unipept 0.2.1 → 0.2.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: d8d91d4254c7c6b86be958cb0b10e2a4665c8b4f
+  metadata.gz: 7a8c0e99c89c6bc8304ff54fb44c0f432021f2db
+  data.tar.gz: 29e5c50c53cc1246212d9bf1e184ac0760c90739
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+  data.tar.gz: 205a9c2c8b6c2594bd26464f4f45201940fa5dd041ffc8f620aa08a3425c491bbe56c67cf8c61f5a90e8cd5e3138bb868f304c9b4b3e59ac74eb3589bc181dda

data/Rakefile

@@ -24,7 +24,7 @@ Jeweler::Tasks.new do |gem|
   gem.authors = ["Toon Willems"]
   # dependencies defined in Gemfile
   gem.add_dependency 'faraday', '~> 0.9'
-  gem.add_dependency 'cri', '~> 2.5'
+  gem.add_dependency 'cri', '~> 2.6'
   gem.add_dependency 'ruby-progressbar', '~> 1.4'
 end
 Jeweler::RubygemsDotOrgTasks.new

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.2.2

data/bin/unipept

@@ -12,6 +12,8 @@ require_relative '../lib/unipept'
 
 class ApiRunner < Cri::CommandRunner
 
+  attr_accessor :progress
+
   def initialize(args, opts, cmd)
     super
     host = Unipept::Configuration.new['host']
@@ -19,9 +21,14 @@ class ApiRunner < Cri::CommandRunner
       puts "WARNING: no host has been set, you can set the host with `unipept config host http://localhost:3000/`"
       exit 1
     end
+    if !host.start_with? "http://"
+      host = "http://#{host}"
+    end
+
     @url = "#{host}/api/v1/#{mapping[cmd.name]}.json"
   end
 
+
   def mapping
     {'pept2taxa' => 'single', 'pept2lca' => 'lca'}
   end
@@ -41,55 +48,78 @@ class ApiRunner < Cri::CommandRunner
   end
 
   def url_options(sub_part)
+    filter = options[:select] ? options[:select] : []
+    if filter.empty?
+      names = true
+    else
+      names = filter.any? {|f| /.*name.*/.match f}
+    end
     {:sequences => sub_part,
      :equate_il => options[:equate],
-     :full_lineage => options[:lineage]}
+     :full_lineage => options[:lineage],
+     :names => names,
+    }
   end
 
   def run
     formatter = Unipept::Formatter.new_for_format(options[:format])
     peptides = read_input
 
-    filter = options[:select] rescue nil
-    filter = glob_to_regex(filter) if filter
-
-    progress = ProgressBar.create(total: peptides.size, output: $stderr)
+    filter_list = options[:select] ? options[:select] : []
+    filter_list = filter_list.map {|f| glob_to_regex(f) }
+    output = STDOUT.tty? ? STDOUT : STDERR
+    self.progress = ProgressBar.create(total: peptides.size, output: output)
 
+    printed_header = false
     result = []
-    peptides.each_slice(self.batch_size) do |sub_division|
 
+    peptides.each_slice(self.batch_size) do |sub_division|
       begin
         sub_result = JSON[Faraday.post(@url, url_options(sub_division)).body]
       rescue
-        puts "API endpoint gave an error, exiting."
+        STDERR.puts "API endpoint gave an error, exiting."
         exit 1
       end
 
       sub_result = [sub_result] if not sub_result.kind_of? Array
 
-      sub_result.map! {|r| r.select! {|k,v| filter.match k } } if filter
+      sub_result.map! {|r| r.select! {|k,v| filter_list.any? {|f| f.match k } } } if ! filter_list.empty?
 
       result << sub_result
 
+      if ! printed_header
+        write_to_output formatter.header(sub_result)
+        printed_header = true
+      end
+
+      write_to_output formatter.format(sub_result)
       progress.progress += sub_division.size
     end
 
     begin
       download_xml(result)
     rescue
-      puts "Something went wrong while downloading xml information! please check the output"
+      STDERR.puts "Something went wrong while downloading xml information! please check the output"
     end
 
-    result = formatter.format(result)
-    if options[:output]
-      File.open(options[:output], 'w') do |f|
-        f.write result
+  end
+
+  def write_to_output(string)
+      if options[:output]
+        File.open(options[:output], 'a') do |f|
+          f.write string
+        end
+      else
+        if STDOUT.tty?
+          progress.log string
+        else
+          puts string
+        end
       end
-    else
-      puts result
-    end
+
   end
 
+
   def download_xml(result)
     if options[:xml]
       File.open(options[:xml] + ".xml", "wb") do |f|
@@ -117,11 +147,9 @@ class Taxa2lca < ApiRunner
   end
 
   def batch_size
-    100000
+    Float::INFINITY
   end
 
-
-
 end
 
 class Pept2pro < ApiRunner
@@ -177,7 +205,7 @@ root_cmd.define_command('pept2taxa') do
   description 'Search Unipept for the given peptide and return taxons'
 
   flag :e, :equate, "equate I and L"
-  option :s, :select, "select the attributes", :argument => :required
+  option :s, :select, "select the attributes", :argument => :required, :multiple => true
   option :l, :lineage, "Show full lineage"
   option :x, :xml, "Download taxonomy from NCBI as xml (specify output filename)", :argument => :required
 
@@ -191,7 +219,7 @@ root_cmd.define_command('pept2lca') do
   description 'Search Unipept for the given peptide and return the lowest common ancestor'
 
   flag :e, :equate, "equate I and L"
-  option :s, :select, "select the attributes", :argument => :required
+  option :s, :select, "select the attributes", :argument => :required, :multiple => true
   option :l, :lineage, "Show full lineage"
 
   runner ApiRunner
@@ -203,7 +231,7 @@ root_cmd.define_command('taxa2lca') do
   summary     'Give lowest common ancestor for taxon ids'
   description 'Search Unipept for the given taxon ids and return the lowest common ancestor'
 
-  option :s, :select, "select the attributes", :argument => :required
+  option :s, :select, "select the attributes", :argument => :required, :multiple => true
   option :l, :lineage, "Show full lineage"
 
   runner Taxa2lca
@@ -216,7 +244,7 @@ root_cmd.define_command('pept2pro') do
   description 'Search Unipept for the given peptides and return the lowest common ancestor'
 
   flag :e, :equate, "equate I and L"
-  option :s, :select, "select the attributes", :argument => :required
+  option :s, :select, "select the attributes", :argument => :required, :multiple => true
   option :x, :xml, "download uniprot record in specified directory", :argument => :required
 
   runner Pept2pro

data/lib/unipept/formatters.rb

@@ -22,7 +22,11 @@ module Unipept
     end
 
     def self.default
-      'json'
+      'csv'
+    end
+
+    def header(sample_data)
+      ""
     end
 
     # JSON formatted data goes in, something other comes out
@@ -45,14 +49,18 @@ module Unipept
 
     register :csv
 
-    def format(data)
+    def header(data)
       CSV.generate do |csv|
         first = data.first
         if first.kind_of? Array
           first = first.first
         end
         csv << first.keys.map(&:to_s)
+      end
+    end
 
+    def format(data)
+      CSV.generate do |csv|
         data.each do |o|
           if o.kind_of? Array
             o.each {|h| csv << h.values }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.2
 platform: ruby
 authors:
 - Toon Willems
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-11 00:00:00.000000000 Z
+date: 2014-04-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -100,14 +100,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.5'
+        version: '2.6'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.5'
+        version: '2.6'
 - !ruby/object:Gem::Dependency
   name: ruby-progressbar
   requirement: !ruby/object:Gem::Requirement