1 files changed, 114 insertions, 0 deletions
diff --git a/pc.rb b/pc.rb
new file mode 100644
index 0000000..3718eeb
--- /dev/null
+++ b/pc.rb
@@ -0,0 +1,114 @@
+# pc.rb
+# (P)hysico (C)hemical descriptor calculation
+# Author: Andreas Maunz
+
+
+# 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'
+  list = (algorithms.keys.sort << "AllDescriptors").collect { |name| url_for("/pc/#{name}",:full) }.join("\n") + "\n"
+  case request.env['HTTP_ACCEPT']
+  when /text\/html/
+    content_type "text/html"
+    OpenTox.text_to_html list
+  else
+    content_type 'text/uri-list'
+    list
+  end
+end
+
+# 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" } ]
+      
+  if params[:descriptor] != "AllDescriptors"
+    descriptors = descriptors[params[:descriptor]]
+  else
+    alg_params << { DC.description => "Physico-chemical type, one or more of '#{descriptors.collect { |id, info| info[:pc_type] }.uniq.sort.join(",")}'", OT.paramScope => "optional", DC.title => "pc_type" }
+    alg_params << { DC.description => "Software Library, one or more of '#{descriptors.collect { |id, info| info[:lib] }.uniq.sort.join(",")}'", OT.paramScope => "optional", DC.title => "lib" }
+    descriptors = {:id => "AllDescriptors", :name => "All PC descriptors" }
+  end
+
+  if descriptors 
+
+    # Contents
+    algorithm = OpenTox::Algorithm::Generic.new(url_for("/pc/#{params[:descriptor]}",:full))
+    algorithm.metadata = {
+      DC.title => params[:descriptor],
+      DC.creator => "andreas@maunz.de",
+      DC.description => descriptors[:name],
+      RDF.type => [OTA.DescriptorCalculation],
+    }
+    algorithm.metadata[OT.parameters] = alg_params
+    algorithm.metadata[DC.description] << (", pc_type: " + descriptors[:pc_type]) unless descriptors[:id] == "AllDescriptors"
+    algorithm.metadata[DC.description] << (", lib: " + descriptors[:lib]) unless descriptors[:id] == "AllDescriptors"
+
+    # Deliver
+    case request.env['HTTP_ACCEPT']
+    when /text\/html/
+      content_type "text/html"
+      OpenTox.text_to_html algorithm.to_yaml
+    when /yaml/
+      content_type "application/x-yaml"
+      algorithm.to_yaml
+    else
+      response['Content-Type'] = 'application/rdf+xml'  
+      algorithm.to_rdfxml
+    end
+
+  else
+    raise OpenTox::NotFoundError.new "Unknown descriptor #{params[:descriptor]}."
+  end
+end
+
+# 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/AllDescriptors' do
+  response['Content-Type'] = 'text/uri-list'
+  raise OpenTox::NotFoundError.new "Parameter 'dataset_uri' missing." unless params[:dataset_uri]
+
+  descriptors = YAML::load_file File.join(ENV['HOME'], ".opentox", "config", "pc_descriptors.yaml")
+  params[:pc_type] = descriptors.collect { |id,info| info[:pc_type]}.uniq.sort.join(',')  unless params[:pc_type]
+
+  task = OpenTox::Task.create("PC descriptor calculation for dataset ", @uri) do |task|
+    Rjb.load(nil,["-Xmx64m"]) # start vm
+    byteArray = Rjb::import('java.io.ByteArrayOutputStream'); printStream = Rjb::import('java.io.PrintStream'); 
+    out = byteArray.new() ; Rjb::import('java.lang.System').out = printStream.new(out) # joelib is too verbose
+    s = Rjb::import('JoelibFc') # import main class
+
+    LOGGER.debug "Running PC with pc_type '#{params[:pc_type]}' and lib '#{params[:lib]}'"
+    OpenTox::Algorithm.pc_descriptors( { :dataset_uri => params[:dataset_uri], :pc_type => params[:pc_type], :rjb => s, :add_uri => true, :task => task, :lib => params[:lib], :subjectid => @subjectid} )
+  end
+  raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
+  halt 202,task.uri.to_s+"\n"
+end
+
+# 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
+post '/pc/:descriptor' do
+  response['Content-Type'] = 'text/uri-list'
+  raise OpenTox::NotFoundError.new "Parameter 'dataset_uri' missing." unless params[:dataset_uri]
+
+  descriptors = YAML::load_file File.join(ENV['HOME'], ".opentox", "config", "pc_descriptors.yaml")
+  params[:pc_type] = descriptors.collect { |id,info| info[:pc_type]}.uniq.sort.join(',')
+
+  task = OpenTox::Task.create("PC descriptor calculation for dataset ", @uri) do |task|
+    Rjb.load(nil,["-Xmx64m"]) # start vm
+    byteArray = Rjb::import('java.io.ByteArrayOutputStream'); printStream = Rjb::import('java.io.PrintStream'); 
+    out = byteArray.new() ; Rjb::import('java.lang.System').out = printStream.new(out) # joelib is too verbose
+    s = Rjb::import('JoelibFc') # import main class
+    OpenTox::Algorithm.pc_descriptors( { :dataset_uri => params[:dataset_uri], :pc_type => params[:pc_type], :descriptor => params[:descriptor], :rjb => s, :add_uri => false, :task => task, :subjectid => @subjectid} )
+  end
+  raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
+  halt 202,task.uri.to_s+"\n"
+end
+