Patch iops 4298 genomics validation issues

.github/workflows/firely-validation.yml

@@ -5,11 +5,11 @@ name: Firely Validation
 # Controls when the action will run. 
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
-  push:
-    branches: 
-      - '**'
-  pull_request:
-   branches: [ master, main ]
+  #push:
+    #branches: 
+      #- '**'
+  #pull_request:
+   #branches: [ master, main ]
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 

.github/workflows/terminology.yml

@@ -5,7 +5,7 @@ on:
   # Triggers the workflow on push or pull request events but only for the master branch
   # Allows you to run this workflow manually from the Actions tab
 
-  #push:
+  push:
 
   # Allows you to run this workflow manually from the Actions tab
 

StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json

@@ -46,23 +46,6 @@
         "id": "BodyStructure.locationQualifier",
         "path": "BodyStructure.locationQualifier",
         "definition": "SHALL be provided where relevant. SHOULD use SNOMED CT encoding."
-      },
-      {
-        "id": "BodyStructure.patient",
-        "path": "BodyStructure.patient",
-        "type": [
-          {
-            "code": "Reference",
-            "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics",
-              "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient"
-            ],
-            "aggregation": [
-              "referenced",
-              "bundled"
-            ]
-          }
-        ]
       }
     ]
   }

StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json

@@ -2,11 +2,11 @@
   "resourceType": "StructureDefinition",
   "id": "NHSEngland-Composition-GenomicsEULabReport",
   "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport",
-  "version": "0.3.0",
+  "version": "0.4.0",
   "name": "NHSEngland_Composition_GenomicsEULabReport",
   "title": "NHSEngland Composition GenomicsEULabReport",
   "status": "active",
-  "date": "2026-04-16",
+  "date": "2026-06-03",
   "publisher": "NHS England",
   "contact": [
     {
@@ -32,81 +32,6 @@
   "derivation": "constraint",
   "differential": {
     "element": [
-      {
-        "id": "Composition.extension:basedOn-order-or-requisition",
-        "path": "Composition.extension",
-        "sliceName": "basedOn-order-or-requisition",
-        "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the ServiceRequest which this report is in response to."
-      },
-      {
-        "id": "Composition.extension:basedOn-order-or-requisition.value[x]:valueReference",
-        "path": "Composition.extension.value[x]",
-        "sliceName": "valueReference",
-        "type": [
-          {
-            "code": "Reference",
-            "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics",
-              "http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab"
-            ],
-            "aggregation": [
-              "referenced",
-              "bundled"
-            ]
-          }
-        ]
-      },
-      {
-        "id": "Composition.extension:information-recipient",
-        "path": "Composition.extension",
-        "sliceName": "information-recipient",
-        "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the recipient for a report, could potentially be used to reference additional recipients over the subject and original requester for the request."
-      },
-      {
-        "id": "Composition.extension:information-recipient.value[x]",
-        "path": "Composition.extension.value[x]",
-        "type": [
-          {
-            "code": "Reference",
-            "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics",
-              "http://hl7.eu/fhir/laboratory/StructureDefinition/Practitioner-eu-lab",
-              "http://hl7.org/fhir/StructureDefinition/Device",
-              "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab",
-              "http://hl7.org/fhir/StructureDefinition/RelatedPerson",
-              "http://hl7.eu/fhir/laboratory/StructureDefinition/PractitionerRole-eu-lab",
-              "http://hl7.org/fhir/StructureDefinition/Organization"
-            ],
-            "aggregation": [
-              "referenced",
-              "bundled"
-            ]
-          }
-        ]
-      },
-      {
-        "id": "Composition.extension:diagnosticReport-reference",
-        "path": "Composition.extension",
-        "sliceName": "diagnosticReport-reference",
-        "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the focal DiagnosticReport this Composition is for."
-      },
-      {
-        "id": "Composition.extension:diagnosticReport-reference.value[x]",
-        "path": "Composition.extension.value[x]",
-        "type": [
-          {
-            "code": "Reference",
-            "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport",
-              "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab"
-            ],
-            "aggregation": [
-              "referenced",
-              "bundled"
-            ]
-          }
-        ]
-      },
       {
         "id": "Composition.status",
         "path": "Composition.status",
@@ -116,89 +41,21 @@
       {
         "id": "Composition.type",
         "path": "Composition.type",
-        "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)"
-      },
-      {
-        "id": "Composition.type.coding",
-        "path": "Composition.type.coding",
-        "slicing": {
-          "discriminator": [
+        "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)",
+        "fixedCodeableConcept": {
+          "coding": [
             {
-              "type": "pattern",
-              "path": "$this"
+              "system": "http://snomed.info/sct",
+              "code": "1054161000000101"
             }
-          ],
-          "rules": "open"
-        }
-      },
-      {
-        "id": "Composition.type.coding.display.extension:translation",
-        "path": "Composition.type.coding.display.extension",
-        "sliceName": "translation"
-      },
-      {
-        "id": "Composition.type.coding.display.extension:translation.extension",
-        "path": "Composition.type.coding.display.extension.extension",
-        "min": 2
-      },
-      {
-        "id": "Composition.type.coding:codingGenomics",
-        "path": "Composition.type.coding",
-        "sliceName": "codingGenomics",
-        "fixedCoding": {
-          "system": "http://snomed.info/sct",
-          "code": "1054161000000101",
-          "display": "Genetic report"
+          ]
         }
       },
-      {
-        "id": "Composition.type.coding:codingGenomics.display.extension:translation",
-        "path": "Composition.type.coding.display.extension",
-        "sliceName": "translation"
-      },
-      {
-        "id": "Composition.type.coding:codingGenomics.display.extension:translation.extension",
-        "path": "Composition.type.coding.display.extension.extension",
-        "min": 2
-      },
-      {
-        "id": "Composition.type.text.extension:translation",
-        "path": "Composition.type.text.extension",
-        "sliceName": "translation"
-      },
-      {
-        "id": "Composition.type.text.extension:translation.extension",
-        "path": "Composition.type.text.extension.extension",
-        "min": 2
-      },
       {
         "id": "Composition.category",
         "path": "Composition.category",
-        "slicing": {
-          "rules": "open"
-        },
         "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)."
       },
-      {
-        "id": "Composition.category.coding.display.extension:translation",
-        "path": "Composition.category.coding.display.extension",
-        "sliceName": "translation"
-      },
-      {
-        "id": "Composition.category.coding.display.extension:translation.extension",
-        "path": "Composition.category.coding.display.extension.extension",
-        "min": 2
-      },
-      {
-        "id": "Composition.category.text.extension:translation",
-        "path": "Composition.category.text.extension",
-        "sliceName": "translation"
-      },
-      {
-        "id": "Composition.category.text.extension:translation.extension",
-        "path": "Composition.category.text.extension.extension",
-        "min": 2
-      },
       {
         "id": "Composition.category:studyType",
         "path": "Composition.category",
@@ -235,8 +92,7 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics",
-              "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab",
+              "http://hl7.eu/fhir/base/StructureDefinition/patient-eu-core",
               "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab",
               "http://hl7.org/fhir/StructureDefinition/Group",
               "http://hl7.org/fhir/StructureDefinition/Location",
@@ -265,46 +121,19 @@
         "definition": "SHALL match the SNOMED CT display used within Composition.type",
         "fixedString": "Genetic report"
       },
-      {
-        "id": "Composition.section",
-        "path": "Composition.section",
-        "slicing": {
-          "rules": "open"
-        },
-        "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development."
-      },
-      {
-        "id": "Composition.section.code.coding.display.extension:translation",
-        "path": "Composition.section.code.coding.display.extension",
-        "sliceName": "translation"
-      },
-      {
-        "id": "Composition.section.code.coding.display.extension:translation.extension",
-        "path": "Composition.section.code.coding.display.extension.extension",
-        "min": 2
-      },
-      {
-        "id": "Composition.section.code.text.extension:translation",
-        "path": "Composition.section.code.text.extension",
-        "sliceName": "translation"
-      },
-      {
-        "id": "Composition.section.code.text.extension:translation.extension",
-        "path": "Composition.section.code.text.extension.extension",
-        "min": 2
-      },
       {
         "id": "Composition.section:sectionUGR",
         "path": "Composition.section",
         "sliceName": "sectionUGR",
-        "definition": "Sections included within the UGR: patient-demographics | investigations-and-procedures-requested | investigation-results | consent-for-information-sharing |  family-history "
+        "definition": "Sections included within UGR",
+        "min": 0,
+        "max": "*"
       },
       {
         "id": "Composition.section:sectionUGR.code",
         "path": "Composition.section.code",
         "binding": {
           "strength": "extensible",
-          "description": "UK Core Composition Section Codes",
           "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode"
         }
       }

StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json

@@ -2,11 +2,11 @@
   "resourceType": "StructureDefinition",
   "id": "NHSEngland-DiagnosticReport-GenomicReport",
   "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport",
-  "version": "0.3.0",
+  "version": "0.4.0",
   "name": "NHSEngland_DiagnosticReport_GenomicReport",
   "title": "NHSEngland DiagnosticReport GenomicReport",
   "status": "active",
-  "date": "2026-04-16",
+  "date": "2026-06-03",
   "publisher": "NHS England",
   "contact": [
     {
@@ -61,21 +61,6 @@
         "path": "DiagnosticReport.extension.value[x].type",
         "fixedCode": "citation"
       },
-      {
-        "id": "DiagnosticReport.extension:diagnosticReportCompositionR5",
-        "path": "DiagnosticReport.extension",
-        "sliceName": "diagnosticReportCompositionR5",
-        "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: DiagnosticReport Profile). A reference to the Composition which wraps this report for data sharing.",
-        "type": [
-          {
-            "code": "Extension",
-            "profile": [
-              "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition"
-            ]
-          }
-        ],
-        "isModifier": false
-      },
       {
         "id": "DiagnosticReport.identifier",
         "path": "DiagnosticReport.identifier",
@@ -169,7 +154,6 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics",
               "http://hl7.org/fhir/StructureDefinition/CarePlan",
               "http://hl7.org/fhir/StructureDefinition/ImmunizationRecommendation",
               "http://hl7.org/fhir/StructureDefinition/MedicationRequest",
@@ -190,9 +174,6 @@
       {
         "id": "DiagnosticReport.category",
         "path": "DiagnosticReport.category",
-        "slicing": {
-          "rules": "open"
-        },
         "definition": "Potentially multiple categories to specify the specialty the report is relevant for. Different codings are expected by the Genomic Report and EU Lab profiles."
       },
       {
@@ -245,7 +226,6 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics",
               "http://hl7.org/fhir/StructureDefinition/Patient",
               "http://hl7.org/fhir/StructureDefinition/Group",
               "http://hl7.org/fhir/StructureDefinition/Device",
@@ -270,7 +250,6 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization",
               "http://hl7.org/fhir/StructureDefinition/Practitioner",
               "http://hl7.org/fhir/StructureDefinition/PractitionerRole",
               "http://hl7.org/fhir/StructureDefinition/Organization",
@@ -306,7 +285,6 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics",
               "http://hl7.org/fhir/StructureDefinition/Practitioner",
               "http://hl7.org/fhir/StructureDefinition/PractitionerRole",
               "http://hl7.org/fhir/StructureDefinition/Organization",
@@ -328,7 +306,6 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Specimen-Genomics",
               "http://hl7.org/fhir/StructureDefinition/Specimen"
             ],
             "aggregation": [
@@ -373,7 +350,6 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DocumentReference-Genomics",
               "http://hl7.org/fhir/StructureDefinition/Resource"
             ],
             "aggregation": [