#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# Copyright (C) 2007-2011 Martin A. Hansen.
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
require 'test/unit'
+require 'test/helper'
require 'maasha/biopieces'
require 'stringio'
-require 'pp'
Biopieces::TEST = true
OptionHandler::TEST = true
class BiopiecesTest < Test::Unit::TestCase
# >>>>>>>>>>>>>>>>>>>> Testing Options.new <<<<<<<<<<<<<<<<<<<<
- def test_Biopieces_options_parse_with_all_cast_keys_dont_raise
+ test "Biopieces.options_parse with all cast keys dont raise" do
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
assert_nothing_raised(CastError) { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_with_illegal_long_cast_values_raises
+ test "Biopieces.options_parse with illegal long cast values raises" do
[nil, true, false, 1, 0, "a"].each do |long|
argv = []
casts = [{:long=>long, :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_legal_long_cast_values_dont_raise
+ test "Biopieces.options_parse with legal long cast values dont raise" do
["foo", "!!", "0123"].each do |long|
argv = []
casts = [{:long=>long, :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_illegal_short_cast_values_raises
+ test "Biopieces.options_parse with illegal short cast values raises" do
[nil, true, false, "foo"].each do |short|
argv = []
casts = [{:long=>"foo", :short=>short, :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_legal_short_cast_values_dont_raise
+ test "Biopieces.options_parse with legal short cast values dont raise" do
["!", "1", "a"].each do |short|
argv = []
casts = [{:long=>"foo", :short=>short, :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_illegal_type_cast_values_raises
+ test "Biopieces.options_parse with illegal type cast values raises" do
[nil, true, false, "foo", 12, 0].each do |type|
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>type, :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_legal_type_cast_values_dont_raise
+ test "Biopieces.options_parse with legal type cast values dont raise" do
TYPES.each do |type|
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>type, :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_illegal_mandatory_cast_values_raises
+ test "Biopieces.options_parse with illegal mandatory cast values raises" do
["yes", 12, 0, nil].each do |mandatory|
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>mandatory, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_legal_mandatory_cast_values_dont_raise
+ test "Biopieces.options_parse with legal mandatory cast values dont raise" do
[true, false].each do |mandatory|
argv = [ "--foo", "1" ]
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>mandatory, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_illegal_default_cast_values_raises
+ test "Biopieces.options_parse with illegal default cast values raises" do
[true, false, [], {}].each do |default|
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>default, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_legal_default_cast_values_dont_raise
+ test "Biopieces.options_parse with legal default cast values dont raise" do
[nil, 0, 1, -1].each do |default|
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>default, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_illegal_allowed_cast_values_raises
+ test "Biopieces.options_parse with illegal allowed cast values raises" do
[true, false, {}, [], 0, 0.1].each do |allowed|
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>allowed, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_legal_allowed_cast_values_dont_raise
+ test "Biopieces.options_parse with legal allowed cast values dont raise" do
["foo,bar,0",nil].each do |allowed|
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>allowed, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_illegal_disallowed_cast_values_raises
+ test "Biopieces.options_parse with illegal disallowed cast values raises" do
[true, false, {}, [], 0, 0.1].each do |disallowed|
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>disallowed}]
end
end
- def test_Biopieces_options_parse_with_legal_disallowed_cast_values_dont_raise
+ test "Biopieces.options_parse with legal disallowed cast values dont raise" do
["foo,bar,0",nil].each do |disallowed|
argv = []
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>disallowed}]
end
end
- def test_Biopieces_options_parse_with_duplicate_long_cast_values_raises
+ test "Biopieces.options_parse with duplicate long cast values raises" do
argv = []
casts = []
casts << {:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
assert_raise(CastError) { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_with_duplicate_short_cast_values_raises
+ test "Biopieces.options_parse with duplicate short cast values raises" do
argv = []
casts = []
casts << {:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
assert_raise(CastError) { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_without_duplicate_long_and_short_cast_values_dont_raise
+ test "Biopieces.options_parse without duplicate long and short cast values dont raise" do
argv = []
casts = []
casts << {:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
# >>>>>>>>>>>>>>>>>>>> Testing Options.parse <<<<<<<<<<<<<<<<<<<<
- def test_Biopieces_options_parse_with_empty_argv_and_missing_wiki_file_raises
+ test "Biopieces.options_parse with empty argv and missing wiki file raises" do
argv = []
casts = []
assert_raise(RuntimeError) { Biopieces.options_parse(argv,casts, "foo") }
end
- def test_Biopieces_options_parse_with_empty_argv_and_existing_wiki_file_dont_raise
+ test "Biopieces.options_parse with empty argv and existing wiki file dont raise" do
argv = []
casts = []
assert_nothing_raised { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_with_help_in_argv_and_existing_wiki_output_long_usage
+ test "Biopieces.options_parse with help in argv and existing wiki output long usage" do
argv = ["--help"]
assert_nothing_raised { Biopieces.options_parse(argv,[],SCRIPT_PATH) }
end
-# # FIXME This one fails because any argument to a flag is ignored and the flag value is set to true. Should it raise?
-# test "Options.parse with type cast flag with an argument raises
-# casts = [{:long=>"foo", :short=>"f", :type=>"flag", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
-# opt_parser = Options.new(casts)
-# assert_raise(ArgumentError) { opt_parser.parse(["--foo", "bar"],SCRIPT_PATH) }
-# end
-
- def test_Biopieces_options_parse_with_stream_in_argv_returns_correct_options
+ test "Biopieces.options_parse with stream in argv returns correct options" do
argv = ["--stream_in", DUMMY_FILE]
options = Biopieces.options_parse(argv,[],SCRIPT_PATH)
assert_equal(DUMMY_FILE, options[:stream_in])
end
- def test_Biopieces_options_parse_with_I_argv_returns_correct_options
+ test "Biopieces.options_parse with I argv returns correct options" do
argv = ["-I", DUMMY_FILE]
casts = []
options = Biopieces.options_parse(argv, casts, SCRIPT_PATH)
assert_equal(DUMMY_FILE, options[:stream_in])
end
- def test_Biopieces_options_parse_use_cast_default_value_if_no_argument_given
+ test "Biopieces.options_parse use cast default value if no argument given" do
argv = ["-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>"bar", :allowed=>nil, :disallowed=>nil}]
options = Biopieces.options_parse(argv, casts, SCRIPT_PATH)
assert_equal(options[:foo], "bar")
end
- def test_Biopieces_options_parse_dont_use_default_value_if_argument_given
+ test "Biopieces.options_parse dont use default value if argument given" do
argv = ["--foo", "bleh", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>"bar", :allowed=>nil, :disallowed=>nil}]
options = Biopieces.options_parse(argv, casts, SCRIPT_PATH)
- assert_equal(options[:foo], "bleh".to_sym)
+ assert_equal(options[:foo], "bleh")
end
- def test_Biopieces_options_parse_with_mandatory_cast_and_no_argument_raises
+ test "Biopieces.options_parse with mandatory cast and no argument raises" do
argv = ["-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}]
assert_raise(ArgumentError) { Biopieces.options_parse(argv,casts,SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_with_mandatory_cast_and_argument_dont_raise
+ test "Biopieces.options_parse with mandatory cast and argument dont raise" do
argv = ["--foo", "bar", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}]
assert_nothing_raised(ArgumentError) { Biopieces.options_parse(argv,casts,SCRIPT_PATH) }
end
- # # This one results in an error: "OptionParser::InvalidArgument: invalid argument: --foo bar"
-# # So it appears that this is tested in OptionParser already.
-# test "Options.parse with type cast int and non-int value raises" do
-# ["bar" ].each do |val| # what about nil, false, true, [], {}, 0.1 ?
-# casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
-# opt_parser = Options.new(casts)
-# assert_raise(ArgumentError) { opt_parser.parse(["--foo", "#{val}"],SCRIPT_PATH) }
-# end
-# end
-
- def test_Biopieces_options_parse_with_type_cast_int_dont_raise
+ test "Biopieces.options_parse with type cast int dont raise" do
[0,-1,1,327649123746293746374276347824].each do |val|
argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- # TODO similar test for uint as "test "Options.parse with type cast int and non-int value raises" do"
-
- def test_Biopieces_options_parse_with_type_cast_uint_dont_raise
+ test "Biopieces.options_parse with type cast uint dont raise" do
[0,1,327649123746293746374276347824].each do |val|
argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"uint", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_file_cast_and_file_dont_exists_raises
+ test "Biopieces.options_parse with file cast and file dont exists raises" do
argv = ["--foo", "bleh", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"file!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
assert_raise(ArgumentError) { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_with_file_cast_and_existing_file_dont_raise
+ test "Biopieces.options_parse with file cast and existing file dont raise" do
argv = ["--foo", DUMMY_FILE, "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"file!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
assert_nothing_raised(ArgumentError) { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_with_files_cast_and_a_file_dont_exists_raises
+ test "Biopieces.options_parse with files cast and a file dont exists raises" do
argv = ["--foo", DUMMY_FILE + ",bleh", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
assert_raise(ArgumentError) { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_with_files_cast_and_files_exists_dont_raise
+ test "Biopieces.options_parse with files cast and files exists dont raise" do
argv = ["--foo", DUMMY_FILE + "," + DUMMY_FILE, "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
assert_nothing_raised(ArgumentError) { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
-# # TODO replace the absolute part below the file location with File.dirname(__FILE__)
-# def test_Biopieces_options_parse_with_glob_argument_expands_correctly
-# flunk("This test is flawed and need fixing")
-# argv = ["--foo", "/Users/maasha/unit_test/foo*,/Users/maasha/unit_test/my_dir/*.fna", "-I", DUMMY_FILE]
-# casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
-# options = Biopieces.options_parse(argv, casts, SCRIPT_PATH)
-# assert_equal(["/Users/maasha/unit_test/foo.fna", "/Users/maasha/unit_test/my_dir/bar.fna"], options[:foo])
-# end
+ test "Biopieces.options_parse with glob argument expands correctly" do
+ path = File.join(ENV['BP_DIR'], "bp_test")
+ argv = ["--foo", "#{path}/te*,#{path}/lib/*.sh", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ options = Biopieces.options_parse(argv, casts, SCRIPT_PATH)
+ assert_equal(["#{path}/test_all", "#{path}/lib/test.sh"], options[:foo])
+ end
- def test_Biopieces_options_parse_with_dir_cast_and_dir_dont_exists_raises
+ test "Biopieces.options_parse with dir cast and dir dont exists raises" do
argv = ["--foo", "bleh", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"dir!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
assert_raise(ArgumentError) { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_with_dir_cast_and_dir_exists_dont_raise
+ test "Biopieces.options_parse with dir cast and dir exists dont raise" do
argv = ["--foo", "/", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"dir!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
assert_nothing_raised(ArgumentError) { Biopieces.options_parse(argv, casts, SCRIPT_PATH) }
end
- def test_Biopieces_options_parse_with_allowed_cast_and_not_allowed_value_raises
+ test "Biopieces.options_parse with allowed cast and not allowed value raises" do
["bleh", "2", "3.3"].each do |val|
argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>"0,-1,0.0,1,bar", :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_allowed_cast_and_allowed_values_dont_raise
+ test "Biopieces.options_parse with allowed cast and allowed values dont raise" do
["0", "-1", "0.0", "1", "bar"].each do |val|
argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>"0,-1,0.0,1,bar", :disallowed=>nil}]
end
end
- def test_Biopieces_options_parse_with_disallowed_cast_and_disallowed_value_raises
+ test "Biopieces.options_parse with disallowed cast and disallowed value raises" do
["0", "-1", "0.0", "1", "bar"].each do |val|
argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0,-1,0.0,1,bar"}]
end
end
- def test_Biopieces_options_parse_with_disallowed_cast_and_allowed_values_dont_raise
+ test "Biopieces.options_parse with disallowed cast and allowed values dont raise" do
["bleh", "2", "3.3"].each do |val|
argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0,-1,0.0,1,bar"}]
projects / biopieces.git / blobdiff