unipept 0.8.0 → 0.9.0

data/test/commands/unipept/test_api_runner.rb

@@ -14,7 +14,6 @@ module Unipept
       assert_equal(%w(a b c), runner.arguments)
       assert(!runner.configuration.nil?)
       assert_equal('http://test_host/api/v1/test.json', runner.url)
-      assert_equal('http://test_host/api/v1/messages.json', runner.message_url)
       assert(/Unipept CLI - unipept [0-9]\.[0-9]\.[0-9]/.match runner.user_agent)
     end
 
@@ -108,8 +107,35 @@ module Unipept
       assert_equal(%w(a b c), output)
     end
 
+    def test_default_batch_size
+      assert_raises NotImplementedError do
+        new_runner.default_batch_size
+      end
+    end
+
     def test_batch_size
-      assert_equal(100, new_runner.batch_size)
+      r = new_runner
+      def r.default_batch_size
+        100
+      end
+      assert_equal(100, r.batch_size)
+    end
+
+    def test_argument_batch_size
+      runner = new_runner('test',  host: 'http://param_host', batch: '123')
+      assert_equal(123, runner.batch_size)
+    end
+
+    def test_number_of_parallel_requests
+      assert_equal(10, new_runner.concurrent_requests)
+      runner = new_runner('test',  host: 'http://param_host', parallel: '123')
+      assert_equal(123, runner.concurrent_requests)
+    end
+
+    def test_queue_size
+      assert_equal(200, new_runner.queue_size)
+      runner = new_runner('test',  host: 'http://param_host', parallel: '100')
+      assert_equal(2000, runner.queue_size)
     end
 
     def test_default_formatter
@@ -152,24 +178,6 @@ module Unipept
       assert_equal([/^field.*$/], runner.selected_fields)
     end
 
-    def test_never_recently_fetched
-      runner = new_runner
-      runner.configuration.delete('last_fetch_date')
-      assert(!runner.recently_fetched?)
-    end
-
-    def test_old_recently_fetched
-      runner = new_runner
-      runner.configuration['last_fetch_date'] = Time.now - 60 * 60 * 25
-      assert(!runner.recently_fetched?)
-    end
-
-    def test_recently_recently_fetched
-      runner = new_runner
-      runner.configuration['last_fetch_date'] = Time.now - 60 * 60 * 1
-      assert(runner.recently_fetched?)
-    end
-
     def test_basic_construct_request_body
       runner = new_runner('test',  host: 'http://param_host')
       body = runner.construct_request_body('test')
@@ -215,104 +223,6 @@ module Unipept
       assert_equal(false, body[:names])
     end
 
-    def test_print_server_message
-      runner = new_runner
-      runner.stub(:recently_fetched?, false) do
-        runner.stub(:fetch_server_message, 'message') do
-          out, _err = capture_io_while do
-            def $stdout.tty?
-              true
-            end
-            runner.print_server_message
-          end
-          assert_equal('message', out.chomp)
-        end
-      end
-    end
-
-    def test_quiet_print_server_message
-      runner = new_runner('test', host: 'bla', quiet: true)
-      runner.stub(:recently_fetched?, false) do
-        runner.stub(:fetch_server_message, 'message') do
-          out, _err = capture_io_while do
-            def $stdout.tty?
-              true
-            end
-            $stdout.tty?
-            runner.print_server_message
-          end
-          assert_equal('', out)
-        end
-      end
-    end
-
-    def test_no_tty_print_server_message
-      runner = new_runner
-      runner.stub(:recently_fetched?, false) do
-        runner.stub(:fetch_server_message, 'message') do
-          out, _err = capture_io_while do
-            def $stdout.tty?
-              false
-            end
-            runner.print_server_message
-          end
-          assert_equal('', out)
-        end
-      end
-    end
-
-    def test_recent_print_server_message
-      runner = new_runner
-      runner.stub(:recently_fetched?, true) do
-        runner.stub(:fetch_server_message, 'message') do
-          out, _err = capture_io_while do
-            def $stdout.tty?
-              true
-            end
-            runner.print_server_message
-          end
-          assert_equal('', out)
-        end
-      end
-    end
-
-    def test_empty_print_server_message
-      runner = new_runner
-      runner.stub(:recently_fetched?, false) do
-        runner.stub(:fetch_server_message, '') do
-          out, _err = capture_io_while do
-            def $stdout.tty?
-              true
-            end
-            runner.print_server_message
-          end
-          assert_equal('', out)
-        end
-      end
-    end
-
-    def test_fetch_server_message
-      runner = new_runner('test', host: 'http://api.unipept.ugent.be')
-      assert(!runner.fetch_server_message.nil?)
-    end
-
-    def test_stdout_write_to_output
-      runner = new_runner
-      out, _err = capture_io_while do
-        runner.write_to_output('hello world')
-      end
-      assert_equal('hello world', out.chomp)
-    end
-
-    def test_file_write_to_output
-      runner = new_runner('test', host: 'test', output: 'output_file')
-      out, _err = capture_io_while do
-        runner.write_to_output('hello world')
-      end
-      assert_equal('', out)
-      assert_equal('hello world', IO.foreach('output_file').next.chomp)
-    end
-
     def test_glob_to_regex
       runner = new_runner
       assert(/^simple$/, runner.glob_to_regex('simple'))
@@ -418,9 +328,6 @@ module Unipept
     def test_run
       runner = new_runner('taxonomy', host: 'http://api.unipept.ugent.be')
       out, err = capture_io_while do
-        def runner.print_server_message
-          puts 'server message'
-        end
         def runner.input_iterator
           %w(0 1 2).each
         end
@@ -431,7 +338,6 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert_equal('server message', lines.next.chomp)
       assert(lines.next.start_with? 'taxon_id')
       assert(lines.next.start_with? '1,root')
       assert(lines.next.start_with? '2,Bacteria')

data/test/commands/unipept/test_pept2lca.rb

@@ -2,12 +2,24 @@ require_relative '../../../lib/commands'
 
 module Unipept
   class UnipeptPept2lcaTestCase < Unipept::TestCase
+    def test_default_batch_size
+      command = Cri::Command.define { name 'pept2lca' }
+      pept2lca = Commands::Pept2lca.new({ host: 'http://api.unipept.ugent.be' }, [], command)
+      assert_equal(1000, pept2lca.default_batch_size)
+      pept2lca.options[:all] = true
+      assert_equal(100, pept2lca.default_batch_size)
+    end
+
+    def test_argument_batch_size
+      command = Cri::Command.define { name 'pept2lca' }
+      pept2lca = Commands::Pept2lca.new({ host: 'http://api.unipept.ugent.be', batch: '123' }, [], command)
+      assert_equal(123, pept2lca.batch_size)
+    end
+
     def test_batch_size
       command = Cri::Command.define { name 'pept2lca' }
       pept2lca = Commands::Pept2lca.new({ host: 'http://api.unipept.ugent.be' }, [], command)
       assert_equal(1000, pept2lca.batch_size)
-      pept2lca.options[:all] = true
-      assert_equal(100, pept2lca.batch_size)
     end
 
     def test_help
@@ -36,5 +48,43 @@ module Unipept
       assert(lines.next.start_with? 'AALTER,1,root,no rank')
       assert_raises(StopIteration) { lines.next }
     end
+
+    def test_run_with_fasta_multiple_batches
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 >test AALTER AALER >tost AALTER))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      assert(lines.next.start_with? 'fasta_header,peptide,taxon_id')
+      assert(lines.next.start_with? '>test,AALTER,1,root,no rank')
+      assert(lines.next.start_with? '>test,AALER,1,root,no rank')
+      assert(lines.next.start_with? '>tost,AALTER,1,root,no rank')
+      assert_raises(StopIteration) { lines.next }
+    end
+
+    def test_run_with_fasta_multiple_batches_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 --format json >test AALTER AALER >tost AALTER))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(output.include? 'fasta_header')
+    end
+
+    def test_run_with_fasta_multiple_batches_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 --format xml >test AALTER AALER >tost AALTER))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+      assert(output.include? '<fasta_header>')
+    end
   end
 end

data/test/commands/unipept/test_pept2prot.rb

@@ -2,12 +2,12 @@ require_relative '../../../lib/commands'
 
 module Unipept
   class UnipeptPept2protTestCase < Unipept::TestCase
-    def test_batch_size
+    def test_default_batch_size
       command = Cri::Command.define { name 'pept2prot' }
       pept2prot = Commands::Pept2prot.new({ host: 'http://api.unipept.ugent.be' }, [], command)
-      assert_equal(10, pept2prot.batch_size)
+      assert_equal(10, pept2prot.default_batch_size)
       pept2prot.options[:all] = true
-      assert_equal(5, pept2prot.batch_size)
+      assert_equal(5, pept2prot.default_batch_size)
     end
 
     def test_help
@@ -35,5 +35,42 @@ module Unipept
       assert(lines.next.start_with? 'peptide,uniprot_id,taxon_id')
       assert(lines.next.start_with? 'ENFVYIAK,')
     end
+
+    def test_run_with_fasta_multiple_batches
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2prot --host http://api.unipept.ugent.be --batch 2 >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      assert(lines.next.start_with? 'fasta_header,peptide,uniprot_id,taxon_id')
+      assert(lines.select { |line| line.start_with? '>test,EGGAGSSTGQR,' }.size >= 1)
+      assert(lines.select { |line| line.start_with? '>test,ENFVYIAK,' }.size >= 1)
+      assert(lines.select { |line| line.start_with? '>tost,EGGAGSSTGQR,' }.size >= 1)
+    end
+
+    def test_run_with_fasta_multiple_batches_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2prot --host http://api.unipept.ugent.be --batch 2 --format json >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(output.include? 'fasta_header')
+    end
+
+    def test_run_with_fasta_multiple_batches_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2prot --host http://api.unipept.ugent.be --batch 2 --format xml >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+      assert(output.include? '<fasta_header>')
+    end
   end
 end

data/test/commands/unipept/test_pept2taxa.rb

@@ -2,12 +2,12 @@ require_relative '../../../lib/commands'
 
 module Unipept
   class UnipeptPept2taxaTestCase < Unipept::TestCase
-    def test_batch_size
+    def test_default_batch_size
       command = Cri::Command.define { name 'pept2taxa' }
       pept2taxa = Commands::Pept2taxa.new({ host: 'http://api.unipept.ugent.be' }, [], command)
-      assert_equal(10, pept2taxa.batch_size)
+      assert_equal(10, pept2taxa.default_batch_size)
       pept2taxa.options[:all] = true
-      assert_equal(5, pept2taxa.batch_size)
+      assert_equal(5, pept2taxa.default_batch_size)
     end
 
     def test_help
@@ -35,5 +35,42 @@ module Unipept
       assert(lines.next.start_with? 'peptide,taxon_id,taxon_name,taxon_rank')
       assert(lines.next.start_with? 'ENFVYIAK,')
     end
+
+    def test_run_with_fasta_multiple_batches
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2taxa --host http://api.unipept.ugent.be --batch 2 >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      assert(lines.next.start_with? 'fasta_header,peptide,taxon_id,taxon_name,taxon_rank')
+      assert(lines.select { |line| line.start_with? '>test,EGGAGSSTGQR,' }.size >= 1)
+      assert(lines.select { |line| line.start_with? '>test,ENFVYIAK,' }.size >= 1)
+      assert(lines.select { |line| line.start_with? '>tost,EGGAGSSTGQR,' }.size >= 1)
+    end
+
+    def test_run_with_fasta_multiple_batches_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2taxa --host http://api.unipept.ugent.be --batch 2 --format json >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(output.include? 'fasta_header')
+    end
+
+    def test_run_with_fasta_multiple_batches_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2taxa --host http://api.unipept.ugent.be --batch 2 --format xml >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+      assert(output.include? '<fasta_header>')
+    end
   end
 end

data/test/commands/unipept/test_taxa2lca.rb

@@ -2,11 +2,11 @@ require_relative '../../../lib/commands'
 
 module Unipept
   class UnipeptTaxa2lcaTestCase < Unipept::TestCase
-    def test_batch_size
+    def test_default_batch_size
       command = Cri::Command.define { name 'taxa2lca' }
       taxa2lca = Commands::Taxa2lca.new({ host: 'http://api.unipept.ugent.be' }, [], command)
       assert_raises RuntimeError do
-        taxa2lca.batch_size
+        taxa2lca.default_batch_size
       end
     end
 
@@ -35,5 +35,29 @@ module Unipept
       assert(lines.next.start_with? 'taxon_id,taxon_name,taxon_rank')
       assert(lines.next.start_with? '1678,Bifidobacterium,genus')
     end
+
+    def test_run_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(taxa2lca --host http://api.unipept.ugent.be --format xml 216816 1680))
+      end
+      lines = out.each_line
+      output = lines.to_a.join('').chomp
+      assert_equal('', err)
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+    end
+
+    def test_run_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(taxa2lca --host http://api.unipept.ugent.be --format json 216816 1680))
+      end
+      lines = out.each_line
+      output = lines.to_a.join('').chomp
+      assert_equal('', err)
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(!output.include?(']['))
+    end
   end
 end

data/test/commands/unipept/test_taxonomy.rb

@@ -2,10 +2,10 @@ require_relative '../../../lib/commands'
 
 module Unipept
   class UnipeptTaxonomyTestCase < Unipept::TestCase
-    def test_batch_size
+    def test_default_batch_size
       command = Cri::Command.define { name 'taxonomy' }
       taxonomy = Commands::Taxonomy.new({ host: 'http://api.unipept.ugent.be' }, [], command)
-      assert_equal(100, taxonomy.batch_size)
+      assert_equal(100, taxonomy.default_batch_size)
     end
 
     def test_help
@@ -33,5 +33,42 @@ module Unipept
       assert(lines.next.start_with? 'taxon_id,taxon_name,taxon_rank')
       assert(lines.next.start_with? '1,root,no rank')
     end
+
+    def test_run_with_fasta_multiple_batches
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(taxonomy --host http://api.unipept.ugent.be --batch 2 >test 1 216816 >tost 1))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      assert(lines.next.start_with? 'fasta_header,taxon_id,taxon_name,taxon_rank')
+      assert(lines.select { |line| line.start_with? '>test,1,' }.size >= 1)
+      assert(lines.select { |line| line.start_with? '>test,216816,' }.size >= 1)
+      assert(lines.select { |line| line.start_with? '>tost,1,' }.size >= 1)
+    end
+
+    def test_run_with_fasta_multiple_batches_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(taxonomy --host http://api.unipept.ugent.be --batch 2 --format json >test 1 216816 >tost 1))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(output.include? 'fasta_header')
+    end
+
+    def test_run_with_fasta_multiple_batches_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(taxonomy --host http://api.unipept.ugent.be --batch 2 --format xml >test 1 216816 >tost 1))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+      assert(output.include? '<fasta_header>')
+    end
   end
 end

data/test/test_formatters.rb

@@ -33,20 +33,60 @@ module Unipept
       assert_equal('csv', formatter.type)
     end
 
+    def test_group_by_first_key
+      array = [{ key1: 'v1', key2: 'v2' }, { key1: 'v1', key2: 'v3' }, { key1: 'v4', key2: 'v2' }]
+      grouped = formatter.group_by_first_key(array)
+      assert_equal({ 'v1' => [{ key1: 'v1', key2: 'v2' }, { key1: 'v1', key2: 'v3' }], 'v4' => [{ key1: 'v4', key2: 'v2' }] }, grouped)
+    end
+
+    def test_integrate_fasta_headers
+      fasta = [['>test', '5']]
+      object = [TestObject.test_object, TestObject.test_object]
+      integrated = Array.new(2, { fasta_header: '>test' }.merge(TestObject.test_object))
+      assert_equal(integrated, formatter.integrate_fasta_headers(object, fasta))
+    end
+
     def formatter
       Formatter.new
     end
 
     def test_header
-      assert_equal('', formatter.header(TestObject.test_object))
+      assert_raises NotImplementedError do
+        formatter.header(TestObject.test_object, nil)
+      end
+    end
+
+    def test_footer
+      assert_raises NotImplementedError do
+        formatter.footer
+      end
     end
 
     def test_type
-      assert_equal('', formatter.type)
+      assert_raises NotImplementedError do
+        formatter.type
+      end
     end
 
     def test_format
-      assert_equal(TestObject.test_object, formatter.format(TestObject.test_object))
+      f = formatter
+      def f.integrate_fasta_headers(_a, _b)
+        puts 'header'
+      end
+      def f.convert(_a, _b)
+        'body'
+      end
+      assert_equal('body', f.format(TestObject.test_object, nil, false))
+      out, _err = capture_io_while do
+        assert_equal('body', f.format(TestObject.test_object, [], false))
+      end
+      assert_equal('header', out.chomp)
+    end
+
+    def test_convert
+      assert_raises NotImplementedError do
+        formatter.convert(TestObject.test_object, false)
+      end
     end
   end
 
@@ -56,15 +96,27 @@ module Unipept
     end
 
     def test_header
-      assert_equal('', formatter.header(TestObject.test_object))
+      assert_equal('[', formatter.header(TestObject.test_object, nil))
+    end
+
+    def test_footer
+      assert_equal("]\n", formatter.footer)
     end
 
     def test_type
       assert_equal('json', formatter.type)
     end
 
-    def test_format
-      assert_equal(TestObject.as_json, formatter.format(TestObject.test_object))
+    def test_convert
+      assert_equal(TestObject.as_json, formatter.convert([TestObject.test_object], true))
+      assert_equal(',' + TestObject.as_json, formatter.convert([TestObject.test_object], false))
+    end
+
+    def test_format_with_fasta
+      fasta = [['>test', '5']]
+      output = formatter.format([TestObject.test_object], fasta, true)
+      json = '{"fasta_header":">test","integer":5,"string":"string","list":["a",2,false]}'
+      assert_equal(json, output)
     end
   end
 
@@ -80,21 +132,26 @@ module Unipept
       assert_equal('fasta_header,' + TestObject.as_csv_header, formatter.header(object, fasta))
     end
 
+    def test_footer
+      assert_equal('', formatter.footer)
+    end
+
     def test_type
       assert_equal('csv', formatter.type)
     end
 
-    def test_format
+    def test_convert
       object = [TestObject.test_object, TestObject.test_object]
       csv = [TestObject.as_csv, TestObject.as_csv, ''].join("\n")
-      assert_equal(csv, formatter.format(object))
+      assert_equal(csv, formatter.convert(object, true))
+      assert_equal(csv, formatter.convert(object, false))
     end
 
     def test_format_with_fasta
       fasta = [['>test', '5']]
       object = [TestObject.test_object, TestObject.test_object]
       csv = ['>test,' + TestObject.as_csv, '>test,' + TestObject.as_csv, ''].join("\n")
-      assert_equal(csv, formatter.format(object, fasta))
+      assert_equal(csv, formatter.format(object, fasta, false))
     end
   end
 
@@ -104,15 +161,28 @@ module Unipept
     end
 
     def test_header
-      assert_equal('', formatter.header(TestObject.test_object))
+      assert_equal('<results>', formatter.header(TestObject.test_object))
+    end
+
+    def test_footer
+      assert_equal("</results>\n", formatter.footer)
     end
 
     def test_type
       assert_equal('xml', formatter.type)
     end
 
-    def test_format
-      assert_equal(TestObject.as_xml, formatter.format(TestObject.test_object))
+    def test_convert
+      xml = '<result>' + TestObject.as_xml + '</result>'
+      assert_equal(xml, formatter.convert([TestObject.test_object], true))
+      assert_equal(xml, formatter.convert([TestObject.test_object], false))
+    end
+
+    def test_format_with_fasta
+      fasta = [['>test', '5']]
+      output = formatter.format([TestObject.test_object], fasta, false)
+      xml = '<result><fasta_header>>test</fasta_header>' + TestObject.as_xml + '</result>'
+      assert_equal(xml, output)
     end
   end
 
@@ -126,7 +196,7 @@ module Unipept
     end
 
     def self.as_xml
-      '<integer>5</integer><string>string</string><list size="3"><item>a</item><item>2</item><item>false</item></list>'
+      '<integer>5</integer><string>string</string><list><item>a</item><item>2</item><item>false</item></list>'
     end
 
     def self.as_csv

data/test/test_output_writer.rb

@@ -0,0 +1,29 @@
+require_relative '../lib/output_writer'
+
+module Unipept
+  class OutputWriterTestCase < Unipept::TestCase
+    def test_init
+      assert_equal($stdout, OutputWriter.new(nil).output)
+      assert_equal(File, OutputWriter.new('output.txt').output.class)
+    end
+
+    def test_stdout_write_to_output
+      out, _err = capture_io_while do
+        writer = OutputWriter.new(nil)
+        writer.write_line('hello world')
+        writer.output.flush
+      end
+      assert_equal('hello world', out.chomp)
+    end
+
+    def test_file_write_to_output
+      out, _err = capture_io_while do
+        writer = OutputWriter.new('output_file')
+        writer.write_line('hello world')
+        writer.output.flush
+      end
+      assert_equal('', out)
+      assert_equal('hello world', IO.foreach('output_file').next.chomp)
+    end
+  end
+end