health-data-standards 0.7.1 → 0.8.0

data/lib/health-data-standards/import/provider_import_utils.rb

@@ -0,0 +1,23 @@
+module ProviderImportUtils
+  
+  def extract_provider(performer)
+    provider_data = extract_provider_data(performer, false)
+    find_or_create_provider(provider_data)
+  end
+  
+  def find_or_create_provider(provider_hash)
+    provider = Provider.first(conditions: {npi: provider_hash[:npi]}) if provider_hash[:npi] && !provider_hash[:npi].empty?
+    provider ||= Provider.create(provider_hash)
+  end
+
+  # Returns nil if result is an empty string, block allows text munging of result if there is one
+  def extract_data(subject, query)
+    result = subject.at_xpath(query)
+    if result.nil? || result.content.empty?
+      nil
+    else
+      result.content
+    end
+  end
+  
+end

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

@@ -0,0 +1,11 @@
+class Address
+  include Mongoid::Document
+  
+  field :street, type: Array
+  field :city, type: String
+  field :state, type: String
+  field :zip, type: String
+  field :country, type: String
+  
+  embedded_in :locatable, polymorphic: true
+end

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

@@ -1,4 +1,5 @@
 class Allergy < Entry
+  field :type, type: String
   field :reaction, type: Hash
   field :severity, type: Hash
 end

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

@@ -3,7 +3,7 @@ class Condition < Entry
   field :causeOfDeath,  type: Boolean
   field :name,          type: String
   
-  # embeds_many :treating_provider,  class_name: "Provider"
+  embeds_many :treating_provider,  class_name: "Provider"
   
   alias   :cause_of_death         :causeOfDeath
   alias   :cause_of_death=        :causeOfDeath=

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

@@ -1,12 +1,17 @@
 class Encounter < Entry
-  field :performer, type: Hash
-  field :facility, type: Hash
   field :admitType, type: Hash
-  field :dischargeDisp, type: Hash
-  embeds_one :reason, class_name: "Entry"
+  field :dischargeDisposition, type: Hash
+  field :free_text, type: String
   
+  embeds_one :facility, class_name: "Organization"
+  embeds_one :reason, class_name: "Entry"
+
+  belongs_to :performer, class_name: "Provider"
+
   alias :admit_type :admitType
   alias :admit_type= :admitType=
-  alias :discharge_disp :dischargeDisp
-  alias :discharge_disp= :dischargeDisp=
+  alias :discharge_disposition :dischargeDisposition
+  alias :discharge_disposition= :dischargeDisposition=
+  alias :freeText :free_text
+  alias :freeText= :free_text=
 end

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

@@ -2,9 +2,12 @@ class Entry
 
   include Mongoid::Document
 
-  embedded_in :entry_list, polymorphic: true
-
+  # embedded_in :entry_list, polymorphic: true
+  
+  embedded_in :record
+  
   field :description, type: String
+  field :specifics, type: String
   field :time, type: Integer
   field :start_time, type: Integer
   field :end_time, type: Integer
@@ -27,11 +30,12 @@ class Entry
   
   # 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
+  def preferred_code(preferred_code_sets, codes_attribute=:codes)
+    codes_value = send(codes_attribute)
+    matching_code_sets = preferred_code_sets & codes_value.keys
     if matching_code_sets.present?
       code_set = matching_code_sets.first
-      {'code' => codes[code_set].first, 'code_set' => code_set}
+      {'code' => codes_value[code_set].first, 'code_set' => code_set}
     else
       nil
     end
@@ -92,6 +96,9 @@ class Entry
     if event['description']
       entry.description = event['description']
     end
+    if event['specifics']
+      entry.specifics = event['specifics']
+    end
     if event['status']
       entry.status = event['status']
     end
@@ -195,6 +202,10 @@ class Entry
     if description
       entry_hash['description'] = description
     end
+
+    if specifics
+      entry_hash['specifics'] = specifics
+    end
     
     entry_hash
   end

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

@@ -2,17 +2,15 @@ class FulfillmentHistory
   include Mongoid::Document
   
   field :prescriptionNumber, type: String
-  field :provider, type: Hash
-  field :dispensingPharmacyLocation, type: Hash
   field :dispenseDate, type: Integer
   field :quantityDispensed, type: Hash
   field :fillNumber, type: Integer
-  field :fillStatus, type: Hash
+  field :fillStatus, type: String
   
+  belongs_to :provider, class_name: "Provider"
+
   alias :prescription_number :prescriptionNumber
   alias :prescription_number= :prescriptionNumber=
-  alias :dispensing_pharmacy_location :dispensingPharmacyLocation
-  alias :dispensing_pharmacy_location= :dispensingPharmacyLocation=
   alias :dispense_date :dispenseDate
   alias :dispense_date= :dispenseDate=
   alias :quantity_dispensed :quantityDispensed

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

@@ -1,10 +1,16 @@
 class Immunization < Entry
   field :refusalInd, type: Boolean
-  field :performer, type: Hash
   field :refusalReason, type: Hash
+  field :seriesNumber, type: Integer
+  
+  belongs_to :performer, class_name: "Provider"
+  
+  embeds_one :medication_product
   
   alias :refusal_ind :refusalInd
   alias :refusal_ind= :refusalInd=
   alias :refusal_reason :refusalReason
   alias :refusal_reason= :refusalReason=
+  alias :series_number :seriesNumber
+  alias :series_number= :seriesNumber=
 end

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

@@ -2,11 +2,11 @@ class Medication < Entry
   field :administrationTiming, type: Hash
   field :freeTextSig, type: String
   field :dose, type: Hash
-  field :brandName, type: String
   field :typeOfMedication, type: Hash
   field :statusOfMedication, type: Hash
   embeds_many :fulfillmentHistory, class_name: 'FulfillmentHistory'
   embeds_many :orderInformation, class_name: 'OrderInformation'
+
   field :route, type: Hash
   field :site, type: Hash
   field :doseRestriction, type: Hash
@@ -17,13 +17,12 @@ class Medication < Entry
   field :reaction, type: Hash
   field :deliveryMethod, type: Hash
   field :patientInstructions, type: String
+  field :doseIndicator, type: String
   
   alias :administration_timing :administrationTiming
   alias :administration_timing= :administrationTiming=
   alias :free_text_sig :freeTextSig
   alias :free_text_sig= :freeTextSig=
-  alias :brand_name :brandName
-  alias :brand_name= :brandName=
   alias :type_of_medication :typeOfMedication
   alias :type_of_medication= :typeOfMedication=
   alias :status_of_medication :statusOfMedication
@@ -42,4 +41,6 @@ class Medication < Entry
   alias :delivery_method= :deliveryMethod=
   alias :patient_instructions :patientInstructions
   alias :patient_instructions= :patientInstructions=
+  alias :dose_indicator :doseIndicator
+  alias :dose_indicator= :doseIndicator=
 end

data/lib/health-data-standards/models/metadata/author.rb

@@ -0,0 +1,16 @@
+module Metadata
+  class Author
+    include Mongoid::Document
+    
+    embedded_in :pedigree, class_name: "Metadata::Pedigree"
+    
+    Types = %w(authenticator authorcustodiandataEnterer informant 
+    legalAuthenticator participant performer recordTarget)
+    
+    field :name, type: String
+    field :type, type: String
+    field :role, type: String
+    
+    validates_inclusion_of :type, in: Types, allow_nil: true
+  end
+end

data/lib/health-data-standards/models/metadata/base.rb

@@ -0,0 +1,20 @@
+# Represents the metadata associated with a hData section
+module Metadata
+  NS = 'http://www.hl7.org/schemas/hdata/2009/11/metadata'
+
+  class Base
+    include Mongoid::Document
+ 
+    field :mime_types, type: Array
+    field :confidentiality, type: String
+    field :original_creation_time, type: Time
+    
+    embedded_in :entry
+    
+    embeds_many :pedigrees, class_name: "Metadata::Pedigree"
+    embeds_many :modified_dates, class_name: "Metadata::ChangeInfo"
+    embeds_many :copied_dates, class_name: "Metadata::ChangeInfo"
+    embeds_many :linked_documents, class_name: "Metadata::LinkInfo"
+
+  end
+end

data/lib/health-data-standards/models/metadata/change_info.rb

@@ -0,0 +1,9 @@
+module Metadata
+  class ChangeInfo
+    include Mongoid::Document
+    
+    embeds_one :pedigree, class_name: "Metadata::Pedigree"
+    
+    field :timestamp, type: Time
+  end
+end

data/lib/health-data-standards/models/metadata/link_info.rb

@@ -0,0 +1,9 @@
+module Metadata
+  class LinkInfo
+    include Mongoid::Document
+
+    field :href, type: String
+    field :extension, type: String
+
+  end
+end

data/lib/health-data-standards/models/metadata/pedigree.rb

@@ -0,0 +1,15 @@
+module Metadata
+  class Pedigree
+    include Mongoid::Document
+
+    field :organization, type: String
+    field :signature, type: String
+    field :document_method, type: String
+    field :derived, type: Boolean
+    
+    embeds_one :author, class_name: "Metadata::Author"
+    embeds_many  :source_pedigrees, class_name: "Metadata::Pedigree"
+    embeds_many  :source_documents, class_name: "Metadata::LinkInfo"
+    
+  end
+end

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

@@ -0,0 +1,8 @@
+class Organization
+  include Mongoid::Document
+  
+  field :name, type: String
+  
+  embeds_many :addresses, as: :locatable
+  embeds_many :telecoms, as: :contactable
+end

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

@@ -1,4 +1,7 @@
 class Procedure < Entry
-  field :performer, type: Hash
-  field :site, type: Hash
+  field :type,          type: String
+  field :site,          type: Hash
+  field :description,   type: String
+  
+  belongs_to :performer, class_name: "Provider"
 end

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

@@ -12,7 +12,11 @@ class Provider
   
   validates_uniqueness_of :npi, allow_blank: true
   
-  
+  embeds_many :addresses, as: :locatable
+  embeds_many :telecoms, as: :contactable
+  embeds_one :organization
+
+
   def records(effective_date=nil)
     Record.by_provider(self, effective_date)
   end
@@ -21,6 +25,7 @@ class Provider
   # checksum using the Luhn algorithm with additional special handling as described in
   # https://www.cms.gov/NationalProvIdentStand/Downloads/NPIcheckdigit.pdf 
   def self.valid_npi?(npi)
+    return false unless npi
     return false if npi.length != 10 and npi.length != 15
     return false if npi.gsub(/\d/, '').length > 0 # npi must be all digits
     return false if npi.length == 15 and (npi =~ /^80840/)==nil # 15 digit npi must start with 80840

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

@@ -15,15 +15,15 @@ class Record
 
   embeds_many :allergies
   embeds_many :care_goals, class_name: "Entry"
-  embeds_many :conditions, class_name: "Entry"
+  embeds_many :conditions
   embeds_many :encounters
   embeds_many :immunizations
   embeds_many :medical_equipment, class_name: "Entry"
   embeds_many :medications
   embeds_many :procedures
   embeds_many :results, class_name: "LabResult"
-  embeds_many :social_history, class_name: "Entry"
-  embeds_many :vital_signs, class_name: "Entry"
+  embeds_many :social_history
+  embeds_many :vital_signs
 
   Sections = [:allergies, :care_goals, :conditions, :encounters, :immunizations, :medical_equipment,
    :medications, :procedures, :results, :social_history, :vital_signs]
@@ -40,4 +40,14 @@ class Record
   def over_18?
     Time.at(birthdate) < Time.now.years_ago(18)
   end
+  
+  private 
+  
+  def self.provider_queries(provider_id, effective_date)
+   {'$or' => [provider_query(provider_id, effective_date,effective_date), provider_query(provider_id, nil,effective_date), provider_query(provider_id, effective_date,nil)]}
+  end
+  def self.provider_query(provider_id, start_before, end_after)
+    {'provider_performances' => {'$elemMatch' => {'provider_id' => provider_id, '$and'=>[{'$or'=>[{'start_date'=>nil},{'start_date'=>{'$lt'=>start_before}}]}, {'$or'=>[{'end_date'=>nil},{'end_date'=> {'$gt'=>end_after}}]}] } }}
+  end
+  
 end

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

@@ -0,0 +1,3 @@
+class SocialHistory < Entry
+  field :type, type: Hash
+end

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

@@ -0,0 +1,9 @@
+class Telecom
+  include Mongoid::Document
+  
+  field :use, type: String
+  field :value, type: String
+  field :preferred, type: Boolean
+  
+  embedded_in :contactable, polymorphic: true
+end

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

@@ -0,0 +1,2 @@
+class VitalSign < LabResult
+end

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

@@ -13,7 +13,9 @@ module HealthDataStandards
         '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'
+        '2.16.840.1.113883.5.83' => 'HITSP C80 Observation Status',
+        "2.16.840.1.113883.3.26.1.1" => "NCI Thesaurus",
+        "2.16.840.1.113883.3.88.12.80.20" => "FDA"
       }
       
       # Returns the name of a code system given an oid

data/templates/_address.gc32.erb

@@ -0,0 +1,9 @@
+<% tag_name ||= "address"%>
+<<%=tag_name%>>
+  <% address.street.each do |street| %>
+    <streetAddressLine><%= street %></streetAddressLine>
+  <% end %>
+  <city><%= address.city %></city>
+  <state><%= address.state %></state>
+  <postalCode><%= address.zip %></postalCode>
+</<%=tag_name%>>

data/templates/_allergies.c32.erb

@@ -20,7 +20,7 @@
         <code nullFlavor="NA"/>
         <statusCode code="active"/>
         <effectiveTime>
-          <low value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+          <low <%= value_or_null_flavor(entry.as_point_in_time) %>/>
         </effectiveTime>
         <entryRelationship typeCode="SUBJ" inversionInd="false">
           <observation classCode="OBS" moodCode="EVN">
@@ -37,7 +37,7 @@
             </text>
             <statusCode code="completed"/>
             <effectiveTime>
-              <low value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+              <low <%= value_or_null_flavor(entry.as_point_in_time) %>/>
             </effectiveTime>
             <value xsi:type="CD" nullFlavor="UNK"/>
             <participant typeCode="CSM">

data/templates/_allergy.gc32.erb

@@ -0,0 +1,13 @@
+<allergy xmlns="urn:hl7-org:greencda:c32">
+  <id><%= allergy.id%></id>
+  <status><%= allergy.status%></status>
+  <%== code_display allergy, "tag_name" => "code", 'preferred_code_sets' => ['SNOMED-CT', "RxNorm", "FDA"] %>
+  <type><%= allergy.type%></type>
+  <effectiveTime>
+    <start><%= time_if_not_nil(allergy.start_time, allergy.time) %></start>
+    <end><%= time_if_not_nil(allergy.end_time) %></end>
+  </effectiveTime>
+  <%== code_display allergy, "tag_name" => "reaction", 'preferred_code_sets' => ['SNOMED-CT'] %>
+  <%== code_display allergy, "tag_name" => "severity", 'preferred_code_sets' => ['SNOMED-CT'] %>
+</allergy>
+

data/templates/_care_goals.c32.erb

@@ -17,7 +17,7 @@
         <id root="<%= UUID.generate %>"/>
         <%== code_display(entry, :preferred_code_sets => ['SNOMED-CT']) %>
         <statusCode code="new"/>
-        <effectiveTime value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+        <effectiveTime <%= value_or_null_flavor(entry.as_point_in_time) %>/>
       </observation>
     </entry>
     <% end -%>