dataset-large tests pass

3 files changed, 13 insertions, 11 deletions

diff --git a/lib/4store.rb b/lib/4store.rb
index 43e41c8..cbce7bb 100644
--- a/lib/4store.rb
+++ b/lib/4store.rb
@@ -29,14 +29,22 @@ module OpenTox
         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
-        RestClient.post File.join(four_store_uri,"data")+"/", :data => rdf, :graph => uri, "mime-type" => mime_type 
+        begin
+          RestClient.post File.join(four_store_uri,"data")+"/", :data => rdf, :graph => uri, "mime-type" => mime_type 
+        rescue
+          rest_call_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"
-        RestClient.put File.join(four_store_uri,"data",uri), rdf, :content_type => mime_type 
+        begin
+          RestClient.put File.join(four_store_uri,"data",uri), rdf, :content_type => mime_type 
+        rescue
+          rest_call_error $!.message, File.join(four_store_uri,"data",uri)
+        end
       end
 
       def self.delete uri
@@ -49,9 +57,6 @@ module OpenTox
 
       def self.query sparql, mime_type
         if sparql =~ /SELECT/i
-#         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 'application/sparql-results+xml' 
@@ -75,6 +80,7 @@ module OpenTox
             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
@@ -85,6 +91,8 @@ module OpenTox
           # TODO: check if this prevents SPARQL injections
           bad_request_error "Only SELECT and CONSTRUCT are accepted SPARQL statements."
         end
+      rescue
+        rest_call_error $!.message, sparql_uri
       end
 
       def self.klass
diff --git a/lib/opentox-server.rb b/lib/opentox-server.rb
index 3f04acc..afcce4b 100644
--- a/lib/opentox-server.rb
+++ b/lib/opentox-server.rb
@@ -2,8 +2,6 @@ require 'opentox-client'
 require 'rack'
 require 'rack/contrib'
 require 'sinatra'
-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__),"authorization-helper.rb")
diff --git a/opentox-server.gemspec b/opentox-server.gemspec
index 8628c5e..cc9d160 100644
--- a/opentox-server.gemspec
+++ b/opentox-server.gemspec
@@ -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 'roo'
-  s.add_runtime_dependency 'spreadsheet', "= 0.6.8" # cannot load 0.7.0
   s.add_runtime_dependency 'unicorn'
 end