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#
# = test/unit/bio/io/flatfile/test_buffer.rb - unit test for Bio::FlatFile::BufferedInputStream
#
# Copyright (C) 2006 Naohisa Goto <ng@bioruby.org>
#
# License:: The Ruby License
#
# $Id:$
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'stringio'
require 'bio/io/flatfile/buffer'
module Bio::TestFlatFileBufferedInputStream
TestDataPath = BioRubyTestDataPath
TestDataFastaFormat01 = File.join(TestDataPath, 'fasta', 'example1.txt')
class TestBufferedInputStreamParseFileOpenArg < Test::Unit::TestCase
K = Bio::FlatFile::BufferedInputStream
def _parse_file_open_mode(mode)
K.module_eval { _parse_file_open_mode(mode) }
end
private :_parse_file_open_mode
def _parse_file_open_arg(*arg)
K.module_eval { _parse_file_open_arg(*arg) }
end
private :_parse_file_open_arg
def test_parse_file_open_mode_nil
assert_equal(nil, _parse_file_open_mode(nil))
end
def test_parse_file_open_mode_integer
assert_equal({ :fmode_integer => 127 },
_parse_file_open_mode(127))
end
def test_parse_file_open_mode_str
assert_equal({ :fmode_string => "r+b" },
_parse_file_open_mode("r+b"))
end
def test_parse_file_open_mode_str_with_ext_enc
assert_equal({ :fmode_string => "r+t",
:external_encoding => "UTF-8" },
_parse_file_open_mode("r+t:UTF-8"))
end
def test_parse_file_open_mode_str_with_enc
assert_equal({ :fmode_string => "rb",
:external_encoding => "EUC-JP",
:internal_encoding => "UTF-8" },
_parse_file_open_mode("rb:EUC-JP:UTF-8"))
end
def test_parse_file_open_arg_nil
assert_equal({}, _parse_file_open_arg(nil))
end
def test_parse_file_open_arg_integer
assert_equal({ :fmode_integer => 127 },
_parse_file_open_arg(127))
end
def test_parse_file_open_arg_str
assert_equal({ :fmode_string => "r+b" },
_parse_file_open_arg("r+b"))
end
def test_parse_file_open_arg_str_with_ext_enc
assert_equal({ :fmode_string => "r+t",
:external_encoding => "UTF-8" },
_parse_file_open_arg("r+t:UTF-8"))
end
def test_parse_file_open_arg_str_with_enc
assert_equal({ :fmode_string => "rb",
:external_encoding => "EUC-JP",
:internal_encoding => "UTF-8" },
_parse_file_open_arg("rb:EUC-JP:UTF-8"))
end
def test_parse_file_open_arg_str_perm
assert_equal({ :fmode_string => "r+b",
:perm => 0644 },
_parse_file_open_arg("r+b", 0644))
end
def test_parse_file_open_arg_int_perm
assert_equal({ :fmode_integer => 255,
:perm => 0755 },
_parse_file_open_arg(255, 0755))
end
def test_parse_file_open_arg_int_perm_opt
assert_equal({ :fmode_integer => 191,
:perm => 0600,
:textmode => true,
:internal_encoding => "EUC-JP" },
_parse_file_open_arg(191, 0600,
:textmode => true,
:internal_encoding => "EUC-JP"))
end
def test_parse_file_open_arg_int_opt
assert_equal({ :fmode_integer => 191,
:textmode => true,
:internal_encoding => "EUC-JP" },
_parse_file_open_arg(191,
:textmode => true,
:internal_encoding => "EUC-JP"))
end
def test_parse_file_open_arg_str_perm_opt
assert_equal({ :fmode_string => "a",
:perm => 0644,
:binmode => true,
:external_encoding => "UTF-8" },
_parse_file_open_arg("a", 0644,
:binmode => true,
:external_encoding => "UTF-8"))
end
def test_parse_file_open_arg_str_opt
assert_equal({ :fmode_string => "a",
:binmode => true,
:external_encoding => "UTF-8" },
_parse_file_open_arg("a",
:binmode => true,
:external_encoding => "UTF-8"))
end
def test_parse_file_open_arg_opt
assert_equal({ :fmode_string => "r",
:binmode => true,
:external_encoding => "UTF-8" },
_parse_file_open_arg(:mode => "r",
:binmode => true,
:external_encoding => "UTF-8"))
end
def test_parse_file_open_arg_opt_with_integer_mode
assert_equal({ :fmode_integer => 123,
:perm => 0600,
:textmode => true,
:external_encoding => "EUC-JP" },
_parse_file_open_arg(:mode => 123,
:perm => 0600,
:textmode => true,
:external_encoding => "EUC-JP"))
end
end #class TestBufferedInputStreamParseFileOpenArg
class TestBufferedInputStreamClassMethod < Test::Unit::TestCase
def test_self_for_io
io = File.open(TestDataFastaFormat01)
obj = Bio::FlatFile::BufferedInputStream.for_io(io)
assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
assert_equal(TestDataFastaFormat01, obj.path)
end
def test_self_open_file
obj = Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01)
assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
assert_equal(TestDataFastaFormat01, obj.path)
end
def test_self_open_file_with_block
obj2 = nil
Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01) do |obj|
assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
assert_equal(TestDataFastaFormat01, obj.path)
obj2 = obj
end
# Since Ruby 2.3.0, calling IO#close to closed IO object is allowed
# without error.
if RUBY_VERSION >= "2.3.0"
assert_nothing_raised { obj2.close }
else
assert_raise(IOError) { obj2.close }
end
end
end #class TestBufferedInputStreamClassMethod
class TestBufferedInputStream < Test::Unit::TestCase
def setup
io = File.open(TestDataFastaFormat01)
io.binmode
path = TestDataFastaFormat01
@obj = Bio::FlatFile::BufferedInputStream.new(io, path)
end
def test_to_io
assert_kind_of(IO, @obj.to_io)
end
def test_close
assert_nil(@obj.close)
end
def test_rewind
@obj.prefetch_gets
@obj.rewind
assert_equal('', @obj.prefetch_buffer)
end
def test_pos
@obj.gets
@obj.gets
@obj.prefetch_gets
assert_equal(117, @obj.pos) #the number depends on original data
end
def test_pos=()
str = @obj.gets
assert_equal(0, @obj.pos = 0)
assert_equal(str, @obj.gets)
end
def test_eof_false_first
assert_equal(false, @obj.eof?)
end
def test_eof_false_after_prefetch
while @obj.prefetch_gets; nil; end
assert_equal(false, @obj.eof?)
end
def test_eof_true
while @obj.gets; nil; end
assert_equal(true, @obj.eof?)
end
def test_gets
@obj.gets
@obj.gets
assert_equal("gagcaaatcgaaaaggagagatttctgcatatcaagagaaaattcgagctgagatacattccaagtgtggctactc", @obj.gets.chomp)
end
def test_gets_equal_prefetch_gets
@obj.prefetch_gets
str = @obj.prefetch_gets
@obj.prefetch_gets
@obj.gets
assert_equal(@obj.gets, str)
end
def test_gets_rs
rs = 'tggtg'
str = <<__END_OF_STR__
aggcactagaattgagcagtgaa
gaagatgaggaagatgaagaagaagatgaggaagaaatcaagaaagaaaaatgcgaattttctgaagatgtagacc
gatttatatggacggttgggcaggactatggtttggatgatctggtcgtgcggcgtgctctcgccaagtacctcga
agtggatgtttcggacatattggaaagatacaatgaactcaagcttaagaatgatggaactgctggtg
__END_OF_STR__
@obj.gets(rs)
@obj.gets(rs)
assert_equal(str.chomp, @obj.gets(rs))
end
def test_gets_rs_equal_prefetch_gets
rs = 'tggtg'
@obj.prefetch_gets(rs)
str = @obj.prefetch_gets(rs)
@obj.prefetch_gets(rs)
@obj.gets(rs)
assert_equal(@obj.gets(rs), str)
end
def test_gets_rs_within_buffer
rs = 'tggtg'
a = []
20.times {a.push @obj.gets }
@obj.ungets(a.join(''))
assert_equal(">At1g02580 mRNA (2291 bp) UTR's and CDS\naggcgagtggttaatggagaaggaaaaccatgaggacgatggtg", @obj.gets(rs))
assert_equal('ggctgaaagtgattctgtgattggtaagagacaaatctattatttgaatggtg',
@obj.gets(rs).split(/\n/)[-1])
assert_equal('aggcactagaattgagcagtgaa',
@obj.gets(rs).split(/\n/)[0])
assert_equal('aggcttct', @obj.gets(rs).split(/\n/)[0])
assert_equal('agacacc', @obj.gets(rs).split(/\n/)[0])
end
def test_gets_paragraph_mode
@obj.gets('')
@obj.gets('')
assert_equal('>At1g65300: mRNA 837bp (shortened at end)',
@obj.gets('').split(/\n/)[0])
end
def test_gets_paragraph_mode_equal_prefetch_gets
rs = ''
@obj.prefetch_gets(rs)
str = @obj.prefetch_gets(rs)
@obj.prefetch_gets(rs)
@obj.gets(rs)
assert_equal(@obj.gets(rs), str)
end
def test_gets_paragraph_mode_within_buffer
@obj.gets('')
a = []
20.times {a.push @obj.gets }
@obj.ungets(a.join(''))
assert_equal('>At1g65300: mRNA 837bp',
@obj.gets('').split(/\n/)[0])
assert_equal('>At1g65300: mRNA 837bp (shortened at end)',
@obj.gets('').split(/\n/)[0])
assert_equal('>At1g65300: mRNA 837bp (shortened from start)',
@obj.gets('').split(/\n/)[0])
end
def test_ungets
@obj.gets
@obj.gets
str1 = @obj.gets
str2 = @obj.gets
assert_nil(@obj.ungets(str2))
assert_nil(@obj.ungets(str1))
assert_equal(str1, @obj.gets)
assert_equal(str2, @obj.gets)
end
def test_getc
assert_equal(?>, @obj.getc)
end
def test_getc_after_prefetch
@obj.prefetch_gets
assert_equal(?>, @obj.getc)
end
def test_ungetc
c = @obj.getc
assert_nil(@obj.ungetc(c))
assert_equal(c, @obj.getc)
end
def test_ungetc_after_prefetch
str = @obj.prefetch_gets
c = @obj.getc
assert_nil(@obj.ungetc(c))
assert_equal(str, @obj.gets)
end
def test_prefetch_buffer
str = @obj.prefetch_gets
str += @obj.prefetch_gets
assert_equal(str, @obj.prefetch_buffer)
end
def test_prefetch_gets
@obj.prefetch_gets
@obj.prefetch_gets
@obj.gets
str = @obj.prefetch_gets
@obj.gets
assert_equal(str, @obj.gets)
end
def test_prefetch_gets_with_arg
# test @obj.gets
str = @obj.prefetch_gets("\n>")
assert_equal(str, @obj.gets("\n>"))
# test using IO object
io = @obj.to_io
io.rewind
assert_equal(str, io.gets("\n>"))
end
def test_skip_spaces
@obj.gets('CDS')
assert_nil(@obj.skip_spaces)
assert_equal(?a, @obj.getc)
end
end #class TestBufferedInputStream
end #module Bio::TestFlatFile
|
