merge with helma/development

6 files changed, 155 insertions, 33 deletions

diff --git a/Rakefile b/Rakefile
index d52f60d..e60ffc7 100644
--- a/Rakefile
+++ b/Rakefile
@@ -30,10 +30,10 @@ namespace "fminer" do
     end
     puts `make ruby`
     Dir.chdir('../../last-utils')
-    puts `git fetch`
+    #puts `git fetch`
     # AM LAST: need branch 'experimental' until merged to master in last-utils
-    puts `git checkout -f -b experimental origin/experimental` 
-    puts `git checkout experimental`
+    #puts `git checkout -f -b experimental origin/experimental` 
+    puts `git checkout master`
     puts `git pull`
   end
 
@@ -63,10 +63,10 @@ namespace "fminer" do
     end
     puts `make ruby`
     Dir.chdir('../../last-utils')
-    puts `git fetch`
+    #puts `git fetch`
     # AM LAST: need branch 'experimental' until merged to master in last-utils
-    puts `git checkout -f -b experimental origin/experimental`
-    puts `git checkout experimental`
+    #puts `git checkout -f -b experimental origin/experimental`
+    puts `git checkout master`
     puts `git pull`
   end
 end
diff --git a/config.ru b/config.ru
index 67d8493..a1aab0d 100644
--- a/config.ru
+++ b/config.ru
@@ -2,3 +2,5 @@ require 'rubygems'
 require 'opentox-ruby'
 require 'config/config_ru'
 run Sinatra::Application
+set :raise_errors, false
+set :show_exceptions, false
\ No newline at end of file
diff --git a/last-utils b/last-utils
-Subproject 9bba490c02a5fea57d65b61e7f68e88ed72893c
+Subproject 324a179b992c7b8b6f52963d4912ce5f92fe81c
diff --git a/lazar.rb b/lazar.rb
index fc037a9..c8cf6ea 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -25,8 +25,8 @@ end
 # @param [String] dataset_uri Training dataset URI
 # @param [optional,String] prediction_feature URI of the feature to be predicted
 # @param [optional,String] feature_generation_uri URI of the feature generation algorithm 
-# @param [optional] - further parameters for the feature generation service 
-# @ return [text/uri-list] Task URI 
+# @param [optional,String] - further parameters for the feature generation service 
+# @return [text/uri-list] Task URI 
 post '/lazar/?' do 
 
   halt 404, "No dataset_uri parameter." unless params[:dataset_uri]
diff --git a/libfminer b/libfminer
-Subproject c72bb7d99bb7f583f009e44be426910fb44cd4f
+Subproject e0eee431ecb954328ff64e3cc48840c7003a276
diff --git a/openbabel.rb b/openbabel.rb
index a261866..3a873c0 100644
--- a/openbabel.rb
+++ b/openbabel.rb
@@ -1,28 +1,148 @@
-get '/openbabel/:smiles/:property/?' do 
+OBMOL_METHODS = {
+  "NumAtoms" =>       "Number of atoms",
+  "NumBonds" =>       "Number of bonds",
+  "NumHvyAtoms" =>    "Number of heavy atoms",
+  "NumResidues" =>    "Number of residues",
+  "NumRotors" =>      "Number of rotatable bonds",
+  "GetEnergy" =>      "Heat of formation for this molecule (in kcal/mol)",
+  "GetMolWt" =>       "Standard molar mass given by IUPAC atomic masses (amu)",
+  "GetExactMass" =>   "Mass given by isotopes (or most abundant isotope, if not specified)",
+  "GetTotalCharge" => "Total charge",
+}
+
+OBDESCRIPTOR_METHODS = { 
+  "HBA1" =>           "Number of hydrogen bond acceptors 1 (JoelLib)",
+  "HBA2" =>           "Number of hydrogen bond acceptors 2 (JoelLib)",
+  "HBD" =>            "Number of hydrogen bond donors (JoelLib)",
+  "L5" =>             "Lipinski rule of five",
+  "logP" =>           "Octanol/water partition coefficient",
+  "MR" =>             "Molar refractivity",
+  "MW" =>             "Molecular weight",
+  "nF" =>             "Number of fluorine atoms",
+  "nHal" =>           "Number of halogen atoms",
+  "spinMult" =>       "Total spin multiplicity",
+  "TPSA" =>           "Topological polar surface area",
+}
+
+# Get a list of OpenBabel algorithms
+# @return [text/uri-list] URIs of OpenBabel algorithms
+get '/openbabel' do
+  algorithms = OBMOL_METHODS.collect{|name,description| url_for("/openbabel/#{name}",:full)}
+  algorithms << OBDESCRIPTOR_METHODS.collect{|name,description| url_for("/openbabel/#{name}",:full)}
+  response['Content-Type'] = 'text/uri-list'
+  algorithms.join("\n")
+end
+
+# Get RDF/XML representation of OpenBabel algorithm
+# @return [application/rdf+xml] OWL-DL representation of OpenBabel algorithm
+get '/openbabel/:property' do
+  description = OBMOL_METHODS[params[:property]] if OBMOL_METHODS.include? params[:property]
+  description = OBDESCRIPTOR_METHODS[params[:property]] if OBDESCRIPTOR_METHODS.include? params[:property]
+  if description
+    algorithm = OpenTox::Algorithm::Generic.new(url_for("/openbabel/#{params[:property]}",:full))
+    algorithm.metadata = {
+      DC.title => params[:property],
+      DC.creator => "helma@in-silico.ch",
+      DC.description => description,
+      OT.isA => OTA.DescriptorCalculation,
+    }
+    response['Content-Type'] = 'application/rdf+xml'
+    algorithm.to_rdfxml
+  else
+    halt 404, "Unknown OpenBabel descriptor #{params[:property]}."
+  end
+end
+
+# Calculate OpenBabel descriptors
+# Supports the following OpenBabel methods (see OpenBabel API http://openbabel.org/api/2.2.0/)
+#   - NumAtoms       Number of atoms
+#   - NumBonds       Number of bonds
+#   - NumHvyAtoms    Number of heavy atoms
+#   - NumResidues    Number of residues
+#   - NumRotors      Number of rotatable bonds
+#   - GetEnergy      Heat of formation for this molecule (in kcal/mol)
+#   - GetMolWt       Standard molar mass given by IUPAC atomic masses (amu)
+#   - GetExactMass   Mass given by isotopes (or most abundant isotope, if not specified)
+#   - GetTotalCharge Total charge
+#   - HBA1           Number of hydrogen bond acceptors 1 (JoelLib)
+#   - HBA2           Number of hydrogen bond acceptors 2 (JoelLib)
+#   - HBD            Number of hydrogen bond donors (JoelLib)
+#   - L5             Lipinski rule of five
+#   - logP           Octanol/water partition coefficient
+#   - MR             Molar refractivity
+#   - MW             Molecular weight
+#   - nF             Number of fluorine atoms
+#   - nHal           Number of halogen atoms
+#   - spinMult       Total spin multiplicity
+#   - TPSA           Topological polar surface area
+# @param [String] compound_uri Compound URI
+# @return [String] descriptor value
+post '/openbabel/:property' do
 	obconversion = OpenBabel::OBConversion.new
 	obmol = OpenBabel::OBMol.new
-	obconversion.set_in_and_out_formats 'smi', 'can'
-	case params[:property]
-	when 'logP'
-		#logP = OpenBabel::OBLogP.new
-		#logP.predict(obmol)
-		"not yet implemented"
-	when 'psa'
-		#psa = OpenBabel::OBPSA.new
-		"not yet implemented"
-	when 'mr'
-		#mr = OpenBabel::OBMR.new
-		"not yet implemented"
-	else
-		begin
-			obconversion.read_string obmol, params[:smiles]
-		rescue
-			halt 404, "Incorrect Smiles string #{params[:smiles]}"
-		end
-		begin
-			eval("obmol.#{params[:property]}").to_s
-		rescue
-			halt 404, "Could not calculate property #{params[:property]}"
-		end
-	end
+  compound = OpenTox::Compound.new params[:compound_uri]
+	obconversion.set_in_and_out_formats 'inchi', 'can'
+  obconversion.read_string obmol, compound.to_inchi
+  if OBMOL_METHODS.keys.include? params[:property]
+    eval("obmol.#{params[:property].underscore}").to_s
+  elsif OBDESCRIPTOR_METHODS.keys.include? params[:property]
+    descriptor = OpenBabel::OBDescriptor.find_type(params[:property])
+    descriptor.predict(obmol).to_s
+  else
+    halt 404, "Cannot calculate property #{params[:property]} with OpenBabel"
+  end
+end
+
+# Calculate all OpenBabel descriptors for a dataset
+# @param [String] dataset_uri Dataset URI
+# @return [text/uri-list] Task URI
+post '/openbabel' do
+  task = OpenTox::Task.create("Calculating OpenBabel descriptors for #{params[:dataset_uri]}", url_for('/openbabel',:full)) do 
+
+    dataset = OpenTox::Dataset.find(params[:dataset_uri])
+    result_dataset = OpenTox::Dataset.create
+    result_dataset.add_metadata({
+      DC.title => "OpenBabel descriptors for " + dataset.metadata[DC.title].to_s,
+      DC.creator => url_for('/openbabel',:full),
+      OT.hasSource => url_for('/openbabel', :full),
+      OT.parameters => [
+        { DC.title => "dataset_uri", OT.paramValue => params[:dataset_uri] },
+      ]
+    })
+
+    obconversion = OpenBabel::OBConversion.new
+    obmol = OpenBabel::OBMol.new
+    obconversion.set_in_and_out_formats 'inchi', 'can'
+
+    OBMOL_METHODS.merge(OBDESCRIPTOR_METHODS).each do |name,description|
+      feature_uri = File.join result_dataset.uri, "feature", "openbabel", name
+      metadata = {
+        OT.hasSource => url_for("/openbabel/#{name}", :full),
+        DC.description => description,
+        DC.title => name,
+      }
+      result_dataset.add_feature feature_uri, metadata
+    end
+
+    dataset.compounds.each do |compound_uri|
+      compound = OpenTox::Compound.new(compound_uri)
+      obconversion.read_string obmol, compound.to_inchi
+      #result_dataset.add_compound compound_uri
+      OBMOL_METHODS.keys.each do |name|
+        feature_uri = File.join result_dataset.uri, "feature", "openbabel", name
+        value = eval("obmol.#{name.underscore}").to_f
+        result_dataset.add compound_uri, feature_uri, value
+      end
+      OBDESCRIPTOR_METHODS.keys.each do |name|
+        feature_uri = File.join result_dataset.uri, "feature", "openbabel", name
+        value = OpenBabel::OBDescriptor.find_type(params[:property]).predict(obmol).to_f
+        result_dataset.add compound_uri, feature_uri, value
+      end
+    end
+    result_dataset.save
+    result_dataset.uri
+  end
+  response['Content-Type'] = 'text/uri-list'
+  halt 503,task.uri+"\n" if task.status == "Cancelled"
+  halt 202,task.uri.to_s+"\n"
 end