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use native bash script instead of dip for people that do not have ruby
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@syphax-bouazzouni
syphax-bouazzouni committed Nov 15, 2023
1 parent c141c7f commit b7ca6cd
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1 change: 1 addition & 0 deletions Gemfile.lock
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Expand Up @@ -7,6 +7,7 @@ GEM

PLATFORMS
x86_64-darwin-23
x86_64-linux-musl

DEPENDENCIES
dip
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2 changes: 0 additions & 2 deletions docker-compose.yml
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@@ -1,5 +1,3 @@
name: ontoportal

x-app: &api
stdin_open: true
tty: true
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208 changes: 104 additions & 104 deletions run
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#!/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=<YOUR ONTOPORTAL API KEY>/, "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="${env_content//OP_APIKEY=<YOUR ONTOPORTAL API KEY>/OP_APIKEY=$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,[email protected]] > /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 --rm -d 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")
echo "Server is up and running!"

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