unipept 0.6.2 → 0.6.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 567da9af48d82125a8bb3d330d25ee0f51429833
-  data.tar.gz: d176b5daec3dc2287fe453d3567d9d7ce86032e8
+  metadata.gz: 4e2985df7d45eb45a982bb73099e92c001155829
+  data.tar.gz: fc79cba4a15df4511af91a85eb9b09f7172b93e9
 SHA512:
-  metadata.gz: e2ca1389cfd0bf5b341222aca4ac8c878b1928d2872ed8d6d2ea8440d2e2f7bb39b51fde803888721fcd85a3b03a3ce2848943348e14cb235556e4f692c2eacd
-  data.tar.gz: 44e9af1dde7132c883fac6f95a0a6d2bf23bb8676f59ece0e51537ed8a101ab141c7056deca40aaee978d6273b557b8389b800cf40178d7d499b0adbc7110d74
+  metadata.gz: 9f0269ffa7a80d490ebf3e85a0a090f5ab89d2d8c75e9f4ca2e904a848ba155b8721d6a0d3fc28289ccab9cf931236074e9ab20d6a1a126a0ddd208cc1240222
+  data.tar.gz: 5381cafb81ac0c32a0f2475e51b0df439e886187ea296a52fb340507763740e4db63918e049434e926f0e360120e4f2609cfbbe80e57518b05be0d951d605637

data/VERSION

@@ -1 +1 @@
-0.6.2
+0.6.4

data/lib/unipept/commands/api_runner.rb

@@ -6,9 +6,10 @@ module Unipept::Commands
     def initialize(args, opts, cmd)
       super
       @configuration = Unipept::Configuration.new
-
       set_configuration
 
+      @user_agent = "Unipept CLI - unipept " + Unipept::VERSION
+
       @url = "#{@host}/api/v1/#{cmd.name}.json"
       @message_url = "#{@host}/api/v1/messages.json"
     end
@@ -100,16 +101,16 @@ module Unipept::Commands
           @url,
           method: :post,
           body: url_options(sub_division),
-          accept_encoding: "gzip"
+          accept_encoding: "gzip",
+          headers: {"User-Agent" => @user_agent}
         )
         request.on_complete do |resp|
-
           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 = [sub_result] unless sub_result.is_a? Array
 
-            sub_result.map! {|r| r.select! {|k,v| filter_list.any? {|f| f.match k } } } if ! filter_list.empty?
+            sub_result.map! { |r| r.select! { |k, _v| filter_list.any? { |f| f.match k } } } unless filter_list.empty?
 
             if options[:xml]
               result << sub_result
@@ -117,8 +118,8 @@ module Unipept::Commands
 
             # wait till it's our turn to write
             batch_order.wait(i) do
-              if ! sub_result.empty?
-                if ! printed_header
+              unless sub_result.empty?
+                unless printed_header
                   write_to_output formatter.header(sub_result, fasta_input)
                   printed_header = true
                 end
@@ -129,26 +130,25 @@ module Unipept::Commands
           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")
+              $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"
+              $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}")
+              $stderr.puts "received a non-successful http response #{resp.code}, continuing anyway, but results might be incomplete"
+              save_error("Got #{resp.code}: #{resp.response_body}\nRequest headers: #{resp.request.options}\nRequest body:\n#{resp.request.encoded_body}\n\n")
             end
 
           end
-
         end
 
         hydra.queue request
@@ -171,9 +171,9 @@ module Unipept::Commands
     end
 
     def save_error(message)
-      path = File.expand_path(File.join(Dir.home, ".unipept", "unipept-#{Time.now.strftime("%F-%T")}.log"))
+      path = File.expand_path(File.join(Dir.home, '.unipept', "unipept-#{Time.now.strftime('%F-%T')}.log"))
       FileUtils.mkdir_p File.dirname(path)
-      File.open(path, "w") do |f|
+      File.open(path, 'w') do |f|
         f.write message
       end
       $stderr.puts "API request failed! log can be found in #{path}"

data/lib/unipept/version.rb

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

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 0.6.2 ruby lib
+# stub: unipept 0.6.4 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept"
-  s.version = "0.6.2"
+  s.version = "0.6.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
-  s.date = "2015-04-30"
+  s.date = "2015-05-17"
   s.description = "Command line interface to Unipept web services."
   s.email = "unipept@ugent.be"
   s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.6.2
+  version: 0.6.4
 platform: ruby
 authors:
 - Toon Willems
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-30 00:00:00.000000000 Z
+date: 2015-05-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri