rbbt-util 5.17.52 → 5.17.53

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 87b240245aaa39720c9348169c476d3279b01e0f
-  data.tar.gz: 77d89d8d0070ac010513780925f8d91a5b0abaab
+  metadata.gz: 9998932f7037c551f4aef97c75fa09296f0e4cba
+  data.tar.gz: c52cab12dc83feea2d889ecffbc2e07472e02b61
 SHA512:
-  metadata.gz: 8a4b612c7a7e4930f2e76c6771cc2872191b036035c8b172098aceb0d224c382ec01f3c59196efcaf47995aca35f7e645e5bb1975497d9801d107f512331c8d5
-  data.tar.gz: cf2b158c03ac3c3426e723e77b0cea503393c8c0fc08e2e75c5027cc54a4d08a764fca2edeeff1ad0d6c73db375a2cf4fe38b1abd0e0e29ec65ad778b0e330a2
+  metadata.gz: b7030c7870cc8ea1ca80d76509c4526ae5435321dcd22561a661c6b57fb190d641a010b9b222e1295504807c7fd226fb4642e8c00e9ac2b02c33aa678b9a0141
+  data.tar.gz: 02546e560b57a8bce92689137e58b4dfe8165e5095cf9382a98f6c588b19970b2b2a75dace012ba2067fb38312b9cdd83d4fea17769f85d7bae6265bf9f8592b

data/lib/rbbt/rest/client/step.rb

@@ -132,7 +132,7 @@ class WorkflowRESTClient
                       end
                     end
       end
-      noload ? path : @result
+      noload ? path + '?_format=raw' : @result
     end
 
     def exec(*args)

data/lib/rbbt/util/misc/omics.rb

@@ -116,9 +116,6 @@ module Misc
     "TGA" => "*",
   }
 
-  def self.correct_mutation(pos, ref, mut_str)
-  end
-
   def self.correct_icgc_mutation(pos, ref, mut_str)
     mut = mut_str
     mut = '-' * (mut_str.length - 1) if mut =~/^-[ACGT]/

data/lib/rbbt/util/misc/pipes.rb

@@ -174,6 +174,8 @@ module Misc
     else
       Log.medium "Consuming stream #{Misc.fingerprint io}"
       begin
+        into = into.find if Path === into
+        into = Open.open(into, :mode => 'w') if String === into 
         into.sync == true if IO === into
         while not io.closed? and block = io.read(2048)
           into << block if into
@@ -295,7 +297,7 @@ module Misc
     end
   end
 
-  def self.sort_stream(stream, header_hash = "#", cmd_args = " -u ")
+  def self.sort_stream(stream, header_hash = "#", cmd_args = "-u")
     Misc.open_pipe do |sin|
       begin
         if defined? Step and Step === stream

data/lib/rbbt/util/tmpfile.rb

@@ -34,7 +34,11 @@ module TmpFile
       tmpfile += ".#{options[:extension]}"
     end
 
-    File.open(tmpfile, 'w') do |f| f.write content end if content != nil
+    if IO === content
+      Misc.consume_stream(content, false, tmpfile)
+    else
+      File.open(tmpfile, 'w') do |f| f.write content end if content != nil
+    end
 
     result = yield(tmpfile)
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.52
+  version: 5.17.53
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-06 00:00:00.000000000 Z
+date: 2015-07-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake