Class: Ms::Generators::UnimodDb

Inherits:
Tap::Generator::Base
  • Object
show all
Defined in:
lib/ms/generators/unimod_db.rb

Overview

:startdoc::generator generate a new unimod database

Downloads and generates a Unimod database (sqlite):

% tap generate unimod
% sqlite3 unimod.sqlite
sqlite> select * from elements;
1|H|Hydrogen|1.007825035|1.00794
2|2H|Deuterium|2.014101779|2.014101779
3|Li|Lithium|7.016003|6.941
...

The database data is downloaded from the unimod website.

Instance Method Summary collapse

Instance Method Details

#manifest(m, database = "unimod.sqlite") ⇒ Object 



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# File 'lib/ms/generators/unimod_db.rb', line 30

def manifest(m, database="unimod.sqlite")
  m.file database do |db|
    db.close
    db = Sequel.sqlite(db.path)
    
    log :get, uri
    doc = Hpricot.XML(open(uri))
    
    db.transaction do
      Ms::Unimod::TABLES.each_pair do |table_name, schema|
        log :create_table, table_name
        db.create_table(table_name, &schema)
        table = db[table_name]
    
        rows = doc.search("unimod/#{table_name}/#{table_name}_row")
        rows.each do |row|
          attributes = row.attributes
          record_id = attributes["record_id"]
      
          log(:insert, record_id)
          table.insert(attributes)
        end
      end
    end
    
    db.disconnect
  end
end