biomart 0.2.2 → 0.2.3

data/Gemfile.lock

@@ -1,13 +1,14 @@
 PATH
   remote: .
   specs:
-    biomart (0.2.1)
-      builder
+    biomart (0.2.2)
+      builder (>= 3.0)
 
 GEM
   remote: http://rubygems.org/
   specs:
-    builder (2.1.2)
+    awesome_print (0.4.0)
+    builder (3.0.0)
     shoulda (2.11.3)
     simplecov (0.4.0)
       simplecov-html (~> 0.4.0)
@@ -17,6 +18,7 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
+  awesome_print
   biomart!
   shoulda (>= 2.10)
   simplecov

data/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.

data/biomart.gemspec

@@ -19,7 +19,8 @@ Gem::Specification.new do |s|
   s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
   s.require_paths = ["lib"]
   
-  s.add_runtime_dependency("builder", [">= 0"])
+  s.add_runtime_dependency("builder", [">= 3.0"])
   s.add_development_dependency("shoulda", [">= 2.10"])
   s.add_development_dependency("simplecov", [">= 0"])
+  s.add_development_dependency("awesome_print", [">= 0"])
 end

data/lib/biomart/dataset.rb

@@ -223,7 +223,7 @@ module Biomart
             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 @@ module Biomart
         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 @@ module Biomart
           
           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

data/lib/biomart/version.rb

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

data/test/test_biomart.rb

@@ -46,6 +46,7 @@ class BiomartTest < Test::Unit::TestCase
       @htgt_trap   = @htgt.datasets["htgt_trap"]
       @kermits     = @htgt.datasets["kermits"]
       @ensembl     = @htgt.datasets["mmusculus_gene_ensembl"]
+      @phenotyping = @htgt.datasets["phenotyping"]
       @ensembl_var = Biomart::Dataset.new( "http://www.ensembl.org/biomart", { :name => "hsapiens_snp" } )
       @emma        = Biomart::Dataset.new( "http://www.emmanet.org/biomart", { :name => "strains" } )
       @dcc         = Biomart::Dataset.new( "http://www.knockoutmouse.org/biomart", { :name => "dcc" } )
@@ -75,11 +76,11 @@ class BiomartTest < Test::Unit::TestCase
       htgt_count = @htgt_targ.count()
       assert( htgt_count.is_a?( Integer ), "Biomart::Dataset.count is not returning integers." )
       assert( htgt_count > 0, "Biomart::Dataset.count is returning zero - this is wrong!" )
-
+    
       htgt_count_single_filter = @htgt_targ.count( :filters => { "is_eucomm" => "1" } )
       assert( htgt_count_single_filter.is_a?( Integer ), "Biomart::Dataset.count (with single filter) is not returning integers." )
       assert( htgt_count_single_filter > 0, "Biomart::Dataset.count (with single filter) is returning zero - this is wrong!" )
-
+    
       htgt_count_single_filter_group_value = @htgt_targ.count( :filters => { "marker_symbol" => ["Cbx1","Cbx7","Art4"] } )
       assert( htgt_count_single_filter_group_value.is_a?( Integer ), "Biomart::Dataset.count (with single filter, group value) is not returning integers." )
       assert( htgt_count_single_filter_group_value > 0, "Biomart::Dataset.count (with single filter, group value) is returning zero - this is wrong!" )
@@ -89,12 +90,12 @@ class BiomartTest < Test::Unit::TestCase
       search = @htgt_trap.search()
       assert( search.is_a?( Hash ), "Biomart::Dataset.search (no options) is not returning a hash." )
       assert( search[:data].is_a?( Array ), "Biomart::Dataset.search[:data] (no options) is not returning an array." )
-
+    
       search1 = @htgt_targ.search( :filters => { "marker_symbol" => "Cbx1" }, :process_results => true )
       assert( search1.is_a?( Array ), "Biomart::Dataset.search (filters defined with processing) is not returning an array." )
       assert( search1.first.is_a?( Hash ), "Biomart::Dataset.search (filters defined with processing) is not returning an array of hashes." )
       assert( search1.first["marker_symbol"] == "Cbx1", "Biomart::Dataset.search (filters defined with processing) is not returning the correct info." )
-
+    
       search2 = @htgt_targ.search( :filters => { "marker_symbol" => "Cbx1" }, :attributes => ["marker_symbol","ensembl_gene_id"], :process_results => true )
       assert( search2.is_a?( Array ), "Biomart::Dataset.search (filters and attributes defined with processing) is not returning an array." )
       assert( search2.first.is_a?( Hash ), "Biomart::Dataset.search (filters and attributes defined with processing) is not returning an array of hashes." )
@@ -143,6 +144,20 @@ class BiomartTest < Test::Unit::TestCase
       assert( search2.is_a?( Hash ), "Biomart::Dataset.search (no options) is not returning a hash. (EMMA Query)" )
       assert( search2[:data].is_a?( Array ), "Biomart::Dataset.search[:data] (no options) is not returning an array. (EMMA Query)" )
       assert( search2[:data].size > 0, "Biomart::Dataset.search[:data] for poorly formatted TSV data is empty. (EMMA Query)" )
+      
+      search3 = @phenotyping.search(
+        :timeout    => 240,
+        :filters    => {},
+        :attributes => [
+          'param_level_heatmap_colony_prefix',
+          'param_level_heatmap_mp_id',
+          'param_level_heatmap_mp_term'
+        ]
+      )
+      
+      assert( search3.is_a?( Hash ), "Biomart::Dataset.search (no options) is not returning a hash. (MGP Phenotyping Query)" )
+      assert( search3[:data].is_a?( Array ), "Biomart::Dataset.search[:data] (no options) is not returning an array. (MGP Phenotyping Query)" )
+      assert( search3[:data].size > 0, "Biomart::Dataset.search[:data] for poorly formatted TSV data is empty. (MGP Phenotyping Query)" )
     end
     
     should "perform federated search queries" do
@@ -169,7 +184,7 @@ class BiomartTest < Test::Unit::TestCase
       assert( results[:data].is_a?(Array), "Biomart::Dataset.search[:data] is not returning an array. [federated search]" )
       assert( results[:data][0].size === 3, "Biomart::Dataset.search[:data] is not returning 3 attributes. [federated search]" )
       assert( results[:headers].size === 3, "Biomart::Dataset.search[:headers] is not returning 3 elements. [federated search]" )
-
+    
       assert_raise( Biomart::ArgumentError ) { @htgt_targ.count( search_opts ) }
       
       assert_raise Biomart::ArgumentError do
@@ -260,7 +275,8 @@ class BiomartTest < Test::Unit::TestCase
       search_opts = {
         :filters         => { 'with_variation_annotation' => true, 'ensembl_gene' => 'ENSG00000244734' },
         :attributes      => [ 'refsnp_id','chr_name','chrom_start' ],
-        :process_results => true
+        :process_results => true,
+        :timeout         => 1000
       }
       
       true_results = {}

data/test/test_helper.rb

@@ -4,6 +4,7 @@ $:.unshift( "#{File.expand_path(File.dirname(__FILE__))}/../lib" )
 require 'rubygems'
 require 'bundler/setup'
 require 'shoulda'
+require 'awesome_print'
 
 # Set-up SimpleCov (code coverage tool for Ruby 1.9)
 if /^1.9/ === RUBY_VERSION

metadata

@@ -1,12 +1,8 @@
 --- !ruby/object:Gem::Specification 
 name: biomart
 version: !ruby/object:Gem::Version 
-  prerelease: false
-  segments: 
-  - 0
-  - 2
-  - 2
-  version: 0.2.2
+  prerelease: 
+  version: 0.2.3
 platform: ruby
 authors: 
 - Darren Oakley
@@ -14,8 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-02-18 00:00:00 +00:00
-default_executable: 
+date: 2011-07-14 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: builder
@@ -25,9 +20,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        version: "0"
+        version: "3.0"
   type: :runtime
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
@@ -38,9 +31,6 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        segments: 
-        - 2
-        - 10
         version: "2.10"
   type: :development
   version_requirements: *id002
@@ -52,11 +42,20 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        segments: 
-        - 0
         version: "0"
   type: :development
   version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: awesome_print
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  version_requirements: *id004
 description: A ruby API for interacting with Biomart XML based webservices.
 email: 
 - daz.oakley@gmail.com
@@ -89,7 +88,6 @@ files:
 - tasks/yard.rake
 - test/test_biomart.rb
 - test/test_helper.rb
-has_rdoc: true
 homepage: http://github.com/dazoakley/biomart
 licenses: []
 
@@ -103,21 +101,17 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      segments: 
-      - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      segments: 
-      - 0
       version: "0"
 requirements: []
 
 rubyforge_project: biomart
-rubygems_version: 1.3.7
+rubygems_version: 1.8.5
 signing_key: 
 specification_version: 3
 summary: A ruby API for interacting with Biomart services.