Code de-duplicate ok to edit metadata.

lib/galaxy/managers/datasets.py

@@ -343,12 +343,13 @@ class DatasetAssociationManager(base.ModelManager,
             rval["modify_item_roles"] = modify_item_role_list
         return rval
 
-    def __ok_to_edit_metadata(self, trans, dataset_id):
+    def ok_to_edit_metadata(self, dataset_id):
         # prevent modifying metadata when dataset is queued or running as input/output
         # This code could be more efficient, i.e. by using mappers, but to prevent slowing down loading a History panel, we'll leave the code here for now
-        for job_to_dataset_association in trans.sa_session.query(
+        sa_session = self.app.model.context
+        for job_to_dataset_association in sa_session.query(
                 self.app.model.JobToInputDatasetAssociation).filter_by(dataset_id=dataset_id).all() \
-                + trans.sa_session.query(self.app.model.JobToOutputDatasetAssociation).filter_by(dataset_id=dataset_id).all():
+                + sa_session.query(self.app.model.JobToOutputDatasetAssociation).filter_by(dataset_id=dataset_id).all():
             if job_to_dataset_association.job.state not in [job_to_dataset_association.job.states.OK, job_to_dataset_association.job.states.ERROR, job_to_dataset_association.job.states.DELETED]:
                 return False
         return True
@@ -357,7 +358,7 @@ class DatasetAssociationManager(base.ModelManager,
         """Sniff and assign the datatype to a given dataset association (ldda or hda)"""
         data = trans.sa_session.query(self.model_class).get(dataset_assoc.id)
         if data.datatype.allow_datatype_change:
-            if not self.__ok_to_edit_metadata(trans, data.id):
+            if not self.ok_to_edit_metadata(data.id):
                 raise exceptions.ItemAccessibilityException('This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them.')
             else:
                 path = data.dataset.file_name
@@ -369,15 +370,22 @@ class DatasetAssociationManager(base.ModelManager,
         else:
             raise exceptions.InsufficientPermissionsException('Changing datatype "%s" is not allowed.' % (data.extension))
 
-    def set_metadata(self, trans, dataset_assoc):
+    def set_metadata(self, trans, dataset_assoc, overwrite=False):
         """Trigger a job that detects and sets metadata on a given dataset association (ldda or hda)"""
         data = trans.sa_session.query(self.model_class).get(dataset_assoc.id)
-        if not self.__ok_to_edit_metadata(trans, data.id):
+        if not self.ok_to_edit_metadata(data.id):
             raise exceptions.ItemAccessibilityException('This dataset is currently being used as input or output. You cannot edit metadata until the jobs have completed or you have canceled them.')
         else:
-            trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
-                trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming={'input1': data},
-                overwrite=False)  # overwrite is False as per existing behavior
+            if overwrite:
+                for name, spec in data.metadata.spec.items():
+                    # We need to be careful about the attributes we are resetting
+                    if name not in ['name', 'info', 'dbkey', 'base_name']:
+                        if spec.get('default'):
+                            setattr(data.metadata, name, spec.unwrap(spec.get('default')))
+
+            self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
+                self.app.datatypes_registry.set_external_metadata_tool, trans, incoming={'input1': data},
+                overwrite=overwrite)
 
     def update_permissions(self, trans, dataset_assoc, **kwd):
         action = kwd.get('action', 'set_permissions')

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -19,7 +19,7 @@ from galaxy import (
 )
 from galaxy.datatypes import sniff
 from galaxy.datatypes.display_applications.util import decode_dataset_user, encode_dataset_user
-from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.exceptions import MessageException, RequestParameterInvalidException
 from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
 from galaxy.util import (
     inflector,
@@ -393,14 +393,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
     def set_edit(self, trans, payload=None, **kwd):
         """Allows user to modify parameters of an HDA."""
         def __ok_to_edit_metadata(dataset_id):
-            # prevent modifying metadata when dataset is queued or running as input/output
-            # This code could be more efficient, i.e. by using mappers, but to prevent slowing down loading a History panel, we'll leave the code here for now
-            for job_to_dataset_association in trans.sa_session.query(
-                    self.app.model.JobToInputDatasetAssociation).filter_by(dataset_id=dataset_id).all() \
-                    + trans.sa_session.query(self.app.model.JobToOutputDatasetAssociation).filter_by(dataset_id=dataset_id).all():
-                if job_to_dataset_association.job.state not in [job_to_dataset_association.job.states.OK, job_to_dataset_association.job.states.ERROR, job_to_dataset_association.job.states.DELETED]:
-                    return False
-            return True
+            return self.hda_manager.ok_to_edit_metadata(dataset_id)
 
         status = 'success'
         operation = payload.get('operation')
@@ -466,17 +459,10 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         elif operation == 'autodetect':
             # The user clicked the Auto-detect button on the 'Edit Attributes' form
             # prevent modifying metadata when dataset is queued or running as input/output
-            if not __ok_to_edit_metadata(data.id):
-                return self.message_exception(trans, 'This dataset is currently being used as input or output.  You cannot change metadata until the jobs have completed or you have canceled them.')
-            else:
-                for name, spec in data.metadata.spec.items():
-                    # We need to be careful about the attributes we are resetting
-                    if name not in ['name', 'info', 'dbkey', 'base_name']:
-                        if spec.get('default'):
-                            setattr(data.metadata, name, spec.unwrap(spec.get('default')))
-                message = 'Attributes have been queued to be updated.'
-                trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming={'input1': data})
-                trans.sa_session.flush()
+            try:
+                self.hda_manager.set_metadata(trans, data, overwrite=True)
+            except MessageException as e:
+                return self.message_exception(trans, e.err_msg)
         elif operation == 'conversion':
             target_type = payload.get('target_type')
             if target_type: