biomart 0.1.2 → 0.1.3

data/History.txt

@@ -1,10 +1,13 @@
-=== 0.1.0 2009-08-29
+=== 0.1.3 2009-10-30
 
-* 1 major enhancement:
-  * Initial release:
-    * Basic gathering of information about a Biomart server.
-    * Counting functionality.
-    * Basic searching of a single dataset.
+* 1 major bugfix:
+  * Ruby 1.9 compatibility added.
+
+=== 0.1.2 2009-10-29
+
+* 1 major bugfix:
+  * Added in code to handle poorly formatted tab-separated data 
+    coming back from a biomart query.
 
 === 0.1.1 2009-10-21
 
@@ -13,8 +16,10 @@
     to allow a user to ping a biomart server to make sure it is online 
     and functioning as expected.
 
-=== 0.1.2 2009-10-29
+=== 0.1.0 2009-08-29
 
-* 1 major bugfix:
-  * Added in code to handle poorly formatted tab-separated data 
-    coming back from a biomart query.
+* 1 major enhancement:
+  * Initial release:
+    * Basic gathering of information about a Biomart server.
+    * Counting functionality.
+    * Basic searching of a single dataset.

data/README.rdoc

@@ -1,9 +1,9 @@
 = Biomart
 
-http://biomart.rubyforge.org
-
 http://github.com/dazoakley/biomart
 
+http://rubyforge.org/projects/biomart
+
 Biomart provides a simple interface for working with Biomart servers 
 (see http://www.biomart.org for more info on Biomart itself), so you 
 don't have to get down and dirty with the basic webservice calls yourself.
@@ -96,10 +96,10 @@ Alternatively you can also set your proxy url in the environment variable
 
 Written by Darren Oakley (daz dot oakley at gmail dot com)
 
-http://biomart.rubyforge.org
-
 http://github.com/dazoakley/biomart
 
+http://rubyforge.org/projects/biomart
+
 == License
 
 (The MIT License)

data/biomart.gemspec

@@ -2,11 +2,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{biomart}
-  s.version = "0.1.2"
+  s.version = "0.1.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Darren Oakley"]
-  s.date = %q{2009-10-29}
+  s.date = %q{2009-10-30}
   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

@@ -7,7 +7,7 @@ require "rubygems"
 require "builder"
 
 module Biomart
-  VERSION = "0.1.2"
+  VERSION = "0.1.3"
   
   # 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/database.rb

@@ -43,7 +43,16 @@ module Biomart
       def fetch_datasets
         url = @url + "?type=datasets&mart=#{@name}"
         document = request( :url => url )
-        tsv_data = CSV.parse( document, "\t" )
+        tsv_data = []
+        
+        if CSV.const_defined? :Reader
+          # Ruby < 1.9 CSV code
+          tsv_data = CSV.parse( document, "\t" )
+        else
+          # Ruby >= 1.9 CSV code
+          tsv_data = CSV.parse( document, { :col_sep => "\t" } )
+        end
+        
         tsv_data.each do |t|
           if t[1] and ( t[3] === "1" )
             dataset_attr = {

data/lib/biomart/dataset.rb

@@ -190,10 +190,21 @@ module Biomart
           end
         end
 
-        begin
-          parsed_data = CSV.parse( tsv, "\t" )
-        rescue CSV::IllegalFormatError => e
-          parsed_data = parse_tsv_line_by_line( headers.size, tsv )
+        parsed_data = []
+        if CSV.const_defined? :Reader
+          # Ruby < 1.9 CSV code
+          begin
+            parsed_data = CSV.parse( tsv, "\t" )
+          rescue CSV::IllegalFormatError => e
+            parsed_data = parse_tsv_line_by_line( headers.size, tsv )
+          end
+        else
+          # Ruby >= 1.9 CSV code
+          begin
+            parsed_data = CSV.parse( tsv, { :col_sep => "\t" } )
+          rescue CSV::MalformedCSVError => e
+            parsed_data = parse_tsv_line_by_line( headers.size, tsv )
+          end
         end
         
         return {
@@ -211,7 +222,19 @@ module Biomart
         
         data_by_line = tsv.split("\n")
         data_by_line.each do |line|
-          elements = CSV::parse_line( line, "\t" )
+          elements = []
+          
+          if CSV.const_defined? :Reader
+            # Ruby < 1.9 CSV code
+            elements = CSV::parse_line( line, "\t" )
+          else
+            # Ruby >= 1.9 CSV code
+            begin
+              elements = CSV::parse_line( line, { :col_sep => "\t" } )
+            rescue CSV::MalformedCSVError => e
+              elements = []
+            end
+          end
           
           if elements.size == 0
             # This is a bad line (causing the above Exception), try and use split to recover.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: biomart
 version: !ruby/object:Gem::Version 
-  version: 0.1.2
+  version: 0.1.3
 platform: ruby
 authors: 
 - Darren Oakley
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-10-29 00:00:00 +00:00
+date: 2009-10-30 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency