Merge branch 'development' of github.com:opentox/opentox-server into development

6 files changed, 76 insertions, 56 deletions

diff --git a/.gitignore b/.gitignore
index 5a5fa8c..c9daf01 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
+Gemfile.lock
 *.gem
 .bundle
 pkg/*
-Gemfile.lock
 *~
diff --git a/VERSION b/VERSION
index bcab45a..3eefcb9 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.0.3
+1.0.0
diff --git a/lib/4store.rb b/lib/4store.rb
index b20af00..f2e3fcd 100644
--- a/lib/4store.rb
+++ b/lib/4store.rb
@@ -2,8 +2,6 @@ module OpenTox
   module Backend
     class FourStore
 
-      #TODO: catch 4store errors
-
       @@mime_format = {
         "application/rdf+xml" => :rdfxml,
         "text/turtle" => :turtle,
@@ -14,8 +12,8 @@ module OpenTox
         #"text/x-yaml" => :yaml,
         #"text/yaml" => :yaml,
         "text/html" => :html,
-        # TODO: compression, forms
         #/sparql/ => :sparql #removed to prevent sparql injections
+        'application/sparql-results+xml' => :sparql
       }
 
       @@format_mime = {
@@ -26,19 +24,19 @@ module OpenTox
         #:json => "application/json",
         #:yaml => "text/yaml",
         :html => "text/html",
+        :sparql => 'application/sparql-results+xml'
       }
 
-      @@accept_formats = [:rdfxml, :turtle, :ntriples, :uri_list, :html] #, :json, :yaml]
+      @@accept_formats = [:rdfxml, :turtle, :ntriples, :uri_list, :html, :sparql] #, :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}>. }"
+          sparql = "SELECT DISTINCT ?g WHERE {GRAPH ?g {?s ?p ?o} }"
         elsif mime_type =~ /turtle|html|rdf|plain/
-          sparql = "CONSTRUCT {?s ?p ?o.} WHERE {?s <#{RDF.type}> <#{@@class}>; ?p ?o. }"
+          sparql = "CONSTRUCT {?s ?p ?o.} WHERE {?s <#{RDF.type}> <#{klass}>; ?p ?o. }"
         end
         query sparql, mime_type
       end
@@ -46,19 +44,22 @@ module OpenTox
       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)
+        not_found_error "#{uri} not found." unless available? 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'
+        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] or mime_type == "multipart/form-data"
+        rdf = convert rdf, @@mime_format[mime_type], :ntriples
+        rdf = "<#{uri}> <#{RDF.type}> <#{klass}>." unless rdf # create empty resource
+        rdf += "\n<#{uri}> <#{RDF::DC.date}> \"#{DateTime.now}\"." unless rdf.match(%r{#{RDF::DC.date}})
         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]
+        bad_request_error "Reqest body empty." unless rdf # create empty resource
         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
@@ -66,19 +67,23 @@ module OpenTox
         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
+        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
-          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"]}
+          return RestClient.get(sparql_uri, :params => { :query => sparql }, :accept => mime_type).body.gsub(/<|>/,'').split("\n") if mime_type == 'application/sparql-results+xml' 
+          list = RestClient.get(sparql_uri, :params => { :query => sparql }, :accept => "text/plain").body.gsub(/<|>/,'').split("\n") 
+          list.shift
+          return list unless mime_type
           case mime_type
           when /json/
             return list.to_json
@@ -98,7 +103,7 @@ module OpenTox
           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 += convert(nt,:ntriples, :turtle).gsub(%r{<(.*)>},'&lt;<a href="\1">\1</a>&gt;').gsub(/\n/,'<br/>')
             html += "</body></html>"
             return html
           when "application/rdf+xml" 
@@ -112,6 +117,17 @@ module OpenTox
 
       private
 
+      def self.klass
+        RDF::OT[SERVICE.capitalize]
+      end
+
+      def self.available? uri
+        #sparql = "SELECT DISTINCT ?s WHERE {GRAPH <#{uri}> {?s ?p ?o} }"
+        sparql = "SELECT DISTINCT ?s WHERE {GRAPH <#{uri}> {?s <#{RDF.type}> <#{klass}>} }"
+        r = query(sparql, nil)
+        r.size == 1 and r.first == uri
+      end
+
       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
@@ -122,7 +138,7 @@ module OpenTox
         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
+            subject = statement.subject if statement.predicate == RDF.type and statement.object == klass
             statements << statement
           end 
         end
@@ -144,8 +160,9 @@ module OpenTox
 
       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|
+          prefixes = {:rdf => "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"}
+          ['OT', 'DC', 'XSD'].each{|p| prefixes[p.downcase.to_sym] = eval("RDF::#{p}.to_s") }
+          string = RDF::N3::Writer.for(format).buffer(:prefixes => prefixes)  do |writer|
             rdf.each{|statement| writer << statement}
           end
         else
@@ -157,6 +174,7 @@ module OpenTox
       end
 
       def self.four_store_uri
+        # TODO remove credentials from URI 9security risk in tasks)
         $four_store[:uri].sub(%r{//},"//#{$four_store[:user]}:#{$four_store[:password]}@")
       end
 
@@ -164,24 +182,12 @@ module OpenTox
         File.join(four_store_uri, "sparql") + '/'
       end
 
-      def self.data_uri uri
-        File.join(four_store_uri, "data","?graph=#{uri}")
+      def self.update_uri 
+        File.join(four_store_uri, "update") + '/'
       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
+      def self.data_uri uri
+        File.join(four_store_uri, "data","?graph=#{uri}")
       end
 
     end
diff --git a/lib/authorization-helper.rb b/lib/authorization-helper.rb
index 4b534a5..46834c6 100644
--- a/lib/authorization-helper.rb
+++ b/lib/authorization-helper.rb
@@ -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
\ No newline at end of file
+end
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 7a73d66..31a6e82 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -1,7 +1,8 @@
 require 'sinatra/base'
-require "sinatra/reloader"
-
 ENV["RACK_ENV"] ||= "production"
+require "sinatra/reloader" if ENV["RACK_ENV"] == "development"
+require File.join(ENV["HOME"],".opentox","config","#{SERVICE}.rb")
+
 
 logfile = File.join(ENV['HOME'], ".opentox","log","#{ENV["RACK_ENV"]}.log")
 $logger = OTLogger.new(logfile) 
@@ -23,6 +24,19 @@ module OpenTox
 
     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/
+    end
+
+    helpers do
+      def parse_input
+        if request.content_type == "multipart/form-data"
+          @body = File.read(params[:file][:tempfile])
+          @content_type = params[:file][:type]
+        else
+          @body = request.body.read
+          @content_type = request.content_type
+        end
+      end
     end
 
     # Attention: Error within tasks are catched by Task.create
@@ -43,38 +57,36 @@ module OpenTox
     # 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
+    get "/#{SERVICE}/?" 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 == ''
+    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 '/:id/?' do
-      FourStore.get(uri("/#{params[:id]}"), request.env['HTTP_ACCEPT'])
+    get "/#{SERVICE}/:id/?" do
+      FourStore.get(uri("/#{SERVICE}/#{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
+    post "/#{SERVICE}/:id/?" do
+      FourStore.post uri("/#{SERVICE}/#{params[:id]}"), @body, @content_type
     end
 
     # Create or updata a resource
-    put '/:id/?' do
-      FourStore.put uri("/#{params[:id]}"), request.body.read, request.content_type
+    put "/#{SERVICE}/:id/?" do
+      FourStore.put uri("/#{SERVICE}/#{params[:id]}"), @body, @content_type
     end
 
     # Delete a resource
-    delete '/:id/?' do
-      FourStore.delete uri("/#{params[:id]}")
+    delete "/#{SERVICE}/:id/?" do
+      FourStore.delete uri("/#{SERVICE}/#{params[:id]}")
     end
 
   end
diff --git a/opentox-server.gemspec b/opentox-server.gemspec
index 1074fbf..199a67a 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     = "0.0.3"
+  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"
@@ -25,6 +25,7 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency 'sinatra'
   s.add_runtime_dependency 'sinatra-contrib'
   s.add_runtime_dependency 'roo'
+  s.add_runtime_dependency 'spreadsheet', "= 0.6.8" # cannot load 0.7.0
   s.add_runtime_dependency 'unicorn'
   s.add_runtime_dependency 'rdf-n3'
 end