mimiweb 0.1.1
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- data/.document +5 -0
- data/Gemfile +15 -0
- data/Gemfile.lock +30 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +54 -0
- data/Rakefile +53 -0
- data/VERSION +1 -0
- data/lib/mimiweb.rb +37 -0
- data/mimiweb.gemspec +65 -0
- data/test/helper.rb +20 -0
- data/test/test_mimiweb.rb +4 -0
- metadata +128 -0
data/.document
ADDED
data/Gemfile
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source "http://rubygems.org"
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# Add dependencies required to use your gem here.
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# Example:
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# gem "activesupport", ">= 2.3.5"
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# Add dependencies to develop your gem here.
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# Include everything needed to run rake, tests, features, etc.
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group :development do
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gem "shoulda", ">= 0"
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gem "bundler", "~> 1.0.0"
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gem "jeweler", "~> 1.6.4"
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gem "rcov", ">= 0"
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gem "httparty"
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gem "hashie"
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end
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data/Gemfile.lock
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GEM
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remote: http://rubygems.org/
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specs:
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git (1.2.5)
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hashie (1.1.0)
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httparty (0.8.1)
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multi_json
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multi_xml
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jeweler (1.6.4)
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bundler (~> 1.0)
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git (>= 1.2.5)
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rake
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multi_json (1.0.3)
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multi_xml (0.4.1)
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rake (0.9.2)
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rcov (0.9.10)
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rcov (0.9.10-java)
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shoulda (2.11.3)
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PLATFORMS
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java
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ruby
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DEPENDENCIES
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bundler (~> 1.0.0)
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hashie
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httparty
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jeweler (~> 1.6.4)
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rcov
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shoulda
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data/LICENSE.txt
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Copyright (c) 2011 Jose Irizarry
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.rdoc
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= mimiweb
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Mimiweb is a ruby client for the MiMI and Metabolomics databases provided by NCIBI
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http://portal.ncibi.org/gateway/
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http://mimi.ncibi.org/MimiWeb/main-page.jsp
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= Usage
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There are four methods on the Mimiweb Web Service. With this client you can access them as follows
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== Free text search
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ruby-1.9.2-p290 :001 > results = Mimiweb.search("pwp1")
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== GeneID search
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ruby-1.9.2-p290 :001 > results = Mimiweb.entrez(1436)
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or
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Pass a type as a second parameter
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:compounds
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:reactions
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:nlp
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:interactions # default
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ruby-1.9.2-p290 :001 > results = Mimiweb.entrez(1436, type)
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== KEGG CompundID search
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ruby-1.9.2-p290 :001 > results = Mimiweb.kegg_compund("C00061")
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== KEGG ReactionID search
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ruby-1.9.2-p290 :001 > results = Mimiweb.kegg_reaction("R00548")
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== Contributing to mimiweb
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* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
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* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
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* Fork the project
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* Start a feature/bugfix branch
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* Commit and push until you are happy with your contribution
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* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
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* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
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== Copyright
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Copyright (c) 2011 Jose Irizarry. See LICENSE.txt for
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further details.
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data/Rakefile
ADDED
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# encoding: utf-8
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake'
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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# gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
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gem.name = "mimiweb"
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gem.homepage = "http://github.com/crm114/mimiweb"
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gem.license = "MIT"
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gem.summary = %Q{Ruby client for MiMI Web}
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gem.description = %Q{Access to MiMI and Metabolomics databases via a web service provided by NCIBI.}
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gem.email = "jose@mrkp.co"
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gem.authors = ["Jose Irizarry"]
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# dependencies defined in Gemfile
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end
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Jeweler::RubygemsDotOrgTasks.new
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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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end
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require 'rcov/rcovtask'
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Rcov::RcovTask.new do |test|
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test.libs << 'test'
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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test.rcov_opts << '--exclude "gems/*"'
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end
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task :default => :test
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require 'rake/rdoctask'
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "mimiweb #{version}"
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/VERSION
ADDED
@@ -0,0 +1 @@
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1
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0.1.1
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data/lib/mimiweb.rb
ADDED
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require 'httparty'
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require 'hashie'
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module Mimiweb
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class << self
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include HTTParty
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BASE_URL = 'http://mimi.ncibi.org/MimiWeb/fetch.jsp?'
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def search(term)
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get_results(:search, term)
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end
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def entrez(id, type="interactions")
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get_results(:geneid, id, type)
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end
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def kegg_compound(id)
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results = get_results(:cid, id)
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end
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def kegg_reaction(id)
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get_results(:rid, id)
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end
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private
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def get_results(search_type, term, type)
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if search_type == :geneid
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response = HTTParty.get(BASE_URL, {:query => {search_type => term, :type => type}}).parsed_response rescue "server error"
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else
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response = HTTParty.get(BASE_URL, {:query => {search_type => term}}).parsed_response rescue "server error"
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end
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results = Hashie::Mash.new(response)
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if results.NCIBI.MiMI.Response.Result.nil? && results.NCIBI.MiMI.Response.ResultSet.nil?
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raise "No results found for #{term}"
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else
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return results.NCIBI.MiMI.Response.Result || results.NCIBI.MiMI.Response.ResultSet.Result
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end
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end
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end
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end
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data/mimiweb.gemspec
ADDED
@@ -0,0 +1,65 @@
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# Generated by jeweler
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# DO NOT EDIT THIS FILE DIRECTLY
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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 = "mimiweb"
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s.version = "0.1.1"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Jose Irizarry"]
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s.date = "2011-10-08"
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s.description = "Access to MiMI and Metabolomics databases via a web service provided by NCIBI."
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s.email = "jose@mrkp.co"
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s.extra_rdoc_files = [
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"LICENSE.txt",
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"README.rdoc"
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]
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s.files = [
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".document",
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"Gemfile",
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"Gemfile.lock",
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"LICENSE.txt",
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"README.rdoc",
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"Rakefile",
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"VERSION",
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"lib/mimiweb.rb",
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"mimiweb.gemspec",
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"test/helper.rb",
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"test/test_mimiweb.rb"
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]
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s.homepage = "http://github.com/crm114/mimiweb"
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s.licenses = ["MIT"]
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s.require_paths = ["lib"]
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s.rubygems_version = "1.8.10"
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s.summary = "Ruby client for MiMI Web"
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+
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if s.respond_to? :specification_version then
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s.specification_version = 3
|
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+
|
41
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+
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
42
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+
s.add_development_dependency(%q<shoulda>, [">= 0"])
|
43
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+
s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
|
44
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+
s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
|
45
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+
s.add_development_dependency(%q<rcov>, [">= 0"])
|
46
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+
s.add_development_dependency(%q<httparty>, [">= 0"])
|
47
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+
s.add_development_dependency(%q<hashie>, [">= 0"])
|
48
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+
else
|
49
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+
s.add_dependency(%q<shoulda>, [">= 0"])
|
50
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+
s.add_dependency(%q<bundler>, ["~> 1.0.0"])
|
51
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+
s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
|
52
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+
s.add_dependency(%q<rcov>, [">= 0"])
|
53
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+
s.add_dependency(%q<httparty>, [">= 0"])
|
54
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+
s.add_dependency(%q<hashie>, [">= 0"])
|
55
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+
end
|
56
|
+
else
|
57
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+
s.add_dependency(%q<shoulda>, [">= 0"])
|
58
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+
s.add_dependency(%q<bundler>, ["~> 1.0.0"])
|
59
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+
s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
|
60
|
+
s.add_dependency(%q<rcov>, [">= 0"])
|
61
|
+
s.add_dependency(%q<httparty>, [">= 0"])
|
62
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+
s.add_dependency(%q<hashie>, [">= 0"])
|
63
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+
end
|
64
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+
end
|
65
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data/test/helper.rb
ADDED
@@ -0,0 +1,20 @@
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|
1
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require 'rubygems'
|
2
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+
require 'bundler'
|
3
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+
require 'httparty'
|
4
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+
require 'hashie'
|
5
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+
begin
|
6
|
+
Bundler.setup(:default, :development)
|
7
|
+
rescue Bundler::BundlerError => e
|
8
|
+
$stderr.puts e.message
|
9
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
10
|
+
exit e.status_code
|
11
|
+
end
|
12
|
+
require 'test/unit'
|
13
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require 'shoulda'
|
14
|
+
|
15
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+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
16
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+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
17
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require 'mimiweb'
|
18
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+
|
19
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class Test::Unit::TestCase
|
20
|
+
end
|
metadata
ADDED
@@ -0,0 +1,128 @@
|
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1
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--- !ruby/object:Gem::Specification
|
2
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+
name: mimiweb
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.1.1
|
5
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prerelease:
|
6
|
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platform: ruby
|
7
|
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authors:
|
8
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- Jose Irizarry
|
9
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autorequire:
|
10
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+
bindir: bin
|
11
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+
cert_chain: []
|
12
|
+
date: 2011-10-08 00:00:00.000000000Z
|
13
|
+
dependencies:
|
14
|
+
- !ruby/object:Gem::Dependency
|
15
|
+
name: shoulda
|
16
|
+
requirement: &79493870 !ruby/object:Gem::Requirement
|
17
|
+
none: false
|
18
|
+
requirements:
|
19
|
+
- - ! '>='
|
20
|
+
- !ruby/object:Gem::Version
|
21
|
+
version: '0'
|
22
|
+
type: :development
|
23
|
+
prerelease: false
|
24
|
+
version_requirements: *79493870
|
25
|
+
- !ruby/object:Gem::Dependency
|
26
|
+
name: bundler
|
27
|
+
requirement: &79493550 !ruby/object:Gem::Requirement
|
28
|
+
none: false
|
29
|
+
requirements:
|
30
|
+
- - ~>
|
31
|
+
- !ruby/object:Gem::Version
|
32
|
+
version: 1.0.0
|
33
|
+
type: :development
|
34
|
+
prerelease: false
|
35
|
+
version_requirements: *79493550
|
36
|
+
- !ruby/object:Gem::Dependency
|
37
|
+
name: jeweler
|
38
|
+
requirement: &79493170 !ruby/object:Gem::Requirement
|
39
|
+
none: false
|
40
|
+
requirements:
|
41
|
+
- - ~>
|
42
|
+
- !ruby/object:Gem::Version
|
43
|
+
version: 1.6.4
|
44
|
+
type: :development
|
45
|
+
prerelease: false
|
46
|
+
version_requirements: *79493170
|
47
|
+
- !ruby/object:Gem::Dependency
|
48
|
+
name: rcov
|
49
|
+
requirement: &79492870 !ruby/object:Gem::Requirement
|
50
|
+
none: false
|
51
|
+
requirements:
|
52
|
+
- - ! '>='
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '0'
|
55
|
+
type: :development
|
56
|
+
prerelease: false
|
57
|
+
version_requirements: *79492870
|
58
|
+
- !ruby/object:Gem::Dependency
|
59
|
+
name: httparty
|
60
|
+
requirement: &79492560 !ruby/object:Gem::Requirement
|
61
|
+
none: false
|
62
|
+
requirements:
|
63
|
+
- - ! '>='
|
64
|
+
- !ruby/object:Gem::Version
|
65
|
+
version: '0'
|
66
|
+
type: :development
|
67
|
+
prerelease: false
|
68
|
+
version_requirements: *79492560
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: hashie
|
71
|
+
requirement: &79492280 !ruby/object:Gem::Requirement
|
72
|
+
none: false
|
73
|
+
requirements:
|
74
|
+
- - ! '>='
|
75
|
+
- !ruby/object:Gem::Version
|
76
|
+
version: '0'
|
77
|
+
type: :development
|
78
|
+
prerelease: false
|
79
|
+
version_requirements: *79492280
|
80
|
+
description: Access to MiMI and Metabolomics databases via a web service provided
|
81
|
+
by NCIBI.
|
82
|
+
email: jose@mrkp.co
|
83
|
+
executables: []
|
84
|
+
extensions: []
|
85
|
+
extra_rdoc_files:
|
86
|
+
- LICENSE.txt
|
87
|
+
- README.rdoc
|
88
|
+
files:
|
89
|
+
- .document
|
90
|
+
- Gemfile
|
91
|
+
- Gemfile.lock
|
92
|
+
- LICENSE.txt
|
93
|
+
- README.rdoc
|
94
|
+
- Rakefile
|
95
|
+
- VERSION
|
96
|
+
- lib/mimiweb.rb
|
97
|
+
- mimiweb.gemspec
|
98
|
+
- test/helper.rb
|
99
|
+
- test/test_mimiweb.rb
|
100
|
+
homepage: http://github.com/crm114/mimiweb
|
101
|
+
licenses:
|
102
|
+
- MIT
|
103
|
+
post_install_message:
|
104
|
+
rdoc_options: []
|
105
|
+
require_paths:
|
106
|
+
- lib
|
107
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
108
|
+
none: false
|
109
|
+
requirements:
|
110
|
+
- - ! '>='
|
111
|
+
- !ruby/object:Gem::Version
|
112
|
+
version: '0'
|
113
|
+
segments:
|
114
|
+
- 0
|
115
|
+
hash: -105208845
|
116
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
117
|
+
none: false
|
118
|
+
requirements:
|
119
|
+
- - ! '>='
|
120
|
+
- !ruby/object:Gem::Version
|
121
|
+
version: '0'
|
122
|
+
requirements: []
|
123
|
+
rubyforge_project:
|
124
|
+
rubygems_version: 1.8.10
|
125
|
+
signing_key:
|
126
|
+
specification_version: 3
|
127
|
+
summary: Ruby client for MiMI Web
|
128
|
+
test_files: []
|