unipept 1.1.2 → 1.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f1754c5a267fc5f4693eac69a39829976faf9ef2
-  data.tar.gz: 51466d18f6e9938285c3a6f9c0ff792744a37f67
+  metadata.gz: 17fb4ae25816764349c1961d48289be0841b3e6a
+  data.tar.gz: b484dc7db887da7172d408c75611083914d34049
 SHA512:
-  metadata.gz: df489439d29c756b4694d400ab23770fef551e5368023c2cd626e3c0eceaef377c1d46b4bfe912a157efc1d88f92fb8a3bef3938c3726176a57dc6933fcab1f9
-  data.tar.gz: 3cf20e18248e59b2f1f777b69ca022da8b83b2964fa9ea06301e77ca6946507a53043472156e44cce5e8a6e861b292b3e1558e65b7a9a17265adff407f500a38
+  metadata.gz: b4066aae51893a28a45fcaccb77f847c41ab39d8fa997e7445a16683904a9270a9b663e01e99860c0d65c5dd08cf941ce8d938081e252d677d6c9512d0ecd2b7
+  data.tar.gz: ef1144113dc60261e27b23d90c351f59410bdb7701203b81309e37d2e72aa21f1c7e8c663ef3488d019d9cab763f14b7da437a8a49a2cb034b271490728d084c

data/.rubocop.yml

@@ -8,6 +8,8 @@ AllCops:
 Style/ClassAndModuleChildren:
   EnforcedStyle: compact
   Enabled: false
+Style/FrozenStringLiteralComment:
+  Enabled: false
 
 # disable for now
 Lint/NestedMethodDefinition:
@@ -26,3 +28,5 @@ Metrics/LineLength:
   Enabled: false
 Metrics/MethodLength:
   Enabled: false
+Metrics/BlockLength:
+  Enabled: false

data/.ruby-version

@@ -0,0 +1 @@
+2.4.0

data/.travis.yml

@@ -1,9 +1,13 @@
 language: ruby
 rvm:
+  - 2.4.0
   - 2.3.3
-  - 2.2.5
+  - 2.2.6
   - 2.1.9
   - 2.0.0
 
+install:
+  - bundle install --without release
+
 notifications:
   slack: zeuswpi:yBidVPnaP2JuP2zfa36Ew0E1

data/Gemfile

@@ -2,14 +2,16 @@ source 'http://rubygems.org'
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
-
 gem 'cri', '~> 2.7'
-gem 'typhoeus', '0.7.2'
+gem 'typhoeus', '~> 1.1'
 
 group :development do
   gem 'rake', '~> 10.4'
   gem 'minitest', '~> 5.7'
   gem 'rubocop', '~>0.32'
-  gem 'jeweler', '~> 2.0'
   gem 'coveralls', '~> 0', require: false
 end
+
+group :release do
+  gem 'jeweler'
+end

data/Gemfile.lock

@@ -1,103 +1,94 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    addressable (2.3.8)
-    ast (2.0.0)
-    astrolabe (1.3.0)
-      parser (>= 2.2.0.pre.3, < 3.0)
-    builder (3.2.2)
+    addressable (2.5.0)
+      public_suffix (~> 2.0, >= 2.0.2)
+    ast (2.3.0)
+    builder (3.2.3)
     colored (1.2)
-    coveralls (0.8.2)
-      json (~> 1.8)
-      rest-client (>= 1.6.8, < 2)
-      simplecov (~> 0.10.0)
+    coveralls (0.8.18)
+      json (>= 1.8, < 3)
+      simplecov (~> 0.12.0)
       term-ansicolor (~> 1.3)
       thor (~> 0.19.1)
-    cri (2.7.0)
+      tins (~> 1.6)
+    cri (2.7.1)
       colored (~> 1.2)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
     docile (1.1.5)
-    domain_name (0.5.24)
-      unf (>= 0.0.5, < 1.0.0)
-    ethon (0.7.4)
+    ethon (0.10.1)
       ffi (>= 1.3.0)
-    faraday (0.9.1)
+    faraday (0.9.2)
       multipart-post (>= 1.2, < 3)
-    ffi (1.9.10)
-    git (1.2.9.1)
-    github_api (0.12.3)
+    ffi (1.9.17)
+    git (1.3.0)
+    github_api (0.11.3)
       addressable (~> 2.3)
-      descendants_tracker (~> 0.0.4)
+      descendants_tracker (~> 0.0.1)
       faraday (~> 0.8, < 0.10)
-      hashie (>= 3.3)
+      hashie (>= 1.2)
       multi_json (>= 1.7.5, < 2.0)
-      nokogiri (~> 1.6.3)
+      nokogiri (~> 1.6.0)
       oauth2
-    hashie (3.4.2)
-    highline (1.7.2)
-    http-cookie (1.0.2)
-      domain_name (~> 0.5)
-    jeweler (2.0.1)
+    hashie (3.4.6)
+    highline (1.7.8)
+    jeweler (2.3.2)
       builder
       bundler (>= 1.0)
       git (>= 1.2.5)
-      github_api
+      github_api (~> 0.11.0)
       highline (>= 1.6.15)
       nokogiri (>= 1.5.10)
+      psych (~> 2.2)
       rake
       rdoc
-    json (1.8.3)
-    jwt (1.5.1)
-    mime-types (2.6.1)
-    mini_portile (0.6.2)
-    minitest (5.7.0)
-    multi_json (1.11.1)
-    multi_xml (0.5.5)
+      semver2
+    json (2.0.3)
+    jwt (1.5.6)
+    mini_portile2 (2.1.0)
+    minitest (5.10.1)
+    multi_json (1.12.1)
+    multi_xml (0.6.0)
     multipart-post (2.0.0)
-    netrc (0.10.3)
-    nokogiri (1.6.6.2)
-      mini_portile (~> 0.6.0)
-    oauth2 (1.0.0)
-      faraday (>= 0.8, < 0.10)
+    nokogiri (1.6.8.1)
+      mini_portile2 (~> 2.1.0)
+    oauth2 (1.3.0)
+      faraday (>= 0.8, < 0.11)
       jwt (~> 1.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
-      rack (~> 1.2)
-    parser (2.3.0.pre.2)
-      ast (>= 1.1, < 3.0)
+      rack (>= 1.2, < 3)
+    parser (2.3.3.1)
+      ast (~> 2.2)
     powerpack (0.1.1)
-    rack (1.6.4)
-    rainbow (2.0.0)
-    rake (10.4.2)
-    rdoc (4.2.0)
-      json (~> 1.4)
-    rest-client (1.8.0)
-      http-cookie (>= 1.0.2, < 2.0)
-      mime-types (>= 1.16, < 3.0)
-      netrc (~> 0.7)
-    rubocop (0.32.1)
-      astrolabe (~> 1.3)
-      parser (>= 2.2.2.5, < 3.0)
+    psych (2.2.2)
+    public_suffix (2.0.5)
+    rack (2.0.1)
+    rainbow (2.2.1)
+    rake (10.5.0)
+    rdoc (5.0.0)
+    rubocop (0.47.0)
+      parser (>= 2.3.3.1, < 3.0)
       powerpack (~> 0.1)
       rainbow (>= 1.99.1, < 3.0)
-      ruby-progressbar (~> 1.4)
-    ruby-progressbar (1.7.5)
-    simplecov (0.10.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (~> 1.0, >= 1.0.1)
+    ruby-progressbar (1.8.1)
+    semver2 (3.4.2)
+    simplecov (0.12.0)
       docile (~> 1.1.0)
-      json (~> 1.8)
+      json (>= 1.8, < 3)
       simplecov-html (~> 0.10.0)
     simplecov-html (0.10.0)
-    term-ansicolor (1.3.2)
+    term-ansicolor (1.4.0)
       tins (~> 1.0)
-    thor (0.19.1)
+    thor (0.19.4)
     thread_safe (0.3.5)
-    tins (1.5.4)
-    typhoeus (0.7.2)
-      ethon (>= 0.7.4)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.7.1)
+    tins (1.13.0)
+    typhoeus (1.1.2)
+      ethon (>= 0.9.0)
+    unicode-display_width (1.1.3)
 
 PLATFORMS
   ruby
@@ -105,11 +96,11 @@ PLATFORMS
 DEPENDENCIES
   coveralls (~> 0)
   cri (~> 2.7)
-  jeweler (~> 2.0)
+  jeweler
   minitest (~> 5.7)
   rake (~> 10.4)
   rubocop (~> 0.32)
-  typhoeus (= 0.7.2)
+  typhoeus (~> 1.1)
 
 BUNDLED WITH
-   1.10.3
+   1.13.7

data/Rakefile

@@ -12,25 +12,28 @@ end
 require 'rake'
 require 'rake/testtask'
 require 'rubocop/rake_task'
-
-require 'jeweler'
-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.homepage = 'http://unipept.ugent.be'
-  gem.license = 'MIT'
-  gem.summary = 'Command line interface to Unipept web services.'
-  gem.description = <<-EOS
-  Command line interface to the Unipept (http://unipept.ugent.be) web services
-  (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
-  commands for handling proteins using the command line.
-  EOS
-  gem.email = 'unipept@ugent.be'
-  gem.authors = ['Toon Willems', 'Bart Mesuere', 'Tom Naessens']
-  gem.required_ruby_version = '>= 2.0.0'
+begin
+  require 'jeweler'
+  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.homepage = 'http://unipept.ugent.be'
+    gem.license = 'MIT'
+    gem.summary = 'Command line interface to Unipept web services.'
+    gem.description = <<-EOS
+    Command line interface to the Unipept (http://unipept.ugent.be) web services
+    (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
+    commands for handling proteins using the command line.
+    EOS
+    gem.email = 'unipept@ugent.be'
+    gem.authors = ['Toon Willems', 'Bart Mesuere', 'Tom Naessens']
+    gem.required_ruby_version = '>= 2.0.0'
+  end
+  Jeweler::RubygemsDotOrgTasks.new
+rescue LoadError
+# do nothing
 end
-Jeweler::RubygemsDotOrgTasks.new
 
 task :test_unit do
   require './test/helper.rb'

data/VERSION

@@ -1 +1 @@
-1.1.2
+1.1.3

data/lib/batch_iterator.rb

@@ -39,7 +39,7 @@ module Unipept
     # Splits the input lines in fasta format into slices, based on the
     # batch_size of the current command. Executes the given block for each of
     # the batches.
-    def fasta_iterator(first_line, next_lines, &block)
+    def fasta_iterator(first_line, next_lines)
       current_fasta_header = first_line.chomp
       next_lines.each_slice(batch_size).with_index do |slice, i|
         fasta_mapper = []
@@ -55,7 +55,7 @@ module Unipept
           end
         end
 
-        block.call(input_set.to_a, i, fasta_mapper)
+        yield(input_set.to_a, i, fasta_mapper)
       end
     end
 

data/lib/commands/peptfilter.rb

@@ -98,7 +98,7 @@ module Unipept::Commands
     #
     # @return [Boolean] true if the peptide satisfies all requirements
     def self.filter_lacks(peptide, lacks)
-      (peptide.chars.to_a & lacks).size == 0
+      (peptide.chars.to_a & lacks).empty?
     end
 
     # Checks if a peptide satisfies the contains requirement.

data/lib/commands/unipept/api_runner.rb

@@ -25,7 +25,7 @@ module Unipept
       host = 'http://api.unipept.ugent.be' if host.nil? || host.empty?
 
       # add http:// if needed
-      if host.start_with?('http://') || host.start_with?('https://')
+      if host.start_with?('http://', 'https://')
         host
       else
         "http://#{host}"
@@ -48,7 +48,7 @@ module Unipept
 
     # Returns the default default_batch_size of a command.
     def default_batch_size
-      fail NotImplementedError, 'This must be implemented in a subclass.'
+      raise NotImplementedError, 'This must be implemented in a subclass.'
     end
 
     # returns the effective batch_size of a command
@@ -102,8 +102,7 @@ module Unipept
       { input: input,
         equate_il: options[:equate] == true,
         extra: options[:all] == true,
-        names: options[:all] == true && names
-      }
+        names: options[:all] == true && names }
     end
 
     # Runs the command
@@ -114,7 +113,7 @@ module Unipept
       last_id = 0
 
       batch_iterator.iterate(input_iterator) do |input_slice, batch_id, fasta_mapper|
-        last_id =  batch_id
+        last_id = batch_id
         request = ::RetryableTyphoeus::Request.new(
           @url,
           method: :post,
@@ -129,7 +128,7 @@ module Unipept
         end
 
         hydra.queue request
-        hydra.run if batch_id % queue_size == 0
+        hydra.run if (batch_id % queue_size).zero?
       end
 
       hydra.run
@@ -166,8 +165,8 @@ module Unipept
 
       lambda do
         unless result.empty?
-          output_writer.write_line formatter.header(result, fasta_mapper) if batch_id == 0
-          output_writer.write_line formatter.format(result, fasta_mapper, batch_id == 0)
+          output_writer.write_line formatter.header(result, fasta_mapper) if batch_id.zero?
+          output_writer.write_line formatter.format(result, fasta_mapper, batch_id.zero?)
         end
       end
     end
@@ -175,7 +174,7 @@ module Unipept
     def handle_failed_response(response)
       if response.timed_out?
         -> { save_error('request timed out, continuing anyway, but results might be incomplete') }
-      elsif response.code == 0
+      elsif response.code.zero?
         -> { save_error('could not get an http response, continuing anyway, but results might be incomplete' + response.return_message) }
       else
         -> { save_error("Got #{response.code}: #{response.response_body}\nRequest headers: #{response.request.options}\nRequest body:\n#{response.request.encoded_body}\n\n") }

data/lib/commands/unipept/config.rb

@@ -1,7 +1,7 @@
 module Unipept
   class Commands::Config < Cri::CommandRunner
     def run
-      abort command.help if arguments.size == 0 || arguments.size > 2
+      abort command.help if arguments.empty? || arguments.size > 2
 
       key, value = *arguments
 

data/lib/commands/unipept/taxa2lca.rb

@@ -6,13 +6,13 @@ module Unipept::Commands
     end
 
     def default_batch_size
-      fail 'NOT NEEDED FOR TAXA2LCA'
+      raise 'NOT NEEDED FOR TAXA2LCA'
     end
   end
 
   class SimpleBatchIterator
-    def iterate(input, &block)
-      block.call(input.to_a, 0)
+    def iterate(input)
+      yield(input.to_a, 0)
     end
   end
 end

data/lib/configuration.rb

@@ -14,11 +14,11 @@ module Unipept
     # config from
     def initialize(file = nil)
       @file_name = file ? file : File.join(Dir.home, '.unipeptrc')
-      if !File.exist? file_name
-        @config = {}
-      else
-        @config = YAML.load_file file_name
-      end
+      @config = if !File.exist? file_name
+                  {}
+                else
+                  YAML.load_file file_name
+                end
     end
 
     # Saves the config to disk. If the file doesn't exist yet, a new one will be

data/lib/formatters.rb

@@ -42,7 +42,7 @@ module Unipept
 
     # @return [String] The type of the current formatter
     def type
-      fail NotImplementedError, 'This must be implemented in a subclass.'
+      raise NotImplementedError, 'This must be implemented in a subclass.'
     end
 
     # Returns the header row for the given sample_data and fasta_mapper. This
@@ -58,7 +58,7 @@ module Unipept
     #
     # @return [String] The header row
     def header(_sample_data, _fasta_mapper = nil)
-      fail NotImplementedError, 'This must be implemented in a subclass.'
+      raise NotImplementedError, 'This must be implemented in a subclass.'
     end
 
     # Returns the footer row. This row is output only once at the end of the
@@ -66,7 +66,7 @@ module Unipept
     #
     # @return [String] The footer row
     def footer
-      fail NotImplementedError, 'This must be implemented in a subclass.'
+      raise NotImplementedError, 'This must be implemented in a subclass.'
     end
 
     # Converts the given input data and corresponding fasta headers to another
@@ -82,7 +82,7 @@ module Unipept
     # @param [Boolean] Is this the first output batch?
     #
     # @return [String] The converted input data
-    def format(data, fasta_mapper = nil, first)
+    def format(data, fasta_mapper, first)
       data = integrate_fasta_headers(data, fasta_mapper) if fasta_mapper
       convert(data, first)
     end
@@ -95,7 +95,7 @@ module Unipept
     #
     # @return [String] The converted input data
     def convert(_data, _first)
-      fail NotImplementedError, 'This must be implemented in a subclass.'
+      raise NotImplementedError, 'This must be implemented in a subclass.'
     end
 
     # Integrates the fasta headers into the data object