Adding filters to fix CAT I export errors

lib/c4_helper.rb

@@ -1,4 +1,5 @@
 require 'date'
+require_relative './cypress/scoop_and_filter.rb'
 
 module C4Helper
   class Cat1Exporter
@@ -107,11 +108,13 @@ def headergenerater(patient)
 
     def pluck(outfilepath, patients)
       begin
+      patient_scoop_and_filter = Cypress::ScoopAndFilter.new(@measures)
       #, Zip::File::CREATE
       if patients && patients.length > 0
         Zip::OutputStream.open(outfilepath) do |zout|
             patients.each do |patient_hash|
               patient=patient_hash[:record]
+              patient_scoop_and_filter.scoop_and_filter(patient)
               #Including Provider Details In a way CQM-Report wants it
               provider = Provider.where('_id' => patient.provider_ids[0]).first
               @options[:provider] = provider

lib/cypress/scoop_and_filter.rb

@@ -0,0 +1,92 @@
+module Cypress
+  class ScoopAndFilter
+    def initialize(measures)
+      @valuesets = measures.collect(&:value_sets).flatten.uniq
+      @relevant_codes = codes_in_measures
+      @de_category_statuses_for_measures = get_non_demographic_category_statuses(measures)
+    end
+
+    # return an array of all of the concepts in all of the valueset for the measure
+    def codes_in_measures
+      code_list = @valuesets.collect(&:concepts).flatten
+      code_list.map { |cl| { code: cl.code, codeSystemOid: cl.code_system_oid } }
+    end
+
+    def get_non_demographic_category_statuses(measures)
+      measures.collect do |measure|
+        measure.source_data_criteria.map { |cr| data_element_category_and_status(cr) unless cr.qdmCategory == 'patient_characteristic' }
+      end.flatten.uniq
+    end
+
+    def scoop_and_filter(patient)
+      demographic_criteria = patient.qdmPatient.dataElements.collect { |de| de if de.qdmCategory == 'patient_characteristic' }.compact
+      # If a negated code belongs to multiple valuesets, we need to add a cloned entry for each valueset.
+      # This array stores the cloned entries to be added
+      multi_vs_negation_elements = []
+      patient.qdmPatient.dataElements.keep_if { |de| data_element_used_by_measure(de) }
+      patient.qdmPatient.dataElements.each do |data_element|
+        scoop_and_filter_data_element_codes(data_element, multi_vs_negation_elements)
+      end
+      # keep data element if codes is not empty
+      patient.qdmPatient.dataElements.keep_if { |data_element| data_element.dataElementCodes.present? }
+      patient.qdmPatient.dataElements.concat(demographic_criteria)
+      patient.qdmPatient.dataElements.concat(multi_vs_negation_elements)
+      patient
+    end
+
+    private
+
+    # Method to remove codes from a data element that are not relevant to measure.
+    # Multi_vs_negation_elements is an array of cloned elements to add to patient record to capture all of the negated valuesets
+    def scoop_and_filter_data_element_codes(data_element, multi_vs_negation_elements)
+      # keep if data_element code and codesystem is in one of the relevant_codes
+      data_element.dataElementCodes.keep_if { |de_code| @relevant_codes.include?(code: de_code.code, codeSystemOid: de_code.codeSystemOid) }
+      # Do not try to replace with negated valueset if all codes are removed
+      return if data_element.dataElementCodes.blank?
+
+      add_description_to_data_element(data_element)
+      return unless data_element.respond_to?('negationRationale') && data_element.negationRationale
+
+      replace_negated_code_with_valueset(data_element, multi_vs_negation_elements)
+    end
+
+    def data_element_category_and_status(data_element)
+      { category: data_element.qdmCategory, status: data_element['qdmStatus'] }
+    end
+
+    # returns true if a patients data element is used by a measure
+    def data_element_used_by_measure(data_element)
+      @de_category_statuses_for_measures.include?(category: data_element['qdmCategory'], status: data_element['qdmStatus'])
+    end
+
+    def add_description_to_data_element(data_element)
+      de = data_element
+      vsets = @valuesets.select { |vs| vs.concepts.any? { |c| c.code == de.codes.first.code && c.code_system_oid == de.codes.first.codeSystemOid } }
+      # A data element may have codes from multiple valusets, pick the first valueset for the description
+      vs = vsets.first
+      de.description = vs.display_name
+    end
+
+    # For negated elements, replace codes (that aren't direct reference codes) with valuesets.
+    # If a code is in multiple valuesets, create new entries to be added to record
+    def replace_negated_code_with_valueset(data_element, multi_vs_negation_elements)
+      de = data_element
+      neg_vs = @valuesets.select { |vs| vs.concepts.any? { |c| c.code == de.codes.first.code && c.code_system_oid == de.codes.first.codeSystemOid } }
+
+      negated_valueset = neg_vs.first
+      neg_vs.drop(1).each do |additional_vs|
+        next if additional_vs.oid[0, 3] == 'drc'
+
+        de_for_additional_vs = data_element.clone
+        de_for_additional_vs.id = QDM::Id.new(value: BSON::ObjectId.new.to_s)
+        de_for_additional_vs.dataElementCodes = [{ code: additional_vs.oid, codeSystemOid: '1.2.3.4.5.6.7.8.9.10' }]
+        multi_vs_negation_elements << de_for_additional_vs
+      end
+
+      # If the first three characters of the valueset oid is drc, this is a direct reference code, not a valueset.  Do not negate a valueset here.
+      return if negated_valueset.oid[0, 3] == 'drc'
+
+      data_element.dataElementCodes = [{ code: negated_valueset.oid, codeSystemOid: '1.2.3.4.5.6.7.8.9.10' }]
+    end
+  end
+end