initial model service

1 files changed, 10 insertions, 112 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