initial dataset tests

1 files changed, 2 insertions, 159 deletions

diff --git a/lib/opentox.rb b/lib/opentox.rb
index 6c6fcb5..c97f7d9 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -1,164 +1,10 @@
-require 'sinatra/base'
-require "sinatra/reloader"
-require 'mongo'
-
-ENV["RACK_ENV"] ||= "production"
-require File.join(ENV["HOME"],".opentox","config","default.rb") if File.exist? File.join(ENV["HOME"],".opentox","config","default.rb")
-require File.join(ENV["HOME"],".opentox","config","#{SERVICE}.rb")
-$aa[SERVICE.to_sym] = $aa
-
-logfile = File.join(ENV['HOME'], ".opentox","log","#{ENV["RACK_ENV"]}.log")
-$logger = OTLogger.new(logfile)
-
-Mongo::Logger.logger = $logger
-Mongo::Logger.logger.level = Logger::WARN 
-$mongo = Mongo::Client.new($mongodb[:uri])
-#$mongo[SERVICE].create if $mongo[SERVICE].find.count == 0
-# TODO create collections $mongo[SERVICE].create if $mongo[SERVICE].find.count == 0
+require_relative 'helper.rb'
 
 module OpenTox
 
   # Base class for OpenTox services
   class Service < Sinatra::Base
 
-    # use OpenTox error handling
-    set :raise_errors, false
-    set :show_exceptions, false
-    set :static, false
-
-    configure :development do
-      register Sinatra::Reloader
-      also_reload "./*.rb"
-      also_reload "./**/*.rb"
-      also_reload "../opentox-client/lib/*.rb"
-      also_reload File.join(ENV["HOME"],".opentox","config","#{SERVICE}.rb")
-    end
-
-    before do
-      @uri = uri(request.env['PATH_INFO']) # prevent /algorithm/algorithm in algorithm service
-      @uuid = params[:id]
-      get_subjectid if respond_to? :get_subjectid
-      # fix for IE, and set accept to 'text/html' as we do exact-matching later (sth. like text/html,application/xhtml+xml,*/* is not supported)
-      request.env['HTTP_ACCEPT'] = "text/html" if request.env["HTTP_USER_AGENT"]=~/MSIE/ or request.env['HTTP_ACCEPT']=~/text\/html/
-      # support set accept via url by adding ?media=<type> to the url
-      request.env['HTTP_ACCEPT'] = request.params["media"] if request.params["media"]
-      # default is turtle ??
-      #request.env['HTTP_ACCEPT'] = "text/turtle" if request.env['HTTP_ACCEPT'].size==0 or request.env['HTTP_ACCEPT']=~/\*\/\*/
-      # default is application/json
-      request.env['HTTP_ACCEPT'] = "application/json" if request.env['HTTP_ACCEPT'].size==0 or request.env['HTTP_ACCEPT']=~/\*\/\*/
-      @accept = request.env['HTTP_ACCEPT']
-
-      request.content_type ? response['Content-Type'] = request.content_type : response['Content-Type'] = request.env['HTTP_ACCEPT']
-      parse_input if request.request_method =~ /POST|PUT/
-      Authorization.check_policy(@uri) if env['REQUEST_METHOD'] == "PUT" && $aa[SERVICE.to_sym][:uri] && $aa[SERVICE.to_sym]
-      response['Content-Type'] = @accept
-    end
-
-    after do
-      Authorization.check_policy(@uri) if env['REQUEST_METHOD'].to_s == "POST" && $aa[SERVICE.to_sym][:uri] && $aa[SERVICE.to_sym]
-      Authorization.delete_policies_from_uri(@uri) if env['REQUEST_METHOD'].to_s == "DELETE" && $aa[SERVICE.to_sym][:uri] && $aa[SERVICE.to_sym]
-    end
-
-
-    helpers do
-      def parse_input
-        case request.content_type
-        when /multipart/
-          if params[:file]
-            @body = params[:file][:tempfile].read
-            # sdf files are incorrectly detected
-            @content_type = params[:file][:type]
-            @content_type = "chemical/x-mdl-sdfile" if File.extname(params[:file][:filename]) == ".sdf"
-          end
-        else
-          @body = request.body.read
-          @content_type = request.content_type
-        end
-      end
-
-      # format output according to accept header
-      def render object
-        content_type @accept
-        return nil if object.nil?
-        if @accept == "application/json"
-          #object.delete("_id") if object and object["_id"]
-          return object.to_json
-        else
-          if object.class == String
-            case @accept
-            when /text\/html/
-              object.to_html
-            else
-              content_type 'text/uri-list'
-              object
-            end
-          elsif object.class == Array
-            content_type 'text/uri-list'
-            object.join "\n"
-          else
-            case @accept
-            when "application/rdf+xml"
-              object.to_rdfxml
-            when /text\/html/
-              object.to_html
-            when /turtle/
-              object.to_turtle
-            when 'text/plain'
-              object.to_ntriples
-            else
-              bad_request_error "Mime type '#{@accept}' is not supported."
-            end
-
-          end
-        end
-      end
-    end
-
-
-    # ERROR HANDLING (for errors outside of tasks, errors inside of tasks are taken care of in Task.run)
-    def return_ot_error(ot_error)
-      case @accept
-      when /text\/html/
-        content_type "text/html"
-        halt ot_error.http_code, ot_error.to_html
-      else
-        content_type "application/json"
-        halt ot_error.http_code, ot_error.to_json
-      end
-    end
-
-    error Exception do # wraps non-opentox-errors like NoMethodError within an InternalServerError
-      error = request.env['sinatra.error']
-      return_ot_error(OpenTox::Error.new(500,error.message,nil,error.backtrace))
-    end
-
-    error OpenTox::Error do # this covers all opentox errors
-      return_ot_error(request.env['sinatra.error'])
-    end
-
-    def return_task( task )
-      raise "http_code == nil" unless task.code!=nil
-      case request.env['HTTP_ACCEPT']
-      when /rdf/
-        response['Content-Type'] = "application/rdf+xml"
-        halt task.code,task.to_rdfxml
-      when /yaml/
-        response['Content-Type'] = "application/x-yaml"
-        halt task.code,task.to_yaml # PENDING differs from task-webservice
-      when /html/
-        response['Content-Type'] = "text/html"
-        # html -> task created with html form -> redirect to task uri
-        redirect task.uri
-      else # default /uri-list/
-        response['Content-Type'] = "text/uri-list"
-        if task.completed?
-          halt task.code,task.resultURI+"\n"
-        else
-          halt task.code,task.uri+"\n"
-        end
-      end
-    end
-
     # Default methods, may be overwritten by derived services
     # see http://jcalcote.wordpress.com/2008/10/16/put-or-post-the-rest-of-the-story/
 
@@ -196,10 +42,7 @@ module OpenTox
 
     # internal route not in API
     get "/#{SERVICE}/last/ordered/?" do # REQUIRED?
-      FourStore.query("SELECT DISTINCT ?s WHERE
-      {GRAPH ?g
-        {?s <#{RDF.type}> <#{RDF::OT}#{SERVICE.capitalize}>; <#{RDF::DC.date}> ?o. }
-      } ORDER BY ?o ", @accept)
+      render $mongo[SERVICE].find.sort(:date).distinct(:uri)
     end
 
     # Create a new resource