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| name: ci | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| permissions: | ||
| contents: write | ||
| jobs: | ||
| deploy: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - name: Configure Git Credentials | ||
| run: | | ||
| git config user.name github-actions[bot] | ||
| git config user.email 41898282+github-actions[bot]@users.noreply.github.com | ||
| - uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: 3.x | ||
| - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV | ||
| - uses: actions/cache@v4 | ||
| with: | ||
| key: mkdocs-material-${{ env.cache_id }} | ||
| path: .cache | ||
| restore-keys: | | ||
| mkdocs-material- | ||
| - run: pip install mkdocs-material | ||
| - run: mkdocs gh-deploy --force |
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@@ -58,3 +58,4 @@ build/ | |
| /application.yaml | ||
| /application.properties | ||
| .Rproj.user | ||
| site/ | ||
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| # Contributing to Armadillo | ||
|
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| ## Running Armadillo from source code | ||
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| You can run from source code as follows: | ||
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| 1. Install Java and Docker | ||
| 2. Checkout the source using `git clone https://github.com/molgenis/molgenis-service-armadillo.git` | ||
| 3. Optionally copy `application.template.yml` to `application.yml` to change settings (will be .gitignored) | ||
| 4. Compile and execute the code using `./gradlew run` | ||
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| Note: contact MOLGENIS team if you want to contribute and need a testing OIDC config that you can run against localhost. | ||
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| # Developing Armadillo | ||
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| We use gradle to build: | ||
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| ## Running locally | ||
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| ```bash | ||
| ./gradlew run | ||
| ``` | ||
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| As we now have the option to download the logfile from the application we need to have one to begin with: | ||
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| ```bash | ||
| # Leave out the -a to overwrite instead of append | ||
| ./gradlew run | tee -a logs/armadillo.log | ||
| ``` | ||
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| ## Running tests | ||
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| ```bash | ||
| ./gradlew test | ||
| ``` | ||
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| ## Upgrade plugins | ||
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| Use the commands listed below. | ||
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| ```bash | ||
| ./gradlew useLatestVersions | ||
| ./gradlew useLatestVersionsCheck | ||
| ``` | ||
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| Some plugins need manually editing the build files. | ||
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| To help find the right `build.gradle` use the command below with your keyword. | ||
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| ```bash | ||
| find . -type f -name "build.gradle" -exec echo {} \; -exec grep YOUR_KEY_WORD {} \; | ||
| ``` | ||
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| ## Upgrading gradle | ||
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| ```bash | ||
| ./gradlew wrapper --gradle-version 8.6 | ||
| ``` | ||
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| ## Check for updates | ||
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| To get a list of new dependencies run | ||
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| ```bash | ||
| ./gradlew dependencyUpdates | ||
| ``` | ||
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| ## Tools | ||
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| We use intellij to develop | ||
| * To run or debug in intellij, right click on armadillo/src/main/java/org.molgenis.armdadillo/ArmadilloServiceAppliction and choose 'Run/Debug Armadillo...' | ||
| * To run using oidc, create a copy of [application.yml](application.template.yml) in root of your project | ||
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| We have a swagger-ui to quickly see and test available web services at http://localhost:8080/swagger-ui/ | ||
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| ## Components | ||
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| We have several components | ||
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| - [Armadillo](./armadillo/src/) source | ||
| - [UI](./ui/README.md) readme | ||
| - [R](./r/) java integration source | ||
| - [docker](./docker/README.md) | ||
| - [ci](./docker/ci/README.md) | ||
| - [scripts](./scripts/README.md) migration | ||
| - [install](./scripts/install/README.md) | ||
| - [release](./scripts/release/README.md) | ||
| - [ops](./scripts/ops/README.md) | ||
| - [upgrade](./scripts/upgrade/README.md) | ||
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| ## Releasing | ||
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| Releases are done whenever the version number gets bumped. For more information see the `Commit messages and versioning (Major, Minor, Patch updates)` section below. | ||
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| We use mooltiverse [Nyx](https://mooltiverse.github.io/nyx/guide/user/introduction/how-nyx-works/) for changelog and publishing to github. | ||
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| Run `./gradlew tasks --group Release` to see all release tasks | ||
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| Use `./gradlew nyxMake` to see what is build in [build/distributions](./build/distributions/). | ||
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| ### Commit messages and versioning (Major, Minor, Patch updates) | ||
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| Versionnumbers are updated according to [Semantic versioning](https://semver.org/), using [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/). | ||
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| Please be aware that new releases will only be done when one of the above prefixes is used. | ||
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| Other prefixes do not indicate user-facing changes and will therefore not result in a version bump, consequently not resulting in a new (pre) release. | ||
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| Each commit with `!` just before the colon `:` is a major update, indicating a breaking change. So use it wisely. You can also add `BREAKING CHANGE:` in the long commit message format. | ||
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| - Use `feat!: ...` or `fix!: ...` for a major upgrade, indicating a breaking change. | ||
| - Use `feat: ...` for a minor upgrade, indicating a new feature. | ||
| - Use `fix: ...` for a patch update, indicating a bugfix. | ||
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| ### Checking log messages | ||
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| As [changelog template](./changelog-notes.tpl) uses the commit message it is good to check their quality. | ||
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| List messages to see usage of conventional commits from the past. | ||
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| ```sh | ||
| # How many colon usages | ||
| git log --pretty=format:"%s" | cut -d: -f1 | sort | uniq -c | sort -n | ||
| ``` | ||
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| ### Building locally | ||
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| ```sh | ||
| ./gradlew clean assemble | ||
| ``` | ||
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| ## Continuous integration | ||
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| - We test on each PR and merges on master | ||
| - We build docker compose set for CI testing and demo purposes. | ||
| - [CI testing](./docker/ci/README.md) | ||
| - Demo zip file is a delivery you as artifact | ||
| - Master build have a armadillo-compose.zip for download | ||
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| ### Local CI build | ||
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| ``` | ||
| ./gradlew docker | ||
| ./docker/bin/prepare.bash ci | ||
| cd build/docker/armadillo-compose | ||
| # Follow README.md to see Armadillo and R images run in container | ||
| docker compose build | ||
| docker compose up | ||
| ``` | ||
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| then run `./release-test.R` against this. | ||
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| ### Local CI test of armadillo-compose | ||
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| Follow [docker CI README.md](./docker/ci/README.md) to run `release-test.R` using `molgenis/r-cicd` image | ||
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| ## Profile xenon with resourcer whitelisted returns a host.docker.internal error | ||
| When developing locally, it might be possible to come across the container error: `Could not resolve host: host.docker.internal`, | ||
| especially when developing on a non-supported operating system when resourcer is whitelisted (such as xenon). | ||
| Sadly, the only way around this error is to edit the JAVA source code of Armadillo to include starting with an extra host. | ||
| To enable this feature, you must edit the private method `installImage` of [DockerService.java](https://github.com/molgenis/molgenis-service-armadillo/blob/master/armadillo/src/main/java/org/molgenis/armadillo/profile/DockerService.java) `CreateContainerCmd cmd` from `.withHostConfig(new HostConfig().withPortBindings(portBindings))` to `.withHostConfig(new HostConfig().withPortBindings(portBindings).withExtraHosts("host.docker.internal:host-gateway"))`. | ||
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| Please note that in order for this change to work, you must use Intellij to run Armadillo or compile the new source code. | ||
| Also, if you already have a xenon container build and running, stop and remove that container. | ||
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| # Developing DataSHIELD packages in Armadillo | ||
| As package developer will want to push your new packages into a DataSHIELD profile | ||
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| * You can start Armadillo with defaults as described above; then use admin/admin as authentication | ||
| * to see what profile are available and has been selected: | ||
| ``` | ||
| curl -u admin:admin http://localhost:8080/profiles | ||
| ``` | ||
| * to change selected profile 'my-profile': | ||
| ``` | ||
| curl -X POST http://localhost:8080/select-profile \ | ||
| -H 'Content-Type: application/json' \ | ||
| -d 'default' | ||
| ``` | ||
| * to install-packages in DataSHIELD current using admin user: | ||
| ``` | ||
| curl -u admin:admin -v \ | ||
| -H 'Content-Type: multipart/form-data' \ | ||
| -F "file=@dsBase_6.3.0.tar.gz" \ | ||
| -X POST http://localhost:8080/install-package | ||
| ``` | ||
| * to update whitelist of your current profile: | ||
| ``` | ||
| curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase | ||
| ``` | ||
| * to get whitelist of current profile: | ||
| ``` | ||
| curl -u admin:admin http://localhost:8080/whitelist | ||
| ``` | ||
| We really appreciate anyone wanting to contribute to Armadillo. For more information on doing so, visit our | ||
| [Developer guides](https://molgenis.github.io/molgenis-service-armadillo/pages/dev_guides/) |
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armadillo/src/main/java/org/molgenis/armadillo/audit/AuthenticationAuditListener.java
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