unipept 1.4.0 → 1.4.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.rubocop.yml +5 -2
- data/.travis.yml +4 -5
- data/Gemfile +3 -4
- data/Gemfile.lock +2 -2
- data/Rakefile +5 -7
- data/VERSION +1 -1
- data/lib/batch_order.rb +1 -0
- data/lib/commands/unipept/api_runner.rb +4 -2
- data/lib/commands/uniprot.rb +2 -2
- data/lib/configuration.rb +1 -1
- data/lib/formatters.rb +2 -2
- data/lib/server_message.rb +1 -0
- data/test/commands/test_peptfilter.rb +23 -23
- data/test/commands/test_prot2pept.rb +11 -11
- data/test/commands/test_unipept.rb +4 -4
- data/test/commands/test_uniprot.rb +25 -25
- data/test/commands/unipept/test_api_runner.rb +26 -26
- data/test/commands/unipept/test_config.rb +5 -5
- data/test/commands/unipept/test_pept2lca.rb +7 -7
- data/test/commands/unipept/test_pept2prot.rb +7 -7
- data/test/commands/unipept/test_pept2taxa.rb +7 -7
- data/test/commands/unipept/test_taxa2lca.rb +5 -5
- data/test/commands/unipept/test_taxonomy.rb +7 -7
- data/test/helper.rb +2 -2
- data/test/test_batch_iterator.rb +4 -4
- data/unipept.gemspec +12 -12
- metadata +15 -15
@@ -5,14 +5,14 @@ module Unipept
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def test_help
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out, _err = capture_io_while do
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assert_raises SystemExit do
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Commands::Unipept.run(%w
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Commands::Unipept.run(%w[-h])
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end
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end
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assert(out.include?('show help for this command'))
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out, _err = capture_io_while do
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assert_raises SystemExit do
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Commands::Unipept.run(%w
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Commands::Unipept.run(%w[--help])
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end
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end
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assert(out.include?('show help for this command'))
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@@ -21,7 +21,7 @@ module Unipept
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def test_no_valid_subcommand
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_out, err = capture_io_while do
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assert_raises SystemExit do
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Commands::Unipept.run(%w
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Commands::Unipept.run(%w[])
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end
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end
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assert(err.include?('show help for this command'))
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@@ -29,7 +29,7 @@ module Unipept
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def test_version
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out, _err = capture_io_while do
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Commands::Unipept.run(%w
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Commands::Unipept.run(%w[-v])
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end
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assert_equal(VERSION, out.chomp)
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end
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@@ -4,56 +4,56 @@ module Unipept
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class UniprotTestCase < Unipept::TestCase
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def test_argument_input
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out, _err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[Q6GZX3])
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end
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assert_equal(1, out.split(/\n/).length)
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out, _err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[Q6GZX3 Q6GZX4])
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end
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assert_equal(2, out.split(/\n/).length)
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out, _err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[-f fasta Q6GZX3 Q6GZX4])
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end
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assert_equal(2, out.count('>'))
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out, _err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[--format fasta Q6GZX3 Q6GZX4])
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end
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assert_equal(2, out.count('>'))
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end
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def test_stdin_input
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out, _err = capture_io_with_input('Q6GZX3') do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[])
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end
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assert_equal(1, out.split(/\n/).length)
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out, _err = capture_io_with_input(%w
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Commands::Uniprot.run(%w
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out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
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Commands::Uniprot.run(%w[])
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end
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assert_equal(2, out.split(/\n/).length)
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out, _err = capture_io_with_input(%w
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Commands::Uniprot.run(%w
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out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
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Commands::Uniprot.run(%w[-f fasta])
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end
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assert_equal(2, out.count('>'))
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out, _err = capture_io_with_input(%w
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Commands::Uniprot.run(%w
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out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
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Commands::Uniprot.run(%w[--format fasta])
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end
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assert_equal(2, out.count('>'))
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end
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def test_argument_input_priority
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out, _err = capture_io_with_input('Q6GZX3') do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[Q6GZX3 Q6GZX4])
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end
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assert_equal(2, out.split(/\n/).length)
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out, _err = capture_io_with_input(%w
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Commands::Uniprot.run(%w
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out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
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Commands::Uniprot.run(%w[Q6GZX3])
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end
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assert_equal(1, out.split(/\n/).length)
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end
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@@ -61,7 +61,7 @@ module Unipept
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def test_invalid_format
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out, err = capture_io_while do
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assert_raises SystemExit do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[--format xxx])
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end
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end
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assert_equal('', out)
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def test_default_format
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out_default, _err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[Q6GZX3])
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end
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assert_equal(1, out_default.split(/\n/).length)
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out_sequence, _err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[-f sequence Q6GZX3])
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end
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assert_equal(out_default, out_sequence)
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out_sequence, _err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[--format sequence Q6GZX3])
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end
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assert_equal(out_default, out_sequence)
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end
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def test_format_options
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# fasta txt xml rdf gff sequence
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out, err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[-f fasta Q6GZX3])
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end
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assert(!out.empty?)
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assert(err.empty?)
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out, err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[-f txt Q6GZX3])
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end
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assert(!out.empty?)
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assert(err.empty?)
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out, err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[-f xml Q6GZX3])
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end
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assert(!out.empty?)
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assert(err.empty?)
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out, err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[-f rdf Q6GZX3])
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end
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assert(!out.empty?)
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assert(err.empty?)
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out, err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[-f gff Q6GZX3])
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end
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assert(!out.empty?)
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assert(err.empty?)
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out, err = capture_io_while do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[-f sequence Q6GZX3])
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end
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assert(!out.empty?)
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assert(err.empty?)
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def test_help
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out, _err = capture_io_while do
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assert_raises SystemExit do
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Commands::Uniprot.run(%w
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Commands::Uniprot.run(%w[-h])
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end
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end
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assert(out.include?('show help for this command'))
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class UnipeptAPIRunnerTestCase < Unipept::TestCase
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def test_init
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runner = new_runner('test', { host: 'test_host' }, %w
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runner = new_runner('test', { host: 'test_host' }, %w[a b c])
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assert_equal('test', runner.command.name)
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assert_equal('test_host', runner.options[:host])
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assert_equal(%w
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assert_equal(%w[a b c], runner.arguments)
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assert(!runner.configuration.nil?)
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assert_equal('http://test_host/api/v1/test.json', runner.url)
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assert(/Unipept CLI - unipept [0-9]*\.[0-9]*\.[0-9]*/.match runner.user_agent)
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end
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def test_config_host
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runner = new_runner('test', { host: 'http://param_host' }, %w
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runner = new_runner('test', { host: 'http://param_host' }, %w[a b c])
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runner.options.delete(:host)
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runner.configuration['host'] = 'http://config_host'
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host = runner.host
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end
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def test_param_host
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runner = new_runner('test', { host: 'http://param_host' }, %w
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runner = new_runner('test', { host: 'http://param_host' }, %w[a b c])
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runner.configuration.delete('host')
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host = runner.host
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assert_equal('http://param_host', host)
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end
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def test_no_host
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runner = new_runner('test', { host: 'param_host' }, %w
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runner = new_runner('test', { host: 'param_host' }, %w[a b c])
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runner.configuration.delete('host')
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runner.options.delete(:host)
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host = runner.host
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end
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def test_host_priority
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runner = new_runner('test', { host: 'http://param_host' }, %w
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runner = new_runner('test', { host: 'http://param_host' }, %w[a b c])
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runner.configuration['host'] = 'http://config_host'
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host = runner.host
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assert_equal('http://param_host', host)
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end
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def test_http_host
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runner = new_runner('test', { host: 'param_host' }, %w
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runner = new_runner('test', { host: 'param_host' }, %w[a b c])
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host = runner.host
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assert_equal('http://param_host', host)
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end
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def test_https_host
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runner = new_runner('test', { host: 'https://param_host' }, %w
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runner = new_runner('test', { host: 'https://param_host' }, %w[a b c])
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host = runner.host
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assert_equal('https://param_host', host)
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end
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def test_input_iterator_args
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runner = new_runner('test', { host: 'https://param_host' }, %w
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runner = new_runner('test', { host: 'https://param_host' }, %w[a b c])
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output = []
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runner.input_iterator.each { |el| output << el.chomp }
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assert_equal(%w
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assert_equal(%w[a b c], output)
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end
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def test_input_iterator_file
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File.open('input_file', 'w') { |file| file.write(%w
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File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
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runner = new_runner('test', host: 'https://param_host', input: 'input_file')
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output = []
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runner.input_iterator.each { |el| output << el.chomp }
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assert_equal(%w
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assert_equal(%w[a b c], output)
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end
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def test_input_iterator_stdin
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runner = new_runner('test', host: 'https://param_host')
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output = []
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_out, _err = capture_io_with_input(%w
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_out, _err = capture_io_with_input(%w[a b c]) do
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runner.input_iterator.each { |el| output << el.chomp }
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end
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assert_equal(%w
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assert_equal(%w[a b c], output)
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end
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def test_input_iterator_arguments_priority
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File.open('input_file', 'w') { |file| file.write(%w
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runner = new_runner('test', { host: 'https://param_host', input: 'input_file' }, %w
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File.open('input_file', 'w') { |file| file.write(%w[1 2 3].join("\n")) }
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runner = new_runner('test', { host: 'https://param_host', input: 'input_file' }, %w[a b c])
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output = []
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_out, _err = capture_io_with_input(%w
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_out, _err = capture_io_with_input(%w[1 2 3]) do
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runner.input_iterator.each { |el| output << el.chomp }
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end
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assert_equal(%w
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assert_equal(%w[a b c], output)
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end
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def test_input_iterator_file_priority
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File.open('input_file', 'w') { |file| file.write(%w
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File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
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runner = new_runner('test', host: 'https://param_host', input: 'input_file')
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output = []
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_out, _err = capture_io_with_input(%w
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_out, _err = capture_io_with_input(%w[1 2 3]) do
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runner.input_iterator.each { |el| output << el.chomp }
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end
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assert_equal(%w
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assert_equal(%w[a b c], output)
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end
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def test_required_fields
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end
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def test_multiple_selected_fields
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runner = new_runner('test', host: 'http://param_host', select: %w
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runner = new_runner('test', host: 'http://param_host', select: %w[field1 field2])
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assert_equal([/^field1$/, /^field2$/], runner.selected_fields)
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end
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@@ -348,7 +348,7 @@ module Unipept
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lambda = runner.handle_response(response, 0, nil)
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assert(lambda.lambda?)
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def runner.save_error(input)
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-
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warn(input)
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end
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out, err = capture_io_while(&lambda)
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354
|
assert_equal('', out)
|
@@ -361,7 +361,7 @@ module Unipept
|
|
361
361
|
lambda = runner.handle_response(response, 0, nil)
|
362
362
|
assert(lambda.lambda?)
|
363
363
|
def runner.save_error(input)
|
364
|
-
|
364
|
+
warn(input)
|
365
365
|
end
|
366
366
|
out, err = capture_io_while(&lambda)
|
367
367
|
assert_equal('', out)
|
@@ -374,7 +374,7 @@ module Unipept
|
|
374
374
|
lambda = runner.handle_response(response, 0, nil)
|
375
375
|
assert(lambda.lambda?)
|
376
376
|
def runner.save_error(input)
|
377
|
-
|
377
|
+
warn(input)
|
378
378
|
end
|
379
379
|
out, err = capture_io_while(&lambda)
|
380
380
|
assert_equal('', out)
|
@@ -385,7 +385,7 @@ module Unipept
|
|
385
385
|
runner = new_runner('taxonomy', host: 'http://api.unipept.ugent.be')
|
386
386
|
out, err = capture_io_while do
|
387
387
|
def runner.input_iterator
|
388
|
-
%w
|
388
|
+
%w[0 1 2].each
|
389
389
|
end
|
390
390
|
|
391
391
|
def runner.batch_size
|
@@ -5,14 +5,14 @@ module Unipept
|
|
5
5
|
def test_help
|
6
6
|
out, _err = capture_io_while do
|
7
7
|
assert_raises SystemExit do
|
8
|
-
Commands::Unipept.run(%w
|
8
|
+
Commands::Unipept.run(%w[config -h])
|
9
9
|
end
|
10
10
|
end
|
11
11
|
assert(out.include?('show help for this command'))
|
12
12
|
|
13
13
|
out, _err = capture_io_while do
|
14
14
|
assert_raises SystemExit do
|
15
|
-
Commands::Unipept.run(%w
|
15
|
+
Commands::Unipept.run(%w[config --help])
|
16
16
|
end
|
17
17
|
end
|
18
18
|
assert(out.include?('show help for this command'))
|
@@ -21,7 +21,7 @@ module Unipept
|
|
21
21
|
def test_no_args
|
22
22
|
_out, err = capture_io_while do
|
23
23
|
assert_raises SystemExit do
|
24
|
-
Commands::Unipept.run(%w
|
24
|
+
Commands::Unipept.run(%w[config])
|
25
25
|
end
|
26
26
|
end
|
27
27
|
assert(err.include?('show help for this command'))
|
@@ -30,7 +30,7 @@ module Unipept
|
|
30
30
|
def test_too_many_args
|
31
31
|
_out, err = capture_io_while do
|
32
32
|
assert_raises SystemExit do
|
33
|
-
Commands::Unipept.run(%w
|
33
|
+
Commands::Unipept.run(%w[config a b c])
|
34
34
|
end
|
35
35
|
end
|
36
36
|
assert(err.include?('show help for this command'))
|
@@ -54,7 +54,7 @@ module Unipept
|
|
54
54
|
config['test'] = value
|
55
55
|
config.save
|
56
56
|
out, _err = capture_io_while do
|
57
|
-
Commands::Unipept.run(%w
|
57
|
+
Commands::Unipept.run(%w[config test])
|
58
58
|
end
|
59
59
|
config.delete('test')
|
60
60
|
config.save
|
@@ -31,14 +31,14 @@ module Unipept
|
|
31
31
|
def test_help
|
32
32
|
out, _err = capture_io_while do
|
33
33
|
assert_raises SystemExit do
|
34
|
-
Commands::Unipept.run(%w
|
34
|
+
Commands::Unipept.run(%w[pept2lca -h])
|
35
35
|
end
|
36
36
|
end
|
37
37
|
assert(out.include?('show help for this command'))
|
38
38
|
|
39
39
|
out, _err = capture_io_while do
|
40
40
|
assert_raises SystemExit do
|
41
|
-
Commands::Unipept.run(%w
|
41
|
+
Commands::Unipept.run(%w[pept2lca --help])
|
42
42
|
end
|
43
43
|
end
|
44
44
|
assert(out.include?('show help for this command'))
|
@@ -46,7 +46,7 @@ module Unipept
|
|
46
46
|
|
47
47
|
def test_run
|
48
48
|
out, err = capture_io_while do
|
49
|
-
Commands::Unipept.run(%w
|
49
|
+
Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be AALTER])
|
50
50
|
end
|
51
51
|
lines = out.each_line
|
52
52
|
assert_equal('', err)
|
@@ -57,7 +57,7 @@ module Unipept
|
|
57
57
|
|
58
58
|
def test_run_with_fasta_multiple_batches
|
59
59
|
out, err = capture_io_while do
|
60
|
-
Commands::Unipept.run(%w
|
60
|
+
Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be --batch 2 >test AALTER AALER >tost AALTER])
|
61
61
|
end
|
62
62
|
lines = out.each_line
|
63
63
|
assert_equal('', err)
|
@@ -70,7 +70,7 @@ module Unipept
|
|
70
70
|
|
71
71
|
def test_run_with_fasta_multiple_batches_and_select
|
72
72
|
out, err = capture_io_while do
|
73
|
-
Commands::Unipept.run(%w
|
73
|
+
Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be --batch 2 --select taxon_id >test AALTER AALER >tost AALTER])
|
74
74
|
end
|
75
75
|
lines = out.each_line
|
76
76
|
assert_equal('', err)
|
@@ -83,7 +83,7 @@ module Unipept
|
|
83
83
|
|
84
84
|
def test_run_with_fasta_multiple_batches_json
|
85
85
|
out, err = capture_io_while do
|
86
|
-
Commands::Unipept.run(%w
|
86
|
+
Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be --batch 2 --format json >test AALTER AALER >tost AALTER])
|
87
87
|
end
|
88
88
|
lines = out.each_line
|
89
89
|
assert_equal('', err)
|
@@ -96,7 +96,7 @@ module Unipept
|
|
96
96
|
|
97
97
|
def test_run_with_fasta_multiple_batches_xml
|
98
98
|
out, err = capture_io_while do
|
99
|
-
Commands::Unipept.run(%w
|
99
|
+
Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be --batch 2 --format xml >test AALTER AALER >tost AALTER])
|
100
100
|
end
|
101
101
|
lines = out.each_line
|
102
102
|
assert_equal('', err)
|