Merge branch 'main' into update-dependencies

.github/workflows/build-and-test.yml.yml

@@ -0,0 +1,78 @@
+#
+# This source file is part of the Stanford Biodesign Digital Health ENGAGE-HF open-source project
+#
+# SPDX-FileCopyrightText: 2023 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+name: Build and Test
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+  workflow_dispatch:
+  workflow_call:
+
+jobs:
+  reuseaction:
+    name: REUSE Compliance Check
+    uses: StanfordBDHG/.github/.github/workflows/reuse.yml@v2
+  markdownlinkcheck:
+    name: Markdown Link Check
+    uses: StanfordBDHG/.github/.github/workflows/markdown-link-check.yml@v2
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: 'true'
+      - name: Git LFS Pull
+        run: git lfs pull
+      - name: Use Node.js 22.x
+        uses: actions/setup-node@v4
+        with:
+          node-version: 22.6.x
+      - name: Install Dependencies
+        run: npm run install
+      - name: Build
+        run: npm run build
+      - name: Lint
+        run: npm run lint:strict
+    permissions:
+      contents: read
+  buildandtest:
+    name: Build and Test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: 'true'
+      - name: Git LFS Pull
+        run: git lfs pull
+      - name: Use Node.js 22.x
+        uses: actions/setup-node@v4
+        with:
+          node-version: 22.6.x
+      - name: Install Dependencies
+        run: npm run install
+      - name: Install Firebase CLI
+        run: npm install -g firebase-tools
+      - name: Build
+        run: npm run build
+      - name: Test
+        id: test
+        run: npm run test:ci
+      - name: Archive Regenerated Test Results
+        uses: actions/upload-artifact@v4
+        with:
+          name: test results
+          path: functions/src/tests/resources
+    permissions:
+      contents: read

.github/workflows/codeql.yml

@@ -0,0 +1,38 @@
+#
+# This source file is part of the Stanford Biodesign Digital Health ENGAGE-HF open-source project
+#
+# SPDX-FileCopyrightText: 2023 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+name: CodeQL
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  schedule:
+    - cron: '0 8 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: 'ubuntu-latest'
+    permissions:
+      security-events: write
+      packages: read
+      actions: read
+      contents: read
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: javascript-typescript
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3

.github/workflows/deployment.yml

@@ -0,0 +1,86 @@
+#
+# This source file is part of the Stanford Biodesign Digital Health ENGAGE-HF open-source project
+#
+# SPDX-FileCopyrightText: 2023 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+name: Deployment
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+    inputs:
+      environment:
+        description: |
+          The GitHub deployment environment.
+        required: true
+        default: 'development'
+        type: choice
+        options:
+          - development
+          - staging
+          - production
+  workflow_call:
+    inputs:
+      environment:
+        description: |
+          The GitHub deployment environment.
+        required: false
+        type: string
+        default: development
+
+concurrency:
+  group: deployment
+  cancel-in-progress: false
+
+jobs:
+  determineenvironment:
+    name: Determine Environment
+    runs-on: ubuntu-latest
+    outputs:
+      environment: ${{ steps.set-env.outputs.environment }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Determine Environment
+        id: set-env
+        run: |
+          if [[ -z "${{ inputs.environment }}" ]]; then
+            echo "environment=staging" >> $GITHUB_OUTPUT
+          else
+            echo "environment=${{ inputs.environment }}" >> $GITHUB_OUTPUT
+          fi
+  vars:
+    name: Inject Environment Variables In Deployment Workflow
+    needs: determineenvironment
+    runs-on: ubuntu-latest
+    environment: ${{ needs.determineenvironment.outputs.environment }}
+    outputs:
+      FIREBASE_PROJECT_ID: ${{ vars.FIREBASE_PROJECT_ID }}
+    steps:
+      - run: |
+          echo "Injecting Environment Variables In Deployment Workflow: ${{ vars.FIREBASE_PROJECT_ID }}"
+  buildandtest:
+    name: Build and Test
+    needs: determineenvironment
+    uses: ./.github/workflows/build-and-test.yml
+    permissions:
+      contents: read
+      checks: write
+    secrets: inherit
+  deployfirebase:
+    name: Deploy Firebase Project
+    needs: [buildandtest, determineenvironment, vars]
+    uses: StanfordBDHG/.github/.github/workflows/firebase-deploy.yml@v2
+    permissions:
+      contents: read
+    with:
+      customcommand: "npm run install"
+      environment: ${{ needs.determineenvironment.outputs.environment }}
+      arguments: '--project ${{ needs.vars.outputs.FIREBASE_PROJECT_ID }}'
+    secrets:
+      GOOGLE_APPLICATION_CREDENTIALS_BASE64: ${{ secrets.GOOGLE_APPLICATION_CREDENTIALS_BASE64 }}

.github/workflows/monthly-markdown-link-check.yml

@@ -0,0 +1,18 @@
+#
+# This source file is part of the Stanford Biodesign Digital Health ENGAGE-HF open-source project
+#
+# SPDX-FileCopyrightText: 2023 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+name: Monthly Markdown Link Check
+
+on:
+  schedule:
+    - cron: '0 8 1 * *'
+
+jobs:
+  markdown_link_check:
+    name: Markdown Link Check
+    uses: StanfordBDHG/.github/.github/workflows/markdown-link-check.yml@v2

.github/workflows/release-models-package.yml → .github/workflows/production.yml

@@ -1,20 +1,35 @@
 #
-# This source file is part of the ENGAGE-HF project based on the Stanford Spezi Template Application project
+# This source file is part of the Stanford Biodesign Digital Health ENGAGE-HF open-source project
 #
-# SPDX-FileCopyrightText: 2023 Stanford University
+# SPDX-FileCopyrightText: 2023 Stanford University and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
 #
 
-name: Release Models Package
+name: Production Deployment
 
 on:
   release:
     types: [published]
   workflow_dispatch:
 
+concurrency:
+  group: production
+  cancel-in-progress: false
+
 jobs:
-  build:
+  deployment:
+    name: Production Deployment
+    uses: ./.github/workflows/deployment.yml
+    permissions:
+      contents: read
+      actions: read
+      security-events: write
+    secrets: inherit
+    with:
+      environment: production
+  publishpackage:
+    name: Publish Package
     runs-on: ubuntu-latest
     permissions:
       contents: read
@@ -25,7 +40,6 @@ jobs:
         working-directory: ./functions/models
     steps:
       - uses: actions/checkout@v4
-        # Setup .npmrc file to publish to npm
       - uses: actions/setup-node@v4
         with:
           node-version: '22.x'

README.md

@@ -291,7 +291,7 @@ Based on [FHIR AllergyIntolerance](https://hl7.org/fhir/R4B/allergyintolerance.h
 |-|-|-|-|
 |id|string|-|[Resource](https://hl7.org/fhir/R4B/resource.html): Logical id of this artifact|
 |type|optional [allergyIntoleranceType](https://hl7.org/fhir/R4B/valueset-allergy-intolerance-type.html)|e.g. "allergy", "intolerance"|In addition to the FHIR defined value set, we also use "financial" - these values shall not be exposed to EHR systems.|
-|code|CodableContent|e.g. "{"coding":[{"system":"https://hl7.org/fhir/R4B/valueset-allergyintolerance-code.html","code":"293963004","display":"Cardioselective beta-blocker allergy"}],"text":"Cardioselective beta-blocker allergy"}"|Uses either [AllergyIntoleranceCode](https://hl7.org/fhir/R4B/valueset-allergyintolerance-code.html), `medicationId` as used in /medications/$medicationId$ and/or `medicationId` as used in /medicationClasses/$medicationClassId$.|
+|code|CodableContent|e.g. `{"coding":[{"system":"https://hl7.org/fhir/R4B/valueset-allergyintolerance-code.html","code":"293963004","display":"Cardioselective beta-blocker allergy"}],"text":"Cardioselective beta-blocker allergy"}`|Uses either [AllergyIntoleranceCode](https://hl7.org/fhir/R4B/valueset-allergyintolerance-code.html), `medicationId` as used in /medications/$medicationId$ and/or `medicationId` as used in /medicationClasses/$medicationClassId$.|
 |patient|string|-|`userId` as used in /users/$userId$ and related collections.|
 
 We use RxNorm codes to identify contraindications using the following rules: