From 077a4435cb3cb8dd7f786cb92241fe21432a6c91 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Thu, 9 Jul 2026 16:31:10 +0100 Subject: [PATCH 1/5] Remove empty slicing & R5 Extensions Remove empty slicing & R5 Extensions --- .github/workflows/firely-validation.yml | 10 ++--- .github/workflows/terminology.yml | 2 +- ...ngland-DiagnosticReport-GenomicReport.json | 18 --------- .../NHSEngland-Patient-Genomics.json | 3 -- .../NHSEngland-ServiceRequest-Genomics.json | 3 -- .../NHSEngland-Specimen-Genomics.json | 13 ------- package.json | 10 ++--- private.package.yaml | 39 +++++++++++++++++++ 8 files changed, 48 insertions(+), 50 deletions(-) create mode 100644 private.package.yaml diff --git a/.github/workflows/firely-validation.yml b/.github/workflows/firely-validation.yml index bb8cbd9..3e8518e 100644 --- a/.github/workflows/firely-validation.yml +++ b/.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: diff --git a/.github/workflows/terminology.yml b/.github/workflows/terminology.yml index 5174c15..a6f2ed8 100644 --- 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: # Allows you to run this workflow manually from the Actions tab diff --git a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json index be3df23..8d9a8e7 100644 --- a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json +++ b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json @@ -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", @@ -191,9 +176,6 @@ { "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." }, { diff --git a/StructureDefinition/NHSEngland-Patient-Genomics.json b/StructureDefinition/NHSEngland-Patient-Genomics.json index 5bee313..53a7a56 100644 --- a/StructureDefinition/NHSEngland-Patient-Genomics.json +++ b/StructureDefinition/NHSEngland-Patient-Genomics.json @@ -107,9 +107,6 @@ { "id": "Patient.identifier", "path": "Patient.identifier", - "slicing": { - "rules": "open" - }, "definition": "SHALL be present for Patients within the Genomic Order Management ecosystem. It is preferred that all patients with an NHS number have this included within the Patient resource upon submission of a test order. Patient who do not have an NHS number SHOULD have a temporary one registered/assigned with PDS.\r\nFor patient records where the NHS number has been traced from PDS, the trace status SHOULD be provided within the NHS Number identifier slice.\r\n\r\nAdditional identifiers SHOULD include an appropriate naming system scheme which clearly identifies the assigner (to disambiguate the identifier from other resources where these are not nationally unique). Alternatively, the OID for local identifier MAY be used, with the 'assigner' organization explicitly referenced.", "min": 1 }, diff --git a/StructureDefinition/NHSEngland-ServiceRequest-Genomics.json b/StructureDefinition/NHSEngland-ServiceRequest-Genomics.json index 30c3dfe..bcdd207 100644 --- a/StructureDefinition/NHSEngland-ServiceRequest-Genomics.json +++ b/StructureDefinition/NHSEngland-ServiceRequest-Genomics.json @@ -222,9 +222,6 @@ { "id": "ServiceRequest.category", "path": "ServiceRequest.category", - "slicing": { - "rules": "open" - }, "definition": "Category SHALL be populated with the reason for the request being ordered e.g. Diagnostic, Carrier, Predictive, Stored DNA etc. The final list of applicable codes which can be selected is still under review, the Genomic-ReasonforTesting ValueSet SHOULD be used for this categorisation.", "min": 1 }, diff --git a/StructureDefinition/NHSEngland-Specimen-Genomics.json b/StructureDefinition/NHSEngland-Specimen-Genomics.json index 9aadddf..54dfe10 100644 --- a/StructureDefinition/NHSEngland-Specimen-Genomics.json +++ b/StructureDefinition/NHSEngland-Specimen-Genomics.json @@ -302,19 +302,6 @@ "definition": "The UK Core STU3 version of Specimen backports the R5 changes to the container BackboneElement to support capturing of storage location for a sample (through `container.location`) and recursive capture of device identifiers (e.g. tube, well, rack, freezer through `container.device`).\r\nThe container.identifier should match the identifier associated with the barcode for the tube/collection device. This can be searched using the container-id SearchParameter.\r\n\r\nAdditional examples/guidance will be provided within this IG once use of the fields has been appropriately tested.\r\n\r\nSample tracking information SHOULD be added to Tasks acting on Specimen resources, e.g. Tasks marked SamplePreparation or SampleProcessing, on either the output or input elements. This information MAY include consignment number, destination, date sent etc.\r\n\r\nIf known, the container type SHOULD be populated, using the example bound ValueSet, in SNOMED CT. If an appropraite code cannot be found, the specimen container type should be populated using free text, in Specimen.container.type.text. Additional container elements, such as capacity or specimenQuantity MAY be populated if known.", "max": "1" }, - { - "id": "Specimen.container.extension:specimenContainerLocationR5", - "path": "Specimen.container.extension", - "sliceName": "specimenContainerLocationR5", - "type": [ - { - "code": "Extension", - "profile": [ - "http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.container.location" - ] - } - ] - }, { "id": "Specimen.condition", "path": "Specimen.condition", diff --git a/package.json b/package.json index 6510d2f..b83f8ec 100644 --- a/package.json +++ b/package.json @@ -3,19 +3,15 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", - "hl7.fhir.uv.xver-r5.r4": "0.1.0", +"hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "2.0.0", "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pars": "0.1.2-alpha", - "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "hl7.fhir.uv.tools.r4": "1.1.2", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", - "fhir.r4.ukcore.stu3.currentbuild": "0.29.0-pre-release" + "fhir.r4.ukcore.stu3.currentbuild": "0.29.0-pre-release", + "fhir.r4.nhsengland.pathology": "0.2.4-alpha" }, "fhirVersions": [ "4.0.1" diff --git a/private.package.yaml b/private.package.yaml new file mode 100644 index 0000000..789b101 --- /dev/null +++ b/private.package.yaml @@ -0,0 +1,39 @@ +implementationguides: + hl7-fhir-uv-extensions-r4: + name: hl7.fhir.uv.extensions.r4 + version: 5.3.0-ballot-tc1 + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7-fhir-uv-xver-r5-r4: + name: hl7.fhir.uv.xver-r5.r4 + version: 0.1.0 + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7-fhir-uv-ips: + name: hl7.fhir.uv.ips + version: 2.0.0 + installMode: STORE_AND_INSTALL + fetchDependencies: false + fhir-r4-nhsengland-pathology: + name: fhir.r4.nhsengland.pathology + version: 0.1.4-alpha + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7-fhir-uv-tools-r4: + name: hl7.fhir.uv.tools.r4 + version: 1.1.2 + installMode: STORE_AND_INSTALL + fhir-r4-nhsengland-nhse-identifiers: + name: fhir.r4.nhsengland.nhse-identifiers + version: 0.1.1-alpha + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7.fhir.us.core: + name: hl7.fhir.us.core + version: 6.1.0 + installMode: STORE_AND_INSTALL + hl7.fhir.us.mcode: + name: hl7.fhir.us.mcode + version: 4.0.0 + installMode: STORE_AND_INSTALL + fetchDependencies: false \ No newline at end of file From a97d977f2a78c6530c81917281e91cb8d1e67e0d Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Thu, 9 Jul 2026 16:35:28 +0100 Subject: [PATCH 2/5] Pathology-nhse-as-private move Pathology-nhse-as-private package --- package.json | 3 +-- private.package.yaml | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index b83f8ec..37dd20c 100644 --- a/package.json +++ b/package.json @@ -10,8 +10,7 @@ "fhir.r4.nhsengland.pars": "0.1.2-alpha", "hl7.fhir.uv.tools.r4": "1.1.2", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", - "fhir.r4.ukcore.stu3.currentbuild": "0.29.0-pre-release", - "fhir.r4.nhsengland.pathology": "0.2.4-alpha" + "fhir.r4.ukcore.stu3.currentbuild": "0.29.0-pre-release" }, "fhirVersions": [ "4.0.1" diff --git a/private.package.yaml b/private.package.yaml index 789b101..1ec8db8 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -16,7 +16,7 @@ implementationguides: fetchDependencies: false fhir-r4-nhsengland-pathology: name: fhir.r4.nhsengland.pathology - version: 0.1.4-alpha + version: 0.2.4-alpha installMode: STORE_AND_INSTALL fetchDependencies: false hl7-fhir-uv-tools-r4: From 2918efec105c47cb32aaf418fea9321facf78bba Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Thu, 9 Jul 2026 16:44:36 +0100 Subject: [PATCH 3/5] Empty Slicing issues Empty Slicing issues --- .../CodeSystem-Genomics-DGTS-testpackage-modality.json | 2 +- .../NHSEngland-Composition-GenomicsEULabReport.json | 6 ------ 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/CodeSystem/CodeSystem-Genomics-DGTS-testpackage-modality.json b/CodeSystem/CodeSystem-Genomics-DGTS-testpackage-modality.json index 75b16ca..30b67f4 100644 --- a/CodeSystem/CodeSystem-Genomics-DGTS-testpackage-modality.json +++ b/CodeSystem/CodeSystem-Genomics-DGTS-testpackage-modality.json @@ -26,7 +26,7 @@ "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", "caseSensitive": true, "content": "complete", - "count": 7, + "count": 9, "concept": [ { "code": "solid-cancer", diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index c31e397..ca4fa03 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -174,9 +174,6 @@ { "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)." }, { @@ -268,9 +265,6 @@ { "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." }, { From d341d3ab4c5fdb14b877aecdae335f45f618c0f9 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 9 Jul 2026 18:53:45 +0100 Subject: [PATCH 4/5] Update fhirpkg.lock.json Update fhirpkg.lock.json --- fhirpkg.lock.json | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 1237a67..64c0436 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,19 +1,27 @@ { - "updated": "2026-05-06T10:21:55.9845039+01:00", + "updated": "2026-07-09T18:47:18.0145474+01:00", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", - "hl7.fhir.uv.xver-r5.r4": "0.1.0", + "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "2.0.0", + "hl7.terminology.r4": "7.1.0", + "hl7.fhir.uv.extensions.r4": "5.2.0", + "hl7.fhir.uv.xver-r5.r4": "0.1.0", + "hl7.fhir.eu.extensions.r4": "1.3.0", + "hl7.fhir.eu.base": "2.0.0", + "ihe.pharm.mpd.r4": "1.0.0-comment-2", "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", + "us.nlm.vsac": "0.9.0", + "ihe.iti.balp": "1.1.4", "fhir.r4.nhsengland.pars": "0.1.2-alpha", - "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.uv.tools.r4": "1.1.2", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", + "fhir.r4.ukcore.stu2": "2.0.2", + "hl7.fhir.uv.ips": "2.0.0", + "hl7.fhir.uv.ipa": "1.1.0", + "hl7.fhir.uv.smart-app-launch": "2.0.0", + "fhir.r4.nhsengland.stu1": "1.5.0", + "hl7.fhir.uv.tools.r4": "1.1.2", "fhir.r4.ukcore.stu3.currentbuild": "0.29.0-pre-release" }, "missing": {} -} \ No newline at end of file +} From 6566cf73c39258a2158f2eef48c0b1846d25d10b Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 9 Jul 2026 18:59:25 +0100 Subject: [PATCH 5/5] Update fhirpkg.lock.json update --- fhirpkg.lock.json | 1 - 1 file changed, 1 deletion(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 69078a9..725585f 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -22,7 +22,6 @@ "hl7.fhir.uv.ipa": "1.1.0", "hl7.fhir.uv.smart-app-launch": "2.0.0", "fhir.r4.nhsengland.stu1": "1.5.0", - "hl7.fhir.uv.tools.r4": "1.1.2", "fhir.r4.ukcore.stu3.currentbuild": "0.29.0-pre-release" }, "missing": {}