#184: Add trailing commas to meet flake8 output

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
@@ -189,7 +189,7 @@ def get_investigations_for_instrument_in_facility_cycle_with_filters(
 
     @abstractmethod
     def get_investigations_for_instrument_in_facility_cycle_count_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 the count of the

datagateway_api/common/database/backend.py

@@ -110,31 +110,31 @@ 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
+        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

@@ -53,14 +53,14 @@ 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)
 
@@ -85,7 +85,7 @@ 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}",
             )
 
 

datagateway_api/common/database/helpers.py

@@ -47,7 +47,7 @@
 else:
     raise ApiError(
         "Cannot select which implementation of filters to import, check the config file"
-        " has a valid backend type"
+        " has a valid backend type",
     )
 
 log = logging.getLogger()
@@ -521,7 +521,7 @@ def __init__(self, instrument_id, facility_cycle_id):
 
 
 def get_investigations_for_instrument_in_facility_cycle(
-    instrument_id, facility_cycle_id, filters
+    instrument_id, facility_cycle_id, filters,
 ):
     """
     Given an instrument id and facility cycle id, get investigations that use the given
@@ -534,7 +534,7 @@ def get_investigations_for_instrument_in_facility_cycle(
     """
     filter_handler = FilterOrderHandler()
     with InstrumentFacilityCycleInvestigationsQuery(
-        instrument_id, facility_cycle_id
+        instrument_id, facility_cycle_id,
     ) as query:
         return get_filtered_read_query_results(filter_handler, filters, query)
 
@@ -558,7 +558,7 @@ def __init__(self, instrument_id, facility_cycle_id):
 
 
 def get_investigations_for_instrument_in_facility_cycle_count(
-    instrument_id, facility_cycle_id, filters
+    instrument_id, facility_cycle_id, filters,
 ):
     """
     Given an instrument id and facility cycle id, get the count of the investigations
@@ -570,7 +570,7 @@ def get_investigations_for_instrument_in_facility_cycle_count(
     :return: The investigations count
     """
     with InstrumentFacilityCycleInvestigationsCountQuery(
-        instrument_id, facility_cycle_id
+        instrument_id, facility_cycle_id,
     ) as query:
         filter_handler = FilterOrderHandler()
         filter_handler.add_filters(filters)

datagateway_api/common/database/models.py

@@ -74,7 +74,7 @@ def get_entity_object_from_name(entity_name):
             return globals()[entity_name.upper()]
         except KeyError:
             raise ApiError(
-                f"Entity class cannot be found. Please create a class for {entity_name}"
+                f"Entity class cannot be found, missing class for {entity_name}",
             )
 
     def to_dict(self):
@@ -132,17 +132,17 @@ def _nest_dictionary_include(self, dictionary, include):
         related_entity = self.get_related_entity(list(include)[0])
         if not isinstance(related_entity, InstrumentedList):
             dictionary[related_entity.__tablename__] = related_entity.to_nested_dict(
-                include[list(include)[0]]
+                include[list(include)[0]],
             )
         else:
             for entity in related_entity:
                 if entity.__tablename__ in dictionary.keys():
                     dictionary[entity.__tablename__].append(
-                        entity.to_nested_dict(include[list(include)[0]])
+                        entity.to_nested_dict(include[list(include)[0]]),
                     )
                 else:
                     dictionary[entity.__tablename__] = [
-                        entity.to_nested_dict(include[list(include)[0]])
+                        entity.to_nested_dict(include[list(include)[0]]),
                     ]
 
     def _nest_string_include(self, dictionary, include):
@@ -289,7 +289,7 @@ class DATACOLLECTIONPARAMETER(Base, EntityHelper):
     __tablename__ = "DATACOLLECTIONPARAMETER"
     __table_args__ = (
         Index(
-            "UNQ_DATACOLLECTIONPARAMETER_0", "DATACOLLECTION_ID", "PARAMETER_TYPE_ID"
+            "UNQ_DATACOLLECTIONPARAMETER_0", "DATACOLLECTION_ID", "PARAMETER_TYPE_ID",
         ),
     )
 
@@ -306,7 +306,7 @@ class DATACOLLECTIONPARAMETER(Base, EntityHelper):
     STRING_VALUE = Column(String(4000))
     DATACOLLECTION_ID = Column(ForeignKey("DATACOLLECTION.ID"), nullable=False)
     PARAMETER_TYPE_ID = Column(
-        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True
+        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True,
     )
 
     DATACOLLECTION = relationship(
@@ -347,7 +347,7 @@ class DATAFILE(Base, EntityHelper):
         backref="DATAFILE",
     )
     DATASET = relationship(
-        "DATASET", primaryjoin="DATAFILE.DATASET_ID == DATASET.ID", backref="DATAFILE"
+        "DATASET", primaryjoin="DATAFILE.DATASET_ID == DATASET.ID", backref="DATAFILE",
     )
 
 
@@ -392,7 +392,7 @@ class DATAFILEPARAMETER(Base, EntityHelper):
     STRING_VALUE = Column(String(4000))
     DATAFILE_ID = Column(ForeignKey("DATAFILE.ID"), nullable=False)
     PARAMETER_TYPE_ID = Column(
-        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True
+        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True,
     )
 
     DATAFILE = relationship(
@@ -433,7 +433,7 @@ class DATASET(Base, EntityHelper):
         backref="DATASET",
     )
     SAMPLE = relationship(
-        "SAMPLE", primaryjoin="DATASET.SAMPLE_ID == SAMPLE.ID", backref="DATASET"
+        "SAMPLE", primaryjoin="DATASET.SAMPLE_ID == SAMPLE.ID", backref="DATASET",
     )
     DATASETTYPE = relationship(
         "DATASETTYPE",
@@ -461,7 +461,7 @@ class DATASETPARAMETER(Base, EntityHelper):
     STRING_VALUE = Column(String(4000))
     DATASET_ID = Column(ForeignKey("DATASET.ID"), nullable=False)
     PARAMETER_TYPE_ID = Column(
-        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True
+        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True,
     )
 
     DATASET = relationship(
@@ -622,7 +622,7 @@ class INVESTIGATIONGROUP(Base, EntityHelper):
     ROLE = Column(String(255), nullable=False)
     GROUP_ID = Column(ForeignKey("GROUPING.ID"), nullable=False)
     INVESTIGATION_ID = Column(
-        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True
+        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True,
     )
 
     GROUPING = relationship(
@@ -682,7 +682,7 @@ class INVESTIGATIONPARAMETER(Base, EntityHelper):
     STRING_VALUE = Column(String(4000))
     INVESTIGATION_ID = Column(ForeignKey("INVESTIGATION.ID"), nullable=False)
     PARAMETER_TYPE_ID = Column(
-        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True
+        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True,
     )
 
     INVESTIGATION = relationship(
@@ -730,7 +730,7 @@ class INVESTIGATIONUSER(Base, EntityHelper):
     MOD_TIME = Column(DateTime, nullable=False)
     ROLE = Column(String(255), nullable=False)
     INVESTIGATION_ID = Column(
-        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True
+        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True,
     )
     USER_ID = Column(ForeignKey("USER_.ID"), nullable=False)
 
@@ -760,7 +760,9 @@ class JOB(Base, EntityHelper):
     OUTPUTDATACOLLECTION_ID = Column(ForeignKey("DATACOLLECTION.ID"), index=True)
 
     APPLICATION = relationship(
-        "APPLICATION", primaryjoin="JOB.APPLICATION_ID == APPLICATION.ID", backref="JOB"
+        "APPLICATION",
+        primaryjoin="JOB.APPLICATION_ID == APPLICATION.ID",
+        backref="JOB",
     )
     DATACOLLECTION = relationship(
         "DATACOLLECTION",
@@ -780,7 +782,7 @@ class KEYWORD(Base, EntityHelper):
     MOD_TIME = Column(DateTime, nullable=False)
     NAME = Column(String(255), nullable=False)
     INVESTIGATION_ID = Column(
-        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True
+        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True,
     )
 
     INVESTIGATION = relationship(
@@ -840,7 +842,7 @@ class PERMISSIBLESTRINGVALUE(Base, EntityHelper):
     MOD_TIME = Column(DateTime, nullable=False)
     VALUE = Column(String(255), nullable=False)
     PARAMETERTYPE_ID = Column(
-        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True
+        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True,
     )
 
     PARAMETERTYPE = relationship(
@@ -864,7 +866,7 @@ class PUBLICATION(Base, EntityHelper):
     REPOSITORYID = Column(String(255))
     URL = Column(String(255))
     INVESTIGATION_ID = Column(
-        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True
+        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True,
     )
 
     INVESTIGATION = relationship(
@@ -932,7 +934,7 @@ class RULE(Base, EntityHelper):
     GROUPING_ID = Column(ForeignKey("GROUPING.ID"), index=True)
 
     GROUPING = relationship(
-        "GROUPING", primaryjoin="RULE.GROUPING_ID == GROUPING.ID", backref="RULE"
+        "GROUPING", primaryjoin="RULE.GROUPING_ID == GROUPING.ID", backref="RULE",
     )
 
 
@@ -978,7 +980,7 @@ class SAMPLEPARAMETER(Base, EntityHelper):
     STRING_VALUE = Column(String(4000))
     SAMPLE_ID = Column(ForeignKey("SAMPLE.ID"), nullable=False)
     PARAMETER_TYPE_ID = Column(
-        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True
+        ForeignKey("PARAMETERTYPE.ID"), nullable=False, index=True,
     )
 
     PARAMETERTYPE = relationship(
@@ -1049,10 +1051,12 @@ class USERGROUP(Base, EntityHelper):
     USER_ID = Column(ForeignKey("USER_.ID"), nullable=False)
 
     GROUPING = relationship(
-        "GROUPING", primaryjoin="USERGROUP.GROUP_ID == GROUPING.ID", backref="USERGROUP"
+        "GROUPING",
+        primaryjoin="USERGROUP.GROUP_ID == GROUPING.ID",
+        backref="USERGROUP",
     )
     USER_ = relationship(
-        "USER", primaryjoin="USERGROUP.USER_ID == USER.ID", backref="USERGROUP"
+        "USER", primaryjoin="USERGROUP.USER_ID == USER.ID", backref="USERGROUP",
     )
 
 
@@ -1068,7 +1072,7 @@ class STUDYINVESTIGATION(Base, EntityHelper):
     MOD_ID = Column(String(255), nullable=False)
     MOD_TIME = Column(DateTime, nullable=False)
     INVESTIGATION_ID = Column(
-        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True
+        ForeignKey("INVESTIGATION.ID"), nullable=False, index=True,
     )
     STUDY_ID = Column(ForeignKey("STUDY.ID"), nullable=False)
 
@@ -1099,7 +1103,7 @@ class STUDY(Base, EntityHelper):
     USER_ID = Column(ForeignKey("USER_.ID"), index=True)
 
     USER_ = relationship(
-        "USER", primaryjoin="STUDY.USER_ID == USER.ID", backref="STUDY"
+        "USER", primaryjoin="STUDY.USER_ID == USER.ID", backref="STUDY",
     )
 
 

datagateway_api/common/database/session_manager.py

@@ -5,7 +5,7 @@
 from datagateway_api.common.constants import Constants
 
 engine = create_engine(
-    Constants.DATABASE_URL, poolclass=QueuePool, pool_size=100, max_overflow=0
+    Constants.DATABASE_URL, poolclass=QueuePool, pool_size=100, max_overflow=0,
 )
 session_factory = sessionmaker(engine)
 

datagateway_api/common/date_handler.py

@@ -55,7 +55,7 @@ def str_to_datetime_object(data):
             raise BadRequestError(
                 "Bad request made, the date entered is not in the correct format. Use"
                 f" the {Constants.ACCEPTED_DATE_FORMAT} format to submit dates to the"
-                " API"
+                " API",
             )
 
         return data

datagateway_api/common/exceptions.py

@@ -22,7 +22,7 @@ def __init__(
         self,
         msg="Bad request, only one include filter may be given per request",
         *args,
-        **kwargs
+        **kwargs,
     ):
         super().__init__(msg, *args, **kwargs)
         self.status_code = 400

datagateway_api/common/filters.py

@@ -31,7 +31,7 @@ def __init__(self, field, value, operation):
             if not isinstance(self.value, list):
                 raise BadRequestError(
                     "When using the 'in' operation for a WHERE filter, the values must"
-                    " be in a list format e.g. [1, 2, 3]"
+                    " be in a list format e.g. [1, 2, 3]",
                 )
 
 

datagateway_api/common/helpers.py

@@ -64,7 +64,7 @@ def get_session_id_from_auth_header():
         raise MissingCredentialsError(f"No credentials provided in auth header")
     if len(auth_header) != 2 or auth_header[0] != "Bearer":
         raise AuthenticationError(
-            f" Could not authenticate consumer with auth header {auth_header}"
+            f" Could not authenticate consumer with auth header {auth_header}",
         )
     return auth_header[1]
 
@@ -97,7 +97,7 @@ def get_filters_from_query_string():
         for arg in request.args:
             for value in request.args.getlist(arg):
                 filters.append(
-                    QueryFilterFactory.get_query_filter({arg: json.loads(value)})
+                    QueryFilterFactory.get_query_filter({arg: json.loads(value)}),
                 )
         return filters
     except Exception as e: