clinical 0.2.2

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data/.document ADDED
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+ README.rdoc
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+ lib/**/*.rb
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+ bin/*
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+ features/**/*.feature
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+ LICENSE
data/.gitignore ADDED
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+ *.sw?
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+ .DS_Store
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+ coverage
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+ rdoc
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+ pkg
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+ tmp
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+ features_rcov
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+ coverage.data
data/LICENSE ADDED
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+ Copyright (c) 2009 Dan Pickett
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+
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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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+
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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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+
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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.
data/README.rdoc ADDED
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+ = clinical
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+
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+ Description goes here.
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+
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+ == Copyright
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+
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+ Copyright (c) 2009 Dan Pickett. See LICENSE for details.
data/Rakefile ADDED
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+ require 'rubygems'
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+ require 'rake'
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+
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+ begin require "metric_fu" rescue LoadError; end
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+
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+ begin
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+ require 'jeweler'
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+ Jeweler::Tasks.new do |gem|
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+ gem.name = "clinical"
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+ gem.summary = %Q{a library for accessing data from ClinicalTrials.gov}
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+ gem.email = "dpickett@enlightsolutions.com"
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+ gem.homepage = "http://github.com/dpickett/clinical"
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+ gem.authors = ["Dan Pickett"]
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+ gem.add_dependency("jnunemaker-httparty", ">= 0.4.3")
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+ gem.add_dependency("jnunemaker-happymapper", ">= 0.2.5")
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+ gem.add_dependency("mislav-will_paginate", ">= 2.3.11")
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+ gem.add_dependency("nokogiri", ">= 1.3.3")
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+
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+ # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
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+ end
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+
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+ rescue LoadError
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+ puts "Jeweler (or a dependency) not available. Install it with: sudo gem install jeweler"
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+ end
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+
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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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+
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+ namespace :rcov do
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+ require 'rcov/rcovtask'
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+ Rcov::RcovTask.new(:tests) do |test|
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+ test.libs << 'test'
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+ test.pattern = 'test/**/*_test.rb'
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+ test.rcov_opts = %w{--aggregate coverage.data --exclude osx\/objc,gems\/,spec\/}
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+ test.verbose = true
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+ end
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+
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+ require 'cucumber/rake/task'
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+ Cucumber::Rake::Task.new(:cucumber) do |t|
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+ t.rcov = true
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+ t.rcov_opts = %w{--aggregate coverage.data --exclude osx\/objc,gems\/,features\/,spec\/ -o "features_rcov"}
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+ end
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+ end
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+ begin
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+ desc "Run both specs and features to generate aggregated coverage"
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+ task :rcov do |t|
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+ rm "coverage.data" if File.exist?("coverage.data")
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+ Rake::Task["rcov:cucumber"].invoke
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+ Rake::Task["rcov:tests"].invoke
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+ end
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+ rescue LoadError
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+ task :rcov do
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+ abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
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+ end
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+ end
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+
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+ begin
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+ require 'cucumber/rake/task'
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+ Cucumber::Rake::Task.new(:features)
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+
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+ rescue LoadError
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+ task :features do
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+ abort "Cucumber is not available. In order to run features, you must: sudo gem install cucumber"
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+ end
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+ end
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+
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+ task :default => :test
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+
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+ require 'rake/rdoctask'
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+ Rake::RDocTask.new do |rdoc|
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+ if File.exist?('VERSION.yml')
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+ config = YAML.load(File.read('VERSION.yml'))
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+ version = "#{config[:major]}.#{config[:minor]}.#{config[:patch]}"
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+ else
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+ version = ""
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+ end
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+
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+ rdoc.rdoc_dir = 'rdoc'
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+ rdoc.title = "clinical #{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
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+ 0.2.2
data/clinical.gemspec ADDED
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+ # -*- encoding: utf-8 -*-
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+
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+ Gem::Specification.new do |s|
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+ s.name = %q{clinical}
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+ s.version = "0.2.2"
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+
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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 = ["Dan Pickett"]
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+ s.date = %q{2009-07-28}
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+ s.email = %q{dpickett@enlightsolutions.com}
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+ s.extra_rdoc_files = [
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+ "LICENSE",
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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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+ ".gitignore",
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+ "LICENSE",
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+ "README.rdoc",
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+ "Rakefile",
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+ "VERSION",
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+ "clinical.gemspec",
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+ "features/finding_clinical_trials.feature",
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+ "features/getting_keywords_and_categories.feature",
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+ "features/step_definitions/clinical_steps.rb",
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+ "features/support/env.rb",
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+ "lib/clinical.rb",
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+ "lib/clinical/address.rb",
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+ "lib/clinical/agency.rb",
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+ "lib/clinical/collaborator.rb",
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+ "lib/clinical/collection.rb",
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+ "lib/clinical/condition.rb",
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+ "lib/clinical/contact.rb",
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+ "lib/clinical/extensions.rb",
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+ "lib/clinical/intervention.rb",
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+ "lib/clinical/lead_sponsor.rb",
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+ "lib/clinical/location.rb",
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+ "lib/clinical/outcome.rb",
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+ "lib/clinical/primary_outcome.rb",
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+ "lib/clinical/secondary_outcome.rb",
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+ "lib/clinical/sponsor.rb",
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+ "lib/clinical/status.rb",
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+ "lib/clinical/trial.rb",
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+ "test/clinical/trial_test.rb",
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+ "test/fixtures/lupus_single.xml",
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+ "test/fixtures/open_set.xml",
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+ "test/test_helper.rb"
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+ ]
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+ s.has_rdoc = true
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+ s.homepage = %q{http://github.com/dpickett/clinical}
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+ s.rdoc_options = ["--charset=UTF-8"]
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+ s.require_paths = ["lib"]
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+ s.rubygems_version = %q{1.3.2}
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+ s.summary = %q{a library for accessing data from ClinicalTrials.gov}
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+ s.test_files = [
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+ "test/clinical/trial_test.rb",
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+ "test/test_helper.rb"
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+ ]
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+
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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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+ s.specification_version = 3
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+
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+ if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
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+ s.add_runtime_dependency(%q<jnunemaker-httparty>, [">= 0.4.3"])
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+ s.add_runtime_dependency(%q<jnunemaker-happymapper>, [">= 0.2.5"])
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+ s.add_runtime_dependency(%q<mislav-will_paginate>, [">= 2.3.11"])
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+ s.add_runtime_dependency(%q<nokogiri>, [">= 1.3.3"])
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+ else
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+ s.add_dependency(%q<jnunemaker-httparty>, [">= 0.4.3"])
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+ s.add_dependency(%q<jnunemaker-happymapper>, [">= 0.2.5"])
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+ s.add_dependency(%q<mislav-will_paginate>, [">= 2.3.11"])
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+ s.add_dependency(%q<nokogiri>, [">= 1.3.3"])
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+ end
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+ else
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+ s.add_dependency(%q<jnunemaker-httparty>, [">= 0.4.3"])
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+ s.add_dependency(%q<jnunemaker-happymapper>, [">= 0.2.5"])
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+ s.add_dependency(%q<mislav-will_paginate>, [">= 2.3.11"])
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+ s.add_dependency(%q<nokogiri>, [">= 1.3.3"])
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+ end
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+ end
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+ Feature: As a potential participant for a clinical study
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+ I want to search for clinical trials
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+ So that I can find out more information about them
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+
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+ Scenario: Find open studies
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+ Given I am searching for trials where "recruiting" is "true"
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+ When I perform the search
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+ Then I should get trials that are "open"
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+
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+ Scenario: Find closed studies
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+ Given I am searching for trials where "recruiting" is "false"
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+ When I perform the search
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+ Then I should get trials that are not "open"
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+
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+ Scenario: Find a specific condition
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+ Given I am searching for trials where "condition" is "hemophelia"
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+ When I perform the extended search
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+ Then I should get trials where the "conditions" contains "hemophelia"
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+
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+ Scenario: Find a specific intervention
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+ Given I am searching for trials where "intervention" is "drug"
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+ When I perform the extended search
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+ Then I should get trials where the "interventions" contains "drug"
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+
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+ Scenario: Find a specific outcome
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+ Given I am searching for trials where "outcome" is "toxic"
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+ When I perform the extended search
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+ Then I should get trials where the "outcomes" contains "toxic"
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+
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+ Scenario: Find a specific sponsor
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+ Given I am searching for trials where "sponsor" is "Eli Lilly"
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+ When I perform the extended search
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+ Then I should get trials where the "sponsors" contains "Eli Lilly"
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+
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+ Scenario: Find a specific trial
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+ When I attempt to retrieve trial "NCT00001372"
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+ Then I should get a trial
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+ And the trial should have an "id" of "NCT00001372"
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+
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+ Scenario: Find a specific trial with extended attributes
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+ When I attempt to retrieve trial "NCT00454363"
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+ Then I should get a trial
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+ And the trial should have a "phase" of "2"
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+ And the trial should have "conditions" like "Lung Cancer"
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+ And the trial should have a "minimum_age" of "21 Years"
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+ And the trial should have "sponsors" like "M.D. Anderson"
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+
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+ Scenario: Find a non-existant trial
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+ When I attempt to retrieve trial "4325785"
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+ Then I should not get a trial
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+
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+
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+ Feature: As a user of the clinical library
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+ I want to retrieve keywords, categories, and terms from ClinicalTrials.gov
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+ So that I can associate related trials
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+
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+ Scenario: Get keywords, categories, and terms
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+ When I attempt to retrieve keywords for trial "NCT00001372"
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+ Then the trial should have "keywords" like "Autoimmunity"
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+ And the trial should have "categories" like "Urologic Diseases"
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+ And the trial should have "terms" like "Connective Tissue Diseases"
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+ Given /^I am searching for trials where "([^\"]*)" is "([^\"]*)"$/ do |field, value|
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+ @params ||= {}
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+
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+ if value == "true"
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+ value = true
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+ elsif value == "false"
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+ value = false
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+ end
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+
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+ @params[field.to_sym] = value
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+ end
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+
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+ When /^I perform the search$/ do
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+ @trials = Clinical::Trial.find(:conditions => @params)
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+ end
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+
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+ When /^I perform the extended search$/ do
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+ @trials = Clinical::Trial.find(:conditions => @params, :extended => true)
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+ end
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+
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+ When /^I attempt to retrieve trial "([^\"]*)"$/ do |id|
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+ @trial = Clinical::Trial.find_by_id(id)
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+ end
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+
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+ When /^I attempt to retrieve keywords for trial "([^\"]*)"$/ do |id|
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+ @trial = Clinical::Trial.find_by_id(id)
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+ @trial.get_metadata
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+ end
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+
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+ Then /^I should get trials that are (not )?"([^\"]*)"$/ do |not_included, field|
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+ if not_included
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+ result = false
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+ else
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+ result = true
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+ end
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+
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+ @trials.each do |trial|
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+ trial.send(field + "?").should(eql(result))
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+ end
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+ end
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+
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+ Then /^I should get trials where the "([^\"]*)" contains "([^\"]*)"$/ do |field, value|
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+ @trials.each do |trial|
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+ item_values = []
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+ result = trial.send(field)
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+ if result.is_a?(Array)
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+ found = false
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+ result.each do |i|
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+ found = true if i.to_s =~ /#{value}/i
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+ end
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+ found.should be_true
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+ else
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+ result.to_s.should =~ /#{value}/i
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+ end
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+ end
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+ end
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+
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+ Then /^I should get a trial$/ do
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+ @trial.should_not be_nil
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+ end
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+
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+ Then /^the trial should have an? "([^\"]*)" of "([^\"]*)"$/ do |field, value|
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+ @trial.send(field).to_s.should eql(value)
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+ end
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+
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+ Then /^the trial should have "([^\"]*)" like "([^\"]*)"$/ do |field, value|
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+ @trial.send(field).to_s.should =~ /#{Regexp.escape(value)}/
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+ end
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+
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+
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+ Then /^I should not get a trial$/ do
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+ @trial.should be_nil
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+ end
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+
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+ $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
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+ require 'clinical'
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+
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+ require 'test/unit/assertions'
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+
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+ World(Test::Unit::Assertions)
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+ module Clinical
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+ class Address
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+ include HappyMapper
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+
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+ element :city, String
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+ element :state, String
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+ element :zip, String
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+ element :country, String
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+ end
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+ end
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+ module Clinical
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+ class Agency
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+ include Clinical::Sponsor
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+ tag "sponsors/agency"
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+ end
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+ end
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+ module Clinical
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+ class Collaborator
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+ include Clinical::Sponsor
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+ tag "sponsors/collaborator"
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+ end
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+ end
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+ module Clinical
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+ class Collection < WillPaginate::Collection
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+ include HappyMapper
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+ attr_accessor :count
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+ class << self
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+ def create_from_results(page, per_page, body)
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+ results = SearchResult.parse(body)
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+ col = create(page, per_page, results.count || 0) do |pager|
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+ pager.replace(results.trials)
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+ end
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+ col.count = results.count
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+ col
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+ end
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+ end
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+
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+ class SearchResult
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+ include HappyMapper
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+ tag "search_results"
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+ attribute "count", Integer
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+
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+ has_many :trials, Clinical::Trial
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+ end
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+ end
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+ end
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+ module Clinical
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+ class Condition
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+ attr_accessor :name
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+ include HappyMapper
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+
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+ def to_s
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+ self.name || ""
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+ end
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+
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+ class << self
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+ def parse(xml, options)
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+ xml.find("condition").collect do |n|
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+ item = new
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+ item.name = n.content.chomp.strip
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+ item
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+ end
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+ end
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+ end
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+ end
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+ end
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+ module Clinical
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+ class Contact
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+ include HappyMapper
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+
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+ element :first_name, String
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+ element :middle_name, String
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+ element :last_name, String
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+ element :degrees, String
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+ element :phone, String
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+ element :phone_ext, String
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+ element :email, String
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+ end
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+ end
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+ #thanks Rails Core!
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+ module Clinical
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+ module Extensions
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+ module Array
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+ def extract_options!
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+ last.is_a?(::Hash) ? pop : {}
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+ end
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+
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+ end
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+
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+ module String
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+ def underscore(camel_cased_word)
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+ camel_cased_word.to_s.gsub(/::/, '/').
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+ gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
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+ gsub(/([a-z\d])([A-Z])/,'\1_\2').
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+ tr("-", "_").
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+ downcase
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+ end
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+ end
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+ end
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+ end
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+
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+ unless String.instance_methods.include?("underscore")
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+ String.send(:include, Clinical::Extensions::String)
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+ end
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+ unless Array.instance_methods.include?("extract_options!")
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+ Array.send(:include, Clinical::Extensions::Array)
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+ end
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+ module Clinical
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+ class Intervention
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+ include HappyMapper
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+
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+ element :type, String, :tag => "intervention_type"
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+ element :description, String
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+ element :name, String, :tag => "intervention_name"
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+
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+ def to_s
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+ "#{self.name} (#{self.type}): #{self.description}"
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+ end
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+ end
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+ end
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+ module Clinical
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+ class LeadSponsor
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+ include Clinical::Sponsor
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+ tag "sponsors/lead_sponsor"
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+ end
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+ end
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+ module Clinical
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+ class Location
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+ include HappyMapper
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+
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+ element :facility, String
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+ has_one :status, Clinical::Status, :parser => :parse
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+ has_one :contact, Clinical::Contact
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+ has_one :address, Clinical::Address
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+ end
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+ end
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+ module Clinical
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+ module Outcome
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+
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+ def self.included(base)
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+ base.send(:include, InstanceMethods)
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+ base.class_eval do
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+ include InstanceMethods
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+ include HappyMapper
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+ element :measure, String
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+ element :time_frame, String
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+ element :safety_issue, String
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+ end
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+ end
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+
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+ module InstanceMethods
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+ def primary?
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+ self.class.tag_name == "primary_outcome"
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+ end
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+
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+ def to_s
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+ val = "#{measure}"
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+ val << ", TIME FRAME: #{time_frame}" if time_frame
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+ val << ",SAFETY ISSUE: #{safety_issue}" if safety_issue
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+ val
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+ end
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+ end
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+
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+ end
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+ end
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+ module Clinical
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+ class PrimaryOutcome
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+ include Outcome
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+ tag :primary_outcome
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+ end
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+ end
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+ module Clinical
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+ class SecondaryOutcome
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+ include Outcome
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+ tag :secondary_outcome
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+ end
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+ end
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+ module Clinical
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+ module Sponsor
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+ def self.included(base)
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+ base.class_eval do
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+ attr_accessor :name
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+ include HappyMapper
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+ end
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+ base.extend(ClassMethods)
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+ base.send(:include, InstanceMethods)
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+ end
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+
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+ module InstanceMethods
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+ def to_s
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+ name
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+ end
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+ end
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+ module ClassMethods
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+ def parse(xml, options = {})
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+ xml.find(tag_name).collect do |n|
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+ item = new
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+ item.name = n.content.chomp.strip
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+ item
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+ end
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+ end
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+ end
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+ end
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+ end
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+ module Clinical
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+ class Status
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+ STATUSES = [
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+ :not_yet_recruiting,
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+ :recruiting,
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+ :enrolling_by_invitation,
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+ :active,
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+ :not_recruiting,
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+ :completed,
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+ :suspended,
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+ :terminated,
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+ :withdrawn,
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+ :available,
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+ :no_longer_available
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+ ]
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+
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+ OPEN_STATUSES = [
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+ :not_yet_recruiting,
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+ :recruiting
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+ ]
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+
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+ attr_reader :name
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+
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+ def initialize(sym)
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+ @name = sym
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+ end
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+
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+ def open?
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+ OPEN_STATUSES.include?(name)
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+ end
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+
32
+ def to_s
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+ @name.to_s
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+ end
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+
36
+ class << self
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+ def parse(s)
38
+ s.nil? ? nil : Status.new(s.downcase.gsub(" ", "_").to_sym)
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+ end
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+ end
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+ end
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+ end