biomart 0.1.4 → 0.1.5

data/History.txt

@@ -1,3 +1,10 @@
+=== 0.1.5 2010-02-04
+
+* 1 major bugfix:
+  * Poorly formatted tab-separated data (coming from biomart) was not 
+    being processed correctly (as a result some data was being dropped). 
+    This hole has now been fixed...
+
 === 0.1.4 2010-01-20
 
 * 1 minor enhancement:

data/biomart.gemspec

@@ -2,11 +2,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{biomart}
-  s.version = "0.1.4"
+  s.version = "0.1.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Darren Oakley"]
-  s.date = %q{2010-01-20}
+  s.date = %q{2010-02-04}
   s.description = %q{A ruby API for interacting with Biomart services.}
   s.email = ["daz.oakley@gmail.com"]
   s.extra_rdoc_files = ["History.txt", "Manifest.txt", "README.rdoc"]

data/lib/biomart.rb

@@ -15,7 +15,7 @@ require "builder"
 #CURB_AVAILABLE = use_curb
 
 module Biomart
-  VERSION = "0.1.4"
+  VERSION = "0.1.5"
   
   # This is the base Biomart error/exception class. Rescue it if 
   # you want to catch any exceptions that this code might raise.

data/lib/biomart/dataset.rb

@@ -256,9 +256,13 @@ module Biomart
           
           if elements.size == 0
             # This is a bad line (causing the above Exception), try and use split to recover.
-            # Alse add an empty value as split will miss the final value...
             elements = line.split("\t")
-            elements.push(nil)
+            if line =~ /\t$/
+              # If the last attribute resturn is empty add a nil
+              # value to the array as it would have been missed 
+              # by the split function!
+              elements.push(nil)
+            end
             
             # Substitute blank strings for nils
             elements.map! do |elem|

data/test/test_biomart.rb

@@ -43,6 +43,7 @@ class BiomartTest < Test::Unit::TestCase
       @htgt_targ = @htgt.datasets["htgt_targ"]
       @htgt_trap = @htgt.datasets["htgt_trap"]
       @kermits   = @htgt.datasets["kermits"]
+      @emma      = Biomart::Dataset.new( "http://www.emmanet.org/biomart", { :name => "strains" } )
     end
     
     should "have basic metadata" do
@@ -105,9 +106,22 @@ class BiomartTest < Test::Unit::TestCase
           "is_latest_for_gene", "targeted_trap"
         ]
       )
-      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." )
-      assert( search[:data].size > 0, "Biomart::Dataset.search[:data] for poorly formatted TSV data is empty." )
+      assert( search.is_a?( Hash ), "Biomart::Dataset.search (no options) is not returning a hash. (HTGT Query)" )
+      assert( search[:data].is_a?( Array ), "Biomart::Dataset.search[:data] (no options) is not returning an array. (HTGT Query)" )
+      assert( search[:data].size > 20, "Biomart::Dataset.search[:data] for poorly formatted TSV data is empty. (HTGT Query)" )
+      
+      search2 = @emma.search(
+        :filters    => { "emma_id" => ["EM:03629"] },
+        :attributes => [
+          "emma_id", "international_strain_name", "synonym", "maintained_background", 
+          "mutation_main_type", "mutation_sub_type", "alls_form", "genetic_description", 
+          "phenotype_description", "reference", "pubmed_id", "availability", "owner"
+        ]
+      )
+      
+      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)" )
     end
     
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: biomart
 version: !ruby/object:Gem::Version 
-  version: 0.1.4
+  version: 0.1.5
 platform: ruby
 authors: 
 - Darren Oakley
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-01-20 00:00:00 +00:00
+date: 2010-02-04 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency