medvane 0.0.1

data/.document

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+README.rdoc
+lib/**/*.rb
+bin/*
+features/**/*.feature
+LICENSE

data/.gitignore

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+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+
+## PROJECT::SPECIFIC

data/LICENSE

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+Copyright (c) 2009 Joon Lee
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= medvane
+
+Description goes here.
+
+== Note on Patches/Pull Requests
+ 
+* Fork the project.
+* Make your feature addition or bug fix.
+* Add tests for it. This is important so I don't break it in a
+  future version unintentionally.
+* Commit, do not mess with rakefile, version, or history.
+  (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
+* Send me a pull request. Bonus points for topic branches.
+
+== Copyright
+
+Copyright (c) 2010 Joon Lee. See LICENSE for details.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "medvane"
+    gem.summary = %Q{Medvane common library gem}
+    gem.description = %Q{Medvane common library for accessing PubMed}
+    gem.email = "seouri@gmail.com"
+    gem.homepage = "http://github.com/seouri/medvane"
+    gem.authors = ["Joon Lee"]
+    gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
+end
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+begin
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new do |test|
+    test.libs << 'test'
+    test.pattern = 'test/**/test_*.rb'
+    test.verbose = true
+  end
+rescue LoadError
+  task :rcov do
+    abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
+  end
+end
+
+task :test => :check_dependencies
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "medvane #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/medvane.rb

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+require 'cgi'
+require 'net/http'
+require 'uri'
+
+module Medvane
+  module Eutils
+    EUTILS_URL  = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
+    TOOL_NAME   = "medvane.org"
+    TOOL_EMAIL  = "eutils@medvane.org"
+
+    def esearch(query, db = "pubmed")
+      server = EUTILS_URL + "esearch.fcgi"
+      params = {
+        "db"          => db,
+        "term"        => query,
+        "tool"        => TOOL_NAME,
+        "email"       => TOOL_EMAIL,
+        "retmax"      => 0,
+        "usehistory"  => "y",
+      }
+      response = Net::HTTP.post_form(URI.parse(server), params)
+      result = response.body
+      count = result.scan(/<Count>(.*?)<\/Count>/m).flatten.first.to_i
+      webenv = result.scan(/<WebEnv>(.*?)<\/WebEnv>/m).flatten.first.to_s
+      return webenv, count
+    end
+    module_function :esearch
+
+    def efetch(webenv, retstart = 0, retmax = 1000000, rettype = "uilist", db = "pubmed")
+      server = EUTILS_URL + "efetch.fcgi"
+      params = {
+        "db"          => db,
+        "tool"        => TOOL_NAME,
+        "email"       => TOOL_EMAIL,
+        "WebEnv"      => webenv,
+        "retmax"      => retmax,
+        "rettype"     => rettype,
+        "retmode"     => "text",
+        "retstart"    => retstart,
+        "query_key"   => 1,
+      }
+      response = Net::HTTP.post_form(URI.parse(server), params)
+      medline = []
+      unless response.body.blank?
+        case rettype
+        when "uilist"
+          medline = response.body.split(/\n/)
+        when "medline"
+          medline = response.body.split(/\n\n+/).map {|e| Bio::MEDLINE.new(e) }
+        end
+      end
+      return medline
+    end
+    module_function :efetch
+
+    def esearchgis(query, db = "nuccore", retmax = 24)
+      server = EUTILS_URL + "esearch.fcgi"
+      params = {
+        "db"          => db,
+        "term"        => query,
+        "tool"        => TOOL_NAME,
+        "email"       => TOOL_EMAIL,
+        "retmax"      => retmax,
+      }
+      response = Net::HTTP.post_form(URI.parse(server), params)
+      result = response.body
+      gis = result.scan(/<Id>(\d+)<\/Id>/).flatten
+      return gis
+    end
+    module_function :esearchgis
+
+    def efetchids(ids, db = "nuccore", retstart = 0, retmax = 10000, rettype = "gb", retmode = "xml")
+      server = EUTILS_URL + "efetch.fcgi"
+      params = {
+         "id"          => ids,
+         "db"          => db,
+         "tool"        => TOOL_NAME,
+         "email"       => TOOL_EMAIL,
+         "retmax"      => retmax,
+         "rettype"     => rettype,
+         "retmode"     => retmode,
+         "retstart"    => retstart,
+       }
+       response = Net::HTTP.post_form(URI.parse(server), params)
+       return response.body
+    end
+    module_function :efetchids
+
+    def epost(ids)
+      server = EUTILS_URL + "epost.fcgi"
+      params = {
+        "db"          => "pubmed",
+        "id"          => ids.join(","),
+        "tool"        => TOOL_NAME,
+        "email"       => TOOL_EMAIL,
+      }
+      response = Net::HTTP.post_form(URI.parse(server), params)
+      result = response.body
+      webenv = result.scan(/<WebEnv>(.*?)<\/WebEnv>/m).flatten.first.to_s
+      return webenv
+    end
+    module_function :epost
+  end
+end

data/medvane.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{medvane}
+  s.version = "0.0.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Joon Lee"]
+  s.date = %q{2010-08-17}
+  s.description = %q{Medvane common library for accessing PubMed}
+  s.email = %q{seouri@gmail.com}
+  s.extra_rdoc_files = [
+    "LICENSE",
+     "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+     ".gitignore",
+     "LICENSE",
+     "README.rdoc",
+     "Rakefile",
+     "VERSION",
+     "lib/medvane.rb",
+     "medvane.gemspec",
+     "test/helper.rb",
+     "test/test_medvane.rb"
+  ]
+  s.homepage = %q{http://github.com/seouri/medvane}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.6}
+  s.summary = %q{Medvane common library gem}
+  s.test_files = [
+    "test/helper.rb",
+     "test/test_medvane.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
+      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+    else
+      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+  end
+end
+

data/test/helper.rb

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+require 'rubygems'
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'medvane'
+
+class Test::Unit::TestCase
+end

data/test/test_medvane.rb

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+require 'helper'
+
+class TestMedvane < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: medvane
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 1
+  version: 0.0.1
+platform: ruby
+authors: 
+- Joon Lee
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-08-17 00:00:00 -04:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: thoughtbot-shoulda
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id001
+description: Medvane common library for accessing PubMed
+email: seouri@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- .document
+- .gitignore
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/medvane.rb
+- medvane.gemspec
+- test/helper.rb
+- test/test_medvane.rb
+has_rdoc: true
+homepage: http://github.com/seouri/medvane
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.6
+signing_key: 
+specification_version: 3
+summary: Medvane common library gem
+test_files: 
+- test/helper.rb
+- test/test_medvane.rb