health-data-standards 3.1.1 → 3.2.0

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

@@ -0,0 +1,60 @@
+module HealthDataStandards
+	module CQM
+	  class PatientCache
+			include Mongoid::Document
+	    store_in collection: 'patient_cache'
+			index "value.last" => 1
+	  	index "bundle_id" => 1
+	    embeds_one :value, class_name: "HealthDataStandards::CQM::PatientCacheValue", inverse_of: :patient_cache
+
+		  def record
+		  	Record.where(:medical_record_number => value['medical_record_id'], :test_id => value["test_id"]).first
+		  end
+
+		  def self.smoking_gun_rational(hqmf_id,sub_ids=nil, filter ={})
+
+		  	match = {"value.IPP" => {"$gt" => 0},
+		  				   "value.measure_id" => hqmf_id
+		  	}.merge filter
+
+		  	if sub_ids
+		  		match["value.sub_id"] = {"$in" => sub_ids}
+		  	end
+
+		  	group = {"$group" => {"_id" => "$value.medical_record_id", "rational" => {"$push"=> "$value.rationale"}}}
+		    aggregate = self.mongo_session.command(:aggregate => 'patient_cache', :pipeline => [{"$match" =>match},group])
+
+		    merged = {}
+		    aggregate["result"].each do |agg|
+		    	mrn = agg["_id"]
+		    	rational = {}
+		    	merged[mrn] = rational
+		      agg["rational"].each do |r|
+		    		rational.merge! r 
+		    	end
+		    end
+
+		    merged
+		  end
+		end
+
+	  class PatientCacheValue
+
+		  include Mongoid::Document
+
+		  embedded_in :patient_cache, inverse_of: :value
+
+		  field :DENOM, type: Integer
+		  field :NUMER, type: Integer
+		  field :DENEX, type: Integer
+		  field :DENEXCEP, type: Integer
+		  field :MSRPOPL, type: Integer
+		  field :OBSERV
+		  field :antinumerator, type: Integer
+		  field :IPP, type: Integer
+		  field :measure_id, type: String
+		  field :sub_id, type: String\
+		end
+
+	end
+end

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

@@ -23,4 +23,15 @@ class Encounter < Entry
   alias :transfer_to= :transferTo=
   alias :transfer_from :transferFrom
   alias :transfer_from= :transferFrom=
+
+  def shift_dates(date_diff)
+    super
+    if self.facility
+      self.facility.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

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

@@ -198,4 +198,12 @@ class Entry
     
     entry_hash
   end
+
+
+  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)
+    self.time = self.time.nil? ? nil : (self.time + date_diff)
+  end
+
 end

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

@@ -9,4 +9,9 @@ class Facility
   
   embeds_many :addresses, as: :locatable
   embeds_many :telecoms, as: :contactable
+
+   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

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

@@ -21,4 +21,8 @@ class FulfillmentHistory
   alias :fill_status= :fillStatus=
   alias :prescription_number :prescriptionNumber
   alias :prescription_number= :prescriptionNumber=
+
+  def shift_dates(date_diff)
+    self.dispenseDate = (self.dispenseDate.nil?) ? nil : self.dispenseDate + date_diff
+  end
 end

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

@@ -8,4 +8,9 @@ class Guarantor
   field :start_time, type: Integer
   field :end_time, type: Integer
   
+
+  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

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

@@ -17,4 +17,14 @@ class InsuranceProvider
   field :name, type: String
   field :free_text, type: String
   
+
+  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
+    self.time = self.time.nil? ? nil : self.time + date_diff
+    self.guarantors.each do |g|
+      g.shift_dates(date_diff)
+    end
+    
+  end
 end

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

@@ -8,4 +8,9 @@ class MedicalEquipment < Entry
   alias :anatomical_structure= :anatomicalStructure=
   alias :removal_time :removalTime
   alias :removal_time= :removalTime=
+
+   def shift_dates(date_diff)
+   	super
+    self.removalTime = self.removalTime.nil? ? nil : self.removalTime + date_diff
+  end
 end

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

@@ -47,4 +47,15 @@ class Medication < Entry
   alias :dose_indicator= :doseIndicator=
   alias :cumulative_medication_duration :cumulativeMedicationDuration
   alias :cumulative_medication_duration= :cumulativeMedicationDuration=
+
+  def shift_dates(date_diff)
+    super
+    self.fulfillmentHistory.each do |fh|
+      fh.shift_dates(date_diff)
+    end
+    self.orderInformation.each do |oi|
+      oi.shift_dates(date_diff)
+    end
+  end
+
 end

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

@@ -17,4 +17,10 @@ class OrderInformation
   alias :order_expiration_date_time= :orderExpirationDateTime=
   alias :order_date_time :orderDateTime
   alias :order_date_time= :orderDateTime=
+
+
+  def shift_dates(date_diff)
+    self.orderDateTime = self.orderDateTime.nil? ? nil : self.orderDateTime + date_diff
+    self.orderExpirationDateTime = self.orderExpirationDateTime.nil? ? nil : self.orderExpirationDateTime + date_diff
+  end
 end

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

@@ -8,4 +8,9 @@ class Procedure < Entry
 
   alias :incision_time :incisionTime
   alias :incision_time= :incisionTime=
+
+  def shift_dates(date_diff)
+  	super
+  	self.incisionTime = self.incisionTime.nil? ? nil : self.incisionTime + date_diff
+  end
 end

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

@@ -7,4 +7,9 @@ class ProviderPerformance
   belongs_to :provider
   embedded_in :record
   
+
+  def shift_dates(date_diff)
+    self.start_date = self.start_date.nil? ? nil : self.start_date + date_diff
+    self.end_date = self.end_date.nil? ? nil : self.end_date + date_diff
+  end
 end

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

@@ -96,6 +96,19 @@ class Record
     Record::Sections.each {|section| self.dedup_section!(section)}
   end
 
+  def shift_dates(date_diff)
+    self.birthdate = (self.birthdate.nil?) ? nil : self.birthdate + date_diff
+    self.deathdate = (self.deathdate.nil?) ? nil : self.deathdate + date_diff
+    self.provider_performances.each {|pp| pp.shift_dates(date_diff)}
+    Sections.each do |sec|
+      (self.send sec || []).each do |ent|
+        ent.shift_dates(date_diff)
+      end
+
+    end
+
+  end
+
   private 
   
   def self.provider_queries(provider_id, effective_date)
@@ -105,4 +118,7 @@ class Record
     {'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/thing_with_codes.rb

@@ -17,12 +17,22 @@ module ThingWithCodes
   
   # 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, codes_attribute=:codes)
+  def preferred_code(preferred_code_sets, codes_attribute=:codes, value_set_map=nil)
     codes_value = send(codes_attribute)
-    matching_code_sets = preferred_code_sets & codes_value.keys
+    preferred_code_sets = value_set_map ? (preferred_code_sets & value_set_map.collect{|cs| cs["set"]}) : preferred_code_sets
+    matching_code_sets = preferred_code_sets & codes_value.keys 
     if matching_code_sets.present?
+      if value_set_map
+        matching_code_sets.each do |matching_code_set|
+           matching_codes = codes_value[matching_code_set] & value_set_map.collect{|cs| cs["set"] == matching_code_set ? cs["values"] : []}.flatten.compact
+           if matching_codes.present?
+             return {'code' => matching_codes.first, 'code_set' => matching_code_set}
+           end
+        end
+      else
       code_set = matching_code_sets.first
       {'code' => codes_value[code_set].first, 'code_set' => code_set}
+      end
     else
       nil
     end
@@ -31,17 +41,37 @@ module ThingWithCodes
   # 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)
+  def translation_codes(preferred_code_sets,value_set_map=nil)
     tx_codes = []
-    codes.each_pair do |code_set, code_list|
+    matching_codes = value_set_map ? codes_in_code_set(value_set_map) : codes
+    matching_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)]
+    tx_codes - [preferred_code(preferred_code_sets, :codes, value_set_map)]
+  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
+  #                The hash has a key of "set" for the code system name and "values"
+  #                for the actual code list
+  # @return [all codes that are in the code set
+  def codes_in_code_set(code_set)
+    matching = {}
+    codes.keys.each do |code_system|
+      matching_codes = []
+      matching[code_system] = matching_codes
+      all_codes_in_system = code_set.find_all {|set| set['set'] == code_system}
+      all_codes_in_system.each do |codes_in_system|
+        matching_codes.concat codes_in_system['values'] & codes[code_system]
+      end
+    end
+    matching
   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

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

@@ -14,7 +14,7 @@ module HealthDataStandards
         '2.16.840.1.113883.6.90' =>   'ICD-10-CM',
         '2.16.840.1.113883.6.14' =>   'HCPCS',
         '2.16.840.1.113883.5.2' => "HL7 Marital Status",
-        '2.16.840.1.113883.6.59' =>   'CVX',
+        '2.16.840.1.113883.12.292' => 'CVX',
         '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',
@@ -31,18 +31,27 @@ module HealthDataStandards
         '2.16.840.1.113883.1.11.19717' => "HL7 ActNoImmunicationReason",
         '2.16.840.1.113883.3.88.12.80.33' => "NUBC",
         '2.16.840.1.113883.1.11.78' => "HL7 Observation Interpretation",
-        '2.16.840.1.114222.4.11.3591' => "Source of Payment Typology"
+        '2.16.840.1.113883.3.221.5' => "Source of Payment Typology",
+        '2.16.840.1.113883.6.13' => 'CDT'
       }
       
       CODE_SYSTEM_ALIASES = {
         'FDA SPL' => 'NCI Thesaurus',
-        'HSLOC' => 'HL7 Healthcare Service Location'
+        'HSLOC' => 'HL7 Healthcare Service Location',
+        'SOP' => "Source of Payment Typology"
+      }
+      
+      # Some old OID are still around in data, this hash maps retired OID values to 
+      # the new value
+      OID_ALIASES = {
+        '2.16.840.1.113883.6.59' => '2.16.840.1.113883.12.292' # CVX
       }
       
       # 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)
+        oid = OID_ALIASES[oid] if OID_ALIASES[oid]
         CODE_SYSTEMS[oid] || "Unknown"
       end
       

data/lib/hqmf-model/data_criteria.json

@@ -126,7 +126,7 @@
       "property":"ethnicity",
       "standard_category":"individual_characteristic",
       "qds_data_type":"individual_characteristic",
-      "not_supported":true},
+      "not_supported":false},
   "patient_characteristic_expired":{
       "title":"patient characteristic, expired",
       "category":"characteristic",
@@ -150,7 +150,7 @@
       "property":"payer",
       "standard_category":"individual_characteristic",
       "qds_data_type":"individual_characteristic",
-      "not_supported":true},
+      "not_supported":false},
   "patient_characteristic_race":{
       "title":"patient characteristic, race",
       "category":"characteristic",

data/lib/hqmf-model/document.rb

@@ -135,9 +135,16 @@ module HQMF
     
     # Get the source data criteria that are specific occurrences
     # @return [Array] an array of HQMF::DataCriteria describing the data elements used by the measure that are specific occurrences
-    def specific_occurrence_source_data_criteria
+    def specific_occurrence_source_data_criteria(force_sources=nil)
       return [] if @source_data_criteria.nil?
-      @source_data_criteria.select {|dc| !dc.specific_occurrence.nil?}
+      matching = @source_data_criteria.select {|dc| !dc.specific_occurrence.nil?}
+
+      if force_sources
+        existing = matching.map(&:id)
+        matching.concat @source_data_criteria.select {|dc| !existing.include?(dc.id) && force_sources.include?(dc.id)} 
+      end
+
+      matching
     end
     
 

data/lib/hqmf-parser/1.0/document.rb

@@ -15,7 +15,12 @@ module HQMF1
       @data_criteria = @doc.xpath('//cda:section[cda:code/@code="57025-9"]/cda:entry').collect do |entry|
         DataCriteria.new(entry, occurrence_counters)
       end
-      
+
+      @supplemental= @doc.xpath('//cda:section[cda:code/@code="69670-8"]/cda:entry').collect do |entry|
+        DataCriteria.new(entry, occurrence_counters)
+      end
+
+      @data_criteria.concat @supplemental
       backfill_derived_code_lists
       
       @attributes = @doc.xpath('//cda:subjectOf/cda:measureAttribute').collect do |attr|

data/templates/_author.hdata.erb

@@ -0,0 +1,3 @@
+<hrf-md:Author <%if author.type%>typeCode="<%= author.type %>"<% end %> <% if author.role %><%= author.role %><% end %>
+  <%=author.name%>
+</hrf-md:Author>

data/templates/_pedigree.hdata.erb

@@ -1,24 +1,25 @@
-<PedigreeInfo>
+<hrf-md:PedigreeInfo>
   <% unless pedigree.source_documents.empty? && pedigree.source_documents.empty?%>
-  <Source derived="true">
+  <hrf-md:Source derived="true">
     <% pedigree.source_documents.each do |source| %>
-    <PedigreeInfo>
-      <Author><%=source.author.name%></Author>
-      <Organization><%= source.organization %></Organization>
-    </PedigreeInfo>
+    <hrf-md:PedigreeInfo>
+      <% if source.author %>
+        <%== render :partial => "author", locals: {author: source.author }%>
+      <% end %>
+      <hrf-md:Organization><%= source.organization %></hrf-md:Organization>
+    </hrf-md:PedigreeInfo>
     <% end %>
     <% pedigree.source_documents.each do |doc|%>
-    <Document>
-      <Target <% if doc.extension %> targetExtension="<%=doc.extension%>" <% end %>><%= doc.uri %></Target>
-    </Document>
-  </Source>
+    <hrf-md:Document>
+      <hrf-md:Target <% if doc.extension %> targetExtension="<%=doc.extension%>" <% end %>><%= doc.uri %></hrf-md:Target>
+    </hrf-md:Document>
+    <% end %>
+  </hrf-md:Source>
   <% end %>
   <% if pedigree.author %>
-    <Author typeCode="<%= pedigree.author.type %>" role="<%= pedigree.author.role%>">
-      <%= pedigree.author.name %>
-    </Author>
+      <%== render :partial => "author", locals: {author: pedigree.author }%>
   <% end %>
   <% if pedigree.organization %>
-  <Organization><%= pedigree.organization %></Organization>
+  <hrf-md:Organization><%= pedigree.organization %></hrf-md:Organization>
   <% end %>
-</PedigreeInfo>
+</hrf-md:PedigreeInfo>

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

@@ -13,6 +13,7 @@
     </effectiveTime>
     <%== 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}\"") %>
   </observation>
 </entry>