health-data-standards 2.2.1 → 3.0.3

data/Gemfile

@@ -15,4 +15,9 @@ group :test do
   gem "cane", '~> 2.3.0'
   gem 'simplecov', :require => false
   gem 'webmock'
+
+  gem 'minitest'
+  gem 'turn', :require => false
+  gem 'awesome_print', :require => 'ap'
+
 end

data/lib/health-data-standards.rb

@@ -5,6 +5,8 @@ require 'uuid'
 require 'builder'
 require 'csv'
 require 'nokogiri'
+require 'ostruct'
+require 'log4r'
 
 # Freedom patches
 require_relative 'health-data-standards/ext/symbol'
@@ -22,9 +24,11 @@ require_relative 'health-data-standards/export/c32'
 require_relative 'health-data-standards/export/ccda'
 require_relative 'health-data-standards/export/ccr'
 require_relative 'health-data-standards/export/csv'
+require_relative 'health-data-standards/export/helper/html_view_helper'
 require_relative 'health-data-standards/export/html'
 require_relative 'health-data-standards/export/hdata/metadata'
 
+require_relative 'health-data-standards/export/helper/gc32_view_helper'
 require_relative 'health-data-standards/export/green_c32/record'
 require_relative 'health-data-standards/export/green_c32/entry'
 require_relative 'health-data-standards/export/green_c32/export_generator'
@@ -69,20 +73,28 @@ require_relative 'health-data-standards/models/metadata/change_info'
 require_relative 'health-data-standards/models/metadata/link_info'
 require_relative 'health-data-standards/models/metadata/pedigree'
 
-require_relative 'health-data-standards/import/c32/locatable_import_utils'
-require_relative 'health-data-standards/import/c32/section_importer'
-require_relative 'health-data-standards/import/c32/allergy_importer'
-require_relative 'health-data-standards/import/c32/encounter_importer'
+require_relative 'health-data-standards/export/qrda/entry_template_resolver'
+require_relative 'health-data-standards/export/helper/cat1_view_helper'
+require_relative 'health-data-standards/export/cat_1'
+
+require_relative 'health-data-standards/import/cda/narrative_reference_handler'
+require_relative 'health-data-standards/import/cda/entry_finder'
+require_relative 'health-data-standards/import/cda/locatable_import_utils'
+require_relative 'health-data-standards/import/cda/section_importer'
+require_relative 'health-data-standards/import/cda/provider_importer'
+require_relative 'health-data-standards/import/cda/organization_importer'
+require_relative 'health-data-standards/import/cda/allergy_importer'
+require_relative 'health-data-standards/import/cda/condition_importer'
+require_relative 'health-data-standards/import/cda/encounter_importer'
+require_relative 'health-data-standards/import/cda/medical_equipment_importer'
+require_relative 'health-data-standards/import/cda/medication_importer'
+require_relative 'health-data-standards/import/cda/procedure_importer'
+require_relative 'health-data-standards/import/cda/result_importer'
+require_relative 'health-data-standards/import/cda/vital_sign_importer'
+
 require_relative 'health-data-standards/import/c32/condition_importer'
 require_relative 'health-data-standards/import/c32/immunization_importer'
-require_relative 'health-data-standards/import/c32/medication_importer'
-require_relative 'health-data-standards/import/c32/procedure_importer'
-require_relative 'health-data-standards/import/c32/result_importer'
-require_relative 'health-data-standards/import/c32/vital_sign_importer'
 require_relative 'health-data-standards/import/c32/patient_importer'
-require_relative 'health-data-standards/import/c32/provider_importer'
-require_relative 'health-data-standards/import/c32/organization_importer'
-require_relative 'health-data-standards/import/c32/medical_equipment_importer'
 require_relative 'health-data-standards/import/c32/insurance_provider_importer'
 require_relative 'health-data-standards/import/c32/care_goal_importer'
 
@@ -119,4 +131,35 @@ require_relative 'health-data-standards/import/green_c32/immunization_importer'
 require_relative 'health-data-standards/import/green_c32/support_importer'
 require_relative 'health-data-standards/import/green_c32/advance_directive_importer'
 require_relative 'health-data-standards/import/green_c32/medical_equipment_importer'
-require_relative 'health-data-standards/import/green_c32/care_goal_importer'
+require_relative 'health-data-standards/import/green_c32/care_goal_importer'
+
+require_relative 'health-data-standards/import/cat1/gestational_age_importer'
+require_relative 'health-data-standards/import/cat1/procedure_intolerance_importer'
+require_relative 'health-data-standards/import/cat1/procedure_order_importer'
+require_relative 'health-data-standards/import/cat1/diagnosis_active_importer'
+require_relative 'health-data-standards/import/cat1/diagnosis_inactive_importer'
+require_relative 'health-data-standards/import/cat1/patient_importer'
+require_relative 'health-data-standards/import/cat1/lab_order_importer'
+require_relative 'health-data-standards/import/cat1/medication_dispensed_importer'
+require_relative 'health-data-standards/import/cat1/encounter_order_importer'
+require_relative 'health-data-standards/import/cat1/diagnostic_study_order_importer'
+require_relative 'health-data-standards/import/cat1/tobacco_use_importer'
+require_relative 'health-data-standards/import/cat1/entry_package'
+
+require_relative 'health-data-standards/models/cqm/bundle'
+require_relative 'health-data-standards/models/cqm/measure'
+require_relative 'health-data-standards/import/bundle/importer'
+
+
+module HealthDataStandards
+  class << self
+    attr_accessor :logger
+  end
+end
+
+if defined?(Rails)
+  require_relative 'health-data-standards/railtie' 
+else
+  HealthDataStandards.logger = Log4r::Logger.new("Health Data Standards")
+  HealthDataStandards.logger.outputters = Log4r::Outputter.stdout
+end

data/lib/health-data-standards/export/c32.rb

@@ -1,14 +1,15 @@
 module HealthDataStandards
   module Export
-    module C32
-      include TemplateHelper
+    class C32
+      def initialize
+        template_helper = TemplateHelper.new('c32', 'c32')
+        @rendering_context = RenderingContext.new
+        @rendering_context.template_helper = template_helper
+      end
 
       def export(patient)
-        self.template_format = "c32"
-        render(:template => 'show', :locals => {:patient => patient})
+        @rendering_context.render(:template => 'show', :locals => {:patient => patient})
       end
-
-      extend self
     end
   end
 end

data/lib/health-data-standards/export/cat_1.rb

@@ -0,0 +1,18 @@
+module HealthDataStandards
+  module Export
+    class Cat1
+      def initialize
+        template_helper = HealthDataStandards::Export::TemplateHelper.new('cat1', 'cat1')
+        @rendering_context = HealthDataStandards::Export::RenderingContext.new
+        @rendering_context.template_helper = template_helper
+        @rendering_context.extensions = [HealthDataStandards::Export::Helper::Cat1ViewHelper]
+      end
+
+      @@vs_map = nil
+      def export(patient, measures, start_date, end_date)
+        @rendering_context.render(:template => 'show', :locals => {:patient => patient, :measures => measures, 
+                                                :start_date => start_date, :end_date => end_date})
+      end
+    end
+  end
+end

data/lib/health-data-standards/export/ccda.rb

@@ -1,15 +1,15 @@
 module HealthDataStandards
   module Export
-    module CCDA
-      include TemplateHelper
-      
-      def export(patient)
-        self.template_format = "ccda"
-        self.template_subdir = "ccda"
-        render(:template => 'show', :locals => {:patient => patient})
+    class CCDA
+      def initialize
+        template_helper = TemplateHelper.new('ccda', 'ccda')
+        @rendering_context = RenderingContext.new
+        @rendering_context.template_helper = template_helper
       end
 
-      extend self
+      def export(patient)
+        @rendering_context.render(:template => 'show', :locals => {:patient => patient})
+      end      
     end
   end
 end

data/lib/health-data-standards/export/green_c32/entry.rb

@@ -1,14 +1,17 @@
 module HealthDataStandards
   module Export
     module GreenC32
-      module Entry
-        include TemplateHelper
+      class Entry
+        def initialize
+          template_helper = TemplateHelper.new('gc32', 'gc32')
+          @rendering_context = RenderingContext.new
+          @rendering_context.template_helper = template_helper
+          @rendering_context.extensions = [HealthDataStandards::Export::Helper::GC32ViewHelper]
+        end
         
         def export(object, object_type)
-          self.template_format = "gc32"
-          render(partial: object_type, locals: {object_type => object, type: object_type})
+          @rendering_context.render(partial: object_type, locals: {object_type => object, type: object_type})
         end
-        extend self
       end
     end
   end

data/lib/health-data-standards/export/green_c32/export_generator.rb

@@ -12,7 +12,7 @@ module HealthDataStandards
         def create_exporter_for(section)
           object = Object.new
           object.define_singleton_method(:export) do |section_instance|
-            HealthDataStandards::Export::GreenC32::Entry.export(section_instance, section)
+            HealthDataStandards::Export::GreenC32::Entry.new.export(section_instance, section)
           end
           object
         end

data/lib/health-data-standards/export/green_c32/record.rb

@@ -1,14 +1,17 @@
 module HealthDataStandards
   module Export
     module GreenC32
-      module Record
-        include TemplateHelper
-        
-        def export(object)
-          self.template_format = "gc32"
-          render(template: "record", locals: {record: object})
+      class Record
+        def initialize
+          template_helper = TemplateHelper.new('gc32', 'gc32')
+          @rendering_context = RenderingContext.new
+          @rendering_context.template_helper = template_helper
+          @rendering_context.extensions = [HealthDataStandards::Export::Helper::GC32ViewHelper]
+        end
+
+        def export(patient)
+          @rendering_context.render(:template => 'record', :locals => {:record => patient})
         end
-        extend self
       end
     end
   end

data/lib/health-data-standards/export/hdata/metadata.rb

@@ -1,15 +1,16 @@
 module HealthDataStandards
   module Export
     module Hdata
-      module Metadata
-        include TemplateHelper
+      class Metadata
+        def initialize
+          template_helper = TemplateHelper.new('hdata')
+          @rendering_context = RenderingContext.new
+          @rendering_context.template_helper = template_helper
+        end
 
         def export(entry, metadata)
-          self.template_format = "hdata"
-          render(:template => 'metadata', :locals => {entry: entry, metadata: metadata})
+          @rendering_context.render(:template => 'metadata', :locals => {entry: entry, metadata: metadata})
         end
-        
-        extend self
       end
     end
   end

data/lib/health-data-standards/export/helper/cat1_view_helper.rb

@@ -0,0 +1,133 @@
+module HealthDataStandards
+  module Export
+    module Helper
+      module Cat1ViewHelper
+        include HealthDataStandards::Util
+        include HealthDataStandards::SVS
+
+        def value_set_map
+          @@vs_map ||= Hash[*ValueSet.all.map{ |p| [p.oid, p] }.flatten]
+        end
+
+        # Find all of the entries on a patient that match the given data criteria
+        def entries_for_data_criteria(data_criteria, patient)
+          data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition, 
+                                                                                      data_criteria.status || '',
+                                                                                      data_criteria.negation)
+          filtered_entries = []
+          case data_criteria_oid
+          when '2.16.840.1.113883.3.560.1.404'
+            filtered_entries = handle_patient_expired(patient)
+          when '2.16.840.1.113883.3.560.1.401'
+            filtered_entries = handle_clinical_trial_participant(patient)
+          when '2.16.840.1.113883.3.560.1.405'
+            filtered_entries = handle_payer_information(patient)
+          else
+            entries = patient.entries_for_oid(data_criteria_oid)
+            codes = []
+            vs = value_set_map[data_criteria.code_list_id]
+            if vs
+              codes = vs.code_set_map
+            else
+              HealthDataStandards.logger.warn("No codes for #{data_criteria.code_list_id}")
+            end
+            filtered_entries = entries.find_all do |entry|
+              # This special case is for when the code list is a reason
+              if data_criteria.code_list_id =~ /2\.16\.840\.1\.113883\.3\.526\.3\.100[7-9]/
+                entry.negation_reason.present? && codes.first['values'].include?(entry.negation_reason['code'])
+              else
+                # The !! hack makes sure that negation_ind is a boolean
+                entry.is_in_code_set?(codes) && !!entry.negation_ind == data_criteria.negation
+              end
+            end
+          end
+          if filtered_entries.empty?
+            HealthDataStandards.logger.debug("No entries for #{data_criteria.title}")
+          end
+
+          filtered_entries
+        end
+
+        # Given a set of measures, find the data criteria/value set pairs that are unique across all of them
+        # Returns an Array of Hashes. Hashes will have a three key/value pairs. One for the data criteria oid,
+        # one for the value set oid and one for the data criteria itself
+        def unique_data_criteria(measures)
+          all_data_criteria = measures.map {|measure| measure.all_data_criteria}.flatten
+          dc_oids_and_vs_oids = all_data_criteria.map do |data_criteria|
+            data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition, 
+                                                                              (data_criteria.status || ""),
+                                                                              data_criteria.negation)
+            value_set_oid = data_criteria.code_list_id
+            {'data_criteria_oid' => data_criteria_oid, 'value_set_oid' => value_set_oid, 'data_criteria' => data_criteria}
+          end
+          dc_oids_and_vs_oids.uniq_by {|thingy| [thingy['data_criteria_oid'], thingy['value_set_oid']]}
+        end
+
+        def render_data_criteria(dc_oid, vs_oid, entries)
+          html_array = entries.map do |entry|
+            if dc_oid == '2.16.840.1.113883.3.560.1.1001'
+              # This is a special case. This HQMF OID maps to more than one QRDA OID.
+              # So we need to try to figure out what template we should use based on the
+              # content of the entry
+              if vs_oid == '2.16.840.1.113883.3.526.3.1279'
+                # Patient Characteristic Observation Assertion template for
+                # Patient Characteristic: ECOG Performance Status-Poor
+                render(:partial => '2.16.840.1.113883.10.20.24.3.103', :locals => {:entry => entry,
+                                                                                   :value_set_oid => vs_oid})
+              elsif vs_oid == "2.16.840.1.113883.3.117.1.7.1.402" || vs_oid == "2.16.840.1.113883.3.117.1.7.1.403" 
+                # Patient Charasteristic Gestational Age
+                render(:partial => '2.16.840.1.113883.10.20.24.3.101', :locals => {:entry => entry,
+                                                                                   :value_set_oid => vs_oid})
+              elsif vs_oid == "2.16.840.1.113883.3.526.3.1189" || vs_oid == "2.16.840.1.113883.3.526.3.1170"
+                # Patient Characteristic Tobacco User/Non-User
+                render(:partial => '2.16.840.1.113883.10.20.22.4.85', :locals => {:entry => entry,
+                                                                                   :value_set_oid => vs_oid})  
+              end
+            else
+              render(:partial => HealthDataStandards::Export::QRDA::EntryTemplateResolver.partial_for(dc_oid), :locals => {:entry => entry,
+                                                                                                               :value_set_oid => vs_oid})
+            end
+          end
+          html_array.join("\n")
+        end
+
+        def render_patient_data(patient, measures)
+          udcs = unique_data_criteria(measures)
+          data_criteria_html = udcs.map do |udc|
+            entries = entries_for_data_criteria(udc['data_criteria'], patient)
+            render_data_criteria(udc['data_criteria_oid'], udc['value_set_oid'], entries)          
+          end
+          data_criteria_html.compact.join("\n")
+        end
+
+        def negation_indicator(entry)
+          if entry.negation_ind
+            'negationInd="true"'
+          else
+            ''
+          end
+        end
+
+        def handle_clinical_trial_participant(patient)
+          if patient.clinical_trial_participant
+            [{dummy_entry: true}]
+          else
+            []
+          end
+        end
+
+        def handle_patient_expired(patient)
+          if patient.expired
+            [OpenStruct.new(start_date: patient.deathdate)]
+          else
+            []
+          end
+        end
+
+        def handle_payer_information(patient)
+          patient.insurance_providers
+        end
+      end
+    end
+  end
+end

data/lib/health-data-standards/export/helper/gc32_view_helper.rb

@@ -0,0 +1,39 @@
+module HealthDataStandards
+  module Export
+    module Helper
+      module GC32ViewHelper
+        def gc32_code_display(entry, options={})
+          code_display(entry, options.merge("exclude_null_flavor" => true))
+        end
+        
+        def gc32_effective_time(entry)
+          if entry.time
+            "<effectiveTime value=\"#{Time.at(entry.time).xmlschema}\" />"
+          elsif entry.start_time || entry.end_time
+            gc32_interval(entry, "effectiveTime", :start_time, :end_time)
+          else
+            "<effectiveTime />"
+          end
+        end
+        
+        def gc32_interval(entry, tag_name, start_attribute, end_attribute)
+          time = "<#{tag_name}>"
+          time += "<start value=\"#{Time.at(entry.send(start_attribute)).xmlschema}\" />"  if entry.send(start_attribute)
+          time += "<end value=\"#{Time.at(entry.send(end_attribute)).xmlschema}\" />" if entry.send(end_attribute)
+          time += "</#{tag_name}>"
+        end
+
+        def quantity_display(value, tag_name="value")
+          return unless value
+          if value.respond_to?(:scalar)
+            "<#{tag_name} amount=\"#{value.scalar}\" unit=\"#{value.units}\" />"
+          elsif value['scalar'].present?
+            "<#{tag_name} amount=\"#{value['scalar']}\" unit=\"#{value['units']}\" />"  
+          else
+            "<#{tag_name} amount=\"#{value['value']}\" unit=\"#{value['unit']}\" />"
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,23 @@
+module HealthDataStandards
+  module Export
+    module Helper
+      module HTMLViewHelper
+        def decode_hqmf_section(section, oid)
+          if oid
+            HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['definition'].pluralize.to_sym
+          else
+            section
+          end
+        end
+
+        def decode_hqmf_status(status, oid)
+          if oid
+            HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['status']
+          else
+            status
+          end
+        end
+      end
+    end
+  end
+end