unipept 1.4.0 → 1.4.1

data/test/commands/test_unipept.rb

@@ -5,14 +5,14 @@ module Unipept
     def test_help
       out, _err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Unipept.run(%w(-h))
+          Commands::Unipept.run(%w[-h])
         end
       end
       assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Unipept.run(%w(--help))
+          Commands::Unipept.run(%w[--help])
         end
       end
       assert(out.include?('show help for this command'))
@@ -21,7 +21,7 @@ module Unipept
     def test_no_valid_subcommand
       _out, err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Unipept.run(%w())
+          Commands::Unipept.run(%w[])
         end
       end
       assert(err.include?('show help for this command'))
@@ -29,7 +29,7 @@ module Unipept
 
     def test_version
       out, _err = capture_io_while do
-        Commands::Unipept.run(%w(-v))
+        Commands::Unipept.run(%w[-v])
       end
       assert_equal(VERSION, out.chomp)
     end

data/test/commands/test_uniprot.rb

@@ -4,56 +4,56 @@ module Unipept
   class UniprotTestCase < Unipept::TestCase
     def test_argument_input
       out, _err = capture_io_while do
-        Commands::Uniprot.run(%w(Q6GZX3))
+        Commands::Uniprot.run(%w[Q6GZX3])
       end
       assert_equal(1, out.split(/\n/).length)
 
       out, _err = capture_io_while do
-        Commands::Uniprot.run(%w(Q6GZX3 Q6GZX4))
+        Commands::Uniprot.run(%w[Q6GZX3 Q6GZX4])
       end
       assert_equal(2, out.split(/\n/).length)
 
       out, _err = capture_io_while do
-        Commands::Uniprot.run(%w(-f fasta Q6GZX3 Q6GZX4))
+        Commands::Uniprot.run(%w[-f fasta Q6GZX3 Q6GZX4])
       end
       assert_equal(2, out.count('>'))
 
       out, _err = capture_io_while do
-        Commands::Uniprot.run(%w(--format fasta Q6GZX3 Q6GZX4))
+        Commands::Uniprot.run(%w[--format fasta Q6GZX3 Q6GZX4])
       end
       assert_equal(2, out.count('>'))
     end
 
     def test_stdin_input
       out, _err = capture_io_with_input('Q6GZX3') do
-        Commands::Uniprot.run(%w())
+        Commands::Uniprot.run(%w[])
       end
       assert_equal(1, out.split(/\n/).length)
 
-      out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
-        Commands::Uniprot.run(%w())
+      out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
+        Commands::Uniprot.run(%w[])
       end
       assert_equal(2, out.split(/\n/).length)
 
-      out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
-        Commands::Uniprot.run(%w(-f fasta))
+      out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
+        Commands::Uniprot.run(%w[-f fasta])
       end
       assert_equal(2, out.count('>'))
 
-      out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
-        Commands::Uniprot.run(%w(--format fasta))
+      out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
+        Commands::Uniprot.run(%w[--format fasta])
       end
       assert_equal(2, out.count('>'))
     end
 
     def test_argument_input_priority
       out, _err = capture_io_with_input('Q6GZX3') do
-        Commands::Uniprot.run(%w(Q6GZX3 Q6GZX4))
+        Commands::Uniprot.run(%w[Q6GZX3 Q6GZX4])
       end
       assert_equal(2, out.split(/\n/).length)
 
-      out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
-        Commands::Uniprot.run(%w(Q6GZX3))
+      out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
+        Commands::Uniprot.run(%w[Q6GZX3])
       end
       assert_equal(1, out.split(/\n/).length)
     end
@@ -61,7 +61,7 @@ module Unipept
     def test_invalid_format
       out, err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Uniprot.run(%w(--format xxx))
+          Commands::Uniprot.run(%w[--format xxx])
         end
       end
       assert_equal('', out)
@@ -70,17 +70,17 @@ module Unipept
 
     def test_default_format
       out_default, _err = capture_io_while do
-        Commands::Uniprot.run(%w(Q6GZX3))
+        Commands::Uniprot.run(%w[Q6GZX3])
       end
       assert_equal(1, out_default.split(/\n/).length)
 
       out_sequence, _err = capture_io_while do
-        Commands::Uniprot.run(%w(-f sequence Q6GZX3))
+        Commands::Uniprot.run(%w[-f sequence Q6GZX3])
       end
       assert_equal(out_default, out_sequence)
 
       out_sequence, _err = capture_io_while do
-        Commands::Uniprot.run(%w(--format sequence Q6GZX3))
+        Commands::Uniprot.run(%w[--format sequence Q6GZX3])
       end
       assert_equal(out_default, out_sequence)
     end
@@ -88,37 +88,37 @@ module Unipept
     def test_format_options
       # fasta txt xml rdf gff sequence
       out, err = capture_io_while do
-        Commands::Uniprot.run(%w(-f fasta Q6GZX3))
+        Commands::Uniprot.run(%w[-f fasta Q6GZX3])
       end
       assert(!out.empty?)
       assert(err.empty?)
 
       out, err = capture_io_while do
-        Commands::Uniprot.run(%w(-f txt Q6GZX3))
+        Commands::Uniprot.run(%w[-f txt Q6GZX3])
       end
       assert(!out.empty?)
       assert(err.empty?)
 
       out, err = capture_io_while do
-        Commands::Uniprot.run(%w(-f xml Q6GZX3))
+        Commands::Uniprot.run(%w[-f xml Q6GZX3])
       end
       assert(!out.empty?)
       assert(err.empty?)
 
       out, err = capture_io_while do
-        Commands::Uniprot.run(%w(-f rdf Q6GZX3))
+        Commands::Uniprot.run(%w[-f rdf Q6GZX3])
       end
       assert(!out.empty?)
       assert(err.empty?)
 
       out, err = capture_io_while do
-        Commands::Uniprot.run(%w(-f gff Q6GZX3))
+        Commands::Uniprot.run(%w[-f gff Q6GZX3])
       end
       assert(!out.empty?)
       assert(err.empty?)
 
       out, err = capture_io_while do
-        Commands::Uniprot.run(%w(-f sequence Q6GZX3))
+        Commands::Uniprot.run(%w[-f sequence Q6GZX3])
       end
       assert(!out.empty?)
       assert(err.empty?)
@@ -127,7 +127,7 @@ module Unipept
     def test_help
       out, _err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Uniprot.run(%w(-h))
+          Commands::Uniprot.run(%w[-h])
         end
       end
       assert(out.include?('show help for this command'))

data/test/commands/unipept/test_api_runner.rb

@@ -8,17 +8,17 @@ module Unipept
 
   class UnipeptAPIRunnerTestCase < Unipept::TestCase
     def test_init
-      runner = new_runner('test', { host: 'test_host' }, %w(a b c))
+      runner = new_runner('test', { host: 'test_host' }, %w[a b c])
       assert_equal('test', runner.command.name)
       assert_equal('test_host', runner.options[:host])
-      assert_equal(%w(a b c), runner.arguments)
+      assert_equal(%w[a b c], runner.arguments)
       assert(!runner.configuration.nil?)
       assert_equal('http://test_host/api/v1/test.json', runner.url)
       assert(/Unipept CLI - unipept [0-9]*\.[0-9]*\.[0-9]*/.match runner.user_agent)
     end
 
     def test_config_host
-      runner = new_runner('test', { host: 'http://param_host' }, %w(a b c))
+      runner = new_runner('test', { host: 'http://param_host' }, %w[a b c])
       runner.options.delete(:host)
       runner.configuration['host'] = 'http://config_host'
       host = runner.host
@@ -26,14 +26,14 @@ module Unipept
     end
 
     def test_param_host
-      runner = new_runner('test', { host: 'http://param_host' }, %w(a b c))
+      runner = new_runner('test', { host: 'http://param_host' }, %w[a b c])
       runner.configuration.delete('host')
       host = runner.host
       assert_equal('http://param_host', host)
     end
 
     def test_no_host
-      runner = new_runner('test', { host: 'param_host' }, %w(a b c))
+      runner = new_runner('test', { host: 'param_host' }, %w[a b c])
       runner.configuration.delete('host')
       runner.options.delete(:host)
       host = runner.host
@@ -41,66 +41,66 @@ module Unipept
     end
 
     def test_host_priority
-      runner = new_runner('test', { host: 'http://param_host' }, %w(a b c))
+      runner = new_runner('test', { host: 'http://param_host' }, %w[a b c])
       runner.configuration['host'] = 'http://config_host'
       host = runner.host
       assert_equal('http://param_host', host)
     end
 
     def test_http_host
-      runner = new_runner('test', { host: 'param_host' }, %w(a b c))
+      runner = new_runner('test', { host: 'param_host' }, %w[a b c])
       host = runner.host
       assert_equal('http://param_host', host)
     end
 
     def test_https_host
-      runner = new_runner('test', { host: 'https://param_host' }, %w(a b c))
+      runner = new_runner('test', { host: 'https://param_host' }, %w[a b c])
       host = runner.host
       assert_equal('https://param_host', host)
     end
 
     def test_input_iterator_args
-      runner = new_runner('test', { host: 'https://param_host' }, %w(a b c))
+      runner = new_runner('test', { host: 'https://param_host' }, %w[a b c])
       output = []
       runner.input_iterator.each { |el| output << el.chomp }
-      assert_equal(%w(a b c), output)
+      assert_equal(%w[a b c], output)
     end
 
     def test_input_iterator_file
-      File.open('input_file', 'w') { |file| file.write(%w(a b c).join("\n")) }
+      File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
       runner = new_runner('test',  host: 'https://param_host', input: 'input_file')
       output = []
       runner.input_iterator.each { |el| output << el.chomp }
-      assert_equal(%w(a b c), output)
+      assert_equal(%w[a b c], output)
     end
 
     def test_input_iterator_stdin
       runner = new_runner('test', host: 'https://param_host')
       output = []
-      _out, _err = capture_io_with_input(%w(a b c)) do
+      _out, _err = capture_io_with_input(%w[a b c]) do
         runner.input_iterator.each { |el| output << el.chomp }
       end
-      assert_equal(%w(a b c), output)
+      assert_equal(%w[a b c], output)
     end
 
     def test_input_iterator_arguments_priority
-      File.open('input_file', 'w') { |file| file.write(%w(1 2 3).join("\n")) }
-      runner = new_runner('test', { host: 'https://param_host', input: 'input_file' }, %w(a b c))
+      File.open('input_file', 'w') { |file| file.write(%w[1 2 3].join("\n")) }
+      runner = new_runner('test', { host: 'https://param_host', input: 'input_file' }, %w[a b c])
       output = []
-      _out, _err = capture_io_with_input(%w(1 2 3)) do
+      _out, _err = capture_io_with_input(%w[1 2 3]) do
         runner.input_iterator.each { |el| output << el.chomp }
       end
-      assert_equal(%w(a b c), output)
+      assert_equal(%w[a b c], output)
     end
 
     def test_input_iterator_file_priority
-      File.open('input_file', 'w') { |file| file.write(%w(a b c).join("\n")) }
+      File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
       runner = new_runner('test',  host: 'https://param_host', input: 'input_file')
       output = []
-      _out, _err = capture_io_with_input(%w(1 2 3)) do
+      _out, _err = capture_io_with_input(%w[1 2 3]) do
         runner.input_iterator.each { |el| output << el.chomp }
       end
-      assert_equal(%w(a b c), output)
+      assert_equal(%w[a b c], output)
     end
 
     def test_required_fields
@@ -199,7 +199,7 @@ module Unipept
     end
 
     def test_multiple_selected_fields
-      runner = new_runner('test', host: 'http://param_host', select: %w(field1 field2))
+      runner = new_runner('test', host: 'http://param_host', select: %w[field1 field2])
       assert_equal([/^field1$/, /^field2$/], runner.selected_fields)
     end
 
@@ -348,7 +348,7 @@ module Unipept
       lambda = runner.handle_response(response, 0, nil)
       assert(lambda.lambda?)
       def runner.save_error(input)
-        $stderr.puts(input)
+        warn(input)
       end
       out, err = capture_io_while(&lambda)
       assert_equal('', out)
@@ -361,7 +361,7 @@ module Unipept
       lambda = runner.handle_response(response, 0, nil)
       assert(lambda.lambda?)
       def runner.save_error(input)
-        $stderr.puts(input)
+        warn(input)
       end
       out, err = capture_io_while(&lambda)
       assert_equal('', out)
@@ -374,7 +374,7 @@ module Unipept
       lambda = runner.handle_response(response, 0, nil)
       assert(lambda.lambda?)
       def runner.save_error(input)
-        $stderr.puts(input)
+        warn(input)
       end
       out, err = capture_io_while(&lambda)
       assert_equal('', out)
@@ -385,7 +385,7 @@ module Unipept
       runner = new_runner('taxonomy', host: 'http://api.unipept.ugent.be')
       out, err = capture_io_while do
         def runner.input_iterator
-          %w(0 1 2).each
+          %w[0 1 2].each
         end
 
         def runner.batch_size

data/test/commands/unipept/test_config.rb

@@ -5,14 +5,14 @@ module Unipept
     def test_help
       out, _err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Unipept.run(%w(config -h))
+          Commands::Unipept.run(%w[config -h])
         end
       end
       assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Unipept.run(%w(config --help))
+          Commands::Unipept.run(%w[config --help])
         end
       end
       assert(out.include?('show help for this command'))
@@ -21,7 +21,7 @@ module Unipept
     def test_no_args
       _out, err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Unipept.run(%w(config))
+          Commands::Unipept.run(%w[config])
         end
       end
       assert(err.include?('show help for this command'))
@@ -30,7 +30,7 @@ module Unipept
     def test_too_many_args
       _out, err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Unipept.run(%w(config a b c))
+          Commands::Unipept.run(%w[config a b c])
         end
       end
       assert(err.include?('show help for this command'))
@@ -54,7 +54,7 @@ module Unipept
       config['test'] = value
       config.save
       out, _err = capture_io_while do
-        Commands::Unipept.run(%w(config test))
+        Commands::Unipept.run(%w[config test])
       end
       config.delete('test')
       config.save

data/test/commands/unipept/test_pept2lca.rb

@@ -31,14 +31,14 @@ module Unipept
     def test_help
       out, _err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Unipept.run(%w(pept2lca -h))
+          Commands::Unipept.run(%w[pept2lca -h])
         end
       end
       assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Unipept.run(%w(pept2lca --help))
+          Commands::Unipept.run(%w[pept2lca --help])
         end
       end
       assert(out.include?('show help for this command'))
@@ -46,7 +46,7 @@ module Unipept
 
     def test_run
       out, err = capture_io_while do
-        Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be AALTER))
+        Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be AALTER])
       end
       lines = out.each_line
       assert_equal('', err)
@@ -57,7 +57,7 @@ module Unipept
 
     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))
+        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)
@@ -70,7 +70,7 @@ module Unipept
 
     def test_run_with_fasta_multiple_batches_and_select
       out, err = capture_io_while do
-        Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 --select taxon_id >test AALTER AALER >tost AALTER))
+        Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be --batch 2 --select taxon_id >test AALTER AALER >tost AALTER])
       end
       lines = out.each_line
       assert_equal('', err)
@@ -83,7 +83,7 @@ module Unipept
 
     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))
+        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)
@@ -96,7 +96,7 @@ module Unipept
 
     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))
+        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)