From fe9623b9f618a43ea6772f5094190209916ced2c Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Wed, 21 Oct 2020 11:15:56 +0000
Subject: [PATCH 01/10]  #166: Fix Swagger data parsing for entity by ID
 endpoints

---
 src/resources/entities/entity_endpoint.py        | 6 +++---
 src/resources/table_endpoints/table_endpoints.py | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/resources/entities/entity_endpoint.py b/src/resources/entities/entity_endpoint.py
index 0addd080..26202bbb 100644
--- a/src/resources/entities/entity_endpoint.py
+++ b/src/resources/entities/entity_endpoint.py
@@ -181,7 +181,7 @@ def get(self, id_):
             parameters:
                 - in: path
                   required: true
-                  name: id
+                  name: id_
                   description: The id of the entity to retrieve
                   schema:
                     type: integer
@@ -215,7 +215,7 @@ def delete(self, id_):
             parameters:
                 - in: path
                   required: true
-                  name: id
+                  name: id_
                   description: The id of the entity to delete
                   schema:
                     type: integer
@@ -246,7 +246,7 @@ def patch(self, id_):
             parameters:
                 - in: path
                   required: true
-                  name: id
+                  name: id_
                   description: The id of the entity to update
                   schema:
                     type: integer
diff --git a/src/resources/table_endpoints/table_endpoints.py b/src/resources/table_endpoints/table_endpoints.py
index d2584c89..aed0e1e7 100644
--- a/src/resources/table_endpoints/table_endpoints.py
+++ b/src/resources/table_endpoints/table_endpoints.py
@@ -24,7 +24,7 @@ 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
@@ -71,7 +71,7 @@ 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

From 7d0205c8e3ea8c4d5715e972a852234222e3ec02 Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Wed, 21 Oct 2020 11:26:33 +0000
Subject: [PATCH 02/10]  #166: Adapt example filter inputs for ICAT backend

---
 src/swagger/initialise_spec.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/swagger/initialise_spec.py b/src/swagger/initialise_spec.py
index 5147b3ff..17347d49 100644
--- a/src/swagger/initialise_spec.py
+++ b/src/swagger/initialise_spec.py
@@ -101,11 +101,11 @@ def initialise_spec(spec):
                 },
             },
             "examples": {
-                "eq": {"value": [{"ID": {"eq": 1}}]},
-                "like": {"value": [{"NAME": {"like": "dog"}}]},
-                "gte": {"value": [{"ID": {"gte": 50}}]},
-                "lte": {"value": [{"ID": {"lte": 50}}]},
-                "in": {"value": [{"ID": {"in": [1, 2, 3]}}]},
+                "eq": {"value": {"id": {"eq": 1}}},
+                "like": {"value": [{"name": {"like": "dog"}}]},
+                "gte": {"value": [{"id": {"gte": 50}}]},
+                "lte": {"value": [{"id": {"lte": 50}}]},
+                "in": {"value": [{"id": {"in": [1, 2, 3]}}]},
             },
         },
     )
@@ -118,7 +118,7 @@ def initialise_spec(spec):
             "name": "order",
             "description": "Apply order filters to the query. Given a field and direction, order the returned entities.",
             "schema": {"type": "array", "items": {"type": "string"}},
-            "examples": {"asc": {"value": ["ID asc"]}, "desc": {"value": ["ID desc"]}},
+            "examples": {"asc": {"value": ["id asc"]}, "desc": {"value": ["id desc"]}},
         },
     )
 

From 6666f292d1a412d244f809b8495e4f8bde98632d Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Wed, 21 Oct 2020 11:41:06 +0000
Subject: [PATCH 03/10]  #166: Add not equal to DB where filter

- This will match the functionality seen in the Python ICAT version of the WHERE filter, so I can put an example of this operation in the Swagger docs
---
 common/database/filters.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/common/database/filters.py b/common/database/filters.py
index 8eba4e36..a6a33d08 100644
--- a/common/database/filters.py
+++ b/common/database/filters.py
@@ -71,6 +71,8 @@ def apply_filter(self, query):
 
         if self.operation == "eq":
             query.base_query = query.base_query.filter(field == self.value)
+        elif self.operation == "ne":
+            query.base_query = query.base_query.filter(field != self.value)
         elif self.operation == "like":
             query.base_query = query.base_query.filter(field.like(f"%{self.value}%"))
         elif self.operation == "lt":

From 27249111d892468e9b659e7a76e780e0bbd4e1c0 Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Wed, 21 Oct 2020 11:59:19 +0000
Subject: [PATCH 04/10]  #166: Add examples to match all possible WHERE filter
 operations

- Also modified description to aid users if they're having issues getting example values to work
---
 src/swagger/initialise_spec.py | 55 +++++++++++++++++++++++++++++-----
 1 file changed, 48 insertions(+), 7 deletions(-)

diff --git a/src/swagger/initialise_spec.py b/src/swagger/initialise_spec.py
index 17347d49..56af459f 100644
--- a/src/swagger/initialise_spec.py
+++ b/src/swagger/initialise_spec.py
@@ -25,7 +25,7 @@ def initialise_spec(spec):
         {
             "in": "query",
             "name": "where",
-            "description": "Apply where filters to the query. The possible operators are like, gte, lte, in and eq",
+            "description": "Apply where filters to the query. The possible operators are like, gte, lte, in and eq. Please modify the examples before executing a request if you are having issues with the example values.",
             "schema": {
                 "type": "array",
                 "items": {
@@ -53,9 +53,28 @@ def initialise_spec(spec):
                             },
                             {
                                 "type": "object",
-                                "title": "Greater than or equal",
+                                "title": "Inequality",
                                 "properties": {
-                                    "gte": {
+                                    "ne": {
+                                        "oneOf": [
+                                            {"type": "string"},
+                                            {"type": "number"},
+                                            {"type": "integer"},
+                                            {"type": "boolean"},
+                                        ]
+                                    }
+                                },
+                            },
+                            {
+                                "type": "object",
+                                "title": "Substring equality",
+                                "properties": {"like": {"type": "string"}},
+                            },
+                            {
+                                "type": "object",
+                                "title": "Less than",
+                                "properties": {
+                                    "lt": {
                                         "oneOf": [
                                             {"type": "number"},
                                             {"type": "integer"},
@@ -77,8 +96,27 @@ def initialise_spec(spec):
                             },
                             {
                                 "type": "object",
-                                "title": "Substring equality",
-                                "properties": {"like": {"type": "string"}},
+                                "title": "Greater than",
+                                "properties": {
+                                    "gt": {
+                                        "oneOf": [
+                                            {"type": "number"},
+                                            {"type": "integer"},
+                                        ]
+                                    }
+                                },
+                            },
+                            {
+                                "type": "object",
+                                "title": "Greater than or equal",
+                                "properties": {
+                                    "gte": {
+                                        "oneOf": [
+                                            {"type": "number"},
+                                            {"type": "integer"},
+                                        ]
+                                    }
+                                },
                             },
                             {
                                 "type": "object",
@@ -101,10 +139,13 @@ def initialise_spec(spec):
                 },
             },
             "examples": {
-                "eq": {"value": {"id": {"eq": 1}}},
+                "eq": {"value": [{"id": {"eq": 1}}]},
+                "ne": {"value": [{"id": {"ne": 1}}]},
                 "like": {"value": [{"name": {"like": "dog"}}]},
-                "gte": {"value": [{"id": {"gte": 50}}]},
+                "lt": {"value": [{"id": {"lt": 10}}]},
                 "lte": {"value": [{"id": {"lte": 50}}]},
+                "gt": {"value": [{"id": {"gt": 10}}]},
+                "gte": {"value": [{"id": {"gte": 50}}]},  
                 "in": {"value": [{"id": {"in": [1, 2, 3]}}]},
             },
         },

From 588158c3e20de986baaa74a4a2141175ca7a2209 Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Wed, 21 Oct 2020 12:00:15 +0000
Subject: [PATCH 05/10]  #166: Add modified OpenAPI YAML from recent
 modifications

---
 src/swagger/openapi.yaml | 294 ++++++++++++++++++++++-----------------
 1 file changed, 165 insertions(+), 129 deletions(-)

diff --git a/src/swagger/openapi.yaml b/src/swagger/openapi.yaml
index db6fbe18..0146a91f 100644
--- a/src/swagger/openapi.yaml
+++ b/src/swagger/openapi.yaml
@@ -69,10 +69,10 @@ components:
       examples:
         asc:
           value:
-          - ID asc
+          - id asc
         desc:
           value:
-          - ID desc
+          - id desc
       in: query
       name: order
       schema:
@@ -88,31 +88,44 @@ components:
         type: integer
     WHERE_FILTER:
       description: Apply where filters to the query. The possible operators are like,
-        gte, lte, in and eq
+        gte, lte, in and eq. Please modify the examples before executing a request
+        if you are having issues with the example values.
       examples:
         eq:
           value:
-          - ID:
+          - id:
               eq: 1
+        gt:
+          value:
+          - id:
+              gt: 10
         gte:
           value:
-          - ID:
+          - id:
               gte: 50
         in:
           value:
-          - ID:
+          - id:
               in:
               - 1
               - 2
               - 3
         like:
           value:
-          - NAME:
+          - name:
               like: dog
+        lt:
+          value:
+          - id:
+              lt: 10
         lte:
           value:
-          - ID:
+          - id:
               lte: 50
+        ne:
+          value:
+          - id:
+              ne: 1
       in: query
       name: where
       schema:
@@ -132,11 +145,25 @@ components:
               title: Equality
               type: object
             - properties:
-                gte:
+                ne:
                   oneOf:
+                  - type: string
                   - type: number
                   - type: integer
-              title: Greater than or equal
+                  - type: boolean
+              title: Inequality
+              type: object
+            - properties:
+                like:
+                  type: string
+              title: Substring equality
+              type: object
+            - properties:
+                lt:
+                  oneOf:
+                  - type: number
+                  - type: integer
+              title: Less than
               type: object
             - properties:
                 lte:
@@ -146,9 +173,18 @@ components:
               title: Less than or equal
               type: object
             - properties:
-                like:
-                  type: string
-              title: Substring equality
+                gt:
+                  oneOf:
+                  - type: number
+                  - type: integer
+              title: Greater than
+              type: object
+            - properties:
+                gte:
+                  oneOf:
+                  - type: number
+                  - type: integer
+              title: Greater than or equal
               type: object
             - properties:
                 in:
@@ -1871,7 +1907,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -1895,7 +1931,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -1924,7 +1960,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2122,7 +2158,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2146,7 +2182,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2175,7 +2211,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2375,7 +2411,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2399,7 +2435,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2428,7 +2464,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2629,7 +2665,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2653,7 +2689,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2682,7 +2718,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2882,7 +2918,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2906,7 +2942,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -2935,7 +2971,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3133,7 +3169,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3157,7 +3193,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3186,7 +3222,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3384,7 +3420,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3408,7 +3444,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3437,7 +3473,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3636,7 +3672,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3660,7 +3696,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3689,7 +3725,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3887,7 +3923,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3911,7 +3947,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -3940,7 +3976,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4139,7 +4175,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4163,7 +4199,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4192,7 +4228,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4390,7 +4426,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4414,7 +4450,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4443,7 +4479,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4641,7 +4677,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4665,7 +4701,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4694,7 +4730,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4892,7 +4928,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4916,7 +4952,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -4945,7 +4981,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5143,7 +5179,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5167,7 +5203,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5196,7 +5232,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5394,7 +5430,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5418,7 +5454,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5447,7 +5483,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5646,7 +5682,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5670,7 +5706,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5699,7 +5735,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5897,7 +5933,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5921,7 +5957,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -5950,7 +5986,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6150,7 +6186,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6174,7 +6210,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6203,7 +6239,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6403,7 +6439,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6427,7 +6463,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6456,7 +6492,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6656,7 +6692,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6680,7 +6716,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6709,7 +6745,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6908,7 +6944,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6932,7 +6968,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -6961,7 +6997,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7160,7 +7196,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7184,7 +7220,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7213,7 +7249,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7410,7 +7446,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7434,7 +7470,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7463,7 +7499,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7661,7 +7697,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7685,7 +7721,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7714,7 +7750,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7912,7 +7948,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7936,7 +7972,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -7965,7 +8001,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8163,7 +8199,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8187,7 +8223,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8216,7 +8252,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8416,7 +8452,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8440,7 +8476,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8469,7 +8505,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8667,7 +8703,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8691,7 +8727,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8720,7 +8756,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8918,7 +8954,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8942,7 +8978,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -8971,7 +9007,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9169,7 +9205,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9193,7 +9229,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9222,7 +9258,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9420,7 +9456,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9444,7 +9480,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9473,7 +9509,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9672,7 +9708,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9696,7 +9732,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9725,7 +9761,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9922,7 +9958,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9946,7 +9982,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -9975,7 +10011,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10172,7 +10208,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10196,7 +10232,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10225,7 +10261,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10422,7 +10458,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10446,7 +10482,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10475,7 +10511,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10673,7 +10709,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10697,7 +10733,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10726,7 +10762,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10925,7 +10961,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10949,7 +10985,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -10978,7 +11014,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -11175,7 +11211,7 @@ paths:
       parameters:
       - description: The id of the entity to delete
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -11199,7 +11235,7 @@ paths:
       parameters:
       - description: The id of the entity to retrieve
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -11228,7 +11264,7 @@ paths:
       parameters:
       - description: The id of the entity to update
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -11425,7 +11461,7 @@ paths:
       parameters:
       - description: The id of the instrument to retrieve the facility cycles of
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer
@@ -11465,7 +11501,7 @@ paths:
       parameters:
       - description: The id of the instrument to count the facility cycles of
         in: path
-        name: id
+        name: id_
         required: true
         schema:
           type: integer

From efb732c9c5ba670e10cb7edbdf584649f4604094 Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Wed, 21 Oct 2020 13:28:28 +0000
Subject: [PATCH 06/10]  #134: Make file adhere to Black's 88 character/line
 rule

- Since the Python files in the repo adhere to this limit, it seems sensible that the README file also following this formatting rule where possible
---
 README.md | 93 +++++++++++++++++++++++++++++++------------------------
 1 file changed, 52 insertions(+), 41 deletions(-)

diff --git a/README.md b/README.md
index 600507d7..ee5b7cfb 100644
--- a/README.md
+++ b/README.md
@@ -17,10 +17,9 @@ ICAT API to interface with the Data Gateway
   - [Running Tests](#running-tests)
 
 
-
-
 ## Requirements
-All requirements can be installed with `pip install -r requirements.txt`, and all development requirements can be installed with `pip install -r dev-requirements.txt`
+All requirements can be installed with `pip install -r requirements.txt`, and all
+development requirements can be installed with `pip install -r dev-requirements.txt`
 
 The required python libraries:  
    - [SQLAlchemy](https://www.sqlalchemy.org/)    
@@ -30,17 +29,20 @@ The required python libraries:
    - [pip-tools](https://github.com/jazzband/pip-tools) (For generating requirements.txt)
 
 ## Setup and running the API   
-The database connection needs to be set up first. This is set in config.json, an example config file called `config.json.example` is provided.
+The database connection needs to be set up first. This is set in config.json, an example
+config file called `config.json.example` is provided.
 
 Ideally the API would be run with:  
 `python -m src.main`
 However it can be run with the flask run command as shown below:
   
   
-**Warning: the host, port and debug config options will not be respected when the API is run this way**
+**Warning: the host, port and debug config options will not be respected when the API is 
+run this way**
 
-To use `flask run`, the enviroment variable `FLASK_APP` should be set to `src/main.py`. Once this is 
-set the API can be run with `flask run` while inside the root directory of the project. The `flask run` command gets installed with flask.   
+To use `flask run`, the enviroment variable `FLASK_APP` should be set to `src/main.py`.
+Once this is set the API can be run with `flask run` while inside the root directory of
+the project. The `flask run` command gets installed with flask.
 
 Examples shown:  
 Unix
@@ -69,10 +71,10 @@ e.g.
 `http://localhost:5000/sessions`
 
 
-
 ## Project structure
-The project consists of 3 main packages: common, src and test. common contains modules shared across test and src such as the database mapping classes.
-src contains the api resources and their http method definitions, and test contains tests for each endpoint.
+The project consists of 3 main packages: common, src and test. common contains modules
+shared across test and src such as the database mapping classes. src contains the api
+resources and their http method definitions, and test contains tests for each endpoint.
 
 This is illustrated below.
 
@@ -118,59 +120,67 @@ This is illustrated below.
     └── config.json
  `````
 #### Main
-`main.py` is where the flask_restful api is set up. This is where each endpoint resource class is generated and mapped 
-to an endpoint.
+`main.py` is where the flask_restful api is set up. This is where each endpoint resource
+class is generated and mapped to an endpoint.
 
 Example:  
- `api.add_resource(get_endpoint(entity_name, endpoints[entity_name]), f"/{entity_name.lower()}")`	   
+```python
+api.add_resource(get_endpoint(entity_name, endpoints[entity_name]), f"/{entity_name.lower()}")
+```
    
 
 #### Endpoints
-The logic for each endpoint are within `/src/resources`. They are split into entities, non_entities and 
-table_endpoints. The entities package contains `entities_map` which maps entity names to their sqlalchemy
-model. The `entity_endpoint` module contains the function that is used to generate endpoints at start up.
-`table_endpoints` contains the endpoint classes that are table specific. Finally, non_entities contains the
-session endpoint.
+The logic for each endpoint are within `/src/resources`. They are split into entities,
+non_entities and table_endpoints. The entities package contains `entities_map` which
+maps entity names to their sqlalchemy model. The `entity_endpoint` module contains the
+function that is used to generate endpoints at start up. `table_endpoints` contains the
+endpoint classes that are table specific. Finally, non_entities contains the session
+endpoint.
 
 
 #### Mapped classes
-The classes mapped from the database are stored in `/common/database/models.py`. Each model was 
-automatically generated using sqlacodegen. A class `EntityHelper` is defined so that each model may
-inherit two methods `to_dict()` and `update_from_dict(dictionary)`, both used for returning entities 
-and updating them, in a form easily converted to JSON.  
-
-
+The classes mapped from the database are stored in `/common/database/models.py`. Each
+model was automatically generated using sqlacodegen. A class `EntityHelper` is defined
+so that each model may inherit two methods `to_dict()` and 
+`update_from_dict(dictionary)`, both used for returning entities and updating them, in a
+form easily converted to JSON.  
 
 
 ## Database Generator
-There is a tool to generate mock data into the database. It is located in `util/icat_db_generator.py`
-By default it will generate 20 years worth of data (approx 70,000 entities). The script makes use of 
-`random` and `Faker` and is seeded with a seed of 1. The seed and number of years of data generated can 
-be changed by using the arg flags `-s` or `--seed` for the seed, and `-y` or `--years` for the number of years.
-For example:  
-`python -m util.icat_db_generator -s 4 -y 10` Would set the seed to 4 and generate 10 years of data.
+There is a tool to generate mock data into the database. It is located in
+`util/icat_db_generator.py`. By default it will generate 20 years worth of data (approx
+70,000 entities). The script makes use of `random` and `Faker` and is seeded with a seed
+of 1. The seed and number of years of data generated can be changed by using the arg
+flags `-s` or `--seed` for the seed, and `-y` or `--years` for the number of years. For
+example: `python -m util.icat_db_generator -s 4 -y 10` Would set the seed to 4 and
+generate 10 years of data.
 
 
 #### Querying and filtering:
-The querying and filtering logic is located in `/common/database_helpers.py`. In this module the abstract `Query` and
-`QueryFilter` classes are defined as well as their implementations. The functions that are used by various endpoints to
-query the database are also in this module.
-Class diagrams for this module:
+The querying and filtering logic is located in `/common/database_helpers.py`. In this
+module the abstract `Query` and `QueryFilter` classes are defined as well as their
+implementations. The functions that are used by various endpoints to query the database
+are also in this module.
+
+
+#### Class diagrams for this module:
 ![image](https://user-images.githubusercontent.com/44777678/67954353-ba69ef80-fbe8-11e9-81e3-0668cea3fa35.png)  
 ![image](https://user-images.githubusercontent.com/44777678/67954834-7fb48700-fbe9-11e9-96f3-ffefc7277ebd.png)
 
 
 #### Authentication
-Each request requires a valid session ID to be provided in the Authorization header. This header should take the form of `{"Authorization":"Bearer <session_id>"}` A session ID can be obtained by
-sending a post request to `/sessions/`  
-All endpoint methods that require a session id are decorated with `@requires_session_id`
+Each request requires a valid session ID to be provided in the Authorization header.
+This header should take the form of `{"Authorization":"Bearer <session_id>"}` A session
+ID can be obtained by sending a post request to `/sessions/`. All endpoint methods that
+require a session id are decorated with `@requires_session_id`
 
 
 
 #### Generating the swagger spec: `openapi.yaml`
-The swagger generation script is located in `/src/swagger/swagger_generator.py`. The script will only run when
-the config option `generate_swagger` is set to true in `config.json`. The generator decorates the first endpoint
-resource class in it's module to get the name of the entity. It then creates the correct paths using the name of the 
+The swagger generation script is located in `/src/swagger/swagger_generator.py`. The
+script will only run when the config option `generate_swagger` is set to true in
+`config.json`. The generator decorates the first endpoint resource class in it's module
+to get the name of the entity. It then creates the correct paths using the name of the
 entity and outputs the swagger spec to `openapi.yaml` 
 
 Example of the decorator:
@@ -191,6 +201,7 @@ To run the tests use `python -m unittest discover`
 When writing code for this repository, [Black](https://black.readthedocs.io/en/stable/)
 is used as the code linter/formatter to ensure the code is kept Pythonic. Installing
 the dev requirements will ensure this package is installed. This repository uses the
-default settings for Black; to use, execute the following command on the root directory of this repo:
+default settings for Black; to use, execute the following command on the root directory
+of this repo:
 
 `black .`

From c2e8099f00861e3c61cf945415091ecc03131c3b Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Wed, 21 Oct 2020 15:45:08 +0000
Subject: [PATCH 07/10]  #134: Edit Swagger doc section of README to reflect
 changes in generation

---
 README.md | 31 +++++++++++++++----------------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/README.md b/README.md
index ee5b7cfb..d67fceec 100644
--- a/README.md
+++ b/README.md
@@ -175,23 +175,22 @@ ID can be obtained by sending a post request to `/sessions/`. All endpoint metho
 require a session id are decorated with `@requires_session_id`
 
 
-
 #### Generating the swagger spec: `openapi.yaml`
-The swagger generation script is located in `/src/swagger/swagger_generator.py`. The
-script will only run when the config option `generate_swagger` is set to true in
-`config.json`. The generator decorates the first endpoint resource class in it's module
-to get the name of the entity. It then creates the correct paths using the name of the
-entity and outputs the swagger spec to `openapi.yaml` 
-
-Example of the decorator:
-```python
-@swagger_gen.resource_wrapper()
-class DataCollectionDatasets(Resource):
-    @requires_session_id
-    @queries_records
-    def get(self):
-        return get_rows_by_filter(DATACOLLECTIONDATASET, get_filters_from_query_string()), 200
-```
+When the config option `generate_swagger` is set to true in `config.json`, a YAML
+file defining the API using OpenAPI standards will be created at
+`src/swagger/openapi.yaml`. [apispec](https://apispec.readthedocs.io/en/latest/) is used
+to help with this, with an `APISpec()` object created in `src/main.py` which is added to
+(using `APISpec.path()`) when the endpoints are created for Flask. These paths are 
+iterated over and ordered alphabetically, to ensure `openapi.yaml` only changes if there
+have been changes to the Swagger docs of the API; without that code, Git will detect
+changes on that file everytime startup occurs (preventing a clean development repo). The
+contents of the `APISpec` object are written to a YAML file and is used when the user
+goes to the configured (root) page in their browser.
+
+The endpoint related files in `src/resources/` contain `__doc__` which have the Swagger
+docs for each type of endpoint. `src/resources/swagger/` contain code to aid Swagger doc
+generation, with a plugin (`RestfulPlugin`) created for `apispec` to extract Swagger
+documentation from `flask-restful` functions.
 
 
 ## Running Tests

From da21adb735c842b72da6bcb4e6806e286f974786 Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Wed, 21 Oct 2020 15:49:14 +0000
Subject: [PATCH 08/10]  #134: Misc. changes of existing sections in README

- Also updated `requirements.in` (with a freshly compiled `requirements.txt`) to reflect the requirement of Python ICAT
---
 README.md        | 12 +++++++++---
 requirements.in  |  2 +-
 requirements.txt |  2 +-
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index d67fceec..da152ef1 100644
--- a/README.md
+++ b/README.md
@@ -10,6 +10,8 @@ ICAT API to interface with the Data Gateway
       - [Main](#main)
       - [Endpoints](#endpoints)
       - [Mapped classes](#mapped-classes)
+      - [Database Generator](#database-generator)
+      - [Class Diagrams](#class-diagrams-for-this-module)
       - [Querying and filtering](#querying-and-filtering)
       - [Swagger Generation](#generating-the-swagger-spec-openapiyaml)
       - [Authentication](#authentication)
@@ -25,8 +27,12 @@ The required python libraries:
    - [SQLAlchemy](https://www.sqlalchemy.org/)    
    - [flask-restful](https://github.com/flask-restful/flask-restful/)  
    - [pymysql](https://pymysql.readthedocs.io/en/latest/)  
-   - [pyyaml](https://pyyaml.org/wiki/PyYAMLDocumentation) (For the swagger generation)
-   - [pip-tools](https://github.com/jazzband/pip-tools) (For generating requirements.txt)
+   - [apispec](https://apispec.readthedocs.io/en/latest/) (For the swagger generation)
+   - [pip-tools](https://github.com/jazzband/pip-tools) (For generating
+    requirements.txt)
+   - [python-icat](https://python-icat.readthedocs.io/en/stable) (For ICAT backend)
+    
+
 
 ## Setup and running the API   
 The database connection needs to be set up first. This is set in config.json, an example
@@ -196,7 +202,7 @@ documentation from `flask-restful` functions.
 ## Running Tests
 To run the tests use `python -m unittest discover`
 
-## Linter
+## Code Formatter
 When writing code for this repository, [Black](https://black.readthedocs.io/en/stable/)
 is used as the code linter/formatter to ensure the code is kept Pythonic. Installing
 the dev requirements will ensure this package is installed. This repository uses the
diff --git a/requirements.in b/requirements.in
index 8b8d42d8..1db77744 100644
--- a/requirements.in
+++ b/requirements.in
@@ -4,4 +4,4 @@ pymysql == 0.9.3
 flask-cors == 3.0.8
 apispec == 3.3.0
 flask-swagger-ui == 3.25.0
-pyyaml == 5.1.2
\ No newline at end of file
+python-icat == 0.17.0
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 752e3265..f6055a6c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -15,8 +15,8 @@ itsdangerous==1.1.0       # via flask
 jinja2==2.10.1            # via flask
 markupsafe==1.1.1         # via jinja2
 pymysql==0.9.3            # via -r requirements.in
+python-icat==0.17.0       # via -r requirements.in
 pytz==2019.2              # via flask-restful
-pyyaml==5.1.2             # via -r requirements.in
 six==1.12.0               # via flask-cors, flask-restful
 sqlalchemy==1.3.8         # via -r requirements.in
 werkzeug==0.16.0          # via flask

From 80943adebfdb2ffa3ae8677d1f6d327197e5f136 Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Thu, 22 Oct 2020 17:58:49 +0000
Subject: [PATCH 09/10]  #147: Misc. code formatting changes

---
 common/icat/helpers.py |  8 ++------
 common/icat/query.py   | 13 ++-----------
 2 files changed, 4 insertions(+), 17 deletions(-)

diff --git a/common/icat/helpers.py b/common/icat/helpers.py
index d1f8440a..85d9cc7b 100644
--- a/common/icat/helpers.py
+++ b/common/icat/helpers.py
@@ -487,9 +487,7 @@ def get_facility_cycles_for_instrument(
     log.info("Getting a list of facility cycles from the specified instrument for ISIS")
 
     query_aggregate = "COUNT:DISTINCT" if count_query else "DISTINCT"
-    query = ICATQuery(
-        client, "FacilityCycle", aggregate=query_aggregate
-    )
+    query = ICATQuery(client, "FacilityCycle", aggregate=query_aggregate)
 
     instrument_id_check = PythonICATWhereFilter(
         "facility.instruments.id", instrument_id, "eq"
@@ -572,9 +570,7 @@ def get_investigations_for_instrument_in_facility_cycle(
     )
 
     query_aggregate = "COUNT:DISTINCT" if count_query else "DISTINCT"
-    query = ICATQuery(
-        client, "Investigation", aggregate=query_aggregate
-    )
+    query = ICATQuery(client, "Investigation", aggregate=query_aggregate)
 
     instrument_id_check = PythonICATWhereFilter(
         "facility.instruments.id", instrument_id, "eq"
diff --git a/common/icat/query.py b/common/icat/query.py
index 99fa2d03..1808167f 100644
--- a/common/icat/query.py
+++ b/common/icat/query.py
@@ -15,12 +15,7 @@
 
 class ICATQuery:
     def __init__(
-        self,
-        client,
-        entity_name,
-        conditions=None,
-        aggregate=None,
-        includes=None,
+        self, client, entity_name, conditions=None, aggregate=None, includes=None,
     ):
         """
         Create a Query object within Python ICAT 
@@ -58,7 +53,6 @@ def __init__(
                 " suggesting an invalid argument"
             )
 
-
     def execute_query(self, client, return_json_formattable=False):
         """
         Execute the ICAT Query object and return in the format specified by the
@@ -93,10 +87,7 @@ def execute_query(self, client, return_json_formattable=False):
                 count_query = True
                 log.debug("This ICATQuery is used for COUNT purposes")
 
-        if (
-            self.query.aggregate == "DISTINCT"
-            and not count_query
-        ):
+        if self.query.aggregate == "DISTINCT" and not count_query:
             log.info("Extracting the distinct fields from query's conditions")
             # Check query's conditions for the ones created by the distinct filter
             distinct_attributes = self.iterate_query_conditions_for_distinctiveness()

From 511a8ef6c26625dd7f9289a5a101962b9a4b3b3f Mon Sep 17 00:00:00 2001
From: Matthew Richards <matthew.richards@stfc.ac.uk>
Date: Fri, 23 Oct 2020 15:37:21 +0000
Subject: [PATCH 10/10]  #147: Override handle_error on extended Api class

---
 src/main.py | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/main.py b/src/main.py
index f93805f8..819d7080 100644
--- a/src/main.py
+++ b/src/main.py
@@ -35,18 +35,21 @@
     security=[{"session_id": []}],
 )
 
-app = Flask(__name__)
-cors = CORS(app)
-app.url_map.strict_slashes = False
-api = Api(app)
-
 
-def handle_error(e):
-    return str(e), e.status_code
+class CustomErrorHandledApi(Api):
+    """
+    This class overrides `handle_error` function from the API class from `flask_restful`
+    to correctly return response codes and exception messages from uncaught exceptions
+    """
 
+    def handle_error(self, e):
+        return str(e), e.status_code
 
-app.register_error_handler(ApiError, handle_error)
 
+app = Flask(__name__)
+cors = CORS(app)
+app.url_map.strict_slashes = False
+api = CustomErrorHandledApi(app)
 
 swaggerui_blueprint = get_swaggerui_blueprint(
     "", "/openapi.json", config={"app_name": "DataGateway API OpenAPI Spec"},