clinical 0.2.2

data/.document

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

data/.gitignore

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+*.sw?
+.DS_Store
+coverage
+rdoc
+pkg
+tmp
+features_rcov
+coverage.data

data/LICENSE

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+Copyright (c) 2009 Dan Pickett
+
+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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+= clinical
+
+Description goes here.
+
+== Copyright
+
+Copyright (c) 2009 Dan Pickett. See LICENSE for details.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin require "metric_fu" rescue LoadError; end
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "clinical"
+    gem.summary = %Q{a library for accessing data from ClinicalTrials.gov}
+    gem.email = "dpickett@enlightsolutions.com"
+    gem.homepage = "http://github.com/dpickett/clinical"
+    gem.authors = ["Dan Pickett"]
+    gem.add_dependency("jnunemaker-httparty", ">= 0.4.3")
+    gem.add_dependency("jnunemaker-happymapper", ">= 0.2.5")
+    gem.add_dependency("mislav-will_paginate", ">= 2.3.11")
+    gem.add_dependency("nokogiri", ">= 1.3.3")
+    
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: sudo 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
+
+namespace :rcov do
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new(:tests) do |test|
+    test.libs << 'test'
+    test.pattern = 'test/**/*_test.rb'
+    test.rcov_opts = %w{--aggregate coverage.data --exclude osx\/objc,gems\/,spec\/}
+    test.verbose = true
+  end  
+  
+  require 'cucumber/rake/task'  
+  Cucumber::Rake::Task.new(:cucumber) do |t|    
+    t.rcov = true
+    t.rcov_opts = %w{--aggregate coverage.data --exclude osx\/objc,gems\/,features\/,spec\/ -o "features_rcov"}
+  end
+end
+begin
+  desc "Run both specs and features to generate aggregated coverage"
+  task :rcov do |t|
+    rm "coverage.data" if File.exist?("coverage.data")
+    Rake::Task["rcov:cucumber"].invoke
+    Rake::Task["rcov:tests"].invoke
+  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
+
+begin
+  require 'cucumber/rake/task'
+  Cucumber::Rake::Task.new(:features)
+  
+rescue LoadError
+  task :features do
+    abort "Cucumber is not available. In order to run features, you must: sudo gem install cucumber"
+  end
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  if File.exist?('VERSION.yml')
+    config = YAML.load(File.read('VERSION.yml'))
+    version = "#{config[:major]}.#{config[:minor]}.#{config[:patch]}"
+  else
+    version = ""
+  end
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "clinical #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+

data/VERSION

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+0.2.2

data/clinical.gemspec

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+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{clinical}
+  s.version = "0.2.2"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Dan Pickett"]
+  s.date = %q{2009-07-28}
+  s.email = %q{dpickett@enlightsolutions.com}
+  s.extra_rdoc_files = [
+    "LICENSE",
+     "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+     ".gitignore",
+     "LICENSE",
+     "README.rdoc",
+     "Rakefile",
+     "VERSION",
+     "clinical.gemspec",
+     "features/finding_clinical_trials.feature",
+     "features/getting_keywords_and_categories.feature",
+     "features/step_definitions/clinical_steps.rb",
+     "features/support/env.rb",
+     "lib/clinical.rb",
+     "lib/clinical/address.rb",
+     "lib/clinical/agency.rb",
+     "lib/clinical/collaborator.rb",
+     "lib/clinical/collection.rb",
+     "lib/clinical/condition.rb",
+     "lib/clinical/contact.rb",
+     "lib/clinical/extensions.rb",
+     "lib/clinical/intervention.rb",
+     "lib/clinical/lead_sponsor.rb",
+     "lib/clinical/location.rb",
+     "lib/clinical/outcome.rb",
+     "lib/clinical/primary_outcome.rb",
+     "lib/clinical/secondary_outcome.rb",
+     "lib/clinical/sponsor.rb",
+     "lib/clinical/status.rb",
+     "lib/clinical/trial.rb",
+     "test/clinical/trial_test.rb",
+     "test/fixtures/lupus_single.xml",
+     "test/fixtures/open_set.xml",
+     "test/test_helper.rb"
+  ]
+  s.has_rdoc = true
+  s.homepage = %q{http://github.com/dpickett/clinical}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.2}
+  s.summary = %q{a library for accessing data from ClinicalTrials.gov}
+  s.test_files = [
+    "test/clinical/trial_test.rb",
+     "test/test_helper.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_runtime_dependency(%q<jnunemaker-httparty>, [">= 0.4.3"])
+      s.add_runtime_dependency(%q<jnunemaker-happymapper>, [">= 0.2.5"])
+      s.add_runtime_dependency(%q<mislav-will_paginate>, [">= 2.3.11"])
+      s.add_runtime_dependency(%q<nokogiri>, [">= 1.3.3"])
+    else
+      s.add_dependency(%q<jnunemaker-httparty>, [">= 0.4.3"])
+      s.add_dependency(%q<jnunemaker-happymapper>, [">= 0.2.5"])
+      s.add_dependency(%q<mislav-will_paginate>, [">= 2.3.11"])
+      s.add_dependency(%q<nokogiri>, [">= 1.3.3"])
+    end
+  else
+    s.add_dependency(%q<jnunemaker-httparty>, [">= 0.4.3"])
+    s.add_dependency(%q<jnunemaker-happymapper>, [">= 0.2.5"])
+    s.add_dependency(%q<mislav-will_paginate>, [">= 2.3.11"])
+    s.add_dependency(%q<nokogiri>, [">= 1.3.3"])
+  end
+end

data/features/finding_clinical_trials.feature

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+Feature: As a potential participant for a clinical study
+  I want to search for clinical trials
+  So that I can find out more information about them
+
+  Scenario: Find open studies
+    Given I am searching for trials where "recruiting" is "true"
+    When I perform the search
+    Then I should get trials that are "open"
+
+  Scenario: Find closed studies
+    Given I am searching for trials where "recruiting" is "false"
+    When I perform the search
+    Then I should get trials that are not "open"
+
+  Scenario: Find a specific condition
+    Given I am searching for trials where "condition" is "hemophelia"
+    When I perform the extended search
+    Then I should get trials where the "conditions" contains "hemophelia"
+
+  Scenario: Find a specific intervention
+    Given I am searching for trials where "intervention" is "drug"
+    When I perform the extended search
+    Then I should get trials where the "interventions" contains "drug"
+
+  Scenario: Find a specific outcome
+    Given I am searching for trials where "outcome" is "toxic"
+    When I perform the extended search
+    Then I should get trials where the "outcomes" contains "toxic"
+
+  Scenario: Find a specific sponsor
+    Given I am searching for trials where "sponsor" is "Eli Lilly"
+    When I perform the extended search
+    Then I should get trials where the "sponsors" contains "Eli Lilly"
+
+  Scenario: Find a specific trial
+    When I attempt to retrieve trial "NCT00001372"
+    Then I should get a trial
+    And the trial should have an "id" of "NCT00001372"
+
+  Scenario: Find a specific trial with extended attributes
+    When I attempt to retrieve trial "NCT00454363"
+    Then I should get a trial
+    And the trial should have a "phase" of "2"
+    And the trial should have "conditions" like "Lung Cancer"
+    And the trial should have a "minimum_age" of "21 Years"
+    And the trial should have "sponsors" like "M.D. Anderson"
+
+  Scenario: Find a non-existant trial
+    When I attempt to retrieve trial "4325785"
+    Then I should not get a trial
+    
+

data/features/getting_keywords_and_categories.feature

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+Feature: As a user of the clinical library
+  I want to retrieve keywords, categories, and terms from ClinicalTrials.gov
+  So that I can associate related trials
+
+  Scenario: Get keywords, categories, and terms
+    When I attempt to retrieve keywords for trial "NCT00001372"
+    Then the trial should have "keywords" like "Autoimmunity"
+    And the trial should have "categories" like "Urologic Diseases"
+    And the trial should have "terms" like "Connective Tissue Diseases"

data/features/step_definitions/clinical_steps.rb

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+Given /^I am searching for trials where "([^\"]*)" is "([^\"]*)"$/ do |field, value|
+  @params ||= {}
+
+  if value == "true"
+    value = true
+  elsif value == "false"
+    value = false
+  end
+
+  @params[field.to_sym] = value
+end
+
+When /^I perform the search$/ do
+  @trials = Clinical::Trial.find(:conditions => @params)
+end
+
+When /^I perform the extended search$/ do
+  @trials = Clinical::Trial.find(:conditions => @params, :extended => true)
+end
+
+When /^I attempt to retrieve trial "([^\"]*)"$/ do |id|
+  @trial = Clinical::Trial.find_by_id(id)
+end
+
+When /^I attempt to retrieve keywords for trial "([^\"]*)"$/ do |id|
+  @trial = Clinical::Trial.find_by_id(id)
+  @trial.get_metadata
+end
+
+Then /^I should get trials that are (not )?"([^\"]*)"$/ do |not_included, field|
+  if not_included
+    result = false
+  else
+    result = true
+  end
+
+  @trials.each do |trial|
+    trial.send(field + "?").should(eql(result))
+  end
+end
+
+Then /^I should get trials where the "([^\"]*)" contains "([^\"]*)"$/ do |field, value|
+  @trials.each do |trial|
+    item_values = []
+    result = trial.send(field)
+    if result.is_a?(Array)
+      found = false
+      result.each do |i|
+        found = true if i.to_s =~ /#{value}/i
+      end
+      found.should be_true
+    else
+      result.to_s.should =~ /#{value}/i
+    end
+  end
+end
+
+Then /^I should get a trial$/ do
+  @trial.should_not be_nil
+end
+
+Then /^the trial should have an? "([^\"]*)" of "([^\"]*)"$/ do |field, value|
+  @trial.send(field).to_s.should eql(value)
+end
+
+Then /^the trial should have "([^\"]*)" like "([^\"]*)"$/ do |field, value|
+  @trial.send(field).to_s.should =~ /#{Regexp.escape(value)}/
+end
+
+
+Then /^I should not get a trial$/ do
+  @trial.should be_nil
+end
+

data/features/support/env.rb

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+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+require 'clinical'
+
+require 'test/unit/assertions'
+
+World(Test::Unit::Assertions)

data/lib/clinical/address.rb

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+module Clinical
+  class Address
+    include HappyMapper
+
+    element :city, String
+    element :state, String
+    element :zip, String
+    element :country, String
+  end
+end

data/lib/clinical/agency.rb

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+module Clinical
+  class Agency
+    include Clinical::Sponsor
+    tag "sponsors/agency"
+  end
+end

data/lib/clinical/collaborator.rb

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+module Clinical
+  class Collaborator
+    include Clinical::Sponsor
+    tag "sponsors/collaborator"
+  end
+end

data/lib/clinical/collection.rb

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+module Clinical
+  class Collection < WillPaginate::Collection
+    include HappyMapper
+    attr_accessor :count
+    class << self
+      def create_from_results(page, per_page, body)
+        results = SearchResult.parse(body)
+        col = create(page, per_page, results.count || 0) do |pager|
+          pager.replace(results.trials)
+        end
+        col.count = results.count
+        col
+      end
+    end
+    
+    class SearchResult
+      include HappyMapper
+      tag "search_results"
+      attribute "count", Integer
+
+      has_many :trials, Clinical::Trial
+    end
+  end
+end

data/lib/clinical/condition.rb

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+module Clinical
+  class Condition
+    attr_accessor :name
+    include HappyMapper
+
+    def to_s
+      self.name || ""
+    end
+
+    class << self
+      def parse(xml, options)
+        xml.find("condition").collect do |n|
+          item = new
+          item.name = n.content.chomp.strip
+          item
+        end
+      end
+    end
+  end
+end

data/lib/clinical/contact.rb

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+module Clinical
+  class Contact
+    include HappyMapper
+
+    element :first_name, String
+    element :middle_name, String
+    element :last_name, String
+    element :degrees, String
+    element :phone, String
+    element :phone_ext, String
+    element :email, String
+  end
+end

data/lib/clinical/extensions.rb

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+#thanks Rails Core!
+module Clinical
+  module Extensions
+    module Array
+      def extract_options!
+        last.is_a?(::Hash) ? pop : {}
+      end
+      
+    end
+
+    module String
+      def underscore(camel_cased_word)
+        camel_cased_word.to_s.gsub(/::/, '/').
+        gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
+        gsub(/([a-z\d])([A-Z])/,'\1_\2').
+        tr("-", "_").
+        downcase
+      end
+    end
+  end
+end
+
+unless String.instance_methods.include?("underscore")
+  String.send(:include, Clinical::Extensions::String)
+end
+unless Array.instance_methods.include?("extract_options!")
+  Array.send(:include, Clinical::Extensions::Array) 
+end

data/lib/clinical/intervention.rb

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+module Clinical
+  class Intervention
+    include HappyMapper
+
+    element :type, String, :tag => "intervention_type"
+    element :description, String
+    element :name, String, :tag => "intervention_name"
+
+    def to_s
+      "#{self.name} (#{self.type}): #{self.description}"
+    end
+  end
+end

data/lib/clinical/lead_sponsor.rb

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+module Clinical
+  class LeadSponsor
+    include Clinical::Sponsor
+    tag "sponsors/lead_sponsor"
+  end
+end

data/lib/clinical/location.rb

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+module Clinical
+  class Location
+    include HappyMapper
+
+    element :facility, String
+    has_one :status, Clinical::Status, :parser => :parse
+    has_one :contact, Clinical::Contact
+    has_one :address, Clinical::Address
+  end
+end

data/lib/clinical/outcome.rb

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+module Clinical
+  module Outcome
+
+    def self.included(base)
+      base.send(:include, InstanceMethods)
+      base.class_eval do
+        include InstanceMethods
+        include HappyMapper
+        element :measure, String
+        element :time_frame, String
+        element :safety_issue, String
+      end
+    end
+    
+    module InstanceMethods
+      def primary?
+        self.class.tag_name == "primary_outcome"
+      end
+
+      def to_s
+        val = "#{measure}"
+        val << ", TIME FRAME: #{time_frame}" if time_frame
+        val << ",SAFETY ISSUE: #{safety_issue}" if safety_issue
+        val
+      end
+    end
+    
+  end
+end

data/lib/clinical/primary_outcome.rb

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+module Clinical
+  class PrimaryOutcome
+    include Outcome
+    tag :primary_outcome
+  end
+end

data/lib/clinical/secondary_outcome.rb

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+module Clinical
+  class SecondaryOutcome
+    include Outcome
+    tag :secondary_outcome
+  end
+end

data/lib/clinical/sponsor.rb

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+module Clinical
+  module Sponsor
+     def self.included(base)
+        base.class_eval do
+          attr_accessor :name
+          include HappyMapper
+        end
+        base.extend(ClassMethods)
+        base.send(:include, InstanceMethods)
+      end
+
+    module InstanceMethods
+      def to_s
+        name
+      end
+    end
+    module ClassMethods
+      def parse(xml, options = {})
+        xml.find(tag_name).collect do |n|
+          item = new
+          item.name = n.content.chomp.strip
+          item
+        end
+      end
+    end
+  end
+end

data/lib/clinical/status.rb

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+module Clinical
+  class Status
+    STATUSES = [
+      :not_yet_recruiting, 
+      :recruiting,
+      :enrolling_by_invitation,
+      :active,
+      :not_recruiting, 
+      :completed, 
+      :suspended, 
+      :terminated, 
+      :withdrawn, 
+      :available, 
+      :no_longer_available
+    ]
+
+    OPEN_STATUSES = [
+      :not_yet_recruiting,
+      :recruiting
+    ]
+
+    attr_reader :name
+
+    def initialize(sym)
+      @name = sym
+    end
+
+    def open?
+      OPEN_STATUSES.include?(name)
+    end
+
+    def to_s
+      @name.to_s
+    end
+
+    class << self
+      def parse(s)
+        s.nil? ? nil : Status.new(s.downcase.gsub(" ", "_").to_sym)
+      end
+    end
+  end
+end