Just some quick tidying up. Dropping commented out code, and using the SQLAlchemyAutoSchema to handle serializing db models
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Dan
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40ee20ecca
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047c68b2b5
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@ -7,32 +7,6 @@ from crc.models.data_store import DataStoreModel, DataStoreSchema
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from crc.scripts.data_store_base import DataStoreBase
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# def study_data_set(study_id, key, value):
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# """Set a study data value in the data_store, mimic the script endpoint"""
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# if study_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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# retval = dsb.set_data_common('api', study_id, None, None, None, 'api_study_data_set', key, value)
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# json_value = json.dumps(retval, ensure_ascii=False, indent=2)
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# return json_value
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# def study_data_get(study_id, key, default=None):
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# """Get a study data value in the data_store, mimic the script endpoint"""
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# if study_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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# retval = dsb.get_data_common(study_id, None, 'api_study_data_get', key, default)
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# # json_value = json.dumps(retval, ensure_ascii=False, indent=2) # just return raw text
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# return retval
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def study_multi_get(study_id):
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"""Get all data_store values for a given study_id study"""
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if study_id is None:
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@ -44,57 +18,6 @@ def study_multi_get(study_id):
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return results
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# def study_data_del(study_id, key):
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# """Delete a study data value in the data store"""
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# if study_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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# dsb.del_data_common(study_id, None, 'api_study_data_get', key)
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# json_value = json.dumps('deleted', ensure_ascii=False, indent=2)
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# return json_value
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# def user_data_set(user_id, key, value):
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# """Set a user data value in the data_store, mimic the script endpoint"""
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# if user_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid UserID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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#
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# retval = dsb.set_data_common('api',
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# None,
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# user_id,
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# None,
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# None,
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# 'api_user_data_set',
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# key, value)
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#
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# json_value = json.dumps(retval, ensure_ascii=False, indent=2)
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# return json_value
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# def user_data_get(user_id, key, default=None):
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# """Get a user data value from the data_store, mimic the script endpoint"""
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# if user_id is None:
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# raise ApiError('unknown_study', 'Please provide a valid UserID.')
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#
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# if key is None:
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# raise ApiError('invalid_key', 'Please provide a valid key')
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# dsb = DataStoreBase()
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# retval = dsb.get_data_common(None,
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# user_id,
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# 'api_user_data_get',
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# key, default)
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#
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# # json_value = json.dumps(retval, ensure_ascii=False, indent=2) # just return raw text
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# return retval
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#
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def user_multi_get(user_id):
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"""Get all data values in the data_store for a userid"""
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if user_id is None:
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@ -108,7 +31,7 @@ def user_multi_get(user_id):
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def datastore_del(id):
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"""Delete a data store item for a user_id and a key"""
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"""Delete a data store item for a key"""
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session.query(DataStoreModel).filter_by(id=id).delete()
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session.commit()
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json_value = json.dumps('deleted', ensure_ascii=False, indent=2)
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@ -116,7 +39,7 @@ def datastore_del(id):
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def datastore_get(id):
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"""Delete a data store item for a user_id and a key"""
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"""retrieve a data store item by a key"""
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item = session.query(DataStoreModel).filter_by(id=id).first()
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results = DataStoreSchema(many=False).dump(item)
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return results
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@ -130,12 +53,8 @@ def update_datastore(id, body):
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item = session.query(DataStoreModel).filter_by(id=id).first()
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if item is None:
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raise ApiError('unknown_item', 'The item "' + id + '" is not recognized.')
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#print(body)
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# I'm not sure if there is a generic way to use the
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# schema to both parse the body and update the SQLAlchemy record
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for key in body:
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if hasattr(item, key):
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setattr(item, key, body[key])
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DataStoreSchema().load(body, instance=item, session=session)
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item.last_updated = datetime.now()
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session.add(item)
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session.commit()
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@ -158,6 +77,7 @@ def add_datastore(body):
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if ('user_id' not in body) and ('study_id' not in body) and ('file_id' not in body):
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raise ApiError('conflicting_values', 'A datastore item should have either a study_id, user_id or file_id ')
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present = 0
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for field in ['user_id','study_id','file_id']:
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if field in body:
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@ -166,12 +86,7 @@ def add_datastore(body):
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raise ApiError('conflicting_values', 'A datastore item should have one of a study_id, user_id or a file_id '
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'but not more than one of these')
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item = DataStoreModel(key=body['key'], value=body['value'])
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# I'm not sure if there is a generic way to use the
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# schema to both parse the body and update the SQLAlchemy record
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for key in body:
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if hasattr(item, key):
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setattr(item, key, body[key])
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item = DataStoreSchema().load(body)
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item.last_updated = datetime.now()
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session.add(item)
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session.commit()
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@ -1,5 +1,6 @@
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from flask_marshmallow.sqla import SQLAlchemyAutoSchema
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from marshmallow import EXCLUDE
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from marshmallow_sqlalchemy import ModelSchema
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from sqlalchemy import func
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import marshmallow
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from marshmallow import INCLUDE, fields
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@ -20,13 +21,8 @@ class DataStoreModel(db.Model):
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value = db.Column(db.String)
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class DataStoreSchema(ma.Schema):
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id = fields.Integer(required=False)
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key = fields.String(required=True)
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last_updated = fields.DateTime(server_default=func.now(), onupdate=func.now())
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workflow_id = fields.Integer()
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study_id = fields.Integer(allow_none=True)
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task_id = fields.String()
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spec_id = fields.String()
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user_id = fields.String(allow_none=True)
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value = fields.String()
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class DataStoreSchema(SQLAlchemyAutoSchema):
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class Meta:
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model = DataStoreModel
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load_instance = True
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sqla_session = db.session
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@ -19,8 +19,8 @@ class DataStoreTest(BaseTest):
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"task_id": "MyTask",
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"spec_id": "My Spec Name",
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"value": "Some Value"
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}
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def add_test_study_data(self):
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study_data = DataStoreSchema().dump(self.TEST_STUDY_ITEM)
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rv = self.app.post('/v1.0/datastore',
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@ -60,11 +60,9 @@ class DataStoreTest(BaseTest):
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d = api_response.get_data(as_text=True)
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study_data = DataStoreSchema().loads(d)
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self.assertEqual(study_data['key'], self.TEST_STUDY_ITEM['key'])
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self.assertEqual(study_data['value'], self.TEST_STUDY_ITEM['value'])
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self.assertEqual(study_data['user_id'], None)
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self.assertEqual(study_data.key, self.TEST_STUDY_ITEM['key'])
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self.assertEqual(study_data.value, self.TEST_STUDY_ITEM['value'])
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self.assertEqual(study_data.user_id, None)
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def test_update_datastore(self):
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self.load_example_data()
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@ -72,20 +70,18 @@ class DataStoreTest(BaseTest):
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new_study = session.query(DataStoreModel).filter_by(id=new_study["id"]).first()
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new_study.value = 'MyNewValue'
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api_response = self.app.put('/v1.0/datastore/%i' % new_study.id,
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data=DataStoreSchema().dump(new_study),
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data=DataStoreSchema().dumps(new_study),
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headers=self.logged_in_headers(), content_type="application/json")
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self.assert_success(api_response)
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api_response = self.app.get('/v1.0/datastore/%i' % new_study.id,
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headers=self.logged_in_headers(), content_type="application/json")
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self.assert_success(api_response)
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study_data = DataStoreSchema().loads(api_response.get_data(as_text=True))
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self.assertEqual(study_data['key'], self.TEST_STUDY_ITEM['key'])
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self.assertEqual(study_data['value'], 'MyNewValue')
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self.assertEqual(study_data['user_id'], None)
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self.assertEqual(study_data.key, self.TEST_STUDY_ITEM['key'])
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self.assertEqual(study_data.value, 'MyNewValue')
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self.assertEqual(study_data.user_id, None)
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def test_delete_datastore(self):
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self.load_example_data()
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@ -97,10 +93,8 @@ class DataStoreTest(BaseTest):
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studyreponse = session.query(DataStoreModel).filter_by(id=oldid).first()
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self.assertEqual(studyreponse,None)
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def test_data_crosstalk(self):
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"""Test to make sure that data saved for user or study is not acessible from the other method"""
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"""Test to make sure that data saved for user or study is not accessible from the other method"""
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self.load_example_data()
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new_study = self.add_test_study_data()
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