Fix handling of collecting discovered but purged outputs

galaxyproject · Jun 9, 2024 · 0467e96 · 0467e96
1 parent 64adb9d
commit 0467e96
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Showing 2 changed files with 16 additions and 3 deletions.
diff --git a/lib/galaxy/job_execution/output_collect.py b/lib/galaxy/job_execution/output_collect.py
@@ -521,7 +521,8 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex
                 outdata.designation = designation
                 outdata.dataset.external_filename = None  # resets filename_override
                 # Move data from temp location to dataset location
-                job_context.object_store.update_from_file(outdata.dataset, file_name=filename, create=True)
+                if not outdata.dataset.purged:
+                    job_context.object_store.update_from_file(outdata.dataset, file_name=filename, create=True)
                 primary_output_assigned = True
                 continue
             if name not in primary_datasets:
@@ -554,6 +555,7 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex
                 dataset_attributes=new_primary_datasets_attributes,
                 creating_job_id=job_context.get_job_id() if job_context else None,
                 storage_callbacks=storage_callbacks,
+                purged=outdata.dataset.purged,
             )
             # Associate new dataset with job
             job_context.add_output_dataset_association(f"__new_primary_file_{name}|{designation}__", primary_data)
@@ -563,7 +565,13 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex
         if primary_output_assigned:
             outdata.name = new_outdata_name
             outdata.init_meta()
-            outdata.set_meta()
+            if not outdata.dataset.purged:
+                try:
+                    outdata.set_meta()
+                except Exception:
+                    # We don't want to fail here on a single "bad" discovered dataset
+                    log.debug("set meta failed for %s", outdata, exc_info=True)
+                    outdata.state = HistoryDatasetAssociation.states.FAILED_METADATA
             outdata.set_peek()
             outdata.discovered = True
             sa_session = job_context.sa_session

diff --git a/lib/galaxy/model/store/discover.py b/lib/galaxy/model/store/discover.py
@@ -91,6 +91,7 @@ def create_dataset(
         creating_job_id=None,
         output_name=None,
         storage_callbacks=None,
+        purged=False,
     ):
         tag_list = tag_list or []
         sources = sources or []
@@ -190,7 +191,11 @@ def create_dataset(
 
         if info is not None:
             primary_data.info = info
-        if filename:
+
+        if purged:
+            primary_data.dataset.purged = True
+            primary_data.purged = True
+        if filename and not purged:
             if storage_callbacks is None:
                 self.finalize_storage(
                     primary_data=primary_data,