initial model service

6 files changed, 15 insertions, 308 deletions

diff --git a/application.rb b/application.rb
index 8d79812..5f38ef8 100644
--- a/application.rb
+++ b/application.rb
@@ -1,116 +1,14 @@
-require 'rubygems'
-gem "opentox-ruby", "~> 4"
-require 'opentox-ruby'
-
-set :lock, true
-
-@@datadir = "data"
-
-class PredictionCache < Ohm::Model
-  attribute :compound_uri
-  attribute :model_uri
-  attribute :dataset_uri
-
-  index :compound_uri
-  index :model_uri
-end
-
-before do
-  @accept = request.env['HTTP_ACCEPT']
-  @accept = 'application/rdf+xml' if @accept == '*/*' or @accept == '' or @accept.nil?
-  response['Content-Type'] = @accept
-  @id = request.path_info.match(/^\/\d+/)
-  unless @id.nil?
-    @id = @id.to_s.sub(/\//,'').to_i
-
-    @uri = uri @id
-    @json_file = "#{@@datadir}/#{@id}.json"
-    raise OpenTox::NotFoundError.new "Model #{@id} not found." unless File.exists? @json_file
-
-    extension = File.extname(request.path_info)
-    unless extension.empty?
-      case extension
-      when ".html"
-        @accept = 'text/html'
-      when ".yaml"
-        @accept = 'application/x-yaml'
-      when ".json"
-        @accept = 'application/json'
-      when ".rdfxml"
-        @accept = 'application/rdf+xml'
-      else
-        raise OpenTox::NotFoundError.new "File format #{extension} not supported."
+module OpenTox
+  class Application < Service
+    post "/model/:id/?" do
+      [RDF::OT.featureCalculationAlgorithm, RDF::OT.predictionAlgorithm, RDF::OT.similarityAlgorithm, RDF::OT.trainingDataset , RDF::OT.dependentVariables , RDF::OT.featureDataset].each do |param|
+        query = "SELECT ?uri FROM <#{@uri}> WHERE {<#{@uri}> <#{param.to_s}> ?uri}"
+        param_uri = FourStore.query query, "text/uri-list"
+        param_name = param.to_s.split("#").last.underscore
+        params[param_name] = param_uri
       end
+      #puts params.inspect
+      RestClientWrapper.post File.join($algorithm[:uri],"lazar","predict"), params
     end
   end
-
-  # make sure subjectid is not included in params, subjectid is set as member variable
-  params.delete(:subjectid) 
-end
-
-require 'lazar.rb'
-
-helpers do
-
-  def next_id
-    id = Dir["./#{@@datadir}/*json"].collect{|f| File.basename(f.sub(/.json/,'')).to_i}.sort.last
-    id = 0 if id.nil?
-    id + 1
-  end
-
-  def uri(id)
-    url_for "/#{id}", :full
-  end
-
-  def activity(a)
-    case a.to_s
-    when "true"
-      act = "active"
-    when "false"
-      act = "inactive"
-    else
-      act = "not available"
-    end
-    act
-  end
-end
-
-get '/?' do # get index of models
-  uri_list = Dir["./#{@@datadir}/*json"].collect{|f| File.basename(f.sub(/.json/,'')).to_i}.sort.collect{|n| uri n}.join("\n") + "\n"
-  case @accept
-  when /html/
-    response['Content-Type'] = 'text/html'
-    OpenTox.text_to_html uri_list
-  else
-    response['Content-Type'] = 'text/uri-list'
-    uri_list
-  end
-end
-
-delete '/:id/?' do
-  LOGGER.debug "Deleting model with id "+@id.to_s
-  begin
-    FileUtils.rm @json_file
-    if @subjectid and !File.exists? @json_file and @uri
-      begin
-        res = OpenTox::Authorization.delete_policies_from_uri(@uri, @subjectid)
-        LOGGER.debug "Policy deleted for Model URI: #{@uri} with result: #{res}"
-      rescue
-        LOGGER.warn "Policy delete error for Model URI: #{@uri}"
-      end
-    end
-    response['Content-Type'] = 'text/plain'
-    "Model #{@id} deleted."
-  rescue
-    raise OpenTox::NotFoundError.new "Model #{@id} does not exist."
-  end
-end
-
-
-delete '/?' do
-  # TODO delete datasets
-  FileUtils.rm Dir["#{@@datadir}/*.json"]
-  PredictionCache.all.each {|cache| cache.delete }
-  response['Content-Type'] = 'text/plain'
-  "All models and cached predictions deleted."
 end
diff --git a/config.ru b/config.ru
index ec39d1b..24f4dce 100644
--- a/config.ru
+++ b/config.ru
@@ -1,7 +1,5 @@
-require 'rubygems'
-require 'opentox-ruby'
-require 'config/config_ru'
-set :app_file, __FILE__ # to get the view path right
-run Sinatra::Application
-set :raise_errors, false
-set :show_exceptions, false
\ No newline at end of file
+SERVICE = "model"
+require 'bundler'
+Bundler.require
+require './application.rb'
+run OpenTox::Application
diff --git a/data/.gitignore b/data/.gitignore
deleted file mode 100644
index 59e3edd..0000000
--- a/data/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-*.rdfxml
-*.xls
-*.yaml
diff --git a/lazar.rb b/lazar.rb
deleted file mode 100644
index e4ae4c9..0000000
--- a/lazar.rb
+++ /dev/null
@@ -1,176 +0,0 @@
-require "haml" 
-
-helpers do
-
-  def yaml_file(id)
-    file = "#{@@datadir}/#{id}.yaml"
-    unless File.exists? file # lazy yaml generation
-      lazar = OpenTox::Model::Lazar.from_json(File.read(@json_file))
-      File.open(file,"w+") { |f| f.puts lazar.to_yaml }
-    end
-    file
-  end
-
-  def lazar
-    OpenTox::Model::Lazar.from_json(File.read(@json_file))
-  end
-
-  #def metadata
-    #lazar.metadata
-  #end
-
-end
-
-# Get model representation
-# @return [application/rdf+xml,application/x-yaml,aapplication/json] Model representation
-get '/:id/?' do
-  raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @json_file
-  case @accept
-  when /application\/rdf\+xml/
-    response['Content-Type'] = 'application/rdf+xml'
-    s = OpenTox::Serializer::Owl.new
-    s.add_model(@uri,lazar.metadata)
-    s.to_rdfxml
-  when /yaml/
-    send_file yaml_file(params[:id]), :type => 'application/x-yaml' 
-  when /json/
-    send_file @json_file, :type => 'application/json' 
-  when /html/
-    response['Content-Type'] = 'text/html'
-    #OpenTox.text_to_html File.read(yaml_file(params[:id]))
-    OpenTox.text_to_html JSON.pretty_generate(JSON.parse(File.read(@json_file)))
-  else
-    raise OpenTox::BadRequestError.new "Unsupported MIME type '#{@accept}'"
-  end
-end
-
-get '/:id/metadata.?:ext?' do
-  raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @json_file
-  @accept = "application/x-yaml" if params[:ext] and params[:ext].match(/yaml/)
-  case @accept
-  when /yaml/
-    lazar.metadata.to_yaml
-  else #when /rdf/ and anything else
-    serializer = OpenTox::Serializer::Owl.new
-    serializer.add_metadata @uri, lazar.metadata
-    serializer.to_rdfxml
-  end
-end
-
-get '/:id/dependent.?:ext?' do
-  raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @json_file
-  @accept = "application/x-yaml" if params[:ext] and params[:ext].match(/yaml/)
-  feature_uri = lazar.metadata[OT.dependentVariables]
-  case @accept
-  when /yaml/
-    OpenTox::Feature.find(feature_uri, @subjectid).to_yaml
-  when "text/uri-list"
-    feature_uri
-  when /rdf/ 
-    OpenTox::Feature.find(feature_uri, @subjectid).to_rdfxml
-  when /html/
-    OpenTox.text_to_html OpenTox::Feature.find(feature_uri, @subjectid).to_yaml
-  else
-    raise OpenTox::BadRequestError.new "Unsupported MIME type '#{@accept}'"
-  end
-end
-
-get '/:id/predicted/:prop' do
-  raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @json_file
-  if params[:prop] == "value" or params[:prop] == "confidence"
-    #feature = eval "YAML.load_file(@json_file).prediction_#{params[:prop]}_feature"
-    feature = eval "lazar.prediction_#{params[:prop]}_feature"
-    case @accept
-    when /yaml/
-      content_type "application/x-yaml"
-      feature.metadata.to_yaml
-    when /rdf/
-      content_type "application/rdf+xml"
-      feature.to_rdfxml
-    when /html/
-      content_type "text/html"
-      OpenTox.text_to_html feature.metadata.to_yaml
-    else
-      raise OpenTox::BadRequestError.new "Unsupported MIME type '#{@accept}'"
-    end
-  else
-      raise OpenTox::BadRequestError.new "Unknown URI #{@uri}"
-  end
-end
-
-get '/:id/predicted.?:ext?' do
-  raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @json_file
-  @accept = "application/x-yaml" if params[:ext] and params[:ext].match(/yaml/)
-  features = lazar.prediction_features
-  case @accept
-  when  "text/uri-list"
-    "#{features.collect{|f| f.uri}.join("\n")}\n"
-  when /yaml/
-    features.to_yaml
-  when /rdf/ 
-    serializer = OpenTox::Serializer::Owl.new
-    features.each{|f| serializer.add_feature(f.uri,f.metadata)}
-    serializer.to_rdfxml
-  when /html/
-    OpenTox.text_to_html features.to_yaml
-  else
-    raise OpenTox::BadRequestError.new "Unsupported MIME type '#{@accept}'"
-  end
-end
-
-# Store a lazar model. This method should not be called directly, use OpenTox::Algorithm::Lazar to create a lazar model
-# @param [Body] lazar Model representation in YAML format
-# @return [String] Model URI
-post '/?' do # create model
-  raise OpenTox::BadRequestError.new "MIME type \"#{request.content_type}\" not supported." unless request.content_type.match(/json/)
-  @id = next_id
-  @uri = uri @id
-  @json_file = "#{@@datadir}/#{@id}.json"
-  hash = Yajl::Parser.parse request.env["rack.input"].read
-  hash["uri"] = @uri
-  value_feature_uri = File.join( @uri, "predicted", "value")
-  confidence_feature_uri = File.join( @uri, "predicted", "confidence")
-  hash["metadata"][OT.predictedVariables] = [value_feature_uri, confidence_feature_uri]
-  File.open(@json_file,"w+"){|f| f.puts Yajl::Encoder.encode(hash)}
-  OpenTox::Authorization.check_policy(@uri, @subjectid) if File.exists? @json_file
-  response['Content-Type'] = 'text/uri-list'
-  @uri
-end
-
-# Make a lazar prediction. Predicts either a single compound or all compounds from a dataset 
-# @param [optional,String] dataset_uri URI of the dataset to be predicted
-# @param [optional,String] compound_uri URI of the compound to be predicted
-# @param [optional,Header] Accept Content-type of prediction, can be either `application/rdf+xml or application/x-yaml`
-# @return [text/uri-list] URI of prediction task (dataset prediction) or prediction dataset (compound prediction)
-post '/:id/?' do
-
-  raise OpenTox::NotFoundError.new "Model #{params[:id]} does not exist." unless File.exists? @json_file
-  
-  raise OpenTox::NotFoundError.new "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri]
-  #@lazar = YAML.load_file @json_file
-
-  response['Content-Type'] = 'text/uri-list'
-
-  if compound_uri
-    cache = PredictionCache.find(:model_uri => lazar.uri, :compound_uri => compound_uri).first
-    if cache and uri_available?(cache.dataset_uri)
-      return cache.dataset_uri
-    else
-      begin
-        prediction_uri = lazar.predict(compound_uri,true,@subjectid).uri
-        PredictionCache.create(:model_uri => lazar.uri, :compound_uri => compound_uri, :dataset_uri => prediction_uri)
-        prediction_uri
-      rescue
-        LOGGER.error "Lazar prediction failed for #{compound_uri} with #{$!} "
-        raise "Prediction of #{compound_uri} with #{lazar.uri} failed."
-      end
-    end
-  elsif dataset_uri
-    task = OpenTox::Task.create("Predict dataset",url_for("/#{lazar.id}", :full)) do |task|
-      lazar.predict_dataset(dataset_uri, @subjectid, task).uri
-    end
-    raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
-    halt 202,task.uri
-  end
-
-end
diff --git a/public/robots.txt b/public/robots.txt
deleted file mode 100644
index 1f53798..0000000
--- a/public/robots.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-User-agent: *
-Disallow: /
diff --git a/views/model.builder b/views/model.builder
deleted file mode 100644
index dbb1ca1..0000000
--- a/views/model.builder
+++ /dev/null
@@ -1,8 +0,0 @@
-xml.instruct!
-xml.model do
-	xml.uri url_for("/", :full) + @model.id.to_s
-	xml.name @model.name
-	xml.training_dataset_uri @model.training_dataset_uri
-	xml.feature_dataset_uri @model.feature_dataset_uri
-	xml.finished @model.finished
-end