diff --git a/doc/source/dev/create_release.rst b/doc/source/dev/create_release.rst index 59e0cb96ac15..75d1ff7d469d 100644 --- a/doc/source/dev/create_release.rst +++ b/doc/source/dev/create_release.rst @@ -1,7 +1,7 @@ Creating Galaxy Releases ======================== -The "main" release process is an interactive checklist with instructions (see `Publication of Galaxy Release v 23.2 https://github.com/galaxyproject/galaxy/issues/16742>`_ for an example). +The "main" release process is an interactive checklist with instructions (see `Publication of Galaxy Release v 23.2 `_ for an example). This issue is generated via `make release-issue`. The final result of the release process are @@ -24,7 +24,7 @@ The command is shipped with the `galaxy-release-util Optional[int]: sample_lines = dataset_read.count("\n") return int(sample_lines * (float(dataset.get_size()) / float(sample_size))) except UnicodeDecodeError: - log.error(f"Unable to estimate lines in file {dataset.get_file_name()}") + log.warning(f"Unable to estimate lines in file {dataset.get_file_name()}, likely not a text file.") return None def count_data_lines(self, dataset: HasFileName) -> Optional[int]: @@ -1069,7 +1069,7 @@ def count_data_lines(self, dataset: HasFileName) -> Optional[int]: if line and not line.startswith("#"): data_lines += 1 except UnicodeDecodeError: - log.error(f"Unable to count lines in file {dataset.get_file_name()}") + log.warning(f"Unable to count lines in file {dataset.get_file_name()}, likely not a text file.") return None return data_lines diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py index 05c2398da190..5f744f0933b6 100644 --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -382,7 +382,14 @@ def stop_job(self, job_wrapper): commands.execute(cmd) log.info(f"({job.id}/{ext_id}) Removed from DRM queue at user's request") except drmaa.InvalidJobException: - log.exception(f"({job.id}/{ext_id}) User killed running job, but it was already dead") + log.warning(f"({job.id}/{ext_id}) User killed running job, but it was already dead") + except drmaa.InternalException as e: + if "already completing or completed" in str(e): + log.warning(f"({job.id}/{ext_id}) User killed running job, but job already terminal in DRM queue") + else: + log.exception( + f"({job.id}/{ext_id}) User killed running job, but error encountered removing from DRM queue" + ) except commands.CommandLineException as e: log.error(f"({job.id}/{ext_id}) User killed running job, but command execution failed: {unicodify(e)}") except Exception: