Added some error handling / reporting to the http requests. Closes #3

lib/biomart.rb

@@ -12,18 +12,19 @@ module Biomart
   # Specialised classes for error reporting
   class BiomartError < StandardError
     attr_reader :data
-
+    
     def initialize(data)
       @data = data
       super
     end
   end
-
-  class Unauthorized  < StandardError; end
-  class Unavailable   < StandardError; end
-  class NotFound      < StandardError; end
 
-  @@url = 'http://www.biomart.org/biomart/martservice'
+  class HTTPError             < StandardError; end
+  class BiomartFilterError    < BiomartError; end
+  class BiomartAttributeError < BiomartError; end
+  class BiomartDatasetError   < BiomartError; end
+
+  @@url    = 'http://www.biomart.org/biomart/martservice'
   @@client = Net::HTTP
 
   def request( params={} )
@@ -42,6 +43,23 @@ def request( params={} )
       res = get( params )
     end
 
+    # Process the response code/body to catch errors.
+    if res.code != "200"
+      raise HTTPError, "HTTP error #{res.code}, please check your biomart server and URL settings."
+    else
+      if res.body =~ /ERROR/
+        if res.body =~ /Filter (.+) NOT FOUND/
+          raise BiomartFilterError.new(res.body), "Biomart error. Filter #{$1} not found."
+        elsif res.body =~ /Attribute (.+) NOT FOUND/
+          raise BiomartAttributeError.new(res.body), "Biomart error. Attribute #{$1} not found."
+        elsif res.body =~ /Dataset (.+) NOT FOUND/
+          raise BiomartDatasetError.new(res.body), "Biomart error. Dataset #{$1} not found."
+        else
+          raise BiomartError.new(res.body), "Biomart error."
+        end
+      end
+    end
+
     return res.body
   end
 

test/test_biomart.rb

@@ -93,4 +93,46 @@ def setup
       assert( search2.first["marker_symbol"] == "Cbx1", "Biomart::Dataset.search (filters and attributes defined with processing) is not returning the correct info." )
     end
   end
+
+  context "The Biomart module" do
+    setup do
+      @not_biomart = Biomart::Server.new('http://www.sanger.ac.uk')
+      @htgt_targ   = @htgt.datasets["htgt_targ"]
+      @bad_dataset = Biomart::Dataset.new( "http://www.sanger.ac.uk/htgt/biomart", { :name => "wibble" } )
+    end
+
+    should "handle user/configuration errors (i.e. incorrect URLs etc)" do
+      begin
+        @not_biomart.list_databases
+      rescue Biomart::HTTPError => e
+        http_error = e
+      end
+
+      assert( http_error.is_a?( Biomart::HTTPError ), "Biomart.request is not processing HTTP errors correctly." )
+    end
+
+    should "handle biomart server errors gracefully" do
+      begin
+        @htgt_targ.count( :filters => { "wibbleblibbleblip" => "1" } )
+      rescue Biomart::BiomartFilterError => e
+        filter_error = e
+      end
+
+      begin
+        @htgt_targ.search( :attributes => ["wibbleblibbleblip"] )
+      rescue Biomart::BiomartAttributeError => e
+        attribute_error = e
+      end
+
+      begin
+        @bad_dataset.count()
+      rescue Biomart::BiomartDatasetError => e
+        dataset_error = e
+      end
+
+      assert( filter_error.is_a?( Biomart::BiomartFilterError ), "Biomart.request is not handling Biomart filter errors correctly." )
+      assert( attribute_error.is_a?( Biomart::BiomartAttributeError ), "Biomart.request is not handling Biomart attribute errors correctly." )
+      assert( dataset_error.is_a?( Biomart::BiomartDatasetError ), "Biomart.request is not handling Biomart dataset errors correctly." )
+    end
+  end
 end