Fix imports for new directory structure

- Directory structure due to implementation of search API

datagateway_api/common/datagateway_api/backends.py

@@ -1,7 +1,7 @@
 import sys
 
-from datagateway_api.common.database.backend import DatabaseBackend
-from datagateway_api.common.icat.backend import PythonICATBackend
+from datagateway_api.common.datagateway_api.database.backend import DatabaseBackend
+from datagateway_api.common.datagateway_api.icat.backend import PythonICATBackend
 
 
 def create_backend(backend_type):

datagateway_api/common/datagateway_api/database/backend.py

@@ -5,9 +5,9 @@
 from sqlalchemy import inspect
 from sqlalchemy.exc import SQLAlchemyError
 
-from datagateway_api.common.backend import Backend
 from datagateway_api.common.constants import Constants
-from datagateway_api.common.database.helpers import (
+from datagateway_api.common.datagateway_api.backend import Backend
+from datagateway_api.common.datagateway_api.database.helpers import (
     create_rows_from_json,
     db,
     delete_row_by_id,
@@ -24,7 +24,7 @@
     requires_session_id,
     update_row_from_id,
 )
-from datagateway_api.common.database.models import SESSION
+from datagateway_api.common.datagateway_api.database.models import SESSION
 from datagateway_api.common.exceptions import AuthenticationError, DatabaseError
 from datagateway_api.common.helpers import get_entity_object_from_name, queries_records
 

datagateway_api/common/datagateway_api/database/filters.py

@@ -73,7 +73,7 @@ def add_query_join(self, query):
         filter
 
         :param query: The query to have filters applied to
-        :type query: :class:`datagateway_api.common.database.helpers.[QUERY]`
+        :type query: :class:`.common.datagateway_api.database.helpers.[QUERY]`
         """
 
         if self.related_related_field:
@@ -92,7 +92,7 @@ def get_entity_model_for_filter(self, query):
         variables of this class
 
         :param query: The query to have filters applied to
-        :type query: :class:`datagateway_api.common.database.helpers.[QUERY]`
+        :type query: :class:`.common.datagateway_api.database.helpers.[QUERY]`
         :return: Entity model of the field (usually the field relating to the endpoint
             the request is coming from)
         """

datagateway_api/common/datagateway_api/database/helpers.py

@@ -6,25 +6,27 @@
 from flask_sqlalchemy import SQLAlchemy
 from sqlalchemy.orm import aliased
 
-from datagateway_api.common.database.filters import (
+from datagateway_api.common.datagateway_api.database.filters import (
     DatabaseDistinctFieldFilter,
     DatabaseIncludeFilter as IncludeFilter,
     DatabaseWhereFilter as WhereFilter,
 )
-from datagateway_api.common.database.models import (
+from datagateway_api.common.datagateway_api.database.models import (
     FACILITY,
     FACILITYCYCLE,
     INSTRUMENT,
     INVESTIGATION,
     INVESTIGATIONINSTRUMENT,
     SESSION,
 )
+from datagateway_api.common.datagateway_api.filter_order_handler import (
+    FilterOrderHandler,
+)
 from datagateway_api.common.exceptions import (
     AuthenticationError,
     BadRequestError,
     MissingRecordError,
 )
-from datagateway_api.common.filter_order_handler import FilterOrderHandler
 from datagateway_api.common.helpers import map_distinct_attributes_to_results
 
 

datagateway_api/common/datagateway_api/filter_order_handler.py

@@ -1,6 +1,6 @@
 import logging
 
-from datagateway_api.common.icat.filters import (
+from datagateway_api.common.datagateway_api.icat.filters import (
     PythonICATLimitFilter,
     PythonICATOrderFilter,
     PythonICATSkipFilter,

datagateway_api/common/datagateway_api/icat/backend.py

@@ -2,11 +2,9 @@
 
 from icat.exception import ICATError, ICATSessionError
 
-from datagateway_api.common.backend import Backend
 from datagateway_api.common.constants import Constants
-from datagateway_api.common.exceptions import AuthenticationError, PythonICATError
-from datagateway_api.common.helpers import queries_records
-from datagateway_api.common.icat.helpers import (
+from datagateway_api.common.datagateway_api.backend import Backend
+from datagateway_api.common.datagateway_api.icat.helpers import (
     create_entities,
     delete_entity_by_id,
     get_cached_client,
@@ -25,6 +23,8 @@
     update_entities,
     update_entity_by_id,
 )
+from datagateway_api.common.exceptions import AuthenticationError, PythonICATError
+from datagateway_api.common.helpers import queries_records
 
 
 log = logging.getLogger()

datagateway_api/common/datagateway_api/icat/helpers.py

@@ -14,21 +14,22 @@
     ICATValidationError,
 )
 
+from datagateway_api.common.datagateway_api.filter_order_handler import (
+    FilterOrderHandler,
+)
+from datagateway_api.common.datagateway_api.icat.filters import (
+    PythonICATLimitFilter,
+    PythonICATWhereFilter,
+)
+from datagateway_api.common.datagateway_api.icat.lru_cache import ExtendedLRUCache
+from datagateway_api.common.datagateway_api.icat.query import ICATQuery
 from datagateway_api.common.date_handler import DateHandler
 from datagateway_api.common.exceptions import (
     AuthenticationError,
     BadRequestError,
     MissingRecordError,
     PythonICATError,
 )
-from datagateway_api.common.filter_order_handler import FilterOrderHandler
-from datagateway_api.common.icat.filters import (
-    PythonICATLimitFilter,
-    PythonICATWhereFilter,
-)
-from datagateway_api.common.icat.lru_cache import ExtendedLRUCache
-from datagateway_api.common.icat.query import ICATQuery
-
 
 log = logging.getLogger()
 

datagateway_api/common/datagateway_api/query_filter_factory.py

@@ -29,7 +29,7 @@ def get_query_filter(request_filter):
 
         backend_type = config.get_config_value(APIConfigOptions.BACKEND)
         if backend_type == "db":
-            from datagateway_api.common.database.filters import (
+            from datagateway_api.common.datagateway_api.database.filters import (
                 DatabaseDistinctFieldFilter as DistinctFieldFilter,
                 DatabaseIncludeFilter as IncludeFilter,
                 DatabaseLimitFilter as LimitFilter,
@@ -38,7 +38,7 @@ def get_query_filter(request_filter):
                 DatabaseWhereFilter as WhereFilter,
             )
         elif backend_type == "python_icat":
-            from datagateway_api.common.icat.filters import (
+            from datagateway_api.common.datagateway_api.icat.filters import (
                 PythonICATDistinctFieldFilter as DistinctFieldFilter,
                 PythonICATIncludeFilter as IncludeFilter,
                 PythonICATLimitFilter as LimitFilter,

datagateway_api/common/helpers.py

@@ -8,7 +8,10 @@
 from flask_restful import reqparse
 from sqlalchemy.exc import IntegrityError
 
-from datagateway_api.common.database import models
+from datagateway_api.common.datagateway_api.database import models
+from datagateway_api.common.datagateway_api.query_filter_factory import (
+    QueryFilterFactory,
+)
 from datagateway_api.common.date_handler import DateHandler
 from datagateway_api.common.exceptions import (
     ApiError,
@@ -17,8 +20,9 @@
     FilterError,
     MissingCredentialsError,
 )
-from datagateway_api.common.query_filter_factory import QueryFilterFactory
-from datagateway_api.src.resources.entities.entity_endpoint_dict import endpoints
+from datagateway_api.src.resources.datagateway_api.entities.entity_endpoint_dict import (
+    endpoints,
+)
 
 log = logging.getLogger()
 
@@ -115,7 +119,7 @@ def get_entity_object_from_name(entity_name):
     :param entity_name: Name of the entity to fetch a version from this model
     :type entity_name: :class:`str`
     :return: Object of the entity requested (e.g.
-        :class:`datagateway_api.common.database.models.INVESTIGATIONINSTRUMENT`)
+        :class:`.datagateway_api.database.models.INVESTIGATIONINSTRUMENT`)
     :raises: KeyError: If an entity model cannot be found as a class in this model
     """
     try:

datagateway_api/common/search_api/filters.py

@@ -1,4 +1,4 @@
-from datagateway_api.common.icat.filters import (
+from datagateway_api.common.datagateway_api.icat.filters import (
     PythonICATIncludeFilter,
     PythonICATLimitFilter,
     PythonICATSkipFilter,

datagateway_api/common/search_api/models.py

@@ -9,7 +9,7 @@
 
 class PaNOSCAttribute(ABC):
     @abstractclassmethod
-    def from_icat(cls):
+    def from_icat(self):
         pass
 
     @abstractmethod

datagateway_api/common/search_api/session_handler.py

@@ -9,9 +9,12 @@ def requires_session_id(method):
     """
     TODO
     """
+    pass
 
+    """
     @wraps(method)
     def wrapper_requires_session(*args, **kwargs):
         pass
 
     return wrapper_requires_session
+    """

datagateway_api/src/api_start_utils.py

@@ -7,22 +7,28 @@
 from flask_restful import Api
 from flask_swagger_ui import get_swaggerui_blueprint
 
-from datagateway_api.common.backends import create_backend
 from datagateway_api.common.config import APIConfigOptions, config
-from datagateway_api.common.database.helpers import db
-from datagateway_api.common.icat.icat_client_pool import create_client_pool
-from datagateway_api.src.resources.entities.entity_endpoint import (
+from datagateway_api.common.datagateway_api.backends import create_backend
+from datagateway_api.common.datagateway_api.database.helpers import db
+from datagateway_api.common.datagateway_api.icat.icat_client_pool import (
+    create_client_pool,
+)
+from datagateway_api.src.resources.datagateway_api.entities.entity_endpoint import (
     get_count_endpoint,
     get_endpoint,
     get_find_one_endpoint,
     get_id_endpoint,
 )
-from datagateway_api.src.resources.entities.entity_endpoint_dict import endpoints
-from datagateway_api.src.resources.non_entities.ping_endpoint import ping_endpoint
-from datagateway_api.src.resources.non_entities.sessions_endpoints import (
+from datagateway_api.src.resources.datagateway_api.entities.entity_endpoint_dict import (
+    endpoints,
+)
+from datagateway_api.src.resources.datagateway_api.non_entities.ping_endpoint import (
+    ping_endpoint,
+)
+from datagateway_api.src.resources.datagateway_api.non_entities.sessions_endpoints import (
     session_endpoints,
 )
-from datagateway_api.src.resources.table_endpoints.table_endpoints import (
+from datagateway_api.src.resources.datagateway_api.table_endpoints.table_endpoints import (
     count_instrument_facility_cycles_endpoint,
     count_instrument_investigation_endpoint,
     instrument_facility_cycles_endpoint,

datagateway_api/src/resources/datagateway_api/entities/entity_map.py

@@ -3,7 +3,9 @@
 from sqlalchemy.inspection import inspect
 
 from datagateway_api.common.helpers import get_entity_object_from_name
-from datagateway_api.src.resources.entities.entity_endpoint_dict import endpoints
+from datagateway_api.src.resources.datagateway_api.entities.entity_endpoint_dict import (
+    endpoints,
+)
 
 
 def type_conversion(python_type):

datagateway_api/src/swagger/initialise_spec.py

@@ -1,4 +1,6 @@
-from datagateway_api.src.resources.entities.entity_map import create_entity_models
+from datagateway_api.src.resources.datagateway_api.entities.entity_map import (
+    create_entity_models,
+)
 
 
 def initialise_spec(spec):

test/conftest.py

@@ -3,11 +3,11 @@
 from flask import Flask
 import pytest
 
-from datagateway_api.common.database.helpers import (
+from datagateway_api.common.datagateway_api.database.helpers import (
     delete_row_by_id,
     insert_row_into_table,
 )
-from datagateway_api.common.database.models import SESSION
+from datagateway_api.common.datagateway_api.database.models import SESSION
 from datagateway_api.src.api_start_utils import (
     create_api_endpoints,
     create_app_infrastructure,

test/db/conftest.py

@@ -4,11 +4,11 @@
 import pytest
 
 from datagateway_api.common.constants import Constants
-from datagateway_api.common.database.helpers import (
+from datagateway_api.common.datagateway_api.database.helpers import (
     delete_row_by_id,
     insert_row_into_table,
 )
-from datagateway_api.common.database.models import (
+from datagateway_api.common.datagateway_api.database.models import (
     FACILITYCYCLE,
     INSTRUMENT,
     INVESTIGATION,

test/db/endpoints/test_ping_db.py

@@ -3,8 +3,8 @@
 import pytest
 from sqlalchemy.exc import SQLAlchemyError
 
-from datagateway_api.common.backends import create_backend
 from datagateway_api.common.constants import Constants
+from datagateway_api.common.datagateway_api.backends import create_backend
 from datagateway_api.common.exceptions import DatabaseError
 
 

test/db/test_database_filter_utilities.py

@@ -1,7 +1,9 @@
 import pytest
 
-from datagateway_api.common.database.filters import DatabaseFilterUtilities
-from datagateway_api.common.database.helpers import ReadQuery
+from datagateway_api.common.datagateway_api.database.filters import (
+    DatabaseFilterUtilities,
+)
+from datagateway_api.common.datagateway_api.database.helpers import ReadQuery
 from datagateway_api.common.exceptions import FilterError
 from datagateway_api.common.helpers import get_entity_object_from_name
 

test/db/test_entity_helper.py

@@ -1,7 +1,7 @@
 import pytest
 
 from datagateway_api.common.constants import Constants
-from datagateway_api.common.database.models import (
+from datagateway_api.common.datagateway_api.database.models import (
     DATAFILE,
     DATAFILEFORMAT,
     DATASET,

test/db/test_query_filter_factory.py

@@ -1,14 +1,16 @@
 import pytest
 
-from datagateway_api.common.database.filters import (
+from datagateway_api.common.datagateway_api.database.filters import (
     DatabaseDistinctFieldFilter,
     DatabaseIncludeFilter,
     DatabaseLimitFilter,
     DatabaseOrderFilter,
     DatabaseSkipFilter,
     DatabaseWhereFilter,
 )
-from datagateway_api.common.query_filter_factory import QueryFilterFactory
+from datagateway_api.common.datagateway_api.query_filter_factory import (
+    QueryFilterFactory,
+)
 
 
 class TestQueryFilterFactory:

test/icat/endpoints/test_ping_icat.py

@@ -3,10 +3,12 @@
 from icat.exception import ICATError
 import pytest
 
-from datagateway_api.common.backends import create_backend
 from datagateway_api.common.constants import Constants
+from datagateway_api.common.datagateway_api.backends import create_backend
+from datagateway_api.common.datagateway_api.icat.icat_client_pool import (
+    create_client_pool,
+)
 from datagateway_api.common.exceptions import PythonICATError
-from datagateway_api.common.icat.icat_client_pool import create_client_pool
 
 
 class TestICATPing:

test/icat/filters/test_distinct_filter.py

@@ -1,7 +1,9 @@
 import pytest
 
+from datagateway_api.common.datagateway_api.icat.filters import (
+    PythonICATDistinctFieldFilter,
+)
 from datagateway_api.common.exceptions import FilterError
-from datagateway_api.common.icat.filters import PythonICATDistinctFieldFilter
 
 
 class TestICATDistinctFilter:

test/icat/filters/test_include_filter.py

@@ -1,7 +1,7 @@
 import pytest
 
+from datagateway_api.common.datagateway_api.icat.filters import PythonICATIncludeFilter
 from datagateway_api.common.exceptions import FilterError
-from datagateway_api.common.icat.filters import PythonICATIncludeFilter
 
 
 class TestICATIncludeFilter: