NRL-0000 Merge branch 'develop' into feature/imaging

Author: mattdean3-nhs

.github/workflows/pr-env-deploy.yml

@@ -20,6 +20,7 @@ jobs:
   set-environment-id:
     name: Set Environment ID
     runs-on: [self-hosted, ci]
+    environment: pull-request
     steps:
       - name: Set a ID based on the branch name
         id: set_environment_id
@@ -44,6 +45,7 @@ jobs:
   build:
     name: Build Application
     runs-on: [self-hosted, ci]
+    environment: pull-request
     steps:
       - name: Git Clone - ${{ github.event.pull_request.head.ref }}
         uses: actions/checkout@v4

Makefile

@@ -198,18 +198,22 @@ generate-models: check-warn ## Generate Pydantic Models
 		--input ./api/producer/swagger.yaml \
 		--input-file-type openapi \
 		--output ./layer/nrlf/producer/fhir/r4/model.py \
-		--output-model-type "pydantic_v2.BaseModel"
+		--output-model-type "pydantic_v2.BaseModel" \
+		--base-class nrlf.core.parent_model.Parent
 	poetry run datamodel-codegen \
 		--strict-types {str,bytes,int,float,bool} \
 		--input ./api/producer/swagger.yaml \
 		--input-file-type openapi \
 		--output ./layer/nrlf/producer/fhir/r4/strict_model.py \
+		--base-class nrlf.core.parent_model.Parent \
 		--output-model-type "pydantic_v2.BaseModel"
 
+
 	@echo "Generating consumer model"
 	mkdir -p ./layer/nrlf/consumer/fhir/r4
 	poetry run datamodel-codegen \
 		--input ./api/consumer/swagger.yaml \
 		--input-file-type openapi \
 		--output ./layer/nrlf/consumer/fhir/r4/model.py \
+		--base-class nrlf.core.parent_model.Parent \
 		--output-model-type "pydantic_v2.BaseModel"

api/consumer/searchDocumentReference/tests/test_search_document_reference_consumer.py

@@ -3,6 +3,7 @@
 from moto import mock_aws
 
 from api.consumer.searchDocumentReference.search_document_reference import handler
+from nrlf.consumer.fhir.r4.model import CodeableConcept, Identifier
 from nrlf.core.constants import (
     CATEGORY_ATTRIBUTES,
     TYPE_ATTRIBUTES,
@@ -66,7 +67,9 @@ def test_search_document_reference_accession_number_in_pointer(
 ):
     doc_ref = load_document_reference("Y05868-736253002-Valid")
     doc_ref.identifier = [
-        {"type": {"text": "Accession-Number"}, "value": "Y05868.123456789"}
+        Identifier(
+            type=CodeableConcept(text="Accession-Number"), value="Y05868.123456789"
+        )
     ]
     doc_pointer = DocumentPointer.from_document_reference(doc_ref)
     repository.create(doc_pointer)

api/producer/createDocumentReference/tests/test_create_document_reference.py

@@ -239,6 +239,36 @@ def test_create_document_reference_invalid_body():
                 "diagnostics": "Request body could not be parsed (status: Field required)",
                 "expression": ["status"],
             },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (type: Field required)",
+                "expression": ["type"],
+            },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (category: Field required)",
+                "expression": ["category"],
+            },
             {
                 "severity": "error",
                 "code": "invalid",

api/producer/swagger.yaml

@@ -1381,12 +1381,12 @@ components:
           enum: ["entered-in-error", "amended", "preliminary", "final"]
           description: The status of the underlying document.
         type:
-          $ref: "#/components/schemas/CodeableConcept"
+          $ref: "#/components/schemas/NRLCodeableConcept"
           description: Specifies the particular kind of document referenced  (e.g. History and Physical, Discharge Summary, Progress Note). This usually equates to the purpose of making the document referenced.
         category:
           type: array
           items:
-            $ref: "#/components/schemas/CodeableConcept"
+            $ref: "#/components/schemas/NRLCodeableConcept"
             description: A categorization for the type of document referenced – helps for indexing and searching. This may be implied by or derived from the code specified in the DocumentReference.type.
         subject:
           $ref: "#/components/schemas/Reference"
@@ -1413,7 +1413,7 @@ components:
             description: Relationships that this document has with other document references that already exist.
         description:
           type: string
-          pattern: "[ \\r\\n\\t\\S]+"
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: Human–readable description of the source document.
         securityLabel:
           type: array
@@ -1435,6 +1435,8 @@ components:
         - content
         - author
         - context
+        - type
+        - category
     Bundle:
       type: object
       properties:
@@ -1634,7 +1636,7 @@ components:
           $ref: "#/components/schemas/CodeableConcept"
           description: The kind of facility where the patient was seen.
         practiceSetting:
-          $ref: "#/components/schemas/CodeableConcept"
+          $ref: "#/components/schemas/NRLCodeableConcept"
           description: This property may convey specifics about the practice setting where the content was created, often reflecting the clinical specialty.
         sourcePatientInfo:
           $ref: "#/components/schemas/Reference"
@@ -1720,7 +1722,7 @@ components:
           description: The calculated hash of the data using SHA–1. Represented using base64.
         title:
           type: string
-          pattern: "[ \\r\\n\\t\\S]+"
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: A label or set of text to display in place of the data.
         creation:
           type: string
@@ -1743,8 +1745,29 @@ components:
             description: A reference to a code defined by a terminology system.
         text:
           type: string
-          pattern: "[ \\r\\n\\t\\S]+"
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
+          description: A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.
+    NRLCodeableConcept:
+      type: object
+      properties:
+        id:
+          type: string
+          pattern: "[A-Za-z0-9\\-\\.]{1,64}"
+          description: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
+        coding:
+          type: array
+          items:
+            $ref: "#/components/schemas/NRLCoding"
+            description: A reference to a code defined by a terminology system.
+          minItems: 1
+          maxItems: 1
+        text:
+          type: string
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.
+      required:
+        - coding
+
     Coding:
       type: object
       properties:
@@ -1754,23 +1777,53 @@ components:
           description: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
         system:
           type: string
-          pattern: \S*
+          pattern: \S+
           description: The identification of the code system that defines the meaning of the symbol in the code.
         version:
           type: string
-          pattern: "[ \\r\\n\\t\\S]+"
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: The version of the code system which was used when choosing this code. Note that a well–maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.
         code:
           type: string
           pattern: "[^\\s]+(\\s[^\\s]+)*"
           description: A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post–coordination).
         display:
           type: string
-          pattern: "[ \\r\\n\\t\\S]+"
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: A representation of the meaning of the code in the system, following the rules of the system.
         userSelected:
           type: boolean
           description: Indicates that this coding was chosen by a user directly – e.g. off a pick list of available items (codes or displays).
+    NRLCoding:
+      type: object
+      properties:
+        id:
+          type: string
+          pattern: "[A-Za-z0-9\\-\\.]{1,64}"
+          description: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
+        system:
+          type: string
+          pattern: \S+
+          description: The identification of the code system that defines the meaning of the symbol in the code.
+        version:
+          type: string
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
+          description: The version of the code system which was used when choosing this code. Note that a well–maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.
+        code:
+          type: string
+          pattern: "[^\\s]+(\\s[^\\s]+)*"
+          description: A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post–coordination).
+        display:
+          type: string
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
+          description: A representation of the meaning of the code in the system, following the rules of the system.
+        userSelected:
+          type: boolean
+          description: Indicates that this coding was chosen by a user directly – e.g. off a pick list of available items (codes or displays).
+      required:
+        - system
+        - code
+        - display
     Extension:
       type: object
       properties:
@@ -1874,11 +1927,11 @@ components:
           description: A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.
         system:
           type: string
-          pattern: \S*
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: Establishes the namespace for the value – that is, a URL that describes a set values that are unique.
         value:
           type: string
-          pattern: "[ \\r\\n\\t\\S]+"
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: The portion of the identifier typically relevant to the user and which is unique within the context of the system.
         period:
           $ref: "#/components/schemas/Period"
@@ -1917,11 +1970,11 @@ components:
           description: How the value should be understood and represented &ndash; whether the actual value is greater or less than the stated value due to measurement issues; e.g. if the comparator is "<" , then the real value is < stated value.
         unit:
           type: string
-          pattern: "[ \\r\\n\\t\\S]+"
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: A human&ndash;readable form of the unit.
         system:
           type: string
-          pattern: \S*
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: The identification of the system that provides the coded form of the unit.
         code:
           type: string
@@ -1936,11 +1989,11 @@ components:
           description: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
         reference:
           type: string
-          pattern: "[ \\r\\n\\t\\S]+"
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.
         type:
           type: string
-          pattern: \S*
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: |-
             The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.
             The type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. "Patient" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).
@@ -1949,7 +2002,7 @@ components:
           description: An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.
         display:
           type: string
-          pattern: "[ \\r\\n\\t\\S]+"
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: Plain text narrative that identifies the resource in addition to the resource reference.
     Signature:
       type: object
@@ -2007,13 +2060,13 @@ components:
           description: When the resource last changed &ndash; e.g. when the version changed.
         source:
           type: string
-          pattern: \S*
+          pattern: "[\\S]+[ \\r\\n\\t\\S]*"
           description: A uri that identifies the source system of the resource. This provides a minimal amount of [Provenance](provenance.html#) information that can be used to track or differentiate the source of information in the resource. The source may identify another FHIR server, document, message, database, etc.
         profile:
           type: array
           items:
             type: string
-            pattern: \S*
+            pattern: "[\\S]+[ \\r\\n\\t\\S]*"
             description: A list of profiles (references to [StructureDefinition](structuredefinition.html#) resources) that this resource claims to conform to. The URL is a reference to [StructureDefinition.url](structuredefinition&ndash;definitions.html#StructureDefinition.url).
         security:
           type: array

api/producer/updateDocumentReference/tests/test_update_document_reference.py

@@ -195,7 +195,7 @@ def test_create_document_reference_no_body():
     }
 
 
-def test_create_document_reference_invalid_body():
+def test_update_document_reference_invalid_body():
     event = create_test_api_gateway_event(
         headers=create_headers(),
         path_parameters={"id": "Y05868-99999-99999-999999"},
@@ -246,6 +246,36 @@ def test_create_document_reference_invalid_body():
                 "diagnostics": "Request body could not be parsed (status: Field required)",
                 "expression": ["status"],
             },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (type: Field required)",
+                "expression": ["type"],
+            },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (category: Field required)",
+                "expression": ["category"],
+            },
             {
                 "severity": "error",
                 "code": "invalid",
@@ -562,7 +592,6 @@ def test_update_document_reference_immutable_fields(repository):
             )
         ],
         text=None,
-        extension=None,
     )
 
     event = create_test_api_gateway_event(

api/producer/upsertDocumentReference/tests/test_upsert_document_reference.py

@@ -324,6 +324,36 @@ def test_upsert_document_reference_invalid_body():
                 "diagnostics": "Request body could not be parsed (status: Field required)",
                 "expression": ["status"],
             },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (type: Field required)",
+                "expression": ["type"],
+            },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (category: Field required)",
+                "expression": ["category"],
+            },
             {
                 "severity": "error",
                 "code": "invalid",