health-data-standards 3.7.0 → 4.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8ef5b18109b56fc92d3ed2097aee343760bf477c
-  data.tar.gz: '008f520093afb25e312ecbed501c3bfdf4cb2761'
+  metadata.gz: c4c0614b648a5d2d1326f343bf970d7df12483c3
+  data.tar.gz: f780aa9e0615261edf2dd984dd4a37d0acb6bed6
 SHA512:
-  metadata.gz: 3632559346961e5110f26aae8949d7a3d85cdeb937379e11850cbc40dcde4ec3d5bfc14f5aa010c1fd6f403d734efba052fd5bfafb4992001cdd0f30313b4c39
-  data.tar.gz: c211b9f4922b81411fbce83bf193c22a003a12561a86bef90b9c022c54531776f7ad3072e9aca165c4320a6f8c3a5f9887fc59ffa690fb5e029b46d2dc5ff155
+  metadata.gz: e0022c55d49a80f85bcf53f7b5bda28075ce2331ad16e7db89fc0eb2ef1a5ae67368ef3c98480292c10ad99d3500f72bbb52f7423f387b6c5fee3cf41433899e
+  data.tar.gz: 395455bb02a984b04f87c9ce24eab9c3c7c3929664045eed618566dd28204f21fb853e358503a16a52ba941558f585773bfa6caaf0f1a66e6922e318e3797262

data/lib/health-data-standards.rb

@@ -70,7 +70,9 @@ require_relative 'health-data-standards/models/telecom'
 require_relative 'health-data-standards/models/transfer'
 require_relative 'health-data-standards/models/svs/value_set'
 require_relative 'health-data-standards/models/svs/concept'
+require_relative 'health-data-standards/models/admission_source'
 require_relative 'health-data-standards/models/facility'
+require_relative 'health-data-standards/models/component'
 require_relative 'health-data-standards/models/metadata/base'
 require_relative 'health-data-standards/models/metadata/author'
 require_relative 'health-data-standards/models/metadata/change_info'
@@ -81,6 +83,7 @@ require_relative 'health-data-standards/models/patient_preference'
 require_relative 'health-data-standards/models/care_goal'
 require_relative 'health-data-standards/models/encounter_principal_diagnosis'
 require_relative 'health-data-standards/models/assessment'
+require_relative 'health-data-standards/models/adverse_event'
 
 require_relative 'health-data-standards/models/qrda/id'
 require_relative 'health-data-standards/models/qrda/device'

data/lib/health-data-standards/export/helper/html_view_helper.rb

@@ -6,9 +6,9 @@ module HealthDataStandards
 
         def decode_hqmf_section(section, oid)
           if oid
-	    definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)
-	    definition ||= HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid, 'r2')
-	    definition['definition'].pluralize.to_sym
+            definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)
+            definition ||= HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid, 'r2')
+            definition['definition'].pluralize.to_sym
           else
             section
           end
@@ -16,9 +16,9 @@ module HealthDataStandards
 
         def decode_hqmf_status(status, oid)
           if oid
-	    definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)
-	    definition ||= HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid, 'r2')
-	    definition['status']
+            definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)
+            definition ||= HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid, 'r2')
+            definition['status']
           else
             status
           end
@@ -26,14 +26,14 @@ module HealthDataStandards
 
         def decode_hqmf_description(description, oid)
           if oid
-	    definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)
-	    definition ||= HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid, 'r2')
-	    definition_text = definition['definition']
-	    status_text = definition['status']
+            definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)
+            definition ||= HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid, 'r2')
+            definition_text = definition['definition']
+            status_text = definition['status']
             unless status.blank?
-	      "#{definition_text.titleize}, #{status_text.titleize}".to_sym
+              "#{definition_text.titleize}, #{status_text.titleize}".to_sym
             else
-	      "#{definition_text.titleize}".to_sym
+              "#{definition_text.titleize}".to_sym
             end
           else
             description

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

@@ -7,7 +7,7 @@ module HealthDataStandards
         failed_dir ||= File.join(source_dir, '../', 'failed_imports')
         files = Dir.glob(File.join(source_dir, '*.*'))
         files.each do |file|
-	   self.import_file(file,File.new(file).read,failed_dir)
+          self.import_file(file,File.new(file).read,failed_dir)
         end
       end
 
@@ -27,7 +27,7 @@ module HealthDataStandards
             end
             next if entry.directory?
             data = zipfile.read(entry.name)
-	          status = self.import_file(entry.name,data,failed_dir)
+            status = self.import_file(entry.name,data,failed_dir)
             raise StandardError, status[:message] if status.is_a?(Hash) && status[:status] === 'error'
           end
         end
@@ -61,9 +61,9 @@ module HealthDataStandards
         begin
           ext = File.extname(name)
           if ext == ".json"
-	    self.import_json(data)
+            self.import_json(data)
           else
-	    self.import(data)
+            self.import(data)
           end
         rescue
           FileUtils.mkdir_p(File.dirname(File.join(failed_dir,name)))

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

@@ -42,7 +42,7 @@ module HealthDataStandards
             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
+            encounter.facility = facility.as_json()
           end
         end
     
@@ -88,4 +88,4 @@ module HealthDataStandards
       end
     end
   end
-end
+end

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

@@ -0,0 +1,11 @@
+class AdmissionSource
+  include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
+  
+  embedded_in :encounter, class_name: "Encounter", inverse_of: nil
+  
+  field :code, type: String
+  field :code_system, type: String
+  field :title, type: String
+  
+end

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

@@ -0,0 +1,6 @@
+# QDM 5.0 addition
+class AdverseEvent < Entry
+  field :type, type: Hash
+  field :severity, type: Hash
+  field :facility, type: Hash
+end

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

@@ -1,5 +1,6 @@
+# This is used for QDM 5.0 Allergy/Intollerance. The only fields used are type and severity.
 class Allergy < Entry
   field :type, type: Hash
   field :reaction, type: Hash
   field :severity, type: Hash
-end
+end

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

@@ -1,3 +1,4 @@
 class Assessment < Entry
   field :method,              type: Hash
+  field :components,          type: Hash
 end

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

@@ -1,4 +1,3 @@
 class CareGoal < Entry
-  field :relatedTo,     type: Hash, as: :related_to
   field :targetOutcome, type: Hash, as: :target_outcome
 end

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

@@ -0,0 +1,14 @@
+class Component
+  include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
+  
+  field :type, type: String
+  field :code, type: Hash    # Hash of HQMF::Coded
+  field :result, type: Hash  # Hash of HQMF::Value
+  
+end
+
+class ResultComponent < Component
+  field :range, type: Hash # Hash of HQMF::Range 
+
+end

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

@@ -3,14 +3,15 @@ class Encounter < Entry
   field :dischargeDisposition, as: :discharge_disposition, type: Hash
   field :admitTime, as: :admit_time, type: Integer
   field :dischargeTime, as: :discharge_time, type: Integer
+  field :diagnosis, type: Hash # This is a Hash to align with the 'Collection' object
+  field :facility, type: Hash
 
   embeds_one :principalDiagnosis, class_name: "EncounterPrincipalDiagnosis"
-  embeds_one :diagnosis, class_name: "EncounterPrincipalDiagnosis"
   
   embeds_one :transferTo, class_name: "Transfer"
   embeds_one :transferFrom, class_name: "Transfer"
 
-  embeds_one :facility
+  embeds_one :admission_source, class_name: "AdmissionSource"
   embeds_one :reason, class_name: "Entry"
 
   belongs_to :performer, class_name: "Provider"
@@ -21,23 +22,19 @@ class Encounter < Entry
   alias :transfer_from= :transferFrom=
   alias :principal_diagnosis :principalDiagnosis
   alias :principal_diagnosis= :principalDiagnosis=
+  alias :admissionSource :admission_source
+  alias :admissionSource= :admission_source=
 
   def shift_dates(date_diff)
     super
     if self.facility
-      self.facility.shift_dates(date_diff)
+      # Facility is now stored as a Hash; shift its dates by updating its start_time and end_time values.
+      self.facility['start_time'] += date_diff if self.facility['start_time']
+      self.facility['end_time'] += date_diff if self.facility['end_time']
     end
-
-    if self.transferTo
-      self.transferTo.shift_dates(date_diff)
-    end
-
-    if self.transferFrom
-      self.transferFrom.shift_dates(date_diff)
-    end
-
+    
     self.admitTime = (self.admitTime.nil?) ? nil : self.admitTime + date_diff
     self.dischargeTime = (self.dischargeTime.nil?) ? nil : self.dischargeTime + date_diff
   end
 
-end
+end

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

@@ -25,7 +25,7 @@ class Entry
   field :oid, type: String
   field :reason, type: Hash
   field :health_record_field, type: Hash
-  
+    
   attr_protected :version
   attr_protected :_id
   attr_protected :created_at

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

@@ -11,8 +11,9 @@ class Facility
   embeds_many :addresses, as: :locatable
   embeds_many :telecoms, as: :contactable
 
-   def shift_dates(date_diff)
+  def shift_dates(date_diff)
     self.start_time = (self.start_time.nil?) ? nil : self.start_time + date_diff
     self.end_time = (self.end_time.nil?) ? nil : self.end_time + date_diff
   end
-end
+
+end

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

@@ -1,13 +1,19 @@
 class LabResult < Entry
+  # NOT used for QDM 5.0 referenceRange
   field :referenceRange, as: :reference_range, type: String
+  # used for QDM 5.0 referenceRange
   field :referenceRangeHigh, as: :reference_range_high, type: String
+  # used for QDM 5.0 referenceRange
   field :referenceRangeLow, as: :reference_range_low, type: String
-  field :interpretation, type: Hash  
-  field :reaction,   type: Hash
-  field :method,  type: Hash
+  field :interpretation,      type: Hash  
+  field :reaction,            type: Hash
+  field :method,              type: Hash
   # The resulting status of a procedure as defined in the QDM documentation. This is different
   # than the status associated with the `Entry` object, which relates to the data criteria
   # status as defined in health-data-standards/lib/hqmf-model/data_criteria.json.
-  field :qdm_status, type: Hash
+  field :qdm_status,          type: Hash
+  field :components,          type: Hash
   
+  # QDM 5.0 addition to Laboratory Test, Performed
+  field :result_date_time,    type: Integer
 end

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

@@ -1,7 +1,10 @@
 class Medication < Entry
   field :administrationTiming, as: :administration_timing, type: Hash
   field :freeTextSig, type: String
+  # QDM 5.0 disambiguates dose to be dosage and suppy. 'dose' here represents the QDM 5.0 'dosage'.
+  # Bonnie displays this as 'dosage'.
   field :dose, type: Hash
+  field :supply, type: Hash
   field :typeOfMedication, as: :type_of_medication, type: Hash
   field :statusOfMedication, as: :status_of_medication, type: Hash
   embeds_many :fulfillmentHistory, class_name: 'FulfillmentHistory'

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

@@ -13,9 +13,14 @@ class Procedure < Entry
   field :qdm_status,          type: Hash
 
   field :radiation_dose,      type: Hash 
-  field :radiation_duration,  type: Hash 
+  field :radiation_duration,  type: Hash
 
-  embeds_one :facility
+  # QDM 5.0 addition to Diagnostic Study, Performed
+  field :result_date_time,    type: Integer
+  # Component attribute is for Diagnostic, Performed which is classified as a procedure
+  field :components,          type: Hash
+ 
+  field :facility, type: Hash
 
   belongs_to :performer, class_name: "Provider"
 

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

@@ -26,7 +26,7 @@ class Record
   index medical_record_number: 1
   index test_id: 1
   index bundle_id: 1
-  embeds_many :allergies
+  embeds_many :allergies # used for QDM 5.0 allergy/intollerance
   embeds_many :care_goals, class_name: "Entry" # This can be any number of different entry types
   embeds_many :conditions
   embeds_many :encounters
@@ -40,6 +40,10 @@ class Record
   embeds_many :socialhistories, class_name: "Entry"
   embeds_many :care_experiences
   embeds_many :assessments
+  # TODO: (LDY 9/29/16) Will the below work? These are not defined in the JSON in the HQMF stuff because we're not parsing HQMF.
+  # also, allergy_intolerance would translate to allergies_intolerances. If this is done automatically, it won't be done correclty.
+  # Does it make sense to do a `class_name` thing like above?
+  embeds_many :adverse_events
 
   alias :social_history :socialhistories
   alias :social_history= :socialhistories=
@@ -52,7 +56,7 @@ class Record
 
   Sections = [:allergies, :care_goals, :conditions, :encounters, :immunizations, :medical_equipment,
    :medications, :procedures, :results, :communications, :family_history, :social_history, :vital_signs, :support, :advance_directives,
-   :insurance_providers, :functional_statuses, :care_experiences, :assessments]
+   :insurance_providers, :functional_statuses, :care_experiences, :assessments, :adverse_events]
 
   embeds_many :provider_performances
   embeds_many :addresses, as: :locatable

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

@@ -6,9 +6,4 @@ class Transfer
   field :time, type: Integer 
 
   embedded_in :encounter, class_name: "Encounter", inverse_of: nil
-
-  def shift_dates(date_diff)
-    self.time = (self.time.nil?) ? nil : self.time + date_diff
-  end
-
 end

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

@@ -11,7 +11,8 @@ module HealthDataStandards
         if @id_map.blank?
           @id_map = {
             'r1' => JSON.parse(File.read(File.expand_path('../hqmf_template_oid_map.json', __FILE__))),
-            'r2' => JSON.parse(File.read(File.expand_path('../hqmfr2_template_oid_map.json', __FILE__)))
+            'r2' => JSON.parse(File.read(File.expand_path('../hqmfr2_template_oid_map.json', __FILE__))),
+            'r2cql' => JSON.parse(File.read(File.expand_path('../hqmfr2cql_template_oid_map.json', __FILE__)))
           }
         end
         @id_map[version]
@@ -23,7 +24,7 @@ module HealthDataStandards
           kv_pair = template_id_map(version).find {|k, v| v['definition'] == definition &&
                                                  v['status'] == status &&
                                                  v['negation'] == negation}
-        when "r2"
+        when "r2", "r2cql"
           kv_pair = template_id_map(version).find {|k, v| v['definition'] == definition &&
                                                  v['status'] == status}
         end

data/lib/health-data-standards/util/hqmfr2_template_oid_map.json

@@ -378,5 +378,13 @@
   "2.16.840.1.113883.10.20.28.3.118":{
     "definition":"assessment",
     "status":"recommended",
+    "negation":false},
+  "2.16.840.1.113883.10.20.28.3.120": {
+    "definition":"adverse_event",
+    "status":"",
+    "negation":false},
+  "2.16.840.1.113883.10.20.28.3.119": {
+    "definition":"allergy_intolerance",
+    "status":"",
     "negation":false}
 }

data/lib/health-data-standards/util/hqmfr2cql_template_oid_map.json

@@ -0,0 +1,390 @@
+{
+  "2.16.840.1.113883.10.20.28.4.53":{
+      "definition":"patient_characteristic",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.54":{
+      "definition":"patient_characteristic_birthdate",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.6":{
+      "definition":"patient_characteristic",
+      "status":"clinical_trial_participant",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.55":{
+      "definition":"patient_characteristic_gender",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.56":{
+      "definition":"patient_characteristic_ethnicity",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.57":{
+      "definition":"patient_characteristic_expired",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.58":{
+      "definition":"patient_characteristic_payer",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.59":{
+      "definition":"patient_characteristic_race",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.4":{
+      "definition":"encounter",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.26":{
+      "definition":"encounter",
+      "status":"active",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.5":{
+      "definition":"encounter",
+      "status":"performed",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.27":{
+      "definition":"encounter",
+      "status":"ordered",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.28":{
+      "definition":"encounter",
+      "status":"recommended",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.67":{
+      "definition":"procedure",
+      "status":"performed",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.66":{
+      "definition":"procedure",
+      "status":"ordered",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.69":{
+      "definition":"procedure_result",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.64":{
+      "definition":"procedure_adverse_event",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.65":{
+      "definition":"procedure_intolerance",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.68":{
+      "definition":"procedure",
+      "status":"recommended",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.1":{
+      "definition":"diagnosis",
+      "status":"active",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.19":{
+      "definition":"diagnosis",
+      "status":"resolved",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.17":{
+      "definition":"diagnosis",
+      "status":"family_history",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.18":{
+      "definition":"diagnosis",
+      "status":"inactive",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.110":{
+      "definition":"diagnosis",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.111":{
+      "definition":"family_history",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.23":{
+      "definition":"diagnostic_study",
+      "status":"performed",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.25":{
+      "definition":"diagnostic_study_result",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.20":{
+      "definition":"diagnostic_study_adverse_event",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.21":{
+      "definition":"diagnostic_study_intolerance",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.22":{
+      "definition":"diagnostic_study",
+      "status":"ordered",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.23":{
+      "definition":"diagnostic_study",
+      "status":"performed",
+      "negation":true},
+  "2.16.840.1.113883.10.20.28.4.24":{
+      "definition":"diagnostic_study",
+      "status":"recommended",
+      "negation":true},
+  "2.16.840.1.113883.10.20.28.4.49":{
+      "definition":"medication",
+      "status":"dispensed",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.51":{
+      "definition":"medication",
+      "status":"ordered",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.48":{
+      "definition":"medication",
+      "status":"discharge",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.44":{
+      "definition":"medication",
+      "status":"active",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.45":{
+      "definition":"medication",
+      "status":"administered",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.46":{
+      "definition":"medication_adverse_effects",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.47":{
+      "definition":"medication_allergy",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.10.20.28.4.50":{
+      "definition":"medication_intolerance",
+      "status":"",
+      "negation":false},
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