Merge remote-tracking branch 'origin/master'

crc/__init__.py

@@ -33,4 +33,5 @@ cors = CORS(connexion_app.app)
 def load_example_data():
     """Load example data into the database."""
     from example_data import ExampleDataLoader
+    ExampleDataLoader.clean_db()
     ExampleDataLoader().load_all()

crc/api.yml

@@ -290,12 +290,7 @@ paths:
                 example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
   # /v1.0/workflow/0
   /workflow/{workflow_id}:
-    get:
-      operationId: crc.api.workflow.get_workflow
-      summary: Detailed information for a specific workflow instance
-      tags:
-        - Workflows and Tasks
-      parameters:
+    parameters:
         - name: workflow_id
           in: path
           required: true
@@ -303,6 +298,11 @@ paths:
           schema:
             type: integer
             format: int32
+    get:
+      operationId: crc.api.workflow.get_workflow
+      summary: Detailed information for a specific workflow instance
+      tags:
+        - Workflows and Tasks
       responses:
         '200':
           description: Returns details about the workflows state and current task
@@ -316,6 +316,14 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/Error"
+    delete:
+      operationId: crc.api.workflow.delete
+      summary: Removes an existing workflow
+      tags:
+        - Workflows and Tasks
+      responses:
+        '204':
+          description: The workflow was removed
   /workflow/{workflow_id}/tasks:
     get:
       operationId: crc.api.workflow.get_tasks

crc/api/study.py

@@ -50,4 +50,4 @@ def add_workflow_to_study(study_id, body):
                              workflow_spec_id=workflow_spec_model.id)
     db.session.add(workflow)
     db.session.commit()
-    return get_study_workflows(study_id)
+    return WorkflowSchema().dump(workflow)

crc/api/workflow.py

@@ -14,6 +14,8 @@ def get_workflow(workflow_id):
     workflow = db.session.query(WorkflowModel).filter_by(id=workflow_id).first()
     return schema.dump(workflow)
 
+def delete(workflow_id):
+    db.session.query(WorkflowModel).filter_by(id=workflow_id).delete()
 
 def get_tasks(workflow_id):
     workflow = db.session.query(WorkflowModel).filter_by(id=workflow_id).first()

example_data.py

@@ -50,6 +50,13 @@ class ExampleDataLoader:
     file = open(filename, "rb")
     workflow_data = [FileDataModel(data=file.read(), file_model=workflow_spec_files[0])]
 
+    @staticmethod
+    def clean_db():
+        db.session.flush()  # Clear out any transactions before deleting it all to avoid spurious errors.
+        for table in reversed(db.metadata.sorted_tables):
+            db.session.execute(table.delete())
+        db.session.flush()
+
     def load_all(self):
         db.session.bulk_save_objects(ExampleDataLoader.studies)
         db.session.bulk_save_objects(ExampleDataLoader.workflow_specs)

tests/base_test.py

@@ -5,7 +5,7 @@ import os
 os.environ["TESTING"] = "true"
 
 from crc import app, db
-
+from example_data import ExampleDataLoader
 
 # UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
 # import logging
@@ -13,11 +13,7 @@ from crc import app, db
 # logging.getLogger('sqlalchemy.engine').setLevel(logging.INFO)
 
 
-def clean_db():
-    db.session.flush() # Clear out any transactions before deleting it all to avoid spurious errors.
-    for table in reversed(db.metadata.sorted_tables):
-        db.session.execute(table.delete())
-    db.session.flush()
+
 
 
 # Great class to inherit from, as it sets up and tears down
@@ -43,13 +39,13 @@ class BaseTest:
         self.ctx.push()
 
     def tearDown(self):
-        clean_db()  # This does not seem to work, some colision of sessions.
+        ExampleDataLoader.clean_db()  # This does not seem to work, some colision of sessions.
         self.ctx.pop()
         self.auths = {}
 
     def load_example_data(self):
-        clean_db()
         from example_data import ExampleDataLoader
+        ExampleDataLoader.clean_db()
         ExampleDataLoader().load_all()
 
     def assert_success(self, rv, msg=""):

tests/test_api.py

@@ -68,6 +68,20 @@ class TestStudy(BaseTest, unittest.TestCase):
         workflows = WorkflowSchema(many=True).load(json_data, session=db.session)
         self.assertEqual(workflows[0].id, workflow.id)
 
+    def test_delete_workflow(self):
+        self.load_example_data()
+        study = db.session.query(StudyModel).first()
+        spec = db.session.query(WorkflowSpecModel).first()
+        rv = self.app.post('/v1.0/study/%i/workflows' % study.id,content_type="application/json",
+                           data=json.dumps(WorkflowSpecSchema().dump(spec)))
+        self.assertEqual(1, db.session.query(WorkflowModel).count())
+        json_data = json.loads(rv.get_data(as_text=True))
+        workflow = WorkflowSchema().load(json_data, session=db.session)
+        rv = self.app.delete('/v1.0/workflow/%i' % workflow.id)
+        self.assert_success(rv)
+        self.assertEqual(0, db.session.query(WorkflowModel).count())
+
+
     def test_get_current_user_tasks(self):
         self.load_example_data()
         study = db.session.query(StudyModel).first()