health-data-standards 3.6.1 → 3.7.0

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

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

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

@@ -0,0 +1,2 @@
+class CareExperience < Entry
+end

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

@@ -0,0 +1,4 @@
+class CareGoal < Entry
+  field :relatedTo,     type: Hash, as: :related_to
+  field :targetOutcome, type: Hash, as: :target_outcome
+end

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

@@ -0,0 +1,3 @@
+class Communication < Entry
+  field :direction,           type: String
+end

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

@@ -1,14 +1,17 @@
 class Condition < Entry
-  field :type,          type: String
-  field :causeOfDeath,  type: Boolean
-  field :time_of_death, type: Integer
-  field :priority,      type: Integer
-  field :name,          type: String
-  field :ordinality,    type: Hash
-  field :severity,      type: Hash # Currently unsupported by any importers
+  field :type,              type: String
+  field :causeOfDeath,      type: Boolean
+  field :time_of_death,     type: Integer
+  field :priority,          type: Integer
+  field :name,              type: String
+  field :ordinality,        type: Hash
+  field :severity,          type: Hash
+  field :laterality,        type: Hash
+  field :anatomical_target, type: Hash
+  field :anatomical_location, type: Hash
 
   embeds_many :treating_provider,  class_name: "Provider"
-  
+
   alias   :cause_of_death         :causeOfDeath
   alias   :cause_of_death=        :causeOfDeath=
 
@@ -16,4 +19,4 @@ class Condition < Entry
     super
     self.time_of_death = self.time_of_death.nil? ? nil : self.time_of_death + date_diff
   end
-end
+end

data/lib/health-data-standards/models/cqm/bundle.rb

@@ -16,6 +16,7 @@ module HealthDataStandards
       field :measure_period_start
       field :records, type: Array
       field :active, type: Boolean
+      field :done_importing, type: Boolean, default: false
 
       validates_presence_of :version
 
@@ -47,4 +48,4 @@ module HealthDataStandards
       end
      end
   end
-end
+end

data/lib/health-data-standards/models/cqm/measure.rb

@@ -87,7 +87,8 @@ module HealthDataStandards
         pipeline << {'$project' => {'category' => '$_id', 'measures' => 1, '_id' => 0}}
 
         pipeline << {'$sort' => {"category" => 1}}
-        Mongoid.default_session.command(aggregate: 'measures', pipeline: pipeline)['result']
+        
+        Mongoid.default_client.command(aggregate: 'measures', pipeline: pipeline).documents[0]["result"]
       end
 
 

data/lib/health-data-standards/models/cqm/patient_cache.rb

@@ -24,10 +24,10 @@ module HealthDataStandards
         end
 
         group = {"$group" => {"_id" => "$value.medical_record_id", "rational" => {"$push"=> "$value.rationale"}}}
-        aggregate = self.mongo_session.command(:aggregate => 'patient_cache', :pipeline => [{"$match" =>match},group])
-
+        aggregate = self.mongo_client.command(:aggregate => 'patient_cache', :pipeline => [{"$match" =>match},group])
+        aggregate_document = aggregate.documents[0]
         merged = {}
-        aggregate["result"].each do |agg|
+        aggregate_document["result"].each do |agg|
           mrn = agg["_id"]
           rational = {}
           merged[mrn] = rational
@@ -48,15 +48,19 @@ module HealthDataStandards
 
       field :DENOM, type: Integer
       field :NUMER, type: Integer
+      field :NUMEX, type: Integer
       field :DENEX, type: Integer
       field :DENEXCEP, type: Integer
       field :MSRPOPL, type: Integer
+      field :MSRPOPLEX, type: Integer
       field :OBSERV
       field :antinumerator, type: Integer
       field :IPP, type: Integer
       field :measure_id, type: String
       field :sub_id, type: String
+      field :patient_id, type: BSON::ObjectId
     end
 
   end
+
 end

data/lib/health-data-standards/models/cqm/query_cache.rb

@@ -14,10 +14,12 @@ module HealthDataStandards
       field :IPP, type: Integer
       field :DENOM, type: Integer
       field :NUMER, type: Integer
+      field :NUMEX, type: Integer
       field :antinumerator, type: Integer
       field :DENEX, type: Integer
       field :DENEXCEP, type: Integer
       field :MSRPOPL, type: Integer
+      field :MSRPOPLEX, type: Integer
       field :OBSERV, type: Float
       field :supplemental_data, type: Hash
 

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

@@ -3,6 +3,9 @@ class Encounter < Entry
   field :dischargeDisposition, as: :discharge_disposition, type: Hash
   field :admitTime, as: :admit_time, type: Integer
   field :dischargeTime, as: :discharge_time, type: Integer
+
+  embeds_one :principalDiagnosis, class_name: "EncounterPrincipalDiagnosis"
+  embeds_one :diagnosis, class_name: "EncounterPrincipalDiagnosis"
   
   embeds_one :transferTo, class_name: "Transfer"
   embeds_one :transferFrom, class_name: "Transfer"
@@ -16,13 +19,23 @@ class Encounter < Entry
   alias :transfer_to= :transferTo=
   alias :transfer_from :transferFrom
   alias :transfer_from= :transferFrom=
+  alias :principal_diagnosis :principalDiagnosis
+  alias :principal_diagnosis= :principalDiagnosis=
 
   def shift_dates(date_diff)
     super
     if self.facility
       self.facility.shift_dates(date_diff)
     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

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

@@ -0,0 +1,36 @@
+class EncounterPrincipalDiagnosis
+  include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
+
+  embedded_in :encounter, class_name: "Encounter", inverse_of: nil
+  
+  def preferred_code(preferred_code_sets=nil, codes_attribute=nil, value_set_map=nil)
+    if @attributes.key?('code') and @attributes.key?('code_system')
+      # This encounter principal diagnosis has the standard 'code' and
+      # 'code_system' attributes, so only one code possible.
+      return {'code' => @attributes['code'], 'code_set' => @attributes['code_system']}
+    elsif @attributes.key?('codes')
+      # This encounter principal diagnosis has the special 'codes' attribute
+      # set, so return the first code in the first code set.
+      code_set, code_set_codes = @attributes['codes'].first
+      return {'code' => code_set_codes.first, 'code_set' => code_set}
+    end
+  end
+
+  def translation_codes(preferred_code_sets=nil ,value_set_map=nil)
+    tx_codes = []
+    # Translations are only necessary when the encounter principal diagnosis
+    # contains the special 'codes' attribute rather than the normal 'code' and
+    # 'code_system', as 'codes' supports multiple codes/code sets.
+    if @attributes.key?('codes')
+      @attributes['codes'].each do |code_set, code_set_codes|
+        for code in code_set_codes
+          tx_codes.push({'code' => code, 'code_set' => code_set})
+        end
+      end
+      tx_codes.shift
+    end
+    tx_codes
+  end
+
+end

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

@@ -10,6 +10,9 @@ class Entry
   embeds_one :cda_identifier, class_name: "CDAIdentifier", as: :cda_identifiable
   embeds_many :values, class_name: "ResultValue"
   embeds_many :references
+  embeds_many :provider_preference, class_name: "Entry"
+  embeds_many :patient_preference, class_name: "Entry"
+  
   field :description, type: String
   field :specifics, type: String
   field :time, type: Integer
@@ -21,6 +24,7 @@ class Entry
   field :negationReason, as: :negation_reason, type: Hash
   field :oid, type: String
   field :reason, type: Hash
+  field :health_record_field, type: Hash
   
   attr_protected :version
   attr_protected :_id
@@ -213,4 +217,4 @@ class Entry
     end
   end
 
-end
+end

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

@@ -0,0 +1,4 @@
+class FamilyHistory < Entry
+  field :relationshipToPatient, as: :relationship_to_patient, type: Hash
+  field :onsetAge, as: :onset_age, type: Hash
+end

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

@@ -1,5 +1,6 @@
 class Immunization < Entry
   field :seriesNumber, type: Integer
+  field :reaction, type: Hash
   
   belongs_to :performer, class_name: "Provider"
   

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

@@ -1,4 +1,13 @@
 class LabResult < Entry
   field :referenceRange, as: :reference_range, type: String
+  field :referenceRangeHigh, as: :reference_range_high, type: String
+  field :referenceRangeLow, as: :reference_range_low, type: String
   field :interpretation, type: Hash  
-end
+  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
+  
+end

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

@@ -3,7 +3,8 @@ class MedicalEquipment < Entry
   field :manufacturer, type: String
   field :anatomicalStructure, as: :anatomical_structure, type: Hash
   field :removalTime, as: :removal_time, type: Integer
-
+  field :anatomical_approach , type: Hash 
+  field :reaction, type: Hash 
    def shift_dates(date_diff)
    	super
     self.removalTime = self.removalTime.nil? ? nil : self.removalTime + date_diff

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

@@ -8,7 +8,7 @@ class Medication < Entry
   embeds_many :orderInformation, class_name: 'OrderInformation'
 
   field :route, type: Hash
-  field :site, type: Hash
+  field :anatomical_approach, type: Hash
   field :doseRestriction, as: :dose_restriction, type: Hash
   field :fulfillmentInstructions, as: :fulfillment_instructions, type: String
   field :indication, type: Hash
@@ -19,6 +19,23 @@ class Medication < Entry
   field :patientInstructions, as: :patient_instructions, type: String
   field :doseIndicator, as: :dose_indicator, type: String
 
+  field :method ,   type: Hash 
+  field :active_datetime ,  type: Integer
+  field :signed_datetime ,  type: Integer
+  
+  # This is used for Medicaton, Order. It is the total number of times a dose of a particular
+  # medication can be administered. This, coupled with the administrationTiming will
+  # give the cumulative medication duration.
+  # E.g.
+  #  allowedAdministrations = 90 doses
+  #  administrationTiming = 1 dose / 12 hours
+  #  cumulativeMedicationDuration = allowedAdministrations / administrationTiming * (time conversion)
+  #  cumulativeMedicationDuration = (90 doses) * (12 hours)/(1 dose) * (1 day)/(24 hours) = 45 days
+  # Medication, Order can't use fulfillmentHistory because the fulfillment of the 
+  # medication has not yet happened.
+  # This corresponds to 'repeatNumber' in the QRDA representation
+  field :allowedAdministrations, as: :allowed_administrations, type: Integer
+
   # There are currently no importers that support this field
   # It is expected to be a scalar and value, such as 7 days
   field :cumulativeMedicationDuration, as: :cumulative_medication_duration, type: Hash
@@ -38,4 +55,4 @@ class Medication < Entry
     end
   end
 
-end
+end

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

@@ -0,0 +1,5 @@
+class PatientPreference
+  include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
+
+end

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

@@ -1,13 +1,26 @@
 class Procedure < Entry
-  field :site,                type: Hash
+
   field :incisionTime,        type: Integer,      as: :incision_time 
   field :ordinality,          type: Hash
   field :source,              type: Hash
-  
+  field :anatomical_approach, type: Hash
+  field :anatomical_target,   type: Hash
+  field :method,              type: Hash
+  field :reaction,            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 :radiation_dose,      type: Hash 
+  field :radiation_duration,  type: Hash 
+
+  embeds_one :facility
+
   belongs_to :performer, class_name: "Provider"
 
   def shift_dates(date_diff)
   	super
   	self.incisionTime = self.incisionTime.nil? ? nil : self.incisionTime + date_diff
   end
-end
+end

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

@@ -2,9 +2,10 @@ class Provider
   include Personable
   include Mongoid::Tree
   include Mongoid::Attributes::Dynamic
-  
+
   NPI_OID = '2.16.840.1.113883.4.6'
   TAX_ID_OID = '2.16.840.1.113883.4.2'
+  CCN_OID = '2.16.840.1.113883.4.336'.freeze
 
   field :specialty   , type: String
   field :phone       , type: String
@@ -40,6 +41,21 @@ class Provider
     cda_id_tin ? cda_id_tin.extension : nil
   end
 
+  def ccn=(a_ccn)
+    cda_id_ccn = self.cda_identifiers.where(root: CCN_OID).first
+    if cda_id_ccn
+      cda_id_ccn.extension = a_ccn
+      cda_id_ccn.save!
+    else
+      self.cda_identifiers << CDAIdentifier.new(root: CCN_OID, extension: a_ccn)
+    end
+  end
+
+  def ccn
+    cda_id_ccn = self.cda_identifiers.where(root: CCN_OID).first
+    cda_id_ccn ? cda_id_ccn.extension : nil
+  end
+
   def records(effective_date=nil)
     Record.by_provider(self, effective_date)
   end

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

@@ -0,0 +1,5 @@
+class ProviderPreference
+  include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
+
+end

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

@@ -16,13 +16,11 @@ class Record
   field :ethnicity, type: Hash
   field :languages, type: Array, default: []
   field :test_id, type: BSON::ObjectId
+  field :bundle_id, type: BSON::ObjectId
   field :marital_status, type: Hash
   field :medical_record_number, type: String
   field :medical_record_assigner, type: String
   field :expired, type: Boolean
-  field :clinicalTrialParticipant, as: :clinical_trial_participant, type: Boolean   # Currently not implemented in the C32 importer
-                                                                                    # because it cannot be easily represented in a
-                                                                                    # HITSP C32
 
   index "last" => 1
   index medical_record_number: 1
@@ -32,12 +30,16 @@ class Record
   embeds_many :care_goals, class_name: "Entry" # This can be any number of different entry types
   embeds_many :conditions
   embeds_many :encounters
+  embeds_many :communications
+  embeds_many :family_history
   embeds_many :immunizations
   embeds_many :medical_equipment
   embeds_many :medications
   embeds_many :procedures
   embeds_many :results, class_name: "LabResult"
   embeds_many :socialhistories, class_name: "Entry"
+  embeds_many :care_experiences
+  embeds_many :assessments
 
   alias :social_history :socialhistories
   alias :social_history= :socialhistories=
@@ -49,8 +51,8 @@ class Record
   embeds_many :functional_statuses
 
   Sections = [:allergies, :care_goals, :conditions, :encounters, :immunizations, :medical_equipment,
-   :medications, :procedures, :results, :social_history, :vital_signs, :support, :advance_directives,
-   :insurance_providers, :functional_statuses]
+   :medications, :procedures, :results, :communications, :family_history, :social_history, :vital_signs, :support, :advance_directives,
+   :insurance_providers, :functional_statuses, :care_experiences, :assessments]
 
   embeds_many :provider_performances
   embeds_many :addresses, as: :locatable
@@ -98,9 +100,6 @@ class Record
 
   memoize :entries_for_oid
 
-  alias :clinical_trial_participant :clinicalTrialParticipant
-  alias :clinical_trial_participant= :clinicalTrialParticipant=
-
   # Remove duplicate entries from a section based on cda_identifier or id.
   # This method may lose information because it does not compare entries
   # based on clinical content
@@ -125,7 +124,7 @@ class Record
       else
         unique_entries[entry.identifier] = entry
       end
-      
+
     end
     self.send("#{section}=", unique_entries.values)
   end

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

@@ -20,4 +20,4 @@ class Reference
     end
     self.referenced_id = resolved_reference.id.to_s
   end
-end
+end

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

@@ -6,6 +6,7 @@ module HealthDataStandards
       field :display_name, type: String
       field :version, type: String
       field :user_id, type: String # Eventually we need to delete this from bundles when exporting
+      field :categories, type: Hash
 
       belongs_to :bundle, class_name: "HealthDataStandards::CQM::Bundle", inverse_of: :value_sets
 
@@ -37,20 +38,37 @@ module HealthDataStandards
 
       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")
+        vs_element = doc.at_xpath("/vs:RetrieveValueSetResponse/vs:ValueSet|/vs:RetrieveMultipleValueSetsResponse/vs:DescribedValueSet")
         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|
-            code_system_name = HealthDataStandards::Util::CodeSystemHelper::CODE_SYSTEMS[con["codeSystem"]] || con["codeSystemName"]
-            Concept.new(code: con["code"], 
-                        code_system_name: code_system_name,
-                        code_system_version: con["codeSystemVersion"],
-                        display_name: con["displayName"], code_system: con["codeSystem"])
-          end
-          vs.concepts = concepts
+          vs.concepts = extract_concepts(vs_element)
+          vs.categories = extract_categories(vs_element)
           return vs
         end
       end
+
+      def self.extract_concepts(vs_element)
+        concepts = vs_element.xpath("//vs:Concept").collect do |con|
+        code_system_name = HealthDataStandards::Util::CodeSystemHelper::CODE_SYSTEMS[con["codeSystem"]] || con["codeSystemName"]
+        Concept.new(code: con["code"], 
+                    code_system_name: code_system_name,
+                    code_system_version: con["codeSystemVersion"],
+                    display_name: con["displayName"], code_system: con["codeSystem"])
+        end
+      end
+
+      def self.extract_categories(vs_element)
+        category_hash = Hash.new {|h,k| h[k]=[]}
+        groups_with_categories = vs_element.xpath("//vs:Group/@ID[../@displayName='CATEGORY']")
+        groups_with_categories.each do |group_number|
+          measure = vs_element.xpath("//vs:Group[@displayName='CMS eMeasure ID' and @ID='#{group_number}']/vs:Keyword").text
+          categories_for_group = vs_element.xpath("//vs:Group[@displayName='CATEGORY' and @ID='#{group_number}']/vs:Keyword")
+          categories_for_group.each do |category|
+            category_hash[measure] << category.text
+          end
+        end
+        category_hash.size > 0 ? category_hash : nil
+      end
     end
   end
-end
+end