unipept 1.2.0 → 1.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 064e088ee2208683820c27e5331a8005beeb4753
+  metadata.gz: 6e803f0d77ccd06f8b983f3fac7d51ebc5c170e6
+  data.tar.gz: f30e852d61c6a69c250306148fc2fa1a064f63f7
 SHA512:
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-  data.tar.gz: 326a285c3753138a388c7bfbfce1cd773b9038c2af4c1cd9e3a186989325ebfe983728abb2741c34b044ca33496474953bd1a763470a46f37bd18a9d9c1240f3
+  metadata.gz: fb053972592c1c18b33304c6f39d7db8ebcfcb8dedf1ed99c53a9ad8d73121feff1b8f806c6b7f80bc75bab0c03e9ae272122020ab716093fd9d7a30e1a16c2f
+  data.tar.gz: 7664a300163ceed13732c7286b017e9e28e08ebfc39072b15321cce85d12db60d26de79a52f50f4d70aa2528f4e222e1b451fd3f027fa6072e293895dbe66799

data/.travis.yml

@@ -7,6 +7,7 @@ rvm:
   - 2.0.0
 
 install:
+  - gem update --system
   - bundle install --without release
 
 notifications:

data/VERSION

@@ -1 +1 @@
-1.2.0
+1.3.0

data/lib/commands/unipept.rb

@@ -51,6 +51,7 @@ module Unipept
         EOS
         flag :v, :version, 'displays the version'
         flag :q, :quiet, 'disable service messages'
+        flag nil, :'no-header', 'disable header in csv output', hidden: true
         option :i, :input, 'read input from file', argument: :required
         option nil, :batch, 'specify the batch size', argument: :required, hidden: true
         option nil, :parallel, 'specify the number of parallel requests', argument: :required, hidden: true

data/lib/commands/unipept/api_runner.rb

@@ -15,6 +15,7 @@ module Unipept
       @host = host
       @user_agent = 'Unipept CLI - unipept ' + Unipept::VERSION
       @url = "#{@host}/api/v1/#{cmd.name}.json"
+      @fasta = false
     end
 
     # Returns the host. If a value is defined by both an option and the config
@@ -86,7 +87,7 @@ module Unipept
     def selected_fields
       return @selected_fields unless @selected_fields.nil?
       fields = [*options[:select]].map { |f| f.split(',') }.flatten
-      fields.concat(required_fields) unless fields.empty?
+      fields.concat(required_fields) if @fasta && !fields.empty?
       @selected_fields = fields.map { |f| glob_to_regex(f) }
     end
 
@@ -114,6 +115,7 @@ module Unipept
 
       batch_iterator.iterate(input_iterator) do |input_slice, batch_id, fasta_mapper|
         last_id = batch_id
+        @fasta = !fasta_mapper.nil?
         request = ::RetryableTyphoeus::Request.new(
           @url,
           method: :post,
@@ -165,7 +167,7 @@ module Unipept
 
       lambda do
         unless result.empty?
-          output_writer.write_line formatter.header(result, fasta_mapper) if batch_id.zero?
+          output_writer.write_line formatter.header(result, fasta_mapper) if batch_id.zero? && !options[:"no-header"]
           output_writer.write_line formatter.format(result, fasta_mapper, batch_id.zero?)
         end
       end

data/lib/formatters.rb

@@ -32,7 +32,7 @@ module Unipept
     #
     # @return [Array<String>] The list of available formatters
     def self.available
-      formatters.keys
+      formatters.select { |_key, value| !value.hidden? }.keys
     end
 
     # @return [String] The type of the default formatter: csv
@@ -45,6 +45,10 @@ module Unipept
       raise NotImplementedError, 'This must be implemented in a subclass.'
     end
 
+    def self.hidden?
+      false
+    end
+
     # Returns the header row for the given sample_data and fasta_mapper. This
     # row is output only once at the beginning of the output
     #
@@ -263,6 +267,10 @@ module Unipept
       'blast'
     end
 
+    def self.hidden?
+      true
+    end
+
     def header(_data, _fasta_mapper = nil)
       ''
     end

data/test/commands/unipept/test_api_runner.rb

@@ -170,14 +170,24 @@ module Unipept
       assert_equal([], runner.selected_fields)
     end
 
-    def test_required_fields_are_selected
+    def test_required_fields_are_selected_for_fasta
       runner = new_runner('test', host: 'http://param_host', select: 'field')
       def runner.required_fields
         ['test']
       end
+      runner.instance_variable_set(:@fasta, true)
       assert_equal([/^field$/, /^test$/], runner.selected_fields)
     end
 
+    def test_required_fields_are_not_selected_if_not_fasta
+      runner = new_runner('test', host: 'http://param_host', select: 'field')
+      def runner.required_fields
+        ['test']
+      end
+      runner.instance_variable_set(:@fasta, false)
+      assert_equal([/^field$/], runner.selected_fields)
+    end
+
     def test_single_selected_fields
       runner = new_runner('test', host: 'http://param_host', select: 'field')
       assert_equal([/^field$/], runner.selected_fields)
@@ -308,6 +318,18 @@ module Unipept
       assert_equal('value2,value2', lines.next.chomp)
     end
 
+    def test_success_no_header_option_handle_response
+      runner = new_runner('test', Hash[:host, 'test', :'no-header', true])
+      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('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"}]')

data/test/test_formatters.rb

@@ -7,7 +7,7 @@ module Unipept
       assert(formatters.include?('json'))
       assert(formatters.include?('csv'))
       assert(formatters.include?('xml'))
-      assert(formatters.include?('blast'))
+      assert(!formatters.include?('blast'))
     end
 
     def test_default_formatter

data/unipept.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 1.2.0 ruby lib
+# stub: unipept 1.3.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept".freeze
-  s.version = "1.2.0"
+  s.version = "1.3.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Toon Willems".freeze, "Bart Mesuere".freeze, "Tom Naessens".freeze]
-  s.date = "2017-01-18"
+  s.date = "2017-01-28"
   s.description = "    Command line interface to the Unipept (http://unipept.ugent.be) web services\n    (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility\n    commands for handling proteins using the command line.\n".freeze
   s.email = "unipept@ugent.be".freeze
   s.executables = ["unipept".freeze, "prot2pept".freeze, "peptfilter".freeze, "uniprot".freeze]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 1.2.0
+  version: 1.3.0
 platform: ruby
 authors:
 - Toon Willems
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-01-18 00:00:00.000000000 Z
+date: 2017-01-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri