lib/rbbt/tsv/change_id.rb in rbbt-util-5.41.1 vs lib/rbbt/tsv/change_id.rb in rbbt-util-5.42.0

@@ -6,13 +6,13 @@
   def self.change_key(tsv, format, options = {}, &block)
     options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers
 
     identifiers, persist_input = Misc.process_options options, :identifiers, :persist_input
 
-    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace
+    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? && tsv.namespace && 
+      defined?(Organism) && Organism.identifiers(tsv.namespace).exists?
 
-
     if ! tsv.fields.include?(format)
       new = {}
       tsv.each do |k,v|
         if v === String or v === Array
           new[k] = v.dup 
@@ -56,10 +56,13 @@
   def self.swap_id(tsv, field, format, options = {}, &block)
     options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers, :compact => true
 
     identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
     identifiers = tsv.identifier_files.first if identifiers.nil?
-    identifiers = Organism.identifiers(tsv.namespace) if defined?(Organism) && identifiers.nil? && tsv.namespace && Organism.identifiers(tsv.namespace).exists?
+
+    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? && tsv.namespace && 
+      defined?(Organism) && Organism.identifiers(tsv.namespace).exists?
+
     identifiers.namespace ||= tsv.namespace
 
     fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil 
     #index = identifiers.index :target => format, :fields => fields, :persist => persist_input, :order => true