health-data-standards 2.0.0 → 2.1.0

data/Gemfile

@@ -14,4 +14,5 @@ group :test do
   gem "tailor", '~> 1.1.2'
   gem "cane", '~> 2.3.0'
   gem 'simplecov', :require => false
+  gem 'webmock'
 end

data/lib/health-data-standards.rb

@@ -12,7 +12,8 @@ require_relative 'health-data-standards/ext/string'
 
 require_relative 'health-data-standards/util/hl7_helper'
 require_relative 'health-data-standards/util/code_system_helper'
-require_relative 'health-data-standards/util/qrda_template_helper'
+require_relative 'health-data-standards/util/hqmf_template_helper'
+require_relative 'health-data-standards/util/vs_api'
 
 require_relative 'health-data-standards/export/template_helper'
 require_relative 'health-data-standards/export/view_helper'
@@ -59,6 +60,8 @@ require_relative 'health-data-standards/models/person'
 require_relative 'health-data-standards/models/organization'
 require_relative 'health-data-standards/models/address'
 require_relative 'health-data-standards/models/telecom'
+require_relative 'health-data-standards/models/svs/value_set'
+require_relative 'health-data-standards/models/svs/concept'
 require_relative 'health-data-standards/models/facility'
 require_relative 'health-data-standards/models/metadata/base'
 require_relative 'health-data-standards/models/metadata/author'

data/lib/health-data-standards/export/html.rb

@@ -3,10 +3,10 @@ module HealthDataStandards
     module HTML
       include TemplateHelper
 
-      def export(patient)
+      def export(patient, concept_map=nil)
         self.template_format = "html"
         self.template_subdir = "html"
-        render(:template => 'show', :locals => {:patient => patient})
+        render(:template => 'show', :locals => {:patient => patient, :concept_map=>concept_map})
       end
 
       extend self

data/lib/health-data-standards/export/view_helper.rb

@@ -84,16 +84,16 @@ module HealthDataStandards
         return ["true","false"].include? (str || "").downcase
       end
       
-      def decode_qrda_section(section, oid)
+      def decode_hqmf_section(section, oid)
         if oid
-          HealthDataStandards::Util::QRDATemplateHelper.definition_for_template_id(oid)['definition'].pluralize.to_sym
+          HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['definition'].pluralize.to_sym
         else
           section
         end
       end
-      def decode_qrda_status(status, oid)
+      def decode_hqmf_status(status, oid)
         if oid
-          HealthDataStandards::Util::QRDATemplateHelper.definition_for_template_id(oid)['status']
+          HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['status']
         else
           status
         end

data/lib/health-data-standards/import/c32/encounter_importer.rb

@@ -60,6 +60,7 @@ module HealthDataStandards
             facility.addresses = participant_element.xpath("./cda:addr").try(:map) {|ae| import_address(ae)}
             facility.telecoms = participant_element.xpath("./cda:telecom").try(:map) {|te| import_telecom(te)}
             facility.code = extract_code(participant_element, './cda:code')
+            extract_dates(participant_element.parent, facility, "time")
             encounter.facility = facility
           end
         end

data/lib/health-data-standards/import/c32/section_importer.rb

@@ -108,7 +108,7 @@ module HealthDataStandards
         end
 
         def extract_dates(parent_element, entry, element_name="effectiveTime")
-          if parent_element.at_xpath("cda:#{element_name}")
+          if parent_element.at_xpath("cda:#{element_name}/@value")
             entry.time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}")['value'])
           end
           if parent_element.at_xpath("cda:#{element_name}/cda:low")

data/lib/health-data-standards/import/green_c32/encounter_importer.rb

@@ -17,18 +17,15 @@ module HealthDataStandards
           extract_code(encounter_element, encounter, "./gc32:admissionType", :admit_type)
           extract_code(encounter_element, encounter, "./gc32:reasonForVisit", :reason)
           extract_code(encounter_element, encounter)
-          extract_facility(encounter_element, encounter)
           extract_free_text(encounter_element, encounter)
           
-          encounter
-        end
-        
-        def extract_facility(encounter_element, encounter)
-          facility_element = encounter_element.xpath("./gc32:facility").first
+          facility_element = encounter_element.at_xpath("./gc32:facility")
           if facility_element
-            organization = extract_organization(facility_element)
-            encounter.facility = organization
+            facility = extract_facility(facility_element)
+            encounter.facility = facility
           end
+
+          encounter
         end
         
       end

data/lib/health-data-standards/import/green_c32/section_importer.rb

@@ -122,6 +122,22 @@ module HealthDataStandards
           
           return organization
         end
+
+        def extract_facility(facility_element)
+          facility = Facility.new
+          facility.name = extract_node_text(facility_element.xpath("./gc32:name"))
+          facility.addresses = facility_element.xpath("./gc32:address").map { |addr| extract_address(addr)  }
+          facility.telecoms = facility_element.xpath("./gc32:telecom").map { |tele| extract_telecom(tele) }
+          start_time = facility_element.at_xpath("./gc32:duration/gc32:start").try(:text)
+          if start_time
+            facility.start_time = Time.parse(start_time).utc.to_i
+          end
+          end_time = facility_element.at_xpath("./gc32:duration/gc32:end").try(:text)
+          if end_time
+            facility.end_time = Time.parse(end_time).utc.to_i
+          end
+          facility
+        end
         
         def extract_address(address_element)
           return unless address_element

data/lib/health-data-standards/models/coded_result_value.rb

@@ -1,3 +1,4 @@
 class CodedResultValue < ResultValue
   include ThingWithCodes
+  field :description, type: String
 end

data/lib/health-data-standards/models/facility.rb

@@ -4,6 +4,9 @@ class Facility
   field :name, type: String
   field :code, type: Hash
   
+  field :start_time, type: Integer
+  field :end_time, type: Integer
+  
   embeds_many :addresses, as: :locatable
   embeds_many :telecoms, as: :contactable
 end

data/lib/health-data-standards/models/insurance_provider.rb

@@ -1,6 +1,7 @@
 class InsuranceProvider
   include Mongoid::Document
   
+  embedded_in :record, class_name: 'Record'
   embeds_one :payer, class_name: "Organization"
   embeds_many :guarantors, class_name: "Guarantor"
   embeds_one :subscriber, class_name: "Person"

data/lib/health-data-standards/models/medical_equipment.rb

@@ -1,5 +1,8 @@
 class MedicalEquipment < Entry
   
   field :manufacturer, type: String
-   
+  field :anatomicalStructure, type: Hash
+
+  alias :anatomical_structure :anatomicalStructure
+  alias :anatomical_structure= :anatomicalStructure=
 end

data/lib/health-data-standards/models/procedure.rb

@@ -1,5 +1,9 @@
 class Procedure < Entry
-  field :site,          type: Hash
+  field :site,             type: Hash
+  field :incisionDateTime, type: Integer
   
   belongs_to :performer, class_name: "Provider"
+
+  alias :incision_date_time :incisionDateTime
+  alias :incision_date_time= :incisionDateTime=
 end

data/lib/health-data-standards/models/provider.rb

@@ -5,7 +5,6 @@ class Provider
   field :tin         , type: String
   field :specialty   , type: String
   field :phone       , type: String
-  field :organization, type: String
   
   validates_uniqueness_of :npi, allow_blank: true
   

data/lib/health-data-standards/models/record.rb

@@ -37,8 +37,8 @@ class Record
   embeds_many :functional_statuses
 
   Sections = [:allergies, :care_goals, :conditions, :encounters, :immunizations, :medical_equipment,
-   :medications, :procedures, :results, :social_history, :vital_signs, :support, :advanced_directives,
-   :functional_statuses]
+   :medications, :procedures, :results, :social_history, :vital_signs, :support, :advance_directives,
+   :insurance_providers, :functional_statuses]
 
   embeds_many :provider_performances
   
@@ -52,6 +52,18 @@ class Record
   def over_18?
     Time.at(birthdate) < Time.now.years_ago(18)
   end
+
+  def entries_for_oid(oid)
+    matching_entries_by_section = Sections.map do |section|
+      section_entries = self.send(section)
+      if section_entries.present?
+        section_entries.find_all { |entry| entry.oid == oid }
+      else
+        []
+      end
+    end
+    matching_entries_by_section.flatten
+  end
   
   alias :clinical_trial_participant :clinicalTrialParticipant
   alias :clinical_trial_participant= :clinicalTrialParticipant=

data/lib/health-data-standards/models/svs/concept.rb

@@ -0,0 +1,16 @@
+module HealthDataStandards
+  module SVS
+
+    class Concept
+	
+    	include Mongoid::Document
+    	field :code, type: String
+    	field :code_system_name, type: String
+    	field :code_system_version, type: String
+    	field :display_name, type: String
+      field :code_system, type: String
+      scope :by_code_system_name,  ->(cs){where(code_system_name: cs)}
+      scope :by_code_system,  ->(cs){where(code_system: cs)}
+    end
+  end
+end

data/lib/health-data-standards/models/svs/value_set.rb

@@ -0,0 +1,30 @@
+module HealthDataStandards
+  module SVS
+    class ValueSet
+
+    	include Mongoid::Document
+      field :oid, type: String
+      field :display_name, type: String
+      field :version, type: String
+
+      embeds_many :concepts
+      scope :by_oid, ->(oid){where(:oid => oid)}
+
+      def self.load_from_xml(doc)
+      	  doc.root.add_namespace_definition("vs","urn:ihe:iti:svs:2008")
+      	 	vs_element = doc.at_xpath("/vs:RetrieveValueSetResponse/vs:ValueSet")
+      	 	if vs_element
+      	 		vs = ValueSet.new(oid: vs_element["ID"], display_name: vs_element["displayName"], version: vs_element["version"])
+      	 		concepts = vs_element.xpath("//vs:Concept").collect do |con|
+      	 				Concept.new(code: con["code"], 
+      	 					code_system_name: con["codeSystemName"], 
+      	 					code_system_version: con["code_system_version"],
+      	 				  display_name: con["displayName"],code_system: con["codeSystem"])
+      	 		   end
+                vs.concepts = concepts
+      	 		return vs
+      	 	end
+      end
+    end
+  end
+end

data/lib/health-data-standards/util/code_system_helper.rb

@@ -18,7 +18,9 @@ module HealthDataStandards
         '2.16.840.1.113883.3.88.12.80.20' => 'FDA',
         '2.16.840.1.113883.5.14' => 'HL7 ActStatus',
         '2.16.840.1.113883.6.259' => 'HL7 Healthcare Service Location',
-        '2.16.840.1.113883.5.4' => 'HL7 Act Code'
+        '2.16.840.1.113883.5.4' => 'HL7 Act Code',
+        '2.16.840.1.113883.1.11.18877' => 'HL7 Relationship Code',
+        '2.16.840.1.113883.6.238' => 'CDC Race'
       }
       
       # Returns the name of a code system given an oid

data/lib/health-data-standards/util/hqmf_template_helper.rb

@@ -0,0 +1,28 @@
+module HealthDataStandards
+  module Util
+    # General helpers for working with codes and code systems
+    class HQMFTemplateHelper
+      
+      def self.definition_for_template_id(template_id)
+        template_id_map[template_id]
+      end
+      
+      def self.template_id_map
+        if @id_map.blank?
+          template_id_file = File.expand_path('../hqmf_template_oid_map.json', __FILE__)
+          @id_map = JSON.parse(File.read(template_id_file))  
+        end
+        @id_map
+      end
+
+      def self.template_id_by_definition_and_status(definition, status, negation=false)
+        pairs = template_id_map.select {|k, v| v['definition'] == definition && 
+                                               v['status'] == status && 
+                                               v['negation'] == negation}
+        pairs.keys.first if pairs.present?
+      end
+    end
+  end
+end
+
+

data/lib/health-data-standards/util/vs_api.rb

@@ -0,0 +1,43 @@
+require 'rest_client'
+require 'uri'
+module HealthDataStandards
+  module Util
+		class VSApi			
+			attr_accessor :api_url, :ticket_url,  :username, :password
+
+			def initialize(ticket_url, api_url,username,password)
+				@api_url = api_url
+				@ticket_url = ticket_url
+				@username = username
+				@password = password
+			end
+
+			def get_valueset(oid,&block)
+				vs = RestClient.get api_url, {:params=>{id: oid, ticket: get_ticket}}
+				yield oid,vs if block_given?
+				vs
+			end
+
+			def process_valuesets(oids, &block)
+				oids.each do |oid|
+		     		vs = get_valueset(oid)
+		     		yield oid,vs
+				end
+			end
+
+			def proxy_ticket
+			 	@proxy_ticket ||= get_proxy_ticket
+			end
+
+			def get_proxy_ticket
+				# the content type is set and the body is a string becuase the NLM service does not support urlencoded content and
+				# throws an error on that contnet type
+				 RestClient.post ticket_url, {username: username, password: password}
+			end
+			
+			def get_ticket
+			  RestClient.post "#{ticket_url}/#{proxy_ticket}", {service: "http://umlsks.nlm.nih.gov"}
+		  end
+		end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: health-data-standards
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.1.0
   prerelease: 
 platform: ruby
 authors:
@@ -12,8 +12,24 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-24 00:00:00.000000000 Z
+date: 2012-10-31 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.7
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.7
 - !ruby/object:Gem::Dependency
   name: erubis
   requirement: !ruby/object:Gem::Requirement
@@ -196,13 +212,16 @@ files:
 - lib/health-data-standards/models/record.rb
 - lib/health-data-standards/models/result_value.rb
 - lib/health-data-standards/models/support.rb
+- lib/health-data-standards/models/svs/concept.rb
+- lib/health-data-standards/models/svs/value_set.rb
 - lib/health-data-standards/models/telecom.rb
 - lib/health-data-standards/models/thing_with_codes.rb
 - lib/health-data-standards/models/treating_provider.rb
 - lib/health-data-standards/models/vital_sign.rb
 - lib/health-data-standards/util/code_system_helper.rb
 - lib/health-data-standards/util/hl7_helper.rb
-- lib/health-data-standards/util/qrda_template_helper.rb
+- lib/health-data-standards/util/hqmf_template_helper.rb
+- lib/health-data-standards/util/vs_api.rb
 - lib/health-data-standards.rb
 - templates/_address.gc32.erb
 - templates/_advance_directive.gc32.erb
@@ -273,3 +292,4 @@ signing_key:
 specification_version: 3
 summary: A library for generating and consuming various healthcare related formats.
 test_files: []
+has_rdoc: 

data/lib/health-data-standards/util/qrda_template_helper.rb

@@ -1,20 +0,0 @@
-
-module HealthDataStandards
-  module Util
-    # General helpers for working with codes and code systems
-    class QRDATemplateHelper
-      
-      def self.definition_for_template_id(template_id)
-        template_id_map[template_id]
-      end
-      
-      def self.template_id_map
-        template_id_file = File.expand_path('../qrda_template_oid_map.json', __FILE__)
-        JSON.parse(File.read(template_id_file))
-      end
-      
-    end
-  end
-end
-
-