unipept 0.3.0 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e0cedbb475ea3469e5e59bed186772d043056252
-  data.tar.gz: bae15a7be7890c1c9331f4c12edc148db1273425
+  metadata.gz: e8ceae14f14f26fc95744563b982738ef445d77b
+  data.tar.gz: e3a91a2e7ca3b2b076c19e0d7291bb90c69dfd04
 SHA512:
-  metadata.gz: af89285b238a595f688964b2294db03db2cd9a8943c8677eda59e951108a692c28a2ed28136187c4d3fca87ee6624d228537c196e8c0faff397f9cb983ae2717
-  data.tar.gz: 845bf1890a13ce5e836690781c7dc32f59c0392e8620704734dc8edc13b03e98b3a1678d4b3ce0ff3a20f62e84d2a1d7908bf00035edc1f258dd03ae0bd51f90
+  metadata.gz: 354c5fd790c33c79d638455350a1b27aba0dfddf5e5d8e1b0c23c09ecaee7d185a88b7ad9be8fc14fdb1653e8f5c7bc71809085556da1b3c6bac7771b022eb3e
+  data.tar.gz: 0f86c782e0e1f058f6b5243671897b62619051334cd4f8e8f6f51bf655f160e1aeab28271b7226cd093cfaf9e9ff962ae1e476d37f4767e32882abeaaeb12700

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.3.1

data/bin/unipept

@@ -70,13 +70,15 @@ class ApiRunner < Cri::CommandRunner
     filter_list = filter_list.map {|f| glob_to_regex(f) }
     output = STDOUT.tty? ? STDOUT : STDERR
 
+    batch_order = Unipept::BatchOrder.new
+
     printed_header = false
     result = []
 
     hydra = Typhoeus::Hydra.new(max_concurrency: 20)
     num_req = 0
 
-    peptide_iterator(peptides) do |sub_division|
+    peptide_iterator(peptides).with_index do |sub_division, i|
       if $interupted
         $stdin.close
         exit 1
@@ -100,11 +102,14 @@ class ApiRunner < Cri::CommandRunner
 
             result << sub_result
 
-            if ! printed_header
-              write_to_output formatter.header(sub_result)
-              printed_header = true
+            # wait till it's our turn to write
+            batch_order.wait(i) do
+              if ! printed_header
+                write_to_output formatter.header(sub_result)
+                printed_header = true
+              end
+              write_to_output formatter.format(sub_result)
             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|
@@ -117,9 +122,8 @@ class ApiRunner < Cri::CommandRunner
       hydra.queue request
 
       num_req += 1
-      if num_req == 200
+      if num_req % 200 == 0
         hydra.run
-        num_req = 0
       end
 
     end

data/lib/unipept/batch_order.rb

@@ -0,0 +1,28 @@
+module Unipept
+
+  class BatchOrder
+
+    attr_reader :order
+
+    def initialize
+      @order = {}
+      @current = 0
+    end
+
+    def wait(i, &block)
+      if i == @current
+        # start writing + those who have been waiting as well
+        block.call
+        @current += 1
+        while order[@current]
+          order.delete(@current).call
+          @current += 1
+        end
+      else
+        @order[i] = block
+      end
+    end
+
+  end
+
+end

data/lib/unipept.rb

@@ -1,5 +1,6 @@
 require_relative 'unipept/formatters'
 require_relative 'unipept/configuration'
+require_relative 'unipept/batch_order'
 
 module Unipept
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.1
 platform: ruby
 authors:
 - Toon Willems
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-05 00:00:00.000000000 Z
+date: 2014-05-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -131,6 +131,7 @@ files:
 - bin/unipept
 - bin/uniprot
 - lib/unipept.rb
+- lib/unipept/batch_order.rb
 - lib/unipept/configuration.rb
 - lib/unipept/formatters.rb
 - test/helper.rb