# File lib/bio/io/sql.rb, line 65 65: def self.delete_entry_accession(accession) 66: Bioentry.delete(Bioentry.find_by_accession(accession)) 67: end
no check is made
# File lib/bio/io/sql.rb, line 23 23: def self.establish_connection(configurations, env) 24: #configurations is an hash similar what YAML returns. 25: #{:database=>"biorails_development", :adapter=>"postgresql", :username=>"rails", :password=>nil} 26: configurations.assert_valid_keys('development', 'production','test') 27: configurations[env].assert_valid_keys('hostname','database','adapter','username','password') 28: DummyBase.configurations = configurations 29: DummyBase.establish_connection "#{env}" 30: end
# File lib/bio/io/sql.rb, line 41 41: def self.exists_accession(accession) 42: Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? ? false : true 43: end
# File lib/bio/io/sql.rb, line 45 45: def self.exists_database(name) 46: Bio::SQL::Biodatabase.find_by_name(name).nil? ? false : true 47: end
# File lib/bio/io/sql.rb, line 36 36: def self.fetch_accession(accession) 37: accession = accession.upcase 38: Bio::SQL::Bioentry.exists?(:accession => accession) ? Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession)) : nil 39: end
# File lib/bio/io/sql.rb, line 55 55: def self.list_databases 56: Bio::SQL::Biodatabase.find(:all).collect{|entry| 57: {:id=>entry.biodatabase_id, :name => entry.name} 58: } 59: end