Revert "Merge pull request #816 from jkiang13/SYNPY-1115-store-table-provenance"

This reverts commit effef31, reversing
changes made to 1c55705.

Author: jkiang13

synapseclient/client.py

@@ -999,15 +999,7 @@ def store(self, obj, *, createOrUpdate=True, forceVersion=True, versionLabel=Non
         # _synapse_store hook
         # for objects that know how to store themselves
         if hasattr(obj, '_synapse_store'):
-            obj = obj._synapse_store(self)
-            return self._apply_provenance(
-                obj,
-                activity=activity,
-                used=used,
-                executed=executed,
-                activityName=activityName,
-                activityDescription=activityDescription,
-            )
+            return obj._synapse_store(self)
 
         # Handle all non-Entity objects
         if not (isinstance(obj, Entity) or type(obj) == dict):
@@ -1163,30 +1155,6 @@ def store(self, obj, *, createOrUpdate=True, forceVersion=True, versionLabel=Non
             annotations = self.set_annotations(Annotations(properties['id'], properties['etag'], annotations))
             properties['etag'] = annotations.etag
 
-        properties = self._apply_provenance(
-            properties,
-            activity=activity,
-            used=used,
-            executed=executed,
-            activityName=activityName,
-            activityDescription=activityDescription,
-        )
-
-        # Return the updated Entity object
-        entity = Entity.create(properties, annotations, local_state)
-        return self.get(entity, downloadFile=False)
-
-    def _apply_provenance(
-        self,
-        entity,
-        activity=None,
-        used=None,
-        executed=None,
-        activityName=None,
-        activityDescription=None
-    ):
-        # apply any provenance passed to via the store method to the entity
-
         # If the parameters 'used' or 'executed' are given, create an Activity object
         if used or executed:
             if activity is not None:
@@ -1198,12 +1166,14 @@ def _apply_provenance(
 
         # If we have an Activity, set it as the Entity's provenance record
         if activity:
-            self.setProvenance(entity, activity)
+            self.setProvenance(properties, activity)
 
             # 'etag' has changed, so get the new Entity
-            entity = self._getEntity(entity)
+            properties = self._getEntity(properties)
 
-        return entity
+        # Return the updated Entity object
+        entity = Entity.create(properties, annotations, local_state)
+        return self.get(entity, downloadFile=False)
 
     def _createAccessRequirementIfNone(self, entity):
         """

tests/unit/synapseclient/unit_test_client.py

@@ -36,7 +36,6 @@
     SynapseFileNotFoundError,
     SynapseHTTPError,
     SynapseMd5MismatchError,
-    SynapseProvenanceError,
     SynapseUnmetAccessRestrictions,
 )
 from synapseclient.core.logging_setup import DEFAULT_LOGGER_NAME, DEBUG_LOGGER_NAME, SILENT_LOGGER_NAME
@@ -2445,82 +2444,6 @@ def test_store__existing_no_update(syn):
         assert not mock_updatentity.called
 
 
-def test_store_self_stored_obj__provenance_applied(syn):
-    """Verify that any object with its own _synapse_store mechanism (e.g. a table) will have
-    any passed provenance applied"""
-
-    obj = Mock()
-    del obj._before_synapse_store
-    obj._synapse_store = lambda x: x
-
-    activity_kwargs = {
-        'activity': MagicMock(spec=synapseclient.Activity),
-        'activityName': 'test name',
-        'activityDescription': 'test description',
-        'used': ['syn123'],
-        'executed': ['syn456'],
-    }
-
-    with patch.object(syn, '_apply_provenance') as mock_apply_provenance:
-        stored = syn.store(obj, **activity_kwargs)
-        assert mock_apply_provenance.called_once_with(obj, **activity_kwargs)
-        assert stored == mock_apply_provenance.return_value
-
-
-def test_apply_provenance__duplicate_args(syn):
-    """Verify that a SynapseProvenanceError is raised if both used/executed and an Activity is passed"""
-    with pytest.raises(SynapseProvenanceError):
-        syn._apply_provenance(
-            Mock(),
-            activity=MagicMock(spec=synapseclient.Activity),
-            used=['syn123'],
-            executed=['syn456'],
-            activityName='test name',
-            activityDescription='test description',
-        )
-
-
-def test_apply_provenance__activity(syn):
-    """Verify _apply_provenance behavior when an Activity is passed"""
-
-    obj = Mock()
-    activity = synapseclient.Activity(used=['syn123'])
-    with patch.object(syn, 'setProvenance') as mock_set_provenance, \
-            patch.object(syn, '_getEntity') as mock_get_entity:
-        result = syn._apply_provenance(obj, activity=activity)
-
-        mock_set_provenance.assert_called_once_with(obj, activity)
-        mock_get_entity.assert_called_once_with(obj)
-        assert result is mock_get_entity.return_value
-
-
-def test_apply_provenance__used_executed(syn):
-    """Verify _apply_provenance behavior with used and executed args"""
-
-    obj = Mock()
-
-    used = ['syn123']
-    executed = ['syn456']
-    name = 'test name'
-    description = 'test description'
-
-    expected_activity = synapseclient.Activity(used=used, executed=executed, name=name, description=description)
-
-    with patch.object(syn, 'setProvenance') as mock_set_provenance, \
-            patch.object(syn, '_getEntity') as mock_get_entity:
-        result = syn._apply_provenance(
-            obj,
-            used=used,
-            executed=executed,
-            activityName=name,
-            activityDescription=description
-        )
-
-        mock_set_provenance.assert_called_once_with(obj, expected_activity)
-        mock_get_entity.assert_called_once_with(obj)
-        assert result is mock_get_entity.return_value
-
-
 def test_get_submission_with_annotations(syn):
     """Verify a getSubmission with annotation entityBundleJSON that
     uses the old style annotations is converted to bundle v2 style