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[23.1] Fix metadata setting in extended metadata + outputs_to_working_directory mode #16678

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merged 10 commits into from
Sep 13, 2023
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Fix test_pulsar_embedded_remote_metadata.py::test_tools[job_properties]
mvdbeek committed Sep 12, 2023

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jasonmadigan Jason Madigan
commit 4a4607397aaae24dd37a4e81a616f87025ed62a3
4 changes: 3 additions & 1 deletion lib/galaxy/jobs/runners/pulsar.py
Original file line number Diff line number Diff line change
@@ -2,6 +2,7 @@

More information on Pulsar can be found at https://pulsar.readthedocs.io/ .
"""
import copy
import errno
import logging
import os
@@ -924,7 +925,8 @@ def __build_metadata_configuration(
# false_path to send the metadata command generation module.
work_dir_outputs = self.get_work_dir_outputs(job_wrapper, tool_working_directory=working_directory)
outputs = job_wrapper.job_io.get_output_fnames()
real_path_to_output = {o.real_path: o for o in outputs}
# copy fixes 'test/integration/test_pulsar_embedded_remote_metadata.py::test_tools[job_properties]'
real_path_to_output = {o.real_path: copy.copy(o) for o in outputs}
rewritten_outputs = []
for pulsar_workdir_path, real_path in work_dir_outputs:
work_dir_output = real_path_to_output.pop(real_path, None)