health-data-standards 0.3.0 → 0.5.0

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

@@ -0,0 +1,12 @@
+module HealthDataStandards
+  module Import
+    module C32
+      class VitalSignImporter < ResultImporter
+        def initialize
+          super
+          @entry_xpath = "//cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.14']"
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,4 @@
+class Allergy < Entry
+  field :reaction, type: Hash
+  field :severity, type: Hash
+end

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

@@ -0,0 +1,7 @@
+class Encounter < Entry
+  field :performer, type: Hash
+  field :facility, type: Hash
+  field :admitType, type: Hash, as: 'admit_type'
+  field :dischargeDisp, type: Hash, as: 'discharge_disp'
+  embeds_one :reason, class_name: "Entry"
+end

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

@@ -8,9 +8,9 @@ class Entry
   field :time, type: Integer
   field :start_time, type: Integer
   field :end_time, type: Integer
-  field :status, type: Symbol
-  field :codes, type: Hash
-  field :value, type: Hash
+  field :status, type: String
+  field :codes, type: Hash, default: {}
+  field :value, type: Hash, default: {}
 
   def single_code_value?
     codes.size == 1 && codes.first[1].size == 1
@@ -20,6 +20,32 @@ class Entry
     codes.map {|code_set, codes| "#{code_set}: #{codes.join(', ')}"}.join(' ')
   end
   
+  # Will return a single code and code set if one exists in the code sets that are
+  # passed in. Returns a hash with a key of code and code_set if found, nil otherwise
+  def preferred_code(preferred_code_sets)
+    matching_code_sets = preferred_code_sets & codes.keys
+    if matching_code_sets.present?
+      code_set = matching_code_sets.first
+      {'code' => codes[code_set].first, 'code_set' => code_set}
+    else
+      nil
+    end
+  end
+  
+  # Will return an Array of code and code_set hashes for all codes for this entry
+  # except for the preferred_code. It is intended that these codes would be used in
+  # the translation elements as childern of a CDA code element
+  def translation_codes(preferred_code_sets)
+    tx_codes = []
+    codes.each_pair do |code_set, code_list|
+      code_list.each do |code|
+        tx_codes << {'code' => code, 'code_set' => code_set}
+      end
+    end
+    
+    tx_codes - [preferred_code(preferred_code_sets)]
+  end
+  
   def times_to_s
     if start_time.present? || end_time.present?
       start_string = start_time ? Time.at(start_time).to_formatted_s(:long_ordinal) : 'UNK'
@@ -48,4 +74,106 @@ class Entry
       end
     end
   end
+  
+  def self.from_event_hash(event)
+    entry = Entry.new
+    if event['code']
+      entry.add_code(event['code'], event['code_set'])
+    end
+    entry.time = event['time']
+    if event['value']
+      entry.set_value(event['value'], event['unit'])
+    end
+    if event['description']
+      entry.description = event['description']
+    end
+    if event['status']
+      entry.status = event['status']
+    end
+    entry
+  end
+
+  # Add a code into the Entry
+  # @param [String] code the code to add
+  # @param [String] code_system the code system that the code belongs to
+  def add_code(code, code_system)
+    self.codes[code_system] ||= []
+    self.codes[code_system] << code
+  end
+
+  # Sets the value for the entry
+  # @param [String] scalar the value
+  # @param [String] units the units of the scalar value
+  def set_value(scalar, units=nil)
+    self.value[:scalar] = scalar
+    self.value[:units] = units
+  end
+
+  # Checks if a code is in the list of possible codes
+  # @param [Array] code_set an Array of Hashes that describe the values for code sets
+  # @return [true, false] whether the code is in the list of desired codes
+  def is_in_code_set?(code_set)
+    codes.keys.each do |code_system|
+      all_codes_in_system = code_set.find_all {|set| set['set'] == code_system}
+      all_codes_in_system.each do |codes_in_system|
+        matching_codes = codes_in_system['values'] & codes[code_system]
+        if matching_codes.length > 0
+          return true
+        end
+      end
+    end
+    false
+  end
+
+  # Tries to find a single point in time for this entry. Will first return time if it is present,
+  # then fall back to start_time and finally end_time
+  def as_point_in_time
+    if time
+      time
+    elsif start_time
+      start_time
+    else
+      end_time
+    end
+  end
+
+  # Checks to see if this Entry can be used as a date range
+  # @return [true, false] If the Entry has a start and end time returns true, false otherwise.
+  def is_date_range?
+    start_time.present? && end_time.present?
+  end
+
+  # Checks to see if this Entry is usable for measure calculation. This means that it contains
+  # at least one code and has one of its time properties set (start, end or time)
+  # @return [true, false]
+  def usable?
+    codes.present? && (start_time.present? || end_time.present? || time.present?)
+  end
+  
+  # Creates a Hash for this Entry
+  # @return [Hash] a Hash representing the Entry
+  def to_hash
+    entry_hash = {}
+    entry_hash['codes'] = codes
+    unless value.empty?
+      entry_hash['value'] = value
+    end
+    
+    if is_date_range?
+      entry_hash['start_time'] = start_time
+      entry_hash['end_time'] = end_time
+    else
+      entry_hash['time'] = as_point_in_time
+    end
+    
+    if status
+      entry_hash['status'] = status
+    end
+    
+    if description
+      entry_hash['description'] = description
+    end
+    
+    entry_hash
+  end
 end

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

@@ -0,0 +1,11 @@
+class FulfillmentHistory
+  include Mongoid::Document
+  
+  field :prescriptionNumber, type: String, as: 'prescription_number'
+  field :provider, type: Hash
+  field :dispensingPharmacyLocation, type: Hash, as: 'dispensing_pharmacy_location'
+  field :dispenseDate, type: Integer, as: 'dispense_date'
+  field :quantityDispensed, type: Hash, as: 'quantity_dispensed'
+  field :fillNumber, type: Integer, as: 'fill_number'
+  field :fillStatus, type: Hash, as: 'fill_status'
+end

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

@@ -0,0 +1,5 @@
+class Immunization < Entry
+  field :refusalInd, type: Boolean, as: 'refusal_ind'
+  field :performer, type: Hash
+  field :refusalReason, type: Hash, as: 'refusal_reason'
+end

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

@@ -0,0 +1,4 @@
+class LabResult < Entry
+  field :referenceRange, type: String, as: 'reference_range'
+  field :interpretation, type: Hash
+end

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

@@ -0,0 +1,25 @@
+class Medication < Entry
+  field :administrationTiming, type: Hash, as: 'administration_timing'
+  field :freeTextSig, type: String, as: 'free_text_sig'
+  field :dose, type: Hash
+  field :brandName, type: String, as: 'brand_name'
+  field :typeOfMedication, type: Hash, as: 'type_of_medication'
+  field :statusOfMedication, type: Hash, as: 'status_of_medication'
+  embeds_many :fulfillmentHistory, class_name: 'FulfillmentHistory'
+  embeds_many :orderInformation, class_name: 'OrderInformation'
+  field :route, type: Hash
+  field :site, type: Hash
+  field :doseRestriction, type: Hash, as: 'dose_restriction'
+  field :fulfillmentInstructions, type: String, as: 'fulfillment_instructions'
+  field :indication, type: Hash
+  field :productForm, type: Hash, as: 'product_form'
+  field :vehicle, type: Hash
+  field :reaction, type: Hash
+  field :deliveryMethod, type: Hash, as: 'delivery_method'
+  field :patientInstructions, type: String, as: 'patient_instructions'
+  
+  alias :fulfillment_history :fulfillmentHistory
+  alias :fulfillment_history= :fulfillmentHistory=
+  alias :order_information :orderInformation
+  alias :order_information= :orderInformation=
+end

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

@@ -0,0 +1,9 @@
+class OrderInformation
+  include Mongoid::Document
+  
+  field :orderNumber, type: String, as: 'order_number'
+  field :fills, type: Integer
+  field :quantityOrdered, type: Hash, as: 'quantity_ordered'
+  field :orderExpirationDateTime, type: Integer, as: 'order_expiration_date_time'
+  field :orderDateTime, type: Integer, as: 'order_date_time'
+end

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

@@ -0,0 +1,4 @@
+class Procedure < Entry
+  field :performer, type: Hash
+  field :site, type: Hash
+end

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

@@ -9,6 +9,7 @@ class Record
   field :race, type: String
   field :ethnicity, type: String
   field :test_id, type: BSON::ObjectId
+  field :medical_record_number, type: String
 
   [:allergies, :care_goals, :conditions, :encounters, :immunizations, :medical_equipment,
    :medications, :procedures, :results, :social_history, :vital_signs].each do |section|

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

@@ -0,0 +1,41 @@
+module HealthDataStandards
+  module Util
+    # General helpers for working with codes and code systems
+    class CodeSystemHelper
+      CODE_SYSTEMS = {
+        '2.16.840.1.113883.6.1' =>    'LOINC',
+        '2.16.840.1.113883.6.96' =>   'SNOMED-CT',
+        '2.16.840.1.113883.6.12' =>   'CPT',
+        #'2.16.840.1.113883.3.88.12.80.32' => 'CPT', # Encounter Type from C32, a subset of CPT
+        '2.16.840.1.113883.6.88' =>   'RxNorm',
+        '2.16.840.1.113883.6.103' =>  'ICD-9-CM',
+        '2.16.840.1.113883.6.104' =>  'ICD-9-CM',
+        '2.16.840.1.113883.6.90' =>   'ICD-10-CM',
+        '2.16.840.1.113883.6.14' =>   'HCPCS',
+        '2.16.840.1.113883.6.59' =>   'CVX',
+        '2.16.840.1.113883.5.83' => 'HITSP C80 Observation Status'
+      }
+      
+      # Returns the name of a code system given an oid
+      # @param [String] oid of a code system
+      # @return [String] the name of the code system as described in the measure definition JSON
+      def self.code_system_for(oid)
+        CODE_SYSTEMS[oid] || "Unknown"
+      end
+      
+      # Returns the oid for a code system given a codesystem name
+      # @param [String] the name of the code system
+      # @return [String] the oid of the code system
+      def self.oid_for_code_system(code_system)
+        CODE_SYSTEMS.invert[code_system]
+      end
+      
+      # Returns the whole map of OIDs to code systems
+      # @terurn [Hash] oids as keys, code system names as values
+      def self.code_systems
+        CODE_SYSTEMS
+      end
+    end
+  end
+end
+

data/lib/health-data-standards/util/hl7_helper.rb

@@ -0,0 +1,25 @@
+module HealthDataStandards
+  module Util
+    # General helpers for working with HL7 data types
+    class HL7Helper
+      
+      # Converts an HL7 timestamp into an Integer
+      # @param [String] timestamp the HL7 timestamp. Expects YYYYMMDD format
+      # @return [Integer] Date in seconds since the epoch
+      def self.timestamp_to_integer(timestamp)
+        if timestamp && timestamp.length >= 4
+          year = timestamp[0..3].to_i
+          month = timestamp.length >= 6 ? timestamp[4..5].to_i : 1
+          day = timestamp.length >= 8 ? timestamp[6..7].to_i : 1
+          hour = timestamp.length >= 10 ? timestamp[8..9].to_i : 0
+          min = timestamp.length >= 12 ? timestamp[10..11].to_i : 0
+          sec = timestamp.length >= 14 ? timestamp[12..13].to_i : 0
+          
+          Time.gm(year, month, day, hour, min, sec).to_i
+        else
+          nil
+        end
+      end
+    end
+  end
+end

data/templates/_allergies.c32.erb

@@ -43,7 +43,9 @@
             <participant typeCode="CSM">
               <participantRole classCode="MANU">
                 <playingEntity classCode="MMAT">
-                  <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'allergies'} %>
+                  <%== render :partial => 'code_with_reference', 
+                              :locals => {:entry => entry, :i => i, :section => 'allergies', 
+                                          :preferred_code_sets => ['RxNorm']} %>
                   <name><%= entry.description %></name>
                 </playingEntity>
               </participantRole>

data/templates/_care_goals.c32.erb

@@ -14,7 +14,7 @@
         <templateId root="2.16.840.1.113883.10.20.1.25"/>
         <!-- Plan of Activity activity template -->
         <id root="<%= UUID.generate %>"/>
-        <%== code_display(entry) %>
+        <%== code_display(entry, :preferred_code_sets => ['SNOMED-CT']) %>
         <statusCode code="new"/>
         <effectiveTime value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
       </observation>

data/templates/_code_with_reference.c32.erb

@@ -1,8 +1,13 @@
-<% if entry.single_code_value? 
-  code = entry.codes.first[1].first
-  code_system_oid = QME::Importer::CodeSystemHelper.oid_for_code_system(entry.codes.first[0])
+<% preferred_code = entry.preferred_code(preferred_code_sets)
+  if preferred_code 
+  code_system_oid = HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(preferred_code['code_set'])
   -%>
-<code code="<%= code %>" codeSystem="<%= code_system_oid %>">
+<code code="<%= preferred_code['code'] %>" codeSystem="<%= code_system_oid %>" displayName="<%= entry.description %>">
+<% else -%>
+<code nullFlavor="UNK">
+<% end -%>
   <originalText><reference value="#<%= section %>-desc-<%= i %>"/></originalText>
+  <% entry.translation_codes(preferred_code_sets).each do |translation| -%>
+  <translation code="<%= translation['code'] %>" codeSystem="<%= HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(translation['code_set']) %>" />
+  <% end -%>
 </code>
-<% end -%>

data/templates/_conditions.c32.erb

@@ -7,7 +7,7 @@
     <!--Problems section template-->
     <code code="11450-4" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Problem list"/>
     <title>Problems</title>
-    <%== render :partial => 'narrative_block', :locals => {:entries => entries, :section => 'conditions'} %>
+    <%== render :partial => 'narrative_block', :locals => {:entries => entries, :section => 'conditions', :status => true } %>
     <% entries.each_with_index do |entry, i| -%>
     <entry typeCode="DRIV">
       <act classCode="ACT" moodCode="EVN">
@@ -40,7 +40,7 @@
             <effectiveTime>
               <low value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
             </effectiveTime>
-            <%== code_display(entry, 'value', 'xsi:type="CD"') %>
+            <%== code_display(entry, {'tag_name' => 'value', 'extra_content' => 'xsi:type="CD"', 'preferred_code_sets' => ['SNOMED-CT']}) %>
             <% if entry.status -%>
             <entryRelationship typeCode="REFR">
               <observation classCode="OBS" moodCode="EVN">

data/templates/_encounters.c32.erb

@@ -16,7 +16,8 @@
         <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.14" assigningAuthorityName="IHE PCC"/>
         <!-- Encounter activity template -->
         <id root="<%= UUID.generate %>"/>
-        <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'encounters'} %>
+        <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'encounters',
+                                                                   :preferred_code_sets => ['CPT']} %>
         <text>
           <reference value="#encounters-desc-<%= i %>"/>
         </text>

data/templates/_immunizations.c32.erb

@@ -29,7 +29,8 @@
                   <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.7.2"/>
                   <!-- Product template -->
                   <manufacturedMaterial>
-                    <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'immunizations'} %>
+                    <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'immunizations',
+                                                                               :preferred_code_sets => ['CVX']} %>
                     <name><%= entry.description %></name>
                   </manufacturedMaterial>
                 </manufacturedProduct>

data/templates/_medical_equipment.c32.erb

@@ -23,7 +23,7 @@
             <addr/>
             <telecom/>
             <playingDevice>
-              <%== code_display(entry) %>
+              <%== code_display(entry, {:preferred_code_sets => ['SNOMED-CT']}) %>
             </playingDevice>
           </participantRole>
         </participant>

data/templates/_medications.c32.erb

@@ -28,7 +28,8 @@
             <templateId root="2.16.840.1.113883.3.88.11.83.8.2"/>
             <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.7.2"/>
             <manufacturedMaterial>
-              <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'medications'} %>
+              <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'medications',
+                                                                         :preferred_code_sets => ['RxNorm']} %>
               <name><%= entry.description %></name>
             </manufacturedMaterial>
           </manufacturedProduct>

data/templates/_narrative_block.c32.erb

@@ -5,6 +5,13 @@
         <th>Description</th>
         <th>Codes</th>
         <th>Time</th>
+        <% if status.present? %>
+          <th>Status</th>
+        <% end %>
+        
+         <% if value.present? %>
+          <th>Value</th>
+        <% end %>
       </tr>
     </thead>
     <tbody>
@@ -13,6 +20,13 @@
           <td ID="<%= section %>-desc-<%= i %>"><%= entry.description %></td>
           <td ID="<%= section %>-code-<%= i %>"><%= entry.codes_to_s %></td>
           <td><%= entry.times_to_s %></td>
+           <% if status.present? %>
+            <td><%= entry.status %></td>
+           <% end %>
+           
+            <% if value.present? %>
+              <td><%= entry.value["scalar"] %></td>
+           <% end %>
         </tr>
       <%- end -%>
     </tbody>