opentox-server 0.0.2pre → 1.0.0pre1

data/.gitignore

@@ -1,4 +1,5 @@
+Gemfile.lock
 *.gem
 .bundle
-Gemfile.lock
 pkg/*
+*~

data/ChangeLog

@@ -0,0 +1,2 @@
+v0.0.3 2012-05-07
+* switch from v0.0.2pre to v0.0.3

data/Gemfile

@@ -1,4 +1,4 @@
 source "http://rubygems.org"
 # Specify your gem's dependencies in opentox-server.gemspec
 gemspec
-gem "opentox-client", :path => "~/opentox-client"
+gem "opentox-client", :path => "../opentox-client"

data/VERSION

@@ -0,0 +1 @@
+1.0.0pre1

data/lib/4store.rb

@@ -0,0 +1,121 @@
+module OpenTox
+  module Backend
+    class FourStore
+
+      @@accept_formats = [ "application/rdf+xml", "text/turtle", "text/plain", "text/uri-list", "text/html", 'application/sparql-results+xml' ]
+      @@content_type_formats = [ "application/rdf+xml", "text/turtle", "text/plain" ]
+
+      def self.list service_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.join(", ")} in the Accept Header." unless @@accept_formats.include? mime_type
+        if mime_type =~ /uri-list/
+          sparql = "SELECT DISTINCT ?g WHERE {GRAPH ?g {?s <#{RDF.type}> <#{klass}>; ?p ?o. } }"
+        else 
+          sparql = "CONSTRUCT {?s ?p ?o.} WHERE {?s <#{RDF.type}> <#{klass}>; ?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.join(", ")} in the Accept Header." unless @@accept_formats.include? mime_type
+        sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{uri}> WHERE { ?s ?p ?o. }"
+        rdf = query sparql, mime_type
+        resource_not_found_error "#{uri} not found." if rdf.empty?
+        rdf
+      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.join(", ")}." unless @@content_type_formats.include? mime_type or mime_type == "multipart/form-data"
+        bad_request_error "Reqest body empty." unless rdf 
+        mime_type = "application/x-turtle" if mime_type == "text/plain" # ntriples is turtle in 4store
+        begin
+          RestClient.post File.join(four_store_uri,"data")+"/", :data => rdf, :graph => uri, "mime-type" => mime_type 
+        rescue
+          bad_request_error $!.message, File.join(four_store_uri,"data")+"/"
+        end
+      end
+
+      def self.put uri, rdf, mime_type
+        bad_request_error "'#{mime_type}' is not a supported content type. Please use one of #{@@content_type_formats.join(", ")}." unless @@content_type_formats.include? mime_type
+        bad_request_error "Reqest body empty." unless rdf 
+        mime_type = "application/x-turtle" if mime_type == "text/plain"
+        #begin
+          RestClientWrapper.put File.join(four_store_uri,"data",uri), rdf, :content_type => mime_type 
+        #rescue
+          #bad_request_error $!.message, File.join(four_store_uri,"data",uri)
+        #end
+      end
+
+      def self.delete uri
+        RestClientWrapper.delete data_uri(uri)
+      end
+
+      def self.update sparql
+        RestClient.post(update_uri, :update => sparql )
+      end
+
+      def self.query sparql, mime_type
+        if sparql =~ /SELECT/i
+#         return list unless mime_type
+          case mime_type
+          when 'application/sparql-results+xml' 
+            RestClient.get(sparql_uri, :params => { :query => sparql }, :accept => mime_type).body
+          when "text/uri-list"
+            RestClient.get(sparql_uri, :params => { :query => sparql }, :accept => "text/plain").body.gsub(/"|<|>/,'').split("\n").drop(1).join("\n")
+          else
+            bad_request_error "#{mime_type} is not a supported mime type for SELECT statements."
+          end
+        elsif sparql =~ /CONSTRUCT/i
+          case mime_type
+          when "text/plain", "application/rdf+xml" 
+            RestClient.get(sparql_uri, :params => { :query => sparql }, :accept => mime_type).body
+          when /html|turtle/
+            # TODO: fix and improve
+            nt = RestClient.get(sparql_uri, :params => { :query => sparql }, :accept => "text/plain").body # 4store returns ntriples for turtle
+
+            rdf = RDF::Graph.new
+            RDF::Reader.for(:ntriples).new(nt) do |reader|
+              reader.each_statement { |statement| rdf << statement }
+            end
+            prefixes = {:rdf => "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"}
+            ['OT', 'DC', 'XSD', 'OLO'].each{|p| prefixes[p.downcase.to_sym] = eval("RDF::#{p}.to_s") }
+            # TODO: fails for large datasets?? multi_cell_call
+            turtle = RDF::N3::Writer.for(:turtle).buffer(:prefixes => prefixes)  do |writer|
+              rdf.each{|statement| writer << statement}
+            end
+            turtle =  "<html><body>" + turtle.gsub(%r{<(.*)>},'&lt;<a href="\1">\1</a>&gt;').gsub(/\n/,'<br/>') + "</body></html>" if mime_type =~ /html/ and !turtle.empty?
+            turtle
+          end
+        else
+          # TODO: check if this prevents SPARQL injections
+          bad_request_error "Only SELECT and CONSTRUCT are accepted SPARQL statements."
+        end
+      rescue
+        bad_request_error $!.message, sparql_uri
+      end
+
+      def self.klass
+        RDF::OT[SERVICE.capitalize]
+      end
+
+      def self.four_store_uri
+        # credentials are removed from uri in error.rb
+        $four_store[:uri].sub(%r{//},"//#{$four_store[:user]}:#{$four_store[:password]}@")
+      end
+
+      def self.sparql_uri 
+        File.join(four_store_uri, "sparql") + '/'
+      end
+
+      def self.update_uri 
+        File.join(four_store_uri, "update") + '/'
+      end
+
+      def self.data_uri uri
+        File.join(four_store_uri, "data","?graph=#{uri}")
+      end
+
+    end
+  end
+end

data/lib/authorization-helper.rb

@@ -56,10 +56,10 @@ module OpenTox
         elsif !env["session"] && subjectid
           unless authorized?(subjectid)
             $logger.debug "URI not authorized: clean: " + clean_uri("#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}").sub("http://","https://").to_s + " full: #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']} with request: #{request.env['REQUEST_METHOD']}"
-            raise OpenTox::NotAuthorizedError.new "Not authorized"
+            unauthorized_error "Not authorized #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']} with request: #{request.env['REQUEST_METHOD']}"
           end
         else
-          raise OpenTox::NotAuthorizedError.new "Not authorized" unless authorized?(subjectid)
+          unauthorized_error "Not authorized" unless authorized?(subjectid)
         end
       end
 
@@ -67,7 +67,7 @@ module OpenTox
       # @param [String]subjectid
       def authorized?(subjectid)
         request_method = request.env['REQUEST_METHOD']
-        uri = clean_uri("#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}").sub("http://","https://")
+        uri = clean_uri("#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}") #.sub("http://","https://")
         request_method = "GET" if request_method == "POST" &&  uri =~ /\/model\/\d+\/?$/
         return OpenTox::Authorization.authorized?(uri, request_method, subjectid)
       end
@@ -78,7 +78,8 @@ module OpenTox
         uri = uri.sub(" ", "%20")          #dirty hacks => to fix
         uri = uri[0,uri.index("InChI=")] if uri.index("InChI=")
         out = URI.parse(uri)
-        out.path = out.path[0, out.path.length - (out.path.reverse.rindex(/\/{1}\d+\/{1}/))] if out.path.index(/\/{1}\d+\/{1}/)  #cuts after /id/ for a&a
+        out.path = out.path[0, out.path.length - (out.path.reverse.rindex(/\/{1}\d+\/{1}/))] if out.path.index(/\/{1}\d+\/{1}/)  #cuts after numeric /id/ for a&a
+        out.path.sub! /(\/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}).*/, '\1' # cut after uuid
         out.path = out.path.split('.').first #cut extension
         port = (out.scheme=="http" && out.port==80)||(out.scheme=="https" && out.port==443) ? "" : ":#{out.port.to_s}"
         "#{out.scheme}://#{out.host}#{port}#{out.path.chomp("/")}" #"
@@ -128,4 +129,4 @@ module OpenTox
       end
     end
   end
-end
+end

data/lib/opentox-server.rb

@@ -1,10 +1,7 @@
-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 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")

data/lib/opentox.rb

@@ -1,12 +1,18 @@
 require 'sinatra/base'
-require "sinatra/reloader"
+require "sinatra/reloader" 
+ENV["RACK_ENV"] ||= "production"
+require File.join(ENV["HOME"],".opentox","config","#{SERVICE}.rb")
+
+
+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
@@ -14,38 +20,41 @@ module OpenTox
 
     configure :development do
       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
+      also_reload "./*.rb"
+      also_reload "../opentox-client/lib/*.rb"
+      also_reload File.join(ENV["HOME"],".opentox","config","#{SERVICE}.rb")
     end
 
     before do
+      request.content_type ? response['Content-Type'] = request.content_type : response['Content-Type'] = request.env['HTTP_ACCEPT']
+      parse_input if request.request_method =~ /POST|PUT/
       @accept = request.env['HTTP_ACCEPT']
-      response['Content-Type'] = @accept
-      # TODO: A+A
     end
 
+    before "/#{SERVICE}/:id" do
+      @uri = uri("/#{SERVICE}/#{params[:id]}")
+    end
+
+    helpers do
+      def parse_input
+        case request.content_type 
+        when /multipart/
+          @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"
+        else
+          @body = request.body.read
+          @content_type = request.content_type
+        end
+      end
+    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 +63,42 @@ 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 "/#{SERVICE}/?" do
+      FourStore.list uri("/#{SERVICE}"), @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
+    get "/#{SERVICE}/:id/?" do
+      FourStore.get(@uri, @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
-

data/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     = File.read("./VERSION")
   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"
@@ -14,8 +14,6 @@ Gem::Specification.new do |s|
   s.rubyforge_project = "opentox-server"
 
   s.files         = `git ls-files`.split("\n")
-  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
-  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
   s.require_paths = ["lib"]
 
   # specify any dependencies here; for example:
@@ -24,7 +22,5 @@ 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'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: opentox-server
 version: !ruby/object:Gem::Version
-  version: 0.0.2pre
+  version: 1.0.0pre1
   prerelease: 5
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-02 00:00:00.000000000 Z
+date: 2012-08-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: opentox-client
-  requirement: &84856440 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *84856440
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rack
-  requirement: &84855790 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +37,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *84855790
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rack-contrib
-  requirement: &84855290 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +53,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *84855290
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: sinatra
-  requirement: &84854680 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,21 +69,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *84854680
-- !ruby/object:Gem::Dependency
-  name: sinatra-contrib
-  requirement: &84853820 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: *84853820
 - !ruby/object:Gem::Dependency
-  name: emk-sinatra-url-for
-  requirement: &84852960 !ruby/object:Gem::Requirement
+  name: sinatra-contrib
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,21 +85,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *84852960
-- !ruby/object:Gem::Dependency
-  name: roo
-  requirement: &84851990 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: *84851990
 - !ruby/object:Gem::Dependency
   name: unicorn
-  requirement: &84851710 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,7 +101,12 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *84851710
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Ruby library for opentox services
 email:
 - helma@in-silico.ch
@@ -107,12 +115,14 @@ extensions: []
 extra_rdoc_files: []
 files:
 - .gitignore
+- ChangeLog
 - Gemfile
 - LICENSE
 - README
 - Rakefile
+- VERSION
+- lib/4store.rb
 - lib/authorization-helper.rb
-- lib/environment.rb
 - lib/file-store.rb
 - lib/opentox-server.rb
 - lib/opentox.rb
@@ -138,7 +148,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: 1.3.1
 requirements: []
 rubyforge_project: opentox-server
-rubygems_version: 1.8.11
+rubygems_version: 1.8.18
 signing_key: 
 specification_version: 3
 summary: Ruby library for opentox services

data/lib/environment.rb

@@ -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
-