unipept 0.2.8 → 0.2.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: d6685c8616187aac8a4a8ab39b684f2760df9660
+  metadata.gz: 0ead8dcab7989d462a289d66dcde96b8fd190953
+  data.tar.gz: 239fb70845d676a350a0c2ec0c0ba378c196a3d2
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+  metadata.gz: 98489a9cc2ad823dd787f540e4b5810fb4f98215e5ef73c5ff7756991c7c6cb44d6491218942c115e4fce1e5f9ea809c4d5766d3b56fb1d6a13a987fe4d27448
+  data.tar.gz: 30239e524d0d45121caee7c68a26eef59275eac3cc0c0890c6a66d6a28c6f240945d2c992a41e1bdb13f6e6f376feb68a5d47571cecd9864a82ccc4f95b520a0

data/Rakefile

@@ -25,7 +25,6 @@ Jeweler::Tasks.new do |gem|
   # dependencies defined in Gemfile
   gem.add_dependency 'faraday', '~> 0.9'
   gem.add_dependency 'cri', '~> 2.6'
-  gem.add_dependency 'ruby-progressbar', '~> 1.4'
 end
 Jeweler::RubygemsDotOrgTasks.new
 

data/VERSION

@@ -1 +1 @@
-0.2.8
+0.2.10

data/bin/peptfilter

@@ -1,6 +1,10 @@
 #!/usr/bin/env ruby
 require 'cri'
 
+trap "INT" do
+  $interupted = true
+end
+Signal.trap("PIPE", "EXIT")
 root_cmd = Cri::Command.new_basic_root.modify do
   name 'peptfilter'
   flag :i, :unique, "only output unique peptides"
@@ -14,6 +18,7 @@ root_cmd = Cri::Command.new_basic_root.modify do
     lacks = opts.fetch(:lacks, "").chars.to_a
     contains = opts.fetch(:contains, "").chars.to_a
     $stdin.each_line do |pept|
+      break if $interupted
       pept = pept.chomp
       length_ok = pept.length >= minlen && pept.length <= maxlen
       lacks_ok = (pept.chars.to_a & lacks).size == 0

data/bin/prot2pept

@@ -1,12 +1,19 @@
 #!/usr/bin/env ruby
 require 'cri'
 
+trap "INT" do
+  $interupted = true
+end
+Signal.trap("PIPE", "EXIT")
 root_cmd = Cri::Command.new_basic_root.modify do
   name 'prot2pept'
   required :p, :pattern, "cleavage pattern to split input protein (default: ([KR])([^P]))"
   run do |opts, args, cmd|
     pattern = opts.fetch(:pattern, "([KR])([^P])")
-    $stdin.each_line { |prot| puts prot.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?) }
+    $stdin.each_line do |prot|
+      break if $interupted
+      puts prot.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?)
+    end
   end
 end
 

data/bin/unipept

@@ -8,6 +8,12 @@ require 'fileutils'
 
 require_relative '../lib/unipept'
 
+$interupted = false
+
+trap "INT" do
+  puts "Interupted, exiting..."
+  $interupted = true
+end
 
 class ApiRunner < Cri::CommandRunner
 
@@ -68,6 +74,10 @@ class ApiRunner < Cri::CommandRunner
     result = []
 
     peptide_iterator(peptides) do |sub_division|
+      if $interupted
+        $stdin.close
+        exit 1
+      end
       begin
         sub_result = JSON[Faraday.post(@url, url_options(sub_division)).body]
       rescue
@@ -173,10 +183,16 @@ end
 
 root_cmd = Cri::Command.new_basic_root.modify do
   name 'unipept'
-  flag :v, :verbose, "verbose mode"
+  flag :v, :version, "print version"
   option :i, :input, "input file", :argument => :required
   option :o, :output, "output file", :argument => :required
   option :f, :format, "output format (available: #{Unipept::Formatter.available.join "," }) (default: #{Unipept::Formatter.default})", :argument => :required
+
+  run do |opts, args, cmd|
+    if opts[:version]
+      puts File.read(File.join(File.dirname(__FILE__), "..", "VERSION"))
+    end
+  end
 end
 
 root_cmd.define_command('config') do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.2.8
+  version: 0.2.10
 platform: ruby
 authors:
 - Toon Willems
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-29 00:00:00.000000000 Z
+date: 2014-05-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -108,20 +108,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.6'
-- !ruby/object:Gem::Dependency
-  name: ruby-progressbar
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.4'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.4'
 description: CLI interface to unipept
 email: willemstoon@gmail.com
 executables: