Merge remote-tracking branch 'upstream/release_24.0' into dev

ahmedhamidawan · May 21, 2024 · d6d3aa5 · d6d3aa5
2 parents e796826 + 37551f5
commit d6d3aa5
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diff --git 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 <https://github.com/galaxyproject/galaxy/issues/16742>`_ 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 <https://pypi.org/project/g
  - stage and commit all changes
  - create a new tag,
  - (intelligently) merge forward changes to newer release branches and dev
- - push changes to the repo identified by `--upstream` (defaults to https://github.com/galaxyporject/galaxy.git/)
+ - push changes to the repo identified by `--upstream` (defaults to https://github.com/galaxyproject/galaxy.git/)
 
 The script has 2 important arguments:
 

diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
@@ -1049,7 +1049,7 @@ def estimate_file_lines(self, dataset: DatasetProtocol) -> 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
@@ -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: