LikeC4 diagrams and deployment workflow

.github/workflows/deploy-pages.yml

@@ -0,0 +1,83 @@
+# Sample workflow for building and deploying a website to GitHub Pages
+name: Deploy Pages
+
+on:
+  # Runs on pushes targeting the default branch and c4 files
+  pull_request:
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_call:
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+#permissions:
+#  contents: read
+#  pages: write
+#  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in progress and the latest queued.
+# However, do NOT cancel in-progress runs, as we want to allow these production deployments to be completed.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Validate model following our rules
+  # @see test/validate-model.spec.ts
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - name: Setup bun
+        uses: oven-sh/setup-bun@v2
+
+      - name: Install dependencies
+        run: bun install
+
+      #- name: Validate
+      #  run: bun run test
+
+  # Build job
+  build-pages:
+    runs-on: ubuntu-latest
+    needs: validate
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - name: Setup bun
+        uses: oven-sh/setup-bun@v2
+
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v4
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./dist
+
+      - name: Build
+        run: |
+          bunx likec4@latest build \
+            --base "${{ steps.pages.outputs.base_path || '/docs' }}" \
+            --output dist
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./dist
+
+  # Deployment job
+  #deploy-pages:
+  #  environment:
+  #    name: github-pages
+  #    url: ${{ steps.deployment.outputs.page_url }}
+  #  runs-on: ubuntu-latest
+  #  needs: build-pages
+  #  steps:
+  #    - name: Deploy to GitHub Pages
+  #      id: deployment
+  #      uses: actions/deploy-pages@v4

.gitignore

@@ -319,3 +319,4 @@ cython_debug/
 /cache-directory/
 data
 .vscode
+node_modules

docs/c4_diagrams/likec4_src/README.txt

@@ -0,0 +1,18 @@
+
+## Build commands
+
+`npx likec4 codegen react --no-use-dot -o ../likec4_react/likec4.generated.js`
+
+Note that `--no-use-dot` is needed for general containers which aren't the likec4 dedicated container.
+
+
+## Index image generation
+
+This uses a headless browser session, so the dependencies for playwright have to be installed first
+`npx playwright install`
+`npx playwright install-deps`
+
+Then run the export command
+`npx likec4 export png --no-use-dot`
+Copy the index figure into the public images directory
+`cp index.png ../public/images/likec4_index.png`

docs/c4_diagrams/likec4_src/context.c4

@@ -0,0 +1,45 @@
+model {
+  // ---------------------------------------------------------------------------
+  // Actors
+
+  researcher = external_actor {
+    title 'Researcher'
+    description 'Researcher who wishes to perform analyses on protected data'
+
+    -> ro-crate_service.ro-crate_service 'Submits tasks via'
+    -> tre.tre_app 'Submits tasks via'
+  }
+
+  // ----------------------------------------------------------------------------
+  // Systems
+
+  ro-crate_validator = system {
+    title 'RO-Crate Validator'
+    description 'System for validating RO-Crates'
+    technology '[Docker Compose stack]'
+  }
+
+  tre = system {
+    title 'TRE Stack'
+    description 'TRE stack'
+  }
+
+  // ----------------------------------------------------------------------------
+  // External Systems
+
+  ro-crate_service = system {
+    title 'RO-Crate Service'
+    description 'Service for submitting RO-Crate packaged work'
+    technology '[Python package]'
+  }
+
+}
+
+views {
+  view index {
+    title 'RO-Crate Validation Service - Context'
+    description 'Top level diagram'
+    include *
+    exclude ro-crate_service
+  }
+}

docs/c4_diagrams/likec4_src/ro-crate_service/ro-crate_service.c4

@@ -0,0 +1,18 @@
+model {
+  extend ro-crate_service {
+    ro-crate_service = service {
+      title 'RO-Crate Service'
+      description 'Service for submitting work via RO-Crates'
+
+    -> tre 'Submits tasks via'
+    -> ro-crate_validator.validator_api 'Validates RO-Crates via'
+    }
+}
+}
+
+views {
+  view ro-crate_service of ro-crate_service {
+    title 'RO-Crate Service'
+    include *
+  }
+}

docs/c4_diagrams/likec4_src/ro-crate_validator/ro-crate_validator.c4

@@ -0,0 +1,34 @@
+model {
+  extend ro-crate_validator {
+    validator_api = service {
+      title 'RO-Crate Validator API'
+      description 'API for validating RO-Crates'
+
+      -> redis 'Submits validation tasks to'
+    }
+
+    celery_worker = component {
+      title 'Celery Worker'
+      description 'Processes validation tasks'
+      icon https://github.com/celery/celery/blob/main/docs/images/celery_128.png?raw=true
+
+      -> redis 'Receives validation tasks from'
+      -> tre.minio 'Fetches RO-Crate data from'
+      -> tre.minio 'Stores validation results in'
+      -> validator_api 'Sends validation results to'
+    }
+
+    redis = component {
+      title 'Redis'
+      description 'In-memory data structure store'
+      icon tech:redis
+    }
+  }
+}
+
+views {
+  view ro-crate_validator of ro-crate_validator {
+    title 'RO-Crate Validator Service'
+    include *
+  }
+}

docs/c4_diagrams/likec4_src/specs.c4

@@ -0,0 +1,50 @@
+specification {
+  element external_actor {
+    style {
+      shape person
+      color red
+    }
+  }
+  element internal_actor {
+    style {
+      shape person
+      color green
+    }
+  }
+
+  color orange rgba(255, 153, 0, 100%)
+  element database {
+    style {
+      shape storage
+      color orange
+      multiple true
+    }
+  }
+
+  color system-colour rgba(35, 67, 99, 100%)
+  element system {
+    style {
+      color system-colour
+    }
+  }
+
+  color service-colour rgba(0, 100, 150, 100%)
+  element service {
+    style {
+      color service-colour
+    }
+  }
+
+  color component-colour rgba(0, 0, 0, 100%)
+  element component {
+    style {
+      color component-colour
+    }
+  }
+
+  deploymentNode environment
+
+  deploymentNode vm {
+    notation 'Virtual Machine'
+  }
+}

docs/c4_diagrams/likec4_src/tre/tre.c4

@@ -0,0 +1,32 @@
+model {
+  extend tre {
+    tre_app = service {
+      title 'TRE Application'
+      description 'Application managing tasks in the TRE'
+
+      -> tre_keycloak 'Authenticates requests via'
+      -> minio 'Stores and retrieves data from'
+      -> ro-crate_validator.validator_api 'Sends validation tasks to'
+      -> ro-crate_validator.validator_api 'Receives validation results from'
+    }
+
+    tre_keycloak = component {
+      title 'TRE Keycloak'
+      description 'Authenticates requests throughout the layer'
+      icon https://upload.wikimedia.org/wikipedia/commons/2/29/Keycloak_Logo.png
+    }
+
+    minio = component {
+      title 'Minio'
+      description 'S3 Object Store'
+      icon https://dl.min.io/logo/Minio_logo_light/Minio_logo_light.png
+    }
+  }
+}
+
+views {
+  view tre of tre {
+    title 'TRE Service'
+    include *
+  }
+}

docs/installation.md

@@ -1,5 +1,10 @@
 # Installation & Setup
 
+```likec4-view
+ro-crate_service
+```
+
+## Service Snapshot
 The RO-Crate Validation Service works in two ways: a metadata-only mode, in which the contents of an `ro-crate-metadata.json` file are assessed, and storage-backed validation, where complete RO-Crates (zip or directory) are evaluated. 
 
 ## Quick start

mkdocs.yml

@@ -9,5 +9,6 @@ theme: readthedocs
 plugins:
   - search
   - mermaid2
+  - likec4
 markdown_extensions:
   - admonition