1 files changed, 0 insertions, 125 deletions
diff --git a/webapp/dataset.rb b/webapp/dataset.rb
deleted file mode 100644
index 3ee6c04..0000000
--- a/webapp/dataset.rb
+++ /dev/null
@@ -1,125 +0,0 @@
-# dataset.rb
-# OpenTox dataset
-# Author: Andreas Maunz
-
-module OpenTox
-
-  class Application < Service
-
-
-    # Get a list of descriptor calculation 
-    # @return [text/uri-list] URIs
-    get '/dataset/*/pc' do
-      dataset=params["captures"][0]
-      algorithms = YAML::load_file RestClientWrapper.get(File.join($compound[:uri],"pc_descriptors.yaml"))
-      list = (algorithms.keys.sort << "AllDescriptors").collect { |name| to("/dataset/#{dataset}/pc/#{name}",:full) }.join("\n") + "\n"
-      format_output(list)
-    end
-    
-    # Get representation of descriptor calculation
-    # @return [String] Representation
-    get '/dataset/*/pc/*' do
-      dataset = params[:captures][0]
-      params[:descriptor] = params[:captures][1]
-      descriptors = YAML::load_file RestClientWrapper.get(File.join($compound[:uri],"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" } # Comes from pc_descriptors.yaml for single descriptors
-      end
-    
-      if descriptors 
-        # Contents
-        algorithm = OpenTox::Algorithm.new(to("/dataset/#{dataset}/pc/#{params[:descriptor]}",:full))
-        mmdata = {
-          DC.title => params[:descriptor],
-          DC.creator => "andreas@maunz.de",
-          DC.description => descriptors[:name],
-          RDF.type => [OTA.DescriptorCalculation],
-        }
-        mmdata[DC.description] << (", pc_type: " + descriptors[:pc_type]) unless descriptors[:id] == "AllDescriptors"
-        mmdata[DC.description] << (", lib: " + descriptors[:lib])         unless descriptors[:id] == "AllDescriptors"
-        algorithm.metadata=mmdata
-        algorithm.parameters = alg_params
-        format_output(algorithm)
-      else
-        resource_not_found_error "Unknown descriptor #{params[:descriptor]}."
-      end
-    end
-
-
-    # Calculate PC descriptors
-    # Single descriptors or sets of descriptors can be selected
-    # Sets are selected via lib and/or pc_type, and take precedence, when also a descriptor is submitted
-    # If none of descriptor, lib, and pc_type is submitted, all descriptors are calculated
-    # Set composition is induced by intersecting lib and pc_type sets, if appropriate
-    # @param [optional, HEADER] accept Accept one of 'application/rdf+xml', 'text/csv', defaults to 'application/rdf+xml'
-    # @param [optional, String] descriptor A single descriptor to calculate values for.
-    # @param [optional, String] lib One or more descriptor libraries out of [cdk,joelib,openbabel], for whose descriptors to calculate values.
-    # @param [optional, String] pc_type One or more descriptor types out of [constitutional,topological,geometrical,electronic,cpsa,hybrid], for whose descriptors to calculate values
-    # @return [application/rdf+xml,text/csv] Compound descriptors and values
-    post '/dataset/*/pc' do
-      dataset=params["captures"][0]
-      params.delete('splat')
-      params.delete('captures')
-      params_array = params.collect{ |k,v| [k.to_sym, v]}
-      params = Hash[params_array]
-      params[:dataset] = dataset
-      descriptor = params[:descriptor].nil? ? "" : params[:descriptor]
-      lib = params[:lib].nil? ? "" : params[:lib]
-      pc_type = params[:pc_type].nil? ? "" : params[:pc_type]
-
-      task = OpenTox::Task.create(
-                                 $task[:uri],
-                                 @subjectid,
-                                 { RDF::DC.description => "Calculating PC descriptors",
-                                   RDF::DC.creator => to("/dataset/#{dataset}/pc",:full)
-                                 }
-                                ) do |task|
-
-       result_ds = OpenTox::Dataset.new(nil,@subjectid)
-       ds=OpenTox::Dataset.find("#{$dataset[:uri]}/#{dataset}",@subjectid)
-       ds.compounds.each { |cmpd|
-         ds_string = RestClientWrapper.post("#{$compound[:uri]}/#{cmpd.inchi}/pc", params, {:accept => "application/rdf+xml"})
-         single_cmpd_ds = OpenTox::Dataset.new(OpenTox::Dataset.uri_from_rdf(ds_string),@subjectid)
-         single_cmpd_ds.parse_rdfxml(ds_string)
-         single_cmpd_ds.get(true)
-         unless result_ds.features.size>0 # features present already?
-           result_ds.features = single_cmpd_ds.features # AM: features
-           result_ds.parameters = ["pc_type", "lib", "descriptor"].collect{ |key| # AM: parameters
-             val = single_cmpd_ds.find_parameter_value(key)
-             { DC.title => key, OT.paramValue => (val.nil? ? "" : val) }
-           }
-           result_ds[DC.title] = single_cmpd_ds[DC.title]
-           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]
-       }
-       result_ds.put @subjectid
-       $logger.debug result_ds.uri
-       result_ds.uri
-
-      end
-      response['Content-Type'] = 'text/uri-list'
-      service_unavailable_error "Service unavailable" if task.cancelled?
-      halt 202,task.uri.to_s+"\n"
-    end
-
-  end
-
-end
-