Loading lib/galaxy/jobs/runners/pulsar.py +14 −9 Original line number Diff line number Diff line Loading @@ -657,14 +657,19 @@ class PulsarJobRunner(AsynchronousJobRunner): run_results = client.full_status() remote_metadata_directory = run_results.get("metadata_directory", None) tool_stdout = run_results.get("stdout", "") if tool_stdout is None: tool_stderr = run_results.get("stderr", "") for file in ("tool_stdout", "tool_stderr"): if tool_stdout and tool_stderr: pass try: stdout_path = Path(job_wrapper.working_directory) / "outputs" / "tool_stdout" stdout_file = open(stdout_path, "r") tool_stdout = stdout_file.read() file_path = Path(job_wrapper.working_directory) / "outputs" / file file_content = open(file_path, "r") if tool_stdout is None and file == "tool_stdout": tool_stdout = file_content.read() elif tool_stderr is None and file == "tool_stderr": tool_stderr = file_content.read() except Exception: pass tool_stderr = run_results.get("stderr", "") job_stdout = run_results.get("job_stdout") job_stderr = run_results.get("job_stderr") exit_code = run_results.get("returncode") Loading Loading
lib/galaxy/jobs/runners/pulsar.py +14 −9 Original line number Diff line number Diff line Loading @@ -657,14 +657,19 @@ class PulsarJobRunner(AsynchronousJobRunner): run_results = client.full_status() remote_metadata_directory = run_results.get("metadata_directory", None) tool_stdout = run_results.get("stdout", "") if tool_stdout is None: tool_stderr = run_results.get("stderr", "") for file in ("tool_stdout", "tool_stderr"): if tool_stdout and tool_stderr: pass try: stdout_path = Path(job_wrapper.working_directory) / "outputs" / "tool_stdout" stdout_file = open(stdout_path, "r") tool_stdout = stdout_file.read() file_path = Path(job_wrapper.working_directory) / "outputs" / file file_content = open(file_path, "r") if tool_stdout is None and file == "tool_stdout": tool_stdout = file_content.read() elif tool_stderr is None and file == "tool_stderr": tool_stderr = file_content.read() except Exception: pass tool_stderr = run_results.get("stderr", "") job_stdout = run_results.get("job_stdout") job_stderr = run_results.get("job_stderr") exit_code = run_results.get("returncode") Loading