Merge branch 'master' of github.com:dazoakley/biomart

* 'master' of github.com:dazoakley/biomart:
  Version bump to 0.2.3
  Bugfix - we were creating too many filter objects as the catch for the pointer filters was wrong.
  Update builder dependency.
  Make the TSV parsing a little more robust...

Conflicts:
	Gemfile.lock
	biomart.gemspec
	test/test_biomart.rb
	test/test_helper.rb

Gemfile.lock

@@ -11,6 +11,7 @@ GEM
     builder (3.0.0)
     crack (0.1.8)
     rake (0.8.7)
+    awesome_print (0.4.0)
     shoulda (2.11.3)
     simplecov (0.4.0)
       simplecov-html (~> 0.4.0)
@@ -24,6 +25,7 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
+  awesome_print
   biomart!
   rake
   shoulda (>= 2.10)

History.txt

@@ -1,4 +1,10 @@
-=== 0.2.1 2011-02-18
+=== 0.2.3 2011-07-14
+
+* 2 minor bugfixes:
+  * More robust parsing of the TSV from biomart
+  * Stop creating lots of unnecessary filter objects
+
+=== 0.2.2 2011-02-18
 
 * 1 major bugfix:
   * More forceful filter checking in 0.2.1 was causing queries on 'pointerFilters' to error out unnecessarily.

biomart.gemspec

@@ -23,6 +23,7 @@ Gem::Specification.new do |s|
   s.add_development_dependency("rake", [">= 0"])
   s.add_development_dependency("shoulda", [">= 2.10"])
   s.add_development_dependency("simplecov", [">= 0"])
+  s.add_development_dependency("awesome_print", [">= 0"])
   s.add_development_dependency("vcr", [">= 0"])
   s.add_development_dependency("webmock", [">= 0"])
 end

lib/biomart/dataset.rb

@@ -223,7 +223,7 @@ def fetch_configuration
             if f.attributes["displayType"] != nil
               next if f.attributes["displayType"] == "container"
               @filters[ f.attributes["internalName"] ] = Filter.new( f.attributes )
-            else f.attributes["pointerFilter"] != nil
+            elsif f.attributes["pointerFilter"] != nil
               pointer_filter = Filter.new( f.attributes )
               @filters[ pointer_filter.name ]           = pointer_filter
               @filters[ pointer_filter.pointer_filter ] = pointer_filter
@@ -337,7 +337,7 @@ def process_tsv( args, tsv )
         else
           # Ruby >= 1.9 CSV code
           begin
-            parsed_data = CSV.parse( tsv, { :col_sep => "\t" } )
+            parsed_data = CSV.parse( tsv, { :col_sep => "\t", :skip_blanks => true } )
           rescue CSV::MalformedCSVError => e
             parsed_data = parse_tsv_line_by_line( headers.size, tsv )
           end
@@ -378,11 +378,11 @@ def parse_tsv_line_by_line( expected_row_size, tsv )
 
           if CSV.const_defined? :Reader
             # Ruby < 1.9 CSV code
-            elements = CSV::parse_line( line, "\t" )
+            elements = CSV::parse_line( line, "\t" ) || []
           else
             # Ruby >= 1.9 CSV code
             begin
-              elements = CSV::parse_line( line, { :col_sep => "\t" } )
+              elements = CSV::parse_line( line, { :col_sep => "\t" } ) || []
             rescue CSV::MalformedCSVError => e
               elements = []
             end

lib/biomart/version.rb

@@ -1,3 +1,3 @@
 module Biomart
-  VERSION = "0.2.2"
+  VERSION = "0.2.3"
 end

test/test_biomart_dataset.rb

@@ -231,7 +231,8 @@ def teardown
       search_opts = {
         :filters         => { 'with_variation_annotation' => true, 'ensembl_gene' => 'ENSG00000244734' },
         :attributes      => [ 'refsnp_id','chr_name','chrom_start' ],
-        :process_results => true
+        :process_results => true,
+        :timeout => 2000
       }
 
       true_results = {}

test/test_helper.rb

@@ -15,6 +15,7 @@
 require 'biomart'
 require 'shoulda'
 require 'vcr'
+require 'awesome_print'
 
 # Set-up VCR for mocking up web requests.
 VCR.config do |c|