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/CodeSystem/CodeSystem-Genomics-test-types.json b/CodeSystem/CodeSystem-Genomics-test-types.json deleted file mode 100644 index af1a974..0000000 --- a/CodeSystem/CodeSystem-Genomics-test-types.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "resourceType": "CodeSystem", - "id": "test-type-genomics", - "url": "https://fhir.nhs.uk/CodeSystem/test-type-genomics", - "version": "0.2.0", - "name": "TestTypeGenomics", - "title": "Test Type Genomics", - "status": "draft", - "date": "2022-12-21T11:27:52.3231281+00:00", - "publisher": "NHS England", - "contact": [ - { - "name": "NHS England", - "telecom": [ - { - "system": "email", - "value": "interoperabilityteam@nhs.net", - "use": "work" - } - ] - } - ], - "description": "A set of codes use to identify the category of genomic test types", - "copyright": "Copyright © 2023+ 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", - "concept": [ - { - "code": "RID-WGS", - "display": "Rare and Inherited Diseases - WGS" - }, - { - "code": "C-WGS", - "display": "Cancer (paired tumour normal) - WGS" - } - ] -} \ No newline at end of file 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." }, { diff --git a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json index be3df23..02ae05c 100644 --- a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json +++ b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json @@ -191,9 +191,6 @@ { "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/ValueSet/ValueSet-Genomics-test-types.json b/ValueSet/ValueSet-Genomics-test-types.json deleted file mode 100644 index b885e6d..0000000 --- a/ValueSet/ValueSet-Genomics-test-types.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "resourceType": "ValueSet", - "id": "genomics-test-types", - "url": "https://fhir.nhs.uk/ValueSet/genomics-test-types", - "version": "0.1.1", - "name": "GenomicsTestTypes", - "title": "Genomics Test Types", - "status": "draft", - "date": "2024-09-10T10:17:52.3231281+00:00", - "publisher": "NHS England", - "contact": [ - { - "name": "NHS England", - "telecom": [ - { - "system": "email", - "value": "interoperabilityteam@nhs.net" - } - ] - } - ], - "description": "A ValueSet to identify the category of genomic test types", - "copyright": "Copyright © 2023+ 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.", - "compose": { - "include": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/test-type-genomics", - "version": "0.2.0" - } - ] - } -} \ No newline at end of file diff --git a/package.json b/package.json index ca7e1ce..85b7e92 100644 --- a/package.json +++ b/package.json @@ -3,14 +3,10 @@ "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": "0.2.4-alpha", "hl7.fhir.uv.tools.r4": "1.1.2", @@ -21,4 +17,4 @@ "4.0.1" ], "jurisdiction": "urn:iso:std:iso:3166:-2#GB" -} +} \ No newline at end of file diff --git a/private.package.yaml b/private.package.yaml new file mode 100644 index 0000000..1ec8db8 --- /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: 0.2.4-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