class SequenceServer::Config

Capture our configuration system.

Attributes

config_file[R]
data[R]

Public Class Methods

new(data = {}) click to toggle source
# File lib/sequenceserver/config.rb, line 12
def initialize(data = {})
  @data = normalize data

  @config_file = @data.delete(:config_file)
  if @config_file
    @config_file = File.expand_path(@config_file)
    @data = parse_config_file.deep_merge @data
  end

  @data = defaults.deep_merge @data

  return unless @upgraded

  logger.warn 'You are using old configuration syntax. ' \
              'Run `sequenceserver -s` to update your config file syntax.'
end

Public Instance Methods

[](key) click to toggle source

Get.

# File lib/sequenceserver/config.rb, line 32
def [](key)
  data[key]
end
[]=(key, value) click to toggle source

Set.

# File lib/sequenceserver/config.rb, line 37
def []=(key, value)
  data[key] = value
end
include?(key) click to toggle source

Exists?

# File lib/sequenceserver/config.rb, line 42
def include?(key)
  data.include? key
end
write_config_file() click to toggle source

Write config data to config file.

# File lib/sequenceserver/config.rb, line 47
def write_config_file
  return unless config_file

  File.open(config_file, 'w') do |f|
    f.puts(data.delete_if { |_, v| v.nil? }.to_yaml)
  end
end

Private Instance Methods

convert_deprecated_options(options) click to toggle source
# File lib/sequenceserver/config.rb, line 143
def convert_deprecated_options(options)
  options.each do |blast_algo, algo_config|
    if algo_config.is_a?(Array)
      # Very old config files may have a single array with CLI args.
      # e.g. { blastn: ['-task blastn', '-evalue 1e-5'] }
      # Convert the array values into a single hash naming it 'default' if
      # the values match SequenceServer defaults.
      options[blast_algo] = if algo_config == defaults.dig(:options, blast_algo, :default, :attributes)
                              { default: { attributes: algo_config } }
                            else
                              { custom: { attributes: algo_config } }
                            end
      @upgraded = true
    elsif algo_config.is_a?(Hash)
      # v3.0.1 and older config files contain a flatter structure
      # with an array instead of 'description' and 'attributes' keys.
      # e.g. { blastn: { default: ['-task blastn', '-evalue 1e-5'] }
      algo_config.each do |config_name, config|
        next unless config.is_a?(Array)

        options[blast_algo][config_name] = {
          description: nil,
          attributes: config
        }
        @upgraded = true
      end
    end
  end

  options
end
defaults() click to toggle source

Default configuration data.

# File lib/sequenceserver/config.rb, line 95
def defaults
  @defaults ||= {
    host: '0.0.0.0',
    port: 4567,
    databases_widget: 'classic',
    options: {
      blastn: {
        default: {
          description: nil,
          attributes: ['-task blastn', '-evalue 1e-5']
        }
      },
      blastp: {
        default: {
          description: nil,
          attributes: ['-evalue 1e-5']
        }
      },
      blastx: {
        default: {
          description: nil,
          attributes: ['-evalue 1e-5']
        }
      },
      tblastx: {
        default: {
          description: nil,
          attributes: ['-evalue 1e-5']
        }
      },
      tblastn: {
        default: {
          description: nil,
          attributes: ['-evalue 1e-5']
        }
      }
    },
    num_threads: 1,
    num_jobs: 1,
    job_lifetime: 43_200,
    # Set cloud_share_url to 'disabled' to disable the cloud sharing feature
    cloud_share_url: 'https://share.sequenceserver.com/api/v1/shared-job',
    # Warn in the UI before rendering results larger than this value
    large_result_warning_threshold: 250 * 1024 * 1024,
    optimistic: false # Faster, but does not perform DB compatibility checks
  }
end
file?(file) click to toggle source
# File lib/sequenceserver/config.rb, line 90
def file?(file)
  file && File.exist?(file) && File.file?(file)
end
normalize(data) click to toggle source

Symbolizes keys. Rename/reformat key-values.

# File lib/sequenceserver/config.rb, line 58
def normalize(data)
  return {} unless data

  # Symbolize keys.
  data = data.transform_keys(&:to_sym)

  # Very old config files may have a key called `database`.
  # Rename it to `database_dir`
  if data[:database]
    database_dir = data.delete(:database)
    data[:database_dir] ||= database_dir
    @upgrade = true
  end

  data[:options] = convert_deprecated_options(data[:options]) if data[:options]

  data
end
parse_config_file() click to toggle source

Parses and returns data from config_file if it exists. Returns {} otherwise.

# File lib/sequenceserver/config.rb, line 79
def parse_config_file
  unless file? config_file
    logger.debug "Configuration file not found: #{config_file}"
    return {}
  end
  logger.info "Reading configuration file: #{config_file}."
  normalize YAML.load_file(config_file)
rescue StandardError => e
  raise CONFIG_FILE_ERROR.new(config_file, e)
end