unipept 0.7.1 → 0.8.0

data/test/commands/unipept/test_api_runner.rb

@@ -0,0 +1,486 @@
+require_relative '../../../lib/commands/unipept/api_runner'
+
+module Unipept
+  # make methods public to test them
+  class Commands::ApiRunner
+    public :glob_to_regex, :handle_response, :error_file_path, :filter_result
+  end
+
+  class UnipeptAPIRunnerTestCase < Unipept::TestCase
+    def test_init
+      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(!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
+
+    def test_config_host
+      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
+      assert_equal('http://config_host', host)
+    end
+
+    def test_param_host
+      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.configuration.delete('host')
+      runner.options.delete(:host)
+      _out, err = capture_io_while do
+        assert_raises SystemExit do
+          runner.host
+        end
+      end
+      assert(err.start_with? 'WARNING: no host has been set')
+    end
+
+    def test_host_priority
+      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))
+      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))
+      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))
+      output = []
+      runner.input_iterator.each { |el| output << el.chomp }
+      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")) }
+      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)
+    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
+        runner.input_iterator.each { |el| output << el.chomp }
+      end
+      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))
+      output = []
+      _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)
+    end
+
+    def test_input_iterator_file_priority
+      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
+        runner.input_iterator.each { |el| output << el.chomp }
+      end
+      assert_equal(%w(a b c), output)
+    end
+
+    def test_batch_size
+      assert_equal(100, new_runner.batch_size)
+    end
+
+    def test_default_formatter
+      runner = new_runner
+      assert_equal('csv', runner.formatter.type)
+    end
+
+    def test_param_formatter
+      runner = new_runner('test',  host: 'http://param_host', format: 'json')
+      assert_equal('json', runner.formatter.type)
+    end
+
+    def test_no_selected_fields
+      runner = new_runner
+      assert_equal([], runner.selected_fields)
+    end
+
+    def test_single_selected_fields
+      runner = new_runner('test',  host: 'http://param_host', select: 'field')
+      assert_equal([/^field$/], runner.selected_fields)
+    end
+
+    def test_comma_selected_fields
+      runner = new_runner('test',  host: 'http://param_host', select: 'field1,field2')
+      assert_equal([/^field1$/, /^field2$/], runner.selected_fields)
+    end
+
+    def test_multiple_selected_fields
+      runner = new_runner('test',  host: 'http://param_host', select: %w(field1 field2))
+      assert_equal([/^field1$/, /^field2$/], runner.selected_fields)
+    end
+
+    def test_combined_selected_fields
+      runner = new_runner('test',  host: 'http://param_host', select: ['field1', 'field2,field3'])
+      assert_equal([/^field1$/, /^field2$/, /^field3$/], runner.selected_fields)
+    end
+
+    def test_wildcard_selected_fields
+      runner = new_runner('test',  host: 'http://param_host', select: 'field*')
+      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')
+      assert_equal('test', body[:input])
+      assert_equal(false, body[:equate_il])
+      assert_equal(false, body[:extra])
+      assert_equal(false, body[:names])
+    end
+
+    def test_equate_construct_request_body
+      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])
+      assert_equal(false, body[:extra])
+      assert_equal(false, body[:names])
+    end
+
+    def test_all_no_select_construct_request_body
+      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])
+      assert_equal(true, body[:extra])
+      assert_equal(true, body[:names])
+    end
+
+    def test_all_names_select_construct_request_body
+      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])
+      assert_equal(true, body[:extra])
+      assert_equal(true, body[:names])
+    end
+
+    def test_all_no_names_select_construct_request_body
+      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])
+      assert_equal(true, body[:extra])
+      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'))
+      assert(/^.*simple.*$/, runner.glob_to_regex('*simple*'))
+    end
+
+    def test_save_error
+      runner = new_runner
+      runner.stub(:error_file_path, 'errordir/error.log') do
+        _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_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/')
+    end
+
+    def test_invalid_filter_result
+      runner = new_runner
+      assert_equal([], runner.filter_result('{"key":"value'))
+    end
+
+    def test_array_wrap_filter_result
+      runner = new_runner
+      assert_equal([{ 'key' => 'value' }], runner.filter_result('{"key":"value"}'))
+    end
+
+    def test_filter_filter_result
+      runner = new_runner('test', host: 'test', select: 'key1')
+      result = runner.filter_result('[{"key1":"value1","key2":"value1"},{"key1":"value2","key2":"value2"}]')
+      assert_equal([{ 'key1' => 'value1' }, { 'key1' => 'value2' }], result)
+    end
+
+    def test_success_header_handle_response
+      runner = new_runner
+      response = new_response(success: true, response_body: '[{"key1":"value1","key2":"value1"},{"key1":"value2","key2":"value2"}]')
+      lambda = runner.handle_response(response, 0, nil)
+      assert(lambda.lambda?)
+      out, err = capture_io_while(&lambda)
+      lines = out.each_line
+      assert_equal('', err)
+      assert_equal('key1,key2', lines.next.chomp)
+      assert_equal('value1,value1', lines.next.chomp)
+      assert_equal('value2,value2', lines.next.chomp)
+    end
+
+    def test_success_no_header_handle_response
+      runner = new_runner
+      response = new_response(success: true, response_body: '[{"key1":"value1","key2":"value1"},{"key1":"value2","key2":"value2"}]')
+      lambda = runner.handle_response(response, 1, nil)
+      assert(lambda.lambda?)
+      out, err = capture_io_while(&lambda)
+      lines = out.each_line
+      assert_equal('', err)
+      assert_equal('value1,value1', lines.next.chomp)
+      assert_equal('value2,value2', lines.next.chomp)
+    end
+
+    def test_time_out_handle_response
+      runner = new_runner
+      response = new_response(success: false, timed_out: true)
+      lambda = runner.handle_response(response, 0, nil)
+      assert(lambda.lambda?)
+      def runner.save_error(input)
+        $stderr.puts(input)
+      end
+      out, err = capture_io_while(&lambda)
+      assert_equal('', out)
+      assert(err.chomp.start_with? 'request timed out')
+    end
+
+    def test_code_0_handle_response
+      runner = new_runner
+      response = new_response(success: false, timed_out: false, code: 0)
+      lambda = runner.handle_response(response, 0, nil)
+      assert(lambda.lambda?)
+      def runner.save_error(input)
+        $stderr.puts(input)
+      end
+      out, err = capture_io_while(&lambda)
+      assert_equal('', out)
+      assert(err.chomp.start_with? 'could not get an http')
+    end
+
+    def test_failed_handle_response
+      runner = new_runner
+      response = new_response(success: false, timed_out: false, code: 10)
+      lambda = runner.handle_response(response, 0, nil)
+      assert(lambda.lambda?)
+      def runner.save_error(input)
+        $stderr.puts(input)
+      end
+      out, err = capture_io_while(&lambda)
+      assert_equal('', out)
+      assert(err.chomp.start_with? 'Got 10')
+    end
+
+    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
+        def runner.batch_size
+          2
+        end
+        runner.run
+      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')
+      assert_raises(StopIteration) { lines.next }
+    end
+
+    def new_runner(command_name = 'test', options = { host: 'http://param_host' }, arguments = [])
+      command = Cri::Command.define { name command_name }
+      Commands::ApiRunner.new(options, arguments, command)
+    end
+
+    def new_response(values)
+      response = Class.new do
+        def initialize(values)
+          @values = values
+        end
+
+        def success?
+          @values[:success]
+        end
+
+        def timed_out?
+          @values[:timed_out]
+        end
+
+        def code
+          @values[:code]
+        end
+
+        def response_body
+          @values[:response_body]
+        end
+
+        def return_message
+          ''
+        end
+
+        def request
+          o = Object.new
+          def o.options
+            ''
+          end
+          def o.encoded_body
+            ''
+          end
+          o
+        end
+      end
+      response.new(values)
+    end
+  end
+end

data/test/commands/unipept/test_config.rb

@@ -0,0 +1,64 @@
+require_relative '../../../lib/commands'
+
+module Unipept
+  class UnipeptConfigTestCase < Unipept::TestCase
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          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))
+        end
+      end
+      assert(out.include? 'show help for this command')
+    end
+
+    def test_no_args
+      _out, err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w(config))
+        end
+      end
+      assert(err.include? 'show help for this command')
+    end
+
+    def test_too_many_args
+      _out, err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w(config a b c))
+        end
+      end
+      assert(err.include? 'show help for this command')
+    end
+
+    def test_setting_config
+      value = Random.rand.to_s
+      config = Unipept::Configuration.new
+      config.delete('test')
+      config.save
+      out, _err = capture_io_while do
+        Commands::Unipept.run(['config', 'test', value])
+      end
+      assert_equal('test was set to ' + value, out.chomp)
+      assert_equal(value, Unipept::Configuration.new['test'])
+    end
+
+    def test_getting_config
+      value = Random.rand.to_s
+      config = Unipept::Configuration.new
+      config['test'] = value
+      config.save
+      out, _err = capture_io_while do
+        Commands::Unipept.run(%w(config test))
+      end
+      config.delete('test')
+      config.save
+      assert_equal(value, out.chomp)
+    end
+  end
+end

data/test/commands/unipept/test_pept2lca.rb

@@ -0,0 +1,40 @@
+require_relative '../../../lib/commands'
+
+module Unipept
+  class UnipeptPept2lcaTestCase < Unipept::TestCase
+    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
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          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))
+        end
+      end
+      assert(out.include? 'show help for this command')
+    end
+
+    def test_run
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be AALTER))
+      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_raises(StopIteration) { lines.next }
+    end
+  end
+end

data/test/commands/unipept/test_pept2prot.rb

@@ -0,0 +1,39 @@
+require_relative '../../../lib/commands'
+
+module Unipept
+  class UnipeptPept2protTestCase < Unipept::TestCase
+    def test_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)
+      pept2prot.options[:all] = true
+      assert_equal(5, pept2prot.batch_size)
+    end
+
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w(pept2prot -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(pept2prot --help))
+        end
+      end
+      assert(out.include? 'show help for this command')
+    end
+
+    def test_run
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2prot --host http://api.unipept.ugent.be ENFVYIAK))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      assert(lines.next.start_with? 'peptide,uniprot_id,taxon_id')
+      assert(lines.next.start_with? 'ENFVYIAK,')
+    end
+  end
+end

data/test/commands/unipept/test_pept2taxa.rb

@@ -0,0 +1,39 @@
+require_relative '../../../lib/commands'
+
+module Unipept
+  class UnipeptPept2taxaTestCase < Unipept::TestCase
+    def test_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)
+      pept2taxa.options[:all] = true
+      assert_equal(5, pept2taxa.batch_size)
+    end
+
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w(pept2taxa -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(pept2taxa --help))
+        end
+      end
+      assert(out.include? 'show help for this command')
+    end
+
+    def test_run
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2taxa --host http://api.unipept.ugent.be ENFVYIAK))
+      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,')
+    end
+  end
+end