local inchi conversion, url_for removed, gem dependencies in gemspec

6 files changed, 67 insertions, 15 deletions

diff --git a/Gemfile b/Gemfile
index 47d91b5..2142a18 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,6 +1,4 @@
 source :gemcutter
-#gemspec
+gemspec
 gem "opentox-server", :path => "../opentox-server"
 gem "opentox-client", :path => "../opentox-client"
-gem "emk-sinatra-url-for", "~>0.2.1"
-gem "roo", "~>1.10.1"
diff --git a/application.rb b/application.rb
index cae6066..dd6a62d 100644
--- a/application.rb
+++ b/application.rb
@@ -3,7 +3,7 @@
 # Author: Christoph Helma, Andreas Maunz
 
 require 'roo'
-require 'sinatra/url_for'
+require './compound.rb'
 
 # Library code
 $logger.debug "Dataset booting: #{$dataset.collect{|k,v| "#{k}: '#{v}'"} }"
diff --git a/compound.rb b/compound.rb
new file mode 100644
index 0000000..cb194ff
--- /dev/null
+++ b/compound.rb
@@ -0,0 +1,58 @@
+require "openbabel"
+module OpenTox
+
+  # Perform OpenBabel conversions locally in order to prevent net overhead
+	class Compound 
+
+    attr_writer :smiles, :inchi
+
+    # Create a compound from smiles string
+    # @example
+    #   compound = OpenTox::Compound.from_smiles("c1ccccc1")
+    # @param [String] smiles Smiles string
+    # @return [OpenTox::Compound] Compound
+    def self.from_smiles service_uri, smiles, subjectid=nil
+			inchi = obconversion(smiles,'smi','inchi')
+      compound = Compound.new(File.join service_uri, inchi)
+      compound.inchi = inchi
+      compound.smiles = smiles
+      compound
+    end
+
+    # Create a compound from inchi string
+    # @param [String] smiles InChI string
+    # @return [OpenTox::Compound] Compound
+    def self.from_inchi service_uri, inchi, subjectid=nil
+      compound = Compound.new(File.join service_uri, inchi)
+      compound.inchi = inchi
+      compound
+    end
+
+    # Create a compound from sdf string
+    # @param [String] smiles SDF string
+    # @return [OpenTox::Compound] Compound
+    def self.from_sdf service_uri, sdf, subjectid=nil
+			inchi = obconversion(sdf,'sdf','inchi')
+      compound = Compound.new(File.join service_uri, inchi)
+      compound.inchi = inchi
+      compound
+    end
+
+    private
+    
+    # Convert identifier from OpenBabel input_format to OpenBabel output_format
+    def self.obconversion(identifier,input_format,output_format)
+      obconversion = OpenBabel::OBConversion.new
+      obmol = OpenBabel::OBMol.new
+      obconversion.set_in_and_out_formats input_format, output_format
+      obconversion.read_string obmol, identifier
+      case output_format
+      when /smi|can|inchi/
+        obconversion.write_string(obmol).gsub(/\s/,'').chomp
+      else
+        obconversion.write_string(obmol)
+      end
+    end
+  end
+
+end
diff --git a/dataset.gemspec b/dataset.gemspec
index a6a135b..d82e8b3 100644
--- a/dataset.gemspec
+++ b/dataset.gemspec
@@ -18,8 +18,7 @@ Gem::Specification.new do |s|
 
   # specify any dependencies here; for example:
   s.add_runtime_dependency "opentox-server"
-  s.add_runtime_dependency 'roo'
-  #s.add_runtime_dependency 'axlsx'
-  #s.add_runtime_dependency 'simple_xlsx_writer'
+  s.add_runtime_dependency 'roo', "~>1.10.1"
+  s.add_runtime_dependency "openbabel", "~>2.3.1.5"
   s.post_install_message = "Please configure your service in ~/.opentox/config/dataset.rb"
 end
diff --git a/webapp/dataset.rb b/webapp/dataset.rb
index c75b722..5bf8799 100644
--- a/webapp/dataset.rb
+++ b/webapp/dataset.rb
@@ -12,7 +12,7 @@ module OpenTox
     get '/dataset/*/pc' do
       dataset=params["captures"][0]
       algorithms = YAML::load_file File.join(ENV['HOME'], ".opentox", "config", "pc_descriptors.yaml")
-      list = (algorithms.keys.sort << "AllDescriptors").collect { |name| url_for("/dataset/#{dataset}/pc/#{name}",:full) }.join("\n") + "\n"
+      list = (algorithms.keys.sort << "AllDescriptors").collect { |name| to("/dataset/#{dataset}/pc/#{name}",:full) }.join("\n") + "\n"
       format_output(list)
     end
     
@@ -43,7 +43,7 @@ module OpenTox
     
       if descriptors 
         # Contents
-        algorithm = OpenTox::Algorithm.new(url_for("/dataset/#{dataset}/pc/#{params[:descriptor]}",:full))
+        algorithm = OpenTox::Algorithm.new(to("/dataset/#{dataset}/pc/#{params[:descriptor]}",:full))
         mmdata = {
           DC.title => params[:descriptor],
           DC.creator => "andreas@maunz.de",
@@ -86,7 +86,7 @@ module OpenTox
                                  $task[:uri],
                                  @subjectid,
                                  { RDF::DC.description => "Calculating PC descriptors",
-                                   RDF::DC.creator => url_for("/dataset/#{dataset}/pc",:full)
+                                   RDF::DC.creator => to("/dataset/#{dataset}/pc",:full)
                                  }
                                 ) do |task|
 
@@ -105,8 +105,8 @@ module OpenTox
                { DC.title => key, OT.paramValue => (val.nil? ? "" : val) }
              }
              result_ds[DC.title] = single_cmpd_ds[DC.title]
-             result_ds[DC.creator] = url_for("/dataset/#{dataset}/pc",:full)
-             result_ds[OT.hasSource] = url_for("/dataset/#{dataset}/pc",:full)
+             result_ds[DC.creator] = to("/dataset/#{dataset}/pc",:full)
+             result_ds[OT.hasSource] = to("/dataset/#{dataset}/pc",:full)
            end
            result_ds << [ cmpd ] + single_cmpd_ds.data_entries[0]
          }
diff --git a/webapp/sinatra.rb b/webapp/sinatra.rb
index a516496..fd0d354 100644
--- a/webapp/sinatra.rb
+++ b/webapp/sinatra.rb
@@ -5,9 +5,6 @@
 module OpenTox
   class Application < Service
 
-    # Get url_for support
-    helpers Sinatra::UrlForHelper
-
     # Conveniently accessible from anywhere within the Application class,
     # it negotiates the appropriate output format based on object class
     # and requested MIME type.