removing several halt, adding debug message, getting smiles directly

4 files changed, 17 insertions, 16 deletions

diff --git a/fminer.rb b/fminer.rb
index 81725cd..00d11a0 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -334,7 +334,7 @@ post '/fminer/last/?' do
 
     training_dataset.data_entries.each do |compound,entry|
       begin
-        smiles = OpenTox::Compound.new(compound.to_s).to_smiles
+        smiles = OpenTox::Compound.smiles(compound.to_s)
       rescue
         LOGGER.warn "No resource for #{compound.to_s}"
         next
diff --git a/lazar.rb b/lazar.rb
index 4e5d41d..00f3216 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -37,8 +37,9 @@ end
 # @return [text/uri-list] Task URI 
 post '/lazar/?' do 
 
+  LOGGER.debug "building lazar model with params: "+params.inspect
   params[:subjectid] = @subjectid
-  halt 404, "No dataset_uri parameter." unless params[:dataset_uri]
+  raise OpenTox::NotFoundError.new "No dataset_uri parameter." unless params[:dataset_uri]
 	dataset_uri = params[:dataset_uri]
 
   task = OpenTox::Task.create("Create lazar model",url_for('/lazar',:full)) do |task|
@@ -75,7 +76,7 @@ post '/lazar/?' do
       if feature_generation_uri.match(/fminer/)
         lazar.feature_calculation_algorithm = "Substructure.match"
       else
-        halt 404, "External feature generation services not yet supported"
+        raise OpenTox::NotFoundError.new "External feature generation services not yet supported"
       end
       params[:subjectid] = @subjectid
       prediction_feature = OpenTox::Feature.find params[:prediction_feature], @subjectid
@@ -87,7 +88,7 @@ post '/lazar/?' do
     end
 
     training_features.load_all(@subjectid)
-		halt 404, "Dataset #{feature_dataset_uri} not found." if training_features.nil?
+		raise OpenTox::NotFoundError.new "Dataset #{feature_dataset_uri} not found." if training_features.nil?
 
     # sorted features for index lookups
 
diff --git a/openbabel.rb b/openbabel.rb
index 1644455..fedcb8a 100644
--- a/openbabel.rb
+++ b/openbabel.rb
@@ -49,7 +49,7 @@ get '/openbabel/:property' do
     response['Content-Type'] = 'application/rdf+xml'
     algorithm.to_rdfxml
   else
-    halt 404, "Unknown OpenBabel descriptor #{params[:property]}."
+    raise OpenTox::NotFoundError.new "Unknown OpenBabel descriptor #{params[:property]}."
   end
 end
 
@@ -89,7 +89,7 @@ post '/openbabel/:property' do
     descriptor = OpenBabel::OBDescriptor.find_type(params[:property])
     descriptor.predict(obmol).to_s
   else
-    halt 404, "Cannot calculate property #{params[:property]} with OpenBabel"
+    raise OpenTox::NotFoundError.new "Cannot calculate property #{params[:property]} with OpenBabel"
   end
 end
 
diff --git a/similarity.rb b/similarity.rb
index 060bd2b..faf43f9 100644
--- a/similarity.rb
+++ b/similarity.rb
@@ -2,25 +2,25 @@ require File.join(File.dirname(__FILE__),'dataset.rb')
 
 helpers do
 def find
-# + charges are dropped
-uri = uri(params[:splat].first.gsub(/(InChI.*) (.*)/,'\1+\2')) # reinsert dropped '+' signs in InChIs
-halt 404, "Dataset \"#{uri}\" not found." unless @set = Dataset.find(uri)
+  # + charges are dropped
+  uri = uri(params[:splat].first.gsub(/(InChI.*) (.*)/,'\1+\2')) # reinsert dropped '+' signs in InChIs
+  raise OpenTox::NotFoundError.new "Dataset \"#{uri}\" not found." unless @set = Dataset.find(uri)
 end
 
 def uri(name)
-name = URI.encode(name)
-uri = File.join Dataset.base_uri, name
-end
+  name = URI.encode(name)
+  uri = File.join Dataset.base_uri, name
+  end
 end
 
 get '/tanimoto/dataset/*/dataset/*/?' do
-find
-@set.tanimoto(uri(params[:splat][1]))
+  find
+  @set.tanimoto(uri(params[:splat][1]))
 end
 
 get '/weighted_tanimoto/dataset/*/dataset/*/?' do
-find
-@set.weighted_tanimoto(uri(params[:splat][1]))
+  find
+  @set.weighted_tanimoto(uri(params[:splat][1]))
 end