rbbt-util 5.16.1 → 5.16.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 29417065f1fbfa88cb5c271a16378bd256a4c212
-  data.tar.gz: 93e3c4e913359512c90fc5de892a39a0a485a97f
+  metadata.gz: 34f1d517fbcc392d6fb628b06c1803ccc741c5c7
+  data.tar.gz: 37a629ea804ba0fe4dddfd113ea58b4334de99d8
 SHA512:
-  metadata.gz: 483bcaa453d07b7f7fbb09241dceb3ab8cd8f7b87ff430be52dcaad9998a393b919a82242f6b0eca2005a4a5ad559ce6ac2f73850c765fc22e351a3c8b057b1e
-  data.tar.gz: 4a89efa036fbfadaea7f553d5396469eecd78e7702857f77db829e55249f63511d3b1472afe31e8a2aa0d3e481e9699a6e1936d0e2c4e341ed0eb4dfefed1b6a
+  metadata.gz: 468a5f0148cdbaee168e98d356e3d05989ff6a28b3ed146dec47ed53a470e36e5309170cf474ffff52ab91ce664585dfdec9bb07ea54349faf8c6bd677f12c4c
+  data.tar.gz: 462e3776be3b24f57a61c3d24316d8f60858859c145590f2d3303494f3e5d28729c44e5cfee7dca49c775c537e82c2d371518226c4441c49a4c7a25740b0ad41

data/lib/rbbt/association/index.rb

@@ -59,9 +59,11 @@ module Association
               list.replace [list.first] * size if list.length == 1
             end if recycle and size > 1
 
+
             rest = Misc.zip_fields rest
 
-            annotations = rest.length > 1 ?
+
+            annotations = (Array === rest.first and rest.first.length > 1) ?
               targets.zip(rest) :
               targets.zip(rest * targets.length) 
 

data/lib/rbbt/resource.rb

@@ -74,7 +74,11 @@ module Resource
     begin
       @server_missing_resource_cache ||= Set.new
       raise "Resource Not Found" if @server_missing_resource_cache.include? url
-      lock_filename = Persist.persistence_path(final_path, {:dir => Resource.lock_dir})
+      
+      #lock_filename = Persist.persistence_path(final_path, {:dir => Resource.lock_dir})
+      
+      lock_filename = nil # it seems like this was locked already.
+
       Misc.lock lock_filename do
         Net::HTTP.get_response URI(url) do |response|
           case response

data/lib/rbbt/tsv/index.rb

@@ -116,6 +116,7 @@ module TSV
           end
         end
 
+        new_fields = [] if new_fields.nil?
         TSV.setup(new, :type => index_type, :filename => filename, :fields => [new_key_field], :key_field => new_fields * ", ", :namespace => namespace)
       end
     end

data/test/rbbt/association/test_database.rb

@@ -61,4 +61,19 @@ TP53 NFKB1|GLI1 activation|activation true|true
   def test_gene_ages
     assert Association.database('/home/mvazquezg/git/workflows/genomics/share/gene_ages', :source => "FamilyAge", :merge => true, :target => "Ensembl Gene ID", :persist => false).values.first.length > 1
   end
+
+  def __test_reorder_multiple_mismatch
+
+    text =<<-EOF
+#: :filename=BLADDER_11_and_12#:namespace=Hsa/feb2014#:type=:double
+#Genomic Mutation	Ensembl Gene ID	affected	damaged	splicing	broken	Sample
+12:54423561:A	ENSG00000273049|ENSG00000197757|ENSG00000198353|ENSG00000273046	false|true|false|false	false|true|false|false	false|false|false|false	false|true|false|false	51106212
+    EOF
+
+    tsv = TSV.open(StringIO.new(text))
+  
+    index =  Association.index(tsv, :source => "Sample", :target => "Genomic Mutation", :merge => true, :persist_update => true)
+    assert_equal 4, index["51106212~12:54423561:A"][0].split(";;").length
+
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.16.1
+  version: 5.16.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-01-22 00:00:00.000000000 Z
+date: 2015-01-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake