Merge pull request #186 from ral-facilities/feature/fix-code-linting-…

…#184

Apply Fixes suggested by Linting Tools

.flake8

@@ -2,9 +2,9 @@
 [flake8]
 select = A,B,B9,BLK,C,E,F,I,N,S,W
 ignore = E203,W503,E501
-max-complexity = 10
+max-complexity = 17
 max-line-length = 80
-application-import-names = common,src,test,util
+application-import-names = datagateway_api,test,util
 import-order-style = google
-per-file-ignores = test/*:S101
+per-file-ignores = test/*:S101,util/icat_db_generator.py:S311
 enable-extensions=G

README.md

@@ -146,7 +146,7 @@ nox -s [SESSION/FUNCTION NAME]
 ```
 
 Currently, the following Nox sessions have been created:
-- `format` - this uses [Black](https://black.readthedocs.io/en/stable/) to format Python
+- `black` - this uses [Black](https://black.readthedocs.io/en/stable/) to format Python
   code to a pre-defined style.
 - `lint` - this uses [flake8](https://flake8.pycqa.org/en/latest/) with a number of
   additional plugins (see the included `noxfile.py` to see which plugins are used) to

config.json.example

@@ -4,6 +4,7 @@
   "ICAT_URL": "https://localhost.localdomain:8181",
   "icat_check_cert": false,
   "log_level": "WARN",
+  "log_location": "/home/user1/datagateway-api/logs.log",
   "debug_mode": false,
   "generate_swagger": false,
   "host": "127.0.0.1",

datagateway_api/common/backend.py

@@ -143,7 +143,7 @@ def update_with_id(self, session_id, entity_type, id_, data):
 
     @abstractmethod
     def get_facility_cycles_for_instrument_with_filters(
-        self, session_id, instrument_id, filters
+        self, session_id, instrument_id, filters,
     ):
         """
         Given an instrument_id get facility cycles where the instrument has
@@ -158,7 +158,7 @@ def get_facility_cycles_for_instrument_with_filters(
 
     @abstractmethod
     def get_facility_cycles_for_instrument_count_with_filters(
-        self, session_id, instrument_id, filters
+        self, session_id, instrument_id, filters,
     ):
         """
         Given an instrument_id get the facility cycles count where the instrument has
@@ -173,7 +173,7 @@ def get_facility_cycles_for_instrument_count_with_filters(
 
     @abstractmethod
     def get_investigations_for_instrument_in_facility_cycle_with_filters(
-        self, session_id, instrument_id, facilitycycle_id, filters
+        self, session_id, instrument_id, facilitycycle_id, filters,
     ):
         """
         Given an instrument id and facility cycle id, get investigations that use the
@@ -188,8 +188,8 @@ def get_investigations_for_instrument_in_facility_cycle_with_filters(
         pass
 
     @abstractmethod
-    def get_investigations_for_instrument_in_facility_cycle_count_with_filters(
-        self, session_id, instrument_id, facilitycycle_id, filters
+    def get_investigation_count_for_instrument_facility_cycle_with_filters(
+        self, session_id, instrument_id, facilitycycle_id, filters,
     ):
         """
         Given an instrument id and facility cycle id, get the count of the

datagateway_api/common/backends.py

@@ -1,8 +1,10 @@
-from datagateway_api.common.database.backend import DatabaseBackend
-from datagateway_api.common.icat.backend import PythonICATBackend
+import sys
+
 from datagateway_api.common.backend import Backend
 from datagateway_api.common.config import config
-import sys
+from datagateway_api.common.database.backend import DatabaseBackend
+from datagateway_api.common.icat.backend import PythonICATBackend
+
 
 backend_type = config.get_backend_type()
 

datagateway_api/common/config.py

@@ -1,8 +1,10 @@
 import json
-import sys
+import logging
 from pathlib import Path
+import sys
+
 import requests
-import logging
+
 
 log = logging.getLogger()
 
@@ -11,65 +13,67 @@ class Config(object):
     def __init__(self):
         config_path = Path(__file__).parent.parent.parent / "config.json"
         with open(config_path) as target:
-
             self.config = json.load(target)
         target.close()
 
     def get_backend_type(self):
         try:
             return self.config["backend"]
-        except:
+        except KeyError:
             sys.exit("Missing config value, backend")
 
     def get_db_url(self):
         try:
             return self.config["DB_URL"]
-        except:
+        except KeyError:
             sys.exit("Missing config value, DB_URL")
 
     def get_icat_url(self):
         try:
             return self.config["ICAT_URL"]
-        except:
+        except KeyError:
             sys.exit("Missing config value, ICAT_URL")
 
     def get_icat_check_cert(self):
         try:
             return self.config["icat_check_cert"]
-        except:
-            # This could be set to true if there's no value, and log a warning
-            # that no value has been found from the config - save app from
-            # exiting
+        except KeyError:
             sys.exit("Missing config value, icat_check_cert")
 
     def get_log_level(self):
         try:
             return self.config["log_level"]
-        except:
+        except KeyError:
             sys.exit("Missing config value, log_level")
 
+    def get_log_location(self):
+        try:
+            return self.config["log_location"]
+        except KeyError:
+            sys.exit("Missing config value, log_location")
+
     def is_debug_mode(self):
         try:
             return self.config["debug_mode"]
-        except:
+        except KeyError:
             sys.exit("Missing config value, debug_mode")
 
     def is_generate_swagger(self):
         try:
             return self.config["generate_swagger"]
-        except:
+        except KeyError:
             sys.exit("Missing config value, generate_swagger")
 
     def get_host(self):
         try:
             return self.config["host"]
-        except:
+        except KeyError:
             sys.exit("Missing config value, host")
 
     def get_port(self):
         try:
             return self.config["port"]
-        except:
+        except KeyError:
             sys.exit("Missing config value, port")
 
     def get_icat_properties(self):

datagateway_api/common/database/backend.py

@@ -1,27 +1,28 @@
+import datetime
+import logging
+import uuid
+
 from datagateway_api.common.backend import Backend
 from datagateway_api.common.database.helpers import (
+    create_rows_from_json,
+    delete_row_by_id,
     get_facility_cycles_for_instrument,
     get_facility_cycles_for_instrument_count,
+    get_filtered_row_count,
+    get_first_filtered_row,
     get_investigations_for_instrument_in_facility_cycle,
     get_investigations_for_instrument_in_facility_cycle_count,
-    get_rows_by_filter,
-    create_rows_from_json,
-    patch_entities,
     get_row_by_id,
+    get_rows_by_filter,
     insert_row_into_table,
-    delete_row_by_id,
-    update_row_from_id,
-    get_filtered_row_count,
-    get_first_filtered_row,
+    patch_entities,
     requires_session_id,
+    update_row_from_id,
 )
-from datagateway_api.common.helpers import queries_records
 from datagateway_api.common.database.models import EntityHelper, SESSION
-import uuid
 from datagateway_api.common.exceptions import AuthenticationError
-import datetime
+from datagateway_api.common.helpers import queries_records
 
-import logging
 
 log = logging.getLogger()
 
@@ -110,31 +111,31 @@ def update_with_id(self, session_id, entity_type, id_, data):
     @requires_session_id
     @queries_records
     def get_facility_cycles_for_instrument_with_filters(
-        self, session_id, instrument_id, filters
+        self, session_id, instrument_id, filters,
     ):
         return get_facility_cycles_for_instrument(instrument_id, filters)
 
     @requires_session_id
     @queries_records
     def get_facility_cycles_for_instrument_count_with_filters(
-        self, session_id, instrument_id, filters
+        self, session_id, instrument_id, filters,
     ):
         return get_facility_cycles_for_instrument_count(instrument_id, filters)
 
     @requires_session_id
     @queries_records
     def get_investigations_for_instrument_in_facility_cycle_with_filters(
-        self, session_id, instrument_id, facilitycycle_id, filters
+        self, session_id, instrument_id, facilitycycle_id, filters,
     ):
         return get_investigations_for_instrument_in_facility_cycle(
-            instrument_id, facilitycycle_id, filters
+            instrument_id, facilitycycle_id, filters,
         )
 
     @requires_session_id
     @queries_records
-    def get_investigations_for_instrument_in_facility_cycle_count_with_filters(
-        self, session_id, instrument_id, facilitycycle_id, filters
+    def get_investigation_count_for_instrument_facility_cycle_with_filters(
+        self, session_id, instrument_id, facilitycycle_id, filters,
     ):
         return get_investigations_for_instrument_in_facility_cycle_count(
-            instrument_id, facilitycycle_id, filters
+            instrument_id, facilitycycle_id, filters,
         )

datagateway_api/common/database/filters.py

@@ -1,16 +1,18 @@
+import logging
+
+from sqlalchemy import asc, desc
+
+from datagateway_api.common.database import models
+from datagateway_api.common.exceptions import FilterError, MultipleIncludeError
 from datagateway_api.common.filters import (
-    WhereFilter,
     DistinctFieldFilter,
+    IncludeFilter,
+    LimitFilter,
     OrderFilter,
     SkipFilter,
-    LimitFilter,
-    IncludeFilter,
+    WhereFilter,
 )
-from datagateway_api.common.exceptions import FilterError, MultipleIncludeError
-from datagateway_api.common.database import models
 
-from sqlalchemy import asc, desc
-import logging
 
 log = logging.getLogger()
 
@@ -53,14 +55,14 @@ def apply_filter(self, query):
             field = getattr(query.table, self.field)
         except AttributeError:
             raise FilterError(
-                f"Unknown attribute {self.field} on table {query.table.__name__}"
+                f"Unknown attribute {self.field} on table {query.table.__name__}",
             )
 
         if self.included_included_field:
             included_table = getattr(models, self.field)
             included_included_table = getattr(models, self.included_field)
             query.base_query = query.base_query.join(included_table).join(
-                included_included_table
+                included_included_table,
             )
             field = getattr(included_included_table, self.included_included_field)
 
@@ -87,7 +89,7 @@ def apply_filter(self, query):
             query.base_query = query.base_query.filter(field.in_(self.value))
         else:
             raise FilterError(
-                f" Bad operation given to where filter. operation: {self.operation}"
+                f" Bad operation given to where filter. operation: {self.operation}",
             )