entrez 0.5.0 → 0.5.1

data/lib/entrez/version.rb

@@ -1,3 +1,3 @@
 module Entrez
-  VERSION = "0.5.0"
+  VERSION = "0.5.1"
 end

data/lib/entrez.rb

@@ -21,9 +21,12 @@ class Entrez
     end
 
     # E.g. Entrez.ESearch('genomeprj', {WORD: 'hapmap', SEQS: 'inprogress'}, retmode: :xml)
+    # returns response. For convenience, response.ids() returns array of ID integers from result set.
     def ESearch(db, search_terms = {}, params = {})
       params[:term] = convert_search_term_hash(search_terms)
-      perform '/esearch.fcgi', db, params
+      response = perform '/esearch.fcgi', db, params
+      parse_ids_and_extend response if response[:retmode].nil? || response[:retmode] == :xml
+      response
     end
 
     # E.g. Entrez.ESummary('snp', id: 123, retmode: :xml)
@@ -64,6 +67,15 @@ class Entrez
       end.join('+AND+')
     end
 
+    # Define ids() method which will parse and return the IDs from the XML response.
+    def parse_ids_and_extend(response)
+      response.instance_eval do
+        def ids
+          @ids ||= self['eSearchResult']['IdList']['Id'].map(&:to_i)
+        end
+      end
+    end
+
   end
 
 end

data/lib/query_string_normalizer.rb

@@ -5,8 +5,11 @@ QueryStringNormalizer = proc do |query_hash|
     when Array
       value.join(',')
     else
-      value
+      # If value is a string, it will be frozen, so dup it.
+      value.to_s.dup
     end
+    # Escape spaces.
+    value_string.gsub!(' ', '%20')
     "#{key}=#{value_string}"
   end.join('&')
 end

data/spec/entrez_spec.rb

@@ -27,6 +27,11 @@ describe Entrez do
     response.body.should include('<Name>RS</Name>')
   end
 
+  it '#ESearch response returns IDs for convenience' do
+    response = Entrez.ESearch('genomeprj', {WORD: 'hapmap', SEQS: 'inprogress'}, retmode: :xml)
+    response.ids.should == [60153, 29429, 28911, 48101, 59851, 59849, 59847, 59845, 59839, 59835, 59833, 59831, 51895, 59829, 59827, 60835, 59811, 60831, 60819, 33895]
+  end
+
   it 'should respect query limit' do
     requests = proc { 4.times { Entrez.EFetch('taxonomy', id: 9606) } }
     requests.should take_longer_than(1.0)

data/spec/query_string_normalizer_spec.rb

@@ -2,9 +2,14 @@ require 'spec_helper'
 
 describe QueryStringNormalizer do
 
-  it 'does not escape' do
+  it 'does not escape square brackets' do
     query = {term: '[asdf]', db: 'snp'}
     QueryStringNormalizer.call(query).should == 'term=[asdf]&db=snp'
   end
 
+  it 'escapes spaces' do
+    query = {term: 'a b c'}
+    QueryStringNormalizer.call(query).should == 'term=a%20b%20c'
+  end
+
 end

metadata

@@ -2,7 +2,7 @@
 name: entrez
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.5.0
+  version: 0.5.1
 platform: ruby
 authors: 
 - Jared Ning
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-05-28 00:00:00 -05:00
+date: 2011-05-29 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency