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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
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