health-data-standards 3.0.6 → 3.1.0

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

@@ -1,36 +1,57 @@
 module HealthDataStandards
   module CQM
+    class Measure
+      include Mongoid::Document
+      store_in collection: 'measures'
+      field :id, type: String
+      field :sub_id, type: String
+      field :name, type: String
+      field :subtitle, type: String
+      field :short_subtitle, type: String
+      field :hqmf_id, type: String
+      field :hqmf_set_id, type: String
+      field :hqmf_version_number, type: String
+      field :nqf_id, type: String
+      field :type, type: String
+      field :category, type: String
+      field :population_ids , type: Hash
+      field :oids, type: Array 
+      field :data_criteria, type: Array
 
-  	class Measure
-		  include Mongoid::Document
-		  store_in collection: 'measures'
-		  field :id, type: String
-		  field :sub_id, type: String
-		  field :name, type: String
-		  field :subtitle, type: String
-		  field :short_subtitle, type: String
-		  field :hqmf_id, type: String
-		  field :hqmf_set_id, type: String
-		  field :hqmf_version_number, type: String
-		  field :nqf_id, type: String
-		  field :type, type: String
-		  field :category, type: String
-		  field :population_ids , type: Hash
-		  field :oids, type: Array 
-		  field :data_criteria, type: Array
-		  scope :top_level_by_type , ->(type){where({"type"=> type}).any_of({"sub_id" => nil}, {"sub_id" => "a"})}
-		  scope :top_level , any_of({"sub_id" => nil}, {"sub_id" => "a"})
-		  scope :order_by_id_sub_id, order_by([["id", :asc],["sub_id", :asc]])
-		  index({oids: 1})
-		  index({hqmf_id: 1})
-		  index({category: 1})
-		  index "bundle_id" => 1
-		  
-		  validates_presence_of :id
-		  validates_presence_of :name
-		  
+      scope :top_level_by_type , ->(type){where({"type"=> type}).any_of({"sub_id" => nil}, {"sub_id" => "a"})}
+      scope :top_level , any_of({"sub_id" => nil}, {"sub_id" => "a"})
+      scope :order_by_id_sub_id, order_by([["id", :asc],["sub_id", :asc]])
 
+      index({oids: 1})
+      index({hqmf_id: 1})
+      index({category: 1})
+      index "bundle_id" => 1
+      
+      validates_presence_of :id
+      validates_presence_of :name
 
-		end
-	end
+      def self.categories
+        pipeline = []
+        pipeline << {'$group' => {_id: "$id", 
+                                  name: {"$first" => "$name"},
+                                  description: {"$first" => "$description"},
+                                  sub_ids: {'$push' => "$sub_id"},
+                                  subs: {'$push' => {"sub_id" => "$sub_id", "short_subtitle" => "$short_subtitle"}},
+                                  category: {'$first' => "$category"}}}
+
+        pipeline << {'$group' => {_id: "$category",
+                                  measures: {'$push' => {"id" => "$_id", 
+                                             'name' => "$name",
+                                             'description' => "$description",
+                                             'subs' => "$subs",
+                                             'sub_ids' => "$sub_ids"
+                                            }}}}
+
+        pipeline << {'$project' => {'category' => '$_id', 'measures' => 1, '_id' => 0}}
+  
+        pipeline << {'$sort' => {"category" => 1}}
+        Mongoid.default_session.command(aggregate: 'measures', pipeline: pipeline)['result']
+      end
+    end
+  end
 end

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

@@ -0,0 +1,64 @@
+module HealthDataStandards
+  module CQM
+    class QueryCache
+      include Mongoid::Document
+      store_in collection: 'query_cache'
+
+      field :measure_id, type: String
+      field :sub_id, type: String
+      field :population_ids, type: Hash
+      field :effective_date, type: Integer
+      field :IPP, type: Integer
+      field :DENOM, type: Integer
+      field :NUMER, type: Integer
+      field :antinumerator, type: Integer
+      field :DENEX, type: Integer
+      field :DENEXCEP, type: Integer
+      field :MSRPOPL, type: Integer
+      field :OBSERV, type: Float
+      field :supplemental_data, type: Hash
+
+      def self.aggregate_measure(measure_id, effective_date, test_id=nil)
+        cache_entries = self.where(effective_date: effective_date, measure_id: measure_id, test_id: test_id)
+        aggregate_count = AggregateCount.new
+        aggregate_count.measure_id = 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
+        end
+        aggregate_count
+      end
+
+      def is_stratification?
+        population_ids.has_key?('stratification')
+      end
+
+      def is_cv?
+        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/entry.rb

@@ -6,7 +6,7 @@ class Entry
   # embedded_in :entry_list, polymorphic: true
   
   embedded_in :record
-  
+  embeds_one :cda_identifier, class_name: "CDAIdentifier"
   embeds_many :values, class_name: "ResultValue"
   
   field :description, type: String

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

@@ -1,5 +1,6 @@
 class Record
   include Mongoid::Document
+  extend Memoist
   
   field :title, type: String
   field :first, type: String
@@ -30,7 +31,11 @@ class Record
   embeds_many :medications
   embeds_many :procedures
   embeds_many :results, class_name: "LabResult"
-  embeds_many :social_history, class_name: "Entry"
+  embeds_many :socialhistories, class_name: "Entry"
+
+  alias :social_history :socialhistories
+  alias :social_history= :socialhistories=
+
   embeds_many :vital_signs
   embeds_many :support
   embeds_many :advance_directives, class_name: "Entry"
@@ -47,7 +52,7 @@ 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 providers
     provider_performances.map {|pp| pp.provider }
   end
@@ -67,10 +72,30 @@ class Record
     end
     matching_entries_by_section.flatten
   end
+
+  memoize :entries_for_oid
   
   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)
+    unique_entries = self.send(section).uniq do |entry|
+      if entry.respond_to?(:cda_identifier) && entry.cda_identifier.present?
+        entry.cda_identifier
+      else
+        entry.id
+      end
+    end
+    self.send("#{section}=", unique_entries)
+  end
+
+  def dedup_record!
+    Record::Sections.each {|section| self.dedup_section!(section)}
+  end
+
   private 
   
   def self.provider_queries(provider_id, effective_date)

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

@@ -69,6 +69,26 @@ module HealthDataStandards
           code_set_name
         end
       end
+      def self.denormalize_code_set_name(code_set_name)
+        case code_set_name
+        when'RxNorm'
+          'RXNORM'
+        when'ICD-9-CM'
+          'ICD9CM'
+        when'ICD-10-CM'
+          'ICD10CM'
+        when'ICD-10-PCS'
+          'ICD10PCS'
+        when'SNOMED-CT'
+          'SNOMEDCT'
+        when'CDC Race'
+          'CDCREC'
+        when'HL7 Healthcare Service Location'
+          'HSLOC'
+        else
+          code_set_name
+        end
+      end
     end
   end
 end

data/lib/health-data-standards/tasks/bundle.rake

@@ -4,26 +4,36 @@ db_name = ENV['DB_NAME'] || 'test'
 
 namespace :bundle do
   desc 'Import a quality bundle into the database.'
-  task :import, [:bundle_path,  :delete_existing,  :update_measures, :type] => [:environment] do |task, args|
+  task :import, [:bundle_path,  :delete_existing,  :update_measures, :type, :create_indexes] => [:environment] do |task, args|
     raise "The path to the measures zip file must be specified" unless args.bundle_path
     options = {:delete_existing => (args.delete_existing == "true"),
-    					 :type => args.type ,
+    					 :type => args.type,
     					 :update_measures => (args.update_measures == "true")
     					}
 
     bundle = File.open(args.bundle_path)    
     importer = HealthDataStandards::Import::Bundle::Importer
     bundle_contents = importer.import(bundle, options)
-    
-    ::Rails.application.eager_load!
-    ::Rails::Mongoid.create_indexes
+
+    counts = {measures: bundle_contents.measures.count,
+              records: bundle_contents.records.count,
+              extensions: bundle_contents[:extensions].count,
+              value_sets: bundle_contents.value_sets.count}
+
+    if (args.create_indexes != 'false')
+      ::Rails.application.eager_load!
+      ::Rails::Mongoid.create_indexes
+    end
 
     puts "Successfully imported bundle at: #{args.bundle_path}"
     puts "\t Imported into environment: #{Rails.env.upcase}" if defined? Rails 
     puts "\t Loaded #{args.type || 'all'} measures"
-    puts "\t Measures Loaded: #{bundle_contents.measures.count}"
-    puts "\t Test Patients Loaded: #{bundle_contents.records.count}"
-    puts "\t Extensions Loaded: #{bundle_contents[:extensions].count}"
+    puts "\t Sub-Measures Loaded: #{counts[:measures]}"
+    puts "\t Test Patients Loaded: #{counts[:records]}"
+    puts "\t Extensions Loaded: #{counts[:extensions]}"
+    puts "\t Value Sets Loaded: #{counts[:value_sets]}"
+    
+
   end
   
   # this task is most likely temporary.  Once Bonnie can handle both EP and EH measures together, this would no longer be required.

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

@@ -16,10 +16,14 @@ module HealthDataStandards
       end
 
       def self.template_id_by_definition_and_status(definition, status, negation=false)
-        pairs = template_id_map.select {|k, v| v['definition'] == definition && 
+        kv_pair = template_id_map.find {|k, v| v['definition'] == definition && 
                                                v['status'] == status && 
                                                v['negation'] == negation}
-        pairs.keys.first if pairs.present?
+        if kv_pair
+          kv_pair.first
+        else
+          nil
+        end
       end
     end
   end

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

@@ -223,6 +223,10 @@
       "definition":"medication",
       "status":"discharge",
       "negation":false},
+  "2.16.840.1.113883.3.560.1.200":{
+      "definition":"medication",
+      "status":"discharge",
+      "negation":true},
   "2.16.840.1.113883.3.560.1.13":{
       "definition":"medication",
       "status":"active",

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

@@ -3,24 +3,27 @@ require 'uri'
 module HealthDataStandards
   module Util
 		class VSApi			
-			attr_accessor :api_url, :ticket_url,  :username, :password
+			attr_accessor :api_url, :ticket_url, :username, :password
 
-			def initialize(ticket_url, api_url,username,password)
+			def initialize(ticket_url, api_url, username, password)
 				@api_url = api_url
 				@ticket_url = ticket_url
 				@username = username
 				@password = password
 			end
 
-			def get_valueset(oid,&block)
-				vs = RestClient.get api_url, {:params=>{id: oid, ticket: get_ticket}}
+
+			def get_valueset(oid, effective_date=nil, &block)
+				params = {id: oid, ticket: get_ticket}
+				params[:effectiveDate] = effective_date if effective_date
+				vs = RestClient.get api_url, {:params=>params}
 				yield oid,vs if block_given?
 				vs
 			end
 
-			def process_valuesets(oids, &block)
+			def process_valuesets(oids, effective_date=nil, &block)
 				oids.each do |oid|
-		     		vs = get_valueset(oid)
+		     		vs = get_valueset(oid,effective_date)
 		     		yield oid,vs
 				end
 			end

data/lib/hqmf-model/data_criteria.json

@@ -483,16 +483,16 @@
       "qds_data_type":"medication_administered",
       "not_supported":false},
   "medication_discharge": {
-		  "title":"medication, discharge",
-		  "category":"medications",
-		  "definition":"medication_discharge",
-		  "status":"discharge",
-		  "sub_category":"discharge",
-		  "hard_status":true,
-		  "patient_api_function":"allMedications",
-		  "standard_category":"medication",
-		  "qds_data_type":"medication_discharge",
-		  "not_supported":false},
+      "title":"medication, discharge",
+      "category":"medications",
+      "definition":"medication_discharge",
+      "status":"discharge",
+      "sub_category":"discharge",
+      "hard_status":true,
+      "patient_api_function":"allMedications",
+      "standard_category":"medication",
+      "qds_data_type":"medication_discharge",
+      "not_supported":false},
   "medication_adverse_effects":{
       "title":"medication, adverse effects",
       "category":"medications",

data/lib/hqmf-parser.rb

@@ -49,8 +49,6 @@ require_relative 'hqmf-parser/converter/pass1/simple_population_criteria'
 require_relative 'hqmf-parser/converter/pass2/comparison_converter'
 require_relative 'hqmf-parser/converter/pass2/operator_converter'
 
-require_relative 'hqmf-parser/value_sets/value_set_parser'
-
 require_relative 'hqmf-parser/parser'
 
 require_relative 'hqmf-generator/hqmf-generator'

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

@@ -4,8 +4,20 @@ module HQMF1
   class Value
     include HQMF1::Utilities
     
-    def initialize(entry)
+    def initialize(entry, inclusive=nil)
       @entry = entry
+  
+      if (inclusive.nil?)
+        case attr_val('./@inclusive')
+        when 'true'
+          @inclusive = true
+        else
+          @inclusive = false
+        end
+      else
+        @inclusive = inclusive
+      end
+
     end
     
     def value
@@ -17,12 +29,7 @@ module HQMF1
     end
     
     def inclusive?
-      case attr_val('./@inclusive')
-      when 'true'
-        true
-      else
-        false
-      end
+      @inclusive
     end
     
     def to_json
@@ -40,6 +47,11 @@ module HQMF1
       if @entry
         @low = optional_value('./cda:low')
         @high = optional_value('./cda:high')
+        if (@low == nil && @high == nil)
+          @low = optional_value('.',true)
+          @high = optional_value('.',true)
+          puts "\tfound = relationship parsing temporal reference (bugfix)"
+        end
       end
     end
    
@@ -52,10 +64,10 @@ module HQMF1
     
     private
     
-    def optional_value(xpath)
+    def optional_value(xpath, inclusive=nil)
       value_def = @entry.at_xpath(xpath)
       if value_def
-        Value.new(value_def)
+        Value.new(value_def, inclusive)
       else
         nil
       end