unipept 0.9.0 → 0.10.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: d0d6b1577ca3e5ddc30d334ef0f5cc1500a1b482
+  metadata.gz: 662aed8d64c58c637883ff112a3f7be5a8ea05b1
+  data.tar.gz: 52842a660a7dfe19c47403b7d1b4a83cc5d29525
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+  data.tar.gz: 7559ef5e0dbedf38cac9d0186289ffb8cd6672b131d84fa13389a09f9c1a41003164f949ef40852475479e84e49868dab618bcd0f2280514103fb1f594b9dc83

data/.rubocop.yml

@@ -1,6 +1,6 @@
 AllCops:
   Include:
-    -
+    - ''
   Exclude:
     - 'unipept.gemspec'
     - 'vendor/**/*'
@@ -10,6 +10,8 @@ Style/ClassAndModuleChildren:
   Enabled: false
 
 # disable for now
+Lint/NestedMethodDefinition:
+  Enabled: false
 Style/ClassVars:
   Enabled: false
 Style/Documentation:

data/.travis.yml

@@ -4,6 +4,6 @@ rvm:
   - 2.1.6
   - 2.0.0
   - 1.9.3
-  - jruby-19mode
+#  - jruby-19mode
 notifications:
   slack: zeuswpi:yBidVPnaP2JuP2zfa36Ew0E1

data/Gemfile

@@ -4,12 +4,12 @@ source 'http://rubygems.org'
 #   gem "activesupport", ">= 2.3.5"
 
 gem 'cri', '~> 2.7'
-gem 'typhoeus', '~> 0.6'
+gem 'typhoeus', '0.7.2'
 
 group :development do
-  gem 'rake'
-  gem 'minitest'
-  gem 'rubocop'
-  gem 'jeweler'
+  gem 'rake', '~> 10.4'
+  gem 'minitest', '~> 5.7'
+  gem 'rubocop', '~>0.32'
+  gem 'jeweler', '~> 2.0'
   gem 'coveralls', require: false
 end

data/Gemfile.lock

@@ -7,22 +7,24 @@ GEM
       parser (>= 2.2.0.pre.3, < 3.0)
     builder (3.2.2)
     colored (1.2)
-    coveralls (0.7.1)
-      multi_json (~> 1.3)
-      rest-client
-      simplecov (>= 0.7)
-      term-ansicolor
-      thor
+    coveralls (0.8.2)
+      json (~> 1.8)
+      rest-client (>= 1.6.8, < 2)
+      simplecov (~> 0.10.0)
+      term-ansicolor (~> 1.3)
+      thor (~> 0.19.1)
     cri (2.7.0)
       colored (~> 1.2)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
     docile (1.1.5)
-    ethon (0.7.3)
+    domain_name (0.5.24)
+      unf (>= 0.0.5, < 1.0.0)
+    ethon (0.7.4)
       ffi (>= 1.3.0)
     faraday (0.9.1)
       multipart-post (>= 1.2, < 3)
-    ffi (1.9.8)
+    ffi (1.9.10)
     git (1.2.9.1)
     github_api (0.12.3)
       addressable (~> 2.3)
@@ -32,8 +34,10 @@ GEM
       multi_json (>= 1.7.5, < 2.0)
       nokogiri (~> 1.6.3)
       oauth2
-    hashie (3.4.1)
+    hashie (3.4.2)
     highline (1.7.2)
+    http-cookie (1.0.2)
+      domain_name (~> 0.5)
     jeweler (2.0.1)
       builder
       bundler (>= 1.0)
@@ -43,15 +47,15 @@ GEM
       nokogiri (>= 1.5.10)
       rake
       rdoc
-    json (1.8.2)
-    jwt (1.4.1)
-    mime-types (2.4.3)
+    json (1.8.3)
+    jwt (1.5.1)
+    mime-types (2.6.1)
     mini_portile (0.6.2)
-    minitest (5.6.1)
-    multi_json (1.11.0)
+    minitest (5.7.0)
+    multi_json (1.11.1)
     multi_xml (0.5.5)
     multipart-post (2.0.0)
-    netrc (0.9.0)
+    netrc (0.10.3)
     nokogiri (1.6.6.2)
       mini_portile (~> 0.6.0)
     oauth2 (1.0.0)
@@ -60,36 +64,40 @@ GEM
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (~> 1.2)
-    parser (2.2.0.2)
+    parser (2.3.0.pre.2)
       ast (>= 1.1, < 3.0)
-    powerpack (0.0.9)
-    rack (1.6.0)
+    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 (1.7.2)
+    rest-client (1.8.0)
+      http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 3.0)
       netrc (~> 0.7)
-    rubocop (0.28.0)
+    rubocop (0.32.1)
       astrolabe (~> 1.3)
-      parser (>= 2.2.0.pre.7, < 3.0)
-      powerpack (~> 0.0.6)
+      parser (>= 2.2.2.5, < 3.0)
+      powerpack (~> 0.1)
       rainbow (>= 1.99.1, < 3.0)
       ruby-progressbar (~> 1.4)
-    ruby-progressbar (1.7.1)
+    ruby-progressbar (1.7.5)
     simplecov (0.10.0)
       docile (~> 1.1.0)
       json (~> 1.8)
       simplecov-html (~> 0.10.0)
     simplecov-html (0.10.0)
-    term-ansicolor (1.3.0)
+    term-ansicolor (1.3.2)
       tins (~> 1.0)
     thor (0.19.1)
     thread_safe (0.3.5)
-    tins (1.3.3)
-    typhoeus (0.7.1)
-      ethon (>= 0.7.1)
+    tins (1.5.4)
+    typhoeus (0.7.2)
+      ethon (>= 0.7.4)
+    unf (0.1.4)
+      unf_ext
+    unf_ext (0.0.7.1)
 
 PLATFORMS
   ruby
@@ -97,8 +105,8 @@ PLATFORMS
 DEPENDENCIES
   coveralls
   cri (~> 2.7)
-  jeweler
-  minitest
-  rake
-  rubocop
-  typhoeus (~> 0.6)
+  jeweler (~> 2.0)
+  minitest (~> 5.7)
+  rake (~> 10.4)
+  rubocop (~> 0.32)
+  typhoeus (= 0.7.2)

data/README.md

@@ -23,8 +23,8 @@ The Unipept CLI is available as a *gem*. This means it can easily be installed w
 
 ```bash
 $ gem install unipept
-Successfully installed unipept-0.9.0
-Parsing documentation for unipept-0.9.0
+Successfully installed unipept-0.10.0
+Parsing documentation for unipept-0.10.0
 Done installing documentation for unipept after 0 seconds
 1 gem installed
 ```
@@ -33,7 +33,7 @@ After successful installation, the unipept command should be available:
 
 ```bash
 $ unipept -v
-0.9.0
+0.10.0
 ```
 
 The help can be accessed by running `unipept -h`.

data/VERSION

@@ -1 +1 @@
-0.9.0
+0.10.0

data/lib/commands/unipept.rb

@@ -55,7 +55,7 @@ module Unipept
         option nil, :batch, 'specify the batch size', argument: :required, hidden: true
         option nil, :parallel, 'specify the number of parallel requests', argument: :required, hidden: true
         option :o, :output, 'write output to file', argument: :required
-        option :f, :format, "define the output format (available: #{Unipept::Formatter.available.join ', ' }) (default: #{Unipept::Formatter.default})", argument: :required
+        option :f, :format, "define the output format (available: #{Unipept::Formatter.available.join ', '}) (default: #{Unipept::Formatter.default})", argument: :required
 
         # Configuration options
         option nil, 'host', 'specify the server running the Unipept web service', argument: :required
@@ -104,8 +104,6 @@ module Unipept
         - to standard input
 
         The command will give priority to the first way tryptic peptides are passed, in the order as listed above. Text files and standard input should have one tryptic peptide per line.
-
-        The unipept pept2taxa subcommand yields NCBI Taxonomy records as output.
         EOS
 
         flag :e, :equate, 'equate isoleucine (I) and leucine (L) when matching peptides'
@@ -130,8 +128,6 @@ module Unipept
          - to standard input
 
         The command will give priority to the first way tryptic peptides are passed, in the order as listed above. Text files and standard input should have one tryptic peptide per line.
-
-        The unipept pept2lca subcommand yields an NCBI Taxonomy record as output.
         EOS
 
         flag :e, :equate, 'equate isoleucine (I) and leucine (L) when matching peptides'
@@ -156,8 +152,6 @@ module Unipept
          - to standard input
 
         The command will give priority to the first way NCBI Taxonomy Identifiers are passed, in the order as listed above. Text files and standard input should have one NCBI Taxonomy Identifier per line.
-
-        The unipept taxonomy subcommand yields NCBI Taxonomy records as output.
         EOS
 
         flag :a, :all, 'report all information fields of NCBI Taxonomy records available in Unipept. Note that this may have a performance penalty.'
@@ -181,8 +175,6 @@ module Unipept
         - to standard input
 
         The command will give priority to the first way tryptic peptides are passed, in the order as listed above. Text files and standard input should have one tryptic peptide per line.
-
-        The unipept pept2prot subcommand yields Uniprot records as output.
         EOS
 
         flag :e, :equate, 'equate isoleucine (I) and leucine (L) when matching peptides'
@@ -207,8 +199,6 @@ module Unipept
         - to standard input
 
         The command will give priority to the first way NCBI Taxonomy Identifiers are passed, in the order as listed above. Text files and standard input should have one NCBI Taxonomy Identifier per line.
-
-        The unipept taxonomy subcommand yields NCBI Taxonomy records as output.
         EOS
 
         flag :a, :all, 'report all information fields of NCBI Taxonomy records available in Unipept. Note that this may have a performance penalty.'

data/lib/commands/unipept/api_runner.rb

@@ -1,3 +1,5 @@
+require_relative '../../retryable_typhoeus'
+
 module Unipept
   class Commands::ApiRunner < Cri::CommandRunner
     attr_reader :configuration
@@ -20,11 +22,7 @@ module Unipept
     def host
       # find host in opts first
       host = options[:host] ? options[:host] : @configuration['host']
-
-      # No host has been set?
-      if host.nil? || host.empty?
-        abort 'WARNING: no host has been set, you can set the host with `unipept config host http://api.unipept.ugent.be/`'
-      end
+      host = 'http://api.unipept.ugent.be' if host.nil? || host.empty?
 
       # add http:// if needed
       if host.start_with?('http://') || host.start_with?('https://')
@@ -92,7 +90,7 @@ module Unipept
     # Constructs a request body (a Hash) for set of input strings, using the
     # options supplied by the user.
     def construct_request_body(input)
-      names = selected_fields.empty? || selected_fields.any? { |f| f.to_s.include? 'name' }
+      names = selected_fields.empty? || selected_fields.any? { |f| f.to_s.include?('name') || f.to_s.include?('.*$') }
       { input: input,
         equate_il: options[:equate] == true,
         extra: options[:all] == true,
@@ -109,8 +107,7 @@ module Unipept
 
       batch_iterator.iterate(input_iterator) do |input_slice, batch_id, fasta_mapper|
         last_id =  batch_id
-
-        request = Typhoeus::Request.new(
+        request = ::RetryableTyphoeus::Request.new(
           @url,
           method: :post,
           body: construct_request_body(input_slice),

data/lib/commands/unipept/config.rb

@@ -7,7 +7,7 @@ module Unipept
 
       if arguments.size == 2
         set_config(key, value)
-        puts key +  ' was set to ' + value
+        puts key + ' was set to ' + value
       else
         puts get_config(key)
       end

data/lib/formatters.rb

@@ -200,7 +200,7 @@ module Unipept
     def convert(data, _first)
       CSV.generate do |csv|
         data.each do |o|
-          csv << o.values.map { |v| v == ''  ? nil : v }
+          csv << o.values.map { |v| v == '' ? nil : v }
         end
       end
     end
@@ -217,13 +217,13 @@ module Unipept
 
     class ::Array
       def to_xml(array_name = :array, _item_name = :item)
-        %(<#{array_name}>) + map { |n|n.to_xml(:item) }.join + "</#{array_name}>"
+        %(<#{array_name}>) + map { |n| n.to_xml(:item) }.join + "</#{array_name}>"
       end
     end
 
     class ::Hash
       def to_xml(name = nil)
-        data = to_a.map { |k, v|v.to_xml(k) }.join
+        data = to_a.map { |k, v| v.to_xml(k) }.join
         name ? "<#{name}>#{data}</#{name}>" : data
       end
     end

data/lib/retryable_typhoeus.rb

@@ -0,0 +1,34 @@
+# Retryable Typheous
+# Inspiration: https://gist.github.com/kunalmodi/2939288
+# Patches the request and hydra to allow requests to get resend when they fail
+
+module RetryableTyphoeus
+  require 'typhoeus'
+
+  include Typhoeus
+
+  DEFAULT_RETRIES = 10
+
+  class Request < Typhoeus::Request
+    attr_accessor :retries
+
+    def initialize(base_url, options = {})
+      @retries = (options.delete(:retries) || DEFAULT_RETRIES)
+
+      super
+    end
+
+    def finish(response, bypass_memoization = nil)
+      if response.success? || @retries <= 0
+        super
+      else
+        @retries -= 1
+        if @hydra
+          @hydra.queue_front self
+        else
+          run
+        end
+      end
+    end
+  end
+end

data/test/commands/unipept/test_api_runner.rb

@@ -36,12 +36,8 @@ module Unipept
       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')
+      host = runner.host
+      assert_equal('http://api.unipept.ugent.be', host)
     end
 
     def test_host_priority
@@ -214,6 +210,15 @@ module Unipept
       assert_equal(true, body[:names])
     end
 
+    def test_all_names_wildcard_select_construct_request_body
+      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])
+      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')

data/test/commands/unipept/test_pept2prot.rb

@@ -43,9 +43,9 @@ module Unipept
       lines = out.each_line
       assert_equal('', err)
       assert(lines.next.start_with? 'fasta_header,peptide,uniprot_id,taxon_id')
-      assert(lines.select { |line| line.start_with? '>test,EGGAGSSTGQR,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>test,ENFVYIAK,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>tost,EGGAGSSTGQR,' }.size >= 1)
+      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)
     end
 
     def test_run_with_fasta_multiple_batches_json

data/test/commands/unipept/test_pept2taxa.rb

@@ -43,9 +43,9 @@ module Unipept
       lines = out.each_line
       assert_equal('', err)
       assert(lines.next.start_with? 'fasta_header,peptide,taxon_id,taxon_name,taxon_rank')
-      assert(lines.select { |line| line.start_with? '>test,EGGAGSSTGQR,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>test,ENFVYIAK,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>tost,EGGAGSSTGQR,' }.size >= 1)
+      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)
     end
 
     def test_run_with_fasta_multiple_batches_json

data/test/commands/unipept/test_taxonomy.rb

@@ -41,9 +41,9 @@ module Unipept
       lines = out.each_line
       assert_equal('', err)
       assert(lines.next.start_with? 'fasta_header,taxon_id,taxon_name,taxon_rank')
-      assert(lines.select { |line| line.start_with? '>test,1,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>test,216816,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>tost,1,' }.size >= 1)
+      assert(lines.count { |line| line.start_with? '>test,1,' } >= 1)
+      assert(lines.count { |line| line.start_with? '>test,216816,' } >= 1)
+      assert(lines.count { |line| line.start_with? '>tost,1,' } >= 1)
     end
 
     def test_run_with_fasta_multiple_batches_json

data/test/test_retryable_typhoeus.rb

@@ -0,0 +1,108 @@
+require_relative '../lib/retryable_typhoeus'
+
+module Unipept
+  class BatchIteratorTestCase < Unipept::TestCase
+    def test_request_retry_default_parameter
+      request = new_request
+      assert_equal(10, request.retries)
+      request.retries = 3
+      assert_equal(3, request.retries)
+    end
+
+    def test_request_retry_parameter
+      request = new_request(retries: 5)
+      assert_equal(5, request.retries)
+    end
+
+    def test_succesful_requests_complete
+      hydra = new_hydra
+
+      response = new_response
+      Typhoeus.stub('stubbed.com').and_return(response)
+
+      request = new_request
+
+      hydra.queue request
+      hydra.run
+
+      assert_equal(10, request.retries)
+      assert_equal(true, response.success?)
+    end
+
+    def test_failing_requests_retry_wo_hydra
+      response_fail = new_response(400)
+      response_success = new_response(200)
+      Typhoeus::Expectation.clear
+      Typhoeus.stub('stubbed.com').and_return([response_fail, response_success])
+
+      request = new_request
+      request.run
+
+      assert_equal(9, request.retries)
+    end
+
+    def test_failing_requests_retry_with_hydra
+      hydra = new_hydra
+
+      response_fail = new_response(400)
+      response_success = new_response(200)
+      Typhoeus::Expectation.clear
+      Typhoeus.stub('stubbed.com').and_return([response_fail, response_success])
+
+      request = new_request
+
+      hydra.queue request
+      hydra.run
+
+      assert_equal(9, request.retries)
+    end
+
+    def test_failing_requests_finally_complete_wo_hydra
+      response = new_response(400)
+      Typhoeus.stub('stubbed.com').and_return(response)
+
+      request = new_request
+      request.run
+
+      assert_equal(0, request.retries)
+    end
+
+    def test_failing_requests_finally_complete_with_error
+      hydra = new_hydra
+      response = new_response(400)
+      Typhoeus.stub('stubbed.com').and_return(response)
+
+      request = new_request
+
+      hydra.queue request
+      hydra.run
+
+      assert_equal(0, request.retries)
+      assert_equal(false, response.success?)
+    end
+
+    def new_request(extra_opts = {})
+      ::RetryableTyphoeus::Request.new(
+        'stubbed.com',
+        request_options.merge(extra_opts)
+      )
+    end
+
+    def request_options
+      {
+        method: :post,
+        body: 'body',
+        accept_encoding: 'gzip',
+        headers: { 'User-Agent' => 'user-agent' }
+      }
+    end
+
+    def new_hydra
+      Typhoeus::Hydra.new(max_concurrency: 10)
+    end
+
+    def new_response(code = 200)
+      Typhoeus::Response.new(code: code, body: {}, return_code: :ok)
+    end
+  end
+end

data/unipept.gemspec

@@ -2,15 +2,15 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 0.9.0 ruby lib
+# stub: unipept 0.10.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept"
-  s.version = "0.9.0"
+  s.version = "0.10.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
-  s.date = "2015-06-21"
+  s.date = "2015-07-01"
   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"]
@@ -49,6 +49,7 @@ Gem::Specification.new do |s|
     "lib/configuration.rb",
     "lib/formatters.rb",
     "lib/output_writer.rb",
+    "lib/retryable_typhoeus.rb",
     "lib/server_message.rb",
     "lib/version.rb",
     "test/commands/test_peptfilter.rb",
@@ -63,11 +64,12 @@ Gem::Specification.new do |s|
     "test/commands/unipept/test_taxa2lca.rb",
     "test/commands/unipept/test_taxonomy.rb",
     "test/helper.rb",
-    "test/test_bach_order.rb",
     "test/test_batch_iterator.rb",
+    "test/test_batch_order.rb",
     "test/test_configuration.rb",
     "test/test_formatters.rb",
     "test/test_output_writer.rb",
+    "test/test_retryable_typhoeus.rb",
     "test/test_server_message.rb",
     "unipept.gemspec"
   ]
@@ -83,28 +85,28 @@ 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<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_runtime_dependency(%q<typhoeus>, ["= 0.7.2"])
+      s.add_development_dependency(%q<rake>, ["~> 10.4"])
+      s.add_development_dependency(%q<minitest>, ["~> 5.7"])
+      s.add_development_dependency(%q<rubocop>, ["~> 0.32"])
+      s.add_development_dependency(%q<jeweler>, ["~> 2.0"])
       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<rake>, [">= 0"])
-      s.add_dependency(%q<minitest>, [">= 0"])
-      s.add_dependency(%q<rubocop>, [">= 0"])
-      s.add_dependency(%q<jeweler>, [">= 0"])
+      s.add_dependency(%q<typhoeus>, ["= 0.7.2"])
+      s.add_dependency(%q<rake>, ["~> 10.4"])
+      s.add_dependency(%q<minitest>, ["~> 5.7"])
+      s.add_dependency(%q<rubocop>, ["~> 0.32"])
+      s.add_dependency(%q<jeweler>, ["~> 2.0"])
       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<rake>, [">= 0"])
-    s.add_dependency(%q<minitest>, [">= 0"])
-    s.add_dependency(%q<rubocop>, [">= 0"])
-    s.add_dependency(%q<jeweler>, [">= 0"])
+    s.add_dependency(%q<typhoeus>, ["= 0.7.2"])
+    s.add_dependency(%q<rake>, ["~> 10.4"])
+    s.add_dependency(%q<minitest>, ["~> 5.7"])
+    s.add_dependency(%q<rubocop>, ["~> 0.32"])
+    s.add_dependency(%q<jeweler>, ["~> 2.0"])
     s.add_dependency(%q<coveralls>, [">= 0"])
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.9.0
+  version: 0.10.0
 platform: ruby
 authors:
 - Toon Willems
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-21 00:00:00.000000000 Z
+date: 2015-07-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri
@@ -30,72 +30,72 @@ dependencies:
   name: typhoeus
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: 0.7.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: 0.7.2
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '10.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '10.4'
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '5.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '5.7'
 - !ruby/object:Gem::Dependency
   name: rubocop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.32'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.32'
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
@@ -155,6 +155,7 @@ files:
 - lib/configuration.rb
 - lib/formatters.rb
 - lib/output_writer.rb
+- lib/retryable_typhoeus.rb
 - lib/server_message.rb
 - lib/version.rb
 - test/commands/test_peptfilter.rb
@@ -169,11 +170,12 @@ files:
 - test/commands/unipept/test_taxa2lca.rb
 - test/commands/unipept/test_taxonomy.rb
 - test/helper.rb
-- test/test_bach_order.rb
 - test/test_batch_iterator.rb
+- test/test_batch_order.rb
 - test/test_configuration.rb
 - test/test_formatters.rb
 - test/test_output_writer.rb
+- test/test_retryable_typhoeus.rb
 - test/test_server_message.rb
 - unipept.gemspec
 homepage: https://github.com/unipept/unipept-cli/