diff --git a/.github/workflows/deploy-pages.yml b/.github/workflows/deploy-pages.yml new file mode 100644 index 0000000..2419a85 --- /dev/null +++ b/.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 \ No newline at end of file diff --git a/.gitignore b/.gitignore index 318044e..0f8b44d 100644 --- a/.gitignore +++ b/.gitignore @@ -319,3 +319,4 @@ cython_debug/ /cache-directory/ data .vscode +node_modules diff --git a/docs/c4_diagrams/likec4_src/README.txt b/docs/c4_diagrams/likec4_src/README.txt new file mode 100644 index 0000000..86259f5 --- /dev/null +++ b/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` diff --git a/docs/c4_diagrams/likec4_src/context.c4 b/docs/c4_diagrams/likec4_src/context.c4 new file mode 100644 index 0000000..09c445d --- /dev/null +++ b/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 + } +} \ No newline at end of file diff --git a/docs/c4_diagrams/likec4_src/index.png b/docs/c4_diagrams/likec4_src/index.png new file mode 100644 index 0000000..04ad48d Binary files /dev/null and b/docs/c4_diagrams/likec4_src/index.png differ diff --git a/docs/c4_diagrams/likec4_src/ro-crate_service/ro-crate_service.c4 b/docs/c4_diagrams/likec4_src/ro-crate_service/ro-crate_service.c4 new file mode 100644 index 0000000..17d43d9 --- /dev/null +++ b/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 * + } +} diff --git a/docs/c4_diagrams/likec4_src/ro-crate_service/ro-crate_service.png b/docs/c4_diagrams/likec4_src/ro-crate_service/ro-crate_service.png new file mode 100644 index 0000000..f788804 Binary files /dev/null and b/docs/c4_diagrams/likec4_src/ro-crate_service/ro-crate_service.png differ diff --git a/docs/c4_diagrams/likec4_src/ro-crate_validator/ro-crate_validator.c4 b/docs/c4_diagrams/likec4_src/ro-crate_validator/ro-crate_validator.c4 new file mode 100644 index 0000000..ced9e8d --- /dev/null +++ b/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 * + } +} diff --git a/docs/c4_diagrams/likec4_src/ro-crate_validator/ro-crate_validator.png b/docs/c4_diagrams/likec4_src/ro-crate_validator/ro-crate_validator.png new file mode 100644 index 0000000..1a71b0d Binary files /dev/null and b/docs/c4_diagrams/likec4_src/ro-crate_validator/ro-crate_validator.png differ diff --git a/docs/c4_diagrams/likec4_src/specs.c4 b/docs/c4_diagrams/likec4_src/specs.c4 new file mode 100644 index 0000000..fc0a42b --- /dev/null +++ b/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' + } +} \ No newline at end of file diff --git a/docs/c4_diagrams/likec4_src/tre/tre.c4 b/docs/c4_diagrams/likec4_src/tre/tre.c4 new file mode 100644 index 0000000..88165dd --- /dev/null +++ b/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 * + } +} diff --git a/docs/c4_diagrams/likec4_src/tre/tre.png b/docs/c4_diagrams/likec4_src/tre/tre.png new file mode 100644 index 0000000..e75d3dc Binary files /dev/null and b/docs/c4_diagrams/likec4_src/tre/tre.png differ diff --git a/docs/installation.md b/docs/installation.md index fc43b30..a4878db 100644 --- a/docs/installation.md +++ b/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 diff --git a/mkdocs.yml b/mkdocs.yml index a1ebf4d..8152e71 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -9,5 +9,6 @@ theme: readthedocs plugins: - search - mermaid2 + - likec4 markdown_extensions: - admonition diff --git a/package-lock.json b/package-lock.json new file mode 100644 index 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