cqm-parsers 0.1.0
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- checksums.yaml +7 -0
- data/Gemfile +29 -0
- data/README.md +21 -0
- data/Rakefile +19 -0
- data/lib/ext/code.rb +10 -0
- data/lib/ext/data_element.rb +24 -0
- data/lib/hqmf-model/attribute.rb +63 -0
- data/lib/hqmf-model/data_criteria.rb +467 -0
- data/lib/hqmf-model/document.rb +253 -0
- data/lib/hqmf-model/population_criteria.rb +102 -0
- data/lib/hqmf-model/precondition.rb +94 -0
- data/lib/hqmf-model/types.rb +457 -0
- data/lib/hqmf-model/utilities.rb +52 -0
- data/lib/hqmf-parser.rb +116 -0
- data/lib/hqmf-parser/1.0/attribute.rb +121 -0
- data/lib/hqmf-parser/1.0/comparison.rb +34 -0
- data/lib/hqmf-parser/1.0/data_criteria.rb +92 -0
- data/lib/hqmf-parser/1.0/document.rb +195 -0
- data/lib/hqmf-parser/1.0/expression.rb +60 -0
- data/lib/hqmf-parser/1.0/observation.rb +61 -0
- data/lib/hqmf-parser/1.0/population_criteria.rb +75 -0
- data/lib/hqmf-parser/1.0/precondition.rb +90 -0
- data/lib/hqmf-parser/1.0/range.rb +76 -0
- data/lib/hqmf-parser/1.0/restriction.rb +162 -0
- data/lib/hqmf-parser/1.0/utilities.rb +55 -0
- data/lib/hqmf-parser/2.0/data_criteria.rb +372 -0
- data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_base_extract.rb +80 -0
- data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb +201 -0
- data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_post_processing.rb +85 -0
- data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_specific_occurrences_and_source_data_criteria_extract.rb +117 -0
- data/lib/hqmf-parser/2.0/document.rb +304 -0
- data/lib/hqmf-parser/2.0/document_helpers/doc_population_helper.rb +173 -0
- data/lib/hqmf-parser/2.0/document_helpers/doc_utilities.rb +131 -0
- data/lib/hqmf-parser/2.0/field_value_helper.rb +251 -0
- data/lib/hqmf-parser/2.0/population_criteria.rb +134 -0
- data/lib/hqmf-parser/2.0/precondition.rb +73 -0
- data/lib/hqmf-parser/2.0/source_data_criteria_helper.rb +112 -0
- data/lib/hqmf-parser/2.0/types.rb +448 -0
- data/lib/hqmf-parser/2.0/utilities.rb +45 -0
- data/lib/hqmf-parser/2.0/value_set_helper.rb +104 -0
- data/lib/hqmf-parser/converter/pass1/data_criteria_converter.rb +257 -0
- data/lib/hqmf-parser/converter/pass1/document_converter.rb +133 -0
- data/lib/hqmf-parser/converter/pass1/population_criteria_converter.rb +185 -0
- data/lib/hqmf-parser/converter/pass1/precondition_converter.rb +173 -0
- data/lib/hqmf-parser/converter/pass1/precondition_extractor.rb +201 -0
- data/lib/hqmf-parser/converter/pass1/simple_data_criteria.rb +26 -0
- data/lib/hqmf-parser/converter/pass1/simple_operator.rb +89 -0
- data/lib/hqmf-parser/converter/pass1/simple_population_criteria.rb +10 -0
- data/lib/hqmf-parser/converter/pass1/simple_precondition.rb +51 -0
- data/lib/hqmf-parser/converter/pass1/simple_restriction.rb +64 -0
- data/lib/hqmf-parser/converter/pass2/comparison_converter.rb +112 -0
- data/lib/hqmf-parser/converter/pass2/operator_converter.rb +102 -0
- data/lib/hqmf-parser/cql/data_criteria.rb +57 -0
- data/lib/hqmf-parser/cql/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb +79 -0
- data/lib/hqmf-parser/cql/data_criteria_helpers/dc_post_processing.rb +43 -0
- data/lib/hqmf-parser/cql/document.rb +78 -0
- data/lib/hqmf-parser/cql/document_helpers/doc_population_helper.rb +124 -0
- data/lib/hqmf-parser/cql/value_set_helper.rb +103 -0
- data/lib/hqmf-parser/parser.rb +100 -0
- data/lib/qrda-export/catI-r5/qrda1_r5.rb +125 -0
- data/lib/qrda-export/helper/cat_1_view_helper.rb +142 -0
- data/lib/qrda-export/helper/code_system_helper.rb +77 -0
- data/lib/qrda-export/helper/date_helper.rb +81 -0
- data/lib/qrda-import/base-importers/demographics_importer.rb +47 -0
- data/lib/qrda-import/base-importers/medication_importer.rb +22 -0
- data/lib/qrda-import/base-importers/section_importer.rb +196 -0
- data/lib/qrda-import/cda_identifier.rb +19 -0
- data/lib/qrda-import/data-element-importers/adverse_event_importer.rb +23 -0
- data/lib/qrda-import/data-element-importers/allergy_intolerance_importer.rb +21 -0
- data/lib/qrda-import/data-element-importers/assessment_performed_importer.rb +23 -0
- data/lib/qrda-import/data-element-importers/communication_from_patient_to_provider_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/communication_from_provider_to_patient_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/communication_from_provider_to_provider_importer.rb +20 -0
- data/lib/qrda-import/data-element-importers/device_applied_importer.rb +23 -0
- data/lib/qrda-import/data-element-importers/device_order_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/diagnosis_importer.rb +23 -0
- data/lib/qrda-import/data-element-importers/diagnostic_study_order_importer.rb +20 -0
- data/lib/qrda-import/data-element-importers/diagnostic_study_performed_importer.rb +30 -0
- data/lib/qrda-import/data-element-importers/encounter_order_importer.rb +20 -0
- data/lib/qrda-import/data-element-importers/encounter_performed_importer.rb +41 -0
- data/lib/qrda-import/data-element-importers/immunization_administered_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/intervention_order_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/intervention_performed_importer.rb +22 -0
- data/lib/qrda-import/data-element-importers/laboratory_test_order_importer.rb +20 -0
- data/lib/qrda-import/data-element-importers/laboratory_test_performed_importer.rb +28 -0
- data/lib/qrda-import/data-element-importers/medication_active_importer.rb +17 -0
- data/lib/qrda-import/data-element-importers/medication_administered_importer.rb +17 -0
- data/lib/qrda-import/data-element-importers/medication_discharge_importer.rb +19 -0
- data/lib/qrda-import/data-element-importers/medication_dispensed_importer.rb +19 -0
- data/lib/qrda-import/data-element-importers/medication_order_importer.rb +16 -0
- data/lib/qrda-import/data-element-importers/patient_characteristic_expired.rb +21 -0
- data/lib/qrda-import/data-element-importers/physical_exam_performed_importer.rb +26 -0
- data/lib/qrda-import/data-element-importers/procedure_order_importer.rb +26 -0
- data/lib/qrda-import/data-element-importers/procedure_performed_importer.rb +34 -0
- data/lib/qrda-import/data-element-importers/substance_administered_importer.rb +16 -0
- data/lib/qrda-import/entry_finder.rb +20 -0
- data/lib/qrda-import/entry_package.rb +16 -0
- data/lib/qrda-import/narrative_reference_handler.rb +33 -0
- data/lib/qrda-import/patient_importer.rb +105 -0
- data/lib/util/code_system_helper.rb +76 -0
- data/lib/util/counter.rb +20 -0
- data/lib/util/hqmf_template_helper.rb +39 -0
- metadata +340 -0
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module HQMF2
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# Handles generation of populations for the main document
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class DocumentPopulationHelper
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include HQMF2::Utilities
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def initialize(entry, doc, document, id_generator, reference_ids = {})
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@entry = entry
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@doc = doc
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remove_population_preconditions(@doc)
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@document = document
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@id_generator = id_generator
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@reference_ids = reference_ids
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@populations = []
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@population_criteria = []
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@stratifications = []
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@ids_by_hqmf_id = {}
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@population_counters = {}
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end
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# If a precondition references a population, remove it
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def remove_population_preconditions(doc)
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# population sections
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pop_ids = doc.xpath("//cda:populationCriteriaSection/cda:component[@typeCode='COMP']/*/cda:id",
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HQMF2::Document::NAMESPACES)
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# find the population entries and get their ids
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pop_ids.each do |p_id|
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doc.xpath("//cda:precondition[./cda:criteriaReference/cda:id[@extension='#{p_id['extension']}' and @root='#{p_id['root']}']]",
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HQMF2::Document::NAMESPACES).remove
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end
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end
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# Returns the population descriptions and criteria found in this document
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def extract_populations_and_criteria
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has_observation = extract_observations
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document_populations = @doc.xpath('cda:QualityMeasureDocument/cda:component/cda:populationCriteriaSection',
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HQMF2::Document::NAMESPACES)
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# Sort the populations based on the id/extension, since the populations may be out of order; there doesn't seem to
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# be any other way that order is indicated in the HQMF
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document_populations = document_populations.sort_by do |pop|
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pop.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES).try(:value)
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end
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number_of_populations = document_populations.length
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document_populations.each_with_index do |population_def, population_index|
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population = {}
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handle_base_populations(population_def, population)
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id_def = population_def.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES)
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population['id'] = id_def ? id_def.value : "Population#{population_index}"
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title_def = population_def.at_xpath('cda:title/@value', HQMF2::Document::NAMESPACES)
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population['title'] = title_def ? title_def.value : "Population #{population_index}"
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population['OBSERV'] = 'OBSERV' if has_observation
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@populations << population
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handle_stratifications(population_def, number_of_populations, population, id_def, population_index)
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end
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# Push in the stratification populations after the unstratified populations
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@populations.concat(@stratifications)
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[@populations, @population_criteria]
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end
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# Extracts the measure observations, will return true if one exists
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def extract_observations
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has_observation = false
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# look for observation data in separate section but create a population for it if it exists
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observation_section = @doc.xpath('/cda:QualityMeasureDocument/cda:component/cda:measureObservationSection',
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HQMF2::Document::NAMESPACES)
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unless observation_section.empty?
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observation_section.xpath('cda:definition', HQMF2::Document::NAMESPACES).each do |criteria_def|
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criteria_id = 'OBSERV'
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criteria = PopulationCriteria.new(criteria_def, @document, @id_generator)
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criteria.type = 'OBSERV'
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# This section constructs a human readable id. The first IPP will be IPP, the second will be IPP_1, etc.
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# This allows the populations to be more readable. The alternative would be to have the hqmf ids in the
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# populations, which would work, but is difficult to read the populations.
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if @ids_by_hqmf_id["#{criteria.hqmf_id}"]
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criteria.create_human_readable_id(@ids_by_hqmf_id[criteria.hqmf_id])
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else
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criteria.create_human_readable_id(population_id_with_counter(criteria_id))
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@ids_by_hqmf_id["#{criteria.hqmf_id}"] = criteria.id
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end
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@population_criteria << criteria
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has_observation = true
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end
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end
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has_observation
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end
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# Builds populations based an a predfined set of expected populations
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def handle_base_populations(population_def, population)
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{
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HQMF::PopulationCriteria::IPP => 'initialPopulationCriteria',
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HQMF::PopulationCriteria::DENOM => 'denominatorCriteria',
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HQMF::PopulationCriteria::NUMER => 'numeratorCriteria',
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HQMF::PopulationCriteria::NUMEX => 'numeratorExclusionCriteria',
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HQMF::PopulationCriteria::DENEXCEP => 'denominatorExceptionCriteria',
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HQMF::PopulationCriteria::DENEX => 'denominatorExclusionCriteria',
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HQMF::PopulationCriteria::MSRPOPL => 'measurePopulationCriteria',
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HQMF::PopulationCriteria::MSRPOPLEX => 'measurePopulationExclusionCriteria'
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}.each_pair do |criteria_id, criteria_element_name|
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criteria_def = population_def.at_xpath("cda:component[cda:#{criteria_element_name}]", HQMF2::Document::NAMESPACES)
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if criteria_def
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build_population_criteria(criteria_def, criteria_id, population)
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end
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end
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end
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# Generate the stratifications of populations, if any exist
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def handle_stratifications(population_def, number_of_populations, population, id_def, population_index)
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# handle stratifications (EP137, EP155)
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stratifier_criteria_xpath = "cda:component/cda:stratifierCriteria[not(cda:component/cda:measureAttribute/cda:code[@code = 'SDE'])]/.."
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population_def.xpath(stratifier_criteria_xpath, HQMF2::Document::NAMESPACES)
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.each_with_index do |criteria_def, criteria_def_index|
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# Skip this Stratification if any precondition doesn't contain any preconditions
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next unless PopulationCriteria.new(criteria_def, @document, @id_generator)
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.preconditions.all? { |prcn| prcn.preconditions.length > 0 }
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index = number_of_populations + ((population_index - 1) * criteria_def.xpath('./*/cda:precondition').length) +
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criteria_def_index
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criteria_id = HQMF::PopulationCriteria::STRAT
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stratified_population = population.dup
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stratified_population['stratification'] = criteria_def.at_xpath('./*/cda:id/@root').try(:value) ||
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"#{criteria_id}-#{criteria_def_index}"
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build_population_criteria(criteria_def, criteria_id, stratified_population)
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stratified_population['id'] = id_def ? "#{id_def.value} - Stratification #{criteria_def_index + 1}" : "Population#{index}"
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title_def = population_def.at_xpath('cda:title/@value', HQMF2::Document::NAMESPACES)
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stratified_population['title'] = title_def ? "#{title_def.value} - Stratification #{criteria_def_index + 1}" : "Population #{index}"
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@stratifications << stratified_population
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end
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end
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# Method to generate the criteria defining a population
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def build_population_criteria(criteria_def, criteria_id, population)
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criteria = PopulationCriteria.new(criteria_def, @document, @id_generator)
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# check to see if we have an identical population criteria.
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# this can happen since the hqmf 2.0 will export a DENOM, NUMER, etc for each population, even if identical.
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# if we have identical, just re-use it rather than creating DENOM_1, NUMER_1, etc.
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identical = @population_criteria.select { |pc| pc.to_model.hqmf_id == criteria.to_model.hqmf_id }
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@reference_ids.concat(criteria.to_model.referenced_data_criteria)
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if identical.empty?
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# this section constructs a human readable id. The first IPP will be IPP, the second will be IPP_1, etc.
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# This allows the populations to be more readable. The alternative would be to have the hqmf ids in the
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# populations, which would work, but is difficult to read the populations.
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if @ids_by_hqmf_id["#{criteria.hqmf_id}-#{population['stratification']}"]
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criteria.create_human_readable_id(@ids_by_hqmf_id["#{criteria.hqmf_id}-#{population['stratification']}"])
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else
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criteria.create_human_readable_id(population_id_with_counter(criteria_id))
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@ids_by_hqmf_id["#{criteria.hqmf_id}-#{population['stratification']}"] = criteria.id
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end
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@population_criteria << criteria
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population[criteria_id] = criteria.id
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else
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population[criteria_id] = identical.first.id
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end
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end
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# Returns a unique id for a given population (increments the id if already present)
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def population_id_with_counter(criteria_id)
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if @population_counters[criteria_id]
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@population_counters[criteria_id] += 1
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"#{criteria_id}_#{@population_counters[criteria_id]}"
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else
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@population_counters[criteria_id] = 0
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criteria_id
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end
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end
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end
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end
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module HQMF2
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# Utilities used by the document parser to handle generic tasks
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module DocumentUtilities
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# Create grouper data criteria for encapsulating variable data criteria
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# and update document data criteria list and references map
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def handle_variable(data_criteria, collapsed_source_data_criteria)
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if data_criteria.is_derived_specific_occurrence_variable
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data_criteria.handle_derived_specific_occurrence_variable
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extract_source_data_criteria(data_criteria)
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return
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end
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tmp_id = data_criteria.id
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grouper_data_criteria = data_criteria.extract_variable_grouper
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return unless grouper_data_criteria
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@data_criteria_references[data_criteria.id] = data_criteria
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@data_criteria_references[grouper_data_criteria.id] = grouper_data_criteria
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# create a source data criteria for the grouping data critera we just created
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sdc = SourceDataCriteriaHelper.strip_non_sc_elements(grouper_data_criteria)
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@source_data_criteria << sdc
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# check if the original source has been collapsed when generating the SDC list (we need to reference the collapsed version in the sdc list)
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if collapsed_source_data_criteria[tmp_id]
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+
data_criteria.instance_variable_set(:@source_data_criteria, collapsed_source_data_criteria[tmp_id])
|
28
|
+
else
|
29
|
+
# check if we need to add _source suffix (most source data criteria are segmented with '_source' suffixes)
|
30
|
+
data_criteria_sdc = find(@source_data_criteria, :id, "#{tmp_id}_source")
|
31
|
+
if data_criteria_sdc
|
32
|
+
data_criteria.instance_variable_set(:@source_data_criteria, data_criteria_sdc.id)
|
33
|
+
data_criteria_sdc.instance_variable_set(:@variable, false)
|
34
|
+
# if it's not a derived data criteria then we may need to strip off temporal references, fields, etc as a new source data criteria
|
35
|
+
elsif !['derived', 'satisfies_any', 'satisfies_all'].include?(data_criteria.definition)
|
36
|
+
extract_source_data_criteria(data_criteria)
|
37
|
+
end
|
38
|
+
end
|
39
|
+
|
40
|
+
@data_criteria << grouper_data_criteria
|
41
|
+
end
|
42
|
+
|
43
|
+
def extract_source_data_criteria (data_criteria)
|
44
|
+
# check if we have temporal references other non-SDC elements on this data criteria.
|
45
|
+
# if we do, we need to create a new SDC to reference
|
46
|
+
if !SourceDataCriteriaHelper.already_stripped?(data_criteria)
|
47
|
+
candidate_sdc = SourceDataCriteriaHelper.strip_non_sc_elements(data_criteria.clone)
|
48
|
+
candidate_sdc.instance_variable_set(:@id, "#{candidate_sdc.id}_source")
|
49
|
+
candidate_sdc.instance_variable_set(:@source_data_criteria, candidate_sdc.id)
|
50
|
+
|
51
|
+
existing_candidate = SourceDataCriteriaHelper.find_existing_source_data_criteria(@source_data_criteria, candidate_sdc)
|
52
|
+
if existing_candidate
|
53
|
+
candidate_sdc = existing_candidate
|
54
|
+
else
|
55
|
+
@source_data_criteria << candidate_sdc
|
56
|
+
# Specific occurrence variables need a copy of the source in the data criteria to display variable results
|
57
|
+
@data_criteria << candidate_sdc if data_criteria.is_derived_specific_occurrence_variable
|
58
|
+
end
|
59
|
+
|
60
|
+
data_criteria.instance_variable_set(:@source_data_criteria, candidate_sdc.id)
|
61
|
+
end
|
62
|
+
end
|
63
|
+
|
64
|
+
# Checks if one data criteria is covered by another (has all the appropriate elements of)
|
65
|
+
def criteria_covered_by_criteria?(dc)
|
66
|
+
@reference_ids.uniq
|
67
|
+
|
68
|
+
base_criteria_defs = %w(patient_characteristic_ethnicity patient_characteristic_gender patient_characteristic_payer patient_characteristic_race)
|
69
|
+
to_reject = true
|
70
|
+
# don't reject if anything refers directly to this criteria
|
71
|
+
to_reject &&= @reference_ids.index(dc.id).nil?
|
72
|
+
# don't reject if it is a "base" criteria (no references but must exist)
|
73
|
+
to_reject &&= !base_criteria_defs.include?(dc.definition)
|
74
|
+
# keep referral occurrence
|
75
|
+
to_reject &&= dc.specific_occurrence_const.nil? ||
|
76
|
+
dc.code_list_id != '2.16.840.1.113883.3.464.1003.101.12.1046'
|
77
|
+
to_reject && !@data_criteria.detect do |dc2|
|
78
|
+
similar_criteria = true
|
79
|
+
similar_criteria &&= dc != dc2 # Don't check against itself
|
80
|
+
similar_criteria &&= dc.code_list_id == dc2.code_list_id # Ensure code list ids are the same
|
81
|
+
similar_criteria && detect_criteria_covered_by_criteria(dc, dc2)
|
82
|
+
end.nil? # don't reject unless there is a similar element
|
83
|
+
end
|
84
|
+
|
85
|
+
# Check if one data criteria contains the others information by checking that one has everything the other has
|
86
|
+
# (or more)
|
87
|
+
def detect_criteria_covered_by_criteria(data_criteria, check_criteria)
|
88
|
+
base_checks = true
|
89
|
+
|
90
|
+
# Check whether basic features are the same
|
91
|
+
base_checks &&= data_criteria.definition == check_criteria.definition # same definition
|
92
|
+
base_checks &&= data_criteria.status == check_criteria.status # same status
|
93
|
+
# same children
|
94
|
+
base_checks &&= data_criteria.children_criteria.sort.join(',') == check_criteria.children_criteria.sort.join(',')
|
95
|
+
# Ensure it doesn't contain basic elements that should not be removed
|
96
|
+
base_checks &&= !data_criteria.variable # Ensure it's not a variable
|
97
|
+
base_checks &&= data_criteria.derivation_operator.nil? # Ensure it doesn't have a derivation operator
|
98
|
+
base_checks &&= data_criteria.subset_operators.empty? # Ensure it doesn't have a subset operator
|
99
|
+
# Ensure it doesn't have Temporal References
|
100
|
+
base_checks &&= data_criteria.temporal_references.nil? || data_criteria.temporal_references.empty?
|
101
|
+
|
102
|
+
base_checks && complex_coverage(data_criteria, check_criteria)
|
103
|
+
end
|
104
|
+
|
105
|
+
# Check elements that do not already exist; else, if they do, check if those elements are the same
|
106
|
+
# in a different, potentially matching, data criteria
|
107
|
+
def complex_coverage(data_criteria, check_criteria)
|
108
|
+
same_value = data_criteria.value.nil? ||
|
109
|
+
data_criteria.value.try(:to_model).try(:to_json) == check_criteria.value.try(:to_model).try(:to_json)
|
110
|
+
|
111
|
+
same_field_values = same_field_values_check(data_criteria, check_criteria)
|
112
|
+
|
113
|
+
same_negation_values = data_criteria.negation_code_list_id.nil? ||
|
114
|
+
data_criteria.negation_code_list_id == check_criteria.negation_code_list_id
|
115
|
+
|
116
|
+
same_value && same_negation_values && same_field_values
|
117
|
+
end
|
118
|
+
|
119
|
+
def same_field_values_check(data_criteria, check_criteria)
|
120
|
+
empty = data_criteria.field_values.nil? || data_criteria.field_values.empty?
|
121
|
+
# Ignore STATUS (and ORDINAL for CMS172v5)
|
122
|
+
# The meaning of status has changed over time. Laboratory test and procedure now use status differently.
|
123
|
+
# This change is causing superficial discrepencies between the simplexml and hqmf regarding STATUS.
|
124
|
+
dc_filtered = data_criteria.field_values.except('STATUS').except('ORDINAL')
|
125
|
+
cc_filtered = check_criteria.field_values.except('STATUS').except('ORDINAL')
|
126
|
+
left = dc_filtered.nil? || dc_filtered.empty? ? nil : dc_filtered.try(:to_json)
|
127
|
+
right = cc_filtered.nil? || cc_filtered.empty? ? nil : cc_filtered.try(:to_json)
|
128
|
+
return empty || left == right
|
129
|
+
end
|
130
|
+
end
|
131
|
+
end
|
@@ -0,0 +1,251 @@
|
|
1
|
+
module HQMF2
|
2
|
+
# Generates field values based on understanding of the HQMF 2.1 spec
|
3
|
+
class FieldValueHelper
|
4
|
+
def self.parse_field_values(entry)
|
5
|
+
return if entry.nil?
|
6
|
+
criteria = entry.at_xpath('./cda:actCriteria | ./cda:observationCriteria | ./cda:encounterCriteria |
|
7
|
+
./cda:procedureCriteria | ./cda:supplyCriteria |
|
8
|
+
./cda:substanceAdministrationCriteria | ./cda:grouperCriteria')
|
9
|
+
|
10
|
+
return {} if criteria.nil?
|
11
|
+
fields = {}
|
12
|
+
# Negation is handled in the data criteria parsing class and not as a field value.
|
13
|
+
# Not using the reasonCode element because the QDM HQMF ig states that reason is in an outbound relationship.
|
14
|
+
# parse_dset_cd(criteria.at_xpath('./cda:reasonCode', HQMF2::Document::NAMESPACES), 'REASON', fields) unless
|
15
|
+
# negated.
|
16
|
+
parse_dset_cd(criteria.at_xpath('./cda:priorityCode', HQMF2::Document::NAMESPACES), 'ORDINAL', fields)
|
17
|
+
parse_date_fields(criteria, fields)
|
18
|
+
|
19
|
+
handle_fields_per_criteria(criteria, fields)
|
20
|
+
|
21
|
+
fields
|
22
|
+
end
|
23
|
+
|
24
|
+
def self.handle_fields_per_criteria(criteria, fields)
|
25
|
+
case criteria.name
|
26
|
+
when 'encounterCriteria'
|
27
|
+
parse_encounter_fields(criteria, fields)
|
28
|
+
when 'actCriteria'
|
29
|
+
parse_act_criteria_fields(criteria, fields)
|
30
|
+
when 'observationCriteria'
|
31
|
+
parse_observation_fields(criteria, fields)
|
32
|
+
when 'procedureCriteria'
|
33
|
+
parse_procedure_fields(criteria, fields)
|
34
|
+
when 'supplyCriteria'
|
35
|
+
parse_supply_fields(criteria, fields)
|
36
|
+
when 'substanceAdministrationCriteria'
|
37
|
+
parse_substance_administration_fields(criteria, fields)
|
38
|
+
when 'grouperCriteria'
|
39
|
+
parse_grouper_fields(criteria, fields)
|
40
|
+
end
|
41
|
+
end
|
42
|
+
|
43
|
+
# The next group of "parse_" methods handle extracting values for different types of criteria
|
44
|
+
|
45
|
+
def self.parse_dset_cd(element, field, fields)
|
46
|
+
if element
|
47
|
+
item = element.at_xpath('./cda:item')
|
48
|
+
any = any_flavor(item) || any_flavor(element)
|
49
|
+
fields[field] = AnyValue.new if any
|
50
|
+
fields[field] = Coded.new(item) if item && !any
|
51
|
+
end
|
52
|
+
end
|
53
|
+
|
54
|
+
# The next group of "parse_" methods also first check if the value is of the "ANY" type, and only parse if it isn't
|
55
|
+
|
56
|
+
def self.parse_cd(element, field, fields)
|
57
|
+
any = check_and_set_if_any(element, field, fields)
|
58
|
+
fields[field] = Coded.new(element) if element && !any
|
59
|
+
end
|
60
|
+
|
61
|
+
def self.parse_ts(element, field, fields)
|
62
|
+
any = check_and_set_if_any(element, field, fields)
|
63
|
+
fields[field] = Value.new(element) if element && !any
|
64
|
+
end
|
65
|
+
|
66
|
+
def self.parse_ivl_int(element, field, fields)
|
67
|
+
any = check_and_set_if_any(element, field, fields)
|
68
|
+
fields[field] = Range.new(element) if element && !any
|
69
|
+
end
|
70
|
+
|
71
|
+
def self.parse_cs(element, field, fields)
|
72
|
+
# Only possible result is AnyValue
|
73
|
+
check_and_set_if_any(element, field, fields)
|
74
|
+
end
|
75
|
+
|
76
|
+
def self.parse_pq(element, field, fields)
|
77
|
+
any = check_and_set_if_any(element, field, fields)
|
78
|
+
fields[field] = Range.new(element) if element && !any
|
79
|
+
end
|
80
|
+
|
81
|
+
def self.parse_value(element, field, fields)
|
82
|
+
any = check_and_set_if_any(element, field, fields)
|
83
|
+
fields[field] = DateCriteria.parse_value(element) if element && !any
|
84
|
+
end
|
85
|
+
|
86
|
+
# handle any value
|
87
|
+
def self.parse_any(element, field, fields)
|
88
|
+
any = check_and_set_if_any(element, field, fields)
|
89
|
+
fields[field] = DateCriteria.parse_value(element) if element && !any
|
90
|
+
end
|
91
|
+
|
92
|
+
# Use when checking if the element is a "ANY" type, sets the field key if it is
|
93
|
+
def self.check_and_set_if_any(element, field, fields)
|
94
|
+
any = any_flavor(element)
|
95
|
+
fields[field] = AnyValue.new if any
|
96
|
+
any
|
97
|
+
end
|
98
|
+
|
99
|
+
def self.any_flavor(element)
|
100
|
+
element && (element['flavorId'] == 'ANY.NONNULL' ||
|
101
|
+
element.at_xpath('@xsi:type', HQMF2::Document::NAMESPACES) == 'ANY')
|
102
|
+
end
|
103
|
+
|
104
|
+
def self.parse_date_fields(entry, fields)
|
105
|
+
# handle embded date fields
|
106
|
+
times = [{ key: 'signeddatetime', field: 'SIGNED_DATETIME', highlow: 'high' },
|
107
|
+
{ key: 'startdatetime', field: 'START_DATETIME', highlow: 'low' },
|
108
|
+
{ key: 'stopdatetime', field: 'STOP_DATETIME', highlow: 'high' },
|
109
|
+
{ key: 'recordeddatetime', field: 'RECORDED_DATETIME', highlow: 'high' }
|
110
|
+
]
|
111
|
+
times.each do |e|
|
112
|
+
date = entry.at_xpath("cda:participation[@typeCode='AUT']/cda:role/cda:id/cda:item[@extension = '#{e[:key]}']/../../../cda:time")
|
113
|
+
fields[e[:field]] = Range.new(date, 'IVL_PQ') if date
|
114
|
+
end
|
115
|
+
|
116
|
+
# Special case handle effectiveTime element , by default low is start datetime
|
117
|
+
# and high is stop datetime. This changes for certain elements
|
118
|
+
template_ids = extract_template_ids(entry)
|
119
|
+
low = entry.at_xpath('./cda:effectiveTime/cda:low/..')
|
120
|
+
high = entry.at_xpath('./cda:effectiveTime/cda:high/..')
|
121
|
+
|
122
|
+
fields[low_field_name(template_ids)] = Range.new(low, 'IVL_PQ') if low
|
123
|
+
|
124
|
+
fields[high_field_name(template_ids)] = Range.new(high, 'IVL_PQ') if high
|
125
|
+
end
|
126
|
+
|
127
|
+
# Returns the proper name for the low field given the list of template ids
|
128
|
+
def self.low_field_name(template_ids)
|
129
|
+
if template_ids.include?('2.16.840.1.113883.10.20.28.3.51')
|
130
|
+
'ACTIVE_DATETIME'
|
131
|
+
elsif template_ids.include?('2.16.840.1.113883.10.20.28.3.110') ||
|
132
|
+
template_ids.include?('2.16.840.1.113883.10.20.28.3.116')
|
133
|
+
'ONSET_DATETIME'
|
134
|
+
else
|
135
|
+
'ADMISSION_DATETIME'
|
136
|
+
end
|
137
|
+
end
|
138
|
+
|
139
|
+
# Returns the proper name for the high field given the list of template ids
|
140
|
+
def self.high_field_name(template_ids)
|
141
|
+
if template_ids.include?('2.16.840.1.113883.10.20.28.3.13')
|
142
|
+
'REMOVAL_DATETIME'
|
143
|
+
elsif template_ids.include?('2.16.840.1.113883.10.20.28.3.110') ||
|
144
|
+
template_ids.include?('2.16.840.1.113883.10.20.28.3.116')
|
145
|
+
'ABATEMENT_DATETIME'
|
146
|
+
else
|
147
|
+
'DISCHARGE_DATETIME'
|
148
|
+
end
|
149
|
+
end
|
150
|
+
|
151
|
+
# If type code for this field value is LOC, handle specifics
|
152
|
+
def self.handle_loc(entry, fields)
|
153
|
+
loc = entry.at_xpath("./cda:participation[@typeCode='LOC']/cda:role[@classCode='SDLOC']",
|
154
|
+
HQMF2::Document::NAMESPACES)
|
155
|
+
return unless loc
|
156
|
+
# does it have an effective time?
|
157
|
+
low = loc.at_xpath('./cda:effectiveTime/cda:low/..')
|
158
|
+
high = loc.at_xpath('./cda:effectiveTime/cda:high/..')
|
159
|
+
code = loc.at_xpath('./cda:code')
|
160
|
+
# looking at the 2.4.0 measure bundle these values are set to null if they exist
|
161
|
+
# so that is what I am doing for now
|
162
|
+
fields['FACILITY_LOCATION_ARRIVAL_DATETIME'] = AnyValue.new if low
|
163
|
+
fields['FACILITY_LOCATION_DEPARTURE_DATETIME'] = AnyValue.new if high
|
164
|
+
fields['FACILITY_LOCATION'] = Coded.new(code) if code
|
165
|
+
end
|
166
|
+
|
167
|
+
# Extract template ids from the given entry
|
168
|
+
def self.extract_template_ids(entry)
|
169
|
+
entry.xpath('./cda:templateId/cda:item', HQMF2::Document::NAMESPACES).collect do |template_def|
|
170
|
+
HQMF2::Utilities.attr_val(template_def, '@root')
|
171
|
+
end
|
172
|
+
end
|
173
|
+
|
174
|
+
# The "parse_"s after this point handle extraction of data criteria based on field names
|
175
|
+
|
176
|
+
def self.parse_act_criteria_fields(_entry, _fields)
|
177
|
+
end
|
178
|
+
|
179
|
+
def self.parse_substance_administration_fields(entry, fields)
|
180
|
+
parse_dset_cd(entry.at_xpath('./cda:methodCode', HQMF2::Document::NAMESPACES), 'METHOD', fields)
|
181
|
+
parse_dset_cd(entry.at_xpath('./cda:approachSiteCode', HQMF2::Document::NAMESPACES),
|
182
|
+
'ANATOMICAL_APPROACH_SITE', fields)
|
183
|
+
parse_dset_cd(entry.at_xpath('./cda:targetSiteCode', HQMF2::Document::NAMESPACES),
|
184
|
+
'ANATOMICAL_LOCATION_SITE', fields)
|
185
|
+
parse_cd(entry.at_xpath('./cda:routeCode', HQMF2::Document::NAMESPACES), 'ROUTE', fields)
|
186
|
+
parse_pq(entry.at_xpath('./cda:doseQuantity', HQMF2::Document::NAMESPACES), 'DOSE', fields)
|
187
|
+
parse_pq(entry.at_xpath('./cda:repeatNumber', HQMF2::Document::NAMESPACES), 'REFILLS', fields)
|
188
|
+
end
|
189
|
+
|
190
|
+
def self.parse_observation_fields(entry, fields)
|
191
|
+
parse_dset_cd(entry.at_xpath('./cda:methodCode', HQMF2::Document::NAMESPACES), 'METHOD', fields)
|
192
|
+
parse_dset_cd(entry.at_xpath('./cda:targetSiteCode', HQMF2::Document::NAMESPACES),
|
193
|
+
'ANATOMICAL_LOCATION_SITE', fields)
|
194
|
+
parse_cd(entry.at_xpath("./cda:participation[@typeCode='SBJ']/cda:role[@classCode='PRS']/cda:code",
|
195
|
+
HQMF2::Document::NAMESPACES),
|
196
|
+
'RELATIONSHIP', fields)
|
197
|
+
parse_pq(entry.at_xpath("./cda:outboundRelationship[@typeCode='REFV']/cda:observationCriteria/cda:value/cda:high",
|
198
|
+
HQMF2::Document::NAMESPACES),
|
199
|
+
'REFERENCE_RANGE_HIGH', fields)
|
200
|
+
parse_pq(entry.at_xpath("./cda:outboundRelationship[@typeCode='REFV']/cda:observationCriteria/cda:value/cda:low",
|
201
|
+
HQMF2::Document::NAMESPACES),
|
202
|
+
'REFERENCE_RANGE_LOW', fields)
|
203
|
+
end
|
204
|
+
|
205
|
+
# Ignoring line limits here as it would be hard to create the deep xPaths with these limits.
|
206
|
+
# rubocop:disable Metrics/LineLength
|
207
|
+
def self.parse_encounter_fields(entry, fields)
|
208
|
+
# Added a check for Principal Diagnosis and Diagnosis. QDM 4.2 Update
|
209
|
+
principal = entry.at_xpath("./cda:outboundRelationship[@typeCode='REFR']/cda:actCriteria/cda:code[@code='52534-5']",
|
210
|
+
HQMF2::Document::NAMESPACES)
|
211
|
+
if principal
|
212
|
+
parse_cd(
|
213
|
+
entry.at_xpath(
|
214
|
+
"./cda:outboundRelationship[@typeCode='REFR']/cda:actCriteria/cda:outboundRelationship[@typeCode='SUBJ']/cda:observationCriteria/cda:value",
|
215
|
+
HQMF2::Document::NAMESPACES
|
216
|
+
), 'PRINCIPAL_DIAGNOSIS', fields)
|
217
|
+
end
|
218
|
+
|
219
|
+
diagnosis = entry.at_xpath("./cda:outboundRelationship[@typeCode='REFR']/cda:actCriteria/cda:code[@code='29308-4']",
|
220
|
+
HQMF2::Document::NAMESPACES)
|
221
|
+
if diagnosis
|
222
|
+
parse_cd(
|
223
|
+
entry.at_xpath(
|
224
|
+
"./cda:outboundRelationship[@typeCode='REFR']/cda:actCriteria/cda:outboundRelationship[@typeCode='SUBJ']/cda:observationCriteria/cda:value",
|
225
|
+
HQMF2::Document::NAMESPACES
|
226
|
+
), 'DIAGNOSIS', fields)
|
227
|
+
end
|
228
|
+
|
229
|
+
parse_pq(entry.at_xpath('./cda:lengthOfStayQuantity', HQMF2::Document::NAMESPACES), 'LENGTH_OF_STAY', fields)
|
230
|
+
parse_cd(entry.at_xpath('./cda:dischargeDispositionCode', HQMF2::Document::NAMESPACES), 'DISCHARGE_STATUS', fields)
|
231
|
+
|
232
|
+
handle_loc(entry, fields)
|
233
|
+
end
|
234
|
+
|
235
|
+
# rubocop:enable Metrics/LineLength
|
236
|
+
|
237
|
+
def self.parse_procedure_fields(entry, fields)
|
238
|
+
parse_dset_cd(entry.at_xpath('./cda:methodCode', HQMF2::Document::NAMESPACES), 'METHOD', fields)
|
239
|
+
parse_dset_cd(entry.at_xpath('./cda:approachSiteCode', HQMF2::Document::NAMESPACES),
|
240
|
+
'ANATOMICAL_APPROACH_SITE', fields)
|
241
|
+
parse_dset_cd(entry.at_xpath('./cda:targetSiteCode', HQMF2::Document::NAMESPACES),
|
242
|
+
'ANATOMICAL_LOCATION_SITE', fields)
|
243
|
+
end
|
244
|
+
|
245
|
+
def self.parse_supply_fields(_entry, _fields)
|
246
|
+
end
|
247
|
+
|
248
|
+
def self.parse_grouper_fields(_entry, _fields)
|
249
|
+
end
|
250
|
+
end
|
251
|
+
end
|