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#
# test/unit/bio/test_command.rb - Unit test for Bio::Command
#
# Copyright:: Copyright (C) 2005-2008
# Mitsuteru Nakao <n@bioruby.org>,
# Naohisa Goto <ng@bioruby.org>,
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/command'
module Bio
class TestCommand < Test::Unit::TestCase
def windows_platform?
Bio::Command.module_eval { windows_platform? }
end
private :windows_platform?
def test_command_constants
assert(Bio::Command::UNSAFE_CHARS_UNIX)
assert(Bio::Command::QUOTE_CHARS_WINDOWS)
assert(Bio::Command::UNESCAPABLE_CHARS)
end
def test_escape_shell_windows
str = "bio_ruby.123@456:789"
assert_equal("bio_ruby.123@456:789",
Bio::Command.escape_shell_windows(str))
str = "bio\'\"r u\"b\\y123@456:789"
assert_equal("\"bio'\"\"r u\"\"b\\y123@456:789\"",
Bio::Command.escape_shell_windows(str))
end
def test_escape_shell_unix
str = "bio_ruby.123@456:789"
assert_equal("bio_ruby.123@456:789",
Bio::Command.escape_shell_unix(str))
str = "bio\'\"r u\"b\\y123@456:789"
assert_equal("bio\\'\\\"r\\ u\\\"b\\\\y123@456:789",
Bio::Command.escape_shell_unix(str))
end
def test_escape_shell
str = "bio_ruby.123@456:789"
assert_equal("bio_ruby.123@456:789",
Bio::Command.escape_shell(str))
str = "bio\'\"r u\"b\\y123@456:789"
if windows_platform?
# mswin32, bccwin32, mingw32, etc.
assert_equal("\"bio'\"\"r u\"\"b\\y123@456:789\"",
Bio::Command.escape_shell(str))
else
assert_equal("bio\\'\\\"r\\ u\\\"b\\\\y123@456:789",
Bio::Command.escape_shell(str))
end
end
def test_make_command_line
ary = [ "ruby",
"test.rb", "atgcatgc", "bio\'\"r u\"b\\y123@456:789" ]
if windows_platform?
# mswin32, bccwin32, mingw32, etc.
assert_equal("ruby" +
" test.rb atgcatgc" +
" \"bio'\"\"r u\"\"b\\y123@456:789\"",
Bio::Command.make_command_line(ary))
else
assert_equal("ruby" +
" test.rb atgcatgc" +
" bio\\'\\\"r\\ u\\\"b\\\\y123@456:789",
Bio::Command.make_command_line(ary))
end
end
def test_make_command_line_windows
ary = [ "C:\\Program Files\\Ruby\\bin\\ruby.exe",
"test.rb", "atgcatgc", "bio\'\"r u\"b\\y123@456:789" ]
assert_equal("\"C:\\Program Files\\Ruby\\bin\\ruby.exe\"" +
" test.rb atgcatgc" +
" \"bio'\"\"r u\"\"b\\y123@456:789\"",
Bio::Command.make_command_line_windows(ary))
end
def test_make_command_line_unix
ary = [ "/usr/local/bin/ruby",
"test.rb", "atgcatgc", "bio\'\"r u\"b\\y123@456:789" ]
assert_equal("/usr/local/bin/ruby" +
" test.rb atgcatgc" +
" bio\\'\\\"r\\ u\\\"b\\\\y123@456:789",
Bio::Command.make_command_line_unix(ary))
end
def test_safe_command_line_array
ary1 = [ 'test' ]
assert_equal([ [ 'test', 'test' ] ],
Bio::Command.safe_command_line_array(ary1))
ary1a = [ [ 'test/test1a', 'test' ] ]
assert_equal(ary1a,
Bio::Command.safe_command_line_array(ary1a))
end
def test_safe_command_line_array_passthrough
ary0 = []
assert_equal(ary0,
Bio::Command.safe_command_line_array(ary0))
ary2 = [ 'cmd', 'arg0' ]
assert_equal(ary2,
Bio::Command.safe_command_line_array(ary2))
ary2a = [ [ 'cmd', 'display name' ], 'arg0' ]
assert_equal(ary2a,
Bio::Command.safe_command_line_array(ary2a))
ary3 = [ 'cmd', 'arg0', 'arg1' ]
assert_equal(ary3,
Bio::Command.safe_command_line_array(ary3))
end
def test_make_cgi_params_by_hash_in_symbol
ary = [
"type1=bp",
"type2=bp",
"downstream=",
"upstream=",
"format=fasta",
"options=similarity",
"options=gene",
"action=export",
"_format=Text",
"output=txt",
"submit=Continue+%3E%3E",
"ab%3Dcd%26ef%3Dgh%23ij=pq%3D12%26rs%3D34%23tu",
]
hash = {
:type1 => 'bp',
:type2 => 'bp',
:downstream => '',
:upstream => '',
:format => 'fasta',
:options => ['similarity', 'gene'],
:action => 'export',
:_format => 'Text',
:output => 'txt',
:submit => 'Continue >>',
:"ab=cd&ef=gh#ij" => 'pq=12&rs=34#tu',
}
result = Bio::Command.make_cgi_params(hash)
ary.each do |str|
assert_match(Regexp.new(Regexp.escape(str)), result)
end
# round-trip test
result_hash = {}
CGI.parse(result).each do |k, v|
v = case v.size
when 0
''
when 1
v[0]
else
v
end
result_hash[k.intern] = v
end
assert_equal(hash, result_hash)
end
def test_make_cgi_params_by_hash_in_string
ary = [
"type1=bp",
"type2=bp",
"downstream=",
"upstream=",
"format=fasta",
"options=similarity",
"options=gene",
"action=export",
"_format=Text",
"output=txt",
"submit=Continue+%3E%3E",
"ab%3Dcd%26ef%3Dgh%23ij=pq%3D12%26rs%3D34%23tu",
]
hash = {
"type1" => 'bp',
"type2" => 'bp',
"downstream" => '',
"upstream" => '',
"format" => 'fasta',
"options" => ['similarity', 'gene'],
"action" => 'export',
"_format" => 'Text',
"output" => 'txt',
"submit" => 'Continue >>',
'ab=cd&ef=gh#ij' => 'pq=12&rs=34#tu',
}
result = Bio::Command.make_cgi_params(hash)
ary.each do |str|
assert_match(Regexp.new(Regexp.escape(str)), result)
end
# round-trip test
result_hash = {}
CGI.parse(result).each do |k, v|
v = case v.size
when 0
''
when 1
v[0]
else
v
end
result_hash[k] = v
end
assert_equal(hash, result_hash)
end
def test_make_cgi_params_by_array_of_array
ary = [
"type1=bp",
"type2=bp",
"downstream=",
"upstream=",
"format=fasta",
"options=similarity",
"options=gene",
"action=export",
"_format=Text",
"output=txt",
"submit=Continue+%3E%3E",
"ab%3Dcd%26ef%3Dgh%23ij=pq%3D12%26rs%3D34%23tu",
]
array_of_array = [
["type1", 'bp'],
["type2", 'bp'],
["downstream", ''],
["upstream", ''],
["format", 'fasta'],
["options", ['similarity', 'gene']],
["action", 'export'],
["_format", 'Text'],
["output", 'txt'],
["submit", 'Continue >>'],
[ 'ab=cd&ef=gh#ij', 'pq=12&rs=34#tu' ],
]
result = Bio::Command.make_cgi_params(array_of_array)
# When array of array, order is guaranteed.
assert_equal(ary.join('&'), result)
# round-trip test
result_array = []
CGI.parse(result).each do |k, v|
v = case v.size
when 0
''
when 1
v[0]
else
v
end
result_array.push([ k, v ])
end
assert_equal(array_of_array.sort, result_array.sort)
end
def test_make_cgi_params_by_array_of_hash
ary = [
"type1=bp",
"type2=bp",
"downstream=",
"upstream=",
"format=fasta",
"options=similarity",
"options=gene",
"action=export",
"_format=Text",
"output=txt",
"submit=Continue+%3E%3E",
"ab%3Dcd%26ef%3Dgh%23ij=pq%3D12%26rs%3D34%23tu",
]
array_of_hash = [
{"type1" => 'bp'},
{"type2" => 'bp'},
{"downstream" => ''},
{"upstream" => ''},
{"format" => 'fasta'},
{"options" => ['similarity', 'gene']},
{"action" => 'export'},
{"_format" => 'Text'},
{"output" => 'txt'},
{"submit" => 'Continue >>'},
{'ab=cd&ef=gh#ij' => 'pq=12&rs=34#tu'},
]
result = Bio::Command.make_cgi_params(array_of_hash)
# When array of hash, order is guaranteed.
assert_equal(ary.join('&'), result)
# round-trip test
result_array = []
CGI.parse(result).each do |k, v|
v = case v.size
when 0
''
when 1
v[0]
else
v
end
result_array.push({ k => v })
end
assert_equal(array_of_hash.sort { |x,y| x.keys[0] <=> y.keys[0] },
result_array.sort { |x,y| x.keys[0] <=> y.keys[0] })
end
def test_make_cgi_params_by_array_of_string
str = "type1=bp&type2=bp&downstream=&upstream=&format=fasta&options=similarity&options=gene&action=export&_format=Text&output=txt&submit=Continue+%3E%3E&ab=cd%26ef%3Dgh%23ij%3Dpq%3D12%26rs%3D34%23tu"
array_of_string = [
"type1=bp",
"type2=bp",
"downstream=",
"upstream=",
"format=fasta",
"options=similarity",
"options=gene",
"action=export",
"_format=Text",
"output=txt",
"submit=Continue >>",
# In the following case, 'ab' is regarded as
# the form key, and rest of the string is
# regarded as the value.
'ab=cd&ef=gh#ij=pq=12&rs=34#tu',
]
result = Bio::Command.make_cgi_params(array_of_string)
assert_equal(str, result)
end
def test_make_cgi_params_by_string
##Before BioRuby 1.4.3.0001, only URI escaping was performed.
#string = "type1=bp&type2=bp&downstream=&upstream=&format=fasta&options=similarity&options=gene&action=export&_format=Text&output=txt&submit=Continue%20%3E%3E"
query = " type1=bp&type2=bp&downstream=&upstream=&format=fasta&options=similarity&options=gene&action=export&_format=Text&output=txt&submit=Continue >> "
assert_raise(TypeError) {
Bio::Command.make_cgi_params(query)
}
end
end
end
|
