Fix wrong extension on pick data output

This fixes #18795
galaxyproject · Sep 11, 2024 · ee63214 · ee63214
1 parent 1dce8cf
commit ee63214
Show file tree

Hide file tree

Showing 3 changed files with 20 additions and 4 deletions.
diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
@@ -5704,6 +5704,11 @@ export interface components {
              * @description TODO
              */
             api_type?: "file" | null;
+            /**
+             * Copied From History Dataset Association Id
+             * @description ID of HDA this HDA was copied from.
+             */
+            copied_from_history_dataset_association_id?: string | null;
             /** Copied From Ldda Id */
             copied_from_ldda_id?: string | null;
             /**
@@ -5948,6 +5953,11 @@ export interface components {
              * @enum {string}
              */
             api_type?: "file";
+            /**
+             * Copied From History Dataset Association Id
+             * @description ID of HDA this HDA was copied from.
+             */
+            copied_from_history_dataset_association_id?: string | null;
             /** Copied From Ldda Id */
             copied_from_ldda_id?: string | null;
             /**

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -2880,7 +2880,9 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
                 # if change_datatype PJA is associated with expression tool output the new output already has
                 # the desired datatype, so we use it. If the extension is "data" there's no change_dataset PJA and
                 # we want to use the existing extension.
-                new_ext = output.extension if output.extension != "data" else copy_object.extension
+                new_ext = (
+                    output.extension if output.extension not in ("data", "expression.json") else copy_object.extension
+                )
                 require_metadata_regeneration = copy_object.extension != new_ext
                 output.copy_from(copy_object, include_metadata=not require_metadata_regeneration)
                 output.extension = new_ext
@@ -2895,8 +2897,12 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
                     else:
                         # TODO: move exec_after_process into metadata script so this doesn't run on the headnode ?
                         output.init_meta()
-                        output.set_meta()
-                        output.set_metadata_success_state()
+                        try:
+                            output.set_meta()
+                            output.set_metadata_success_state()
+                        except Exception:
+                            output.state = model.HistoryDatasetAssociation.states.FAILED_METADATA
+                            log.exception("Exception occured while setting metdata")
 
     def parse_environment_variables(self, tool_source):
         """Setup environment variable for inputs file."""

diff --git a/test/unit/app/managers/test_HDAManager.py b/test/unit/app/managers/test_HDAManager.py
@@ -412,7 +412,7 @@ def test_serializers(self):
         assert isinstance(serialized["file_size"], int)
         assert isinstance(serialized["nice_size"], str)
         # TODO: these should be tested w/copy
-        self.assertNullableEncodedId(serialized["copied_from_history_dataset_association_id"])
+        assert isinstance(serialized["copied_from_history_dataset_association_id"], int)
         self.assertNullableEncodedId(serialized["copied_from_library_dataset_dataset_association_id"])
         self.assertNullableBasestring(serialized["info"])
         self.assertNullableBasestring(serialized["blurb"])