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Feature: add ontoportal bash script (#59)
* add ontoportal bash script to run test and development servers * update README.md * update docker CI to work in production releases
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| API_URL=http://localhost:9393 |
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| name: Docker branch Images build - ARM version | ||
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| on: | ||
| push: | ||
| branches: | ||
| - development | ||
| - stage | ||
| - test | ||
| release: | ||
| types: [ published ] | ||
| jobs: | ||
| push_to_registry: | ||
| name: Push Docker branch image to Docker Hub | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Check out the repo | ||
| uses: actions/checkout@v3 | ||
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| - name: Set up QEMU | ||
| uses: docker/setup-qemu-action@v2 | ||
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| - name: Set up Docker Buildx | ||
| uses: docker/setup-buildx-action@v2 | ||
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| - name: Log in to Docker Hub | ||
| uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a | ||
| with: | ||
| username: ${{ secrets.DOCKERHUB_USERNAME }} | ||
| password: ${{ secrets.DOCKERHUB_TOKEN }} | ||
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| - name: Log in to the Container registry | ||
| uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1 | ||
| with: | ||
| registry: ghcr.io | ||
| username: ${{ github.actor }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
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| - name: Extract metadata (tags, labels) for Docker | ||
| id: meta | ||
| uses: docker/metadata-action@v4 | ||
| with: | ||
| images: | | ||
| agroportal/ontologies_api | ||
| ghcr.io/${{ github.repository }} | ||
| - name: Build and push Docker image | ||
| uses: docker/build-push-action@v4 | ||
| with: | ||
| context: . | ||
| platforms: linux/arm64 | ||
| build-args: | | ||
| RUBY_VERSION=2.7 | ||
| push: true | ||
| tags: ${{ steps.meta.outputs.tags }}-${{ env.BRANCH_NAME }}-arm64 | ||
| labels: ${{ steps.meta.outputs.labels }} | ||
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@@ -71,3 +71,5 @@ test/data/ontology_files/catalog-v001.xml | |
| create_permissions.log | ||
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| ontologies_api.iml | ||
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| .env | ||
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@@ -2,7 +2,53 @@ | |
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| ontologies_api provides a RESTful interface for accessing [BioPortal](https://bioportal.bioontology.org/) (an open repository of biomedical ontologies). Supported services include downloads, search, access to terms and concepts, text annotation, and much more. | ||
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| ## Prerequisites | ||
| # Run ontologies_api | ||
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| ## Using OntoPortal api utilities script | ||
| ### See help | ||
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| ```bash | ||
| bin/ontoportal help | ||
| ``` | ||
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| ``` | ||
| Usage: bin/ontoportal {dev|test|run|help} [--reset-cache] [--api-url API_URL] [--api-key API_KEY] | ||
| dev : Start the Ontoportal API development server. | ||
| Example: bin/ontoportal dev --api-url http://localhost:9393 | ||
| Use --reset-cache to remove volumes: bin/ontoportal dev --reset-cache | ||
| test : Run tests. | ||
| run : Run a command in the Ontoportal API Docker container. | ||
| help : Show this help message. | ||
| Description: | ||
| This script provides convenient commands for managing an Ontoportal API | ||
| application using Docker Compose. It includes options for starting the development server, | ||
| running tests, and executing commands within the Ontoportal API Docker container. | ||
| Goals: | ||
| - Simplify common tasks related to Ontoportal API development using Docker. | ||
| - Provide a consistent and easy-to-use interface for common actions. | ||
| ``` | ||
| ### Configuration | ||
| ``` | ||
| cp .env.sample .env | ||
| ``` | ||
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| ### Run dev | ||
| ```bash | ||
| bin/ontoportal dev | ||
| ``` | ||
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| ### Run test with a local OntoPortal API | ||
| ```bash | ||
| bin/ontoportal test | ||
| ``` | ||
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| ## Manually | ||
| ### Prerequisites | ||
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| - [Ruby 2.x](http://www.ruby-lang.org/en/downloads/) (most recent patch level) | ||
| - [rbenv](https://github.com/sstephenson/rbenv) and [ruby-build](https://github.com/sstephenson/ruby-build) (optional) | ||
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@@ -19,7 +65,7 @@ ontologies_api provides a RESTful interface for accessing [BioPortal](https://bi | |
| - [Solr](http://lucene.apache.org/solr/) | ||
| - BioPortal indexes ontology class and property content using Solr (a Lucene-based server) | ||
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| ## Configuring Solr | ||
| ### Configuring Solr | ||
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| To configure Solr for ontologies_api usage, modify the example project included with Solr by doing the following: | ||
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@@ -46,22 +92,22 @@ To configure Solr for ontologies_api usage, modify the example project included | |
| # Edit the ontologieS_api/config/environments/{env}.rb file to point to your running instance: | ||
| # http://localhost:8983/solr/NCBO1 | ||
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| ## Installing | ||
| ### Installing | ||
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| ### Clone the repository | ||
| #### Clone the repository | ||
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| ``` | ||
| $ git clone [email protected]:ncbo/ontologies_api.git | ||
| $ cd ontologies_api | ||
| ``` | ||
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| ### Install the dependencies | ||
| #### Install the dependencies | ||
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| ``` | ||
| $ bundle install | ||
| ``` | ||
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| ### Create an environment configuration file | ||
| #### Create an environment configuration file | ||
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| ``` | ||
| $ cp config/environments/config.rb.sample config/environments/development.rb | ||
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@@ -73,7 +119,7 @@ production.rb<br /> | |
| development.rb<br /> | ||
| test.rb | ||
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| ### Run the unit tests (optional) | ||
| #### Run the unit tests (optional) | ||
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| Requires a configuration file for the test environment: | ||
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@@ -87,7 +133,7 @@ Execute the suite of tests from the command line: | |
| $ bundle exec rake test | ||
| ``` | ||
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| ### Run the application | ||
| #### Run the application | ||
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| ``` | ||
| $ bundle exec rackup --port 9393 | ||
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