Merge pull request #220 from NHSDigital/Feature-Firely-Validation

omarisgreat · web-flow · commit 79530f97e175 · 2026-04-15T10:30:42.000+01:00
QC fixes
diff --git a/.github/workflows/firely-validation-dotnet.yaml b/.github/workflows/firely-validation-dotnet.yaml
diff --git a/.github/workflows/firely-validation.yml b/.github/workflows/firely-validation.yml
@@ -45,8 +45,8 @@ jobs:
           PATH_TO_CONFORMANCE_RESOURCES: StructureDefinition ValueSet CodeSystem
           PATH_TO_EXAMPLES: ActivityDefinition AuditEvent BodyStructure Bundle CapabilityStatement Composition ConceptMap Condition Consent Device DiagnosticReport DocumentReference FamilyMemberHistory GraphDefinition Group Library MessageDefinition MessageHeader NamingSystem Observation OperationDefinition OperationOutcome Organization Parameters Patient PlanDefinition Practitioner PractitionerRole Procedure Provenance Questionnaire QuestionnaireResponse RelatedPerson RequestGroup SearchParameter ServiceRequest Specimen SpecimenDefinition StructureMap Subscription Task
           PATH_TO_QUALITY_CONTROL_RULES: custom
-          DOTNET_VALIDATION_ENABLED: false
-          JAVA_VALIDATION_ENABLED: true
+          DOTNET_VALIDATION_ENABLED: true
+          JAVA_VALIDATION_ENABLED: false
           #EXPECTED_FAILS: VALIDATION_EXAMPLES_JAVA
           SIMPLIFIER_USERNAME: ${{ secrets.SIMPLIFIER_USERNAME }}
           SIMPLIFIER_PASSWORD: ${{ secrets.SIMPLIFIER_PASSWORD }}
diff --git a/.github/workflows/terminology.yml b/.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:
   
   workflow_dispatch:
   
diff --git a/ActivityDefinition/DGTS-ActivityDefinition-Example.json b/ActivityDefinition/DGTS-ActivityDefinition-Example.json
@@ -14,6 +14,7 @@
   }
  ],
  "title": "15q11 critical region (AS/PWS) - MLPA or equivalent",
+ "name": "GT1_ActivityDefinition",
  "version": "1.0",
  "status": "active",
  "experimental": false,
diff --git a/Bundle/Bundle-NonWGSTestOrderForm-Example.json b/Bundle/Bundle-NonWGSTestOrderForm-Example.json
@@ -360,7 +360,7 @@
       {
        "system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
        "code": "inactive",
-       "display": "inactive"
+       "display": "Inactive"
       }
      ]
     },
diff --git a/Bundle/Bundle-NonWGSTestOrderForm-Reanalysis-Example.json b/Bundle/Bundle-NonWGSTestOrderForm-Reanalysis-Example.json
@@ -380,7 +380,7 @@
       {
        "system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
        "code": "inactive",
-       "display": "inactive"
+       "display": "Inactive"
       }
      ]
     },
diff --git a/Bundle/Bundle-WGSTestOrderForm-Example.json b/Bundle/Bundle-WGSTestOrderForm-Example.json
@@ -373,7 +373,7 @@
       {
        "system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
        "code": "inactive",
-       "display": "inactive"
+       "display": "Inactive"
       }
      ]
     },
diff --git a/Condition/Condition-InbornErrorOfMetabolism-Example.json b/Condition/Condition-InbornErrorOfMetabolism-Example.json
@@ -15,7 +15,7 @@
       {
         "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
         "code": "unconfirmed",
-        "display": "unconfirmed"
+        "display": "Unconfirmed"
       }
     ]
   },
diff --git a/Condition/Condition-MonogenicHearingLoss-Example.json b/Condition/Condition-MonogenicHearingLoss-Example.json
@@ -6,7 +6,7 @@
       {
         "system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
         "code": "inactive",
-        "display": "inactive"
+        "display": "Inactive"
       }
     ]
   },
diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json
@@ -1,13 +1,6 @@
 {
  "resourceType": "DiagnosticReport",
  "id": "DiagnosticReport-GenomicVariantAssessment-Example",
- "meta": {
-  "profile": [
-   "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report",
-   "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport",
-   "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab"
-  ]
- },
  "extension": [
   {
    "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition",
diff --git a/Library/DGTS-Library-Example.json b/Library/DGTS-Library-Example.json
@@ -2,6 +2,7 @@
   "resourceType": "Library",
   "id": "DGTS-Library-Example",
   "url": "https://fhir.nhs.uk/Library/GT1",
+  "name": "GT1_Library"
   "type": {
     "coding": [
       {
diff --git a/Observation/Observation-GenomicTherapeuticImplication-Example.json b/Observation/Observation-GenomicTherapeuticImplication-Example.json
@@ -1,12 +1,6 @@
 {
  "resourceType": "Observation",
  "id": "Observation-GenomicTherapeuticImplication-Example",
- "meta": {
-  "profile": [
-   "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication",
-   "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab"
-  ]
- },
  "status": "final",
  "category": [
   {
diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json
@@ -1,12 +1,6 @@
 {
  "resourceType": "Observation",
  "id": "Observation-GenomicsVariantSLC52A2-Example",
- "meta": {
-  "profile": [
-   "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant",
-   "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab"
-  ]
- },
  "status": "final",
  "basedOn": [
   {
diff --git a/PlanDefinition/DGTS-PlanDefinition-Example.json b/PlanDefinition/DGTS-PlanDefinition-Example.json
@@ -14,6 +14,7 @@
   }
  ],
  "title": "Angelman syndrome",
+ "name": "TP321_PlanDefinition",
  "status": "active",
  "experimental": false,
  "version": "1.0",
diff --git a/custom.rules.yaml b/custom.rules.yaml
@@ -1,5 +1,3 @@
- # This is the minimal rule series
- 
 - action: parse
   name: parse-fhir-resources 
   status: "Checking if all FHIR Resource files can be parsed"
@@ -20,11 +18,16 @@
         - eld-16
         - ref-1
         - dom-6
+        - 1012 #ref-1
+        - 4005 # forgotten
+        - CONFIG #errors in dependencies e.g. loops, outdated, pre-release
+        - 6006 #failure to contact term service
+        - 1030 #reference loop
  
 - action: unique
   name: unique-canonicals
   status: "Checking if all StructureDefinitions have a unique canonical"
   category: StructureDefinition
   unique: url 
 
-# - include: manifest
+# - include: manifest
diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json
@@ -1,18 +1,39 @@
 {
-  "updated": "2026-03-26T11:41:42.0351721+00:00",
+  "updated": "2026-04-15T10:02:40.6338296+01:00",
   "dependencies": {
     "hl7.fhir.r4.core": "4.0.1",
-    "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot",
-    "hl7.fhir.uv.ips": "1.1.0",
-    "fhir.dicom": "2022.4.20221006",
-    "hl7.fhir.eu.laboratory": "0.1.0-ballot",
     "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release",
-    "ihe.iti.pcf": "1.0.0-comment",
-    "hl7.fhir.r4b.core": "4.3.0",
-    "us.nlm.vsac": "0.9.0",
-    "ihe.iti.balp": "1.1.1",
     "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1",
-    "hl7.terminology.r4": "7.1.0"
+    "hl7.fhir.uv.xver-r5.r4": "0.1.0",
+    "hl7.terminology.r4": "7.1.0",
+    "hl7.fhir.uv.genomics-reporting": "3.0.0",
+    "hl7.fhir.uv.ips": "2.0.0",
+    "hl7.fhir.uv.ipa": "1.1.0",
+    "hl7.fhir.eu.laboratory": "0.1.1",
+    "hl7.fhir.eu.extensions": "0.1.1",
+    "hl7.terminology.r5": "6.5.0",
+    "hl7.fhir.uv.extensions.r5": "5.2.0",
+    "hl7.fhir.r5.core": "5.0.0",
+    "ihe.iti.pcf": "1.1.0",
+    "ihe.iti.balp": "1.1.4",
+    "hl7.fhir.us.mcode": "4.0.0",
+    "hl7.fhir.us.core": "6.1.0",
+    "hl7.fhir.uv.bulkdata": "2.0.0",
+    "hl7.fhir.uv.smart-app-launch": "2.1.0",
+    "us.nlm.vsac": "0.11.0",
+    "hl7.fhir.uv.sdc": "3.0.0",
+    "hl7.fhir.r4.examples": "4.0.1",
+    "us.cdc.phinvads": "0.12.0",
+    "ihe.formatcode.fhir": "1.1.0",
+    "fhir.r4.nhsengland.pathology": "0.1.4-alpha",
+    "fhir.r4.ukcore.stu2": "2.0.2",
+    "hl7.fhir.eu.extensions.r4": "1.2.0",
+    "hl7.fhir.eu.base": "2.0.0-ballot",
+    "ihe.pharm.mpd.r4": "1.0.0-comment-2",
+    "fhir.r4.nhsengland.programme": "0.23.3-pre-release",
+    "fhir.tx.support.r4": "0.27.0",
+    "fhir.r4.nhsengland.stu1": "1.5.0",
+    "hl7.fhir.uv.tools.r4": "1.1.2"
   },
   "missing": {}
 }
diff --git a/package.json b/package.json
@@ -4,15 +4,20 @@
   "author": "nhsdigital",
   "dependencies": {
     "hl7.fhir.r4.core": "4.0.1",
-    "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot",
-    "hl7.fhir.uv.ips": "1.1.0",
-    "hl7.fhir.eu.laboratory": "0.1.0-ballot",
     "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release",
-    "ihe.iti.pcf": "1.0.0-comment",
-    "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1"
+    "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1",
+    "hl7.fhir.uv.xver-r5.r4": "0.1.0",
+    "hl7.fhir.uv.genomics-reporting": "3.0.0",
+    "hl7.fhir.uv.ips": "2.0.0",
+    "hl7.fhir.eu.laboratory": "0.1.1",
+    "ihe.iti.pcf": "1.1.0",
+    "hl7.fhir.us.mcode": "4.0.0",
+    "fhir.r4.nhsengland.pathology": "0.1.4-alpha",
+    "fhir.r4.nhsengland.programme": "0.23.3-pre-release",
+    "hl7.fhir.uv.tools.r4": "1.1.2"
   },
   "fhirVersions": [
     "4.0.1"
   ],
-  "jurisdiction": "urn:iso:std:iso:3166:-2:GB-ENG"
-}
+  "jurisdiction": "urn:iso:std:iso:3166:-2#GB"
+}

Original file line number	Diff line number	Diff line change
`@@ -14,6 +14,7 @@`
`14`	`14`	`}`
`15`	`15`	`],`
`16`	`16`	`"title": "15q11 critical region (AS/PWS) - MLPA or equivalent",`
	`17`	`+ "name": "GT1_ActivityDefinition",`
`17`	`18`	`"version": "1.0",`
`18`	`19`	`"status": "active",`
`19`	`20`	`"experimental": false,`
Original file line number	Diff line number	Diff line change
`@@ -360,7 +360,7 @@`
`360`	`360`	`{`
`361`	`361`	`"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",`
`362`	`362`	`"code": "inactive",`
`363`		`- "display": "inactive"`
	`363`	`+ "display": "Inactive"`
`364`	`364`	`}`
`365`	`365`	`]`
`366`	`366`	`},`
Original file line number	Diff line number	Diff line change
`@@ -380,7 +380,7 @@`
`380`	`380`	`{`
`381`	`381`	`"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",`
`382`	`382`	`"code": "inactive",`
`383`		`- "display": "inactive"`
	`383`	`+ "display": "Inactive"`
`384`	`384`	`}`
`385`	`385`	`]`
`386`	`386`	`},`
Original file line number	Diff line number	Diff line change
`@@ -373,7 +373,7 @@`
`373`	`373`	`{`
`374`	`374`	`"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",`
`375`	`375`	`"code": "inactive",`
`376`		`- "display": "inactive"`
	`376`	`+ "display": "Inactive"`
`377`	`377`	`}`
`378`	`378`	`]`
`379`	`379`	`},`
Original file line number	Diff line number	Diff line change
`@@ -15,7 +15,7 @@`
`15`	`15`	`{`
`16`	`16`	`"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",`
`17`	`17`	`"code": "unconfirmed",`
`18`		`- "display": "unconfirmed"`
	`18`	`+ "display": "Unconfirmed"`
`19`	`19`	`}`
`20`	`20`	`]`
`21`	`21`	`},`
Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,7 @@`
`6`	`6`	`{`
`7`	`7`	`"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",`
`8`	`8`	`"code": "inactive",`
`9`		`- "display": "inactive"`
	`9`	`+ "display": "Inactive"`
`10`	`10`	`}`
`11`	`11`	`]`
`12`	`12`	`},`
Original file line number	Diff line number	Diff line change
`@@ -1,13 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"resourceType": "DiagnosticReport",`
`3`	`3`	`"id": "DiagnosticReport-GenomicVariantAssessment-Example",`
`4`		`- "meta": {`
`5`		`- "profile": [`
`6`		`- "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report",`
`7`		`- "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport",`
`8`		`- "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab"`
`9`		`- ]`
`10`		`- },`
`11`	`4`	`"extension": [`
`12`	`5`	`{`
`13`	`6`	`"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition",`