health-data-standards 3.7.0 → 4.0.0

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

@@ -66,13 +66,13 @@ module HealthDataStandards
       def get_valueset(oid, options = {}, &block)
         version = options.fetch(:version, nil)
         include_draft = options.fetch(:include_draft, false)
-        profile = options.fetch(:profile, DEFAULT_PROFILE)
+        profile = options.fetch(:profile, nil)
         effective_date = options.fetch(:effective_date, nil)
         program_name = options.fetch(:program, nil)
         params = { id: oid, ticket: get_ticket }
         params[:version] = version if version
-        params[:includeDraft] = 'yes' if include_draft
-        params[:profile] = profile if include_draft
+        params[:includeDraft] = 'yes' if profile && include_draft
+        params[:profile] = profile if profile
         params[:effectiveDate] = effective_date if effective_date
         params[:programType] = program_name if program_name
         begin

data/lib/hqmf-model/data_criteria.json

@@ -157,7 +157,7 @@
       "status":"",
       "sub_category":"payer",
       "hard_status":false,
-      "patient_api_function":"",
+      "patient_api_function":"allProblems",
       "property":"payer",
       "not_supported":false},
   "patient_characteristic_race":{
@@ -1024,5 +1024,23 @@
       "sub_category":"",
       "hard_status":false,
       "patient_api_function":"assessments",
+      "not_supported":false},
+  "adverse_event":{
+      "title":"adverse event",
+      "category":"adverse_events",
+      "definition":"adverse_event",
+      "status":"",
+      "sub_category":"",
+      "hard_status":false,
+      "patient_api_function":"adverseEvents",
+      "not_supported":false},
+  "allergy_intolerance":{
+      "title":"allergy/intolerance",
+      "category":"allergies_intolerances",
+      "definition":"allergy_intolerance",
+      "status":"",
+      "sub_category":"",
+      "hard_status":false,
+      "patient_api_function":"allergies",
       "not_supported":false}
 }

data/lib/hqmf-model/data_criteria.rb

@@ -27,19 +27,27 @@ module HQMF
     FIELDS = {'ABATEMENT_DATETIME' => {title:'Abatement Datetime', coded_entry_method: :end_date, field_type: :timestamp},
               'ACTIVE_DATETIME' => {title:'Active Date/Time', coded_entry_method: :active_date_time, field_type: :timestamp},
               'ADMISSION_DATETIME' => {title:'Admission Date/Time', coded_entry_method: :admit_time, code: '399423000', code_system:'2.16.840.1.113883.6.96', field_type: :timestamp},
+              # QDM 5.0 addition. This is the same as FACILITY_LOCATION.
+              # TODO: (LDY 10/5/2016) this is a new attribute from QDM 5.0. We do not yet have the code or template_id for this. This should be updated when we do.
+              'ADMISSION_SOURCE' => {title:'Admission Source', coded_entry_method: :admission_source, field_type: :value},
               'ANATOMICAL_APPROACH_SITE' => {title:'Anatomical Approach Site', coded_entry_method: :anatomical_approach,  field_type: :value},
               'ANATOMICAL_LOCATION_SITE' => {title:'Anatomical Location Site', coded_entry_method: :anatomical_location,  field_type: :value},
               'ANATOMICAL_STRUCTURE' => {title:'Anatomical Structure', coded_entry_method: :anatomical_structure, code: '91723000', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1000.2', field_type: :value},
               'CAUSE' => {title:'Cause', coded_entry_method: :cause_of_death, code: '42752001', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1017.2', field_type: :value},
+              # TODO: Determine actual code and code_system for component attribute
+              'COMPONENT' => {title: 'Component', coded_entry_method: :components, field_type: :value},
               'CUMULATIVE_MEDICATION_DURATION' => {title:'Cumulative Medication Duration', coded_entry_method: :cumulative_medication_duration, code: '261773006', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1001.3', field_type: :value},
               # MISSING Date - The date that the patient passed away. - Patient Characteristic Expired
               'DIAGNOSIS' => {title:'Diagnosis', coded_entry_method: :diagnosis, field_type: :value},
               'DISCHARGE_DATETIME' => {title:'Discharge Date/Time', coded_entry_method: :discharge_time, code: '442864001', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1025.1', field_type: :timestamp},
-              'DISCHARGE_STATUS' => {title:'Discharge Status', coded_entry_method: :discharge_disposition, code: '309039003', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1003.2', field_type: :value},
-              'DOSE' => {title:'Dose', coded_entry_method: :dose, code: '398232005', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1004.1', field_type: :value},
+              # TODO: (LDY 10/5/2016) this changed from "discharge status" to "discharge disposition". likely there is a code and template id change necessary. these are not yet known.
+              'DISCHARGE_STATUS' => {title:'Discharge Disposition', coded_entry_method: :discharge_disposition, code: '309039003', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1003.2', field_type: :value},
+              # TODO: (LDY 10/4/2016) this changed from "dose" to "dosage". it's possible that there's another code associated with this. this code was not available at the time of this change.
+              'DOSE' => {title:'Dosage', coded_entry_method: :dose, code: '398232005', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1004.1', field_type: :value},
               'FACILITY_LOCATION' => {title:'Facility Location', coded_entry_method: :facility, code: 'SDLOC', field_type: :value},
-              'FACILITY_LOCATION_ARRIVAL_DATETIME' => {title:'Facility Location Arrival Date/Time', coded_entry_method: :facility_arrival, code: 'SDLOC_ARRIVAL', field_type: :nested_timestamp},
-              'FACILITY_LOCATION_DEPARTURE_DATETIME' => {title:'Facility Location Departure Date/Time', coded_entry_method: :facility_departure, code: 'SDLOC_DEPARTURE', field_type: :nested_timestamp},
+              # TODO: (LDY 10/5/2016) this changed from 'facility arrival/departure' to 'location period'. likely there is a code and template id change necessary. these are not yet known.
+              'FACILITY_LOCATION_ARRIVAL_DATETIME' => {title:'Location Period Start Date/Time', coded_entry_method: :facility_arrival, code: 'SDLOC_ARRIVAL', field_type: :nested_timestamp},
+              'FACILITY_LOCATION_DEPARTURE_DATETIME' => {title:'Location Period End Date/Time', coded_entry_method: :facility_departure, code: 'SDLOC_DEPARTURE', field_type: :nested_timestamp},
               'FREQUENCY' => {title:'Frequency', coded_entry_method: :administration_timing, code: '307430002', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1006.1', field_type: :value},
               'HEALTH_RECORD_FIELD' => {title: 'Health Record Field', coded_entry_method: :health_record_field, code: '395676008', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.28.3.102:2014-11-24', field_type: :value},
               'INCISION_DATETIME' => {title:'Incision Date/Time', coded_entry_method: :incision_time, code: '34896006', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.89', field_type: :timestamp},
@@ -59,13 +67,15 @@ module HQMF
               'REACTION'=> {title:'Reaction', coded_entry_method: :reaction, code: '263851003', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.85', field_type: :value},
               'REASON' => {title:'Reason', coded_entry_method: :reason, code: '410666004', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.88', field_type: :value},
               'RECORDED_DATETIME' => {title:'Recorded Datetime', coded_entry_method: :start_date, field_type: :timestamp},
-              'REFERENCE_RANGE_HIGH' => {title:'Reference Range High', coded_entry_method: :reference_range_high, field_type: :value},
-              'REFERENCE_RANGE_LOW' => {title:'Reference Range Low', coded_entry_method: :reference_range_low, field_type: :value},
+              'REFERENCE_RANGE_HIGH' => {title:'Reference Range - High', coded_entry_method: :reference_range_high, field_type: :value},
+              'REFERENCE_RANGE_LOW' => {title:'Reference Range - Low', coded_entry_method: :reference_range_low, field_type: :value},
               'REFILLS' => {title:'Refills', coded_entry_method: :refills,  field_type: :value},
               'RELATED_TO' => {title:'Related To', coded_entry_method: :related_to,  code: 'REL', codeSystem: '2.16.840.1.113883.1.11.11603', field_type: :value},
               'RELATIONSHIP' => {title:'Relationship', coded_entry_method: :relationship_to_patient, field_type: :value},
               'REMOVAL_DATETIME' => {title:'Removal Date/Time', coded_entry_method: :removal_time, code: '118292001', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1032.1', field_type: :timestamp},
               # Result isn't encoded
+              # TODO: (LDY 10/4/2016) RESULT_DATETIME is a new attribute in QDM 5.0. We do not yet have codes/template information for this.
+              'RESULT_DATETIME' => {title:'Result Date/Time', coded_entry_method: :result_date_time, field_type: :timestamp},
               'ROUTE' => {title:'Route', coded_entry_method: :route, code: '263513008', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1020.2', field_type: :value},
               'SEVERITY' => {title:'Severity', coded_entry_method: :severity, code: 'SEV', code_system:'2.16.840.1.113883.5.4', template_id: '2.16.840.1.113883.10.20.22.4.8', field_type: :value},
               'SIGNED_DATETIME' =>  {title:'Signed Date/Time', coded_entry_method: :signed_date_time, field_type: :timestamp},
@@ -73,11 +83,14 @@ module HQMF
               # STATUS is referenced in the code as `qdm_status` because entry/Record already has a `status`/`status_code` field which has a different meaning
               'STATUS' => {title: 'Status', coded_entry_method: :qdm_status, code: '33999-4', code_system:'2.16.840.1.113883.6.1', field_type: :value},
               'STOP_DATETIME' => {title:'Stop Date/Time', coded_entry_method: :end_date, code: '397898000', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1026.1', field_type: :timestamp},
+              # TODO: (LDY 10/4/2016) SUPPLY is a new attribute in QDM 5.0. We do not yet have codes/template information for this.
+              'SUPPLY' => {title:'Supply', coded_entry_method: :supply, field_type: :value},
               'TARGET_OUTCOME' => {title:'Target Outcome', coded_entry_method: :target_outcome, code: '385676005', code_system:'2.16.840.1.113883.6.96', template_id: '', field_type: :value},
               # MISSING Time - The time that the patient passed away
 
               # Custom field values
-              'FLFS' => {title:'Fulfills', coded_entry_method: :fulfills, code: 'FLFS', field_type: :reference},
+              # QDM 5.3 Update: "Related To" replaces Fulfills. We are keeping the fulfills code and only make changes to the UI.
+              'FLFS' => {title:'Related To', coded_entry_method: :fulfills, code: 'FLFS', field_type: :reference},
               'SOURCE' => {title:'Source', coded_entry_method: :source, code: '260753009', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.2001.2', field_type: :value},
               'TRANSFER_FROM' => {title:'Transfer From', coded_entry_method: :transfer_from, code: 'TRANSFER_FROM', template_id: '2.16.840.1.113883.10.20.24.3.81', field_type: :value},
               'TRANSFER_FROM_DATETIME' => {title:'Transfer From Date/Time', coded_entry_method: :transfer_from_time, code: 'ORG_TIME', template_id: '2.16.840.1.113883.10.20.24.3.81', field_type: :nested_timestamp},
@@ -431,6 +444,17 @@ module HQMF
         when 'ACT'
           # Currentlty forcing this as the SimpleXML reresentation contains a fulfills for these types
           value = HQMF::TypedReference.new(json["reference"], 'FLFS', '')
+        when 'CMP'
+          # For ResultComponent, json will have a value or "" for referenceRangeLow_value, for Component, will be nil
+          if json['referenceRangeLow_value']
+            value = ResultComponent.new(json)
+          else
+            value = Component.new(json)
+          end
+        when 'COL'
+          value = HQMF::Collection.from_json(json)
+        when 'FAC'
+          value = Facility.new(json)
         else
           raise "Unknown value type [#{type}]"
         end

data/lib/hqmf-model/document.rb

@@ -9,7 +9,7 @@ module HQMF
 
     include HQMF::Conversion::Utilities
 
-    attr_reader :id, :title, :description, :measure_period, :attributes, :populations, :source_data_criteria, :hqmf_id, :hqmf_set_id, :hqmf_version_number, :cms_id
+    attr_reader :id, :title, :description, :measure_period, :attributes, :populations, :source_data_criteria, :hqmf_id, :hqmf_set_id, :hqmf_version_number, :cms_id, :populations_cql_map, :cql_measure_library, :observations
   
     # Create a new HQMF::Document which can be converted to JavaScript
     # @param [String] id
@@ -24,7 +24,7 @@ module HQMF
     # @param [Array#Attribute] attributes
     # @param [Array#Hash] populations
     # @param [Range] measure_period
-    def initialize(id, hqmf_id, hqmf_set_id, hqmf_version_number, cms_id, title, description, population_criteria, data_criteria, source_data_criteria, attributes, measure_period, populations=nil)
+    def initialize(id, hqmf_id, hqmf_set_id, hqmf_version_number, cms_id, title, description, population_criteria, data_criteria, source_data_criteria, attributes, measure_period, populations=nil, populations_cql_map=nil, cql_measure_library=nil, observations=nil)
       @id = id
       @hqmf_id = hqmf_id
       @hqmf_set_id = hqmf_set_id
@@ -46,6 +46,9 @@ module HQMF
         }
       ]
       @measure_period = measure_period
+      @populations_cql_map = populations_cql_map
+      @cql_measure_library = cql_measure_library
+      @observations = observations
     end
     
     # Create a new HQMF::Document from a JSON hash keyed with symbols
@@ -104,6 +107,12 @@ module HQMF
       
       json[:populations] = @populations
       
+      json[:populations_cql_map] = @populations_cql_map
+
+      json[:observations] = @observations
+
+      json[:cql_measure_library] = @cql_measure_library
+
       json[:measure_period] = @measure_period.to_json
 
       json

data/lib/hqmf-model/types.rb

@@ -155,7 +155,6 @@ module HQMF
   class Coded
     include HQMF::Conversion::Utilities
     attr_reader :type, :system, :code, :code_list_id, :title, :null_flavor, :original_text
-    
     # Create a new HQMF::Coded
     # @param [String] type
     # @param [String] system
@@ -285,9 +284,7 @@ module HQMF
 
     def self.from_json(json)
       type = json["type"] if json["type"]
-
-      value = HQMF::DataCriteria.convert_value(json["value"]) if json["value"]
-      
+      value = HQMF::DataCriteria.convert_value(json["value"]) if json["value"]  
       HQMF::SubsetOperator.new(type,value)
     end
     
@@ -428,4 +425,33 @@ module HQMF
     end
   end
   
-end
+  class Collection
+    include HQMF::Conversion::Utilities
+    attr_accessor :type, :values
+    
+    def initialize(type, values)
+      @type = type || 'COL'
+      @values = values || []
+    end
+
+    def self.from_json(json)
+      json = json.with_indifferent_access
+      values = []
+      type = json['type']
+      json['values'].each { |value| values.push(HQMF::DataCriteria.convert_value(value))}
+      HQMF::Collection.new(type, values)
+    end
+
+    def to_json
+      json = build_hash(self, [:type])
+      json[:values] = []
+      @values.each {|value| json[:values] << value.to_json  }
+      json    
+    end
+
+    def ==(other)
+      check_equality(self,other)
+    end
+  end
+  
+end

data/lib/hqmf-parser.rb

@@ -36,6 +36,13 @@ require_relative 'hqmf-parser/2.0/data_criteria'
 require_relative 'hqmf-parser/2.0/population_criteria'
 require_relative 'hqmf-parser/2.0/precondition'
 
+require_relative 'hqmf-parser/cql/document'
+require_relative 'hqmf-parser/cql/data_criteria_helpers/dc_definition_from_template_or_type_extract'
+require_relative 'hqmf-parser/cql/document_helpers/doc_population_helper'
+require_relative 'hqmf-parser/cql/data_criteria_helpers/dc_post_processing'
+require_relative 'hqmf-parser/cql/data_criteria'
+require_relative 'hqmf-parser/cql/value_set_helper'
+
 require_relative 'hqmf-model/data_criteria.rb'
 require_relative 'hqmf-model/document.rb'
 require_relative 'hqmf-model/population_criteria.rb'

data/lib/hqmf-parser/2.0/data_criteria.rb

@@ -148,7 +148,10 @@ module HQMF2
     # not give us the correct SDC data when we are trying to recreate since we are looping back through
     # the same data criteria before it has finished processing: See: DocUtilities.extract_source_data_criteria
     def clone
-      other = DataCriteria.new(@entry, @data_criteria_references, @occurrences_map)
+      # Using 'self.class.new' in order to allow this DataCriteria class as
+      # well as any future new extending DataCriteria classes to use this clone
+      # function.
+      other = self.class.new(@entry, @data_criteria_references, @occurrences_map)
       other.instance_variable_set(:@id, @id)
       other.instance_variable_set(:@original_id, @original_id)
       other.instance_variable_set(:@property, @property)

data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_base_extract.rb

@@ -67,7 +67,7 @@ module HQMF2
 
     # Extract the negation (and the negation_code_list_id if appropriate)
     def extract_negation
-      negation = (attr_val('./*/@actionNegationInd') == 'true')
+      negation = (attr_val('./*/@actionNegationInd').to_s.downcase == 'true')
       negation_code_list_id = nil
       if negation
         res = @entry.at_xpath('./*/cda:outboundRelationship/*/cda:code[@code="410666004"]/../cda:value/@valueSet',

data/lib/hqmf-parser/2.0/document.rb

@@ -191,8 +191,8 @@ module HQMF2
       value_obj = nil
       value_obj = handle_attribute_value(attribute, value) if attribute.at_xpath('./cda:value', NAMESPACES)
 
-      # Handle the cms_id
-      @cms_id = "CMS#{value}v#{@hqmf_version_number.to_i}" if name.include? 'eMeasure Identifier'
+      # Handle the cms_id - changed to eCQM in MAT 5.4 (QDM 5.3)
+      @cms_id = "CMS#{value}v#{@hqmf_version_number.to_i}" if (name.include? 'eMeasure Identifier') || (name.include? 'eCQM Identifier')
 
       HQMF::Attribute.new(id, code, value, nil, name, id_obj, code_obj, value_obj)
     end
@@ -283,7 +283,7 @@ module HQMF2
         end
       end
     end
-    
+
     # For specific occurrence data criteria, make sure the source data criteria reference points
     # to the correct source data criteria.
     def handle_specific_source_data_criteria_reference(criteria)
@@ -299,6 +299,6 @@ module HQMF2
         original_sdc.instance_variable_set(:@code_list_id, criteria.code_list_id)
       end
     end
-    
+
   end
 end

data/lib/hqmf-parser/2.0/document_helpers/doc_population_helper.rb

@@ -51,7 +51,6 @@ module HQMF2
 
         population['OBSERV'] = 'OBSERV' if has_observation
         @populations << population
-
         handle_stratifications(population_def, number_of_populations, population, id_def, population_index)
       end
 
@@ -116,7 +115,6 @@ module HQMF2
         # Skip this Stratification if any precondition doesn't contain any preconditions
         next unless PopulationCriteria.new(criteria_def, @document, @id_generator)
                     .preconditions.all? { |prcn| prcn.preconditions.length > 0 }
-
         index = number_of_populations + ((population_index - 1) * criteria_def.xpath('./*/cda:precondition').length) +
                 criteria_def_index
         criteria_id = HQMF::PopulationCriteria::STRAT

data/lib/hqmf-parser/2.0/population_criteria.rb

@@ -34,7 +34,7 @@ module HQMF2
       else
         # Extract the data criteria this population references
         dc = handle_observation_criteria
-        @preconditions = [Precondition.new(id_generator.next_id, nil, nil, false, HQMF2::Reference.new(dc.id))]
+        @preconditions = [Precondition.new(id_generator.next_id, nil, nil, false, HQMF2::Reference.new(dc.id))] if dc
       end
     end
 
@@ -76,7 +76,7 @@ module HQMF2
       dc = parse_parts_to_dc(parts)
       @doc.add_data_criteria(dc)
       # Update reference_ids with any newly referenced data criteria
-      dc.children_criteria.each { |cc| @doc.add_reference_id(cc) } unless dc.children_criteria.nil?
+      dc.children_criteria.each { |cc| @doc.add_reference_id(cc) } unless dc&.children_criteria.nil?
       dc
     end
 

data/lib/hqmf-parser/2.0/value_set_helper.rb

@@ -90,7 +90,10 @@ module HQMF2
       '2.16.840.1.113883.10.20.28.3.115' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role/cda:playingMaterial[@classCode='MMAT']/cda:code", result_path: nil },
       '2.16.840.1.113883.10.20.28.3.116' => { valueset_path: './*/cda:value', result_path: nil },
       '2.16.840.1.113883.10.20.28.3.117' => { valueset_path: './*/cda:code', result_path: './*/cda:value' },
-      '2.16.840.1.113883.10.20.28.3.118' => { valueset_path: './*/cda:code', result_path: nil }
+      '2.16.840.1.113883.10.20.28.3.118' => { valueset_path: './*/cda:code', result_path: nil },
+      '2.16.840.1.113883.10.20.28.3.119' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='MANU']/cda:playingEntity[@classCode='MMAT']/cda:code", result_path: nil },
+      '2.16.840.1.113883.10.20.28.3.120' => { valueset_path: "./*/cda:participation[@typeCode='CSM']/cda:role[@classCode='MANU']/cda:playingEntity[@classCode='MMAT']/cda:code", result_path: nil }
+
     }
     # rubocop:enable Metrics/LineLength
 

data/lib/hqmf-parser/cql/data_criteria.rb

@@ -0,0 +1,57 @@
+module HQMF2CQL
+  # Represents a data criteria specification
+  class DataCriteria < HQMF2::DataCriteria
+    include HQMF2CQL::DataCriteriaPostProcessing, HQMF2CQL::DataCriteriaTypeAndDefinitionExtraction
+
+    # Get the title of the criteria, provides a human readable description
+    # @return [String] the title of this data criteria
+    def title
+      disp_value = attr_val("#{@code_list_xpath}/cda:displayName/@value")
+      # Attempt to pull display value from the localVariableName for
+      # MAT 5.3+ exports that appear to no longer include displayName for
+      # code entries.
+      # NOTE: A long term replacement for this and for other portions of the
+      # parsing process should involve reaching out to VSAC for oid information
+      # pulled from the CQL, and then to use that information while parsing.
+      unless disp_value.present?
+        # Grab the localVariableName from the XML
+        disp_value = attr_val('./cda:localVariableName/@value')
+        # Grab everything before the first underscore
+        disp_value = disp_value.partition('_').first unless disp_value.nil?
+      end
+      @title || disp_value || @description || id # allow defined titles to take precedence
+    end
+
+    # Generate the title and description used when producing the model
+    def retrieve_title_and_description_for_model
+      # remove * Value Set from title
+      title_match = title.match(/(.*) \w+ [Vv]alue [Ss]et/)
+      @title = title_match[1] if title_match && title_match.length > 1
+      
+      @description = "#{@description}: #{title}"
+    end
+
+    # In certain situations it is necessary to have a negated data criterion 
+    # copied to a "positive" form.
+    def make_criterion_positive
+      @negation = false
+
+      # Remove negation from description
+      # sometimes "Not Done" used: "Communication: From Provider To Patient, Not Done"
+      # should transform to "Communication: From Provider To Patient"
+      @description.gsub!(', Not Done', '')
+      
+      # sometimes just "Not" used: "Encounter, Not Performed"
+      # should transform to "Encounter, Performed"
+      @description.gsub!(', Not', ',')
+
+      @source_data_criteria = 'Derived from ' + @source_data_criteria
+            
+      # Looking to remove the word 'Not'.  Using lookahead and lookbehind in the regex
+      # criterion.id = criterion.id.gsub(/(?<=[a-z])Not(?=[A-Z])/, '') + '_spoof'
+      @id = @id.gsub(/(?<=[a-z])Not(?=[A-Z])/, '') + '_spoofed'
+
+    end
+    
+  end
+end

data/lib/hqmf-parser/cql/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb

@@ -0,0 +1,79 @@
+module HQMF2CQL
+  # Extracts the type, and modifies the data criteria, based on the template id or definition
+  module DataCriteriaTypeAndDefinitionExtraction
+    extend HQMF2::DataCriteriaTypeAndDefinitionExtraction
+
+    def extract_definition_from_template_or_type
+      # Try to determine what kind of data criteria we are dealing with
+      # First we look for a template id and if we find one just use the definition
+      # status and negation associated with that
+      # If no template id or not one we recognize then try to determine type from
+      # the definition element.
+      extract_definition_from_type unless extract_definition_from_template_id
+    end
+
+    # Given a template id, derive (if available) the definition for the template.
+    # The definitions are stored in hqmf-model/data_criteria.json.
+    def extract_definition_from_template_id
+      found = false
+
+      @template_ids.each do |template_id|
+        # NOTE! (Adam 6/14): The following logic should absolutely be changed
+        # when Bonnie CQL support goes production. The "try this then try
+        # that" approach is an artifact of the template oids changing as of
+        # MAT 5.3; we want to support measures exported using 5.3, but also
+        # measures that were exported using previous versions of the MAT.
+
+        # Try a lookup using the newer template oids.
+        defs = HQMF::DataCriteria.definition_for_template_id(template_id, 'r2cql')
+
+        # If the new template oids didn't work, try a lookup using the older
+        # template oids.
+        defs = HQMF::DataCriteria.definition_for_template_id(template_id, 'r2') unless defs
+
+        if defs
+          @definition = defs['definition']
+          @status = defs['status'].length > 0 ? defs['status'] : nil
+          found ||= true
+        else
+          found ||= handle_known_template_id(template_id)
+        end
+      end
+
+      found
+    end
+
+    # Extract the definition (sometimes status, sometimes other elements) of the data criteria based on the type
+    def extract_definition_from_type
+      if @entry.at_xpath('./cda:grouperCriteria')
+        @definition ||= 'derived'
+        return
+      end
+      # See if we can find a match for the entry definition value and status.
+      entry_type = attr_val('./*/cda:definition/*/cda:id/@extension')
+      handle_entry_type(entry_type)
+    end
+
+    # Generate the definition and/or status from the entry type in most cases.
+    # If the entry type is nil, and the value is a specific occurrence, more parsing may be necessary.
+    def handle_entry_type(entry_type)
+      # settings is required to trigger exceptions, which set the definition
+      HQMF::DataCriteria.get_settings_for_definition(entry_type, @status)
+      @definition = entry_type
+    rescue
+      # if no exact match then try a string match just using entry definition value
+      case entry_type
+      when 'Medication', 'Medications'
+        @definition = 'medication'
+        @status = 'active' unless @status
+      when 'RX'
+        @definition = 'medication'
+        @status = 'dispensed' unless @status
+      when nil
+        definition_for_nil_entry
+      else
+        @definition = extract_definition_from_entry_type(entry_type)
+      end
+    end
+  end
+end