dpickett-clinical 0.1.0

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

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 Exception; 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 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
+
+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
+
+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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+0.1.1

data/clinical.gemspec

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+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{clinical}
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Dan Pickett"]
+  s.date = %q{2009-06-28}
+  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/step_definitions/clinical_steps.rb",
+     "features/support/env.rb",
+     "lib/clinical.rb",
+     "lib/clinical/collection.rb",
+     "lib/clinical/extensions.rb",
+     "lib/clinical/intervention.rb",
+     "lib/clinical/outcome.rb",
+     "lib/clinical/primary_outcome.rb",
+     "lib/clinical/secondary_outcome.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"])
+    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"])
+    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"])
+  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 non-existant trial
+    When I attempt to retrieve trial "4325785"
+    Then I should not get a trial
+    

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
+
+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
+      debugger if !found
+      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).should eql(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/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/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/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/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
+      sym.to_s
+    end
+
+    class << self
+      def parse(s)
+        s.nil? ? nil : Status.new(s.downcase.gsub(" ", "_").to_sym)
+      end
+    end
+  end
+end

data/lib/clinical/trial.rb

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+require "ruby-debug"
+
+module Clinical
+  class Trial
+    include HappyMapper
+    include HTTParty
+
+    base_uri "http://clinicaltrials.gov"
+    default_params :displayxml => true 
+
+    tag "clinical_study"
+    element :nct_id, String, :deep => true
+    element :read_status, Clinical::Status, :tag => "status", :parser => :parse
+    element :overall_status, Clinical::Status, :parser => :parse
+    element :url, String    
+    element :short_title, String, :tag => "title"
+    element :official_title, String
+    element :condition_summary, String
+    has_many :condition_items, String, :tag => "condition"
+
+    element :phase, Integer
+    element :study_type, String
+    element :study_design, String
+
+    element :lead_sponsor, String, :tag => "sponsors/lead_sponsor"
+    has_many :collaborators, String, :tag => "sponsors/collaborator"
+    has_many :agencies, String, :tag => "sponsors/agency"
+
+    has_many :interventions, Intervention, :tag => "intervention"
+    has_many :primary_outcomes, PrimaryOutcome
+    has_many :secondary_outcomes, SecondaryOutcome
+
+    has_many :locations, Location, :tag => "location"
+    element :start_date, Date
+    element :end_date, Date
+
+    element :last_changed_at, Date, :tag => "lastchanged_date"
+
+    element :minimum_age, String
+    element :maximum_age, String
+    element :gender, String
+    element :healthy_volunteers, String
+
+    element :participant_quantity, Integer, :tag => "enrollment"
+
+    element :url, String, :tag => "required_header/url"
+    element :eligibility_criteria, String, :tag => "eligibility/criteria/textblock"
+
+    element :brief_summary, String, :tag => "brief_summary/textblock"
+    element :detailed_description, String, :tag => "brief_summary/textblock"
+
+    def id
+      self.nct_id
+    end
+
+    def open?
+      self.status && self.status.open?
+    end
+
+    def sponsors
+      @sponsors ||= [lead_sponsor, (collaborators || []), (agencies || [])].flatten
+    end
+
+    def outcomes
+      @outcomes ||= [primary_outcomes, secondary_outcomes].flatten
+    end
+
+    def status
+      self.read_status || self.overall_status
+    end
+
+    def conditions
+      if condition_items.nil? || condition_items.empty?
+        condition_summary.split(";")
+      else
+        condition_items
+      end
+    end
+
+    class << self
+      def find_by_id(id)
+        response = get("/show/#{id}")
+        if response.code == 400
+          nil
+        else
+          begin
+            parse(response.body)
+          rescue LibXML::XML::Error
+            return nil
+          end 
+        end
+      end
+
+      def find(*args)
+        options = args.extract_options!
+
+        options[:page] ||= 1
+        options[:per_page] ||= 20
+
+        query = query_hash_for(*[args, options])
+        response = get("/search", :query => query)
+        trials = Collection.create_from_results(options[:page], 
+          options[:per_page], 
+          response.body)
+
+        if options[:extended]
+          fetch_more_details(trials)
+        else
+          trials
+        end
+      end
+
+      def query_hash_for(*args)
+        query = {}
+        options = args.extract_options! || {}
+        
+        conditions = options[:conditions] || {}
+        query["start"] = (options[:per_page] * options[:page]) - (options[:per_page] - 1)
+        unless conditions[:recruiting].nil?
+          query["recr"] = conditions[:recruiting] ? "open" : "closed" 
+        end
+        query["term"] = args.first if args.first.is_a?(String)
+        
+        {
+          :condition => "cond", 
+          :sponsor => "spons",
+          :intervention => "intr",
+          :outcome => "outc",
+          :sponsor => "spons"
+        }.each do |key,value|
+          query[value] = conditions[key] unless conditions[key].nil?
+        end
+
+        query
+      end
+
+      def extract_options!
+        last.is_a?(Hash) ? pop : { }
+      end
+      
+      private
+      def fetch_more_details(trials)
+        detailed_trials = trials.collect {|i| find_by_id(i.id)}
+        Collection.create(trials.current_page, trials.per_page, trials.count || 0) do |pager|
+          pager.replace(detailed_trials)
+        end
+      end
+    end
+  end
+end

data/lib/clinical.rb

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+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+require "will_paginate"
+require "httparty"
+require "happymapper"
+
+require "clinical/extensions"
+
+require "clinical/status"
+require "clinical/intervention"
+require "clinical/outcome"
+require "clinical/primary_outcome"
+require "clinical/secondary_outcome"
+
+require "clinical/address"
+require "clinical/contact"
+require "clinical/location"
+
+require "clinical/trial"
+
+require "clinical/collection"

data/test/clinical/trial_test.rb

@@ -0,0 +1,48 @@
+require "test_helper"
+
+class Clinical::TrialTest < Test::Unit::TestCase
+  context "when finding based on a hash of conditions" do
+    setup do
+      register_response("/search?displayxml=true&start=1&recr=open", "open_set")
+    end
+
+    should "return a paginated list of trials" do
+      @trials = Clinical::Trial.find({:conditions => {:recruiting => true}})
+      assert_instance_of Clinical::Collection, @trials
+    end
+  end   
+
+  context "a trial" do
+    setup do
+      @npi_id = "NPI5245"
+      register_response("/show/NPI5245?displayxml=true", "lupus_single")
+      @trial = Clinical::Trial.find_by_id(@npi_id)
+    end
+
+    should "have a status" do
+      assert_not_nil @trial.status
+    end
+
+    should "indicate whether the trial is open" do
+      assert_equal @trial.open?, @trial.status.open?
+    end
+
+    should "have a location" do
+      assert_not_nil @trial.locations
+      assert !@trial.locations.empty?
+    end
+
+    should "have a start date" do
+      assert_not_nil @trial.start_date
+    end
+
+    should "have a location with an address" do
+      assert !@trial.locations[0].address.nil?
+    end
+
+    should "have a study type" do
+      assert_not_nil @trial.study_type
+    end
+  end
+
+end

data/test/fixtures/lupus_single.xml

@@ -0,0 +1,171 @@
+HTTP/1.1 200 OK
+Date: Sat, 27 Jun 2009 19:11:20 GMT
+Set-Cookie: CTOpts=6ihzm6CLRiWguT0gEyUgzw-R98Ly0RGHhgE; Path=/ct2/
+Expires: Sat, 27 Jun 2009 19:11:21 GMT
+Content-Type: text/xml;charset=UTF-8
+Content-Length: 7971
+Set-Cookie: BIGipServerctgov-http-pool=290524802.22610.0000; path=/
+
+<?xml version="1.0" encoding="UTF-8"?>
+<clinical_study>
+  <required_header>
+    <download_date>Information obtained from ClinicalTrials.gov on June 26, 2009</download_date>
+    <link_text>Link to the current ClinicalTrials.gov record.</link_text>
+    <url>http://clinicaltrials.gov/show/NCT00001372</url>
+  </required_header>
+  <id_info>
+    <org_study_id>940066</org_study_id>
+    <secondary_id>94-AR-0066</secondary_id>
+    <nct_id>NCT00001372</nct_id>
+  </id_info>
+  <brief_title>Study of Systemic Lupus Erythematosus</brief_title>
+  <official_title>Studies of the Pathogenesis and Natural History of Systemic Lupus Erythematosus (SLE)</official_title>
+  <sponsors>
+    <lead_sponsor>
+      <agency>National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)</agency>
+    </lead_sponsor>
+  </sponsors>
+  <source>National Institutes of Health Clinical Center (CC)</source>
+  <oversight_info>
+    <authority>United States: Federal Government</authority>
+  </oversight_info>
+  <brief_summary>
+    <textblock>
+      This protocol will evaluate patients with systemic lupus erythematosus (SLE) and their
+      relatives to learn more about how the disease develops and changes over time.  It will also
+      study genetic factors that make a person susceptible to SLE.
+
+      Patients 10 years of age and older with known or suspected SLE and their relatives may be
+      eligible for this study.  Patients will be evaluated with a medical history and physical
+      examination, blood and urine tests.  Other procedures may include:
+
+        1. Electrocardiogram
+
+        2. 24-hour urine collection
+
+        3. Imaging studies, such as chest and joint X-rays, magnetic resonance imaging (MRI) scans,
+           bone scans, and bone densitometry.
+
+        4. Questionnaire about the degree of disease activity, and survey of risk factors for
+           disease complications.
+
+        5. Apheresis-Collection of plasma (fluid portion of blood) or blood cells for analysis.
+           Whole blood is collected through a needle in an arm vein.  The blood circulates through
+           a machine that separates it into its components.  The required component (plasma or
+           cells) is removed and the rest of the blood is returned to the body through the same
+           needle or through a second needle in the other arm.
+
+        6. Skin biopsy-Removal of a small skin sample for microscopic analysis.  An area of skin is
+           numbed with an anesthetic and a small circular portion (about 1/4 inch in diameter) is
+           removed, using a sharp cookie cutter-type instrument.
+
+        7. Kidney, bone marrow or other organ  biopsy-Removal of a small sample of organ tissue.
+           These biopsies are done only if they can provide information useful in better
+           understanding the disease or making treatment decisions.
+
+        8. Genetic studies-Collection of a blood sample for gene testing.
+
+      Patients will be followed at least once a year with a brief history and physical examination
+      and routine blood and urine tests.  Some patients may be seen more often.  Treatment
+      recommendations will be offered to patients' physicians, and patients who are eligible for
+      other research treatment studies will be invited to enroll.
+
+      Participating relatives of patients will fill out a brief medical history questionnaire and
+      provide a DNA sample (either a blood sample or tissue swab from the inside of the cheek) for
+      genetic testing.
+    </textblock>
+  </brief_summary>
+  <detailed_description>
+    <textblock>
+      This research protocol will evaluate subjects with systemic lupus erythematosus (SLE) and
+      their relatives to study the pathogenesis and natural history of the disease.  Patients will
+      be evaluated by a history and physical examination and routine laboratory studies will be
+      obtained as needed to assess disease activity or complications of the disease and to monitor
+      for drug-related toxicities.  Blood, skin or urine specimens may be requested for
+      laboratory-based research investigations.  DNA will be isolated from eligible subjects for
+      genetic studies.  Patients who are eligible for other research protocols will be offered the
+      opportunity to participate in these studies by signed informed consent.  Any medical care
+      recommended or provided to the patient will be consistent with routine standards of practice
+      and provided in consultation with the patient's referring physician.
+    </textblock>
+  </detailed_description>
+  <overall_status>Recruiting</overall_status>
+  <start_date>February 1994</start_date>
+  <phase>N/A</phase>
+  <study_type>Observational</study_type>
+  <study_design>N/A</study_design>
+  <condition>Lupus Nephritis</condition>
+  <condition>Systemic Lupus Erythematosus</condition>
+  <eligibility>
+    <criteria>
+      <textblock>
+        -  INCLUSION CRITERIA
+
+        SLE or suspected SLE established by ARA criteria.
+
+        Ability to give informed consent .
+
+        Adult and minor relatives (first and second degree) of individuals included in III-A-1
+        (only for genetic studies) .
+
+        Willingness of the patient's or minor relative's parents to give informed consent (only for
+        genetic studies).
+
+        Adult healthy volunteers (for punch biopsy of the skin and bone marrow biopsy).
+
+        EXCLUSION CRITERIA:
+
+        Concomitant medical problems which would confound the interpretation of studies gathered by
+        this protocol.  Included in this is the presence of HIV in the blood if it interferes with
+        interpretation of some lupus studies.
+
+        Concomitant medical, surgical or other conditions for which inadequate facilities are
+        available to support their care at the NIH .
+      </textblock>
+    </criteria>
+    <gender>Both</gender>
+    <minimum_age>N/A</minimum_age>
+    <maximum_age>N/A</maximum_age>
+    <healthy_volunteers>Accepts Healthy Volunteers</healthy_volunteers>
+  </eligibility>
+  <overall_contact>
+    <last_name>Patient Recruitment and Public Liaison Office</last_name>
+    <phone>(800) 411-1222</phone>
+    <email>prpl@mail.cc.nih.gov</email>
+  </overall_contact>
+  <overall_contact_backup>
+    <last_name>TTY</last_name>
+    <phone>1-866-411-1010</phone>
+  </overall_contact_backup>
+  <location>
+    <facility>
+      <name>National Institutes of Health Clinical Center, 9000 Rockville Pike</name>
+      <address>
+        <city>Bethesda</city>
+        <state>Maryland</state>
+        <zip>20892</zip>
+        <country>United States</country>
+      </address>
+    </facility>
+    <status>Recruiting</status>
+  </location>
+  <link>
+    <url>http://clinicalstudies.info.nih.gov/detail/A_1994-AR-0066.html</url>
+    <description>NIH Clinical Center Detailed Web Page</description>
+  </link>
+  <reference>
+    <citation>Boumpas DT, Fessler BJ, Austin HA 3rd, Balow JE, Klippel JH, Lockshin MD.  Systemic lupus erythematosus: emerging concepts. Part 2: Dermatologic and joint disease, the antiphospholipid antibody syndrome, pregnancy and hormonal therapy, morbidity and mortality, and pathogenesis. Ann Intern Med. 1995 Jul 1;123(1):42-53. Review.</citation>
+    <PMID>7762914</PMID>
+  </reference>
+  <reference>
+    <citation>Emlen W, Niebur J, Kadera R.  Accelerated in vitro apoptosis of lymphocytes from patients with systemic lupus erythematosus. J Immunol. 1994 Apr 1;152(7):3685-92.</citation>
+    <PMID>8144943</PMID>
+  </reference>
+  <reference>
+    <citation>Casciola-Rosen LA, Anhalt G, Rosen A.  Autoantigens targeted in systemic lupus erythematosus are clustered in two populations of surface structures on apoptotic keratinocytes. J Exp Med. 1994 Apr 1;179(4):1317-30.</citation>
+    <PMID>7511686</PMID>
+  </reference>
+  <verification_date>October 2008</verification_date>
+  <lastchanged_date>November 25, 2008</lastchanged_date>
+  <firstreceived_date>November 3, 1999</firstreceived_date>
+</clinical_study>

data/test/fixtures/open_set.xml

@@ -0,0 +1,212 @@
+HTTP/1.1 200 OK
+Date: Fri, 26 Jun 2009 21:40:41 GMT
+Set-Cookie: CTOpts=6ihzm6CLRiFiQRcyCyUgzw-R98LyNR4i-CE; Path=/ct2/
+Expires: Fri, 26 Jun 2009 21:40:42 GMT
+Content-Type: text/xml;charset=UTF-8
+Content-Length: 9221
+Set-Cookie: BIGipServerctgov-http-pool=189861506.22610.0000; path=/
+
+<?xml version="1.0" encoding="UTF-8"?>
+<search_results count="28928">
+  <query>( &quot;Recruiting&quot; OR &quot;Not yet recruiting&quot; OR &quot;Available&quot; ) [SUMMARY-STATUS]</query>
+  <clinical_study>
+    <order>1</order>
+    <score>0.9801</score>
+    <nct_id>NCT00004400</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00004400</url>
+    <title>Phase II Randomized Study of Physiologic Testosterone Replacement in Premenopausal, HIV-Positive Women</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>HIV Infections; Cachexia</condition_summary>
+    <last_changed>June 23, 2005</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>2</order>
+    <score>0.9801</score>
+    <nct_id>NCT00005100</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00005100</url>
+    <title>Measurement of Outcome of Surgical Treatment in Patients With Acromegaly</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Acromegaly</condition_summary>
+    <last_changed>June 23, 2005</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>3</order>
+    <score>0.9801</score>
+    <nct_id>NCT00011700</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00011700</url>
+    <title>Stachybotrys Induced Hemorrhage in the Developing Lung</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Idiopathic Pulmonary Hemorrhage</condition_summary>
+    <last_changed>December 1, 2006</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>4</order>
+    <score>0.9801</score>
+    <nct_id>NCT00041600</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00041600</url>
+    <title>Human Epilepsy Genetics--Neuronal Migration Disorders Study</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Epilepsy; Seizures; Cognition Disorders; Neuronal Migration Disorders</condition_summary>
+    <last_changed>February 3, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>5</order>
+    <score>0.9801</score>
+    <nct_id>NCT00044200</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00044200</url>
+    <title>Positron Emission Tomography (PET) to Study Brain Signaling</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Healthy</condition_summary>
+    <last_changed>June 9, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>6</order>
+    <score>0.9801</score>
+    <nct_id>NCT00050700</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00050700</url>
+    <title>Brain Imaging in Depression</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Depression; Bipolar Disorder</condition_summary>
+    <last_changed>June 9, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>7</order>
+    <score>0.9801</score>
+    <nct_id>NCT00062400</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00062400</url>
+    <title>Assessing Women's Attitudes About the Risk of Infertility Related to Adjuvant Therapy for Early Breast Cancer</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Breast Cancer; Psychosocial Effects/Treatment; Sexual Dysfunction and Infertility; Sexuality and Reproductive Issues</condition_summary>
+    <last_changed>June 16, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>8</order>
+    <score>0.9801</score>
+    <nct_id>NCT00083200</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00083200</url>
+    <title>Two Dose Levels of Capecitabine With Docetaxel in Treating Women With Locally Advanced or Metastatic Breast Cancer That Has Not Responded to Previous Anthracycline-Based Chemotherapy</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Breast Cancer</condition_summary>
+    <last_changed>February 26, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>9</order>
+    <score>0.9801</score>
+    <nct_id>NCT00096200</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00096200</url>
+    <title>Sorafenib With or Without Paclitaxel and Carboplatin in Treating Patients With Recurrent Ovarian Cancer, Primary Peritoneal Cancer, or Fallopian Tube Cancer</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Fallopian Tube Cancer; Ovarian Cancer; Peritoneal Cavity Cancer</condition_summary>
+    <last_changed>May 5, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>10</order>
+    <score>0.9801</score>
+    <nct_id>NCT00115700</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00115700</url>
+    <title>Radiotherapy Versus Radiotherapy Plus Chemotherapy in Early Stage Follicular Lymphoma</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Follicular Lymphoma</condition_summary>
+    <last_changed>May 6, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>11</order>
+    <score>0.9801</score>
+    <nct_id>NCT00124800</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00124800</url>
+    <title>The Effect of Tinnitus Retraining Therapy on Subjective and Objective Measures of Chronic Tinnitus</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Tinnitus</condition_summary>
+    <last_changed>February 10, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>12</order>
+    <score>0.9801</score>
+    <nct_id>NCT00136500</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00136500</url>
+    <title>Familial Amyotrophic Lateral Sclerosis (FALS) Study</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Amyotrophic Lateral Sclerosis</condition_summary>
+    <last_changed>February 16, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>13</order>
+    <score>0.9801</score>
+    <nct_id>NCT00135200</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00135200</url>
+    <title>Clinical Trial of Consolidation Treatment With Iodine I 131 Tositumomab for Multiple Myeloma</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Multiple Myeloma</condition_summary>
+    <last_changed>March 7, 2009</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>14</order>
+    <score>0.9801</score>
+    <nct_id>NCT00153400</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00153400</url>
+    <title>California WISEWOMAN Project</title>
+    <status open="Y">Not yet recruiting</status>
+    <condition_summary>Cardiovascular Diseases; Chronic Diseases</condition_summary>
+    <last_changed>February 10, 2006</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>15</order>
+    <score>0.9801</score>
+    <nct_id>NCT00157300</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00157300</url>
+    <title>PROTECT: Prospective Trial on Erythropoietin in Clinical Transplantation</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Patients Receiving a Kidney From a Non-Heart-Beating Donor</condition_summary>
+    <last_changed>September 19, 2007</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>16</order>
+    <score>0.9801</score>
+    <nct_id>NCT00162500</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00162500</url>
+    <title>A Novel Vaccine for the Treatment of MUC1-Expressing Tumor Malignancies</title>
+    <status open="Y">Not yet recruiting</status>
+    <condition_summary>Multiple Myeloma; Tumors</condition_summary>
+    <last_changed>January 9, 2007</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>17</order>
+    <score>0.9801</score>
+    <nct_id>NCT00172900</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00172900</url>
+    <title>MRS and DTI of White Matter in Alzheimer's Disease</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Alzheimer's Disease; Vascular Dementia</condition_summary>
+    <last_changed>December 20, 2005</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>18</order>
+    <score>0.9801</score>
+    <nct_id>NCT00167700</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00167700</url>
+    <title>The Effects of Maternal Nutrition During Pregnancy and Breast Feeding on the Risk of Allergic Disease in Child</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Atopic Eczema; Rhinitis; Asthma</condition_summary>
+    <last_changed>June 9, 2008</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>19</order>
+    <score>0.9801</score>
+    <nct_id>NCT00179400</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00179400</url>
+    <title>Insulin Action in Individuals With Type 2 Diabetes by Natural Fatty Acids or the Medication Pioglitazone</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Type 2 Diabetes Mellitus</condition_summary>
+    <last_changed>September 13, 2005</last_changed>
+  </clinical_study>
+  <clinical_study>
+    <order>20</order>
+    <score>0.9801</score>
+    <nct_id>NCT00182000</nct_id>
+    <url>http://ClinicalTrials.gov/show/NCT00182000</url>
+    <title>Effectiveness of D-Cycloserine as an Aid to Enhance Learning for Individuals With OCD Receiving Behavior Therapy</title>
+    <status open="Y">Recruiting</status>
+    <condition_summary>Obsessive-Compulsive Disorder</condition_summary>
+    <last_changed>September 7, 2007</last_changed>
+  </clinical_study>
+</search_results>

data/test/test_helper.rb

@@ -0,0 +1,23 @@
+require 'rubygems'
+require 'test/unit'
+require 'shoulda'
+require 'fakeweb'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'clinical'
+
+begin require "redgreen" rescue Exceptions; end
+
+FakeWeb.allow_net_connect = false
+
+class Test::Unit::TestCase
+  def register_response(path, fixture)
+    FakeWeb.register_uri("http://clinicaltrials.gov:80#{path}", 
+      :response => xml_fixture_path(fixture))
+  end
+
+  def xml_fixture_path(fixture)
+    File.join(File.dirname(__FILE__), "fixtures", "#{fixture}.xml")
+  end
+end

metadata

@@ -0,0 +1,106 @@
+--- !ruby/object:Gem::Specification 
+name: dpickett-clinical
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: ruby
+authors: 
+- Dan Pickett
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-06-28 00:00:00 -07:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: jnunemaker-httparty
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.4.3
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: jnunemaker-happymapper
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.2.5
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: mislav-will_paginate
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.3.11
+    version: 
+description: 
+email: dpickett@enlightsolutions.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- .document
+- .gitignore
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- clinical.gemspec
+- features/finding_clinical_trials.feature
+- features/step_definitions/clinical_steps.rb
+- features/support/env.rb
+- lib/clinical.rb
+- lib/clinical/collection.rb
+- lib/clinical/extensions.rb
+- lib/clinical/intervention.rb
+- lib/clinical/outcome.rb
+- lib/clinical/primary_outcome.rb
+- lib/clinical/secondary_outcome.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
+has_rdoc: true
+homepage: http://github.com/dpickett/clinical
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.2.0
+signing_key: 
+specification_version: 3
+summary: a library for accessing data from ClinicalTrials.gov
+test_files: 
+- test/clinical/trial_test.rb
+- test/test_helper.rb