Merge branch 'release/v0.0.3'v0.0.3

8 files changed, 248 insertions, 74 deletions

diff --git a/.gitignore b/.gitignore
index 4040c6c..5a5fa8c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 *.gem
 .bundle
-Gemfile.lock
 pkg/*
+Gemfile.lock
+*~
diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..08d2402
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,2 @@
+v0.0.3 2012-05-07
+* switch from v0.0.2pre to v0.0.3
diff --git a/VERSION b/VERSION
new file mode 100644
index 0000000..bcab45a
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+0.0.3
diff --git a/lib/4store.rb b/lib/4store.rb
new file mode 100644
index 0000000..b20af00
--- /dev/null
+++ b/lib/4store.rb
@@ -0,0 +1,189 @@
+module OpenTox
+  module Backend
+    class FourStore
+
+      #TODO: catch 4store errors
+
+      @@mime_format = {
+        "application/rdf+xml" => :rdfxml,
+        "text/turtle" => :turtle,
+        "text/plain" => :ntriples,
+        "text/uri-list" => :uri_list,
+        #"application/json" => :json,
+        #"application/x-yaml" => :yaml,
+        #"text/x-yaml" => :yaml,
+        #"text/yaml" => :yaml,
+        "text/html" => :html,
+        # TODO: compression, forms
+        #/sparql/ => :sparql #removed to prevent sparql injections
+      }
+
+      @@format_mime = {
+        :rdfxml => "application/rdf+xml", 
+        :turtle => "text/turtle",
+        :ntriples => "text/plain",
+        :uri_list => "text/uri-list",
+        #:json => "application/json",
+        #:yaml => "text/yaml",
+        :html => "text/html",
+      }
+
+      @@accept_formats = [:rdfxml, :turtle, :ntriples, :uri_list, :html] #, :json, :yaml]
+      @@content_type_formats = [:rdfxml, :turtle, :ntriples]#, :json, :yaml]
+      @@rdf_formats  = [:rdfxml, :turtle, :ntriples]
+
+      def self.list mime_type
+        mime_type = "text/html" if mime_type.match(%r{\*/\*})
+        bad_request_error "'#{mime_type}' is not a supported mime type. Please specify one of #{@@accept_formats.collect{|f| @@format_mime[f]}.join(", ")} in the Accept Header." unless @@accept_formats.include? @@mime_format[mime_type]
+        if mime_type =~ /json|yaml|uri-list/
+          sparql = "SELECT ?s WHERE {?s <#{RDF.type}> <#{@@class}>. }"
+        elsif mime_type =~ /turtle|html|rdf|plain/
+          sparql = "CONSTRUCT {?s ?p ?o.} WHERE {?s <#{RDF.type}> <#{@@class}>; ?p ?o. }"
+        end
+        query sparql, mime_type
+      end
+
+      def self.get uri, mime_type
+        mime_type = "text/html" if mime_type.match(%r{\*/\*})
+        bad_request_error "'#{mime_type}' is not a supported mime type. Please specify one of #{@@accept_formats.collect{|f| @@format_mime[f]}.join(", ")} in the Accept Header." unless @@accept_formats.include? @@mime_format[mime_type]
+        not_found_error "#{uri} not found." unless list("text/uri-list").split("\n").include?(uri)
+        sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{uri}> WHERE { ?s ?p ?o. }"
+        query sparql, mime_type
+      end
+
+      def self.post uri, rdf, mime_type
+        bad_request_error "'#{mime_type}' is not a supported content type. Please use one of #{@@content_type_formats.collect{|f| @@format_mime[f]}.join(", ")}." unless @@content_type_formats.include? @@mime_format[mime_type]
+        rdf = convert rdf, @@mime_format[mime_type], :ntriples#, uri unless mime_type == 'text/plain'
+        RestClient.post File.join(four_store_uri,"data")+"/", :data => rdf, :graph => uri, "mime-type" => "application/x-turtle" # not very consistent in 4store
+      end
+
+      def self.put uri, rdf, mime_type, skip_rewrite=false
+        bad_request_error "'#{mime_type}' is not a supported content type. Please use one of #{@@content_type_formats.collect{|f| @@format_mime[f]}.join(", ")}." unless @@content_type_formats.include? @@mime_format[mime_type]
+        uuid = uri.sub(/\/$/,'').split('/').last
+        bad_request_error "'#{uri}' is not a valid URI." unless uuid =~ /[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}/
+        if !skip_rewrite
+          rdf = convert rdf, @@mime_format[mime_type], :ntriples, uri 
+        elsif mime_type != "text/plain" # ntriples are not converted
+          rdf = convert rdf, @@mime_format[mime_type], :ntriples
+        end
+        rdf = "<#{uri}> <#{RDF.type}> <#{@@class}>." unless rdf # create empty resource
+        RestClient.put File.join(four_store_uri,"data",uri), rdf, :content_type => "application/x-turtle" # content-type not very consistent in 4store
+      end
+
+      def self.delete uri
+        RestClientWrapper.delete data_uri uri
+      end
+
+      def self.query sparql, mime_type
+        if sparql =~ /SELECT/i
+          xml = RestClient.post File.join(four_store_uri,"sparql")+"/", :query => sparql
+          #TODO request tab delimited format to speed up parsing
+          list = parse_sparql_xml_results(xml).collect{|hash| hash["s"]}
+          case mime_type
+          when /json/
+            return list.to_json
+          when /yaml/
+            return list.to_yaml
+          when /uri-list/
+            return list.join "\n"
+          else
+            bad_request_error "#{mime_type} is not a supported mime type for SELECT statements. Please use one of text/uri-list, application/json, text/yaml, text/html."
+          end
+        elsif sparql =~ /CONSTRUCT/i
+          nt = RestClient.get(sparql_uri, :params => { :query => sparql }, :accept => "text/plain").body
+          return nt if mime_type == 'text/plain'
+          case mime_type
+          when /turtle/
+            return convert(nt,:ntriples, :turtle)
+          when /html/
+            # TODO: fix and improve
+            html = "<html><body>"
+            html += convert(nt,:ntriples, :turtle).gsub(%r{<(.*)>},'&lt;<a href="\1">\1</a>&gt;').gsub(/\n/,'<br/>')#.gsub(/ /,'&nbsp;')
+            html += "</body></html>"
+            return html
+          when "application/rdf+xml" 
+            return convert(nt,:ntriples, :rdfxml)
+          end
+        else
+          # TODO: check if this prevents SPARQL injections
+          bad_request_error "Only SELECT and CONSTRUCT are accepted SPARQL statements."
+        end
+      end
+
+      private
+
+      def self.convert rdf_string, input_format, output_format, rewrite_uri=nil
+        rewrite_uri ?  serialize(parse_and_rewrite_uri(rdf_string,input_format, rewrite_uri), output_format) : serialize(parse(rdf_string,input_format), output_format)
+      end
+
+      def self.parse_and_rewrite_uri string, format, rewrite_uri
+        rdf = RDF::Graph.new
+        subject = nil
+        statements = [] # use array instead of graph for performance reasons
+        RDF::Reader.for(format).new(string) do |reader|
+          reader.each_statement do |statement|
+            subject = statement.subject if statement.predicate == RDF.type and statement.object == @@class
+            statements << statement
+          end 
+        end
+        bad_request_error "No class specified with <#{RDF.type}> statement." unless subject
+        statements.each do |statement|
+          statement.subject = RDF::URI.new rewrite_uri if rewrite_uri and statement.subject == subject
+          rdf << statement
+        end
+        rdf
+      end
+
+      def self.parse string, format
+        rdf = RDF::Graph.new
+        RDF::Reader.for(format).new(string) do |reader|
+          reader.each_statement { |statement| rdf << statement }
+        end
+        rdf
+      end
+
+      def self.serialize rdf, format
+        if format == :turtle # prefixes seen to need RDF::N3
+          # TODO add prefixes
+          string = RDF::N3::Writer.for(format).buffer(:prefixes => {:ot => "http://www.opentox.org/api/1.2#"})  do |writer|
+            rdf.each{|statement| writer << statement}
+          end
+        else
+          string = RDF::Writer.for(format).buffer  do |writer|
+            rdf.each{|statement| writer << statement}
+          end
+        end
+        string
+      end
+
+      def self.four_store_uri
+        $four_store[:uri].sub(%r{//},"//#{$four_store[:user]}:#{$four_store[:password]}@")
+      end
+
+      def self.sparql_uri 
+        File.join(four_store_uri, "sparql") + '/'
+      end
+
+      def self.data_uri uri
+        File.join(four_store_uri, "data","?graph=#{uri}")
+      end
+
+      def self.parse_sparql_xml_results(xml)
+        results = []
+        doc = REXML::Document.new(REXML::Source.new(xml))
+        doc.elements.each("*/results/result") do |result|
+          result_hash = {}
+          result.elements.each do |binding|
+            key = binding.attributes["name"]
+            value = binding.elements[1].text
+            type = binding.elements[1].name 
+            result_hash[key] = value
+          end
+          results.push result_hash
+        end
+        results
+      end
+
+    end
+  end
+end
diff --git a/lib/environment.rb b/lib/environment.rb
deleted file mode 100644
index 3889dfb..0000000
--- a/lib/environment.rb
+++ /dev/null
@@ -1,41 +0,0 @@
-# set default environment
-ENV['RACK_ENV'] = 'production' unless ENV['RACK_ENV']
-
-# load/setup configuration
-basedir = File.join(ENV['HOME'], ".opentox")
-config_dir = File.join(basedir, "config")
-config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
-
-TMP_DIR = File.join(basedir, "tmp")
-LOG_DIR = File.join(basedir, "log")
-
-=begin
-if File.exist?(config_file)
-	CONFIG = YAML.load_file(config_file)
-  not_found_error "Could not load configuration from \"#{config_file.to_s}\"" unless CONFIG
-else
-	FileUtils.mkdir_p TMP_DIR
-	FileUtils.mkdir_p LOG_DIR
-	FileUtils.mkdir_p config_dir
-	puts "Please edit #{config_file} and restart your application."
-	exit
-end
-=end
-
-logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
-$logger = OTLogger.new(logfile) 
-
-=begin
-if CONFIG[:logger] and CONFIG[:logger] == "debug"
-	$logger.level = Logger::DEBUG
-else
-	$logger.level = Logger::WARN 
-end
-
-# TODO: move to opentox-client???
-AA_SERVER = CONFIG[:authorization] ? (CONFIG[:authorization][:server] ? CONFIG[:authorization][:server] : nil) : nil
-CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorization][:authenticate_request]
-CONFIG[:authorization][:authorize_request] =  [""] unless CONFIG[:authorization][:authorize_request]
-CONFIG[:authorization][:free_request] =  [""] unless CONFIG[:authorization][:free_request]
-=end
-
diff --git a/lib/opentox-server.rb b/lib/opentox-server.rb
index 358788b..15cb0cd 100644
--- a/lib/opentox-server.rb
+++ b/lib/opentox-server.rb
@@ -1,10 +1,10 @@
-require "opentox-client"
+require 'opentox-client'
 require 'rack'
 require 'rack/contrib'
 require 'sinatra'
-require 'sinatra/url_for'
 require 'roo'
-require File.join(File.dirname(__FILE__),"environment.rb")
+require 'rdf/n3'
+#require File.join(File.dirname(__FILE__),"environment.rb")
+require File.join(File.dirname(__FILE__),"4store.rb")
 require File.join(File.dirname(__FILE__),"opentox.rb")
-require File.join(File.dirname(__FILE__),"file-store.rb")
 require File.join(File.dirname(__FILE__),"authorization-helper.rb")
diff --git a/lib/opentox.rb b/lib/opentox.rb
index e3c1f3b..7a73d66 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -1,12 +1,17 @@
 require 'sinatra/base'
 require "sinatra/reloader"
 
+ENV["RACK_ENV"] ||= "production"
+
+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
 
-    helpers Sinatra::UrlForHelper
     # use OpenTox error handling
     set :raise_errors, false
     set :show_exceptions, false
@@ -16,36 +21,15 @@ module OpenTox
       register Sinatra::Reloader
     end
 
-    helpers do
-      def uri
-        params[:id] ? url_for("/#{params[:id]}", :full) : "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}"
-      end
-    end
-
     before do
-      @accept = request.env['HTTP_ACCEPT']
-      response['Content-Type'] = @accept
-      # TODO: A+A
+      request.content_type ? response['Content-Type'] = request.content_type : response['Content-Type'] = request.env['HTTP_ACCEPT']
     end
 
+    # Attention: Error within tasks are catched by Task.create
     error do
-      # TODO: convert to OpenTox::Error and set URI
       error = request.env['sinatra.error']
-      #error.uri = uri
       if error.respond_to? :report
-        # Errors are formated according to acccept-header
-        case @accept
-        when 'application/rdf+xml'
-          body = error.report.to_rdfxml
-        when /html/
-          # TODO
-          # body = error.report.to_html
-          body = error.report.to_turtle
-        when "text/n3"
-          body = error.report.to_ntriples
-        else
-          body = error.report.to_turtle
-        end
+        body = error.report.to_turtle
       else
         response['Content-Type'] = "text/plain"
         body = error.message
@@ -54,6 +38,44 @@ module OpenTox
       error.respond_to?(:http_code) ? code = error.http_code : code = 500
       halt code, body
     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/
+
+    # Get a list of objects at the server
+    get '/?' do
+      FourStore.list request.env['HTTP_ACCEPT']
+    end
+
+    # Create a new resource
+    # TODO: handle multipart uploads
+    post '/?' do
+      rdf = request.body.read
+      uri = uri(SecureRandom.uuid)
+      FourStore.put(uri, rdf, request.content_type) unless rdf == ''
+      response['Content-Type'] = "text/uri-list"
+      uri
+    end
+
+    # Get resource representation
+    get '/:id/?' do
+      FourStore.get(uri("/#{params[:id]}"), request.env['HTTP_ACCEPT'])
+    end
+
+    # Modify (i.e. add rdf statments to) a resource
+    post '/:id/?' do
+      FourStore.post uri("/#{params[:id]}"), request.body.read, request.content_type
+    end
+
+    # Create or updata a resource
+    put '/:id/?' do
+      FourStore.put uri("/#{params[:id]}"), request.body.read, request.content_type
+    end
+
+    # Delete a resource
+    delete '/:id/?' do
+      FourStore.delete uri("/#{params[:id]}")
+    end
+
   end
 end
-
diff --git a/opentox-server.gemspec b/opentox-server.gemspec
index 08438f0..1074fbf 100644
--- a/opentox-server.gemspec
+++ b/opentox-server.gemspec
@@ -3,7 +3,7 @@ $:.push File.expand_path("../lib", __FILE__)
 
 Gem::Specification.new do |s|
   s.name        = "opentox-server"
-  s.version     = "0.0.2pre"
+  s.version     = "0.0.3"
   s.authors     = ["Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler"]
   s.email       = ["helma@in-silico.ch"]
   s.homepage    = "http://github.com/opentox/opentox-server"
@@ -24,7 +24,7 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency 'rack-contrib'
   s.add_runtime_dependency 'sinatra'
   s.add_runtime_dependency 'sinatra-contrib'
-  s.add_runtime_dependency 'emk-sinatra-url-for'
   s.add_runtime_dependency 'roo'
   s.add_runtime_dependency 'unicorn'
+  s.add_runtime_dependency 'rdf-n3'
 end