openbabel

lib/classyfire_api.rb

@@ -1,7 +1,7 @@
 require 'JSON'
 require 'csv'
 require 'rest-client'
-require 'openbabel'
+# require 'openbabel'
 # require 'node_resource.rb'
 
 module ClassyFireAPI
@@ -167,7 +167,7 @@ module ClassyFireAPI
         #ID\tSMILES (OR INCHI, OR VALID IUPAC NAME)
         input <<"#{sline[0]}\t#{sline[1]}"
       end
-      input <<"#{sline[0]}"
+      # input <<"#{sline[0]}"
     end
 
     query_ids = []
@@ -184,16 +184,16 @@ module ClassyFireAPI
 
       if i <= subdivised_groups.length
         puts "\n\n\n\n---------------------- -----------"
-        # begin
+        begin
           puts "submitting #{title}"
-          puts subdivised_groups[i-1].join("\n")
+          # puts subdivised_groups[i-1].join("\n")
           q       = submit_query(title,subdivised_groups[i-1].join("\n"),type)
           # puts q
           query_ids << JSON.parse(q)['id']
-        # rescue Exception => e  
-          # puts e.message  
-          # puts e.backtrace.inspect
-        # end
+        rescue Exception => e  
+          puts e.message  
+          puts e.backtrace.inspect
+        end
         i = i + 1
       else
         break
@@ -241,7 +241,7 @@ module ClassyFireAPI
     if File.directory?(folder)
       Dir.foreach(folder) do |filename|
         puts "Filename: #{filename}"
-        ClassyFireAPI.submit_query_input_in_chunks(folder+"/"+filename,slice_length, type) unless filename == "." || filename == ".." || filename == ".DS_Store"
+        ClassyFireAPI.submit_query_input_in_chunks(folder+"/"+filename,slice_length, type) unless filename[0] == "." || File.directory?(filenmae)
       end
     else
       $stderr.puts "#{folder} is not a folder."