Fixes #11: adding a delete endpoint for studies. It won't delete studies that have workflows, you have to delete those first)

Removing the "default" error response from the api.yml, it was all noise.

crc/api.yml

@@ -90,12 +90,6 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/Study"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
     post:
       operationId: crc.api.study.add_study
       summary: Creates a new study with the given parameters.
@@ -113,12 +107,6 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/Study"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
   /study/{study_id}:
     parameters:
       - name: study_id
@@ -140,12 +128,14 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/Study"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
+    delete:
+      operationId: crc.api.study.delete_study
+      summary: Removes the given study completely.
+      tags:
+        - Studies
+      responses:
+        '204':
+          description: The study has been removed.
     put:
       operationId: crc.api.study.update_study
       summary: Updates an existing study with the given parameters.
@@ -163,12 +153,6 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/Study"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
   /study-update/{study_id}:
     post:
       operationId: crc.api.study.post_update_study_from_protocol_builder
@@ -188,12 +172,6 @@ paths:
           description: Study is currently up to date and does not need to be reloaded from Protocol Builder
         '202':
           description: Request accepted, will preform an update. Study state set to "updating"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
   /study/{study_id}/workflows:
     get:
       operationId: crc.api.study.get_study_workflows
@@ -217,12 +195,6 @@ paths:
                 type: array
                 items:
                   $ref: "#/components/schemas/Workflow"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
     post:
       operationId: crc.api.study.add_workflow_to_study
       summary: Starts a new workflow for the given study using the provided spec.  This is atypical, and should be left to the protocol builder.
@@ -250,12 +222,6 @@ paths:
                 type: array
                 items:
                   $ref: "#/components/schemas/Workflow"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
   /workflow-specification:
     get:
       operationId: crc.api.workflow.all_specifications
@@ -271,12 +237,6 @@ paths:
                 type: array
                 items:
                   $ref: "#/components/schemas/WorkflowSpec"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
     post:
       operationId: crc.api.workflow.add_workflow_specification
       summary: Creates a new workflow specification with the given parameters.
@@ -294,12 +254,6 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/WorkflowSpec"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
   /workflow-specification/{spec_id}:
     parameters:
       - name: spec_id
@@ -337,12 +291,6 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/WorkflowSpec"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
     delete:
       operationId: crc.api.workflow.delete_workflow_specification
       summary: Removes an existing workflow specification
@@ -397,12 +345,7 @@ paths:
                 type: array
                 items:
                   $ref: "#/components/schemas/File"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
+
     post:
       operationId: crc.api.file.add_file
       summary: Add a new file
@@ -461,12 +404,6 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/File"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
     delete:
       operationId: crc.api.file.delete_file
       summary: Removes an existing file
@@ -555,12 +492,6 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/Workflow"
-        default:
-          description: unexpected error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/Error"
     delete:
       operationId: crc.api.workflow.delete
       summary: Removes an existing workflow

crc/api/study.py

@@ -1,9 +1,11 @@
+import logging
 from typing import List, Optional, Union, Tuple, Dict
 
 from connexion import NoContent
 from flask import g
+from sqlalchemy.exc import IntegrityError
 
-from crc import session, auth
+from crc import session, auth, app
 from crc.api.common import ApiError, ApiErrorSchema
 from crc.api.workflow import __get_workflow_api_model
 from crc.models.api_models import WorkflowApiSchema
@@ -31,6 +33,7 @@ def add_study(body):
     return StudyModelSchema().dump(study)
 
 
+
 @auth.login_required
 def update_study(study_id, body):
     if study_id is None:
@@ -59,6 +62,16 @@ def get_study(study_id):
     return schema.dump(study)
 
 
+def delete_study(study_id):
+    try:
+        session.query(StudyModel).filter_by(id=study_id).delete()
+    except IntegrityError as ie:
+        session.rollback()
+        app.logger.error("Failed to delete Study #%i due to an Integrity Error: %s" % (study_id, str(ie)))
+        raise ApiError(code="study_integrity_error", message="This study contains running workflows that is "
+                                                             "preventing deletion.  Please delete the workflows " +
+                                                             "before proceeding.")
+
 @auth.login_required
 def update_from_protocol_builder():
     """Updates the list of known studies for a given user based on data received from

tests/base_test.py

@@ -113,11 +113,14 @@ class BaseTest(unittest.TestCase):
             self.assertTrue(200 <= rv.status_code < 300,
                             "BAD Response: %i." % rv.status_code + ". " + msg)
 
-    def assert_failure(self, rv, code=0):
+    def assert_failure(self, rv, status_code=0, error_code=""):
         self.assertFalse(200 <= rv.status_code < 300,
                          "Incorrect Valid Response:" + rv.status + ".")
-        if code != 0:
-            self.assertEqual(code, rv.status_code)
+        if status_code != 0:
+            self.assertEqual(status_code, rv.status_code)
+        if error_code != "":
+            data = json.loads(rv.get_data(as_text=True))
+            self.assertEqual(error_code, data["code"])
 
     @staticmethod
     def user_info_to_query_string(user_info, redirect_url):

tests/test_study_api.py

@@ -141,6 +141,28 @@ class TestStudyApi(BaseTest):
         workflow2 = WorkflowApiSchema().load(json_data)
         self.assertEqual(workflow_model.id, workflow2.id)
 
+    def test_delete_study(self):
+        self.load_example_data()
+        study = session.query(StudyModel).first()
+        rv = self.app.delete('/v1.0/study/%i' % study.id)
+        self.assert_success(rv)
+
+    def test_delete_study_with_workflow(self):
+        self.load_example_data()
+        study = session.query(StudyModel).first()
+
+        spec = session.query(WorkflowSpecModel).first()
+        rv = self.app.post('/v1.0/study/%i/workflows' % study.id,
+                           content_type="application/json",
+                           headers=self.logged_in_headers(),
+                           data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
+
+        rv = self.app.delete('/v1.0/study/%i' % study.id)
+        self.assert_failure(rv, error_code="study_integrity_error")
+
+
+
+
     def test_delete_workflow(self):
         self.load_example_data()
         study = session.query(StudyModel).first()