Merge pull request #5 from sartography/feature/create-study-endpoint

Adds endpoints for creating and updating a Study.

Pipfile.lock

@@ -544,10 +544,10 @@
         },
         "waitress": {
             "hashes": [
-                "sha256:3776cbb9abebefb51e5b654f8728928aa17b656d9f6943c58ce8f48e87cef4e3",
+                "sha256:67a60a376f0eb335ed88967c42b73983a58d66a2a72eb9009a42725f7453b142",
-                "sha256:f4118cbce75985fd60aeb4f0d781aba8dc7ae28c18e50753e913d7a7dee76b62"
+                "sha256:cbf1c62fc41393a6f27cb78483f8f6e252630a3598984668244b7bf4e35856f1"
             ],
-            "version": "==1.4.1"
+            "version": "==1.4.2"
         },
         "webob": {
             "hashes": [
@@ -626,10 +626,10 @@
         },
         "py": {
             "hashes": [
-                "sha256:64f65755aee5b381cea27766a3a147c3f15b9b6b9ac88676de66ba2ae36793fa",
+                "sha256:5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa",
-                "sha256:dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53"
+                "sha256:c20fdd83a5dbc0af9efd622bee9a5564e278f6380fffcacc43ba6f43db2813b0"
             ],
-            "version": "==1.8.0"
+            "version": "==1.8.1"
         },
         "pyparsing": {
             "hashes": [
@@ -655,10 +655,9 @@
         },
         "wcwidth": {
             "hashes": [
-                "sha256:3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e",
+                "sha256:8fd29383f539be45b20bd4df0dc29c20ba48654a41e661925e612311e9f3c603"
-                "sha256:f4ebe71925af7b40a864553f761ed559b43544f8f71746c2d756c7fe788ade7c"
             ],
-            "version": "==0.1.7"
+            "version": "==0.1.8"
         },
         "zipp": {
             "hashes": [

crc/api.yml

@@ -27,6 +27,29 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/Error"
+    post:
+      operationId: crc.api.study.add_study
+      summary: Creates a new study with the given parameters.
+      tags:
+        - Studies
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/Study'
+      responses:
+        '200':
+          description: Study created successfully.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Study"
+        default:
+          description: unexpected error
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Error"
   /study/{study_id}:
     get:
       operationId: crc.api.study.get_study
@@ -54,6 +77,37 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/Error"
+    post:
+      operationId: crc.api.study.update_study
+      summary: Updates an existing study with the given parameters.
+      tags:
+        - Studies
+      parameters:
+        - name: study_id
+          in: path
+          required: true
+          description: The id of the study for which workflows should be returned.
+          schema:
+            type: integer
+            format: int32
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/Study'
+      responses:
+        '200':
+          description: Study updated successfully.
+          content:
+            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

crc/api/file.py

@@ -7,7 +7,7 @@ from flask import send_file
 
 from crc import db
 from crc.api.common import ApiErrorSchema, ApiError
-from crc.models.file import FileSchema, FileModel, FileDataModel, FileType
+from crc.models.file import FileModelSchema, FileModel, FileDataModel, FileType
 
 
 def update_file_from_request(file_model):
@@ -44,7 +44,7 @@ def update_file_from_request(file_model):
 
 def get_files(spec_id):
     if spec_id:
-        schema = FileSchema(many=True)
+        schema = FileModelSchema(many=True)
         return schema.dump(db.session.query(FileModel).filter_by(workflow_spec_id=spec_id).all())
     else:
         error = ApiError('no_files_found', 'Please provide some parameters so we can find the files you need.')
@@ -57,7 +57,7 @@ def add_file():
                                             'Please specify a workflow_spec_id for this file in the form')), 404
     file_model = FileModel(version=0, workflow_spec_id=connexion.request.form['workflow_spec_id'])
     update_file_from_request(file_model)
-    return FileSchema().dump(file_model)
+    return FileModelSchema().dump(file_model)
 
 
 def update_file(file_id):
@@ -65,7 +65,7 @@ def update_file(file_id):
     if file_model is None:
         return ApiErrorSchema().dump(ApiError('no_such_file', 'The file id you provided does not exist')), 404
     update_file_from_request(file_model)
-    return FileSchema().dump(file_model)
+    return FileModelSchema().dump(file_model)
 
 
 def get_file(file_id):
@@ -84,7 +84,7 @@ def get_file_info(file_id):
     file_model = db.session.query(FileModel).filter_by(id=file_id).with_for_update().first()
     if file_model is None:
         return ApiErrorSchema().dump(ApiError('no_such_file', 'The file id you provided does not exist')), 404
-    return FileSchema().dump(file_model)
+    return FileModelSchema().dump(file_model)
 
 
 def delete_file(file_id):

crc/api/study.py

@@ -2,20 +2,44 @@ from connexion import NoContent
 
 from crc import db
 from crc.api.common import ApiError, ApiErrorSchema
-from crc.models.study import StudySchema, StudyModel
+from crc.models.study import StudyModelSchema, StudyModel
-from crc.models.workflow import WorkflowModel, WorkflowSchema, WorkflowSpecModel
+from crc.models.workflow import WorkflowModel, WorkflowModelSchema, WorkflowSpecModel
 from crc.workflow_processor import WorkflowProcessor
 
 
 def all_studies():
     # todo: Limit returned studies to a user
-    schema = StudySchema(many=True)
+    schema = StudyModelSchema(many=True)
     return schema.dump(db.session.query(StudyModel).all())
 
 
+def add_study(body):
+    study = StudyModelSchema().load(body, session=db.session)
+    db.session.add(study)
+    db.session.commit()
+    return StudyModelSchema().dump(study)
+
+
+def update_study(study_id, body):
+    if study_id is None:
+        error = ApiError('unknown_study', 'Please provide a valid Study ID.')
+        return ApiErrorSchema.dump(error), 404
+
+    study = db.session.query(StudyModel).filter_by(id=study_id).first()
+
+    if study is None:
+        error = ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
+        return ApiErrorSchema.dump(error), 404
+
+    study = StudyModelSchema().load(body, session=db.session)
+    db.session.add(study)
+    db.session.commit()
+    return StudyModelSchema().dump(study)
+
+
 def get_study(study_id):
     study = db.session.query(StudyModel).filter_by(id=study_id).first()
-    schema = StudySchema()
+    schema = StudyModelSchema()
     if study is None:
         return NoContent, 404
     return schema.dump(study)
@@ -28,7 +52,7 @@ def post_update_study_from_protocol_builder(study_id):
 
 def get_study_workflows(study_id):
     workflows = db.session.query(WorkflowModel).filter_by(study_id=study_id).all()
-    schema = WorkflowSchema(many=True)
+    schema = WorkflowModelSchema(many=True)
     return schema.dump(workflows)
 
 
@@ -45,4 +69,4 @@ def add_workflow_to_study(study_id, body):
                              workflow_spec_id=workflow_spec_model.id)
     db.session.add(workflow)
     db.session.commit()
-    return WorkflowSchema().dump(workflow)
+    return WorkflowModelSchema().dump(workflow)

crc/api/workflow.py

@@ -1,16 +1,16 @@
 from crc import db
-from crc.models.workflow import WorkflowModel, WorkflowSchema, WorkflowSpecSchema, WorkflowSpecModel, \
+from crc.models.workflow import WorkflowModel, WorkflowModelSchema, WorkflowSpecModelSchema, WorkflowSpecModel, \
     Task, TaskSchema
 from crc.workflow_processor import WorkflowProcessor
 
 
 def all_specifications():
-    schema = WorkflowSpecSchema(many=True)
+    schema = WorkflowSpecModelSchema(many=True)
     return schema.dump(db.session.query(WorkflowSpecModel).all())
 
 
 def get_workflow(workflow_id):
-    schema = WorkflowSchema()
+    schema = WorkflowModelSchema()
     workflow = db.session.query(WorkflowModel).filter_by(id=workflow_id).first()
     return schema.dump(workflow)
 

crc/models/file.py

@@ -1,7 +1,7 @@
 import enum
 
-from flask_marshmallow.sqla import ModelSchema
 from marshmallow_enum import EnumField
+from marshmallow_sqlalchemy import ModelSchema
 from sqlalchemy import func
 
 from crc import db
@@ -20,6 +20,7 @@ class FileDataModel(db.Model):
     file_model_id = db.Column(db.Integer, db.ForeignKey('file.id'))
     file_model = db.relationship("FileModel")
 
+
 class FileModel(db.Model):
     __tablename__ = 'file'
     id = db.Column(db.Integer, primary_key=True)
@@ -32,7 +33,7 @@ class FileModel(db.Model):
     workflow_spec_id = db.Column(db.Integer, db.ForeignKey('workflow_spec.id'))
 
 
-class FileSchema(ModelSchema):
+class FileModelSchema(ModelSchema):
     class Meta:
         model = FileModel
     type = EnumField(FileType)

crc/models/study.py

@@ -25,7 +25,7 @@ class StudyModel(db.Model):
     ind_number = db.Column(db.String)
 
 
-class StudySchema(ModelSchema):
+class StudyModelSchema(ModelSchema):
     class Meta:
         model = StudyModel
 

crc/models/workflow.py

@@ -14,10 +14,11 @@ class WorkflowSpecModel(db.Model):
     description = db.Column(db.Text)
 
 
-class WorkflowSpecSchema(ModelSchema):
+class WorkflowSpecModelSchema(ModelSchema):
     class Meta:
         model = WorkflowSpecModel
 
+
 class WorkflowStatus(enum.Enum):
     new = "new"
     user_input_required = "user_input_required"
@@ -34,7 +35,7 @@ class WorkflowModel(db.Model):
     workflow_spec_id = db.Column(db.Integer, db.ForeignKey('workflow_spec.id'))
 
 
-class WorkflowSchema(ModelSchema):
+class WorkflowModelSchema(ModelSchema):
     class Meta:
         model = WorkflowModel
 
@@ -100,6 +101,7 @@ class FormSchema(ma.Schema):
 class TaskSchema(ma.Schema):
     class Meta:
         fields = ["id", "name", "title", "type", "state", "form", "documentation"]
+
     documentation = marshmallow.fields.String(required=False, allow_none=True)
     form = marshmallow.fields.Nested(FormSchema)
 

tests/test_api.py

@@ -1,10 +1,11 @@
+from datetime import datetime
 import json
 import unittest
 
 from crc import db
-from crc.models.study import StudyModel, StudySchema
+from crc.models.study import StudyModel, StudyModelSchema, ProtocolBuilderStatus
-from crc.models.workflow import WorkflowSpecModel, WorkflowSpecSchema, WorkflowModel, WorkflowStatus, \
+from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
-    WorkflowSchema, TaskSchema
+    WorkflowModelSchema, TaskSchema
 from tests.base_test import BaseTest
 
 
@@ -15,6 +16,45 @@ class TestStudy(BaseTest, unittest.TestCase):
         study = db.session.query(StudyModel).first()
         self.assertIsNotNone(study)
 
+    def test_add_study(self):
+        study = {
+            "id": 12345,
+            "title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents for Interstellar Spacecraft",
+            "last_updated": datetime.now(),
+            "protocol_builder_status": ProtocolBuilderStatus.in_process,
+            "primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
+            "sponsor": "Sirius Cybernetics Corporation",
+            "ind_number": "567890",
+        }
+        rv = self.app.post('/v1.0/study',
+                           content_type="application/json",
+                           data=json.dumps(StudyModelSchema().dump(study)))
+        self.assert_success(rv)
+        db_study = db.session.query(StudyModel).first()
+        self.assertIsNotNone(db_study)
+        self.assertEqual(study["id"], db_study.id)
+        self.assertEqual(study["title"], db_study.title)
+        self.assertEqual(study["last_updated"], db_study.last_updated)
+        self.assertEqual(study["protocol_builder_status"], db_study.protocol_builder_status)
+        self.assertEqual(study["primary_investigator_id"], db_study.primary_investigator_id)
+        self.assertEqual(study["sponsor"], db_study.sponsor)
+        self.assertEqual(study["ind_number"], db_study.ind_number)
+
+    def test_update_study(self):
+        self.load_example_data()
+        study: StudyModel = db.session.query(StudyModel).first()
+        study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility"
+        study.protocol_builder_status = ProtocolBuilderStatus.complete
+
+        rv = self.app.post('/v1.0/study',
+                           content_type="application/json",
+                           data=json.dumps(StudyModelSchema().dump(study)))
+        self.assert_success(rv)
+        db_study = db.session.query(StudyModel).first()
+        self.assertIsNotNone(db_study)
+        self.assertEqual(study.title, db_study.title)
+        self.assertEqual(study.protocol_builder_status, db_study.protocol_builder_status)
+
     def test_study_api_get_single_study(self):
         self.load_example_data()
         study = db.session.query(StudyModel).first()
@@ -23,7 +63,7 @@ class TestStudy(BaseTest, unittest.TestCase):
                           content_type="application/json")
         self.assert_success(rv)
         json_data = json.loads(rv.get_data(as_text=True))
-        study2 = StudySchema().load(json_data, session=db.session)
+        study2 = StudyModelSchema().load(json_data, session=db.session)
         self.assertEqual(study, study2)
         self.assertEqual(study.id, study2.id)
         self.assertEqual(study.title, study2.title)
@@ -41,7 +81,7 @@ class TestStudy(BaseTest, unittest.TestCase):
                           content_type="application/json")
         self.assert_success(rv)
         json_data = json.loads(rv.get_data(as_text=True))
-        specs = WorkflowSpecSchema(many=True).load(json_data, session=db.session)
+        specs = WorkflowSpecModelSchema(many=True).load(json_data, session=db.session)
         spec2 = specs[0]
         self.assertEqual(spec.id, spec2.id)
         self.assertEqual(spec.display_name, spec2.display_name)
@@ -52,8 +92,8 @@ class TestStudy(BaseTest, unittest.TestCase):
         study = db.session.query(StudyModel).first()
         self.assertEqual(0, db.session.query(WorkflowModel).count())
         spec = db.session.query(WorkflowSpecModel).first()
-        rv = self.app.post('/v1.0/study/%i/workflows' % study.id,content_type="application/json",
+        rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
-                           data=json.dumps(WorkflowSpecSchema().dump(spec)))
+                           data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
         self.assert_success(rv)
         self.assertEqual(1, db.session.query(WorkflowModel).count())
         workflow = db.session.query(WorkflowModel).first()
@@ -63,7 +103,7 @@ class TestStudy(BaseTest, unittest.TestCase):
         self.assertEqual(spec.id, workflow.workflow_spec_id)
 
         json_data = json.loads(rv.get_data(as_text=True))
-        workflow = WorkflowSchema().load(json_data, session=db.session)
+        workflow = WorkflowModelSchema().load(json_data, session=db.session)
         self.assertEqual(workflow.id, workflow.id)
 
     def test_delete_workflow(self):
@@ -71,10 +111,10 @@ class TestStudy(BaseTest, unittest.TestCase):
         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)))
+                           data=json.dumps(WorkflowSpecModelSchema().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)
+        workflow = WorkflowModelSchema().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())
@@ -84,7 +124,7 @@ class TestStudy(BaseTest, unittest.TestCase):
         study = db.session.query(StudyModel).first()
         spec = db.session.query(WorkflowSpecModel).filter_by(id='random_fact').first()
         self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
-                      data=json.dumps(WorkflowSpecSchema().dump(spec)))
+                      data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
         rv = self.app.get('/v1.0/workflow/%i/tasks' % study.id, content_type="application/json")
         self.assert_success(rv)
         json_data = json.loads(rv.get_data(as_text=True))
@@ -97,9 +137,9 @@ class TestStudy(BaseTest, unittest.TestCase):
         study = db.session.query(StudyModel).first()
         spec = db.session.query(WorkflowSpecModel).filter_by(id='two_forms').first()
         rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
-                      data=json.dumps(WorkflowSpecSchema().dump(spec)))
+                           data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
         json_data = json.loads(rv.get_data(as_text=True))
-        workflow = WorkflowSchema().load(json_data, session=db.session)
+        workflow = WorkflowModelSchema().load(json_data, session=db.session)
 
         rv = self.app.get('/v1.0/workflow/%i/tasks' % workflow.id, content_type="application/json")
         json_data = json.loads(rv.get_data(as_text=True))

tests/test_api_files.py

@@ -5,7 +5,7 @@ from datetime import datetime
 
 from crc import db
 from crc.models.workflow import WorkflowSpecModel
-from crc.models.file import FileModel, FileType, FileSchema, FileDataModel
+from crc.models.file import FileModel, FileType, FileModelSchema, FileDataModel
 from tests.base_test import BaseTest
 
 
@@ -20,7 +20,7 @@ class TestApiFiles(BaseTest, unittest.TestCase):
         self.assert_success(rv)
         json_data = json.loads(rv.get_data(as_text=True))
         self.assertEqual(1, len(json_data))
-        file = FileSchema(many=True).load(json_data, session=db.session)
+        file = FileModelSchema(many=True).load(json_data, session=db.session)
         self.assertEqual("random_fact.bpmn", file[0].name)
 
     def test_list_multiple_files_for_workflow_spec(self):
@@ -50,7 +50,7 @@ class TestApiFiles(BaseTest, unittest.TestCase):
         self.assert_success(rv)
         self.assertIsNotNone(rv.get_data())
         json_data = json.loads(rv.get_data(as_text=True))
-        file = FileSchema().load(json_data, session=db.session)
+        file = FileModelSchema().load(json_data, session=db.session)
         self.assertEqual(1, file.version)
         self.assertEqual(FileType.svg, file.type)
         self.assertFalse(file.primary)
@@ -60,7 +60,7 @@ class TestApiFiles(BaseTest, unittest.TestCase):
         rv = self.app.get('/v1.0/file/%i' % file.id)
         self.assert_success(rv)
         json_data = json.loads(rv.get_data(as_text=True))
-        file2 = FileSchema().load(json_data, session=db.session)
+        file2 = FileModelSchema().load(json_data, session=db.session)
         self.assertEqual(file, file2)
 
     def test_update_file(self):
@@ -77,7 +77,7 @@ class TestApiFiles(BaseTest, unittest.TestCase):
         self.assert_success(rv)
         self.assertIsNotNone(rv.get_data())
         json_data = json.loads(rv.get_data(as_text=True))
-        file = FileSchema().load(json_data, session=db.session)
+        file = FileModelSchema().load(json_data, session=db.session)
         self.assertEqual(2, file.version)
         self.assertEqual(FileType.bpmn, file.type)
         self.assertTrue(file.primary)