Merge pull request #10 from RemeCare/wip

Initialise project

.github/workflows/ci.yml

@@ -0,0 +1,73 @@
+name: Build And Publish base
+on: 
+  workflow_dispatch:
+  push:
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Runner Info
+        run: |
+          echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
+          echo "🐧 Now running on a ${{ runner.os }} server hosted by GitHub!"
+          echo "🔎 Branch is ${{ github.ref }} ${{ github.repository }} repo"
+          echo "💡 The ${{ github.repository }} repo has been cloned to the runner."
+          echo "The event_name is ${{ github.event_name }}"
+          echo "The event.pull_request.merged is ${{ github.event.pull_request.merged}}"
+          echo "The ref is ${{ github.ref }}"
+          echo "Provided IG is  ${{ inputs.ig }}"
+
+      - name: Checkout Repo
+        uses: actions/checkout@v2
+
+      - name: Setup Ruby
+        uses: actions/setup-ruby@v1
+        with:
+          ruby-version: '3'
+
+      - name: Setup Java / Maven
+        uses: actions/setup-java@v2
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+
+      - name: Install Jekyll
+        run:  |
+          gem install jekyll
+
+      - name: Version Info
+        run:  |
+          java -version
+          npm --version
+          jekyll --version
+          mvn --version
+
+      - name: Install graphviz to support extra plantuml diagrams
+        run:  |
+          sudo apt install graphviz
+
+      - name: Build IG
+        run:  |
+          npm install -g fsh-sushi  
+          sushi .
+          ./_updatePublisher.sh -y && ./_genonce.sh
+  
+      - name: Deploy IG
+        uses: JamesIves/[email protected]
+        with:
+          branch: gh-pages
+          folder: ./output
+          commit-message: Deploy IG ${{ github.ref_name }}
+          target-folder: ${{ github.ref_name }}
+          single-commit: true
+          clean: false 
+
+      # - name: Deploy history
+      #   uses: JamesIves/[email protected]
+      #   with:
+      #     branch: gh-pages
+      #     folder: ./history
+      #     commit-message: Deploy IG history ${{ github.ref_name }}
+      #     target-folder: ${{ github.ref_name }}
+      #     single-commit: true
+      #     clean: false

.gitignore

@@ -22,3 +22,5 @@ Thumbs.db
 # backup files #
 ################
 *.bak
+
+node_modules

README.md

@@ -1,21 +1,48 @@
-Patient Monitoring Outcome
----
+## Patient Monitoring Outcome
+
 IG
 <br> </br>
+
 ###
+
 ### Publication
+
 This ImplementationGuide is published in the following locations:
 
-Continuous Build: 
-__https://hl7-be.github.io/patient-monitoring/__  
-__http://build.fhir.org/ig/hl7-be/patient-monitoring/branches/main/index.html__  
-Canonical / permanent URL: 
+Continuous Build:
+**https://hl7-be.github.io/patient-monitoring/**  
+**http://build.fhir.org/ig/hl7-be/patient-monitoring/branches/main/index.html**  
+Canonical / permanent URL:
 <br> </br>
 
 ### Issues
-Issues and change requests are managed here:  
 
-Issues:  __https://github.com/hl7-be/patient-monitoring/issues__  
-Kanban board:  __https://github.com/hl7-be/patient-monitoring/projects/1__  
+Issues and change requests are managed here:
+
+Issues: **https://github.com/hl7-be/patient-monitoring/issues**  
+Kanban board: **https://github.com/hl7-be/patient-monitoring/projects/1**
 
 ---
+
+### Running locally
+
+1. Install Prerequisites
+   Before running a FHIR IG locally, ensure you have the necessary tools installed:
+
+a. Java
+FHIR tools like the IG Publisher require Java. Download and install Java.
+
+b. Node.js and npm
+Some IGs may use Node.js scripts. Download and install Node.js.
+
+c. FHIR IG Publisher
+The FHIR IG Publisher tool is essential for generating and validating IGs. Download the latest publisher.jar from [here](https://github.com/HL7/fhir-ig-publisher/releases).
+
+d. Jekyll (Optional)
+If your IG uses Jekyll for hosting and templating, install Jekyll. Ensure Ruby and Bundler are installed.
+
+Run Locally:
+
+```
+java -jar path/to/publisher.jar -ig ig.ini
+```

input/fsh/aliases.fsh

@@ -0,0 +1,7 @@
+Alias: $observation-category = http://terminology.hl7.org/CodeSystem/observation-category
+Alias: $loinc = http://loinc.org
+Alias: $vitalsigns = http://hl7.org/fhir/StructureDefinition/vitalsigns
+Alias: $fhir = https://remecare.github.io/patient-monitoring/wip/
+Alias: $snomed = http://snomed.info/sct
+Alias: $cd-hcparty = https://www.ehealth.fgov.be/standards/fhir/core/CodeSystem/cd-hcparty
+Alias: $UCUM = http://unitsofmeasure.org

input/fsh/examples/devices.fsh

@@ -0,0 +1,8 @@
+Instance: vital-signs-box
+InstanceOf: Device
+Usage: #inline
+* identifier.value = "240822yti3tgeyay"
+* deviceName.name = "VS-4"
+* deviceName.type = #other
+* manufacturer = "Byteflies"
+* meta.tag = https://api-vitalsigns.byteflies.net/version#20241028-1511 "API Version 20241028-1511"

input/fsh/examples/organisations.fsh

@@ -0,0 +1,4 @@
+Instance: byteflies
+InstanceOf: Organization
+Usage: #inline
+* name = "Byteflies"

input/fsh/examples/other-qualitative/example-distended-abdomen.fsh

@@ -0,0 +1,14 @@
+Instance: DistendedAbdomenExample	
+InstanceOf: Observation
+Usage: #example
+Title: "INCOMPLETE: Distended abdomen example"
+Description: "NEEDS ATTENTION: Current answer options are no / a little / fierce. These cannot be found in LOINC or SNOMEDCT currently. Change answer options or request new LOINC codes."
+* status = #final
+* code = $snomed#60728008 "Swollen abdomen" 
+* subject.identifier.system = $fhir
+* subject.identifier.value = "D358D4B4-6007-4C3E-A33B-056773F45DC9"
+* valueCodeableConcept = $loinc#LA10138-8 //TODO: Needs correct value
+* effectivePeriod.start = "2024-11-15T09:56:00+00:00"
+* effectivePeriod.end = "2024-11-15T09:57:00+00:00"
+* contained[0] = nurse
+* performer = Reference(nurse)

input/fsh/examples/other-qualitative/example-level-of-responsiveness.fsh

@@ -0,0 +1,13 @@
+Instance: LevelOfResponsivenessExample
+InstanceOf: Observation
+Usage: #example
+Title: "Level of responsiveness example"
+Description: "Level of responsiveness (AVPU scale)"
+* status = #final
+* code = $loinc#67775-7 "Level of responsiveness"
+* subject.identifier.system = $fhir
+* subject.identifier.value = "D358D4B4-6007-4C3E-A33B-056773F45DC9"
+* valueCodeableConcept = $loinc#LA17108-4
+* effectiveDateTime = "2024-11-19T06:48:20+00:00"
+* contained[0] = nurse
+* performer = Reference(nurse)

input/fsh/examples/other-qualitative/example-shortness-of-breath.fsh

@@ -0,0 +1,13 @@
+Instance: ShortnessOfBreathExample
+InstanceOf: Observation
+Usage: #example
+Title: "Shortness of breath example"
+Description: "Possible answers are yes and no"
+* status = #final
+* code = $snomed#267036007 "Shortness of breath"
+* subject.identifier.system = $fhir
+* subject.identifier.value = "D358D4B4-6007-4C3E-A33B-056773F45DC9"
+* valueCodeableConcept = $snomed#373066001
+* effectiveDateTime = "2024-11-19T06:48:20+00:00"
+* contained[0] = nurse
+* performer = Reference(nurse)

input/fsh/examples/other-quantitative/example-national-early-warning-score.fsh

@@ -0,0 +1,13 @@
+Instance: NationalEarlyWarningScoreExample
+InstanceOf: Observation
+Usage: #example
+Title: "National Early Warning Score example"
+Description: "National Early Warning Score (NEWS)"
+* status = #final
+* code = $snomed#1287358002 "National Early Warning Score"
+* subject.identifier.system = $fhir
+* subject.identifier.value = "D358D4B4-6007-4C3E-A33B-056773F45DC9"
+* valueQuantity.value = 6
+* effectiveDateTime = "2024-11-19T06:48:20+00:00"
+* contained[0] = nurse
+* performer = Reference(nurse)

input/fsh/examples/pain/example-abdominal-pain.fsh

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+Instance: AbdominalPainExample
+InstanceOf: Observation
+Usage: #example
+Title: "Abdominal pain example"
+Description: "Pain scale is used as answer"
+* status = #final
+* code = $snomed#21522001 "Abdominal pain"
+* subject.identifier.system = $fhir
+* subject.identifier.value = "D358D4B4-6007-4C3E-A33B-056773F45DC9"
+* valueCodeableConcept = $loinc#LA10138-8
+* effectivePeriod.start = "2024-11-15T09:56:00+00:00"
+* effectivePeriod.end = "2024-11-15T09:57:00+00:00"
+* contained[0] = nurse
+* performer = Reference(nurse)

input/fsh/examples/pain/example-pain-during-urination.fsh

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+Instance: PainDuringUrinationExample
+InstanceOf: Observation
+Usage: #example
+Title: "Pain during urination example"
+Description: "Possible answers are yes and no"
+* status = #final
+* code = $snomed#49650001 "Urination painful"
+* subject.identifier.system = $fhir
+* subject.identifier.value = "D358D4B4-6007-4C3E-A33B-056773F45DC9"
+* valueCodeableConcept = $snomed#373066001
+* effectivePeriod.start = "2024-11-15T09:56:00+00:00"
+* effectivePeriod.end = "2024-11-15T09:57:00+00:00"
+* performer.identifier.system = $fhir
+* performer.identifier.value = "D358D4B4-6007-4C3E-A33B-056773F45DC9"

input/fsh/examples/pain/example-pain-in-calves.fsh

@@ -0,0 +1,14 @@
+Instance: PainInCalvesExample
+InstanceOf: Observation
+Usage: #example
+Title: "Pain in calves example"
+Description: "Possible answers are yes and no"
+* status = #final
+* code = $snomed#1264028004 "Pain in muscle of lower leg"
+* subject.identifier.system = $fhir
+* subject.identifier.value = "D358D4B4-6007-4C3E-A33B-056773F45DC9"
+* valueCodeableConcept = $snomed#373066001
+* effectivePeriod.start = "2024-11-15T09:56:00+00:00"
+* effectivePeriod.end = "2024-11-15T09:57:00+00:00"
+* performer.identifier.system = $fhir
+* performer.identifier.value = "D358D4B4-6007-4C3E-A33B-056773F45DC9"