Merge pull request #370 from sartography/library-listing-453

Library listing #453

crc/api/workflow.py

@@ -31,11 +31,14 @@ def all_specifications(libraries=False,standalone=False):
     if standalone:
         return schema.dump(session.query(WorkflowSpecModel)\
               .filter(WorkflowSpecModel.standalone==True).all())
-    # this still returns standalone workflow specs as well, but by default
-    # we do not return specs marked as library
-    return schema.dump(session.query(WorkflowSpecModel)\
-              .filter((WorkflowSpecModel.library==False)|(
-              WorkflowSpecModel.library==None)).all())
+
+    # return standard workflows (not library, not standalone)
+    return schema.dump(session.query(WorkflowSpecModel)
+                       .filter((WorkflowSpecModel.library==False) | (
+                                WorkflowSpecModel.library==None))
+                       .filter((WorkflowSpecModel.standalone==False) | (
+                                WorkflowSpecModel.standalone==None))
+                       .all())
 
 
 def add_workflow_specification(body):
@@ -43,6 +46,9 @@ def add_workflow_specification(body):
     WorkflowService.cleanup_workflow_spec_display_order(category_id)
     count = session.query(WorkflowSpecModel).filter_by(category_id=category_id).count()
     body['display_order'] = count
+    # Libraries and standalone workflows don't get a category_id
+    if body['library'] is True or body['standalone'] is True:
+        body['category_id'] = None
     new_spec: WorkflowSpecModel = WorkflowSpecModelSchema().load(body, session=session)
     session.add(new_spec)
     session.commit()
@@ -119,6 +125,10 @@ def update_workflow_specification(spec_id, body):
     # There is a separate endpoint for this
     body['display_order'] = spec.display_order
 
+    # Libraries and standalone workflows don't get a category_id
+    if body['library'] is True or body['standalone'] is True:
+        body['category_id'] = None
+
     schema = WorkflowSpecModelSchema()
     spec = schema.load(body, session=session, instance=spec, partial=True)
     session.add(spec)

tests/workflow/test_workflow_spec_api.py

@@ -221,3 +221,18 @@ class TestWorkflowSpec(BaseTest):
         for test_category in categories:
             self.assertEqual(test_order, test_category.display_order)
             test_order += 1
+
+    def test_add_library_with_category_id(self):
+        self.load_example_data()
+        category_id = session.query(WorkflowSpecCategoryModel).first().id
+        spec = WorkflowSpecModel(id='test_spec', name='test_spec', display_name='Test Spec',
+                                 description='Library with a category id', category_id=category_id,
+                                 standalone=False, library=True)
+        rv = self.app.post('/v1.0/workflow-specification',
+                           headers=self.logged_in_headers(),
+                           content_type="application/json",
+                           data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
+        self.assert_success(rv)
+        # libraries don't get category_ids
+        # so, the category_id should not get set
+        self.assertIsNone(rv.json['category_id'])