rbbt-util 5.8.1 → 5.8.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 8d8d53efd7203512d28462d609bf6f52a1c492c0
+  metadata.gz: 242874c88c6d442034c3e929a735f9d8b5613f53
+  data.tar.gz: e7b40e285fbc4faf3961fdda643c9278eba21096
 SHA512:
-  metadata.gz: f858ffbc83f9a199a22c9c1a49b1d40f0de1f1ea8e9979820901040a23a9eb3c7077f354aac6260876c7f04941bd2a2eea976262f6b73a1a46687421fbc441f7
-  data.tar.gz: 3dd1ed9a2dcf25fa5939935f27ad026df16c10a8e464743122e7f6725f8317db82cdee7c5f01b5c7866a442aee9ac9cfc963eca6e276eba372bacc6749ee84d2
+  metadata.gz: 022e09717e9f321571373dcd56e3f1a589fdcf37d731a9db885535964e59f1209c6071017d7efe15a60cdc309538c675d2db9dbf9baae21564c1fc7e071ae13a
+  data.tar.gz: 244ad59bc44e11e54a015efd5ac17f69c496b35051807118ac9b931fb08a3196d47a6030966007dca9d4402e4be6738cbc1f19fd484f8c3a4daa66372bf191fc

data/lib/rbbt/association.rb

@@ -78,12 +78,11 @@ module Association
       :persist => false,
       :key_field => all_fields.index(source), 
       :fields => fields.collect{|f| String === f ? all_fields.index(f): f },
-      :type => options[:type].to_s == :flat ? :flat : :double,
+      :type => (options[:type] and options[:type].to_sym == :flat) ? :flat : :double,
       :unnamed => true,
-      :merge => options[:type].to_s == :flat ? false : true
+      :merge => (options[:type] and options[:type].to_sym == :flat) ? false : true
     })
 
-    # Preserve first line, which would have been considered a header otherwise
     open_options["header_hash"] = "#" if options["header_hash"] == ""
 
     field_headers = all_fields.values_at *open_options[:fields]
@@ -129,6 +128,7 @@ module Association
       end
     end
 
+
     # Translate target 
     if target_final_format and target_field != target_final_format and
       Entity.formats[target_field] and
@@ -140,11 +140,12 @@ module Association
       tsv.key_field = "MASKED"
 
       tsv.with_unnamed do
-        tsv = tsv.swap_id tsv.fields.first, target_final_format, :identifiers => Organism.identifiers(tsv.namespace), :persist => true
+        tsv = tsv.swap_id tsv.fields.first, target_final_format, :identifiers => Organism.identifiers(tsv.namespace), :persist => true, :compact => true
       end
 
       tsv.key_field = save_key_field 
     end
+
     tsv
   end
 

data/lib/rbbt/tsv/attach/util.rb

@@ -307,6 +307,7 @@ module TSV
     in_namespace = options[:in_namespace]
 
     identifiers1 = tsv1.identifier_files || []
+    identifiers1 += options[:identifiers] if options[:identifiers]
     identifiers2 = tsv2.identifier_files || []
 
     identifiers1.unshift tsv1

data/lib/rbbt/tsv/change_id.rb

@@ -17,6 +17,7 @@ module TSV
       else
         tsv = tsv.attach identifiers, :fields => [format], :persist_input => true
       end
+
       tsv = tsv.reorder(format, tsv.fields - [format])
 
       tsv = tsv.to_flat  if orig_type == :flat
@@ -35,9 +36,9 @@ module TSV
   end
 
   def self.swap_id(tsv, field, format, options = {}, &block)
-    options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers
+    options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers, :compact => true
 
-    identifiers, persist_input = Misc.process_options options, :identifiers, :persist
+    identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
 
     fields = identifiers.all_fields.include?(field)? [field] : nil
     index = identifiers.index :target => format, :fields => fields, :persist => persist_input
@@ -54,7 +55,9 @@ module TSV
         end
       else
         tsv.through do |k,v|
-          v[pos] = index.values_at(*v[pos])
+          _values = index.values_at(*v[pos])
+          _values.compact! if compact
+          v[pos] = _values
           tsv[k] = v
         end
       end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.8.1
+  version: 5.8.2
 platform: ruby
 authors:
 - Miguel Vazquez