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require 'sinatra/base'
require "sinatra/reloader"
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)
module OpenTox
# Base class for OpenTox services
class Service < Sinatra::Base
include Backend
# 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
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']=~/\*\/\*/
@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
if object.class == String
case @accept
when /text\/html/
content_type "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"
content_type "application/rdf+xml"
object.to_rdfxml
when /text\/html/
content_type "text/html"
object.to_html
when /turtle/
content_type "text/turtle"
object.to_turtle
else
content_type "text/plain"
object.to_ntriples
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_turtle.to_html
else
content_type "text/turtle"
halt ot_error.http_code, ot_error.to_turtle
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/
# HEAD route for service check
# algorithm, compound and validation overwrite this
head "/#{SERVICE}/?" do
end
# HEAD request for object in backend
# algorithm, dataset, compound and validation overwrite this
head "/#{SERVICE}/:id/?" do
halt 404 unless FourStore.head(@uri.split('?').first)
end
# Get a list of objects at the server or perform a SPARQL query
get "/#{SERVICE}/?" do
if params[:query]
case @accept
when "text/uri-list" # result URIs are protected by A+A
FourStore.query(params[:query], "text/uri-list")
else # prevent searches for protected resources
bad_request_error "Accept header '#{@accept}' is disabled for SPARQL queries at service URIs in order to protect private data. Use 'text/uri-list' and repeat the query at the result URIs.", uri("/#{SERVICE}")
end
else
FourStore.list(@accept)
end
end
# internal route not in API
get "/#{SERVICE}/last/ordered/?" do
FourStore.query("SELECT DISTINCT ?s WHERE
{GRAPH ?g
{?s <#{RDF.type}> <#{RDF::OT}#{SERVICE.capitalize}>; <#{RDF::DC.date}> ?o. }
} ORDER BY ?o ", @accept)
end
# Create a new resource
post "/#{SERVICE}/?" do
@uri = uri("/#{SERVICE}/#{SecureRandom.uuid}")
FourStore.put(@uri, @body, @content_type)
response['Content-Type'] = "text/uri-list"
@uri
end
# Get resource representation or perform a SPARQL query
get "/#{SERVICE}/:id/?" do
params[:query] ? FourStore.query(params[:query], @accept) : FourStore.get(@uri.split('?').first, @accept)
end
# Modify (i.e. add rdf statments to) a resource
post "/#{SERVICE}/:id/?" do
FourStore.post @uri, @body, @content_type
end
# Create or updata a resource
put "/#{SERVICE}/:id/?" do
FourStore.put @uri, @body, @content_type
end
# Delete a resource
delete "/#{SERVICE}/:id/?" do
FourStore.delete @uri
end
end
end
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