#150: General cleanup of recent work

- Sort out linting and remove a few lines of code used for logging etc.

datagateway_api/common/backend.py

@@ -172,7 +172,7 @@ def get_facility_cycles_for_instrument_count_with_filters(
         pass
 
     @abstractmethod
-    def get_investigations_for_instrument_in_facility_cycle_with_filters(
+    def get_investigations_for_instrument_facility_cycle_with_filters(
         self, session_id, instrument_id, facilitycycle_id, filters,
     ):
         """
@@ -188,7 +188,7 @@ def get_investigations_for_instrument_in_facility_cycle_with_filters(
         pass
 
     @abstractmethod
-    def get_investigation_count_for_instrument_facility_cycle_with_filters(
+    def get_investigation_count_instrument_facility_cycle_with_filters(
         self, session_id, instrument_id, facilitycycle_id, filters,
     ):
         """

datagateway_api/common/database/backend.py

@@ -124,7 +124,7 @@ def get_facility_cycles_for_instrument_count_with_filters(
 
     @requires_session_id
     @queries_records
-    def get_investigations_for_instrument_in_facility_cycle_with_filters(
+    def get_investigations_for_instrument_facility_cycle_with_filters(
         self, session_id, instrument_id, facilitycycle_id, filters,
     ):
         return get_investigations_for_instrument_in_facility_cycle(
@@ -133,7 +133,7 @@ def get_investigations_for_instrument_in_facility_cycle_with_filters(
 
     @requires_session_id
     @queries_records
-    def get_investigation_count_for_instrument_facility_cycle_with_filters(
+    def get_investigation_count_instrument_facility_cycle_with_filters(
         self, session_id, instrument_id, facilitycycle_id, filters,
     ):
         return get_investigations_for_instrument_in_facility_cycle_count(

datagateway_api/common/helpers.py

@@ -6,14 +6,14 @@
 from flask_restful import reqparse
 from sqlalchemy.exc import IntegrityError
 
-from datagateway_api.common.query_filter import QueryFilterFactory
 from datagateway_api.common.exceptions import (
     ApiError,
     AuthenticationError,
     BadRequestError,
     FilterError,
     MissingCredentialsError,
 )
+from datagateway_api.common.query_filter import QueryFilterFactory
 
 log = logging.getLogger()
 

datagateway_api/common/icat/backend.py

@@ -136,7 +136,7 @@ def get_facility_cycles_for_instrument_count_with_filters(
 
     @requires_session_id
     @queries_records
-    def get_investigations_for_instrument_in_facility_cycle_with_filters(
+    def get_investigations_for_instrument_facility_cycle_with_filters(
         self, session_id, instrument_id, facilitycycle_id, filters, **kwargs,
     ):
         client = kwargs["client"] if kwargs["client"] else create_client()
@@ -146,7 +146,7 @@ def get_investigations_for_instrument_in_facility_cycle_with_filters(
 
     @requires_session_id
     @queries_records
-    def get_investigation_count_for_instrument_facility_cycle_with_filters(
+    def get_investigation_count_instrument_facility_cycle_with_filters(
         self, session_id, instrument_id, facilitycycle_id, filters, **kwargs,
     ):
         client = kwargs["client"] if kwargs["client"] else create_client()

datagateway_api/common/query_filter.py

@@ -25,7 +25,6 @@ def get_query_filter(request_filter):
         """
 
         backend_type = config.get_backend_type()
-        print(f"Backend inside staticmethod: {backend_type}")
         if backend_type == "db":
             from datagateway_api.common.database.filters import (
                 DatabaseDistinctFieldFilter as DistinctFieldFilter,

datagateway_api/src/main.py

@@ -24,9 +24,9 @@
 )
 from datagateway_api.src.resources.table_endpoints.table_endpoints import (
     count_instrument_facility_cycles_endpoint,
+    count_instrument_investigation_endpoint,
     instrument_facility_cycles_endpoint,
     instrument_investigation_endpoint,
-    count_instrument_investigation_endpoint,
 )
 from datagateway_api.src.swagger.apispec_flask_restful import RestfulPlugin
 from datagateway_api.src.swagger.initialise_spec import initialise_spec
@@ -51,7 +51,7 @@ def create_app_infrastructure(flask_app):
         security=[{"session_id": []}],
     )
 
-    cors = CORS(flask_app)
+    CORS(flask_app)
     flask_app.url_map.strict_slashes = False
     api = Api(flask_app)
 
@@ -70,24 +70,21 @@ def create_api_endpoints(flask_app, api, spec):
     try:
         backend_type = flask_app.config["TEST_BACKEND"]
         config.set_backend_type(backend_type)
-        print(f"test backend: {backend_type}")
     except KeyError:
         backend_type = config.get_backend_type()
-        print(f"config backend: {backend_type}")
 
     # TODO - Add :param backend: to the endpoint functions
     backend = create_backend(backend_type)
-    print(f"Backend: {backend}, Type: {type(backend)}")
 
     for entity_name in endpoints:
         get_endpoint_resource = get_endpoint(
-            entity_name, endpoints[entity_name], backend
+            entity_name, endpoints[entity_name], backend,
         )
         api.add_resource(get_endpoint_resource, f"/{entity_name.lower()}")
         spec.path(resource=get_endpoint_resource, api=api)
 
         get_id_endpoint_resource = get_id_endpoint(
-            entity_name, endpoints[entity_name], backend
+            entity_name, endpoints[entity_name], backend,
         )
         api.add_resource(get_id_endpoint_resource, f"/{entity_name.lower()}/<int:id_>")
         spec.path(resource=get_id_endpoint_resource, api=api)
@@ -114,15 +111,15 @@ def create_api_endpoints(flask_app, api, spec):
     # Table specific endpoints
     instrument_facility_cycle_resource = instrument_facility_cycles_endpoint(backend)
     api.add_resource(
-        instrument_facility_cycle_resource, "/instruments/<int:id_>/facilitycycles"
+        instrument_facility_cycle_resource, "/instruments/<int:id_>/facilitycycles",
     )
     # spec.path(resource=instrument_facility_cycle_resource, api=api)
 
-    count_instrument_facility_cycle_resource = count_instrument_facility_cycles_endpoint(
-        backend
+    count_instrument_facility_cycle_res = count_instrument_facility_cycles_endpoint(
+        backend,
     )
     api.add_resource(
-        count_instrument_facility_cycle_resource,
+        count_instrument_facility_cycle_res,
         "/instruments/<int:id_>/facilitycycles/count",
     )
     # spec.path(resource=count_instrument_facility_cycle_resource, api=api)
@@ -135,7 +132,7 @@ def create_api_endpoints(flask_app, api, spec):
     # spec.path(resource=instrument_investigation_resource, api=api)
 
     count_instrument_investigation_resource = count_instrument_investigation_endpoint(
-        backend
+        backend,
     )
     api.add_resource(
         count_instrument_investigation_resource,

datagateway_api/src/resources/entities/entity_endpoint.py

@@ -1,15 +1,11 @@
 from flask import request
 from flask_restful import Resource
 
-from datagateway_api.common.backends import create_backend
-from datagateway_api.common.config import config
 from datagateway_api.common.helpers import (
     get_filters_from_query_string,
     get_session_id_from_auth_header,
 )
 
-# backend = create_backend(config.get_backend_type())
-
 
 def get_endpoint(name, entity_type, backend):
     """

datagateway_api/src/resources/non_entities/sessions_endpoints.py

@@ -3,22 +3,17 @@
 from flask import request
 from flask_restful import Resource
 
-from datagateway_api.common.backends import create_backend
-from datagateway_api.common.config import config
 from datagateway_api.common.exceptions import AuthenticationError
 from datagateway_api.common.helpers import get_session_id_from_auth_header
 
 
 log = logging.getLogger()
 
-# backend = create_backend(config.get_backend_type())
-
 
 def session_endpoints(backend):
     """
     TODO - Add docstring
     """
-    log.info("test")
 
     class Sessions(Resource):
         def post(self):

datagateway_api/src/resources/table_endpoints/table_endpoints.py

@@ -1,14 +1,10 @@
 from flask_restful import Resource
 
-from datagateway_api.common.backends import create_backend
-from datagateway_api.common.config import config
 from datagateway_api.common.helpers import (
     get_filters_from_query_string,
     get_session_id_from_auth_header,
 )
 
-backend = create_backend(config.get_backend_type())
-
 
 def instrument_facility_cycles_endpoint(backend):
     """
@@ -179,7 +175,7 @@ def get(self, instrument_id, cycle_id):
                     description: No such record - Unable to find a record in ICAT
             """
             return (
-                backend.get_investigations_for_instrument_in_facility_cycle_with_filters(
+                backend.get_investigations_for_instrument_facility_cycle_with_filters(
                     get_session_id_from_auth_header(),
                     instrument_id,
                     cycle_id,
@@ -240,7 +236,7 @@ def get(self, instrument_id, cycle_id):
                     description: No such record - Unable to find a record in ICAT
             """
             return (
-                backend.get_investigation_count_for_instrument_facility_cycle_with_filters(
+                backend.get_investigation_count_instrument_facility_cycle_with_filters(
                     get_session_id_from_auth_header(),
                     instrument_id,
                     cycle_id,

test/icat/endpoints/test_count_with_filters.py

@@ -4,7 +4,7 @@
 class TestCountWithFilters:
     @pytest.mark.usefixtures("single_investigation_test_data")
     def test_valid_count_with_filters(
-        self, flask_test_app_icat, valid_credentials_header
+        self, flask_test_app_icat, valid_credentials_header,
     ):
         test_response = flask_test_app_icat.get(
             '/investigations/count?where={"title": {"like": "Test data for the Python'

test/icat/endpoints/test_create.py

@@ -57,7 +57,7 @@ def test_valid_create_data(self, flask_test_app_icat, valid_credentials_header):
             )
 
     def test_valid_boundary_create_data(
-        self, flask_test_app_icat, valid_credentials_header
+        self, flask_test_app_icat, valid_credentials_header,
     ):
         """Create a single investigation, as opposed to multiple"""
 

test/icat/endpoints/test_delete_by_id.py

@@ -13,7 +13,7 @@ def test_valid_delete_with_id(
         assert test_response.status_code == 204
 
     def test_invalid_delete_with_id(
-        self, flask_test_app_icat, valid_credentials_header
+        self, flask_test_app_icat, valid_credentials_header,
     ):
         """Request with a non-existent ID"""
 

test/icat/endpoints/test_endpoint_rules.py

@@ -61,7 +61,7 @@ def test_entity_endpoints(self, flask_test_app, endpoint_ending, expected_method
         ],
     )
     def test_non_entity_endpoints(
-        self, flask_test_app, endpoint_name, expected_methods
+        self, flask_test_app, endpoint_name, expected_methods,
     ):
         endpoint_found = False
 

test/icat/test_query.py

@@ -122,7 +122,6 @@ def test_include_fields_list_flatten(self, icat_client):
         test_query = ICATQuery(icat_client, "User")
 
         flat_list = test_query.flatten_query_included_fields(included_field_set)
-        print(flat_list)
 
         assert flat_list == [
             "instrumentScientists",

test/icat/test_session_handling.py

@@ -12,14 +12,12 @@ def test_session_id_decorator(self):
         pass
 
     def test_get_valid_session_details(
-        self, flask_test_app_icat, valid_credentials_header
+        self, flask_test_app_icat, valid_credentials_header,
     ):
         session_details = flask_test_app_icat.get(
             "/sessions", headers=valid_credentials_header,
         )
 
-        print(f"JSON: {session_details.json}, Code: {session_details.status_code}")
-
         # Check username is correct
         assert (
             session_details.json["USERNAME"] == f"{config.get_test_mechanism()}/"

test/test_helpers.py

@@ -203,7 +203,7 @@ def test_limit_filter(self):
                 1, len(filters), msg="Returned incorrect number of filters",
             )
             self.assertIs(
-                DatabaseLimitFilter, type(filters[0]), msg="Incorrect type of filter"
+                DatabaseLimitFilter, type(filters[0]), msg="Incorrect type of filter",
             )
 
     def test_order_filter(self):