eutils 0.1.2 → 0.2.0
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- data/VERSION +1 -1
- data/eutils.gemspec +14 -16
- data/lib/eutils.rb +16 -4
- data/test/test_eutils.rb +6 -0
- metadata +10 -7
- data/.gitignore +0 -21
data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.
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1
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+
0.2.0
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data/eutils.gemspec
CHANGED
@@ -1,15 +1,15 @@
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1
1
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# Generated by jeweler
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# DO NOT EDIT THIS FILE DIRECTLY
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3
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-
# Instead, edit Jeweler::Tasks in Rakefile, and run
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+
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
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s.name = %q{eutils}
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8
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-
s.version = "0.
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8
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+
s.version = "0.2.0"
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9
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10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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11
11
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s.authors = ["Joon Lee, aka seouri"]
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12
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-
s.date = %q{
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12
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+
s.date = %q{2011-04-27}
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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.}
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s.email = %q{seouri@gmail.com}
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s.extra_rdoc_files = [
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@@ -17,31 +17,29 @@ Gem::Specification.new do |s|
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]
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s.files = [
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".document",
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-
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-
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-
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-
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24
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-
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25
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-
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-
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27
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-
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-
"test/test_eutils.rb"
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20
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+
"MIT-LICENSE",
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21
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+
"README.rdoc",
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22
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"Rakefile",
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23
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"VERSION",
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24
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+
"eutils.gemspec",
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25
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"lib/eutils.rb",
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26
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"test/helper.rb",
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27
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+
"test/test_eutils.rb"
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29
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]
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s.homepage = %q{http://github.com/seouri/eutils}
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31
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-
s.rdoc_options = ["--charset=UTF-8"]
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32
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s.require_paths = ["lib"]
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33
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-
s.rubygems_version = %q{1.3.
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+
s.rubygems_version = %q{1.3.7}
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s.summary = %q{Lightweight Ruby API for NCBI Eutils}
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35
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s.test_files = [
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"test/helper.rb",
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-
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35
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+
"test/test_eutils.rb"
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]
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39
37
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38
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if s.respond_to? :specification_version then
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
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40
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s.specification_version = 3
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41
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44
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-
if Gem::Version.new(Gem::
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42
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+
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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45
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s.add_development_dependency(%q<shoulda>, [">= 0"])
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s.add_runtime_dependency(%q<activesupport>, [">= 3.0.0"])
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else
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data/lib/eutils.rb
CHANGED
@@ -91,16 +91,28 @@ class Eutils
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91
91
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92
92
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# 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.
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# See also: http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html
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94
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-
def elink
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95
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-
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94
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+
def elink(ids, params = {})
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95
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params["id"] = ids.join(",")
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params["cmd"] ||= "neighbor"
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params["dbfrom"] ||= "pubmed"
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98
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params["db"] ||= "pubmed"
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99
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params["retmode"] ||= "xml"
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100
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server = EUTILS_HOST + "elink.fcgi"
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response = post_eutils(server, params)
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if params["retmode"] == "xml"
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return Hash.from_xml(response)["eLinkResult"]
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else
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return response
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end
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end
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# EGQuery: Provides Entrez database counts in XML for a single search using Global Query.
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# See also: http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/egquery_help.html
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def egquery(term)
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term.strip! if term.class == String
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-
server = EUTILS_HOST + "egquery.fcgi"
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-
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#server = EUTILS_HOST + "egquery.fcgi"
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server = "http://eutils.ncbi.nlm.nih.gov/gquery/"
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params = {"term" => term, "retmode" => "xml"}
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response = post_eutils(server, params)
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return Hash.from_xml(response)["Result"]
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end
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data/test/test_eutils.rb
CHANGED
@@ -78,6 +78,12 @@ class TestEutils < Test::Unit::TestCase
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assert_equal "", eutils.espell(" ")
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end
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81
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should "get a hash from Elink" do
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i = eutils.elink([9298984])
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assert_equal Hash, i.class
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assert_equal "9298984", i["LinkSet"]["IdList"]["Id"]
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end
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86
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should "get hash from EGQuery" do
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i = eutils.egquery("autism")
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assert_equal Hash, i.class
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metadata
CHANGED
@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
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prerelease: false
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segments:
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- 0
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- 1
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- 2
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- 0
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version: 0.2.0
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platform: ruby
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authors:
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- Joon Lee, aka seouri
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@@ -14,13 +14,14 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date:
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date: 2011-04-27 00:00:00 -04:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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name: shoulda
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prerelease: false
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requirement: &id001 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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@@ -33,6 +34,7 @@ dependencies:
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name: activesupport
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prerelease: false
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requirement: &id002 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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@@ -53,7 +55,6 @@ extra_rdoc_files:
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- README.rdoc
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files:
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- .document
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-
- .gitignore
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- MIT-LICENSE
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- README.rdoc
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- Rakefile
|
@@ -67,11 +68,12 @@ homepage: http://github.com/seouri/eutils
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licenses: []
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post_install_message:
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rdoc_options:
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-
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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@@ -79,6 +81,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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- 0
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version: "0"
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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@@ -88,7 +91,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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requirements: []
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rubyforge_project:
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rubygems_version: 1.3.
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rubygems_version: 1.3.7
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signing_key:
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specification_version: 3
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summary: Lightweight Ruby API for NCBI Eutils
|