Merge develop into main

.github/workflows/publish.yml

@@ -10,7 +10,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-  
+
       - name: Install Node
         uses: actions/setup-node@v3
         with:
@@ -34,17 +34,56 @@ jobs:
       - name: Install Jekyll
         run: sudo gem install jekyll jekyll-plantuml
 
+      - name: Install Graphvix
+        run: sudo apt install graphviz
+
       - name: Build IG
-        run: ./_genonce.sh
+        run: ./_genonce.sh ${{ vars.VALIDATOR_OFFLINE }}
+
+      - name: Download and unpack font-awesome
+        run: wget https://fontawesome.com/v4/assets/font-awesome-4.7.0.zip; unzip font-awesome-4.7.0.zip -d output
 
       - name: Publish IG Artefact
         uses: actions/upload-artifact@v3
         with:
           name: IG Archive
           path: ./output/
 
+      - name: Prepare files for GitHub Pages
+        run: |
+          cp -r output _site;
+          chmod -c -R +rX "_site/" | while read line; do
+            echo "::warning title=Invalid file permissions automatically fixed::$line"
+          done
+
+      - name: Publish IG to GitHub Pages
+        uses: actions/upload-pages-artifact@v3
+
       - name: Cache Node modules
         uses: actions/cache@v3
         with:
           path: ~/.npm
           key: ${{ runner.os }}--build-cache-npm-packages-${{ hashFiles('**/package-lock.json') }}
+
+  # Deploy job (https://github.com/actions/deploy-pages)
+  deploy:
+    # Add a dependency to the build job
+    needs: build
+    # Only deploy on development branch
+    # if: github.ref == 'refs/heads/development'
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    # Specify runner + deployment step
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4 # or specific "vX.X.X" version tag for this action

.gitignore

@@ -5,3 +5,11 @@ _site/
 # Ignore folders generated by Bundler
 .bundle/
 vendor/
+input-cache
+node_modules
+output
+temp
+template
+font-awesome*
+fsh-generated
+input/resources/QUERY-OUTPUT*

_updatePublisher.sh

@@ -31,7 +31,7 @@ while [ "$#" -gt 0 ]; do
 done
 
 echo "Checking internet connection"
-curl -sSf tx.fhir.org > /dev/null
+curl -sSf raw.githubusercontent.com > /dev/null
 
 if [ $? -ne 0 ] ; then
   echo "Offline (or the terminology server is down), unable to update.  Exiting"

ig-template/package/content/diagram.bpmn

@@ -0,0 +1,115 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<bpmn:definitions xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_149wjti" targetNamespace="http://bpmn.io/schema/bpmn" exporter="bpmn-js (https://demo.bpmn.io)" exporterVersion="16.4.0">
+  <bpmn:collaboration id="Collaboration_0q56fut">
+    <bpmn:participant id="Participant_18xshys" name="Consent to Treatment" processRef="Process_0q168hd" />
+    <bpmn:textAnnotation id="TextAnnotation_009927h">
+      <bpmn:text>Has capacity to consent?</bpmn:text>
+    </bpmn:textAnnotation>
+    <bpmn:association id="Association_171p978" associationDirection="None" sourceRef="Gateway_1ykpua9" targetRef="TextAnnotation_009927h" />
+  </bpmn:collaboration>
+  <bpmn:process id="Process_0q168hd">
+    <bpmn:laneSet id="LaneSet_1s0cwuu">
+      <bpmn:lane id="Lane_1qewygr" name="API" />
+      <bpmn:lane id="Lane_0vot896" name="Patient Advocate">
+        <bpmn:flowNodeRef>Activity_1s5y9xm</bpmn:flowNodeRef>
+      </bpmn:lane>
+      <bpmn:lane id="Lane_0s229l6" name="Patient">
+        <bpmn:flowNodeRef>Gateway_1ykpua9</bpmn:flowNodeRef>
+        <bpmn:flowNodeRef>Activity_1lxn6f7</bpmn:flowNodeRef>
+      </bpmn:lane>
+      <bpmn:lane id="Lane_0jp784q" name="Practitioner">
+        <bpmn:flowNodeRef>Event_03tz7z4</bpmn:flowNodeRef>
+        <bpmn:flowNodeRef>Activity_00yhqnr</bpmn:flowNodeRef>
+        <bpmn:flowNodeRef>Activity_05dlhv6</bpmn:flowNodeRef>
+      </bpmn:lane>
+    </bpmn:laneSet>
+    <bpmn:startEvent id="Event_03tz7z4">
+      <bpmn:outgoing>Flow_0ws129z</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:task id="Activity_00yhqnr" name="Request Consent">
+      <bpmn:incoming>Flow_0ws129z</bpmn:incoming>
+      <bpmn:outgoing>Flow_1ias2ec</bpmn:outgoing>
+    </bpmn:task>
+    <bpmn:exclusiveGateway id="Gateway_1ykpua9">
+      <bpmn:incoming>Flow_1ias2ec</bpmn:incoming>
+      <bpmn:outgoing>Flow_0c4r6vy</bpmn:outgoing>
+    </bpmn:exclusiveGateway>
+    <bpmn:task id="Activity_05dlhv6" name="Record Consent" />
+    <bpmn:task id="Activity_1lxn6f7" name="Provide Consent">
+      <bpmn:incoming>Flow_0c4r6vy</bpmn:incoming>
+    </bpmn:task>
+    <bpmn:task id="Activity_1s5y9xm" name="Provide Consent" />
+    <bpmn:sequenceFlow id="Flow_0ws129z" sourceRef="Event_03tz7z4" targetRef="Activity_00yhqnr" />
+    <bpmn:sequenceFlow id="Flow_1ias2ec" sourceRef="Activity_00yhqnr" targetRef="Gateway_1ykpua9" />
+    <bpmn:sequenceFlow id="Flow_0c4r6vy" name="Yes" sourceRef="Gateway_1ykpua9" targetRef="Activity_1lxn6f7" />
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Collaboration_0q56fut">
+      <bpmndi:BPMNShape id="Participant_18xshys_di" bpmnElement="Participant_18xshys" isHorizontal="true">
+        <dc:Bounds x="160" y="62" width="1370" height="998" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Lane_1qewygr_di" bpmnElement="Lane_1qewygr" isHorizontal="true">
+        <dc:Bounds x="190" y="810" width="1340" height="250" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Lane_0vot896_di" bpmnElement="Lane_0vot896" isHorizontal="true">
+        <dc:Bounds x="190" y="560" width="1340" height="250" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Lane_0s229l6_di" bpmnElement="Lane_0s229l6" isHorizontal="true">
+        <dc:Bounds x="190" y="312" width="1340" height="248" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Lane_0jp784q_di" bpmnElement="Lane_0jp784q" isHorizontal="true">
+        <dc:Bounds x="190" y="62" width="1340" height="250" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Event_03tz7z4_di" bpmnElement="Event_03tz7z4">
+        <dc:Bounds x="262" y="172" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_00yhqnr_di" bpmnElement="Activity_00yhqnr">
+        <dc:Bounds x="420" y="150" width="100" height="80" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Gateway_1ykpua9_di" bpmnElement="Gateway_1ykpua9" isMarkerVisible="true">
+        <dc:Bounds x="445" y="395" width="50" height="50" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_05dlhv6_di" bpmnElement="Activity_05dlhv6">
+        <dc:Bounds x="900" y="150" width="100" height="80" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_1lxn6f7_di" bpmnElement="Activity_1lxn6f7">
+        <dc:Bounds x="630" y="380" width="100" height="80" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_1s5y9xm_di" bpmnElement="Activity_1s5y9xm">
+        <dc:Bounds x="420" y="640" width="100" height="80" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="Flow_1ias2ec_di" bpmnElement="Flow_1ias2ec">
+        <di:waypoint x="470" y="230" />
+        <di:waypoint x="470" y="395" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0ws129z_di" bpmnElement="Flow_0ws129z">
+        <di:waypoint x="298" y="190" />
+        <di:waypoint x="420" y="190" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0c4r6vy_di" bpmnElement="Flow_0c4r6vy">
+        <di:waypoint x="495" y="420" />
+        <di:waypoint x="630" y="420" />
+        <bpmndi:BPMNLabel>
+          <dc:Bounds x="554" y="402" width="18" height="14" />
+        </bpmndi:BPMNLabel>
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Association_171p978_di" bpmnElement="Association_171p978">
+        <di:waypoint x="450" y="415" />
+        <di:waypoint x="370" y="397" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="TextAnnotation_009927h_di" bpmnElement="TextAnnotation_009927h">
+        <dc:Bounds x="270" y="370" width="99.99998764470521" height="40.48582995951417" />
+        <bpmndi:BPMNLabel />
+      </bpmndi:BPMNShape>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

ig-template/package/includes/_append.fragment-header.html

@@ -1,4 +1,5 @@
 <link rel="stylesheet" href="../font-awesome-4.7.0/css/font-awesome.min.css">
+<link rel="stylesheet" href="./font-awesome-4.7.0/css/font-awesome.min.css">
 
 <!-- Left logo - typically the publisher's logo - project or affiliate -->
         <div id="project-nav">

ig-template/package/includes/fragment-footer.html

@@ -4,6 +4,6 @@
                  <a style="color: #81BEF7" href="qa.html">QA Report</a> 
                  <a style="color: #81BEF7" rel="license" href="{{site.data.fhir.path}}license.html"><img style="border-style: none;" alt="CC0" src="cc0.png"/></a>
 <div>
-</div>
 
-</div>
+<!--Include mermaid for creating diagrams.  Jekyll complains if its not local, possibly configurable...-->
+<script type="text/javascript" src="{{site.data.info.assets}}assets/js/mermaid.min.js"> </script>

input/fsh/aliases.fsh

@@ -0,0 +1,24 @@
+Alias: $consentscope = http://terminology.hl7.org/CodeSystem/consentscope
+Alias: $sct = https://snomed.info/sct
+Alias: $condition-clinical = http://terminology.hl7.org/CodeSystem/condition-clinical
+Alias: $v3-DataOperation = http://terminology.hl7.org/CodeSystem/v3-DataOperation
+Alias: $condition-clinical = http://terminology.hl7.org/CodeSystem/condition-clinical
+Alias: $sct = https://snomed.info/sct
+Alias: $v3-DataOperation = http://terminology.hl7.org/CodeSystem/v3-DataOperation
+Alias: $contractsignertypecodes = http://terminology.hl7.org/CodeSystem/contractsignertypecodes
+Alias: $RoleClass = http://terminology.hl7.org/CodeSystem/v3-RoleClass
+Alias: $RoleCode = http://terminology.hl7.org/CodeSystem/v3-RoleCode
+Alias: $ParticipationFunction = http://terminology.hl7.org/CodeSystem/v3-ParticipationFunction
+Alias: $ParticipationType = http://terminology.hl7.org/CodeSystem/v3-ParticipationType
+Alias: $extra-security-role-type = http://terminology.hl7.org/CodeSystem/extra-security-role-type
+Alias: $CareConnect-SDSJobRoleName-1 = https://fhir.hl7.org.uk/STU3/CodeSystem/CareConnect-SDSJobRoleName-1
+Alias: $ValueSetPatientFlagCategory =  https://fhir.nhs.uk/England/ValueSet/PatientFlagCategory
+Alias: $ValueSetProgrammeFlagCategory =  https://fhir.nhs.uk/England/ValueSet/ProgrammeFlagCategory
+Alias: $ExtensionFlagDetail =  http://hl7.org/fhir/StructureDefinition/flag-detail
+Alias: $ValueSetFlagProvenanceRole =  https://fhir.nhs.uk/England/ValueSet/FlagProvenanceRole
+Alias: $ValueSetRAFlagCode =  https://fhir.nhs.uk/England/ValueSet/RA-FlagCode
+Alias: $ValueSetCPISFlagCode =  https://fhir.nhs.uk/England/ValueSet/CPIS-FlagCode
+Alias: $ValueSetFGMFlagCode =  https://fhir.nhs.uk/England/ValueSet/FGM-FlagCode
+Alias: $ValueSetProgrammeFlagCode =  https://fhir.nhs.uk/England/ValueSet/ProgrammeFlagCode
+Alias: $ValueSetFlagConditionCategory =  https://fhir.nhs.uk/England/ValueSet/FlagConditionCategory
+Alias: $ValueSetFlagConditionCode =  https://fhir.nhs.uk/England/ValueSet/FlagConditionCode

input/fsh/codesystem/CPIS-ConditionCategory.fsh

@@ -0,0 +1,17 @@
+CodeSystem: CPIS-ConditionCategory
+Id: CPIS-ConditionCategory
+Title: "CPIS Condition Category"
+Description: "A CodeSystem to identify the category of a condition within CPIS."
+
+* ^name = "CPISConditionCategory"
+* ^url = "https://fhir.nhs.uk/England/CodeSystem/CPIS-ConditionCategory"
+* ^version = "0.1.0"
+* ^status = #draft
+* ^date = "2024-02-14"
+* ^experimental = false
+
+* insert NHSEngland-Copyright
+
+* ^caseSensitive = true
+* ^content = #complete
+* #cpis-example-condition-category "CPIS example condition category"

input/fsh/codesystem/CPIS-ConditionCode.fsh

@@ -0,0 +1,17 @@
+CodeSystem: CPIS-ConditionCode
+Id: CPIS-ConditionCode
+Title: "CPIS Condition Code"
+Description: "A CodeSystem to identify the SNOMED-CT concept representing an Impairment recorded as part of CPIS"
+
+* ^name = "CPISConditionCode"
+* ^url = "https://fhir.nhs.uk/England/CodeSystem/CPIS-ConditionCode"
+* ^version = "0.1.0"
+* ^status = #draft
+* ^date = "2024-02-14"
+* ^experimental = false
+
+* insert NHSEngland-Copyright
+
+* ^caseSensitive = true
+* ^content = #complete
+* #1 "CPIS example condition code"

input/fsh/codesystem/CPIS-ConsentPurpose.fsh

@@ -0,0 +1,17 @@
+CodeSystem: CPIS-ConsentPurpose
+Id: CPIS-ConsentPurpose
+Title: "CPIS Consent Purpose"
+Description: "A CodeSystem to identify the purpose of the consent given within CPIS"
+
+* ^name = "CPISConsentPurpose"
+* ^url = "https://fhir.nhs.uk/England/CodeSystem/CPIS-ConsentPurpose"
+* ^version = "0.1.0"
+* ^status = #draft
+* ^date = "2024-02-14"
+* ^experimental = false
+
+* insert NHSEngland-Copyright
+
+* ^caseSensitive = true
+* ^content = #complete
+* #CPISCONSENT "CPIS - Consent to record CPIS flags"

input/fsh/codesystem/CPIS-FlagCategory.fsh

@@ -0,0 +1,17 @@
+CodeSystem: CPIS-FlagCategory
+Id: CPIS-FlagCategory
+Title: "CPIS Flag Category"
+Description: "A CodeSystem containing CPIS flag categories"
+
+* ^name = "CPISFlagCategory"
+* ^url = "https://fhir.nhs.uk/England/CodeSystem/CPIS-FlagCategory"
+* ^version = "0.1.0"
+* ^status = #draft
+* ^date = "2024-02-14"
+* ^experimental = false
+
+* insert NHSEngland-Copyright
+
+* ^caseSensitive = true
+* ^content = #complete
+* #001 "Example CPIS category"

input/fsh/codesystem/FGM-ConditionCategory.fsh

@@ -0,0 +1,17 @@
+CodeSystem: FGM-ConditionCategory
+Id: FGM-ConditionCategory
+Title: "FGM Condition Category"
+Description: "A CodeSystem to identify the category of a condition within FGM."
+
+* ^name = "FGMConditionCategory"
+* ^url = "https://fhir.nhs.uk/England/CodeSystem/FGM-ConditionCategory"
+* ^version = "0.1.0"
+* ^status = #draft
+* ^date = "2024-02-14"
+* ^experimental = false
+
+* insert NHSEngland-Copyright
+
+* ^caseSensitive = true
+* ^content = #complete
+* #fgm-example-condition-category "FGM example condition category"