unipept 0.7.1 → 0.8.0

data/test/commands/unipept/test_taxa2lca.rb

@@ -0,0 +1,39 @@
+require_relative '../../../lib/commands'
+
+module Unipept
+  class UnipeptTaxa2lcaTestCase < Unipept::TestCase
+    def test_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
+      end
+    end
+
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w(taxa2lca -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(taxa2lca --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(taxa2lca --host http://api.unipept.ugent.be 216816 1680))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      assert(lines.next.start_with? 'taxon_id,taxon_name,taxon_rank')
+      assert(lines.next.start_with? '1678,Bifidobacterium,genus')
+    end
+  end
+end

data/test/commands/unipept/test_taxonomy.rb

@@ -0,0 +1,37 @@
+require_relative '../../../lib/commands'
+
+module Unipept
+  class UnipeptTaxonomyTestCase < Unipept::TestCase
+    def test_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)
+    end
+
+    def test_help
+      out, _err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Unipept.run(%w(taxonomy -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(taxonomy --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(taxonomy --host http://api.unipept.ugent.be 1))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      assert(lines.next.start_with? 'taxon_id,taxon_name,taxon_rank')
+      assert(lines.next.start_with? '1,root,no rank')
+    end
+  end
+end

data/test/helper.rb

@@ -1,34 +1,80 @@
-require 'simplecov'
-
-module SimpleCov::Configuration
-  def clean_filters
-    @filters = []
-  end
-end
-
-SimpleCov.configure do
-  clean_filters
-  load_adapter 'test_frameworks'
-end
-
-ENV["COVERAGE"] && SimpleCov.start do
-  add_filter "/.rvm/"
-end
 require 'rubygems'
 require 'bundler'
+require 'coveralls'
+Coveralls.wear!
+
 begin
   Bundler.setup(:default, :development)
 rescue Bundler::BundlerError => e
   $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
+  $stderr.puts 'Run `bundle install` to install missing gems'
   exit e.status_code
 end
-require 'test/unit'
-require 'shoulda'
 
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
-require 'unipept'
+require 'minitest'
+require 'minitest/autorun'
+
+module Unipept
+  class TestCase < Minitest::Test
+    def setup
+      # Enter tmp
+      @tmp_dir = Dir.mktmpdir('unipept-test')
+      @orig_wd = FileUtils.pwd
+      FileUtils.cd(@tmp_dir)
+
+      @orig_io = capture_io
+    end
+
+    def teardown
+      uncapture_io(*@orig_io)
 
-class Test::Unit::TestCase
+      # Exit tmp
+      FileUtils.cd(@orig_wd)
+      FileUtils.rm_rf(@tmp_dir)
+    end
+
+    def capture_io_with_input(input, &block)
+      capture_io_while do
+        input = input.join("\n") if input.is_a? Array
+        $stdin.write(input)
+        $stdin.rewind
+        block.call
+      end
+    end
+
+    def capture_io_while(&block)
+      orig_io = capture_io
+      block.call
+      [$stdout.string, $stderr.string]
+    ensure
+      uncapture_io(*orig_io)
+    end
+
+    def lines(string)
+      string.scan(/^.*\n/).map(&:chomp)
+    end
+
+    private
+
+    def capture_io
+      orig_stdout = $stdout
+      orig_stderr = $stderr
+      orig_stdin = $stdin
+
+      $stdout = StringIO.new
+      $stderr = StringIO.new
+      $stdin = StringIO.new
+
+      [orig_stdout, orig_stderr, orig_stdin]
+    end
+
+    def uncapture_io(orig_stdout, orig_stderr, orig_stdin)
+      $stdout = orig_stdout
+      $stderr = orig_stderr
+      $stdin = orig_stdin
+    end
+  end
 end
+
+# Unexpected system exit is unexpected
+::MiniTest::Unit::TestCase::PASSTHROUGH_EXCEPTIONS.delete(SystemExit)

data/test/test_bach_order.rb

@@ -0,0 +1,57 @@
+require_relative '../lib/batch_order'
+
+module Unipept
+  class BatchOrderTestCase < Unipept::TestCase
+    def test_single_batch
+      order = BatchOrder.new
+      out, _err = capture_io_while do
+        run_batch(order, [0])
+      end
+      assert_equal(['0', ''].join("\n"), out)
+    end
+
+    def test_double_batch
+      order = BatchOrder.new
+      out, _err = capture_io_while do
+        run_batch(order, [0, 1])
+      end
+      assert_equal(['0', '1', ''].join("\n"), out)
+    end
+
+    def test_missing_batch
+      order = BatchOrder.new
+      out, _err = capture_io_while do
+        run_batch(order, [1, 2])
+      end
+      assert_equal('', out)
+    end
+
+    def test_out_order_batch
+      order = BatchOrder.new
+      out, _err = capture_io_while do
+        run_batch(order, [1, 0])
+      end
+      assert_equal(['0', '1', ''].join("\n"), out)
+    end
+
+    def test_gap_batch
+      order = BatchOrder.new
+      out, _err = capture_io_while do
+        run_batch(order, [1, 4, 0])
+      end
+      assert_equal(['0', '1', ''].join("\n"), out)
+      out, _err = capture_io_while do
+        run_batch(order, [2, 3, 5])
+      end
+      assert_equal(['2', '3', '4', '5', ''].join("\n"), out)
+    end
+
+    def run_batch(order, list)
+      list.each do |i|
+        order.wait(i) do
+          puts i
+        end
+      end
+    end
+  end
+end

data/test/test_base.rb

@@ -0,0 +1,6 @@
+module Unipept
+  class BaseTestCase < Unipept::TestCase
+    def test_stub
+    end
+  end
+end

data/test/test_batch_iterator.rb

@@ -0,0 +1,87 @@
+require_relative '../lib/batch_iterator'
+
+module Unipept
+  class BatchIteratorTestCase < Unipept::TestCase
+    def test_batch_size
+      iterator = BatchIterator.new(50)
+      assert_equal(50, iterator.batch_size)
+    end
+
+    def test_fasta
+      iterator = BatchIterator.new(50)
+      assert(iterator.fasta? '> test')
+      assert(!(iterator.fasta? '< test'))
+      assert(!(iterator.fasta? 'test'))
+    end
+
+    def test_normal_iterator
+      iterator = BatchIterator.new(2)
+      data = %w(a b c d e)
+      out, _err = capture_io_while do
+        iterator.iterate(data.each) do |batch, batch_id, fasta_mapper|
+          assert_nil(fasta_mapper)
+          puts batch_id
+          puts batch.to_s
+        end
+      end
+      assert_equal(['0', '["a", "b"]', '1', '["c", "d"]', '2', '["e"]', ''].join("\n"), out)
+    end
+
+    def test_fasta_iterator_single_header
+      iterator = BatchIterator.new(2)
+      data = %w(>h1 a b c d e)
+      mappings = []
+      out, _err = capture_io_while do
+        iterator.iterate(data.each) do |batch, batch_id, fasta_mapper|
+          assert(!fasta_mapper.nil?)
+          mappings << fasta_mapper
+          puts batch_id
+          puts batch.to_s
+        end
+      end
+      assert_equal(['0', '["a"]', '1', '["b", "c"]', '2', '["d", "e"]', ''].join("\n"), out)
+      mappings.flatten!(1)
+      data.shift
+      data.each { |element| assert(mappings.include?(['>h1', element])) }
+    end
+
+    def test_fasta_iterator_double_header_single_batch
+      iterator = BatchIterator.new(3)
+      data = %w(>h1 a >h2 b c d e)
+      mappings = []
+      out, _err = capture_io_while do
+        iterator.iterate(data.each) do |batch, batch_id, fasta_mapper|
+          assert(!fasta_mapper.nil?)
+          mappings << fasta_mapper
+          puts batch_id
+          puts batch.to_s
+        end
+      end
+      assert_equal(['0', '["a"]', '1', '["b", "c", "d"]', '2', '["e"]', ''].join("\n"), out)
+      mappings.flatten!(1)
+      assert(mappings.include?(['>h1', 'a']))
+      assert(mappings.include?(['>h2', 'b']))
+      assert(mappings.include?(['>h2', 'c']))
+      assert(mappings.include?(['>h2', 'd']))
+      assert(mappings.include?(['>h2', 'e']))
+    end
+
+    def test_fasta_iterator_multiple_values
+      iterator = BatchIterator.new(4)
+      data = %w(>h1 a >h2 a a)
+      mappings = []
+      out, _err = capture_io_while do
+        iterator.iterate(data.each) do |batch, batch_id, fasta_mapper|
+          assert(!fasta_mapper.nil?)
+          mappings << fasta_mapper
+          puts batch_id
+          puts batch.to_s
+        end
+      end
+      assert_equal(['0', '["a"]', '1', '["a"]', ''].join("\n"), out)
+      assert(mappings[0].include?(['>h1', 'a']))
+      assert(mappings[0].include?(['>h2', 'a']))
+      assert(mappings[1].include?(['>h2', 'a']))
+    end
+  end
+end

data/test/test_configuration.rb

@@ -0,0 +1,43 @@
+require_relative '../lib/configuration'
+
+module Unipept
+  class ConfigurationTestCase < Unipept::TestCase
+    def test_load_without_file
+      config = Configuration.new('no_file')
+      assert_equal({}, config.config)
+    end
+
+    def test_load_with_file
+      hash = { 'key' => 'value' }
+      File.open('new_file', 'w') { |f| f.write hash.to_yaml }
+      config = Configuration.new('new_file')
+      assert_equal(hash, config.config)
+    end
+
+    def test_save
+      file_name = 'no_file'
+      assert(!(File.exist? file_name))
+      config = Configuration.new(file_name)
+      config.config['key'] = 'value'
+      config.save
+      assert((File.exist? file_name))
+      other_config = Configuration.new(file_name)
+      assert_equal('value', other_config.config['key'])
+    end
+
+    def test_assign
+      config = Configuration.new('no_file')
+      config['key'] = 'value'
+      assert_equal('value', config.config['key'])
+      assert_equal('value', config['key'])
+    end
+
+    def test_delete
+      config = Configuration.new('no_file')
+      config['key'] = 'value'
+      assert_equal('value', config['key'])
+      config.delete('key')
+      assert_equal(nil, config['key'])
+    end
+  end
+end

data/test/test_formatters.rb

@@ -0,0 +1,140 @@
+require_relative '../lib/formatters'
+
+module Unipept
+  class FormattersTestCase < Unipept::TestCase
+    def test_available_formatters
+      formatters = Formatter.available
+      assert(formatters.include? 'json')
+      assert(formatters.include? 'csv')
+      assert(formatters.include? 'xml')
+    end
+
+    def test_default_formatter
+      assert_equal('csv', Formatter.default)
+    end
+
+    def test_formatter_registration
+      assert(!(Formatter.available.include? 'test'))
+      Formatter.register(:test)
+      assert(Formatter.available.include? 'test')
+    end
+
+    def test_new_for_format
+      formatter = Formatter.new_for_format('json')
+      assert_equal('json', formatter.type)
+
+      formatter = Formatter.new_for_format('xml')
+      assert_equal('xml', formatter.type)
+
+      formatter = Formatter.new_for_format('csv')
+      assert_equal('csv', formatter.type)
+
+      formatter = Formatter.new_for_format('blah')
+      assert_equal('csv', formatter.type)
+    end
+
+    def formatter
+      Formatter.new
+    end
+
+    def test_header
+      assert_equal('', formatter.header(TestObject.test_object))
+    end
+
+    def test_type
+      assert_equal('', formatter.type)
+    end
+
+    def test_format
+      assert_equal(TestObject.test_object, formatter.format(TestObject.test_object))
+    end
+  end
+
+  class JSONFormatterTestCase < Unipept::TestCase
+    def formatter
+      Formatter.new_for_format('json')
+    end
+
+    def test_header
+      assert_equal('', formatter.header(TestObject.test_object))
+    end
+
+    def test_type
+      assert_equal('json', formatter.type)
+    end
+
+    def test_format
+      assert_equal(TestObject.as_json, formatter.format(TestObject.test_object))
+    end
+  end
+
+  class CSVFormatterTestCase < Unipept::TestCase
+    def formatter
+      Formatter.new_for_format('csv')
+    end
+
+    def test_header
+      fasta = [['peptide', '>test']]
+      object = [TestObject.test_object, TestObject.test_object]
+      assert_equal(TestObject.as_csv_header, formatter.header(object))
+      assert_equal('fasta_header,' + TestObject.as_csv_header, formatter.header(object, fasta))
+    end
+
+    def test_type
+      assert_equal('csv', formatter.type)
+    end
+
+    def test_format
+      object = [TestObject.test_object, TestObject.test_object]
+      csv = [TestObject.as_csv, TestObject.as_csv, ''].join("\n")
+      assert_equal(csv, formatter.format(object))
+    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))
+    end
+  end
+
+  class XMLFormatterTestCase < Unipept::TestCase
+    def formatter
+      Formatter.new_for_format('xml')
+    end
+
+    def test_header
+      assert_equal('', formatter.header(TestObject.test_object))
+    end
+
+    def test_type
+      assert_equal('xml', formatter.type)
+    end
+
+    def test_format
+      assert_equal(TestObject.as_xml, formatter.format(TestObject.test_object))
+    end
+  end
+
+  class TestObject
+    def self.test_object
+      JSON.parse('{"integer": 5, "string": "string", "list": ["a", 2, false]}')
+    end
+
+    def self.as_json
+      '{"integer":5,"string":"string","list":["a",2,false]}'
+    end
+
+    def self.as_xml
+      '<integer>5</integer><string>string</string><list size="3"><item>a</item><item>2</item><item>false</item></list>'
+    end
+
+    def self.as_csv
+      '5,string,"[""a"", 2, false]"'
+    end
+
+    def self.as_csv_header
+      "integer,string,list\n"
+    end
+  end
+end

data/unipept.gemspec

@@ -2,16 +2,15 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 0.7.1 ruby lib
+# stub: unipept 0.8.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept"
-  s.version = "0.7.1"
+  s.version = "0.8.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.require_paths = ["lib"]
   s.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
-  s.date = "2015-05-20"
+  s.date = "2015-06-12"
   s.description = "  Command line interface to the Unipept (http://unipept.ugent.be) web services\n  (pept2lca, taxa2lca, pept2taxa and taxonomy) and some utility commands for\n  handling proteins using the command line.\n"
   s.email = "unipept@ugent.be"
   s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]
@@ -21,6 +20,8 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".document",
+    ".rubocop.yml",
+    ".travis.yml",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
@@ -31,26 +32,47 @@ Gem::Specification.new do |s|
     "bin/prot2pept",
     "bin/unipept",
     "bin/uniprot",
-    "lib/unipept.rb",
-    "lib/unipept/batch_order.rb",
-    "lib/unipept/commands.rb",
-    "lib/unipept/commands/api_runner.rb",
-    "lib/unipept/commands/pept2lca.rb",
-    "lib/unipept/commands/pept2prot.rb",
-    "lib/unipept/commands/pept2taxa.rb",
-    "lib/unipept/commands/taxa2lca.rb",
-    "lib/unipept/commands/taxonomy.rb",
-    "lib/unipept/configuration.rb",
-    "lib/unipept/formatters.rb",
-    "lib/unipept/version.rb",
+    "lib/batch_iterator.rb",
+    "lib/batch_order.rb",
+    "lib/commands.rb",
+    "lib/commands/peptfilter.rb",
+    "lib/commands/prot2pept.rb",
+    "lib/commands/unipept.rb",
+    "lib/commands/unipept/api_runner.rb",
+    "lib/commands/unipept/config.rb",
+    "lib/commands/unipept/pept2lca.rb",
+    "lib/commands/unipept/pept2prot.rb",
+    "lib/commands/unipept/pept2taxa.rb",
+    "lib/commands/unipept/taxa2lca.rb",
+    "lib/commands/unipept/taxonomy.rb",
+    "lib/commands/uniprot.rb",
+    "lib/configuration.rb",
+    "lib/formatters.rb",
+    "lib/version.rb",
+    "test/commands/test_peptfilter.rb",
+    "test/commands/test_prot2pept.rb",
+    "test/commands/test_unipept.rb",
+    "test/commands/test_uniprot.rb",
+    "test/commands/unipept/test_api_runner.rb",
+    "test/commands/unipept/test_config.rb",
+    "test/commands/unipept/test_pept2lca.rb",
+    "test/commands/unipept/test_pept2prot.rb",
+    "test/commands/unipept/test_pept2taxa.rb",
+    "test/commands/unipept/test_taxa2lca.rb",
+    "test/commands/unipept/test_taxonomy.rb",
     "test/helper.rb",
-    "test/test_unipept.rb",
+    "test/test_bach_order.rb",
+    "test/test_base.rb",
+    "test/test_batch_iterator.rb",
+    "test/test_configuration.rb",
+    "test/test_formatters.rb",
     "unipept.gemspec"
   ]
   s.homepage = "https://github.com/unipept/unipept-cli/"
   s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.3")
-  s.rubygems_version = "2.2.2"
+  s.rubygems_version = "2.1.11"
   s.summary = "Command line interface to Unipept web services."
 
   if s.respond_to? :specification_version then
@@ -59,28 +81,28 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<cri>, ["~> 2.7"])
       s.add_runtime_dependency(%q<typhoeus>, ["~> 0.6"])
-      s.add_development_dependency(%q<shoulda>, ["~> 3.5"])
-      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0"])
-      s.add_development_dependency(%q<jeweler>, ["~> 2.0"])
-      s.add_development_dependency(%q<simplecov>, ["~> 0.8"])
+      s.add_development_dependency(%q<rake>, [">= 0"])
+      s.add_development_dependency(%q<minitest>, [">= 0"])
+      s.add_development_dependency(%q<rubocop>, [">= 0"])
+      s.add_development_dependency(%q<jeweler>, [">= 0"])
+      s.add_development_dependency(%q<coveralls>, [">= 0"])
     else
       s.add_dependency(%q<cri>, ["~> 2.7"])
       s.add_dependency(%q<typhoeus>, ["~> 0.6"])
-      s.add_dependency(%q<shoulda>, ["~> 3.5"])
-      s.add_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_dependency(%q<bundler>, ["~> 1.0"])
-      s.add_dependency(%q<jeweler>, ["~> 2.0"])
-      s.add_dependency(%q<simplecov>, ["~> 0.8"])
+      s.add_dependency(%q<rake>, [">= 0"])
+      s.add_dependency(%q<minitest>, [">= 0"])
+      s.add_dependency(%q<rubocop>, [">= 0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
+      s.add_dependency(%q<coveralls>, [">= 0"])
     end
   else
     s.add_dependency(%q<cri>, ["~> 2.7"])
     s.add_dependency(%q<typhoeus>, ["~> 0.6"])
-    s.add_dependency(%q<shoulda>, ["~> 3.5"])
-    s.add_dependency(%q<rdoc>, ["~> 3.12"])
-    s.add_dependency(%q<bundler>, ["~> 1.0"])
-    s.add_dependency(%q<jeweler>, ["~> 2.0"])
-    s.add_dependency(%q<simplecov>, ["~> 0.8"])
+    s.add_dependency(%q<rake>, [">= 0"])
+    s.add_dependency(%q<minitest>, [">= 0"])
+    s.add_dependency(%q<rubocop>, [">= 0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
+    s.add_dependency(%q<coveralls>, [">= 0"])
   end
 end