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Drop legacy stdout/stderr file reading

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This commit is contained in:
mvdbeek
2023-06-06 18:49:00 +02:00
parent 846d5004e2
commit 18a2519662
1 changed files with 4 additions and 17 deletions
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lib/galaxy/jobs/runners/__init__.py
+4 -17
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@@ -590,23 +590,10 @@ class BaseJobRunner:
tool_stdout_path = os.path.join(outputs_directory, "tool_stdout")
tool_stderr_path = os.path.join(outputs_directory, "tool_stderr")
# TODO: These might not exist for running jobs at the upgrade to 19.XX, remove that
# assumption in 20.XX.
if os.path.exists(tool_stdout_path):
with open(tool_stdout_path, "rb") as stdout_file:
tool_stdout = self._job_io_for_db(stdout_file)
else:
# Legacy job, were getting a merged output - assume it is mostly tool output.
tool_stdout = job_stdout
job_stdout = None
if os.path.exists(tool_stderr_path):
with open(tool_stderr_path, "rb") as stdout_file:
tool_stderr = self._job_io_for_db(stdout_file)
else:
# Legacy job, were getting a merged output - assume it is mostly tool output.
tool_stderr = job_stderr
job_stderr = None
with open(tool_stdout_path, "rb") as stdout_file:
tool_stdout = self._job_io_for_db(stdout_file)
with open(tool_stderr_path, "rb") as stdout_file:
tool_stderr = self._job_io_for_db(stdout_file)
check_output_detected_state = job_wrapper.check_tool_output(
tool_stdout,