Merge branch 'release/2.0.0'v2.0.0

1 files changed, 14 insertions, 9 deletions

diff --git a/application.rb b/application.rb
index 0a3794a..eba06a4 100644
--- a/application.rb
+++ b/application.rb
@@ -7,11 +7,12 @@ ENV["CLASSPATH"] = "#{ENV["CLASSPATH"]}:#{java_dir}:#{cdk}:#{jchempaint}"
 
 require 'rubygems'
 require 'rjb'
-gem "opentox-ruby", "~> 1"
+gem "opentox-ruby", "~> 2"
 require 'opentox-ruby'
 
 before do
-  @inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'').sub(/\/smarts.*$/,'').sub(/\/image/,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
+  @inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'').sub(/\/smarts.*$/,'').sub(/\/image/,'').sub(/\?.*$/,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
+  puts @inchi
 end
 
 # Display activating (red) and deactivating (green) substructures. Overlaps betwen activating and deactivating structures are marked in yellow.
@@ -35,12 +36,7 @@ get %r{/(.+)/smarts/activating/(.*)/deactivating/(.*)$} do |inchi,activating,dea
   end
 end
 
-# Get png image
-# @return [image/png] Image data
-get %r{/(.+)/image} do |inchi| # catches all remaining get requests
-  smiles = OpenTox::Compound.from_inchi(@inchi).to_smiles
-  content_type "image/png"
-  attachment "#{smiles}.png"
+def png_from_smiles(smiles)
   begin
     Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
     Rjb::import('Structure').new(smiles,150).show
@@ -49,6 +45,15 @@ get %r{/(.+)/image} do |inchi| # catches all remaining get requests
   end
 end
 
+# Get png image
+# @return [image/png] Image data
+get %r{/(.+)/image} do |inchi| # catches all remaining get requests
+  smiles = OpenTox::Compound.from_inchi(@inchi).to_smiles
+  content_type "image/png"
+  attachment "#{smiles}.png"
+  png_from_smiles(smiles)
+end
+
 # Get compound representation
 # @param [optinal, HEADER] Accept one of `chemical/x-daylight-smiles, chemical/x-inchi, chemical/x-mdl-sdfile, chemical/x-mdl-molfile, text/plain, image/gif, image/png`, defaults to chemical/x-daylight-smiles
 # @example Get smiles
@@ -76,7 +81,7 @@ get %r{/(.+)} do |inchi| # catches all remaining get requests
     OpenTox::Compound.from_inchi(@inchi).to_gif
   when "image/png"
     response['Content-Type'] = "image/png"
-    OpenTox::Compound.from_inchi(@inchi).to_png
+    png_from_smiles(OpenTox::Compound.from_inchi(@inchi).to_smiles)
   when "text/plain"
     response['Content-Type'] = "text/plain"
     uri = File.join @@cactus_uri,@inchi,"names"