Class: CaTissue::Migrator

Inherits:
CaRuby::Migrator
  • Object
show all
Defined in:
lib/catissue/migration/migrator.rb

Overview

Migrates a CSV extract to caTissue. See the #initialize documentation for usage options.

See the Galena Cancer Center Tissue Bank Migration Example for further information about how the options tailor migration, esp. the use of the field mappings and shims.

Constant Summary collapse

NAME =

The default name of this migrator.

'caTissue Migrator'
DEF_CONF_FILE = 
File.join('conf', 'migration.yaml')
SHIM_FILE =

The built-in caTissue migration shims.

File.join(File.dirname(__FILE__), 'shims.rb')

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ Migrator

Creates a new Migrator with the given options.

This migrator must include sufficient information to build a well-formed migration target object. For example, if the target object is a new SpecimenCollectionGroup, then the migration must also be able to build that SCG’s CollectionProtocolRegistration. The CPR in turn must either exist in the database or the migration must build a Participant and a CollectionProtocol.

Parameters:

  • opts (Hash) (defaults to: {}) —

    a customizable set of options

Options Hash (opts):

  • :database (String) —

    target application CaRuby::Database

  • :target (String) —

    required target domain class

  • :input (String) —

    required source file to migrate

  • :shims (String) —

    optional array of shim files to load

  • :unique (String) —

    makes migrated objects unique object for testing mix-in do not conflict with existing or future objects

  • :bad (String) —

    write each invalid record to the given file and continue migration

  • :offset (String) —

    zero-based starting source record number to process (default 0)



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# File 'lib/catissue/migration/migrator.rb', line 37

def initialize(opts={})
  # if there is a configuration file, then add config options into the parameter options
  conf_file = opts.delete(:file)
  if conf_file then
    conf = CaRuby::Properties.new(conf_file, :array => [:shims])
    # add config options but don't override the parameter options
    opts.merge!(conf, :deep) { |key, oldval, newval| oldval }
  end
  # open the log file before building structure
  log_file = opts[:log]
  CaRuby::Log.instance.open(log_file, :debug => opts[:debug]) if log_file

  # tailor the options
  opts[:name] ||= NAME
  opts[:database] ||= CaTissue::Database.instance
  # prepend this migrator's shims
  shims = opts[:shims] ||= []
  shims.unshift(SHIM_FILE)

  # call the CaRuby::Migrator initializer with the augmented options
  super

  # The remaining options are specific to this CaTissue::Migrator subclass.

  # If the unique option is set, then append the CaTissue-specific uniquifier shim.
  if opts[:unique] then
    # add the uniquify shim
    @shims << UNIQUIFY_SHIM
  end

  # The tissue site CV look-up option.
  tissue_sites = opts[:tissue_sites]
  if tissue_sites then
    CaTissue::SpecimenCharacteristics.tissue_site_cv_finder = ControlledValueFinder.new(:tissue_site, tissue_sites)
    logger.info("Migrator enabled controlled value lookup.")
  end

  # The clinical diagnosis CV look-up option.
  diagnoses = opts[:diagnoses]
  if diagnoses then
    CaTissue::SpecimenCollectionGroup.diagnosis_cv_finder = ControlledValueFinder.new(:clinical_diagnosis, diagnoses)
    logger.info("Migrator enabled controlled value lookup.")
  end
end