health-data-standards 3.3.0 → 3.4.0

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

@@ -13,6 +13,7 @@ module HealthDataStandards
           extract_interpretation(entry_element, result)
           extract_reference_range(entry_element, result)
           extract_negation(entry_element, result)
+          extract_reason_description(entry_element, result, nrh)
           result
         end
     

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

@@ -47,13 +47,10 @@ module HealthDataStandards
           if @value_xpath
             extract_value(entry_element, entry)
           end
-          entry.free_text = entry_element.at_xpath("./cda:text").try("text")
+          entry.description = entry_element.at_xpath("./cda:text").try("text")
           if @status_xpath
             extract_status(entry_element, entry)
           end
-          if @description_xpath
-            extract_description(entry_element, entry, nrh)
-          end
           entry
         end
 
@@ -76,7 +73,7 @@ module HealthDataStandards
           end
         end
 
-        def extract_description(parent_element, entry, nrh)
+        def extract_reason_description(parent_element, entry, nrh)
           code_elements = parent_element.xpath(@description_xpath)
           code_elements.each do |code_element|
             tag = code_element['value']

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

@@ -17,7 +17,6 @@ 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_free_text(encounter_element, encounter)
           
           facility_element = encounter_element.at_xpath("./gc32:facility")
           if facility_element

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

@@ -22,7 +22,6 @@ module HealthDataStandards
           extract_med_code_attribute(med_element, medication, :vehicle)
           extract_med_code_attribute(med_element, medication, :reaction)
           extract_med_code_attribute(med_element, medication, :deliveryMethod)
-          extract_free_text(med_element, medication, "freeTextSig")
           medication.fulfillment_instructions = extract_node_text(med_element.at_xpath("./gc32:patientInstructions"))
           medication.dose_indicator = extract_node_text(med_element.at_xpath("./gc32:doseIndicator"))
           medication.fulfillment_history = extract_fulfillment_history(med_element)

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

@@ -105,7 +105,7 @@ module HealthDataStandards
           extract_status(element, entry)
           extract_value(element, entry)
           extract_effective_time(element, entry)
-          entry.free_text = element.at_xpath("./gc32:freeText").try(:inner_text)
+          entry.description = element.at_xpath("./gc32:freeText").try(:inner_text)
           entry
         end
         
@@ -159,10 +159,6 @@ module HealthDataStandards
           telecom.preferred = extract_node_attribute(telecom_element, :preferred)
           telecom
         end
-        
-        def extract_free_text(element, entry, free_text_element="freeText")
-          entry.free_text = extract_node_text(element.at_xpath("./gc32:#{free_text_element}"))
-        end
                 
         private
         

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

@@ -7,7 +7,21 @@ module ProviderImportUtils
   
   def find_or_create_provider(provider_hash)
     provider = Provider.where(npi: provider_hash[:npi]).first if provider_hash[:npi] && !provider_hash[:npi].empty?
-    provider ||= Provider.create(provider_hash)
+    unless provider
+      if provider_hash[:npi]
+        provider = Provider.create(provider_hash)
+      else
+        provider ||= Provider.resolve_provider(provider_hash) if Provider.respond_to? :resolve_provider
+        
+        provider_query = {:title => provider_hash[:title],            
+                            :given_name => provider_hash[:given_name],  
+                            :family_name=> provider_hash[:family_name],
+                            :specialty => provider_hash[:specialty]}
+        provider ||= Provider.where(provider_query).first
+        provider ||= Provider.create(provider_hash)
+      end
+    end
+    provider 
   end
 
   # Returns nil if result is an empty string, block allows text munging of result if there is one

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

@@ -1,6 +1,5 @@
 module HealthDataStandards
   module CQM
-
     module PopulationSelectors
       def numerator
         populations.find {|pop| pop.type == 'NUMER'}
@@ -51,42 +50,86 @@ module HealthDataStandards
         population_groups.values.any? { |pops| pops.size > 1 }
       end
     end
-
     class Population
-      attr_accessor :type, :value, :id
+      attr_accessor :type, :value, :id, :stratifications, :supplemental_data
+
+      def initialize
+        @stratifications = []
+      end
+
+      def add_stratification(id,value)
+        unless stratifications.find{|st| st.id == id}
+          stratifications << Stratification.new(id,value)
+        end
+      end
+
     end
 
     class Stratification
-      attr_accessor :id, :populations
+      attr_accessor :id, :value
+      def initialize(id,value)
+        @id = id
+        @value = value
+      end
+
+    end
+
+    class PopulationGroup
       include PopulationSelectors
+      attr_accessor :populations
+      def performance_rate
+        numerator_count.to_f / 
+          (denominator_count - denominator_exclusions_count - denominator_exceptions_count)
+      end
 
-      def initialize
-        @populations = []
+      def is_cv?
+        populations.any? {|pop| pop.type == 'MSRPOPL'}
       end
+
     end
 
     class AggregateCount
-      attr_accessor :measure_id, :stratifications, :top_level_populations, :supplemental_data
-      alias :populations :top_level_populations
-      include PopulationSelectors
+      attr_accessor :measure_id,  :populations, :population_groups
 
-      def initialize
-        @stratifications = []
-        @top_level_populations = []
+      def initialize(measure_id)
+        @populations = []
+        @measure_id = measure_id
+        @population_groups = []
       end
 
-      def is_cv?
-        top_level_populations.any? {|pop| pop.type == 'MSRPOPL'}
+      def add_entry(cache_entry)
+        entry_populations = []
+        cache_entry.population_ids.each do |population_type, population_id|
+          population = populations.find{|pop| pop.id == population_id}
+          if population.nil? && population_type != 'stratification'
+            population = Population.new
+            population.type = population_type
+            population.id = population_id
+            populations << population
+          end
+          unless population_type == 'stratification'
+            if cache_entry.is_stratification?
+              strat_id = cache_entry.population_ids['stratification']
+              population.add_stratification(strat_id,cache_entry[population_type])
+            else
+              population.value = cache_entry[population_type]
+              population.supplemental_data = cache_entry.supplemental_data[population_type]
+            end
+          end
+          entry_populations << population if population
+        end
+         pgroup = population_groups.find{|pg| pg.populations.collect{|p| p.id}.sort == entry_populations.collect{|p| p.id}.sort }
+         unless pgroup
+          pg = PopulationGroup.new
+          pg.populations = entry_populations
+          population_groups << pg
+         end
       end
 
-      def performance_rate
-        numerator_count.to_f / 
-          (denominator_count - denominator_exclusions_count - denominator_exceptions_count)
+      def is_cv?
+        populations.any? {|pop| pop.type == 'MSRPOPL'}
       end
 
-      def supplemental_data_for(population_type, supplemental_data_type)
-        supplemental_data[population_type][supplemental_data_type]
-      end
     end
   end
 end

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

@@ -23,20 +23,9 @@ module HealthDataStandards
 
       def self.aggregate_measure(measure_id, effective_date, filter=nil, test_id=nil)
         cache_entries = self.where(effective_date: effective_date, measure_id: measure_id, test_id: test_id, filter: filter)
-        aggregate_count = AggregateCount.new
-        aggregate_count.measure_id = measure_id
+        aggregate_count = AggregateCount.new(measure_id)
         cache_entries.each do |cache_entry|
-          if cache_entry.is_stratification?
-            stratification = Stratification.new
-            stratification.populations = cache_entry.build_populations
-            stratification.id = cache_entry.population_ids['stratification']
-            aggregate_count.stratifications << stratification
-          else
-            aggregate_count.top_level_populations = cache_entry.build_populations
-            if cache_entry.supplemental_data.present?
-              aggregate_count.supplemental_data = cache_entry.supplemental_data
-            end
-          end
+          aggregate_count.add_entry(cache_entry)
         end
         aggregate_count
       end
@@ -49,19 +38,7 @@ module HealthDataStandards
         population_ids.has_key?('MSRPOPL')
       end
 
-      def build_populations
-        populations = []
-        population_ids.each do |population_type, population_id|
-          unless population_type == 'stratification'
-            population = Population.new
-            population.type = population_type
-            population.id = population_id
-            population.value = self[population_type]
-            populations << population
-          end
-        end
-        populations
-      end
+      
     end
   end
 end

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

@@ -3,8 +3,9 @@ class Encounter < Entry
   field :dischargeDisposition, type: Hash
   field :admitTime, type: Integer
   field :dischargeTime, type: Integer
-  field :transferTo, type: Hash
-  field :transferFrom, type: Hash
+  
+  embeds_one :transferTo, class_name: "Transfer"
+  embeds_one :transferFrom, class_name: "Transfer"
 
   embeds_one :facility
   embeds_one :reason, class_name: "Entry"

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

@@ -15,7 +15,6 @@ class Entry
   field :start_time, type: Integer
   field :end_time, type: Integer
   field :status_code, type: Hash
-  field :free_text, type: String
   field :mood_code, type: String, default: "EVN"
   field :negationInd, type: Boolean
   field :negationReason, type: Hash
@@ -206,4 +205,12 @@ class Entry
     self.time = self.time.nil? ? nil : (self.time + date_diff)
   end
 
+  def identifier
+    if respond_to?(:cda_identifier) && self.cda_identifier.present?
+      self.cda_identifier
+    else
+      self.id
+    end
+  end
+
 end

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

@@ -8,14 +8,10 @@ class InsuranceProvider < Entry
   embeds_one :subscriber, class_name: "Person"
   
   field :type, type: String
-  field :time, type: Integer
-  field :start_time, type: Integer
-  field :end_time, type: Integer
   field :member_id, type: String
   field :relationship, type: Hash
   field :financial_responsibility_type, type: Hash
   field :name, type: String
-  field :free_text, type: String
   
 
   def shift_dates(date_diff)

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

@@ -47,4 +47,14 @@ class Provider
   
     return sum.to_s
   end
+
+  #this is intentially left blank. When using the ProviderImporter class this method will be called
+  # if a parsed provider can not be found in the database if the parsed provider does not have an 
+  # npi number associated with it.  This allows applications to handle this how they see fit by redefining
+  # this method.  If this method call return nil an attempt will be made to discover the Provider by name 
+  # matching and if that fails a Provider will be created in the db based on the information in the parsed
+  #  hase
+  def self.resolve_provider(provider_hash)
+
+  end
 end

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

@@ -54,6 +54,17 @@ class Record
   scope :by_provider, ->(prov, effective_date) { (effective_date) ? where(provider_queries(prov.id, effective_date)) : where('provider_performances.provider_id'=>prov.id)  }
   scope :by_patient_id, ->(id) { where(:medical_record_number => id) }
 
+  def self.update_or_create(data)
+    existing = Record.where(medical_record_number: data.medical_record_number).first
+    if existing
+      existing.update_attributes!(data.attributes.except('_id'))
+      existing
+    else
+      data.save!
+      data
+    end
+  end
+
   def providers
     provider_performances.map {|pp| pp.provider }
   end
@@ -79,20 +90,32 @@ class Record
   alias :clinical_trial_participant :clinicalTrialParticipant
   alias :clinical_trial_participant= :clinicalTrialParticipant=
 
-  # Removed duplicate entries from a section based on id. This method may
-  # lose information because it does not compare entries based on clinical
-  # content
-  def dedup_section!(section)
+
+  # 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
+  def dedup_section_ignoring_content!(section)
     unique_entries = self.send(section).uniq do |entry|
-      if entry.respond_to?(:cda_identifier) && entry.cda_identifier.present?
-        entry.cda_identifier
+      entry.identifier
+    end
+    self.send("#{section}=", unique_entries)
+  end
+  def dedup_section_merging_codes_and_values!(section)
+    unique_entries = {}
+    self.send(section).each do |entry|
+      if unique_entries[entry.identifier]
+        unique_entries[entry.identifier].codes = unique_entries[entry.identifier].codes.deep_merge(entry.codes)
+        unique_entries[entry.identifier].values.concat(entry.values)
       else
-        entry.id
+        unique_entries[entry.identifier] = entry
       end
     end
-    self.send("#{section}=", unique_entries)
+    self.send("#{section}=", unique_entries.values)
   end
 
+  def dedup_section!(section)
+    [:results, :procedures].include?(section) ? dedup_section_merging_codes_and_values!(section) : dedup_section_ignoring_content!(section)
+  end
   def dedup_record!
     Record::Sections.each {|section| self.dedup_section!(section)}
   end

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

@@ -0,0 +1,8 @@
+class Transfer
+  include Mongoid::Document
+  include ThingWithCodes
+
+  field :time, type: Integer 
+
+  embedded_in :encounter, class_name: "Encounter"
+end

data/templates/cat1/_2.16.840.1.113883.10.20.22.4.85.cat1.erb

@@ -15,5 +15,6 @@
                          'tag_name' => 'value',
                          'value_set_map' => value_set_map,
                          'extra_content' => "xsi:type=\"CD\" sdtc:valueSet=\"#{value_set_oid}\"") %>
+    <text><%= entry.description %></text>  
   </observation>
 </entry>

data/templates/cat1/_2.16.840.1.113883.10.20.24.3.101.cat1.erb

@@ -13,13 +13,16 @@
     <value xsi:type="PQ" 
     <% if entry.codes['SNOMED-CT'].include?('80487005')-%>
            value="39"
-    <% elsif entry.codes['SNOMED-CT'].include?('931004')-%>
-           value="36"
+    <% elsif entry.codes['SNOMED-CT'].include?('13798002')-%>
+           value="38"
     <% elsif entry.codes['SNOMED-CT'].include?('43697006')-%>
            value="37"
+    <% elsif entry.codes['SNOMED-CT'].include?('931004')-%>
+           value="36"
     <% else -%>
            nullFlavor="UNK"
     <% end -%>
-           unit="wk"/>   
+           unit="wk"/>
+    <text><%= entry.description %></text>   
   </observation>
 </entry>

data/templates/cat1/_2.16.840.1.113883.10.20.24.3.103.cat1.erb

@@ -8,5 +8,6 @@
     <%== code_display(entry, 'preferred_code_sets' => ['SNOMED-CT'],
                              'tag_name' => 'value','value_set_map' => value_set_map,
                              'extra_content' => "xsi:type=\"CD\" sdtc:valueSet=\"#{value_set_oid}\"") %>
+    <text><%= entry.description %></text>
   </observation>
 </entry>

data/templates/cat1/_2.16.840.1.113883.10.20.24.3.12.cat1.erb

@@ -43,6 +43,7 @@
         <%== code_display(entry, 'value_set_map' => value_set_map,'preferred_code_sets' => ['SNOMED-CT'],
                          'tag_name' => 'value',
                          'extra_content' => "xsi:type=\"CD\" sdtc:valueSet=\"#{value_set_oid}\"") %>
+        <text><%= entry.description %></text>
       </observation>
     </component>
   </organizer>

data/templates/cat1/_2.16.840.1.113883.10.20.24.3.13.cat1.erb

@@ -18,6 +18,7 @@
   <%== render(:partial => 'ordinality', :locals => {:entry => entry, :ordinality_oids=>field_oids["ORDINAL"]}) %>
 
   <%== code_display(entry, 'value_set_map' => value_set_map,'tag_name' => 'value', 'preferred_code_sets' => ['SNOMED-CT', 'ICD-9-CM', 'ICD-10-CM', 'LOINC'], 'extra_content' => "xsi:type=\"CD\" sdtc:valueSet=\"#{value_set_oid}\"") %>
+  <text><%= entry.description %></text>
   <!-- Status -->
   <entryRelationship typeCode="REFR">
     <observation classCode="OBS" moodCode="EVN">

data/templates/cat1/_2.16.840.1.113883.10.20.24.3.14.cat1.erb

@@ -18,6 +18,7 @@
 
     <%== code_display(entry, 'value_set_map' => value_set_map,'tag_name' => 'value', 'preferred_code_sets' => ['SNOMED-CT', 'ICD-9-CM', 'ICD-10-CM', 'CPT'],
                              'extra_content' => "xsi:type=\"CD\" sdtc:valueSet=\"#{value_set_oid}\"") %>
+    <text><%= entry.description %></text>
     <!-- Status -->
     <entryRelationship typeCode="REFR">
       <observation classCode="OBS" moodCode="EVN">