diff options
| -rw-r--r-- | lib/helper.rb | 163 |
1 files changed, 163 insertions, 0 deletions
diff --git a/lib/helper.rb b/lib/helper.rb new file mode 100644 index 0000000..4199775 --- /dev/null +++ b/lib/helper.rb @@ -0,0 +1,163 @@ +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 + +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 + + end +end |