- Using babel now instead of molconvert to generate inchikeys

lib/classyfire_api.rb

@@ -1,5 +1,6 @@
 require 'JSON'
 require 'csv'
+require 'rest-client'
 
 module ClassyFireAPI
   URL = 'http://classyfire.wishartlab.com'
@@ -60,14 +61,14 @@ module ClassyFireAPI
   # @param format [String] the format of the query, 'text' (either JSON, CSV, or SDF)
   # @return [Text] A text file displaying the classification results for the entity in the specified format.
   def ClassyFireAPI.get_entity_classification(inchikey,format="json")
-    inchikey_id = inchikey.to_s.gsub('InChIKey=','')
+    # inchikey_id = inchikey.to_s.gsub('InChIKey=','')
     begin
       if format == "json"
-        RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :json
+        RestClient.get "#{URL}/entities/#{inchikey}.#{format}", :accept => :json
       elsif format == "sdf"
-        RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :sdf
+        RestClient.get "#{URL}/entities/#{inchikey}.#{format}", :accept => :sdf
       elsif format == "csv"
-        RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :csv
+        RestClient.get "#{URL}/entities/#{inchikey}.#{format}", :accept => :csv
       end 
     rescue RestClient::ResourceNotFound => e
       e.response
@@ -148,7 +149,7 @@ module ClassyFireAPI
   # @param: slice_length [Integer] The maximum number of entries for each query input (the whole file 
   # is fragmented into n part of #slice_length entries each).
   # @param: start [Integer] The starting index. Submit framgments from the index 'start'.
-  def ClassyFireAPI.submit_query_input_in_chunks(input_file,slice_length, start, type='STRUCTURE')
+  def ClassyFireAPI.submit_query_input_in_chunks(input_file,slice_length=1000, start=1, type='STRUCTURE')
     @start_time = Time.now
     absolute_path = File.expand_path(input_file)
     f             = File.open(absolute_path, 'r')
@@ -161,7 +162,7 @@ module ClassyFireAPI
       if sline.length == 1
         input <<"#{sline[0]}"
       elsif sline.length >= 2
-        input <<"#{sline[0]}\t#{sline[1]}"
+        input <<"#{sline[1]}\t#{sline[0]}"
       end
     end
 
@@ -169,12 +170,12 @@ module ClassyFireAPI
     subdivised_groups = input.uniq.each_slice(slice_length).to_a
     puts "nr of subdivised_groups: #{subdivised_groups.length}"
     puts subdivised_groups[0]
-    sleeping_time = 120
+    sleeping_time = 360
-    initial_nr_of_jobs = 60
+    initial_nr_of_jobs = 40
     i = start
 
     while i <  initial_nr_of_jobs
-      title     = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{i}"
+      title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{i}"
 
       if i <= subdivised_groups.length
         begin
@@ -186,6 +187,8 @@ module ClassyFireAPI
           puts e.backtrace.inspect
         end
         i = i + 1
+      else
+        break
       end
     end
 
@@ -193,7 +196,7 @@ module ClassyFireAPI
     sleep(sleeping_time)
     puts "Waking up at #{Time.now - @start_time}"
 
-    while i < subdivised_groups.length
+    while i >= initial_nr_of_jobs && i < subdivised_groups.length
       k = 0
       for k in (i..(i+80))
         title     = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{k}"
@@ -367,7 +370,6 @@ module ClassyFireAPI
         e.message
       end        
     end
-
     res += "]}"
     f_output.print res
   end
@@ -402,7 +404,8 @@ module ClassyFireAPI
         puts i
         # puts "#{key} :: #{h[key]}"
         begin
-          inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
+          inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0] 
+          # inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
           # puts inchikey
           qr = JSON.parse(ClassyFireAPI.get_entity_classification(inchikey,format="json"))
           qr['identifier'] = key
@@ -417,7 +420,8 @@ module ClassyFireAPI
       key = h.keys[-1]
       # puts "#{key} :: #{h[key]}"
       begin
-        inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
+        inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
+        # inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
         # puts inchikey
         qr = JSON.parse(ClassyFireAPI.get_entity_classification(inchikey,format="json"))
         qr['identifier'] = key
@@ -459,7 +463,8 @@ module ClassyFireAPI
         puts i
         # puts "#{key} :: #{h[key]}"
         begin
-          inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
+          inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
+          # inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
           # puts inchikey
           qr = ClassyFireAPI.get_entity_classification(inchikey,format="sdf")
           if qr.include?("The page you were looking for doesn't exist")
@@ -478,9 +483,9 @@ module ClassyFireAPI
         i += 1
       end
       key = h.keys[-1]
-      # puts "#{key} :: #{h[key]}"
       begin
-        inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
+        inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
+        # inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
         # puts inchikey
         qr = ClassyFireAPI.get_entity_classification(inchikey,format="sdf")
         if qr.include?("The page you were looking for doesn't exist")
@@ -497,6 +502,5 @@ module ClassyFireAPI
         e.message
       end        
     end
-    # f_output.print res
   end
 end