unipept 0.5.7 → 0.6.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/LICENSE.txt

@@ -1,20 +1,21 @@
-Copyright (c) 2014 Toon Willems
+The MIT License (MIT)
 
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
+Copyright (c) 2010-2014 Universiteit Gent <unipept@ugent.be>
 
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

@@ -0,0 +1,37 @@
+# unipept-cli
+
+[![Code Climate](https://codeclimate.com/github/unipept/unipept-cli/badges/gpa.svg)](https://codeclimate.com/github/unipept/unipept-cli)
+
+Unipept-cli offers a command line interface to the [Unipept](http://unipept.ugent.be) web service.
+Documentation about the web service can be found at [http://unipept.ugent.be/apidocs](http://unipept.ugent.be/apidocs).
+
+## Installation
+
+To use the Unipept CLI, Ruby version 1.9.3 or higher needs to be installed. You can check this by running `ruby -v` on the commandline:
+
+```
+$ ruby -v
+ruby 2.1.1p76 (2014-02-24 revision 45161) [x86_64-darwin12.0]
+```
+
+More information on installing Ruby can be found at https://www.ruby-lang.org/en/installation/
+
+The Unipept CLI is available as a *gem*. This means it can easily be installed with the following command:
+
+```bash
+$ gem install unipept
+Successfully installed unipept-0.6.0
+Parsing documentation for unipept-0.6.0
+Done installing documentation for unipept after 0 seconds
+1 gem installed
+```
+
+After successful installation, the unipept command should be available:
+
+```bash
+$ unipept -v
+0.6.0
+```
+
+The help can be accessed by running `unipept -h`.
+

data/Rakefile

@@ -16,12 +16,13 @@ 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 = ['unipept', 'prot2pept', 'peptfilter', 'uniprot']
-  gem.homepage = "http://github.ugent.be/bmesuere/unipept/"
+  gem.homepage = "https://github.com/unipept/unipept/"
   gem.license = "MIT"
-  gem.summary = %Q{CLI interface to unipept}
-  gem.description = %Q{CLI interface to unipept}
-  gem.email = "willemstoon@gmail.com"
-  gem.authors = ["Toon Willems"]
+  gem.summary = %Q{Command line interface to Unipept web services.}
+  gem.description = %Q{Command line interface to Unipept web services.}
+  gem.email = "unipept@ugent.be"
+  gem.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
+  gem.required_ruby_version = '>= 1.9.3'
   # dependencies defined in Gemfile
   gem.add_dependency 'typhoeus', '~> 0.6'
   gem.add_dependency 'cri', '~> 2.6'

data/VERSION

@@ -1 +1 @@
-0.5.7
+0.6.1

data/bin/unipept

@@ -8,55 +8,10 @@ require 'fileutils'
 
 require_relative '../lib/unipept'
 
+# Prevent broken pipe errors
 Signal.trap("PIPE", "EXIT")
 Signal.trap("INT", "EXIT")
 
-module Unipept
-  class Taxa2lca < ApiRunner
-
-    def mapping
-      {"taxa2lca" => "taxa2lca"}
-    end
-
-    def peptide_iterator(peptides, &block)
-      block.call(peptides.to_a, 0)
-    end
-
-    def batch_size
-      raise "NOT NEEDED FOR TAXA2LCA"
-    end
-
-  end
-
-  class Pept2prot < ApiRunner
-
-    def mapping
-      {"pept2prot" => "pept2prot"}
-    end
-
-    def download_xml(result)
-      if options[:xml]
-        FileUtils.mkdir_p(options[:xml])
-        result.first.each do |prot|
-          File.open(options[:xml] + "/#{prot['uniprot_id']}.xml", "wb") do |f|
-            f.write Typhoeus.get("http://www.uniprot.org/uniprot/#{prot['uniprot_id']}.xml").response_body
-          end
-        end
-      end
-    end
-
-    def batch_size
-      10
-    end
-  end
-
-  class Taxonomy < ApiRunner
-    def mapping
-      {"taxonomy" => "taxonomy"}
-    end
-  end
-end
-
 root_cmd = Cri::Command.new_basic_root.modify do
   name 'unipept'
   flag :v, :version, "print version"
@@ -101,7 +56,7 @@ root_cmd.define_command('pept2taxa') do
   option :a, :extra, "Show full lineage"
   option :x, :xml, "Download taxonomy from NCBI as xml (specify output filename)", :argument => :required
 
-  runner Unipept::ApiRunner
+  runner Unipept::Commands::Pept2taxa
 end
 
 root_cmd.define_command('pept2lca') do
@@ -114,7 +69,7 @@ root_cmd.define_command('pept2lca') do
   option :s, :select, "select the attributes", :argument => :required, :multiple => true
   option :a, :extra, "Show full lineage"
 
-  runner Unipept::ApiRunner
+  runner Unipept::Commands::Pept2lca
 end
 
 root_cmd.define_command('taxa2lca') do
@@ -126,7 +81,7 @@ root_cmd.define_command('taxa2lca') do
   option :s, :select, "select the attributes", :argument => :required, :multiple => true
   option :a, :extra, "Show full lineage"
 
-  runner Unipept::Taxa2lca
+  runner Unipept::Commands::Taxa2lca
 end
 
 root_cmd.define_command('pept2prot') do
@@ -140,7 +95,7 @@ root_cmd.define_command('pept2prot') do
   option :x, :xml, "download uniprot record in specified directory", :argument => :required
   flag :a, :extra, "include all information. WARNING: will take much longer!"
 
-  runner Unipept::Pept2prot
+  runner Unipept::Commands::Pept2prot
 end
 
 root_cmd.define_command('taxonomy') do
@@ -152,7 +107,7 @@ root_cmd.define_command('taxonomy') do
   option :s, :select, "select the attributes", :argument => :required, :multiple => true
   flag :a, :extra, "include all information. WARNING: will take much longer!"
 
-  runner Unipept::Taxonomy
+  runner Unipept::Commands::Taxonomy
 end
 
 root_cmd.run(ARGV)

data/lib/unipept/{api_runner.rb → commands/api_runner.rb}

@@ -1,4 +1,6 @@
-module Unipept
+require 'set'
+
+module Unipept::Commands
   class ApiRunner < Cri::CommandRunner
 
     def initialize(args, opts, cmd)
@@ -7,7 +9,7 @@ module Unipept
 
       set_configuration
 
-      @url = "#{@host}/api/v1/#{mapping[cmd.name]}.json"
+      @url = "#{@host}/api/v1/#{cmd.name}.json"
       @message_url = "#{@host}/api/v1/messages.json"
     end
 
@@ -31,10 +33,6 @@ module Unipept
       @host = host
     end
 
-    def mapping
-      {'pept2taxa' => 'pept2taxa', 'pept2lca' => 'pept2lca'}
-    end
-
     def input_iterator
       # Argument over file input over stdin
       if !arguments.empty?
@@ -71,7 +69,7 @@ module Unipept
       return unless STDOUT.tty?
       last_fetched = @configuration['last_fetch_date']
       if last_fetched.nil? || (last_fetched + 60 * 60 * 24) < Time.now
-        version = File.read(File.join(File.dirname(__FILE__), "..", "..", "VERSION"))
+        version = Unipept::VERSION
         resp = Typhoeus.get(@message_url, params: {version: version})
         puts resp.body unless resp.body.chomp.empty?
         @configuration['last_fetch_date'] = Time.now
@@ -97,7 +95,7 @@ module Unipept
       hydra = Typhoeus::Hydra.new(max_concurrency: 10)
       num_req = 0
 
-      peptide_iterator(peptides) do |sub_division, i, fasta_mapper|
+      peptide_iterator(peptides) do |sub_division, i, fasta_input|
         request = Typhoeus::Request.new(
           @url,
           method: :post,
@@ -105,35 +103,54 @@ module Unipept
           accept_encoding: "gzip"
         )
         request.on_complete do |resp|
-          if resp.timed_out?
-            $stderr.puts "request timed out, continuing anyway, but results might be incomplete"
-          else
-            if resp.success?
-              # if JSON parsing goes wrong
-              sub_result = JSON[resp.response_body] rescue []
-              sub_result = [sub_result] if not sub_result.kind_of? Array
 
-              sub_result.map! {|r| r.select! {|k,v| filter_list.any? {|f| f.match k } } } if ! filter_list.empty?
+          if resp.success?
+            # if JSON parsing goes wrong
+            sub_result = JSON[resp.response_body] rescue []
+            sub_result = [sub_result] if not sub_result.kind_of? Array
 
-              if options[:xml]
-                result << sub_result
-              end
+            sub_result.map! {|r| r.select! {|k,v| filter_list.any? {|f| f.match k } } } if ! filter_list.empty?
 
-              # wait till it's our turn to write
-              batch_order.wait(i) do
-                if ! sub_result.empty?
-                  if ! printed_header
-                    write_to_output formatter.header(sub_result, fasta_mapper)
-                    printed_header = true
-                  end
-                  write_to_output formatter.format(sub_result, fasta_mapper)
+            if options[:xml]
+              result << sub_result
+            end
+
+            # wait till it's our turn to write
+            batch_order.wait(i) do
+              if ! sub_result.empty?
+                if ! printed_header
+                  write_to_output formatter.header(sub_result, fasta_input)
+                  printed_header = true
                 end
+                write_to_output formatter.format(sub_result, fasta_input)
               end
-            else
-              save_error(resp.response_body)
             end
+
+          elsif resp.timed_out?
+
+            batch_order.wait(i) do
+              $stderr.puts "request timed out, continuing anyway, but results might be incomplete"
+              save_error("request timed out, continuing anyway, but results might be incomplete")
+            end
+
+          elsif resp.code == 0
+
+            batch_order.wait(i) do
+              $stderr.puts "could not get an http response, continuing anyway, but results might be incomplete"
+              save_error(resp.return_message)
+            end
+
+          else
+
+            batch_order.wait(i) do
+              $stderr.puts "received a non-successful http response #{resp.code.to_s}, continuing anyway, but results might be incomplete"
+              save_error("Got #{resp.code.to_s}: #{resp.response_body}")
+            end
+
           end
+
         end
+
         hydra.queue request
 
         num_req += 1
@@ -187,19 +204,24 @@ module Unipept
         # FASTA MODE ENGAGED
         fasta_header = first.chomp
         peptides.each_slice(batch_size).with_index do |sub,i|
-          fasta_mapper = {}
-          sub.map! {|s| s.chomp}
-          j = 0
-          while j < sub.size
-            if sub[j].start_with? '>'
-              fasta_header = sub[j]
+          fasta_input = []
+          # Use a set so we don't ask data twice
+          newsub = Set.new
+
+          # Iterate to find fasta headers
+          sub.each do |s|
+            s.chomp!
+            if s.start_with? '>'
+              # Save the FASTA header when found
+              fasta_header = s
             else
-              fasta_mapper[sub[j]] = fasta_header
+              # Add the input pair to our input list
+              fasta_input << [fasta_header, s]
+              newsub << s
             end
-            j += 1
           end
-          sub -= fasta_mapper.values.uniq
-          block.call(sub, i, fasta_mapper)
+
+          block.call(newsub.to_a, i, fasta_input)
         end
       else
         # shame we have to be this explicit, but it appears to be the only way

data/lib/unipept/commands/pept2lca.rb

@@ -0,0 +1,6 @@
+require_relative 'api_runner'
+module Unipept::Commands
+  class Pept2lca < ApiRunner
+  end
+end
+

data/lib/unipept/commands/pept2prot.rb

@@ -0,0 +1,20 @@
+require_relative 'api_runner'
+
+module Unipept::Commands
+  class Pept2prot < ApiRunner
+    def download_xml(result)
+      if options[:xml]
+        FileUtils.mkdir_p(options[:xml])
+        result.first.each do |prot|
+          File.open(options[:xml] + "/#{prot['uniprot_id']}.xml", "wb") do |f|
+            f.write Typhoeus.get("http://www.uniprot.org/uniprot/#{prot['uniprot_id']}.xml").response_body
+          end
+        end
+      end
+    end
+
+    def batch_size
+      10
+    end
+  end
+end

data/lib/unipept/commands/pept2taxa.rb

@@ -0,0 +1,5 @@
+require_relative 'api_runner'
+module Unipept::Commands
+  class Pept2taxa < ApiRunner
+  end
+end

data/lib/unipept/commands/taxa2lca.rb

@@ -0,0 +1,12 @@
+require_relative 'api_runner'
+module Unipept::Commands
+  class Taxa2lca < ApiRunner
+    def peptide_iterator(peptides, &block)
+      block.call(peptides.to_a, 0)
+    end
+
+    def batch_size
+      raise "NOT NEEDED FOR TAXA2LCA"
+    end
+  end
+end

data/lib/unipept/commands/taxonomy.rb

@@ -0,0 +1,5 @@
+require_relative 'api_runner'
+module Unipept::Commands
+  class Taxonomy < ApiRunner
+  end
+end

data/lib/unipept/commands.rb

@@ -0,0 +1,7 @@
+['pept2lca','pept2taxa','pept2prot','taxa2lca','taxonomy'].each do |cmd|
+  require_relative File.join('commands',cmd)
+end
+module Unipept
+  module Commands
+  end
+end

data/lib/unipept/formatters.rb

@@ -50,13 +50,13 @@ module Unipept
 
     register :csv
 
-    def header(data, fasta_mapper = nil)
+    def header(data, fasta_input = nil)
       CSV.generate do |csv|
         first = data.first
         if first.kind_of? Array
           first = first.first
         end
-        if fasta_mapper
+        if fasta_input
           csv << (['fasta_header'] + first.keys).map(&:to_s) if first
         else
           csv << first.keys.map(&:to_s) if first
@@ -64,26 +64,36 @@ module Unipept
       end
     end
 
-    def format(data, fasta_mapper = nil)
+    def format(data, fasta_input = nil)
       CSV.generate do |csv|
-        data.each do |o|
-          if o.kind_of? Array
-            o.each do |h|
-              if fasta_mapper
-                extra_key = [fasta_mapper[h.values.first]]
-                csv << (extra_key + h.values).map { |v| v == ""  ? nil : v }
-              else
-                csv << h.values.map { |v| v == ""  ? nil : v }
+
+        if fasta_input
+          # Process the output from {key1: value1, key2: value2, ...}
+          # to {value => {key1: value1, key2: value2, ...}}
+          data_dict = {}
+          data.each do |d|
+            data_dict[d.values.first.to_s] ||= []
+            data_dict[d.values.first.to_s] << d
+          end
+
+          # Iterate over the input
+          fasta_input.each do |input_pair|
+            fasta_header, id = input_pair
+
+            # Retrieve the corresponding API result (if any)
+            unless data_dict[id].nil?
+              data_dict[id].each do |r|
+                csv << ([fasta_header] + r.values).map { |v| v == "" ? nil : v }
               end
             end
-          else
-            if fasta_mapper
-              extra_key = [fasta_mapper[o.values.first]]
-              csv << (extra_key + o.values).map { |v| v == ""  ? nil : v }
-            else
-              csv << o.values.map { |v| v == ""  ? nil : v }
-            end
           end
+
+        else
+
+          data.each do |o|
+            csv << o.values.map { |v| v == ""  ? nil : v }
+          end
+
         end
       end
     end

data/lib/unipept/version.rb

@@ -0,0 +1,3 @@
+module Unipept
+  VERSION = File.read(File.join(File.dirname(__FILE__), "..", "..", "VERSION"))
+end

data/lib/unipept.rb

@@ -1,7 +1,8 @@
 require_relative 'unipept/formatters'
 require_relative 'unipept/configuration'
 require_relative 'unipept/batch_order'
-require_relative 'unipept/api_runner'
+require_relative 'unipept/commands'
+require_relative 'unipept/version'
 
 module Unipept
 end

data/unipept.gemspec

@@ -2,29 +2,29 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 0.5.7 ruby lib
+# stub: unipept 0.6.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept"
-  s.version = "0.5.7"
+  s.version = "0.6.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
-  s.authors = ["Toon Willems"]
-  s.date = "2014-06-25"
-  s.description = "CLI interface to unipept"
-  s.email = "willemstoon@gmail.com"
+  s.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
+  s.date = "2015-04-22"
+  s.description = "Command line interface to Unipept web services."
+  s.email = "unipept@ugent.be"
   s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
-    "README.rdoc"
+    "README.md"
   ]
   s.files = [
     ".document",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
-    "README.rdoc",
+    "README.md",
     "Rakefile",
     "VERSION",
     "bin/peptfilter",
@@ -32,18 +32,26 @@ Gem::Specification.new do |s|
     "bin/unipept",
     "bin/uniprot",
     "lib/unipept.rb",
-    "lib/unipept/api_runner.rb",
     "lib/unipept/batch_order.rb",
+    "lib/unipept/commands.rb",
+    "lib/unipept/commands/api_runner.rb",
+    "lib/unipept/commands/pept2lca.rb",
+    "lib/unipept/commands/pept2prot.rb",
+    "lib/unipept/commands/pept2taxa.rb",
+    "lib/unipept/commands/taxa2lca.rb",
+    "lib/unipept/commands/taxonomy.rb",
     "lib/unipept/configuration.rb",
     "lib/unipept/formatters.rb",
+    "lib/unipept/version.rb",
     "test/helper.rb",
     "test/test_unipept.rb",
     "unipept.gemspec"
   ]
-  s.homepage = "http://github.ugent.be/bmesuere/unipept/"
+  s.homepage = "https://github.com/unipept/unipept/"
   s.licenses = ["MIT"]
+  s.required_ruby_version = Gem::Requirement.new(">= 1.9.3")
   s.rubygems_version = "2.2.2"
-  s.summary = "CLI interface to unipept"
+  s.summary = "Command line interface to Unipept web services."
 
   if s.respond_to? :specification_version then
     s.specification_version = 4

metadata

@@ -1,14 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.5.7
+  version: 0.6.1
 platform: ruby
 authors:
 - Toon Willems
+- Bart Mesuere
+- Tom Naessens
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-25 00:00:00.000000000 Z
+date: 2015-04-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -108,8 +110,8 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.6'
-description: CLI interface to unipept
-email: willemstoon@gmail.com
+description: Command line interface to Unipept web services.
+email: unipept@ugent.be
 executables:
 - unipept
 - prot2pept
@@ -118,13 +120,13 @@ executables:
 extensions: []
 extra_rdoc_files:
 - LICENSE.txt
-- README.rdoc
+- README.md
 files:
 - ".document"
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - bin/peptfilter
@@ -132,14 +134,21 @@ files:
 - bin/unipept
 - bin/uniprot
 - lib/unipept.rb
-- lib/unipept/api_runner.rb
 - lib/unipept/batch_order.rb
+- lib/unipept/commands.rb
+- lib/unipept/commands/api_runner.rb
+- lib/unipept/commands/pept2lca.rb
+- lib/unipept/commands/pept2prot.rb
+- lib/unipept/commands/pept2taxa.rb
+- lib/unipept/commands/taxa2lca.rb
+- lib/unipept/commands/taxonomy.rb
 - lib/unipept/configuration.rb
 - lib/unipept/formatters.rb
+- lib/unipept/version.rb
 - test/helper.rb
 - test/test_unipept.rb
 - unipept.gemspec
-homepage: http://github.ugent.be/bmesuere/unipept/
+homepage: https://github.com/unipept/unipept/
 licenses:
 - MIT
 metadata: {}
@@ -151,7 +160,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.9.3
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
@@ -162,5 +171,5 @@ rubyforge_project:
 rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
-summary: CLI interface to unipept
+summary: Command line interface to Unipept web services.
 test_files: []

data/README.rdoc

@@ -1,19 +0,0 @@
-= unipept
-
-Description goes here.
-
-== Contributing to unipept
- 
-* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
-* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
-* Fork the project.
-* Start a feature/bugfix branch.
-* Commit and push until you are happy with your contribution.
-* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
-* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
-
-== Copyright
-
-Copyright (c) 2014 Toon Willems. See LICENSE.txt for
-further details.
-