eutils 0.1.0 → 0.1.1

data/Rakefile

@@ -11,7 +11,7 @@ begin
     gem.homepage = "http://github.com/seouri/eutils"
     gem.authors = ["Joon Lee"]
     gem.add_development_dependency "shoulda", ">= 0"
-    gem.add_dependency "nokogiri"
+    gem.add_dependency "activesupport", ">= 3.0.0.rc2"
     # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
   end
   Jeweler::GemcutterTasks.new

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/eutils.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{eutils}
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Joon Lee"]
-  s.date = %q{2010-08-25}
+  s.date = %q{2010-08-26}
   s.description = %q{This gem only provides API for NCBI Eutils. If you need full access to other NCBI databases, try BioRuby (bio gem) instead.}
   s.email = %q{seouri@gmail.com}
   s.extra_rdoc_files = [
@@ -43,14 +43,14 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_development_dependency(%q<shoulda>, [">= 0"])
-      s.add_runtime_dependency(%q<nokogiri>, [">= 0"])
+      s.add_runtime_dependency(%q<activesupport>, [">= 3.0.0.rc2"])
     else
       s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<nokogiri>, [">= 0"])
+      s.add_dependency(%q<activesupport>, [">= 3.0.0.rc2"])
     end
   else
     s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<nokogiri>, [">= 0"])
+    s.add_dependency(%q<activesupport>, [">= 3.0.0.rc2"])
   end
 end
 

data/lib/eutils.rb

@@ -30,7 +30,7 @@ class Eutils
     if db.nil? || db.empty?
       return response.scan(/<DbName>(\w+)<\/DbName>/).flatten
     else
-      return Hash.from_xml(response)
+      return Hash.from_xml(response)["eInfoResult"]
     end
   end
 
@@ -44,7 +44,7 @@ class Eutils
     params["usehistory"] ||= "y"
     server = EUTILS_HOST + "esearch.fcgi"
     response = post_eutils(server, params)
-    return Hash.from_xml(response)
+    return Hash.from_xml(response)["eSearchResult"]
   end
 
   # EPost: Posts a file containing a list of primary IDs for future use in the user's environment to use with subsequent search strategies.
@@ -68,12 +68,12 @@ class Eutils
     params["db"] = db
     server = EUTILS_HOST + "esummary.fcgi"
     response = post_eutils(server, params)
-    return Hash.from_xml(response)
+    return Hash.from_xml(response)["eSummaryResult"]
   end
 
   # EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user's environment.
   # See also: http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetch_help.html
-  def efetch(db, webenv, query_key, params = {})
+  def efetch(db, webenv, query_key = 1, params = {})
     params["db"] = db
     params["WebEnv"] = webenv
     params["query_key"] = query_key
@@ -102,7 +102,7 @@ class Eutils
     server = EUTILS_HOST + "egquery.fcgi"
     params = {"term" => term}
     response = post_eutils(server, params)
-    return Hash.from_xml(response)
+    return Hash.from_xml(response)["Result"]
   end
 
   # ESpell: Retrieves spelling suggestions.

data/test/test_eutils.rb

@@ -35,15 +35,15 @@ class TestEutils < Test::Unit::TestCase
   should "get a hash from EInfo with db parameter" do
     i = eutils.einfo("pubmed")
     assert_equal Hash, i.class
-    assert_equal "eInfoResult", i.keys.first
-    assert_equal "pubmed", i['eInfoResult']['DbInfo']['DbName']
+    assert_equal "DbInfo", i.keys.first
+    assert_equal "pubmed", i['DbInfo']['DbName']
   end
 
   should "get a hash from ESearch for a term" do
     r = eutils.esearch("cancer")
     assert_equal Hash, r.class
-    assert_equal "cancer", r["eSearchResult"]["TranslationSet"]["Translation"]["From"]
-    assert_equal Array, r["eSearchResult"]["IdList"]["Id"].class
+    assert_equal "cancer", r["TranslationSet"]["Translation"]["From"]
+    assert_equal Array, r["IdList"]["Id"].class
   end
 
   should "get webenv and querykey from EPost for posted ids" do
@@ -60,13 +60,13 @@ class TestEutils < Test::Unit::TestCase
     ids = [11850928, 11482001]
     i = eutils.esummary(ids)
     assert_equal Hash, i.class
-    assert_equal ids[0], i['eSummaryResult']['DocSum'][0]['Id'].to_i
+    assert_equal ids[0], i['DocSum'][0]['Id'].to_i
   end
 
   should "get a hash from EFetch for ESearch result" do
     s = eutils.esearch("cancer")
-    webenv = s["eSearchResult"]["WebEnv"]
-    query_key = s["eSearchResult"]["QueryKey"]
+    webenv = s["WebEnv"]
+    query_key = s["QueryKey"]
     r = eutils.efetch("pubmed", webenv, query_key)
     assert_equal Hash, r.class
     assert_equal "PubmedArticleSet", r.keys.first
@@ -81,7 +81,8 @@ class TestEutils < Test::Unit::TestCase
   should "get hash from EGQuery" do
     i = eutils.egquery("autism")
     assert_equal Hash, i.class
-    assert_equal "Result", i.keys.first
-    assert_equal "autism", i["Result"]["Term"]
+    assert_equal "Term", i.keys.sort.first
+    assert_equal "eGQueryResult", i.keys.sort.last
+    assert_equal "autism", i["Term"]
   end
 end

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 0
-  version: 0.1.0
+  - 1
+  version: 0.1.1
 platform: ruby
 authors: 
 - Joon Lee
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-08-25 00:00:00 -04:00
+date: 2010-08-26 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -30,15 +30,18 @@ dependencies:
   type: :development
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: nokogiri
+  name: activesupport
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
         segments: 
+        - 3
         - 0
-        version: "0"
+        - 0
+        - rc2
+        version: 3.0.0.rc2
   type: :runtime
   version_requirements: *id002
 description: This gem only provides API for NCBI Eutils. If you need full access to other NCBI databases, try BioRuby (bio gem) instead.