lib/gi.rb in mspire-0.1.7 vs lib/gi.rb in mspire-0.2.0

@@ -38,22 +38,27 @@
 
 class GI
   BATCH_SIZE = 500
   # takes an array of gi numbers and returns an array of annotation
   # This allows use of the batch search mode on NCBI
+  # returns nil if no internet connection
   def self.gi2annot(list_of_gi_numbers) 
+    annots = []
     loop do
       batch = list_of_gi_numbers.slice!(0..BATCH_SIZE)
       if batch.size == 0 then break end
       string = batch.join(",")
       url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=protein&retmode=xml&id=#{string}"
       #puts url
-      annots = []
-      open(url) do |handle|
-        annots = parse_etool_output(handle)
+      begin
+        open(url) do |handle|
+          annots.push( *(parse_etool_output(handle)) )
+        end
+      rescue SocketError
+        return nil
       end
-      annots
     end
+    annots
   end
 
   protected
   # Returns a list of Annotation strings
   def self.parse_etool_output(handle)