error and dataset tests added, wait_for_task moved to URI.to_object

6 files changed, 154 insertions, 68 deletions

diff --git a/lib/error.rb b/lib/error.rb
index b65651f..2033c1e 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -5,7 +5,9 @@ class RuntimeError
   attr_accessor :report, :http_code
   def initialize message
     super message
+    self.set_backtrace message.backtrace if message.is_a? Exception
     @http_code ||= 500
+    puts self.class
     @report = OpenTox::ErrorReport.create self
     $logger.error "\n"+@report.to_turtle
   end
@@ -77,9 +79,10 @@ module OpenTox
         errorDetails += "REST paramenters:\n#{error.request.args.inspect}"
       end
       error.respond_to?(:http_code) ? statusCode = error.http_code : statusCode = 500
+      puts error.inspect
       if error.respond_to? :response
-        statusCode = error.response.code 
-        message = error.body
+        statusCode = error.response.code if error.response
+        message = error.response.body
       end
       statusCode = error.http_code if error.respond_to? :http_code
       report.rdf << [subject, RDF::OT.statusCode, statusCode ]
@@ -87,7 +90,6 @@ module OpenTox
       # TODO: remove kludge for old task services
       report.http_code = statusCode
       report.rdf << [subject, RDF::OT.message , message ]
-
       errorDetails += "\nBacktrace:\n" + error.backtrace.short_backtrace if error.respond_to?(:backtrace) and error.backtrace 
       report.rdf << [subject, RDF::OT.errorDetails, errorDetails ]
       # TODO Error cause
@@ -139,7 +141,7 @@ module Kernel
     raise stderr.strip if !status.success?
     return stdout
   rescue Exception 
-    internal_server_error "'#{cmd}' failed with: '#{$!.message}'"
+    internal_server_error $!
   end
 
   alias_method :system!, :system
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 566c458..9ba64bd 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -70,8 +70,7 @@ module OpenTox
 
   def delete headers={}
     headers[:subjectid] ||= @subjectid
-    headers[:accept] ||= 'application/rdf+xml'
-    @response = RestClientWrapper.delete(@uri.to_s,:subjectid => @subjectid)
+    @response = RestClientWrapper.delete(@uri.to_s,nil,nil,headers)
   end
 
   # class methods
@@ -82,23 +81,26 @@ module OpenTox
       subjectid ? eval("#{self}.new(\"#{uri}\", #{subjectid})") : eval("#{self}.new(\"#{uri}\")")
     end
 
-    def from_file service_uri, file, subjectid=nil
-      RestClientWrapper.post(service_uri, :file => File.new(file), :subjectid => subjectid).chomp.to_object
+    def from_file service_uri, filename, subjectid=nil
+      file = File.new filename
+      uri = RestClientWrapper.post(service_uri, {:file => file}, {:subjectid => subjectid, :content_type => file.mime_type, :accept => "text/uri-list"})
+      puts uri
     end
 
     def all service_uri, subjectid=nil
-      uris = RestClientWrapper.get(service_uri, nil, {:accept => 'text/uri-list'}).split("\n").compact
+      uris = RestClientWrapper.get(service_uri, {}, :accept => 'text/uri-list').split("\n").compact
       uris.collect{|uri| subjectid ? eval("#{self}.new(\"#{uri}\", #{subjectid})") : eval("#{self}.new(\"#{uri}\")")}
     end
 
   end
 
-  # create default classes
-  SERVICES.each do |s|
-    eval "class #{s}
+  # create default OpenTox classes
+  SERVICES.each do |klass|
+    c = Class.new do
       include OpenTox
       extend OpenTox::ClassMethods
-    end"
+    end
+    OpenTox.const_set klass,c
   end
 
 end
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index f0dcda9..c7a1d43 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -23,8 +23,13 @@ module URI
   end
 
   def self.accessible? uri, subjectid=nil
-    Net::HTTP.get_response(URI.parse(uri))
-    true
+    if URI.task? uri
+      # just ry to get a response, valid tasks may return codes > 400
+      Net::HTTP.get_response(URI.parse(uri))
+      true
+    else
+      Net::HTTP.get_response(URI.parse(uri)).code.to_i < 400
+    end
   rescue
     false
   end
@@ -36,5 +41,23 @@ module URI
     false
   end
 
+  def self.to_object uri, wait=true
+
+    # TODO add waiting task
+    if task? uri and wait
+      t = OpenTox::Task.new(uri)
+      t.wait
+      uri = t.resultURI
+    end
+
+    klass = 
+    subjectid ? eval("#{self}.new(\"#{uri}\", #{subjectid})") : eval("#{self}.new(\"#{uri}\")")
+  end
+
 end
 
+class File
+  def mime_type 
+    `file -ib #{self.path}`.chomp
+  end
+end
diff --git a/lib/rest-client-wrapper.rb b/lib/rest-client-wrapper.rb
index 64c7d7e..e594729 100644
--- a/lib/rest-client-wrapper.rb
+++ b/lib/rest-client-wrapper.rb
@@ -13,7 +13,7 @@ module OpenTox
     # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @param [wait,Boolean] Set to false to NOT wait for task if result is a task
     # @return [RestClient::Response] REST call response 
-    [:head,:get,:post,:put,:dealete].each do |method|
+    [:head,:get,:post,:put,:delete].each do |method|
 
       define_singleton_method method do |uri,payload={},headers={},waiting_task=nil, wait=true|
       
@@ -25,64 +25,40 @@ module OpenTox
         args[:payload] = payload
         headers.each{ |k,v| headers.delete(k) if v==nil } if headers #remove keys with empty values, as this can cause problems
         args[:headers] = headers 
-        @request = RestClient::Request.new(args)
 
         # check input 
         bad_request_error "Invalid URI: '#{uri}'" unless URI.valid? uri
-        bad_request_error "Unreachable URI: '#{uri}'" unless URI.accessible? uri
+        not_found_error "URI '#{uri}' not found." unless URI.accessible? uri
         bad_request_error "Headers are not a hash: #{headers.inspect}" unless headers==nil or headers.is_a?(Hash)
         # make sure that no header parameters are set in the payload
         [:accept,:content_type,:subjectid].each do |header|
           bad_request_error "#{header} should be submitted in the headers" if payload and payload.is_a?(Hash) and payload[header] 
         end
-        bad_request_error "waiting_task is not 'nil', OpenTox::SubTask or OpenTox::Task: #{waiting_task.class}" unless waiting_task.nil? or waiting_task.is_a?(OpenTox::Task) or waiting_task.is_a?(OpenTox::SubTask)
+        #bad_request_error "waiting_task is not 'nil', OpenTox::SubTask or OpenTox::Task: #{waiting_task.class}" unless waiting_task.nil? or waiting_task.is_a?(OpenTox::Task) or waiting_task.is_a?(OpenTox::SubTask)
 
-        
-        begin
-          @response = @request.execute do |response, request, result|
-            # ignore error codes from Task services (may contain eg 500 which causes exceptions in RestClient and RDF::Reader
-            rest_error "Response code is #{response.code}" unless response.code < 400 or URI.task? uri
-            return response
-          end
-          
-          return @response if @response.code==200 or !wait
+        # perform request
+        @request = RestClient::Request.new(args)
+        #begin
+          # do not throw RestClient exceptions in order to create a @response object (needed for error reports) in every case
+          @response = @request.execute { |response, request, result| return response }
+          # ignore error codes from Task services (may return error codes >= 400 according to API, which causes exceptions in RestClient and RDF::Reader)
+          raise OpenTox::RestCallError.new @request, @response, "Response code is #{@response.code}." unless @response.code < 400 or URI.task? uri
+          #return @response if @response.code==200 or !wait
 
           # wait for task
-          while @response.code==201 or @response.code==202
-            @response = wait_for_task(@response, uri, waiting_task)
-          end
-          return @response
+          #while @response.code==201 or @response.code==202
+            #@response = wait_for_task(@response, uri, waiting_task)
+          #end
+          @response
           
-        rescue
-          rest_error $!.message
-        end
-=begin
-        rescue RestClient::RequestTimeout 
-          raise OpenTox::Error @request, @response, $!.message
-          #received_error ex.message, 408, nil, {:rest_uri => uri, :headers => headers, :payload => payload}
-        rescue Errno::ETIMEDOUT 
-          raise OpenTox::Error @request, @response, $!.message
-          #received_error ex.message, 408, nil, {:rest_uri => uri, :headers => headers, :payload => payload}
-        rescue Errno::ECONNREFUSED
-          raise OpenTox::Error $!.message
-          #received_error ex.message, 500, nil, {:rest_uri => uri, :headers => headers, :payload => payload}
-        rescue RestClient::ExceptionWithResponse
-          # error comming from a different webservice, 
-          received_error ex.http_body, ex.http_code, ex.response.net_http_res.content_type, {:rest_uri => uri, :headers => headers, :payload => payload}
-        #rescue OpenTox::RestCallError => ex
-          # already a rest-error, probably comes from wait_for_task, just pass through
-          #raise ex       
-        #rescue => ex
-          # some internal error occuring in rest-client-wrapper, just pass through
-          #raise ex
-        end
-=end
+        #rescue
+          #rest_error $!.message
+        #end
       end
     end
     
+=begin
     def wait_for_task( response, base_uri, waiting_task=nil )
-      #TODO remove TUM hack
-      # @response.headers[:content_type] = "text/uri-list" if base_uri =~/tu-muenchen/ and @response.headers[:content_type] == "application/x-www-form-urlencoded;charset=UTF-8"
 
       task = nil
       case @response.headers[:content_type]
@@ -97,7 +73,6 @@ module OpenTox
         rest_error "Unknown content-type for task : '"+@response.headers[:content_type].to_s+"'"+" base-uri: "+base_uri.to_s+" content: "+@response[0..200].to_s
       end
       
-      #LOGGER.debug "result is a task '"+task.uri.to_s+"', wait for completion"
       task.wait waiting_task
       unless task.completed? # maybe task was cancelled / error
         if task.errorReport
@@ -111,18 +86,10 @@ module OpenTox
     end
 
     def self.rest_error message
+      puts message
       raise OpenTox::RestCallError.new @request, @response, message
     end
 
-=begin
-    def self.bad_request_error message
-      raise OpenTox::Error.new message
-    end
-
-    def self.not_found_error message
-      raise OpenTox::NotFoundError.new message
-    end
-    
     def self.received_error( body, code, content_type=nil, params=nil )
 
       # try to parse body TODO
diff --git a/test/dataset.rb b/test/dataset.rb
new file mode 100644
index 0000000..13012bd
--- /dev/null
+++ b/test/dataset.rb
@@ -0,0 +1,57 @@
+require 'test/unit'
+$LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
+require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
+
+class DatasetTest < Test::Unit::TestCase
+
+=begin
+  def test_post_get_delete
+    service_uri = "http://ot-dev.in-silico.ch/dataset" 
+    dataset = OpenTox::Dataset.create service_uri
+    assert_match /#{service_uri}/, dataset.uri.to_s
+      puts dataset.uri
+    puts dataset.class
+    puts dataset.to_yaml
+    metadata =  dataset.metadata
+    puts dataset.class
+    assert_equal RDF::OT.Dataset, metadata[RDF.type]
+    assert_equal dataset.uri, metadata[RDF::XSD.anyURI]
+    dataset.delete
+  end
+  def test_all
+    datasets = OpenTox::Dataset.all "http://ot-dev.in-silico.ch/dataset"
+    assert_equal OpenTox::Dataset, datasets.first.class
+  end
+
+  def test_create
+    d = OpenTox::Dataset.create "http://ot-dev.in-silico.ch/dataset"
+    assert_equal OpenTox::Dataset, d.class
+    puts d.delete
+    assert_raise OpenTox::NotFoundError do
+      puts d.get(:accept => 'application/x-yaml')
+    end
+  end
+=end
+
+  def test_create_from_file
+    d = OpenTox::Dataset.from_file "http://ot-dev.in-silico.ch/dataset", "data/EPAFHM.mini.csv"
+    assert_equal OpenTox::Dataset, d.class
+    puts d.inspect
+    
+  end
+
+=begin
+  def test_save
+    d = OpenTox::Dataset.create "http://ot-dev.in-silico.ch/dataset"
+    d.metadata
+    d.metadata[RDF::DC.title] = "test"
+    d.save
+    # TODO: save does not work with datasets
+    #puts d.response.code.inspect
+    #assert_equal "test", d.metadata[RDF::DC.title] # should reload metadata
+    d.delete
+  end
+=end
+
+
+end
diff --git a/test/error.rb b/test/error.rb
new file mode 100644
index 0000000..af5db52
--- /dev/null
+++ b/test/error.rb
@@ -0,0 +1,35 @@
+require 'test/unit'
+$LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
+require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
+
+class ErrorTest < Test::Unit::TestCase
+
+  def test_bad_request
+    object = OpenTox::Feature.new "http://this-is-a/fantasy/url"
+    assert_raise OpenTox::BadRequestError do
+      response = object.get
+    end
+  end
+
+  def test_error_methods
+    assert_raise OpenTox::NotFoundError do
+      not_found_error "This is a test"
+    end
+  end
+
+  def test_exception
+    assert_raise Exception do
+      raise Exception.new "Basic Exception"
+    end
+  end
+
+  def test_backtick
+    assert_raise OpenTox::InternalServerError do
+      `this call will not work`
+    end
+    assert_raise OpenTox::InternalServerError do
+      `ls inexisting_directory`
+    end
+  end
+
+end