handle error

bin/sparql_taxon.rb

@@ -9,7 +9,12 @@
 
 File.read(taxonomy_list).split("\n").each do |taxon|
   i = 0
+  loop_count = 0
   while i % limit == 0
+    if loop_count * limit != i
+      $stderr.puts "Error: Failed to retrieve taxon:#{taxon} in loop_count:#{loop_count}"
+      break
+    end
     query = query_template.sub('{{taxon}}', taxon) + " OFFSET #{i} LIMIT #{limit}"
     cmd = "curl -s -H 'Accept: text/csv' --data-urlencode 'query=#{query}' #{endpoint} | sed -E 1d"
     IO.popen(cmd) do |io|
@@ -18,5 +23,6 @@
         i += 1
       end
     end
+    loop_count += 1
   end
 end