eutils 0.1.2 → 0.2.0

data/VERSION

@@ -1 +1 @@
-0.1.2
+0.2.0

data/eutils.gemspec

@@ -1,15 +1,15 @@
 # Generated by jeweler
 # DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
   s.name = %q{eutils}
-  s.version = "0.1.2"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Joon Lee, aka seouri"]
-  s.date = %q{2010-08-30}
+  s.date = %q{2011-04-27}
   s.description = %q{Lightweight Ruby API for NCBI Eutils. 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 = [
@@ -17,31 +17,29 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".document",
-     ".gitignore",
-     "MIT-LICENSE",
-     "README.rdoc",
-     "Rakefile",
-     "VERSION",
-     "eutils.gemspec",
-     "lib/eutils.rb",
-     "test/helper.rb",
-     "test/test_eutils.rb"
+    "MIT-LICENSE",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "eutils.gemspec",
+    "lib/eutils.rb",
+    "test/helper.rb",
+    "test/test_eutils.rb"
   ]
   s.homepage = %q{http://github.com/seouri/eutils}
-  s.rdoc_options = ["--charset=UTF-8"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.6}
+  s.rubygems_version = %q{1.3.7}
   s.summary = %q{Lightweight Ruby API for NCBI Eutils}
   s.test_files = [
     "test/helper.rb",
-     "test/test_eutils.rb"
+    "test/test_eutils.rb"
   ]
 
   if s.respond_to? :specification_version then
     current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
     s.specification_version = 3
 
-    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_runtime_dependency(%q<activesupport>, [">= 3.0.0"])
     else

data/lib/eutils.rb

@@ -91,16 +91,28 @@ class Eutils
 
   # ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs.  Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles;  creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs.
   # See also: http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html
-  def elink
-    
+  def elink(ids, params = {})
+    params["id"] = ids.join(",")
+    params["cmd"] ||= "neighbor"
+    params["dbfrom"] ||= "pubmed"
+    params["db"] ||= "pubmed"
+    params["retmode"] ||= "xml"
+    server = EUTILS_HOST + "elink.fcgi"
+    response = post_eutils(server, params)
+    if params["retmode"] == "xml"
+      return Hash.from_xml(response)["eLinkResult"]
+    else
+      return response
+    end
   end
 
   # EGQuery: Provides Entrez database counts in XML for a single search using Global Query.
   # See also: http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/egquery_help.html
   def egquery(term)
     term.strip! if term.class == String
-    server = EUTILS_HOST + "egquery.fcgi"
-    params = {"term" => term}
+    #server = EUTILS_HOST + "egquery.fcgi"
+    server = "http://eutils.ncbi.nlm.nih.gov/gquery/"
+    params = {"term" => term, "retmode" => "xml"}
     response = post_eutils(server, params)
     return Hash.from_xml(response)["Result"]
   end

data/test/test_eutils.rb

@@ -78,6 +78,12 @@ class TestEutils < Test::Unit::TestCase
     assert_equal "", eutils.espell(" ")
   end
 
+  should "get a hash from Elink" do
+    i = eutils.elink([9298984])
+    assert_equal Hash, i.class
+    assert_equal "9298984", i["LinkSet"]["IdList"]["Id"]
+  end
+
   should "get hash from EGQuery" do
     i = eutils.egquery("autism")
     assert_equal Hash, i.class

metadata

@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
-  - 1
   - 2
-  version: 0.1.2
+  - 0
+  version: 0.2.0
 platform: ruby
 authors: 
 - Joon Lee, aka seouri
@@ -14,13 +14,14 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-08-30 00:00:00 -04:00
+date: 2011-04-27 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: shoulda
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -33,6 +34,7 @@ dependencies:
   name: activesupport
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -53,7 +55,6 @@ extra_rdoc_files:
 - README.rdoc
 files: 
 - .document
-- .gitignore
 - MIT-LICENSE
 - README.rdoc
 - Rakefile
@@ -67,11 +68,12 @@ homepage: http://github.com/seouri/eutils
 licenses: []
 
 post_install_message: 
-rdoc_options: 
-- --charset=UTF-8
+rdoc_options: []
+
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
@@ -79,6 +81,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
@@ -88,7 +91,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.6
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: Lightweight Ruby API for NCBI Eutils

data/.gitignore

@@ -1,21 +0,0 @@
-## MAC OS
-.DS_Store
-
-## TEXTMATE
-*.tmproj
-tmtags
-
-## EMACS
-*~
-\#*
-.\#*
-
-## VIM
-*.swp
-
-## PROJECT::GENERAL
-coverage
-rdoc
-pkg
-
-## PROJECT::SPECIFIC