ct_gov 0.0.1 → 0.0.2

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: a2cbc97f4cd880185f298bb615c8f3c8c9b67b2b
+  data.tar.gz: fedc4b404245cc5582168ae9c4cd90aad6b4a3c8
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data/Rakefile

@@ -1,2 +1,5 @@
 require "bundler/gem_tasks"
 
+task :console do
+  exec "irb -r ct_gov -I ./lib"
+end

data/lib/ct_gov.rb

@@ -1,5 +1,10 @@
 require "ct_gov/version"
+require 'ct_gov/address'
 require 'ct_gov/clinical_trial'
+require 'ct_gov/contact'
+require 'ct_gov/facility'
+require 'ct_gov/investigator'
+require 'ct_gov/location'
 require 'ct_gov/publication'
 
 require 'saxerator'
@@ -10,7 +15,7 @@ module CtGov
   BASE_OPTIONS = '?displayxml=true'
   
   def self.find_by_nctid(nctid)
-    uri = URI.parse("#{BASE_URL}/ct2/show/#{nctid}#{BASE_OPTIONS}")
+    uri = ::URI.parse("#{BASE_URL}/ct2/show/#{nctid}#{BASE_OPTIONS}")
     http = Net::HTTP.new(uri.host, uri.port)
     http.use_ssl = true
     http.verify_mode = OpenSSL::SSL::VERIFY_NONE

data/lib/ct_gov/address.rb

@@ -0,0 +1,24 @@
+module CtGov
+  class Address
+    
+    def initialize(raw_address)
+      @raw_address = raw_address
+    end
+    
+    def city
+      @raw_address['city']
+    end
+    
+    def country
+      @raw_address['country']
+    end
+    
+    def state
+      @raw_address['state']
+    end
+    
+    def zip
+      @raw_address['zip']
+    end
+  end
+end

data/lib/ct_gov/clinical_trial.rb

@@ -4,6 +4,10 @@ module CtGov
       @raw_trial = raw_trial
     end
     
+    def healthy_volunteers?
+      @raw_trial['eligibility']['accepts_healthy_volunteers'] == 'Accepts Healthy Volunteers'
+    end
+    
     def nctid
       @raw_trial['id_info']['nct_id']
     end
@@ -12,10 +16,52 @@ module CtGov
       @raw_trial['brief_title']
     end
     
+    def browse_conditions
+      @raw_trial['condition_browse'].nil? ? [] : [@raw_trial['condition_browse']['mesh_term']].flatten
+    end
+    
+    def completion_date
+      Date.parse(@raw_trial['completion_date'])
+    end
+    
+    def browse_interventions
+      @raw_trial['intervention_browse'].nil? ? [] : [@raw_trial['intervention_browse']['mesh_term']].flatten
+    end
+    
+    def keywords
+      @raw_trial['keyword'].nil? ? [] : [@raw_trial['keyword']].flatten
+    end
+    
+    def locations
+      if @raw_trial['location'].nil?
+        []
+      else
+        [@raw_trial['location']].flatten.map do |loc|
+          Location.new(loc) unless loc.nil?
+        end
+      end
+    end
+    
     def official_title
       @raw_trial['official_title']
     end
     
+    def overall_contacts
+      contacts = []
+      
+      contacts.push Contact.new(@raw_trial['overall_contact']) if @raw_trial['overall_contact']
+      
+      [@raw_trial['overall_contact_backup']].flatten.each do |contact|
+        contacts.push Contact.new(contact)
+      end
+      
+      contacts
+    end
+    
+    def overall_official
+      CtGov::Investigator.new(@raw_trial['overall_official']) unless @raw_trial['overall_official'].nil?
+    end
+    
     def brief_summary
       @raw_trial['brief_summary']['textblock'].strip
     end
@@ -28,6 +74,14 @@ module CtGov
       @raw_trial['eligibility']['criteria']['textblock']
     end
     
+    def min_age
+      @raw_trial['eligibility']['minimum_age']
+    end
+    
+    def max_age
+      @raw_trial['eligibility']['maximum_age']
+    end
+    
     def overall_status
       @raw_trial['overall_status']
     end
@@ -38,6 +92,10 @@ module CtGov
       end
     end
     
+    def primary_completion_date
+      Date.parse(@raw_trial['primary_completion_date'])
+    end
+    
     def start_date
       Date.parse(@raw_trial['start_date'])
     end

data/lib/ct_gov/contact.rb

@@ -0,0 +1,24 @@
+module CtGov
+  class Contact
+    
+    def initialize(raw_contact)
+      @raw_contact = raw_contact
+    end
+    
+    def name
+      @raw_contact['last_name']
+    end
+    
+    def phone
+      @raw_contact['phone']
+    end
+    
+    def phone_extension
+      @raw_contact['phone_ext']
+    end
+    
+    def email
+      @raw_contact['email']
+    end
+  end
+end

data/lib/ct_gov/facility.rb

@@ -0,0 +1,16 @@
+module CtGov
+  class Facility
+    
+    def initialize(raw_facility)
+      @raw_facility = raw_facility
+    end
+    
+    def name
+      @raw_facility['name']
+    end
+    
+    def address
+      Address.new(@raw_facility['address']) unless @raw_facility['address'].nil?
+    end
+  end
+end

data/lib/ct_gov/investigator.rb

@@ -0,0 +1,21 @@
+module CtGov
+  class Investigator
+    
+    def initialize(raw_investigator)
+      @raw_investigator = raw_investigator
+    end
+    
+    def affiliation
+      @raw_investigator['affiliation']
+    end
+    
+    def name
+      @raw_investigator['last_name']
+    end
+    
+    def role
+      @raw_investigator['role']
+    end
+    
+  end
+end

data/lib/ct_gov/location.rb

@@ -0,0 +1,30 @@
+module CtGov
+  class Location
+    
+    def initialize(raw_location)
+      @raw_location = raw_location
+    end
+    
+    def contact
+      Contact.new(@raw_location['contact']) unless @raw_location['contact'].nil?
+    end
+    
+    def contact_backup
+      Contact.new(@raw_location['contact_backup']) unless @raw_location['contact_backup'].nil?
+    end
+    
+    def facility
+      Facility.new(@raw_location['facility']) unless @raw_location['facility'].nil?
+    end
+    
+    def investigators
+      [@raw_location['investigator']].flatten.map do |investigator|
+        Investigator.new(investigator) unless investigator.nil?
+      end
+    end
+    
+    def status
+      @raw_location['status']
+    end
+  end
+end

data/lib/ct_gov/version.rb

@@ -1,3 +1,3 @@
 module CtGov
-  VERSION = "0.0.1"
+  VERSION = "0.0.2"
 end

data/rspec/ct_gov/address_spec.rb

@@ -0,0 +1,40 @@
+require_relative '../spec_helper'
+
+describe CtGov::Address do
+  
+  let(:raw_address) { 
+    Saxerator.parser('<address>
+        <city>Bethesda</city>
+        <state>Maryland</state>
+        <zip>20892</zip>
+        <country>United States</country>
+      </address>').for_tag(:address).first 
+  }
+      
+  let(:address) { CtGov::Address.new(raw_address) }
+  
+  describe '#city' do
+    subject { address.city }
+    
+    it { expect(subject).to eq 'Bethesda' }
+  end
+  
+  describe '#state' do
+    subject { address.state }
+    
+    it { expect(subject).to eq 'Maryland' }
+  end
+  
+  describe '#zip' do
+    subject { address.zip }
+    
+    it { expect(subject).to eq '20892' }
+  end
+  
+  describe '#country' do
+    subject { address.country }
+    
+    it { expect(subject).to eq 'United States' }
+  end
+  
+end

data/rspec/ct_gov/clinical_trial_spec.rb

@@ -6,10 +6,11 @@ describe CtGov::ClinicalTrial do
   
   let(:study) { described_class.new(raw_trial) }
   
-  describe '#nctid' do
-    subject { study.nctid }
+  
+  describe '#brief_summary' do
+    subject { study.brief_summary }
     
-    it { expect(subject).to eq 'NCT00001372' }
+    it { expect(subject).to eq raw_trial['brief_summary']['textblock'].strip }
   end
   
   describe '#brief_title' do
@@ -18,16 +19,26 @@ describe CtGov::ClinicalTrial do
     it { expect(subject).to eq 'Study of Systemic Lupus Erythematosus' }
   end
   
-  describe '#official_title' do
-    subject { study.official_title }
+  describe '#completion_date' do
+    subject { study.completion_date }
     
-    it { expect(subject).to eq 'Studies of the Pathogenesis and Natural History of Systemic Lupus Erythematosus (SLE)' }
+    it { expect(subject).to eq Date.parse('2015-07-01') }
   end
   
-  describe '#brief_summary' do
-    subject { study.brief_summary }
+  describe '#browse_conditions' do
+    subject { study.browse_conditions }
     
-    it { expect(subject).to eq raw_trial['brief_summary']['textblock'].strip }
+    it 'returns an array of all browse conditions' do
+      expect(subject.count).to eq 2
+      
+      expect(subject).to eq ['Lupus Erythematosus, Systemic', 'Nephritis']
+    end
+    
+    context 'when there are no browse_conditions' do
+      before { raw_trial.delete('condition_browse') }
+      
+      it { expect(subject).to eq [] }
+    end
   end
   
   describe '#detailed_description' do
@@ -36,28 +47,152 @@ describe CtGov::ClinicalTrial do
     it { expect(subject).to eq raw_trial['detailed_description']['textblock'].strip }
   end
   
+  describe '#eligibility_description' do
+    subject { study.eligibility_description }
+    
+    it { expect(subject).to eq raw_trial['eligibility']['criteria']['textblock'] }
+  end
+  
+  describe '#healthy_volunteers?' do
+    subject { study.healthy_volunteers? }
+    
+    context 'when the source value is "Accepts Healthy Volunteers"' do
+      before { raw_trial['eligibility']['accepts_healthy_volunteers'] = 'Accepts Healthy Volunteers' }
+      
+      it { expect(subject).to eq true }
+    end
+    
+    context 'when the source value is anything else' do
+      before { raw_trial['eligibility']['accepts_healthy_volunteers'] = 'No way!' }
+      
+      it { expect(subject).to eq false }
+    end
+  end
+  
+  describe '#browse_interventions' do
+    subject { study.browse_interventions }
+    
+    it 'returns an array of all browse conditions' do
+      expect(subject.count).to eq 2
+      
+      expect(subject).to eq ['Methylprednisolone', 'Mycophenolic']
+    end
+    
+    context 'when there are no browse_conditions' do
+      before { raw_trial.delete('intervention_browse') }
+      
+      it { expect(subject).to eq [] }
+    end
+  end
+  
+  describe '#keywords' do
+    subject { study.keywords }
+    
+    let(:expected_keywords) {[
+      "Systemic Lupus Erythematosus",
+      "Natural History",
+      "Lupus Nephritis",
+      "Lupus",
+      "Systemic Lupus",
+      "SLE"
+    ]}
+    
+    it 'returns an array of all keywords for the study' do
+      expect(subject.count).to eq 6
+      
+      expect(subject - expected_keywords).to eq []
+    end
+  end
+  
+  describe '#locations' do
+    subject { study.locations }
+    
+    it 'returns an array of locations' do
+      expect(subject.first).to be_a CtGov::Location
+    end
+    
+    it 'sets the right values for the locations' do
+      loc = subject.first
+      
+      expect(loc.status).to eq 'Recruiting'
+    end
+    
+    context 'when no location is present' do
+      before { raw_trial.delete('location') }
+      
+      it { expect(subject).to eq [] }
+    end
+    
+    context 'when there are multiple locations' do
+      before { raw_trial['location'] = [{'status' => 'Recruiting'},{'status' => 'Not Recruiting'}] }
+      
+      it 'returns all locations' do
+        expect(subject.count).to eq 2
+        
+        expect(subject.first.status).to eq 'Recruiting'
+        expect(subject.last.status).to eq 'Not Recruiting'
+      end
+    end
+  end
+  
+  describe '#max_age' do
+    subject { study.max_age }
+    
+    it { expect(subject).to eq raw_trial['eligibility']['maximum_age'] }
+  end
+  
+  describe '#min_age' do
+    subject { study.min_age }
+    
+    it { expect(subject).to eq raw_trial['eligibility']['minimum_age'] }
+  end
+  
+  describe '#nctid' do
+    subject { study.nctid }
+    
+    it { expect(subject).to eq 'NCT00001372' }
+  end
+  
+  describe '#official_title' do
+    subject { study.official_title }
+    
+    it { expect(subject).to eq 'Studies of the Pathogenesis and Natural History of Systemic Lupus Erythematosus (SLE)' }
+  end
+  
+  describe '#overall_contacts' do
+    subject { study.overall_contacts }
+    
+    it { expect(subject.count).to eq 2 }
+    
+    it { expect(subject.first).to be_a CtGov::Contact }
+    
+    it { expect(subject.first.name).to eq 'Elizabeth Joyal, R.N.' }
+  end
+  
   describe '#overall_status' do
     subject { study.overall_status }
     
     it { expect(subject).to eq 'Recruiting' }
   end
   
-  describe '#start_date' do
-    subject { study.start_date }
+  describe '#overall_official' do
+    subject { study.overall_official }
     
-    it { expect(subject).to eq Date.parse('1994-02-01') }
-  end
-  
-  describe '#study_type' do
-    subject { study.study_type }
+    it { expect(subject).to be_a CtGov::Investigator }
     
-    it { expect(subject).to eq 'Observational' }
+    it { expect(subject.name).to eq 'Sarfaraz A Hasni, M.D.' }
+    
+    context 'when overall official is not present' do
+      before { raw_trial.delete('overall_official') }
+      
+      it { expect(subject).to be_nil }
+    end
   end
   
-  describe '#eligibility_description' do
-    subject { study.eligibility_description }
+  describe '#primary_completion_date' do
+    subject { study.primary_completion_date }
     
-    it { expect(subject).to eq raw_trial['eligibility']['criteria']['textblock'] }
+    it { expect(subject).to eq Date.parse('2015-08-01') }
   end
   
   describe '#publications' do
@@ -69,4 +204,16 @@ describe CtGov::ClinicalTrial do
     
     it { expect(subject.first.pmid).to eq '7762914' }
   end
+  
+  describe '#start_date' do
+    subject { study.start_date }
+    
+    it { expect(subject).to eq Date.parse('1994-02-01') }
+  end
+  
+  describe '#study_type' do
+    subject { study.study_type }
+    
+    it { expect(subject).to eq 'Observational' }
+  end
 end

data/rspec/ct_gov/contact_spec.rb

@@ -0,0 +1,40 @@
+require_relative '../spec_helper'
+
+describe CtGov::Contact do
+  
+  let(:raw_data) { '
+    <contact>
+      <last_name>Elizabeth Joyal, R.N.</last_name>
+      <phone>(301) 435-4489</phone>
+      <phone_ext>321</phone_ext>
+      <email>ejoyal@mail.cc.nih.gov</email>
+    </contact>'
+  }
+  
+  let(:contact) { CtGov::Contact.new(Saxerator.parser(raw_data).for_tag(:contact).first) }
+  
+  describe '#name' do
+    subject { contact.name }
+    
+    it { expect(subject).to eq 'Elizabeth Joyal, R.N.' }
+  end
+  
+  describe '#phone' do
+    subject { contact.phone }
+    
+    it { expect(subject).to eq '(301) 435-4489' }
+  end
+  
+  describe '#phone_extension' do
+    subject { contact.phone_extension }
+    
+    it { expect(subject).to eq '321' }
+  end
+  
+  describe '#email' do
+    subject { contact.email }
+    
+    it { expect(subject).to eq 'ejoyal@mail.cc.nih.gov' }
+  end
+  
+end

data/rspec/ct_gov/facility_spec.rb

@@ -0,0 +1,36 @@
+require_relative '../spec_helper'
+
+describe CtGov::Facility do
+  let(:raw_facility) {
+    Saxerator.parser('
+    <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>').for_tag(:facility).first
+  }
+  
+  let(:facility) { CtGov::Facility.new(raw_facility) }
+  
+  describe '#name' do
+    subject { facility.name }
+    
+    it { expect(subject).to eq 'National Institutes of Health Clinical Center, 9000 Rockville Pike' }
+  end
+  
+  describe '#address' do
+    subject { facility.address }
+    
+    it 'returns an address' do
+      expect(subject).to be_a CtGov::Address
+    end
+    
+    it 'returns an address with the right values' do
+      expect(subject.city).to eq 'Bethesda'
+    end
+  end
+end

data/rspec/ct_gov/investigator_spec.rb

@@ -0,0 +1,32 @@
+require_relative '../spec_helper'
+
+describe CtGov::Investigator do
+  
+  let(:raw_data) { 
+    '<overall_official>
+      <last_name>Sarfaraz A Hasni, M.D.</last_name>
+      <role>Principal Investigator</role>
+      <affiliation>National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)</affiliation>
+    </overall_official>' 
+  }
+  
+  let(:investigator) { CtGov::Investigator.new(Saxerator.parser(raw_data).for_tag(:overall_official).first) }
+  
+  describe '#name' do
+    subject { investigator.name }
+    
+    it { expect(subject).to eq 'Sarfaraz A Hasni, M.D.' }
+  end
+  
+  describe '#role' do
+    subject { investigator.role }
+    
+    it { expect(subject).to eq 'Principal Investigator' }
+  end
+  
+  describe '#affiliation' do
+    subject { investigator.affiliation }
+    
+    it { expect(subject).to eq 'National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)' }
+  end
+end

data/rspec/ct_gov/location_spec.rb

@@ -0,0 +1,124 @@
+require_relative '../spec_helper'
+
+describe CtGov::Location do
+  
+  let(:raw_location) { Saxerator.parser(
+    '<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>
+      <contact>
+        <last_name>For more information at the NIH Clinical Center contact Patient Recruitment and Public Liaison Office (PRPL)</last_name>
+        <phone>800-411-1222</phone>
+        <phone_ext>TTY8664111010</phone_ext>
+        <email>prpl@mail.cc.nih.gov</email>
+      </contact>
+      <contact_backup>
+        <last_name>David Hyman, MD</last_name>
+        <phone>646-888-4544</phone>
+      </contact_backup>
+      <investigator>
+        <last_name>Matthew Fury, MD, PhD</last_name>
+        <role>Principal Investigator</role>
+      </investigator>
+    </location>'
+  ).for_tag(:location).first }
+  
+  let(:location) { CtGov::Location.new(raw_location) }
+  
+  describe '#contact' do
+    subject { location.contact }
+    
+    it 'returns a contact' do
+      expect(subject).to be_a CtGov::Contact
+    end
+    
+    it 'sets the right values for the contact' do
+      expect(subject.phone).to eq '800-411-1222'
+    end
+    
+    context 'when there is no contact backup' do
+      before { raw_location['contact'] = nil }
+      
+      it { expect(subject).to be_nil }
+    end
+  end
+  
+  describe '#contact_bacup' do
+    subject { location.contact_backup }
+    
+    it 'returns a contact' do
+      expect(subject).to be_a CtGov::Contact
+    end
+    
+    it 'sets the right values for the contact' do
+      expect(subject.phone).to eq '646-888-4544'
+    end
+    
+    context 'when there is no contact backup' do
+      before { raw_location['contact_backup'] = nil }
+      
+      it { expect(subject).to be_nil }
+    end
+  end
+  
+  describe '#investigators' do
+    subject { location.investigators }
+    
+    it 'returns an array of investigators' do
+      investigators = subject
+      expect(subject).to be_a Array
+      investigators.each { |i| expect(i).to be_a CtGov::Investigator }
+    end
+    
+    it 'returns investigators with the right values' do
+      investigator = subject.first
+      expect(investigator.name).to eq 'Matthew Fury, MD, PhD'
+    end
+    
+    context 'when there are multiple investigators' do
+      before { raw_location['investigator'] = [{'last_name' => 'Homer Simpson'}, {'last_name' => 'Peter Griffin'}] }
+      
+      it 'returns both investigaors' do
+        expect(subject.count).to eq 2
+        
+        expect(subject.first.name).to eq 'Homer Simpson'
+        expect(subject.last.name).to eq 'Peter Griffin'
+      end
+    end
+  end
+  
+  describe '#facility' do
+    subject { location.facility }
+    
+    it 'returns a facility object' do 
+      expect(subject).to be_a CtGov::Facility
+    end
+    
+    it 'passes the right values to the facility' do
+      facility = subject
+      expect(facility.name).to eq 'National Institutes of Health Clinical Center, 9000 Rockville Pike'
+      expect(facility.address.city).to eq 'Bethesda'
+    end
+    
+    context 'when there is no facility' do
+      before { raw_location['facility'] = nil }
+      
+      it { expect(subject).to be_nil }
+    end
+  end
+  
+  describe '#status' do
+    subject { location.status }
+    
+    it { expect(subject).to eq 'Recruiting' }
+  end
+  
+end

data/rspec/data/sample_trial.xml

@@ -92,6 +92,9 @@
   </detailed_description>
   <overall_status>Recruiting</overall_status>
   <start_date>February 1994</start_date>
+  <end_date>June 2015</end_date>
+  <completion_date>July 2015</completion_date>
+  <primary_completion_date>August 2015</primary_completion_date>
   <phase>N/A</phase>
   <study_type>Observational</study_type>
   <study_design>N/A</study_design>
@@ -258,6 +261,12 @@
   <condition_browse>
     <!-- CAUTION:  The following MeSH terms are assigned with an imperfect algorithm  -->
     <mesh_term>Lupus Erythematosus, Systemic</mesh_term>
+    <mesh_term>Nephritis</mesh_term>
   </condition_browse>
   <!-- Results have not yet been posted for this study                                -->
+  
+  <intervention_browse>
+    <mesh_term>Methylprednisolone</mesh_term>
+    <mesh_term>Mycophenolic</mesh_term>
+  </intervention_browse>
 </clinical_study>

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ct_gov
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - Dan Carpenter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-01-09 00:00:00.000000000 Z
+date: 2015-01-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: saxerator
@@ -64,12 +64,23 @@ files:
 - LICENSE
 - README.md
 - Rakefile
+- ct_gov-0.0.1.gem
 - ct_gov.gemspec
 - lib/ct_gov.rb
+- lib/ct_gov/address.rb
 - lib/ct_gov/clinical_trial.rb
+- lib/ct_gov/contact.rb
+- lib/ct_gov/facility.rb
+- lib/ct_gov/investigator.rb
+- lib/ct_gov/location.rb
 - lib/ct_gov/publication.rb
 - lib/ct_gov/version.rb
+- rspec/ct_gov/address_spec.rb
 - rspec/ct_gov/clinical_trial_spec.rb
+- rspec/ct_gov/contact_spec.rb
+- rspec/ct_gov/facility_spec.rb
+- rspec/ct_gov/investigator_spec.rb
+- rspec/ct_gov/location_spec.rb
 - rspec/ct_gov/publication_spec.rb
 - rspec/ct_gov_spec.rb
 - rspec/data/sample_trial.xml