Fixed documentation

7 files changed, 29 insertions, 245 deletions

diff --git a/application.rb b/application.rb
index 539ac2b..ef123da 100644
--- a/application.rb
+++ b/application.rb
@@ -1,3 +1,4 @@
+# Java Klimbim
 ENV["JAVA_HOME"] = "/usr/lib/jvm/java-6-sun" unless ENV["JAVA_HOME"]
 ENV["JOELIB2"] = File.join File.expand_path(File.dirname(__FILE__)),"java"
 deps = []
@@ -8,16 +9,20 @@ jars = Dir[ENV["JOELIB2"]+"/*.jar"].collect {|f| File.expand_path(f) }
 deps = deps + jars
 ENV["CLASSPATH"] = deps.join(":")
 
-
 require 'rubygems'
-# AM LAST: can include both libs, no problems
-require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/libbbrc/bbrc') # has to be included before openbabel, otherwise we have strange SWIG overloading problems
-require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/liblast/last') # has to be included before openbabel, otherwise we have strange SWIG overloading problems
-require File.join(File.expand_path(File.dirname(__FILE__)), 'last-utils/lu.rb') # AM LAST
+
+
+# fminer libs to be included before openbabel, otherwise strange SWIG overloading problems
+require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/libbbrc/bbrc') 
+require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/liblast/last')
+require File.join(File.expand_path(File.dirname(__FILE__)), 'last-utils/lu.rb')
+
 gem "opentox-ruby", "~> 3"
 require 'opentox-ruby'
 require 'rjb'
 
+
+# main
 require 'fminer.rb'
 require 'lazar.rb'
 require 'fs.rb'
diff --git a/feature_generation.rb b/feature_generation.rb
deleted file mode 100644
index e822404..0000000
--- a/feature_generation.rb
+++ /dev/null
@@ -1,49 +0,0 @@
-# Get list if pc descriptor calculation algorithms
-#
-# @return [text/uri-list] URIs of pc descriptor calculation algorithms
-get '/pcdesc' do
-algorithm = OpenTox::Algorithm::Generic.new(url_for('/pcdesc',:full))
-  algorithm.metadata = {
-    DC.title => 'Physico-chemical (PC) descriptor calculation',
-    DC.creator => "andreas@maunz.de, vorgrimmlerdavid@gmx.de",
-    RDF.type => [OT.Algorithm,OTA.DescriptorCalculation],
-    OT.parameters => [
-      { DC.description => "Dataset URI", OT.paramScope => "mandatory", DC.title => "dataset_uri" },
-      { DC.description => "PC type", OT.paramScope => "mandatory", DC.title => "pc_type" },
-  ]
-  }
-  case request.env['HTTP_ACCEPT']
-  when /text\/html/
-    content_type "text/html"
-    OpenTox.text_to_html algorithm.to_yaml
-  when /application\/x-yaml/
-    content_type "application/x-yaml"
-    algorithm.to_yaml
-  else
-    response['Content-Type'] = 'application/rdf+xml'  
-    algorithm.to_rdfxml
-  end
-end
-
-# Run pc descriptor calculation algorithm on dataset
-#
-# @param [String] dataset_uri URI of the training dataset
-# @param [String] feature_dataset_uri URI of the feature dataset
-# @return [text/uri-list] Task URI
-post '/pcdesc' do
-  response['Content-Type'] = 'text/uri-list'
-  raise OpenTox::NotFoundError.new "Please submit a dataset_uri." unless params[:dataset_uri]
-  raise "No PC type given" unless params["pc_type"]
-
-  task = OpenTox::Task.create("PC descriptor calculation for dataset ", @uri) do |task|
-    types = params[:pc_type].split(",")
-    if types.include?("joelib")
-      Rjb.load(nil,["-Xmx64m"]) 
-      s = Rjb::import('JoelibFc')
-    end
-    OpenTox::Algorithm.pc_descriptors( { :dataset_uri => params[:dataset_uri], :pc_type => params[:pc_type], :rjb => s, :task => task } )
-  end
-  raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
-  halt 202,task.uri.to_s+"\n"
-end
-
diff --git a/fs.rb b/fs.rb
index 469fa87..7ee8c30 100644
--- a/fs.rb
+++ b/fs.rb
@@ -1,7 +1,11 @@
+# fs.rb
+# Feature Selection
+# Author: Andreas Maunz
+
+
 # Get list of feature selection algorithms
-#
 # @return [text/uri-list] URIs of feature selection algorithms
-get '/feature_selection/?' do
+get '/fs/?' do
   list = [ url_for('/feature_selection/rfe', :full) ].join("\n") + "\n"
   case request.env['HTTP_ACCEPT']
   when /text\/html/
@@ -13,9 +17,9 @@ get '/feature_selection/?' do
   end
 end
 
-# Get RDF/XML representation of feature_selection rfe algorithm
-# @return [application/rdf+xml] OWL-DL representation of feature_selection rfe algorithm
-get "/feature_selection/rfe/?" do
+# Get representation of recursive feature elimination algorithm
+# @return [application/rdf+xml] OWL-DL representation of recursive feature elimination algorithm
+get "/fs/rfe/?" do
   algorithm = OpenTox::Algorithm::Generic.new(url_for('/feature_selection/rfe',:full))
   algorithm.metadata = {
     DC.title => 'recursive feature elimination',
@@ -44,9 +48,9 @@ get "/feature_selection/rfe/?" do
 end
 
 # Run rfe algorithm on dataset
-#
 # @param [String] dataset_uri URI of the training dataset
-# @param [String] feature_dataset_uri URI of the feature dataset
+# @param [String] prediction_feature URI
+# @param [String] feature_dataset_uri URI
 # @return [text/uri-list] Task URI
 post '/feature_selection/rfe/?' do 
 
diff --git a/openbabel.rb b/openbabel.rb
deleted file mode 100644
index 463663e..0000000
--- a/openbabel.rb
+++ /dev/null
@@ -1,148 +0,0 @@
-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,
-      RDF.type => [OTA.DescriptorCalculation],
-    }
-    response['Content-Type'] = 'application/rdf+xml'
-    algorithm.to_rdfxml
-  else
-    raise OpenTox::NotFoundError.new "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
-  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
-    raise OpenTox::NotFoundError.new "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'
-  raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
-  halt 202,task.uri.to_s+"\n"
-end
diff --git a/pc.rb b/pc.rb
index 5c38052..37130dd 100644
--- a/pc.rb
+++ b/pc.rb
@@ -3,8 +3,8 @@
 # Author: Andreas Maunz
 
 
-# Get a list of pc algorithms
-# @return [text/uri-list] URIs of algorithms
+# Get a list of descriptor calculation algorithms
+# @return [text/uri-list] URIs of descriptor calculation algorithms
 get '/pc' do
   algorithms = YAML::load_file File.join(ENV['HOME'], ".opentox", "config", "pc_descriptors.yaml")
   response['Content-Type'] = 'text/uri-list'
@@ -19,8 +19,8 @@ get '/pc' do
   end
 end
 
-# Get RDF/XML representation of OpenBabel algorithm
-# @return [application/rdf+xml] OWL-DL representation of OpenBabel algorithm
+# Get representation of descriptor calculation algorithm
+# @return [application/rdf+xml] OWL-DL representation of descriptor calculation algorithm
 get '/pc/:descriptor' do
   descriptors = YAML::load_file File.join(ENV['HOME'], ".opentox", "config", "pc_descriptors.yaml")
   alg_params = [ { DC.description => "Dataset URI", OT.paramScope => "mandatory", DC.title => "dataset_uri" } ]
@@ -65,9 +65,10 @@ get '/pc/:descriptor' do
   end
 end
 
-# Run pc descriptor calculation algorithm on dataset
-#
+# Run pc descriptor calculation algorithm on dataset for a set of descriptors. Can be constrained to types and libraries.
 # @param [String] dataset_uri URI of the training dataset
+# @param optional [String] pc_type Physico-chemical descriptor type to generate, see TODO
+# @param optional [String] lib Library to use, see TODO
 # @return [text/uri-list] Task URI
 post '/pc' do
   response['Content-Type'] = 'text/uri-list'
@@ -87,7 +88,7 @@ post '/pc' do
   halt 202,task.uri.to_s+"\n"
 end
 
-# Run pc descriptor calculation algorithm on dataset
+# Run pc descriptor calculation algorithm on dataset for a specific descriptor.
 #
 # @param [String] dataset_uri URI of the training dataset
 # @return [text/uri-list] Task URI
diff --git a/similarity.rb b/similarity.rb
deleted file mode 100644
index faf43f9..0000000
--- a/similarity.rb
+++ /dev/null
@@ -1,26 +0,0 @@
-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
-  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
-end
-
-get '/tanimoto/dataset/*/dataset/*/?' do
-  find
-  @set.tanimoto(uri(params[:splat][1]))
-end
-
-get '/weighted_tanimoto/dataset/*/dataset/*/?' do
-  find
-  @set.weighted_tanimoto(uri(params[:splat][1]))
-end
-
-
diff --git a/smarts.rb b/smarts.rb
deleted file mode 100644
index 4ae6949..0000000
--- a/smarts.rb
+++ /dev/null
@@ -1,3 +0,0 @@
-get '/match/compound/*/smarts/*/?' do
-	"#{OpenTox::Compound.from_inchi(params[:splat][0]).match?(params[:splat][1])}"
-end