Feature: add ontoportal bash script

.env.sample

@@ -0,0 +1 @@
+API_URL=http://localhost:9393

.github/workflows/docker-dev-release.yml → .github/workflows/docker-image.yml

@@ -6,7 +6,8 @@ on:
       - development
       - stage
       - test
-
+  release:
+    types: [ published ]
 jobs:
   push_to_registry:
     name: Push Docker branch image to Docker Hub

.github/workflows/ruby-unit-tests.yml

@@ -12,6 +12,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
+    - name: copy-env-config
+      run: cp .env.sample .env
     - name: Build docker-compose
       run: docker-compose --profile 4store build #profile flag is set in order to build all containers in this step
     - name: Run unit tests

.gitignore

@@ -71,3 +71,5 @@ test/data/ontology_files/catalog-v001.xml
 create_permissions.log
 
 ontologies_api.iml
+
+.env

README.md

@@ -2,7 +2,53 @@
 
 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.
 
-## Prerequisites
+# Run ontologies_api
+
+## Using OntoPortal api utilities script 
+### See help
+
+```bash 
+bin/ontoportal help
+```
+
+```
+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 
+```
+
+### Run dev
+```bash 
+bin/ontoportal dev 
+```
+
+### Run test with a local OntoPortal API
+```bash 
+bin/ontoportal test 
+```
+
+
+## Manually 
+### Prerequisites
 
 - [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)
@@ -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)
 
-## Configuring Solr
+### Configuring Solr
 
 To configure Solr for ontologies_api usage, modify the example project included with Solr by doing the following:
 
@@ -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
 
-## Installing
+### Installing
 
-### Clone the repository
+#### Clone the repository
 
 ```
 $ git clone [email protected]:ncbo/ontologies_api.git
 $ cd ontologies_api
 ```
 
-### Install the dependencies
+#### Install the dependencies
 
 ```
 $ bundle install
 ```
 
-### Create an environment configuration file
+#### Create an environment configuration file
 
 ```
 $ cp config/environments/config.rb.sample config/environments/development.rb
@@ -73,7 +119,7 @@ production.rb<br />
 development.rb<br />
 test.rb
 
-### Run the unit tests (optional)
+#### Run the unit tests (optional)
 
 Requires a configuration file for the test environment:
 
@@ -87,7 +133,7 @@ Execute the suite of tests from the command line:
 $ bundle exec rake test 
 ```
 
-### Run the application
+#### Run the application
 
 ```
 $ bundle exec rackup --port 9393 

bin/ontoportal

@@ -0,0 +1,166 @@
+#!/usr/bin/env bash
+
+# Function to display script usage information
+show_help() {
+  echo "Usage: $0 {dev|test|run|help} [--reset-cache] [--api-url API_URL] [--api-key API_KEY]"
+  echo "  dev            : Start the Ontoportal API development server."
+  echo "                  Example: $0 dev --api-url http://localhost:9393"
+  echo "                  Use --reset-cache to remove volumes: $0 dev --reset-cache"
+  echo "  test           : Run tests."
+  echo "  run            : Run a command in the Ontoportal API Docker container."
+  echo "  help           : Show this help message."
+  echo
+  echo "Description:"
+  echo "  This script provides convenient commands for managing an Ontoportal API"
+  echo "  application using Docker Compose. It includes options for starting the development server,"
+  echo "  running tests, and executing commands within the Ontoportal API Docker container."
+  echo
+  echo "Goals:"
+  echo "  - Simplify common tasks related to Ontoportal API development using Docker."
+  echo "  - Provide a consistent and easy-to-use interface for common actions."
+}
+# Function to update or create the .env file with API_URL and API_KEY
+update_env_file() {
+  local api_url="$1"
+
+  # Update  the .env file with the provided values
+  file_content=$(<.env)
+
+  # Make changes to the variable
+  while IFS= read -r line; do
+        if [[ "$line" == "API_URL="* ]]; then
+          echo "API_URL=$api_url"
+        else
+          echo "$line"
+        fi
+  done <<< "$file_content" > .env
+}
+
+# Function to create configuration files if they don't exist
+create_config_files() {
+  if [ ! -f ".env" ]; then
+      echo "Creating .env file from env.sample"
+      cp .env.sample .env
+  fi
+
+  if [ ! -f "config/environments/development.rb" ]; then
+    echo "Creating config/environments/development.rb file from config/environments/config.rb.sample"
+    cp config/bioportal_config_env.rb.sample config/bioportal_config_development.rb
+  fi
+}
+
+# Function to handle the "dev" option
+dev() {
+  echo "Starting Ontoportal API development server..."
+
+  create_config_files
+  local reset_cache=false
+  local api_url=""
+
+
+  # Check for command line arguments
+  while [[ "$#" -gt 0 ]]; do
+    case $1 in
+      --reset-cache)
+        reset_cache=true
+        shift
+        ;;
+      --api-url)
+        api_url="$2"
+        shift 2
+        ;;
+      *)
+        echo "Unknown option: $1"
+        show_help
+        exit 1
+        ;;
+    esac
+  done
+
+
+
+  # Check if arguments are provided
+  if [ -n "$api_url" ] ; then
+    # If arguments are provided, update the .env file
+    update_env_file "$api_url"
+  else
+    # If no arguments, fetch values from the .env file
+    source .env
+    api_url="$API_URL"
+  fi
+
+  if [ -z "$api_url" ] ; then
+    echo "Error: Missing required arguments. Please provide both --api-url or update them in your .env"
+    exit 1
+  fi
+
+  # Check if --reset-cache is present and execute docker compose down --volumes
+  if [ "$reset_cache" = true ]; then
+    echo "Resetting cache. Running: docker compose down --volumes"
+    docker compose down --volumes
+  fi
+
+  echo "Run: bundle exec api s -b 0.0.0.0 -p 3000"
+  docker compose run --rm -it --service-ports api bash -c "(bundle check || bundle install) && bundle exec rackup -o 0.0.0.0 --port 9393"
+}
+
+# Function to handle the "test" option
+test() {
+
+
+  local api_url=""
+  local test_path=""
+  local test_options=""
+
+  # Check for command line arguments
+  while [ "$#" -gt 0 ]; do
+     case "$1" in
+       --api-url)
+         shift
+         api_url="$1"
+         ;;
+       *)
+         if [ -z "$test_path" ]; then
+           test_path="$1"
+         else
+           test_options="$test_options $1"
+         fi
+         ;;
+     esac
+     shift
+  done
+
+
+
+  script="API_URL=$api_url bundle exec rake test TEST=\"$test_path\" TESTOPTS=\"$test_options\""
+  echo "Running tests..."
+  echo "Run: $script"
+
+  docker compose run --rm -it api bash -c "(bundle check || bundle install) && $script"
+}
+
+# Function to handle the "run" option
+run() {
+  echo "Run: $*"
+  docker compose run --rm -it api bash -c "$*"
+}
+
+# Main script logic
+case "$1" in
+  "run")
+    run "${@:2}"
+    ;;
+  "dev")
+    dev "${@:2}"
+    ;;
+  "test")
+    test "${@:2}"
+    ;;
+  "help")
+    show_help
+    ;;
+  *)
+    show_help
+    exit 1
+    ;;
+esac

config/environments/config.rb.sample

@@ -18,7 +18,7 @@ REDIS_PERSISTENT_HOST = ENV.include?("REDIS_PERSISTENT_HOST") ? ENV["REDIS_PERSI
 REDIS_PORT            = ENV.include?("REDIS_PORT")            ? ENV["REDIS_PORT"]            : 6379
 REPORT_PATH           = ENV.include?("REPORT_PATH")           ? ENV["REPORT_PATH"]           : "./test/ontologies_report.json"
 REPOSITORY_FOLDER     = ENV.include?("REPOSITORY_FOLDER")     ? ENV["REPOSITORY_FOLDER"]     : "./test/data/ontology_files/repo"
-REST_URL_PREFIX       = ENV.include?("REST_URL_PREFIX")       ? ENV["REST_URL_PREFIX"]       : "http://localhost:9393"
+REST_URL_PREFIX       = ENV.include?("REST_URL_PREFIX")       ? ENV["REST_URL_PREFIX"]       : ENV["API_URL"] || "http://localhost:9393"
 SOLR_PROP_SEARCH_URL  = ENV.include?("SOLR_PROP_SEARCH_URL")  ? ENV["SOLR_PROP_SEARCH_URL"]  : "http://localhost:8983/solr/prop_search_core1"
 SOLR_TERM_SEARCH_URL  = ENV.include?("SOLR_TERM_SEARCH_URL")  ? ENV["SOLR_TERM_SEARCH_URL"]  : "http://localhost:8983/solr/term_search_core1"
 

docker-compose.yml

@@ -1,10 +1,5 @@
 x-app: &app
-    build:
-      context: .
-      args:
-        RUBY_VERSION: '2.7'
-    # Increase the version number in the image tag every time Dockerfile or its arguments is changed
-    image: ontologies_api:0.0.1
+    image: agroportal/ontologies_api:development
     environment: &env
       BUNDLE_PATH: /srv/ontoportal/bundle
       # default bundle config resolves to /usr/local/bundle/config inside of the container
@@ -39,6 +34,8 @@ x-app: &app
 services:
   api:
     <<: *app
+    env_file:
+      .env
     environment:
       <<: *env
       GOO_BACKEND_NAME: 4store