Merge branch 'master' into feature/configurable-backend-#125

common/backend.py

@@ -128,28 +128,6 @@ def update_with_id(self, session_id, entity_type, id, data):
         """
         pass
 
-    @abstractmethod
-    def get_users_investigations_with_filters(self, session_id, user_id, filters):
-        """
-        Given a user id and a list of filters, return a filtered list of all investigations that belong to that user
-        :param session_id: The session id of the requesting user
-        :param user_id: The id of the user
-        :param filters: The list of filters
-        :return: A list of dictionary representations of the investigation entities
-        """
-        pass
-
-    @abstractmethod
-    def count_users_investigations_with_filters(self, session_id, user_id, filters):
-        """
-        Given a user id and a list of filters, return the count of all investigations that belong to that user
-        :param session_id: The session id of the requesting user
-        :param user_id: The id of the user
-        :param filters: The list of filters
-        :return: The count
-        """
-        pass
-
     @abstractmethod
     def get_instrument_facilitycycles_with_filters(self, session_id, instrument_id, filters):
         """

common/database_backend.py

@@ -1,6 +1,5 @@
 from common.backend import Backend
-from common.database_helpers import get_investigations_for_user, get_investigations_for_user_count, \
-    get_facility_cycles_for_instrument, get_facility_cycles_for_instrument_count, \
+from common.database_helpers import get_facility_cycles_for_instrument, get_facility_cycles_for_instrument_count, \
     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, insert_row_into_table, \
     delete_row_by_id, update_row_from_id, get_filtered_row_count, get_first_filtered_row
@@ -78,16 +77,6 @@ def delete_with_id(self, session_id, table, id):
     def update_with_id(self, session_id, table, id, data):
         return update_row_from_id(table, id, data)
 
-    @requires_session_id
-    @queries_records
-    def get_users_investigations_with_filters(self, session_id, user_id, filters):
-        return get_investigations_for_user(user_id, filters)
-
-    @requires_session_id
-    @queries_records
-    def count_users_investigations_with_filters(self, session_id, user_id, filters):
-        return get_investigations_for_user_count(user_id, filters)
-
     @requires_session_id
     @queries_records
     def get_instrument_facilitycycles_with_filters(self, session_id, instrument_id, filters):

common/database_helpers.py

@@ -516,54 +516,6 @@ def patch_entities(table, json_list):
     return results
 
 
-class UserInvestigationsQuery(ReadQuery):
-    """
-    The query class used for the /users/<:id>/investigations endpoint
-    """
-
-    def __init__(self, user_id):
-        super().__init__(INVESTIGATION)
-        self.base_query = self.base_query.join(INVESTIGATIONUSER).filter(
-            INVESTIGATIONUSER.USER_ID == user_id)
-
-
-def get_investigations_for_user(user_id, filters):
-    """
-    Given a user id and a list of filters, return a filtered list of all investigations that belong to that user
-    :param user_id: The id of the user
-    :param filters: The list of filters
-    :return: A list of dictionary representations of the investigation entities
-    """
-    with UserInvestigationsQuery(user_id) as query:
-        filter_handler = FilterOrderHandler()
-        return get_filtered_read_query_results(filter_handler, filters, query)
-
-
-class UserInvestigationsCountQuery(CountQuery):
-    """
-    The query class used for /users/<:id>/investigations/count
-    """
-
-    def __init__(self, user_id):
-        super().__init__(INVESTIGATION)
-        self.base_query = self.base_query.join(INVESTIGATIONUSER).filter(
-            INVESTIGATIONUSER.USER_ID == user_id)
-
-
-def get_investigations_for_user_count(user_id, filters):
-    """
-    Given a user id and a list of filters, return the count of all investigations that belong to that user
-    :param user_id: The id of the user
-    :param filters: The list of filters
-    :return: The count
-    """
-    with UserInvestigationsCountQuery(user_id) as count_query:
-        filter_handler = FilterOrderHandler()
-        filter_handler.add_filters(filters)
-        filter_handler.apply_filters(count_query)
-        return count_query.get_count()
-
-
 class InstrumentFacilityCyclesQuery(ReadQuery):
     def __init__(self, instrument_id):
         super().__init__(FACILITYCYCLE)

src/main.py

@@ -9,9 +9,8 @@
     get_find_one_endpoint
 from src.resources.entities.entity_map import endpoints
 from src.resources.non_entities.sessions_endpoints import *
-from src.resources.table_endpoints.table_endpoints import UsersInvestigations, UsersInvestigationsCount, \
-    InstrumentsFacilityCycles, InstrumentsFacilityCyclesCount, InstrumentsFacilityCyclesInvestigations, \
-    InstrumentsFacilityCyclesInvestigationsCount
+from src.resources.table_endpoints.table_endpoints import InstrumentsFacilityCycles, InstrumentsFacilityCyclesCount, \
+    InstrumentsFacilityCyclesInvestigations, InstrumentsFacilityCyclesInvestigationsCount
 from common.exceptions import ApiError
 from apispec import APISpec
 from pathlib import Path
@@ -79,11 +78,6 @@ def handle_error(e):
 spec.path(resource=Sessions, api=api)
 
 # Table specific endpoints
-api.add_resource(UsersInvestigations, "/users/<int:id>/investigations")
-spec.path(resource=UsersInvestigations, api=api)
-api.add_resource(UsersInvestigationsCount,
-                 "/users/<int:id>/investigations/count")
-spec.path(resource=UsersInvestigationsCount, api=api)
 api.add_resource(InstrumentsFacilityCycles,
                  "/instruments/<int:id>/facilitycycles")
 spec.path(resource=InstrumentsFacilityCycles, api=api)

src/resources/entities/entity_endpoint.py

@@ -196,7 +196,7 @@ def delete(self, id):
             parameters:
                 - in: path
                   required: true
-                  name: ID
+                  name: id
                   description: The id of the entity to delete
                   schema:
                     type: integer
@@ -227,7 +227,7 @@ def patch(self, id):
             parameters:
                 - in: path
                   required: true
-                  name: ID
+                  name: id
                   description: The id of the entity to update
                   schema:
                     type: integer
@@ -283,6 +283,7 @@ def get(self):
             parameters:
                 - WHERE_FILTER
                 - DISTINCT_FILTER
+                - INCLUDE_FILTER
             responses:
                 200:
                     description: Success - The count of the {table.__name__} objects

src/resources/table_endpoints/table_endpoints.py

@@ -1,90 +1,11 @@
 from flask_restful import Resource
 
-from common.database_helpers import get_investigations_for_user, get_investigations_for_user_count, \
-    get_facility_cycles_for_instrument, get_facility_cycles_for_instrument_count, \
+from common.database_helpers import get_facility_cycles_for_instrument, get_facility_cycles_for_instrument_count, \
     get_investigations_for_instrument_in_facility_cycle, get_investigations_for_instrument_in_facility_cycle_count
 from common.helpers import get_session_id_from_auth_header, get_filters_from_query_string
 from common.backends import backend
 
 
-class UsersInvestigations(Resource):
-    def get(self, id):
-        """
-        ---
-        summary: Get a user's Investigations
-        description: Retrieve the investigations that a user of a given ID is an InvestigationUser on, subject to filters.
-        tags:
-            - Investigations
-        parameters:
-            - in: path
-              required: true
-              name: ID
-              description: The id of the user to retrieve the investigations of
-              schema:
-                type: integer
-            - WHERE_FILTER
-            - ORDER_FILTER
-            - LIMIT_FILTER
-            - SKIP_FILTER
-            - DISTINCT_FILTER
-            - INCLUDE_FILTER
-        responses:
-            200:
-                description: Success - returns a list of the user's investigations that satisfy the filters
-                content:
-                    application/json:
-                        schema:
-                            type: array
-                            items:
-                                $ref: '#/components/schemas/INVESTIGATION'
-            400:
-                description: Bad request - Something was wrong with the request
-            401:
-                description: Unauthorized - No session ID was found in the HTTP Authorization header
-            403:
-                description: Forbidden - The session ID provided is invalid
-            404:
-                description: No such record - Unable to find a record in the database
-        """
-        return backend.get_investigations_for_user(get_session_id_from_auth_header(), id, get_filters_from_query_string()), 200
-
-
-class UsersInvestigationsCount(Resource):
-    def get(self, id):
-        """
-        ---
-        summary: Count a user's Investigations
-        description: Return the count of the Investigations that belong to a given user that would be retrieved given the filters provided
-        tags:
-            - Investigations
-        parameters:
-            - in: path
-              required: true
-              name: ID
-              description: The id of the user to count the investigations of
-              schema:
-                type: integer
-            - WHERE_FILTER
-            - DISTINCT_FILTER
-        responses:
-            200:
-                description: Success - The count of the user's investigations that satisfy the filters
-                content:
-                    application/json:
-                        schema:
-                            type: integer
-            400:
-                description: Bad request - Something was wrong with the request
-            401:
-                description: Unauthorized - No session ID was found in the HTTP Authorization header
-            403:
-                description: Forbidden - The session ID provided is invalid
-            404:
-                description: No such record - Unable to find a record in the database
-        """
-        return backend.get_investigations_for_user_count(get_session_id_from_auth_header(), id, get_filters_from_query_string()), 200
-
-
 class InstrumentsFacilityCycles(Resource):
     def get(self, id):
         """
@@ -96,7 +17,7 @@ def get(self, id):
         parameters:
             - in: path
               required: true
-              name: ID
+              name: id
               description: The id of the instrument to retrieve the facility cycles of
               schema:
                 type: integer
@@ -138,7 +59,7 @@ def get(self, id):
         parameters:
             - in: path
               required: true
-              name: ID
+              name: id
               description: The id of the instrument to count the facility cycles of
               schema:
                 type: integer
@@ -174,13 +95,13 @@ def get(self, instrument_id, cycle_id):
         parameters:
             - in: path
               required: true
-              name: Instrument ID
+              name: instrument_id
               description: The id of the instrument to retrieve the investigations of
               schema:
                 type: integer
             - in: path
               required: true
-              name: Facility Cycle ID
+              name: cycle_id
               description: The id of the facility cycles to retrieve the investigations of
               schema:
                 type: integer
@@ -198,7 +119,7 @@ def get(self, instrument_id, cycle_id):
                         schema:
                             type: array
                             items:
-                                $ref: '#/components/schemas/INVESTIGATIONS'
+                                $ref: '#/components/schemas/INVESTIGATION'
             400:
                 description: Bad request - Something was wrong with the request
             401:
@@ -223,13 +144,13 @@ def get(self, instrument_id, cycle_id):
         parameters:
             - in: path
               required: true
-              name: Instrument ID
+              name: instrument_id
               description: The id of the instrument to retrieve the investigations of
               schema:
                 type: integer
             - in: path
               required: true
-              name: Facility Cycle ID
+              name: cycle_id
               description: The id of the facility cycles to retrieve the investigations of
               schema:
                 type: integer