Module: ActiveUnimod::Database

Defined in:
lib/active_unimod/database.rb

Overview

Methods for managing a local Unimod database. Information normally logged by Rails will be written to ‘unimod_log.txt’ unless ActiveRecord::Base.logger is set when this file is required.

Constant Summary collapse

TABLES = 
[
AltName,  AminoAcid, Brick2element, Brick, Classification, 
Element, FragmentComp, Fragment, Log,  Mod2brick, Modification, 
NeutralLoss, Position,  Spec2nl, Specificity, User, XrefSource, Xref]

Class Method Summary collapse

Class Method Details

.create_tables(verbose = true) ⇒ Object

Creates the ActiveUnimod tables using the default migration (db/migrate/001_active_unimod_schema)



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# File 'lib/active_unimod/database.rb', line 24

def create_tables(verbose=true)
  ActiveRecord::Migration.verbose = verbose
  ActiveRecord::Migrator.migrate(File.dirname(__FILE__) + "/../../db/migrate/")
end

.update_from_web(url = nil, overwrite = false, logger = Logger.new($stdout)) ⇒ Object

Retrieves the unimod_tables.xml from “www.unimod.org/xml/unimod_tables.xml” and uses this datafile in update_from_xml.



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# File 'lib/active_unimod/database.rb', line 76

def update_from_web(url=nil, overwrite=false, logger=Logger.new($stdout))
  url = "http://www.unimod.org/xml/unimod_tables.xml" if url == nil
  
  logger.add(Logger::INFO, "retrieving: #{url}")
  update_from_xml(open(url), overwrite, logger)
end

.update_from_xml(xml, overwrite = false, logger = Logger.new($stdout)) ⇒ Object

Parses the xml into ActiveUnimod records. If overwrite=true the new records will replace existing records by with the same id. Otherwise, non-existant records will be created and the existing records will be checked. Any inconsistent records will be collected and returned as an array of [new_record, existing_record] arrays.

Progress is logged to logger.



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# File 'lib/active_unimod/database.rb', line 37

def update_from_xml(xml, overwrite=false, logger=Logger.new($stdout))
  doc = Hpricot.XML(xml)
  inconsistencies = []

  TABLES.each do |table|
    table.transaction do
      logger.add(Logger::INFO, "updating: #{table.table_name}")

      rows = doc.search("unimod/#{table.table_name}/#{table.table_name}_row")
      rows.each do |row|
        attributes = row.attributes
        id = attributes.delete("record_id")
        record = table.new(attributes)
        record.id = id
      
        if table.exists?(id)
          existing_record = table.find(id) 
          unless record.attributes == existing_record.attributes
            if overwrite
              logger.add(Logger::INFO, "overwritting: #{id}")
              existing_record.attributes = row.attributes
              existing_record.save
            else
              inconsistencies << [record, existing_record]
            end
          end
        else
          logger.add(Logger::INFO, "adding: #{id}")
          record.save
        end
      end
    end
  end
  
  inconsistencies
end