batch download with extra duplicate on ID message column

1 files changed, 12 insertions, 2 deletions

diff --git a/batch.rb b/batch.rb
index 2dd9359..0002279 100644
--- a/batch.rb
+++ b/batch.rb
@@ -65,12 +65,22 @@ module OpenTox
             compound = nil
           end
           if compound.nil? # compound parsers may return nil
-            #warn "Cannot parse #{compound_format} compound '#{identifier}' at line #{i+2} of #{source}, all entries are ignored."
-            batch.compounds  << "Cannot parse #{compound_format} compound '#{identifier}' at line #{i+2} of #{source}."
+            batch.warnings << "Cannot parse #{compound_format} compound '#{identifier}' at line #{i+2} of #{source}."
             next
           end
           batch.compounds << compound.id
         end
+        batch.compounds.duplicates.each do |duplicate|
+          dup = Compound.find duplicate
+          positions = []
+          batch.compounds.each_with_index do |co,i|
+            c = Compound.find co
+            if !c.blank? and c.inchi and c.inchi == dup.inchi
+              positions << i+1
+            end
+          end
+          batch.warnings << "Duplicate compound at ID #{positions.join(' and ')}."
+        end
         batch.save
       end
       batch