module HQMF # Represents a data criteria specification class DataCriteria include HQMF::Conversion::Utilities SOURCE_DATA_CRITERIA_TEMPLATE_ID = '2.16.840.1.113883.3.100.1.1' SOURCE_DATA_CRITERIA_TEMPLATE_TITLE = 'Source data criteria' XPRODUCT = 'XPRODUCT' UNION = 'UNION' INTERSECT = 'INTERSECT' SATISFIES_ALL = 'satisfies_all' SATISFIES_ANY = 'satisfies_any' VARIABLE = 'variable' # An object containing metadata information for all attributes that are used within the measure data criteria being parsed. # # fields include: # `title`: The QDM human readable title for the attribute. # `coded_entry_method`: this appears to be a way that fields here are referenced within Bonnie. # `field_type`: The type of whatever will be stored for this attribute. This will often be `:timestamp` or `:value`. # `code`: The code for the entry. This should be included to make HQMF generation work properly. This is whatever code is dictated in the HQMF. For Diagnosis, this is in [HQMF QDM IG](http://www.hl7.org/implement/standards/product_brief.cfm?product_id=346) vol 2 page 155 and is `29308-4`. # `code_system`: This is the oid for whatever code system contains `code`. For Diagnosis, this is LOINC: `2.16.840.1.113883.6.1`. This is also located at (http://www.hl7.org/implement/standards/product_brief.cfm?product_id=346) vol 2 page 155. # `template_id`: These appear to be related to HQMFr1 template ids. These appear to be dangerously out of date. Don't use. 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}, '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}, '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}, '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}, '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}, 'LATERALITY' => {title:'Laterality', coded_entry_method: :laterality, code: '272741003', code_system:'2.16.840.1.113883.6.96', template_id: '', field_type: :value}, 'LENGTH_OF_STAY' => {title:'Length of Stay', coded_entry_method: :length_of_stay, code: '183797002', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1029.3', field_type: :value}, 'METHOD' => {title:'Method', coded_entry_method: :method, template_id: '', field_type: :value}, # Negation Rationale isn't encoded 'ONSET_AGE' => {title:'Onset Age', coded_entry_method: :onset_age, code: '445518008', code_system:'2.16.840.1.113883.6.96', template_id: '', field_type: :value}, 'ONSET_DATETIME' => {title:'Onset Datetime', coded_entry_method: :start_date, field_type: :timestamp}, 'ORDINAL' => {title:'Ordinality', coded_entry_method: :ordinality, code: '117363000', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1012.2', field_type: :value}, # previous 'ORDINALITY' => {title:'Ordinality', coded_entry_method: :ordinality, code: '117363000', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1012.2', field_type: :value}, 'PATIENT_PREFERENCE' => {title:'Patient Preference', coded_entry_method: :patient_preference, code: 'PAT', code_system: '2.16.840.1.113883.5.8', template_id: '2.16.840.1.113883.10.20.24.3.83', field_type: :value}, 'PRINCIPAL_DIAGNOSIS' => {title:'Principal Diagnosis', coded_entry_method: :principal_diagnosis, field_type: :value}, 'PROVIDER_PREFERENCE' => {title:'Provider Preference', coded_entry_method: :provider_preference, code: '103323008', code_system: '2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.84', field_type: :value}, 'RADIATION_DOSAGE' => {title:'Radiation Dosage', coded_entry_method: :radiation_dose, code: '228815006', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.91', field_type: :value}, 'RADIATION_DURATION' => {title:'Radiation Duration', coded_entry_method: :radiation_duration, code: '306751006', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.10.20.24.3.91', field_type: :value}, '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}, '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 '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}, 'START_DATETIME' => {title:'Start Date/Time', coded_entry_method: :start_date, code: '398201009', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1027.1', field_type: :timestamp}, # 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}, '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}, '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}, 'TRANSFER_TO' => {title:'Transfer To', coded_entry_method: :transfer_to, code: 'TRANSFER_TO', template_id: '2.16.840.1.113883.10.20.24.3.82', field_type: :value}, 'TRANSFER_TO_DATETIME' => {title:'Transfer To Date/Time', coded_entry_method: :transfer_to_time, code: 'DST_TIME', template_id: '2.16.840.1.113883.10.20.24.3.82', field_type: :nested_timestamp} } # maps attribute codes to the attribute keys VALUE_FIELDS = {'399423000' => 'ADMISSION_DATETIME', '42752001' => 'CAUSE', '261773006' => 'CUMULATIVE_MEDICATION_DURATION', '363819003' => 'CUMULATIVE_MEDICATION_DURATION', # previous '442864001' => 'DISCHARGE_DATETIME', '309039003' => 'DISCHARGE_STATUS', '398232005' => 'DOSE', 'SDLOC' => 'FACILITY_LOCATION', 'SDLOC_ARRIVAL' => 'FACILITY_LOCATION_ARRIVAL_DATETIME', 'SDLOC_DEPARTURE' => 'FACILITY_LOCATION_DEPARTURE_DATETIME', '307430002' => 'FREQUENCY', '260864003' => 'FREQUENCY', # previous '395676008' => 'HEALTH_RECORD_FIELD', '34896006' => 'INCISION_DATETIME', '272741003' => 'LATERALITY', '183797002' => 'LENGTH_OF_STAY', '445518008' => 'ONSET_AGE', '117363000' => 'ORDINALITY', 'PAT' => 'PATIENT_PREFERENCE', '103323008' => 'PROVIDER_PREFERENCE', '228815006' => 'RADIATION_DOSAGE', '306751006' => 'RADIATION_DURATION', '263851003' => 'REACTION', '410666004' => 'REASON', 'REL' => 'RELATED_TO', '118292001' => 'REMOVAL_DATETIME', '263513008' => 'ROUTE', 'SEV' => 'SEVERITY', '398201009' => 'START_DATETIME', '33999-4' => 'STATUS', '397898000' => 'STOP_DATETIME', '385676005' => 'TARGET_OUTCOME', # Custom field values '91723000' => 'ANATOMICAL_STRUCTURE', 'FLFS' => 'FLFS', '260753009' => 'SOURCE', 'TRANSFER_FROM' => 'TRANSFER_FROM', 'ORG_TIME' => 'TRANSFER_FROM_DATETIME', 'TRANSFER_TO' => 'TRANSFER_TO', 'DST_TIME' => 'TRANSFER_TO_DATETIME' } attr_reader :title, :description, :code_list_id, :derivation_operator , :specific_occurrence, :specific_occurrence_const, :source_data_criteria, :variable attr_accessor :id, :value, :field_values, :children_criteria, :effective_time, :status, :temporal_references, :subset_operators, :definition, :inline_code_list, :negation_code_list_id, :negation, :display_name, :comments # Create a new data criteria instance # @param [String] id # @param [String] title # @param [String] display_name # @param [String] description # @param [String] code_list_id # @param [String] negation_code_list_id # @param [List] children_criteria (ids of children data criteria) # @param [String] derivation_operator # @param [String] definition # @param [String] status # @param [Value|Range|Coded] value # @param [Hash] field_values # @param [Range] effective_time # @param [Hash] inline_code_list # @param [boolean] negation # @param [String] negation_code_list_id # @param [List] temporal_references # @param [List] subset_operators # @param [String] specific_occurrence # @param [String] specific_occurrence_const # @param [String] source_data_criteria (id for the source data criteria, important for specific occurrences) # @param [String] user comments for the criteria # @param [Boolean] variable defines if the element is a QDM variable def initialize(id, title, display_name, description, code_list_id, children_criteria, derivation_operator, definition, status, value, field_values, effective_time, inline_code_list, negation, negation_code_list_id, temporal_references, subset_operators, specific_occurrence, specific_occurrence_const, source_data_criteria=nil, comments=nil, variable=false) status = normalize_status(definition, status) @settings = HQMF::DataCriteria.get_settings_for_definition(definition, status) @id = id @title = title @description = description @code_list_id = code_list_id @negation_code_list_id = negation_code_list_id @children_criteria = children_criteria @derivation_operator = derivation_operator @definition = definition @status = status @value = value @field_values = field_values @effective_time = effective_time @inline_code_list = inline_code_list @negation = negation @negation_code_list_id = negation_code_list_id @temporal_references = temporal_references @subset_operators = subset_operators @specific_occurrence = specific_occurrence @specific_occurrence_const = specific_occurrence_const @source_data_criteria = source_data_criteria || id @comments = comments @variable = variable end # create a new data criteria given a category and sub_category. A sub category can either be a status or a sub category def self.create_from_category(id, title, description, code_list_id, category, sub_category=nil, negation=false, negation_code_list_id=nil) settings = HQMF::DataCriteria.get_settings_for_definition(category, sub_category) HQMF::DataCriteria.new(id, title, nil, description, code_list_id, nil, nil, settings['definition'], settings['status'], nil, nil, nil, nil, negation, negation_code_list_id, nil, nil, nil,nil) end def type @settings['category'].to_sym end def property @settings['property'].to_sym unless @settings['property'].nil? end def patient_api_function @settings['patient_api_function'].to_sym unless @settings['patient_api_function'].empty? end def hard_status @settings['hard_status'] end def update_copy(hard_status, title, description, derivation_operator, definition) @settings['hard_status'] = hard_status @title = title @description = description @derivation_operator = derivation_operator @definition = definition end def definition=(definition) @definition = definition @settings = HQMF::DataCriteria.get_settings_for_definition(@definition, @status) end def status=(status) @status = status @settings = HQMF::DataCriteria.get_settings_for_definition(@definition, @status) end # Create a new data criteria instance from a JSON hash keyed with symbols def self.from_json(id, json) title = json["title"] if json["title"] display_name = json["display_name"] if json["display_name"] description = json["description"] if json["description"] code_list_id = json["code_list_id"] if json["code_list_id"] children_criteria = json["children_criteria"] if json["children_criteria"] derivation_operator = json["derivation_operator"] if json["derivation_operator"] definition = json["definition"] if json["definition"] status = json["status"] if json["status"] value = convert_value(json["value"]) if json["value"] field_values = json["field_values"].inject({}){|memo,(k,v)| memo[k.to_s] = convert_value(v); memo} if json["field_values"] effective_time = HQMF::Range.from_json(json["effective_time"]) if json["effective_time"] inline_code_list = json["inline_code_list"].inject({}){|memo,(k,v)| memo[k.to_s] = v; memo} if json["inline_code_list"] negation = json["negation"] || false negation_code_list_id = json['negation_code_list_id'] if json['negation_code_list_id'] temporal_references = json["temporal_references"].map {|reference| HQMF::TemporalReference.from_json(reference)} if json["temporal_references"] subset_operators = json["subset_operators"].map {|operator| HQMF::SubsetOperator.from_json(operator)} if json["subset_operators"] specific_occurrence = json['specific_occurrence'] if json['specific_occurrence'] specific_occurrence_const = json['specific_occurrence_const'] if json['specific_occurrence_const'] source_data_criteria = json['source_data_criteria'] if json['source_data_criteria'] comments = json['comments'] if json['comments'] variable = json['variable'] || false HQMF::DataCriteria.new(id, title, display_name, description, code_list_id, children_criteria, derivation_operator, definition, status, value, field_values, effective_time, inline_code_list, negation, negation_code_list_id, temporal_references, subset_operators,specific_occurrence,specific_occurrence_const,source_data_criteria, comments, variable) end def is_same_type?(criteria) return @definition == criteria.definition && @hard_status == criteria.hard_status && @negation == criteria.negation && all_code_set_oids.sort == criteria.all_code_set_oids.sort end def to_json json = base_json {self.id.to_s.to_sym => json} end def base_json x = nil json = build_hash(self, [:title,:display_name,:description,:code_list_id,:children_criteria, :derivation_operator, :property, :type, :definition, :status, :hard_status, :negation, :negation_code_list_id,:specific_occurrence,:specific_occurrence_const,:source_data_criteria,:variable]) json[:children_criteria] = @children_criteria unless @children_criteria.nil? || @children_criteria.empty? json[:value] = ((@value.is_a? String) ? @value : @value.to_json) if @value json[:field_values] = @field_values.inject({}) {|memo,(k,v)| memo[k] = (!v.nil? ? v.to_json : nil); memo} if @field_values json[:effective_time] = @effective_time.to_json if @effective_time json[:inline_code_list] = @inline_code_list if @inline_code_list json[:temporal_references] = x if x = json_array(@temporal_references) json[:subset_operators] = x if x = json_array(@subset_operators) json[:comments] = @comments if @comments json end def has_temporal(temporal_reference) @temporal_references.reduce(false) {|found, item| found ||= item == temporal_reference } end def has_subset(subset_operator) @subset_operators.reduce(false) {|found, item| found ||= item == subset_operator } end def self.statuses_by_definition settings_file = File.expand_path('../data_criteria.json', __FILE__) settings_map = JSON.parse(File.read(settings_file)) all_defs = (settings_map.map {|key, value| {category: value['category'],definition:value['definition'],status:(value['status'].empty? ? nil : value['status']), sub_category: value['sub_category'],title:value['title']} unless value['not_supported']}).compact by_categories = {} all_defs.each do |definition| by_categories[definition[:category]]||={} status = definition[:status] def_key = definition[:definition] if status.nil? and definition[:sub_category] and !definition[:sub_category].empty? status = definition[:sub_category] def_key = def_key.gsub("_#{status}",'') end by_categories[definition[:category]][def_key]||={category:def_key,statuses:[]} by_categories[definition[:category]][def_key][:statuses] << status unless status.nil? end status_by_category = {} by_categories.each {|key, value| status_by_category[key] = value.values} status_by_category.delete('derived') status_by_category.delete('variable') status_by_category.delete('measurement_period') status_by_category.values.flatten end def referenced_data_criteria(document) referenced = [] if (@children_criteria) @children_criteria.each do |id| dc = document.data_criteria(id) referenced << id referenced.concat(dc.referenced_data_criteria(document)) end end if (@temporal_references) @temporal_references.each do |tr| id = tr.reference.id if (id != HQMF::Document::MEASURE_PERIOD_ID) dc = document.data_criteria(id) referenced << id referenced.concat(dc.referenced_data_criteria(document)) end end end referenced end def all_code_set_oids # root oid referenced_oids = [code_list_id] # value oid referenced_oids << value.code_list_id if value != nil and value.type == 'CD' # negation oid referenced_oids << negation_code_list_id if negation_code_list_id != nil # field oids if field_values != nil referenced_oids.concat (field_values.map {|key,field| field.code_list_id if field != nil and field.type == 'CD'}) end referenced_oids end def self.get_settings_map return @settings_map if @settings_map settings_file = File.expand_path('../data_criteria.json', __FILE__) @settings_map = JSON.parse(File.read(settings_file)) end def self.get_settings_for_definition(definition, status) settings_file = File.expand_path('../data_criteria.json', __FILE__) settings_map = get_settings_map key = definition + ((status.nil? || status.empty?) ? '' : "_#{status}") settings = settings_map[key] raise "data criteria is not supported #{key}" if settings.nil? || settings["not_supported"] settings end def self.definition_for_template_id(template_id, version='r1') get_template_id_map(version)[template_id] end def self.template_id_for_definition(definition, status, negation, version="r1") # in r2 negation uses the same template as a positive assertion negation = false if version == "r2" get_template_id_map(version).key({'definition' => definition, 'status' => status || '', 'negation' => negation}) end def self.title_for_template_id(template_id, version='r1') value = get_template_id_map(version)[template_id] if value settings = self.get_settings_for_definition(value['definition'], value['status']) if settings settings['title'] else 'Unknown data criteria' end else 'Unknown template id' end end def self.get_template_id_map(version="r1") read_template_id_map(version) end private def self.read_template_id_map(version) HealthDataStandards::Util::HQMFTemplateHelper.template_id_map(version) end def normalize_status(definition, status) return status if status.nil? case status.downcase when 'completed', 'complete' case definition when 'diagnosis' 'active' else 'performed' end when 'order' 'ordered' else status.downcase end end def self.convert_value(json) return nil unless json.present? type = json["type"] case type when 'TS', 'PQ' value = HQMF::Value.from_json(json) when 'IVL_PQ', 'IVL_TS' value = HQMF::Range.from_json(json) when 'CD' value = HQMF::Coded.from_json(json) when 'ANYNonNull' value = HQMF::AnyValue.from_json(json) when 'FLFS' value = HQMF::TypedReference.from_json(json) when 'ACT' # Currentlty forcing this as the SimpleXML reresentation contains a fulfills for these types value = HQMF::TypedReference.new(json["reference"], 'FLFS', '') else raise "Unknown value type [#{type}]" end value end end end