rbbt-sources 3.0.2 → 3.0.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d0ddae660ee5188e8e9ed08bc38a85a01a3fcbf0
-  data.tar.gz: 42e2f12d00c5147ac2eec9cb087f6094342189c3
+  metadata.gz: a5f75097d1a73830c5ae3c2749b114d50367862e
+  data.tar.gz: 837d1281d60d46d97690eaefb36dcfa1e5636636
 SHA512:
-  metadata.gz: 43b3c30586f24975d6295500dbc447b7c8acdb5aa04361c64bbc6eba6628739810f45dd1360c80b78ab6c479751f7eb182a891e57173661080d2b6aea0034f9c
-  data.tar.gz: 3ee58c4b060418bee1b859bd1387ef97217b14b5d2ef26b0594d3813dee14c64ee983349beb2602b3c293223a242a0da25f45cd90fdf56268ee87df35a426083
+  metadata.gz: 38695de62c02838192de10b51b2be02ab6800aa2a62aa96843049325fe6360140433f348d974f18059967f45b76edc621079f9a59d0d521dca491a5ac8182689
+  data.tar.gz: 7223c40d440690cb5ccab506a580593d3adec269060b3006caf8b2985d68b2b564ac0a6eaf3d5f476cb2e6ae483c940525f20fc2df8be28dae03283cb64fe7f1

data/lib/rbbt/sources/biomart.rb

@@ -167,7 +167,7 @@ module BioMart
       data = get(database, main, [], filters, data, open_options)
     end
 
-    open_options[:filename] ||= "BioMart[#{main}+#{attrs.length}]"
+    open_options[:filename] = "BioMart[#{main}+#{attrs.length}]"
     if filename.nil?
       results = TSV.open data, open_options
       results.key_field = main

data/lib/rbbt/sources/kegg.rb

@@ -110,11 +110,11 @@ if defined? Entity
           self 
         when format == "KEGG Gene ID"
           ensembl = from_kegg.clean_annotations
-          Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => ensembl, :format => new_format).exec.chunked_values_at(ensembl), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
+          Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => ensembl, :format => new_format).run.chunked_values_at(ensembl), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
         when new_format == "KEGG Gene ID"
           to_kegg
         else
-          Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => self, :format => new_format).exec.chunked_values_at(self), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
+          Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => self, :format => new_format).run.chunked_values_at(self), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
         end
       end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.0.2
+  version: 3.0.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-25 00:00:00.000000000 Z
+date: 2014-04-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util