unipept 1.4.0 → 1.4.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: d137e5780251e56b16096d349763e2dad61072aec9986f5e739d81a15c329245
+  metadata.gz: 773e25ed2369843012700a657100181e84254c905365d534136d0c1a68606ab7
+  data.tar.gz: 78830dfab3cab145cf248b2bc41d65806a3a4274ab1d48b9be1d530c7f2eb865
 SHA512:
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-  data.tar.gz: ae2c359ba6591a83c00cd25b77ed741964f06ffc17f458a3541d3279ffc421fc2f28b00dc1f5f3fc5f20560792f03c87f3c2a221dab00e4e468f2ecbb42f45ee
+  metadata.gz: 55648c665eadd51c119e4091a3e8e110189df97ac70eeceee0a9a508e8b7112cd522dbec23ae55c1172e061b95b192cc383190640ec68dbd316273510640b598
+  data.tar.gz: fdcf5b35931caee76a3acfa6a8be7828f902570e9b6669f4d184b55321dcd0177d9bd363214f4d2b4766b13010eebe15e7e1beed549b4b864a95f71684a178ae

data/.rubocop.yml

@@ -1,9 +1,8 @@
 AllCops:
-  Include:
-    - ''
   Exclude:
     - 'unipept.gemspec'
     - 'vendor/**/*'
+    - 'Rakefile'
 
 Style/ClassAndModuleChildren:
   EnforcedStyle: compact
@@ -30,3 +29,7 @@ Metrics/MethodLength:
   Enabled: false
 Metrics/BlockLength:
   Enabled: false
+Naming/HeredocDelimiterNaming:
+  Enabled: false
+Naming/UncommunicativeMethodParamName:
+  Enabled: false

data/.travis.yml

@@ -1,10 +1,9 @@
 language: ruby
 rvm:
-  - 2.4.0
-  - 2.3.3
-  - 2.2.6
-  - 2.1.9
-  - 2.0.0
+  - 2.6.0
+  - 2.5.3
+  - 2.4.4
+  - 2.3.7
 
 install:
   - gem update --system

data/Gemfile

@@ -3,15 +3,14 @@ source 'http://rubygems.org'
 # Example:
 #   gem "activesupport", ">= 2.3.5"
 
-# for now, stay on version 2.11 because of a bug
-gem 'cri', '2.11'
+gem 'cri', '~>2.15.3'
 gem 'typhoeus', '~> 1.1'
 
 group :development do
-  gem 'rake', '~> 10.4'
+  gem 'coveralls', '~> 0', require: false
   gem 'minitest', '~> 5.7'
+  gem 'rake', '~> 10.4'
   gem 'rubocop', '~>0.32'
-  gem 'coveralls', '~> 0', require: false
 end
 
 group :release do

data/Gemfile.lock

@@ -11,7 +11,7 @@ GEM
       term-ansicolor (~> 1.3)
       thor (~> 0.19.4)
       tins (~> 1.6)
-    cri (2.11.0)
+    cri (2.15.3)
       colored (~> 1.2)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
@@ -97,7 +97,7 @@ PLATFORMS
 
 DEPENDENCIES
   coveralls (~> 0)
-  cri (= 2.11)
+  cri (~> 2.15.3)
   jeweler
   minitest (~> 5.7)
   rake (~> 10.4)

data/Rakefile

@@ -1,12 +1,10 @@
-# encoding: utf-8
-
 require 'rubygems'
 require 'bundler'
 begin
   Bundler.setup(:default, :development)
 rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts 'Run `bundle install` to install missing gems'
+  warn e.message
+  warn 'Run `bundle install` to install missing gems'
   exit e.status_code
 end
 require 'rake'
@@ -17,7 +15,7 @@ begin
   Jeweler::Tasks.new do |gem|
     # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
     gem.name = 'unipept'
-    gem.executables = %w(unipept prot2pept peptfilter uniprot)
+    gem.executables = %w[unipept prot2pept peptfilter uniprot]
     gem.homepage = 'http://unipept.ugent.be'
     gem.license = 'MIT'
     gem.summary = 'Command line interface to Unipept web services.'
@@ -32,7 +30,7 @@ begin
   end
   Jeweler::RubygemsDotOrgTasks.new
 rescue LoadError
-# do nothing
+  # do nothing
 end
 
 task :test_unit do
@@ -45,7 +43,7 @@ end
 
 RuboCop::RakeTask.new(:test_style)
 
-task test: [:test_unit, :test_style]
+task test: %i[test_unit test_style]
 
 task default: :test
 

data/VERSION

@@ -1 +1 @@
-1.4.0
+1.4.1

data/lib/batch_order.rb

@@ -11,6 +11,7 @@ module Unipept
     def wait(i, &block)
       @order[i] = block
       return unless i == @current
+
       while order[@current]
         order.delete(@current).call
         @current += 1

data/lib/commands/unipept/api_runner.rb

@@ -22,7 +22,7 @@ module Unipept
     # file, the value of the option is used.
     def host
       # find host in opts first
-      host = options[:host] ? options[:host] : @configuration['host']
+      host = options[:host] || @configuration['host']
       host = 'http://api.unipept.ugent.be' if host.nil? || host.empty?
 
       # add http:// if needed
@@ -40,6 +40,7 @@ module Unipept
     def input_iterator
       return arguments.each unless arguments.empty?
       return IO.foreach(options[:input]) if options[:input]
+
       $stdin.each_line
     end
 
@@ -86,6 +87,7 @@ module Unipept
     # Returns an array of regular expressions containing all the selected fields
     def selected_fields
       return @selected_fields unless @selected_fields.nil?
+
       fields = [*options[:select]].map { |f| f.split(',') }.flatten
       fields.concat(required_fields) if @fasta && !fields.empty?
       @selected_fields = fields.map { |f| glob_to_regex(f) }
@@ -143,7 +145,7 @@ module Unipept
       path = error_file_path
       FileUtils.mkdir_p File.dirname(path)
       File.open(path, 'w') { |f| f.write message }
-      $stderr.puts "API request failed! log can be found in #{path}"
+      warn "API request failed! log can be found in #{path}"
     end
 
     private

data/lib/commands/uniprot.rb

@@ -5,7 +5,7 @@ module Unipept::Commands
     attr_reader :root_command
     attr_reader :valid_formats
 
-    valid_formats = Set.new %w(fasta txt xml rdf gff sequence)
+    valid_formats = Set.new %w[fasta txt xml rdf gff sequence]
     @root_command = Cri::Command.define do
       name 'uniprot'
       summary 'Command line interface to UniProt web services.'
@@ -29,7 +29,7 @@ module Unipept::Commands
       run do |opts, args, _cmd|
         format = opts.fetch(:format, 'sequence')
         unless valid_formats.include? format
-          $stderr.puts format + ' is not a valid output format. Available formats are: ' + valid_formats.to_a.join(', ')
+          warn format + ' is not a valid output format. Available formats are: ' + valid_formats.to_a.join(', ')
           exit 1
         end
         iterator = args.empty? ? $stdin.each_line : args

data/lib/configuration.rb

@@ -13,7 +13,7 @@ module Unipept
     # @param [String] file An optional file name of the YAML file to create the
     # config from
     def initialize(file = nil)
-      @file_name = file ? file : File.join(Dir.home, '.unipeptrc')
+      @file_name = file || File.join(Dir.home, '.unipeptrc')
       @config = if !File.exist? file_name
                   {}
                 else

data/lib/formatters.rb

@@ -17,7 +17,7 @@ module Unipept
     # @return [Formatter] The requested formatter
     def self.new_for_format(format)
       formatters[format].new
-    rescue
+    rescue StandardError
       formatters[default].new
     end
 
@@ -32,7 +32,7 @@ module Unipept
     #
     # @return [Array<String>] The list of available formatters
     def self.available
-      formatters.select { |_key, value| !value.hidden? }.keys
+      formatters.reject { |_key, value| value.hidden? }.keys
     end
 
     # @return [String] The type of the default formatter: csv

data/lib/server_message.rb

@@ -19,6 +19,7 @@ module Unipept
     def print
       return unless $stdout.tty?
       return if recently_fetched?
+
       resp = fetch_server_message
       update_fetched
       puts resp unless resp.empty?

data/test/commands/test_peptfilter.rb

@@ -39,114 +39,114 @@ module Unipept
 
     def test_default_min_length_argument
       out, _err = capture_io_with_input('A' * 6) do
-        Commands::Peptfilter.run(%w())
+        Commands::Peptfilter.run(%w[])
       end
       assert_equal('A' * 6, out.chomp)
 
       out, _err = capture_io_with_input('A' * 5) do
-        Commands::Peptfilter.run(%w())
+        Commands::Peptfilter.run(%w[])
       end
       assert_equal('A' * 5, out.chomp)
 
       out, _err = capture_io_with_input('A' * 4) do
-        Commands::Peptfilter.run(%w())
+        Commands::Peptfilter.run(%w[])
       end
       assert_equal('', out.chomp)
     end
 
     def test_default_max_length_argument
       out, _err = capture_io_with_input('A' * 49) do
-        Commands::Peptfilter.run(%w())
+        Commands::Peptfilter.run(%w[])
       end
       assert_equal('A' * 49, out.chomp)
 
       out, _err = capture_io_with_input('A' * 50) do
-        Commands::Peptfilter.run(%w())
+        Commands::Peptfilter.run(%w[])
       end
       assert_equal('A' * 50, out.chomp)
 
       out, _err = capture_io_with_input('A' * 51) do
-        Commands::Peptfilter.run(%w())
+        Commands::Peptfilter.run(%w[])
       end
       assert_equal('', out.chomp)
     end
 
     def test_with_min_argument
       out, _err = capture_io_with_input('A' * 6) do
-        Commands::Peptfilter.run(%w(--minlen 7))
+        Commands::Peptfilter.run(%w[--minlen 7])
       end
       assert_equal('', out.chomp)
 
       out, _err = capture_io_with_input('A' * 4) do
-        Commands::Peptfilter.run(%w(--minlen 3))
+        Commands::Peptfilter.run(%w[--minlen 3])
       end
       assert_equal('A' * 4, out.chomp)
     end
 
     def test_with_max_argument
       out, _err = capture_io_with_input('A' * 45) do
-        Commands::Peptfilter.run(%w(--maxlen 40))
+        Commands::Peptfilter.run(%w[--maxlen 40])
       end
       assert_equal('', out.chomp)
 
       out, _err = capture_io_with_input('A' * 55) do
-        Commands::Peptfilter.run(%w(--maxlen 60))
+        Commands::Peptfilter.run(%w[--maxlen 60])
       end
       assert_equal('A' * 55, out.chomp)
     end
 
     def test_with_lacks_argument
       out, _err = capture_io_with_input('A' * 10) do
-        Commands::Peptfilter.run(%w(--lacks B))
+        Commands::Peptfilter.run(%w[--lacks B])
       end
       assert_equal('A' * 10, out.chomp)
 
       out, _err = capture_io_with_input('A' * 10) do
-        Commands::Peptfilter.run(%w(-l B))
+        Commands::Peptfilter.run(%w[-l B])
       end
       assert_equal('A' * 10, out.chomp)
 
       out, _err = capture_io_with_input('A' * 10) do
-        Commands::Peptfilter.run(%w(--lacks A))
+        Commands::Peptfilter.run(%w[--lacks A])
       end
       assert_equal('', out.chomp)
 
       out, _err = capture_io_with_input('A' * 10) do
-        Commands::Peptfilter.run(%w(-l A))
+        Commands::Peptfilter.run(%w[-l A])
       end
       assert_equal('', out.chomp)
     end
 
     def test_with_contains_argument
       out, _err = capture_io_with_input('A' * 10) do
-        Commands::Peptfilter.run(%w(--contains A))
+        Commands::Peptfilter.run(%w[--contains A])
       end
       assert_equal('A' * 10, out.chomp)
 
       out, _err = capture_io_with_input('A' * 10) do
-        Commands::Peptfilter.run(%w(-c A))
+        Commands::Peptfilter.run(%w[-c A])
       end
       assert_equal('A' * 10, out.chomp)
 
       out, _err = capture_io_with_input('A' * 10) do
-        Commands::Peptfilter.run(%w(--contains B))
+        Commands::Peptfilter.run(%w[--contains B])
       end
       assert_equal('', out.chomp)
 
       out, _err = capture_io_with_input('A' * 10) do
-        Commands::Peptfilter.run(%w(-c B))
+        Commands::Peptfilter.run(%w[-c B])
       end
       assert_equal('', out.chomp)
     end
 
     def test_fasta_input
       out, _err = capture_io_with_input('>') do
-        Commands::Peptfilter.run(%w())
+        Commands::Peptfilter.run(%w[])
       end
       assert_equal('>', out.chomp)
 
       out, _err = capture_io_with_input(['>', 'A', 'AALTER', '>']) do
-        Commands::Peptfilter.run(%w())
+        Commands::Peptfilter.run(%w[])
       end
       assert_equal(">\nAALTER\n>", out.chomp)
     end
@@ -154,7 +154,7 @@ module Unipept
     def test_no_input
       out, err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Peptfilter.run(%w(some argument))
+          Commands::Peptfilter.run(%w[some argument])
         end
       end
       assert_equal('', out.chomp)
@@ -163,7 +163,7 @@ module Unipept
 
     def test_normal_input
       out, _err = capture_io_with_input(['A', 'A' * 11, 'AAAAB', 'BBBBB', 'CCCCC', 'CCCCCA']) do
-        Commands::Peptfilter.run(%w(--minlen 4 --maxlen 10 --lacks B --contains A))
+        Commands::Peptfilter.run(%w[--minlen 4 --maxlen 10 --lacks B --contains A])
       end
       assert_equal('CCCCCA', out.chomp)
     end
@@ -171,7 +171,7 @@ module Unipept
     def test_help
       out, _err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Peptfilter.run(%w(-h))
+          Commands::Peptfilter.run(%w[-h])
         end
       end
       assert(out.include?('show help for this command'))

data/test/commands/test_prot2pept.rb

@@ -4,46 +4,46 @@ module Unipept
   class Prot2peptTestCase < Unipept::TestCase
     def test_normal_input
       out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
-        Commands::Prot2pept.run(%w())
+        Commands::Prot2pept.run(%w[])
       end
       assert_equal("AALTER\nAALTERPAALTER", out.chomp)
 
       out, _err = capture_io_with_input('AALTERAAL*TERPAALTER') do
-        Commands::Prot2pept.run(%w())
+        Commands::Prot2pept.run(%w[])
       end
       assert_equal("AALTER\nAAL\nTERPAALTER", out.chomp)
 
       out, _err = capture_io_with_input('KRKPR') do
-        Commands::Prot2pept.run(%w())
+        Commands::Prot2pept.run(%w[])
       end
       assert_equal("K\nR\nKPR", out.chomp)
 
-      out, _err = capture_io_with_input(%w(AALTERAALTERPAALTER AALTERAA)) do
-        Commands::Prot2pept.run(%w())
+      out, _err = capture_io_with_input(%w[AALTERAALTERPAALTER AALTERAA]) do
+        Commands::Prot2pept.run(%w[])
       end
       assert_equal("AALTER\nAALTERPAALTER\nAALTER\nAA", out.chomp)
     end
 
     def test_fasta_input
       out, _err = capture_io_with_input(">AKA\nAALTERAALTERPAALTER") do
-        Commands::Prot2pept.run(%w())
+        Commands::Prot2pept.run(%w[])
       end
       assert_equal(">AKA\nAALTER\nAALTERPAALTER", out.chomp)
 
       out, _err = capture_io_with_input(">AKA\nAAL\nT\nERAALTER\nP\nAALTER") do
-        Commands::Prot2pept.run(%w())
+        Commands::Prot2pept.run(%w[])
       end
       assert_equal(">AKA\nAALTER\nAALTERPAALTER", out.chomp)
 
       out, _err = capture_io_with_input(">AKA\nAAL\nT\n>\nERAALTER\nP\nAALTER") do
-        Commands::Prot2pept.run(%w())
+        Commands::Prot2pept.run(%w[])
       end
       assert_equal(">AKA\nAALT\n>\nER\nAALTERPAALTER", out.chomp)
     end
 
     def test_default_pattern
       default_out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
-        Commands::Prot2pept.run(%w())
+        Commands::Prot2pept.run(%w[])
       end
       assert_equal("AALTER\nAALTERPAALTER", default_out.chomp)
 
@@ -60,7 +60,7 @@ module Unipept
 
     def test_pattern
       out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
-        Commands::Prot2pept.run(%w())
+        Commands::Prot2pept.run(%w[])
       end
       assert_equal("AALTER\nAALTERPAALTER", out.chomp)
 
@@ -78,7 +78,7 @@ module Unipept
     def test_help
       out, _err = capture_io_while do
         assert_raises SystemExit do
-          Commands::Prot2pept.run(%w(-h))
+          Commands::Prot2pept.run(%w[-h])
         end
       end
       assert(out.include?('show help for this command'))