From 18a2519662cafe542872daf3cf3ca2cffbcd4241 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 6 Jun 2023 18:49:00 +0200 Subject: [PATCH] Drop legacy stdout/stderr file reading --- lib/galaxy/jobs/runners/__init__.py | 21 ++++----------------- 1 file changed, 4 insertions(+), 17 deletions(-) diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py index 23dcdcf6848..d77004e55aa 100644 --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -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,