unipept 1.1.2 → 1.1.3

data/test/commands/test_peptfilter.rb

@@ -174,7 +174,7 @@ module Unipept
           Commands::Peptfilter.run(%w(-h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
   end
 end

data/test/commands/test_prot2pept.rb

@@ -81,7 +81,7 @@ module Unipept
           Commands::Prot2pept.run(%w(-h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
   end
 end

data/test/commands/test_unipept.rb

@@ -8,14 +8,14 @@ module Unipept
           Commands::Unipept.run(%w(-h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
           Commands::Unipept.run(%w(--help))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
 
     def test_no_valid_subcommand
@@ -24,7 +24,7 @@ module Unipept
           Commands::Unipept.run(%w())
         end
       end
-      assert(err.include? 'show help for this command')
+      assert(err.include?('show help for this command'))
     end
 
     def test_version

data/test/commands/test_uniprot.rb

@@ -65,7 +65,7 @@ module Unipept
         end
       end
       assert_equal('', out)
-      assert(err.include? 'xxx is not a valid output format')
+      assert(err.include?('xxx is not a valid output format'))
     end
 
     def test_default_format
@@ -130,7 +130,7 @@ module Unipept
           Commands::Uniprot.run(%w(-h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
   end
 end

data/test/commands/unipept/test_api_runner.rb

@@ -75,7 +75,7 @@ module Unipept
     end
 
     def test_input_iterator_stdin
-      runner = new_runner('test',  host: 'https://param_host')
+      runner = new_runner('test', host: 'https://param_host')
       output = []
       _out, _err = capture_io_with_input(%w(a b c)) do
         runner.input_iterator.each { |el| output << el.chomp }
@@ -136,13 +136,13 @@ module Unipept
 
     def test_number_of_parallel_requests
       assert_equal(10, new_runner.concurrent_requests)
-      runner = new_runner('test',  host: 'http://param_host', parallel: '123')
+      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')
+      runner = new_runner('test', host: 'http://param_host', parallel: '100')
       assert_equal(2000, runner.queue_size)
     end
 
@@ -152,7 +152,7 @@ module Unipept
     end
 
     def test_param_formatter
-      runner = new_runner('test',  host: 'http://param_host', format: 'json')
+      runner = new_runner('test', host: 'http://param_host', format: 'json')
       assert_equal('json', runner.formatter.type)
     end
 
@@ -170,7 +170,7 @@ module Unipept
     end
 
     def test_required_fields_are_selected
-      runner = new_runner('test',  host: 'http://param_host', select: 'field')
+      runner = new_runner('test', host: 'http://param_host', select: 'field')
       def runner.required_fields
         ['test']
       end
@@ -178,32 +178,32 @@ module Unipept
     end
 
     def test_single_selected_fields
-      runner = new_runner('test',  host: 'http://param_host', select: 'field')
+      runner = new_runner('test', host: 'http://param_host', select: 'field')
       assert_equal([/^field$/], runner.selected_fields)
     end
 
     def test_comma_selected_fields
-      runner = new_runner('test',  host: 'http://param_host', select: 'field1,field2')
+      runner = new_runner('test', host: 'http://param_host', select: 'field1,field2')
       assert_equal([/^field1$/, /^field2$/], runner.selected_fields)
     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
 
     def test_combined_selected_fields
-      runner = new_runner('test',  host: 'http://param_host', select: ['field1', 'field2,field3'])
+      runner = new_runner('test', host: 'http://param_host', select: ['field1', 'field2,field3'])
       assert_equal([/^field1$/, /^field2$/, /^field3$/], runner.selected_fields)
     end
 
     def test_wildcard_selected_fields
-      runner = new_runner('test',  host: 'http://param_host', select: 'field*')
+      runner = new_runner('test', host: 'http://param_host', select: 'field*')
       assert_equal([/^field.*$/], runner.selected_fields)
     end
 
     def test_basic_construct_request_body
-      runner = new_runner('test',  host: 'http://param_host')
+      runner = new_runner('test', host: 'http://param_host')
       body = runner.construct_request_body('test')
       assert_equal('test', body[:input])
       assert_equal(false, body[:equate_il])
@@ -212,7 +212,7 @@ module Unipept
     end
 
     def test_equate_construct_request_body
-      runner = new_runner('test',  host: 'http://param_host', equate: true)
+      runner = new_runner('test', host: 'http://param_host', equate: true)
       body = runner.construct_request_body('test')
       assert_equal('test', body[:input])
       assert_equal(true, body[:equate_il])
@@ -221,7 +221,7 @@ module Unipept
     end
 
     def test_all_no_select_construct_request_body
-      runner = new_runner('test',  host: 'http://param_host', all: true)
+      runner = new_runner('test', host: 'http://param_host', all: true)
       body = runner.construct_request_body('test')
       assert_equal('test', body[:input])
       assert_equal(false, body[:equate_il])
@@ -230,7 +230,7 @@ module Unipept
     end
 
     def test_all_names_select_construct_request_body
-      runner = new_runner('test',  host: 'http://param_host', all: true, select: 'test,names')
+      runner = new_runner('test', host: 'http://param_host', all: true, select: 'test,names')
       body = runner.construct_request_body('test')
       assert_equal('test', body[:input])
       assert_equal(false, body[:equate_il])
@@ -239,7 +239,7 @@ module Unipept
     end
 
     def test_all_names_wildcard_select_construct_request_body
-      runner = new_runner('test',  host: 'http://param_host', all: true, select: 'test,order*')
+      runner = new_runner('test', host: 'http://param_host', all: true, select: 'test,order*')
       body = runner.construct_request_body('test')
       assert_equal('test', body[:input])
       assert_equal(false, body[:equate_il])
@@ -248,7 +248,7 @@ module Unipept
     end
 
     def test_all_no_names_select_construct_request_body
-      runner = new_runner('test',  host: 'http://param_host', all: true, select: 'test')
+      runner = new_runner('test', host: 'http://param_host', all: true, select: 'test')
       body = runner.construct_request_body('test')
       assert_equal('test', body[:input])
       assert_equal(false, body[:equate_il])
@@ -268,14 +268,14 @@ module Unipept
         _out, err = capture_io_while do
           runner.save_error('error message')
         end
-        assert(err.start_with? 'API request failed! log can be found in')
+        assert(err.start_with?('API request failed! log can be found in'))
         assert_equal('error message', IO.foreach('errordir/error.log').next.chomp)
       end
     end
 
     def test_error_file_path
       runner = new_runner
-      assert(runner.error_file_path.include? '/.unipept/')
+      assert(runner.error_file_path.include?('/.unipept/'))
     end
 
     def test_invalid_filter_result
@@ -329,7 +329,7 @@ module Unipept
       end
       out, err = capture_io_while(&lambda)
       assert_equal('', out)
-      assert(err.chomp.start_with? 'request timed out')
+      assert(err.chomp.start_with?('request timed out'))
     end
 
     def test_code_0_handle_response
@@ -342,7 +342,7 @@ module Unipept
       end
       out, err = capture_io_while(&lambda)
       assert_equal('', out)
-      assert(err.chomp.start_with? 'could not get an http')
+      assert(err.chomp.start_with?('could not get an http'))
     end
 
     def test_failed_handle_response
@@ -355,7 +355,7 @@ module Unipept
       end
       out, err = capture_io_while(&lambda)
       assert_equal('', out)
-      assert(err.chomp.start_with? 'Got 10')
+      assert(err.chomp.start_with?('Got 10'))
     end
 
     def test_run
@@ -364,6 +364,7 @@ module Unipept
         def runner.input_iterator
           %w(0 1 2).each
         end
+
         def runner.batch_size
           2
         end
@@ -371,9 +372,9 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'taxon_id')
-      assert(lines.next.start_with? '1,root')
-      assert(lines.next.start_with? '2,Bacteria')
+      assert(lines.next.start_with?('taxon_id'))
+      assert(lines.next.start_with?('1,root'))
+      assert(lines.next.start_with?('2,Bacteria'))
       assert_raises(StopIteration) { lines.next }
     end
 
@@ -413,6 +414,7 @@ module Unipept
           def o.options
             ''
           end
+
           def o.encoded_body
             ''
           end

data/test/commands/unipept/test_config.rb

@@ -8,14 +8,14 @@ module Unipept
           Commands::Unipept.run(%w(config -h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
           Commands::Unipept.run(%w(config --help))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
 
     def test_no_args
@@ -24,7 +24,7 @@ module Unipept
           Commands::Unipept.run(%w(config))
         end
       end
-      assert(err.include? 'show help for this command')
+      assert(err.include?('show help for this command'))
     end
 
     def test_too_many_args
@@ -33,7 +33,7 @@ module Unipept
           Commands::Unipept.run(%w(config a b c))
         end
       end
-      assert(err.include? 'show help for this command')
+      assert(err.include?('show help for this command'))
     end
 
     def test_setting_config

data/test/commands/unipept/test_pept2lca.rb

@@ -34,14 +34,14 @@ module Unipept
           Commands::Unipept.run(%w(pept2lca -h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
           Commands::Unipept.run(%w(pept2lca --help))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
 
     def test_run
@@ -50,8 +50,8 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'peptide,taxon_id')
-      assert(lines.next.start_with? 'AALTER,1,root,no rank')
+      assert(lines.next.start_with?('peptide,taxon_id'))
+      assert(lines.next.start_with?('AALTER,1,root,no rank'))
       assert_raises(StopIteration) { lines.next }
     end
 
@@ -61,10 +61,10 @@ module Unipept
       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(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
 
@@ -74,10 +74,10 @@ module Unipept
       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')
-      assert(lines.next.start_with? '>test,AALER,1')
-      assert(lines.next.start_with? '>tost,AALTER,1')
+      assert(lines.next.start_with?('fasta_header,peptide,taxon_id'))
+      assert(lines.next.start_with?('>test,AALTER,1'))
+      assert(lines.next.start_with?('>test,AALER,1'))
+      assert(lines.next.start_with?('>tost,AALTER,1'))
       assert_raises(StopIteration) { lines.next }
     end
 
@@ -88,10 +88,10 @@ module Unipept
       lines = out.each_line
       assert_equal('', err)
       output = lines.to_a.join('').chomp
-      assert(output.start_with? '[')
-      assert(output.end_with? ']')
+      assert(output.start_with?('['))
+      assert(output.end_with?(']'))
       assert(!output.include?('}{'))
-      assert(output.include? 'fasta_header')
+      assert(output.include?('fasta_header'))
     end
 
     def test_run_with_fasta_multiple_batches_xml
@@ -101,9 +101,9 @@ module Unipept
       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>')
+      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

@@ -22,14 +22,14 @@ module Unipept
           Commands::Unipept.run(%w(pept2prot -h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
           Commands::Unipept.run(%w(pept2prot --help))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
 
     def test_run
@@ -38,8 +38,8 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'peptide,uniprot_id,protein_name,taxon_id')
-      assert(lines.next.start_with? 'ENFVYIAK,')
+      assert(lines.next.start_with?('peptide,uniprot_id,protein_name,taxon_id'))
+      assert(lines.next.start_with?('ENFVYIAK,'))
     end
 
     def test_run_with_fasta_multiple_batches
@@ -48,7 +48,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'fasta_header,peptide,uniprot_id,protein_name,taxon_id')
+      assert(lines.next.start_with?('fasta_header,peptide,uniprot_id,protein_name,taxon_id'))
       assert(lines.count { |line| line.start_with? '>test,EGGAGSSTGQR,' } >= 1)
       assert(lines.count { |line| line.start_with? '>test,ENFVYIAK,' } >= 1)
       assert(lines.count { |line| line.start_with? '>tost,EGGAGSSTGQR,' } >= 1)
@@ -60,7 +60,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'fasta_header,peptide,uniprot_id')
+      assert(lines.next.start_with?('fasta_header,peptide,uniprot_id'))
       assert(lines.count { |line| line.start_with? '>test,EGGAGSSTGQR,' } >= 1)
       assert(lines.count { |line| line.start_with? '>test,ENFVYIAK,' } >= 1)
       assert(lines.count { |line| line.start_with? '>tost,EGGAGSSTGQR,' } >= 1)
@@ -73,10 +73,10 @@ module Unipept
       lines = out.each_line
       assert_equal('', err)
       output = lines.to_a.join('').chomp
-      assert(output.start_with? '[')
-      assert(output.end_with? ']')
+      assert(output.start_with?('['))
+      assert(output.end_with?(']'))
       assert(!output.include?('}{'))
-      assert(output.include? 'fasta_header')
+      assert(output.include?('fasta_header'))
     end
 
     def test_run_with_fasta_multiple_batches_xml
@@ -86,9 +86,9 @@ module Unipept
       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>')
+      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

@@ -22,14 +22,14 @@ module Unipept
           Commands::Unipept.run(%w(pept2taxa -h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
           Commands::Unipept.run(%w(pept2taxa --help))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
 
     def test_run
@@ -38,8 +38,8 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'peptide,taxon_id,taxon_name,taxon_rank')
-      assert(lines.next.start_with? 'ENFVYIAK,')
+      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
@@ -48,7 +48,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'fasta_header,peptide,taxon_id,taxon_name,taxon_rank')
+      assert(lines.next.start_with?('fasta_header,peptide,taxon_id,taxon_name,taxon_rank'))
       assert(lines.count { |line| line.start_with? '>test,EGGAGSSTGQR,' } >= 1)
       assert(lines.count { |line| line.start_with? '>test,ENFVYIAK,' } >= 1)
       assert(lines.count { |line| line.start_with? '>tost,EGGAGSSTGQR,' } >= 1)
@@ -60,7 +60,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'fasta_header,peptide,taxon_id')
+      assert(lines.next.start_with?('fasta_header,peptide,taxon_id'))
       assert(lines.count { |line| line.start_with? '>test,EGGAGSSTGQR,' } >= 1)
       assert(lines.count { |line| line.start_with? '>test,ENFVYIAK,' } >= 1)
       assert(lines.count { |line| line.start_with? '>tost,EGGAGSSTGQR,' } >= 1)
@@ -73,10 +73,10 @@ module Unipept
       lines = out.each_line
       assert_equal('', err)
       output = lines.to_a.join('').chomp
-      assert(output.start_with? '[')
-      assert(output.end_with? ']')
+      assert(output.start_with?('['))
+      assert(output.end_with?(']'))
       assert(!output.include?('}{'))
-      assert(output.include? 'fasta_header')
+      assert(output.include?('fasta_header'))
     end
 
     def test_run_with_fasta_multiple_batches_xml
@@ -86,9 +86,9 @@ module Unipept
       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>')
+      assert(output.start_with?('<results>'))
+      assert(output.end_with?('</results>'))
+      assert(output.include?('<fasta_header>'))
     end
   end
 end