BioDSL 1.0.0

data/test/BioDSL/test_cary.rb

@@ -0,0 +1,176 @@
+#!/usr/bin/env ruby
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program is distributed in the hope that it will be useful,              #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of               #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                #
+# GNU General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# rubocop: disable ClassLength
+
+require 'test/helper'
+
+# Test class for CAry.
+class TestCAry < Test::Unit::TestCase
+  test 'BioDSL::CAry.new with bad count raises' do
+    assert_raise(BioDSL::CAryError) { BioDSL::CAry.new(-10, 4) }
+    assert_raise(BioDSL::CAryError) { BioDSL::CAry.new(0, 4) }
+  end
+
+  test 'BioDSL::CAry.new with bad size raises' do
+    assert_raise(BioDSL::CAryError) { BioDSL::CAry.new(10, -4) }
+    assert_raise(BioDSL::CAryError) { BioDSL::CAry.new(10, 0) }
+  end
+
+  test 'BioDSL::CAry.to_s returns correctly' do
+    assert_equal('0' * 40, BioDSL::CAry.new(5, 1).to_s)
+  end
+
+  test 'BioDSL::CAry.new with ary returns correctly' do
+    assert_equal([1, 2].pack('I*').unpack('B*').first,
+                 BioDSL::CAry.new(2, 4, [1, 2].pack('I*')).to_s)
+  end
+
+  test 'BioDSL::CAry.fill! returns correctly' do
+    cary = BioDSL::CAry.new(5, 1)
+    cary.fill!
+    assert_equal('1' * 40, cary.to_s)
+  end
+
+  test 'BioDSL::CAry.fill returns correctly' do
+    cary = BioDSL::CAry.new(5, 1)
+    new = cary.fill
+    assert_equal('0' * 40, cary.to_s)
+    assert_equal('1' * 40, new.to_s)
+  end
+
+  test 'BioDSL::CAry.zero! returns correctly' do
+    cary = BioDSL::CAry.new(5, 1).fill
+    cary.zero!
+    assert_equal('0' * 40, cary.to_s)
+  end
+
+  test 'BioDSL::CAry.zero returns correctly' do
+    cary = BioDSL::CAry.new(5, 1).fill
+    new  = cary.zero
+    assert_equal('1' * 40, cary.to_s)
+    assert_equal('0' * 40, new.to_s)
+  end
+
+  test 'BioDSL::CAry.& raises with bad object type' do
+    cary = BioDSL::CAry.new(5, 1)
+    assert_raise(BioDSL::CAryError) { cary & 10 }
+  end
+
+  test 'BioDSL::CAry.& raises with uneven counts' do
+    cary1 = BioDSL::CAry.new(5, 1)
+    cary2 = BioDSL::CAry.new(4, 1)
+    assert_raise(BioDSL::CAryError) { cary1 & cary2 }
+  end
+
+  test 'BioDSL::CAry.& raises with uneven sizes' do
+    cary1 = BioDSL::CAry.new(5, 1)
+    cary2 = BioDSL::CAry.new(5, 2)
+    assert_raise(BioDSL::CAryError) { cary1 & cary2 }
+  end
+
+  test 'BioDSL::CAry.& returns correctly' do
+    cary1 = BioDSL::CAry.new(5, 1).fill
+    cary2 = BioDSL::CAry.new(5, 1).fill
+
+    cary1 & cary2
+
+    assert_equal('1' * 40, cary1.to_s)
+    assert_equal('1' * 40, cary1.to_s)
+  end
+
+  test 'BioDSL::CAry.| raises with bad object type' do
+    cary = BioDSL::CAry.new(5, 1)
+    assert_raise(BioDSL::CAryError) { cary | 10 }
+  end
+
+  test 'BioDSL::CAry.| raises with uneven counts' do
+    cary1 = BioDSL::CAry.new(5, 1)
+    cary2 = BioDSL::CAry.new(4, 1)
+    assert_raise(BioDSL::CAryError) { cary1 | cary2 }
+  end
+
+  test 'BioDSL::CAry.| raises with uneven sizes' do
+    cary1 = BioDSL::CAry.new(5, 1)
+    cary2 = BioDSL::CAry.new(5, 2)
+    assert_raise(BioDSL::CAryError) { cary1 | cary2 }
+  end
+
+  test 'BioDSL::CAry.| returns correctly' do
+    cary1 = BioDSL::CAry.new(5, 1)
+    cary2 = BioDSL::CAry.new(5, 1).fill
+
+    cary1 | cary2
+
+    assert_equal('1' * 40, cary1.to_s)
+    assert_equal('1' * 40, cary2.to_s)
+  end
+
+  test 'BioDSL::CAry.^ raises with bad object type' do
+    cary = BioDSL::CAry.new(5, 1)
+    assert_raise(BioDSL::CAryError) { cary ^ 10 }
+  end
+
+  test 'BioDSL::CAry.^ raises with uneven counts' do
+    cary1 = BioDSL::CAry.new(5, 1)
+    cary2 = BioDSL::CAry.new(4, 1)
+    assert_raise(BioDSL::CAryError) { cary1 ^ cary2 }
+  end
+
+  test 'BioDSL::CAry.^ raises with uneven sizes' do
+    cary1 = BioDSL::CAry.new(5, 1)
+    cary2 = BioDSL::CAry.new(5, 2)
+    assert_raise(BioDSL::CAryError) { cary1 ^ cary2 }
+  end
+
+  test 'BioDSL::CAry.^ returns correctly' do
+    cary1 = BioDSL::CAry.new(5, 1)
+    cary2 = BioDSL::CAry.new(5, 1).fill
+
+    cary1 ^ cary2
+
+    assert_equal('1' * 40, cary1.to_s)
+    assert_equal('1' * 40, cary2.to_s)
+  end
+
+  test 'BioDSL::CAry #store and #retrieve returns correctly' do
+    file = Tempfile.new('cary')
+    cary = BioDSL::CAry.new(5, 1).fill
+
+    begin
+      BioDSL::CAry.store(file, cary)
+      cary2 = BioDSL::CAry.retrieve(file)
+      assert_equal(cary.to_s, cary2.to_s)
+    ensure
+      file.close
+      file.unlink
+    end
+  end
+end

data/test/BioDSL/test_command.rb

@@ -0,0 +1,45 @@
+#!/usr/bin/env ruby
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program is distributed in the hope that it will be useful,              #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of               #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                #
+# GNU General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+# Test class for Command.
+class CommandTest < Test::Unit::TestCase
+  test 'BioDSL::Command#to_s w/o options returns OK' do
+    command = BioDSL::Command.new('dump', nil, {})
+    expected = %{dump}
+    assert_equal(expected, command.to_s)
+  end
+
+  test 'BioDSL::Command#to_s with options returns OK' do
+    command = BioDSL::Command.new('read_fasta', nil, input: 'test.fna')
+    expected = %{read_fasta(input: "test.fna")}
+    assert_equal(expected, command.to_s)
+  end
+end