unipept 0.2.10 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: bae15a7be7890c1c9331f4c12edc148db1273425
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data/Rakefile

@@ -23,7 +23,7 @@ Jeweler::Tasks.new do |gem|
   gem.email = "willemstoon@gmail.com"
   gem.authors = ["Toon Willems"]
   # dependencies defined in Gemfile
-  gem.add_dependency 'faraday', '~> 0.9'
+  gem.add_dependency 'typhoeus', '~> 0.6'
   gem.add_dependency 'cri', '~> 2.6'
 end
 Jeweler::RubygemsDotOrgTasks.new

data/VERSION

@@ -1 +1 @@
-0.2.10
+0.3.0

data/bin/unipept

@@ -1,7 +1,7 @@
 #!usr/bin/env ruby
 
 require 'cri'
-require 'faraday'
+require 'typhoeus'
 require 'yaml'
 require 'json'
 require 'fileutils'
@@ -45,7 +45,7 @@ class ApiRunner < Cri::CommandRunner
   end
 
   def batch_size
-    10
+    100
   end
 
   def url_options(sub_part)
@@ -73,32 +73,60 @@ class ApiRunner < Cri::CommandRunner
     printed_header = false
     result = []
 
+    hydra = Typhoeus::Hydra.new(max_concurrency: 20)
+    num_req = 0
+
     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
-        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_list.any? {|f| f.match k } } } if ! filter_list.empty?
-
-      result << sub_result
+      request = Typhoeus::Request.new(
+        @url,
+        method: :post,
+        body: url_options(sub_division)
+      )
+      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?
+
+            result << sub_result
+
+            if ! printed_header
+              write_to_output formatter.header(sub_result)
+              printed_header = true
+            end
+            write_to_output formatter.format(sub_result)
+          else
+            path = File.expand_path(File.join(Dir.home, "unipept.log"))
+            File.open(path, "w") do |f|
+              f.write resp.response_body
+            end
+            $stderr.puts "API request failed! log can be found in #{path}"
+          end
+        end
+      end
+      hydra.queue request
 
-      if ! printed_header
-        write_to_output formatter.header(sub_result)
-        printed_header = true
+      num_req += 1
+      if num_req == 200
+        hydra.run
+        num_req = 0
       end
 
-      write_to_output formatter.format(sub_result)
     end
 
+    hydra.run
+
+
     begin
       download_xml(result)
     rescue
@@ -179,6 +207,10 @@ class Pept2prot < ApiRunner
     end
   end
 
+  def batch_size
+    10
+  end
+
 end
 
 root_cmd = Cri::Command.new_basic_root.modify do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.2.10
+  version: 0.3.0
 platform: ruby
 authors:
 - Toon Willems
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-02 00:00:00.000000000 Z
+date: 2014-05-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -81,19 +81,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0.8'
 - !ruby/object:Gem::Dependency
-  name: faraday
+  name: typhoeus
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.9'
+        version: '0.6'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.9'
+        version: '0.6'
 - !ruby/object:Gem::Dependency
   name: cri
   requirement: !ruby/object:Gem::Requirement
@@ -155,7 +155,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.0
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: CLI interface to unipept