af9b39e4
commit 2b2a4f8840
1 changed files with 3 additions and 2 deletions
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lib/galaxy/jobs/runners/pulsar.py
+3 -2
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@@ -57,6 +57,7 @@ from galaxy.util import (
galaxy_directory,
specs,
string_as_bool_or_none,
unicodify,
)
log = logging.getLogger(__name__)
@@ -649,8 +650,8 @@ class PulsarJobRunner(AsynchronousJobRunner):
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")