diff --git a/.env.sample b/.env.sample index 2c15a1c0..7de8b685 100644 --- a/.env.sample +++ b/.env.sample @@ -1,4 +1,11 @@ API_URL=http://localhost:9393 ONTOLOGIES_LINKED_DATA_PATH= GOO_PATH= -SPARQL_CLIENT_PATH= \ No newline at end of file +SPARQL_CLIENT_PATH= + +## An ontology that will be imported in the starting of the API server +STARTER_ONTOLOGY=STY +## API key of a remote API used to download the starter ontology +OP_API_KEY=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb +## API url of the remote API used to download the starter ontology +OP_API_URL="https://data.bioontology.org" \ No newline at end of file diff --git a/bin/ontoportal b/bin/ontoportal index 66f1a654..9bf8cf5b 100755 --- a/bin/ontoportal +++ b/bin/ontoportal @@ -3,10 +3,11 @@ # Function to display script usage information show_help() { cat << EOL -Usage: $0 {dev|test|run|help} [--reset-cache] [--api-url API_URL] [--api-key API_KEY] [--old-path OLD_PATH] [--goo-path GOO_PATH] [--sparql-client-path SPARQL_CLIENT_PATH] +Usage: $0 {dev|test|run|help} [--reset-cache] [--api-url API_URL] [--api-key API_KEY] [--old-path OLD_PATH] [--goo-path GOO_PATH] [--sparql-client-path SPARQL_CLIENT_PATH] [--with-provision] dev : Start the Ontoportal API development server. Example: $0 dev --api-url http://localhost:9393 Use --reset-cache to remove volumes: $0 dev --reset-cache + Use --with-provision to parse ontology for use test : Run tests. Specify either a test file or use 'all'. Example: $0 test test/controllers/test_users_controller.rb -v --name=name_of_the_test Example (run all tests): $0 test all -v @@ -20,12 +21,13 @@ Description: Options: --reset-cache : Remove Docker volumes (used with 'dev'). + --with-provision : Parse ontology for use. --api-url API_URL : Specify the API URL. --api-key API_KEY : Specify the API key. --old-path OLD_PATH : Specify the path for ontologies_linked_data. --goo-path GOO_PATH : Specify the path for goo. --sparql-client-path : Specify the path for sparql-client. - test_file | all : Specify either a test file or all the tests will be run. + test_file | all : Specify either a test file or all the tests will be run. -v : Enable verbosity. --name=name_of_the_test : Specify the name of the test. @@ -101,6 +103,32 @@ build_docker_run_cmd() { } +provision() { + echo "[+] Running Cron provisioning" + source .env + + echo "[+] Cleaning volumes" + docker compose -f docker-compose.yml --profile 4store down --volumes >/dev/null 2>&1 + docker compose -p ontoportal_docker down --volumes >/dev/null 2>&1 + + commands=( + "bundle exec rake user:create[admin,admin@nodomain.org,password]" + "bundle exec rake user:adminify[admin]" + "bundle exec bin/ncbo_ontology_import --admin-user admin --ontologies $STARTER_ONTOLOGY --from-apikey $OP_API_KEY --from $OP_API_URL" + "bundle exec bin/ncbo_ontology_process -o ${STARTER_ONTOLOGY}" + ) + for cmd in "${commands[@]}"; do + echo "[+] Run: $cmd" + docker_cron_cmd="docker compose -f docker-compose.yml -p ontoportal_docker run --remove-orphans --rm --name cron-service --service-ports ncbo_cron bash -c \"$cmd\" >/dev/null 2>&1" + if ! eval "$docker_cron_cmd"; then + echo "Error: Failed to run provisioning . $cmd" + exit 1 + fi + done + + echo "CRON Setup completed successfully!" +} + # Function to handle the "dev" and "test" options run_command() { local custom_command="$1" @@ -110,6 +138,7 @@ run_command() { local old_path="" local goo_path="" local sparql_client_path="" + local with_provision="" shift # Check for command line arguments @@ -135,6 +164,10 @@ run_command() { sparql_client_path="$2" shift 2 ;; + --with-provision) + with_provision="$1" + shift 1 + ;; *) echo "Unknown option: $1" show_help @@ -147,6 +180,7 @@ run_command() { if [ "$reset_cache" = true ]; then echo "Resetting cache. Running: docker compose down --volumes" docker compose down --volumes + docker compose -p ontoportal_docker down --volumes fi # Check if arguments are provided @@ -168,6 +202,12 @@ run_command() { fi + # run provision + if [ "$with_provision" == "--with-provision" ]; then + provision + else + echo "[+] Skipping Cron provisioning" + fi # Build the Docker run command echo "Run: $custom_command"