Merge branch 'release_24.0' into dev

galaxyproject · May 11, 2024 · 65f258c · 65f258c
2 parents 40177d3 + 375268c
commit 65f258c
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/lib/galaxy/job_execution/actions/post.py b/lib/galaxy/job_execution/actions/post.py
@@ -9,10 +9,7 @@
 
 from galaxy.model import PostJobActionAssociation
 from galaxy.model.base import transaction
-from galaxy.util import (
-    send_mail,
-    unicodify,
-)
+from galaxy.util import send_mail
 from galaxy.util.custom_logging import get_logger
 
 log = get_logger(__name__)
@@ -70,8 +67,8 @@ def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state
             if link_invocation:
                 body += f"\n\nWorkflow Invocation Report:\n{link_invocation}"
             send_mail(app.config.email_from, to, subject, body, app.config)
-        except Exception as e:
-            log.error("EmailAction PJA Failed, exception: %s", unicodify(e))
+        except Exception:
+            log.exception("EmailAction PJA Failed")
 
     @classmethod
     def get_short_str(cls, pja):

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
@@ -1420,8 +1420,8 @@ def fail(
                         try:
                             shutil.move(dataset_path.false_path, dataset_path.real_path)
                             log.debug("fail(): Moved %s to %s", dataset_path.false_path, dataset_path.real_path)
-                        except OSError as e:
-                            log.error("fail(): Missing output file in working directory: %s", unicodify(e))
+                        except FileNotFoundError as e:
+                            log.warning("fail(): Missing output file in working directory: %s", unicodify(e))
             except Exception as e:
                 log.exception(str(e))
             for dataset_assoc in job.output_datasets + job.output_library_datasets:

diff --git a/lib/galaxy/jobs/runners/slurm.py b/lib/galaxy/jobs/runners/slurm.py
@@ -222,6 +222,9 @@ def __check_memory_limit(self, efile_path):
                         return OUT_OF_MEMORY_MSG
                     elif any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS):
                         return PROBABLY_OUT_OF_MEMORY_MSG
+        except FileNotFoundError:
+            # Entirely expected, as __check_memory_limit is only called if the job state is CANCELLED
+            return False
         except Exception:
             log.exception("Error reading end of %s:", efile_path)