@@ -30,6 +30,8 @@ Ucsc::Hg18::DBConnection.connect require File.dirname(__FILE__) + '/ucsc/hg18/activerecord.rb' require File.dirname(__FILE__) + '/ucsc/hg18/slice.rb' -ALL_CNPS = [Dgv, CnpIafrate, CnpLocke, CnpRedon, CnpSebat, CnpSharp, CnpTuzun] -SEGDUPS = [GenomicSuperDup] -ALL_REPEATS = [SimpleRepeat, ExaptedRepeat, InterruptedRepeat, Microsatellite] \ No newline at end of file +module Ucsc + ALL_CNPS = [Dgv, CnpIafrate, CnpLocke, CnpRedon, CnpSebat, CnpSharp, CnpTuzun] + SEGDUPS = [GenomicSuperDup] + ALL_REPEATS = [SimpleRepeat, ExaptedRepeat, InterruptedRepeat, Microsatellite] +end \ No newline at end of file lib/ucsc.rb @@ -1,12 +1,13 @@ require 'rubygems' require 'activerecord' -DB_ADAPTER = 'mysql' -DB_HOST = 'genome-mysql.cse.ucsc.edu' -DB_USERNAME = 'genome' -DB_PASSWORD = '' module Ucsc + DB_ADAPTER = 'mysql' + DB_HOST = 'genome-mysql.cse.ucsc.edu' + DB_USERNAME = 'genome' + DB_PASSWORD = '' + module Hg18 # = DESCRIPTION # The Ucsc::Hg18::DBConnection is the actual connection established @@ -26,11 +27,11 @@ module Ucsc # *Arguments*: none def self.connect establish_connection( - :adapter => DB_ADAPTER, - :host => DB_HOST, + :adapter => Ucsc::DB_ADAPTER, + :host => Ucsc::DB_HOST, :database => 'hg18', - :username => DB_USERNAME, - :password => DB_PASSWORD + :username => Ucsc::DB_USERNAME, + :password => Ucsc::DB_PASSWORD ) end lib/ucsc/db_connection.rb @@ -16,11 +16,11 @@ end ranges.keys.each do |chromosome| all_annotations = Array.new - ALL_CNPS.each do |klass| + Ucsc::ALL_CNPS.each do |klass| all_annotations.push(klass.find_all_by_chrom(chromosome)) end - ALL_REPEATS.each do |klass| + Ucsc::ALL_REPEATS.each do |klass| all_annotations.push(klass.find_all_by_chrom(chromosome)) end samples/tryout.rb @@ -57,7 +57,7 @@ class SimpleRecordsTest < Test::Unit::TestCase def test_exapted_repeat assert_equal(3180908, ExaptedRepeat.find_by_name('exap1').chromStart) end - + # def test_repeatmasker # # end test/unit/test_activerecord.rb 0b5fb4c184b2923f88d5cc5500c7dee76959c9c1 Jan Aerts jan.aerts@gmail.com http://github.com/jandot/ruby-ucsc-api/commit/4b09ddcc431ad4b6e20ad560708db02437bbec4a 4b09ddcc431ad4b6e20ad560708db02437bbec4a 2008-09-17T07:31:06-07:00 2008-09-17T07:31:06-07:00 Put constants in Ucsc namespace to prevent clashes with other APIs a6719341040681aea0d7691b4c30655f4a24ee54 Jan Aerts jan.aerts@gmail.com