From 31dd1a172e55e524688b64cb67eb6d76b57e4db0 Mon Sep 17 00:00:00 2001 From: Syphax bouazzouni Date: Wed, 15 Nov 2023 18:02:12 +0100 Subject: [PATCH] use native bash script instead of dip for people that do not have ruby --- Gemfile.lock | 1 + docker-compose.yml | 2 - run | 208 ++++++++++++++++++++++----------------------- 3 files changed, 105 insertions(+), 106 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 330e89a..3859099 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -7,6 +7,7 @@ GEM PLATFORMS x86_64-darwin-23 + x86_64-linux-musl DEPENDENCIES dip diff --git a/docker-compose.yml b/docker-compose.yml index ae716fe..c46deef 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,5 +1,3 @@ -name: ontoportal - x-app: &api stdin_open: true tty: true diff --git a/run b/run index ca3e69a..e694acd 100755 --- a/run +++ b/run @@ -1,129 +1,129 @@ -#!/usr/bin/env ruby - -require 'optparse' +#!/usr/bin/env bash # Default values -options = { - api_key: nil, - api_url: 'https://data.bioontology.org', - starter_ontology: 'STY' -} - -# OptionParser configuration -OptionParser.new do |opts| - opts.banner = "Usage: #{$PROGRAM_NAME} -k API_KEY -u API_URL -s STARTER_ONTOLOGY" - - opts.on("-k", "--api-key API_KEY", "Your Ontoportal API key") do |api_key| - options[:api_key] = api_key - end - - opts.on("-u", "--api-url API_URL", "Ontoportal API URL (default: https://data.bioontology.org)") do |api_url| - options[:api_url] = api_url - end - - opts.on("-r", "--docker-hub-repository DOCKER_HUB_REPOSITORY", "Ontoportal API image repository (default: bioportal)") do |image_repository| - options[:image_repository] = image_repository || 'bioportal' - end - - opts.on("-t", "--image-tag DOCKER_IMAGE_TAG", "Ontoportal API image version (default: latest)") do |image_tag| - options[:image_tag] = image_tag || 'latest' - end - - - opts.on("-s", "--starter-ontology [STARTER_ONTOLOGY]", "Starter ontology code (default: STY)") do |starter_ontology| - options[:starter_ontology] = starter_ontology || 'STY' - end - - opts.on_tail("-h", "--help", "Show this message") do - puts opts - exit - end -end.parse! +API_URL="https://data.bioontology.org" +STARTER_ONTOLOGY="STY" +IMAGE_REPOSITORY="bioportal" +IMAGE_TAG="latest" + +# Parse command line options +while getopts ":k:u:r:t:s:" opt; do +case $opt in + k) API_KEY="$OPTARG";; + u) API_URL="$OPTARG";; + r) IMAGE_REPOSITORY="$OPTARG";; + t) IMAGE_TAG="$OPTARG";; + s) STARTER_ONTOLOGY="$OPTARG";; + \?) echo "Invalid option: -$OPTARG" >&2; exit 1;; + :) echo "Option -$OPTARG requires an argument." >&2; exit 1;; +esac +done # Check if required arguments are provided -unless options[:api_key] - puts "Error: Missing required arguments. Please provide API_KEY." - puts "See help using -h, --help" - exit 1 -end +if [ -z "$API_KEY" ]; then +echo "Error: Missing required argument. Please provide API_KEY." +echo "See help using -h, --help" +exit 1 +fi + +echo "Running the Ontoportal API and CRON Setup..." -puts "Running the Ontoportal API and CRON Setup..." # Step 1: Clone ontologies_linked_data repo -puts "Cloning ontologies_linked_data repo..." -system("git clone --depth=1 https://github.com/ontoportal-lirmm/ontologies_linked_data.git") +echo "Cloning ontologies_linked_data repo..." +git clone --depth=1 https://github.com/ontoportal-lirmm/ontologies_linked_data.git # Step 2: Generate configsets -puts "Generating Solr configsets..." -Dir.chdir("ontologies_linked_data") do - unless system("./test/solr/generate_ncbo_configsets.sh") - puts "Error: Failed to generate Solr configsets." - exit 1 - end -end +echo "Generating Solr configsets..." +cd ontologies_linked_data || exit 1 +if ! ./test/solr/generate_ncbo_configsets.sh; then + echo "Error: Failed to generate Solr configsets." + exit 1 +fi -puts "Navigating to ontoportal_docker directory..." -Dir.chdir("../ontoportal_docker") || exit(1) +echo "Navigating to ontoportal_docker directory..." +cd .. || exit 1 # Step 4: Install DIP -puts "Installing DIP (Docker in Production) dependencies..." -unless system("bundle install") - puts "Error: Failed to install DIP dependencies." - exit 1 -end +echo "Installing DIP (Docker in Production) dependencies..." +if ! bundle install; then + echo "Error: Failed to install DIP dependencies." + exit 1 +fi -# Copy .env.sample to .env -unless system("cp .env.sample .env") - puts "Error: Failed to copy .env.sample to .env." - exit 1 -end + # Copy .env.sample to .env +if ! cp .env.sample .env; then + echo "Error: Failed to copy .env.sample to .env." + exit 1 +fi -env_file_path = './.env' -# Read the content of .env file -begin - env_content = File.read(env_file_path) -rescue StandardError => e - puts "Error: Failed to read .env file. #{e.message}" - exit 1 -end +env_file_path="./.env" -# Step 5: Export bioportal APIKEY, update OP_APIKEY and OP_API_URL in .env file -puts "Exporting bioportal APIKEY..." -env_content.gsub!(/OP_APIKEY=/, "OP_APIKEY=#{options[:api_key]}") +# Read the content of .env file +env_content=$(<"$env_file_path") -# Step 6: Update OP_API_URL in .env file with provided API_URL argument -puts "Updating OP_API_URL in .env file..." -env_content.gsub!(/OP_API_URL="https:\/\/data.bioontology.org"/, "OP_API_URL=#{options[:api_url]}") +# Export bioportal APIKEY, update OP_APIKEY and OP_API_URL in .env file +echo "Exporting bioportal APIKEY..." +env_content="${env_content//OP_APIKEY=/OP_APIKEY=$API_KEY}" -# Step 7: Update STARTER_ONTOLOGY in .env file with provided STARTER_ONTOLOGY argument -puts "Updating STARTER_ONTOLOGY in .env file..." -env_content.gsub!(/STARTER_ONTOLOGY="STY"/, "STARTER_ONTOLOGY=#{options[:starter_ontology]}") +# Update OP_API_URL in .env file with provided API_URL argument +echo "Updating OP_API_URL in .env file..." +env_content="${env_content//OP_API_URL=\"https:\/\/data.bioontology.org\"/OP_API_URL=$API_URL}" -# Step 7: Update IMAGE_REPOSITORY in .env file with provided IMAGE_REPOSITORY argument -puts "Updating IMAGE_REPOSITORY in .env file..." -env_content.gsub!(/IMAGE_REPOSITORY=bioportal/, "IMAGE_REPOSITORY=#{options[:image_repository]}") +# Update STARTER_ONTOLOGY in .env file with provided STARTER_ONTOLOGY argument +echo "Updating STARTER_ONTOLOGY in .env file..." +env_content="${env_content//STARTER_ONTOLOGY=\"STY\"/STARTER_ONTOLOGY=$STARTER_ONTOLOGY}" +# Update IMAGE_REPOSITORY in .env file with provided IMAGE_REPOSITORY argument +echo "Updating IMAGE_REPOSITORY in .env file..." +env_content="${env_content//IMAGE_REPOSITORY=bioportal/IMAGE_REPOSITORY=$IMAGE_REPOSITORY}" -# Step 7: Update IMAGE_TAG in .env file with provided IMAGE_TAG argument -puts "Updating IMAGE_TAG in .env file..." -env_content.gsub!(/IMAGE_TAG=latest/, "IMAGE_TAG=#{options[:image_tag]}") +# Update IMAGE_TAG in .env file with provided IMAGE_TAG argument +echo "Updating IMAGE_TAG in .env file..." +env_content="${env_content//IMAGE_TAG=latest/IMAGE_TAG=$IMAGE_TAG}" # Write the modified content back to the .env file -begin - File.write(env_file_path, env_content) -rescue StandardError => e - puts "Error: Failed to write to .env file. #{e.message}" - exit 1 -end +echo "$env_content" > "$env_file_path" # Step 8: Run provisioning via dip -puts "Running provisioning via DIP..." -unless system("dip provision") - puts "Error: Failed to run provisioning via DIP." - exit 1 -end - -puts "Setup completed successfully!" +echo "Running provisioning via DIP..." +commands=( + 'docker compose down --volumes > /dev/null 2>&1' + 'docker compose run --rm 4store bash -c "4s-backend-setup ontoportal_kb" > /dev/null 2>&1 ' + 'docker compose run --rm ncbo_cron bundle exec rake user:create[admin,admin@nodomain.org] > /dev/null 2>&1' + "docker compose run --rm ncbo_cron bundle exec 'bin/ncbo_ontology_import --admin-user admin --ontologies $STARTER_ONTOLOGY --from-apikey $API_KEY --from $API_URL' > /dev/null 2>&1 " + "docker compose run --rm ncbo_cron bundle exec 'bin/ncbo_ontology_pull -o $STARTER_ONTOLOGY' > /dev/null 2>&1 " + "docker compose run --rm ncbo_cron bundle exec 'bin/ncbo_ontology_process -o ${STARTER_ONTOLOGY}' > /dev/null 2>&1" +) + +for cmd in "${commands[@]}"; do + echo "Run: $cmd" + if ! eval "$cmd"; then + echo "Error: Failed to run provisioning via DIP. $cmd" + exit 1 + fi +done + +echo "Setup completed successfully!" + + + + + +echo "Running api via DIP..." +docker compose run --service-ports -it --rm api + + # Wait for API to be ready (adjust the sleep time accordingly) +timeout=30 +elapsed=0 +until [ $elapsed -ge $timeout ] || curl -sSf http://localhost:9393 > /dev/null 2>&1; do + echo "Waiting for the server to be up..." + sleep 1 + elapsed=$((elapsed + 1)) +done +if [ $elapsed -ge $timeout ]; then + echo "Timed out waiting for the server to be up." + exit 1 +fi -puts "Running api via DIP..." -system("dip api rackup") \ No newline at end of file +echo "Server is up and running!" \ No newline at end of file