Merge pull request #18231 from mvdbeek/set_peek_on_success_only

[24.0] Don't set dataset peek for errored jobs
galaxyproject · May 27, 2024 · 62b53c5 · 62b53c5
2 parents fef8341 + 54db4e9
commit 62b53c5
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Showing 4 changed files with 19 additions and 16 deletions.
diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
@@ -1546,8 +1546,12 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
     def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
         if not dataset.dataset.purged:
             dataset.peek = get_file_peek(dataset.get_file_name())
-            atom_number = int(dataset.peek.split("\n")[1])
-            dataset.blurb = f"{atom_number} atoms"
+            peek_lines = dataset.peek.split("\n")
+            try:
+                atom_number = int(peek_lines[1])
+                dataset.blurb = f"{atom_number} atoms"
+            except (ValueError, IndexError):
+                dataset.blurb = "file does not look like valid GRO file."
         else:
             dataset.peek = "file does not exist"
             dataset.blurb = "file purged from disk"

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
@@ -1786,13 +1786,9 @@ def _finish_dataset(self, output_name, dataset, job, context, final_job_state, r
                     working_directory=self.working_directory,
                     remote_metadata_directory=remote_metadata_directory,
                 )
-            line_count = context.get("line_count", None)
-            try:
-                # Certain datatype's set_peek methods contain a line_count argument
+            if final_job_state != job.states.ERROR:
+                line_count = context.get("line_count", None)
                 dataset.set_peek(line_count=line_count)
-            except TypeError:
-                # ... and others don't
-                dataset.set_peek()
         else:
             # Handle purged datasets.
             dataset.blurb = "empty"

diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
@@ -506,12 +506,7 @@ def set_meta(new_dataset_instance, file_dict):
                     dataset.dataset.uuid = context["uuid"]
                 if not final_job_state == Job.states.ERROR:
                     line_count = context.get("line_count", None)
-                    try:
-                        # Certain datatype's set_peek methods contain a line_count argument
-                        dataset.set_peek(line_count=line_count)
-                    except TypeError:
-                        # ... and others don't
-                        dataset.set_peek()
+                    dataset.set_peek(line_count=line_count)
                 for context_key in TOOL_PROVIDED_JOB_METADATA_KEYS:
                     if context_key in context:
                         context_value = context[context_key]

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -4652,8 +4652,16 @@ def get_mime(self):
             # extension is None
             return "data"
 
-    def set_peek(self, **kwd):
-        return self.datatype.set_peek(self, **kwd)
+    def set_peek(self, line_count=None, **kwd):
+        try:
+            # Certain datatype's set_peek methods contain a line_count argument
+            return self.datatype.set_peek(self, line_count=line_count, **kwd)
+        except TypeError:
+            # ... and others don't
+            return self.datatype.set_peek(self, **kwd)
+        except Exception:
+            # Never fail peek setting, but do log exception so datatype logic can be fixed
+            log.exception("Setting peek failed")
 
     def init_meta(self, copy_from=None):
         return self.datatype.init_meta(self, copy_from=copy_from)