cqm-parsers 0.1.0

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Files changed (103) hide show
  1. checksums.yaml +7 -0
  2. data/Gemfile +29 -0
  3. data/README.md +21 -0
  4. data/Rakefile +19 -0
  5. data/lib/ext/code.rb +10 -0
  6. data/lib/ext/data_element.rb +24 -0
  7. data/lib/hqmf-model/attribute.rb +63 -0
  8. data/lib/hqmf-model/data_criteria.rb +467 -0
  9. data/lib/hqmf-model/document.rb +253 -0
  10. data/lib/hqmf-model/population_criteria.rb +102 -0
  11. data/lib/hqmf-model/precondition.rb +94 -0
  12. data/lib/hqmf-model/types.rb +457 -0
  13. data/lib/hqmf-model/utilities.rb +52 -0
  14. data/lib/hqmf-parser.rb +116 -0
  15. data/lib/hqmf-parser/1.0/attribute.rb +121 -0
  16. data/lib/hqmf-parser/1.0/comparison.rb +34 -0
  17. data/lib/hqmf-parser/1.0/data_criteria.rb +92 -0
  18. data/lib/hqmf-parser/1.0/document.rb +195 -0
  19. data/lib/hqmf-parser/1.0/expression.rb +60 -0
  20. data/lib/hqmf-parser/1.0/observation.rb +61 -0
  21. data/lib/hqmf-parser/1.0/population_criteria.rb +75 -0
  22. data/lib/hqmf-parser/1.0/precondition.rb +90 -0
  23. data/lib/hqmf-parser/1.0/range.rb +76 -0
  24. data/lib/hqmf-parser/1.0/restriction.rb +162 -0
  25. data/lib/hqmf-parser/1.0/utilities.rb +55 -0
  26. data/lib/hqmf-parser/2.0/data_criteria.rb +372 -0
  27. data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_base_extract.rb +80 -0
  28. data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb +201 -0
  29. data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_post_processing.rb +85 -0
  30. data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_specific_occurrences_and_source_data_criteria_extract.rb +117 -0
  31. data/lib/hqmf-parser/2.0/document.rb +304 -0
  32. data/lib/hqmf-parser/2.0/document_helpers/doc_population_helper.rb +173 -0
  33. data/lib/hqmf-parser/2.0/document_helpers/doc_utilities.rb +131 -0
  34. data/lib/hqmf-parser/2.0/field_value_helper.rb +251 -0
  35. data/lib/hqmf-parser/2.0/population_criteria.rb +134 -0
  36. data/lib/hqmf-parser/2.0/precondition.rb +73 -0
  37. data/lib/hqmf-parser/2.0/source_data_criteria_helper.rb +112 -0
  38. data/lib/hqmf-parser/2.0/types.rb +448 -0
  39. data/lib/hqmf-parser/2.0/utilities.rb +45 -0
  40. data/lib/hqmf-parser/2.0/value_set_helper.rb +104 -0
  41. data/lib/hqmf-parser/converter/pass1/data_criteria_converter.rb +257 -0
  42. data/lib/hqmf-parser/converter/pass1/document_converter.rb +133 -0
  43. data/lib/hqmf-parser/converter/pass1/population_criteria_converter.rb +185 -0
  44. data/lib/hqmf-parser/converter/pass1/precondition_converter.rb +173 -0
  45. data/lib/hqmf-parser/converter/pass1/precondition_extractor.rb +201 -0
  46. data/lib/hqmf-parser/converter/pass1/simple_data_criteria.rb +26 -0
  47. data/lib/hqmf-parser/converter/pass1/simple_operator.rb +89 -0
  48. data/lib/hqmf-parser/converter/pass1/simple_population_criteria.rb +10 -0
  49. data/lib/hqmf-parser/converter/pass1/simple_precondition.rb +51 -0
  50. data/lib/hqmf-parser/converter/pass1/simple_restriction.rb +64 -0
  51. data/lib/hqmf-parser/converter/pass2/comparison_converter.rb +112 -0
  52. data/lib/hqmf-parser/converter/pass2/operator_converter.rb +102 -0
  53. data/lib/hqmf-parser/cql/data_criteria.rb +57 -0
  54. data/lib/hqmf-parser/cql/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb +79 -0
  55. data/lib/hqmf-parser/cql/data_criteria_helpers/dc_post_processing.rb +43 -0
  56. data/lib/hqmf-parser/cql/document.rb +78 -0
  57. data/lib/hqmf-parser/cql/document_helpers/doc_population_helper.rb +124 -0
  58. data/lib/hqmf-parser/cql/value_set_helper.rb +103 -0
  59. data/lib/hqmf-parser/parser.rb +100 -0
  60. data/lib/qrda-export/catI-r5/qrda1_r5.rb +125 -0
  61. data/lib/qrda-export/helper/cat_1_view_helper.rb +142 -0
  62. data/lib/qrda-export/helper/code_system_helper.rb +77 -0
  63. data/lib/qrda-export/helper/date_helper.rb +81 -0
  64. data/lib/qrda-import/base-importers/demographics_importer.rb +47 -0
  65. data/lib/qrda-import/base-importers/medication_importer.rb +22 -0
  66. data/lib/qrda-import/base-importers/section_importer.rb +196 -0
  67. data/lib/qrda-import/cda_identifier.rb +19 -0
  68. data/lib/qrda-import/data-element-importers/adverse_event_importer.rb +23 -0
  69. data/lib/qrda-import/data-element-importers/allergy_intolerance_importer.rb +21 -0
  70. data/lib/qrda-import/data-element-importers/assessment_performed_importer.rb +23 -0
  71. data/lib/qrda-import/data-element-importers/communication_from_patient_to_provider_importer.rb +18 -0
  72. data/lib/qrda-import/data-element-importers/communication_from_provider_to_patient_importer.rb +18 -0
  73. data/lib/qrda-import/data-element-importers/communication_from_provider_to_provider_importer.rb +20 -0
  74. data/lib/qrda-import/data-element-importers/device_applied_importer.rb +23 -0
  75. data/lib/qrda-import/data-element-importers/device_order_importer.rb +18 -0
  76. data/lib/qrda-import/data-element-importers/diagnosis_importer.rb +23 -0
  77. data/lib/qrda-import/data-element-importers/diagnostic_study_order_importer.rb +20 -0
  78. data/lib/qrda-import/data-element-importers/diagnostic_study_performed_importer.rb +30 -0
  79. data/lib/qrda-import/data-element-importers/encounter_order_importer.rb +20 -0
  80. data/lib/qrda-import/data-element-importers/encounter_performed_importer.rb +41 -0
  81. data/lib/qrda-import/data-element-importers/immunization_administered_importer.rb +18 -0
  82. data/lib/qrda-import/data-element-importers/intervention_order_importer.rb +18 -0
  83. data/lib/qrda-import/data-element-importers/intervention_performed_importer.rb +22 -0
  84. data/lib/qrda-import/data-element-importers/laboratory_test_order_importer.rb +20 -0
  85. data/lib/qrda-import/data-element-importers/laboratory_test_performed_importer.rb +28 -0
  86. data/lib/qrda-import/data-element-importers/medication_active_importer.rb +17 -0
  87. data/lib/qrda-import/data-element-importers/medication_administered_importer.rb +17 -0
  88. data/lib/qrda-import/data-element-importers/medication_discharge_importer.rb +19 -0
  89. data/lib/qrda-import/data-element-importers/medication_dispensed_importer.rb +19 -0
  90. data/lib/qrda-import/data-element-importers/medication_order_importer.rb +16 -0
  91. data/lib/qrda-import/data-element-importers/patient_characteristic_expired.rb +21 -0
  92. data/lib/qrda-import/data-element-importers/physical_exam_performed_importer.rb +26 -0
  93. data/lib/qrda-import/data-element-importers/procedure_order_importer.rb +26 -0
  94. data/lib/qrda-import/data-element-importers/procedure_performed_importer.rb +34 -0
  95. data/lib/qrda-import/data-element-importers/substance_administered_importer.rb +16 -0
  96. data/lib/qrda-import/entry_finder.rb +20 -0
  97. data/lib/qrda-import/entry_package.rb +16 -0
  98. data/lib/qrda-import/narrative_reference_handler.rb +33 -0
  99. data/lib/qrda-import/patient_importer.rb +105 -0
  100. data/lib/util/code_system_helper.rb +76 -0
  101. data/lib/util/counter.rb +20 -0
  102. data/lib/util/hqmf_template_helper.rb +39 -0
  103. metadata +340 -0
@@ -0,0 +1,173 @@
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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+ @reference_ids.concat(criteria.to_model.referenced_data_criteria)
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+
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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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+
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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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+
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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
@@ -0,0 +1,131 @@
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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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+
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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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+
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+ tmp_id = data_criteria.id
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+
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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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+
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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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+
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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])
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+ else
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+ # check if we need to add _source suffix (most source data criteria are segmented with '_source' suffixes)
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+ data_criteria_sdc = find(@source_data_criteria, :id, "#{tmp_id}_source")
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+ if data_criteria_sdc
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+ data_criteria.instance_variable_set(:@source_data_criteria, data_criteria_sdc.id)
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+ data_criteria_sdc.instance_variable_set(:@variable, false)
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+ # 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
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+ elsif !['derived', 'satisfies_any', 'satisfies_all'].include?(data_criteria.definition)
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+ extract_source_data_criteria(data_criteria)
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+ end
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+ end
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+
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+ @data_criteria << grouper_data_criteria
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+ end
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+
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+ def extract_source_data_criteria (data_criteria)
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+ # check if we have temporal references other non-SDC elements on this data criteria.
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+ # if we do, we need to create a new SDC to reference
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+ if !SourceDataCriteriaHelper.already_stripped?(data_criteria)
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+ candidate_sdc = SourceDataCriteriaHelper.strip_non_sc_elements(data_criteria.clone)
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+ candidate_sdc.instance_variable_set(:@id, "#{candidate_sdc.id}_source")
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+ candidate_sdc.instance_variable_set(:@source_data_criteria, candidate_sdc.id)
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+
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+ existing_candidate = SourceDataCriteriaHelper.find_existing_source_data_criteria(@source_data_criteria, candidate_sdc)
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+ if existing_candidate
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+ candidate_sdc = existing_candidate
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+ else
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+ @source_data_criteria << candidate_sdc
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+ # Specific occurrence variables need a copy of the source in the data criteria to display variable results
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+ @data_criteria << candidate_sdc if data_criteria.is_derived_specific_occurrence_variable
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+ end
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+
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+ data_criteria.instance_variable_set(:@source_data_criteria, candidate_sdc.id)
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+ end
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+ end
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+
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+ # Checks if one data criteria is covered by another (has all the appropriate elements of)
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+ def criteria_covered_by_criteria?(dc)
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+ @reference_ids.uniq
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+
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+ base_criteria_defs = %w(patient_characteristic_ethnicity patient_characteristic_gender patient_characteristic_payer patient_characteristic_race)
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+ to_reject = true
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+ # don't reject if anything refers directly to this criteria
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+ to_reject &&= @reference_ids.index(dc.id).nil?
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+ # don't reject if it is a "base" criteria (no references but must exist)
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+ to_reject &&= !base_criteria_defs.include?(dc.definition)
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+ # keep referral occurrence
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+ to_reject &&= dc.specific_occurrence_const.nil? ||
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+ dc.code_list_id != '2.16.840.1.113883.3.464.1003.101.12.1046'
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+ to_reject && !@data_criteria.detect do |dc2|
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+ similar_criteria = true
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+ similar_criteria &&= dc != dc2 # Don't check against itself
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+ similar_criteria &&= dc.code_list_id == dc2.code_list_id # Ensure code list ids are the same
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+ similar_criteria && detect_criteria_covered_by_criteria(dc, dc2)
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+ end.nil? # don't reject unless there is a similar element
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+ end
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+
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+ # Check if one data criteria contains the others information by checking that one has everything the other has
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+ # (or more)
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+ def detect_criteria_covered_by_criteria(data_criteria, check_criteria)
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+ base_checks = true
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+
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+ # Check whether basic features are the same
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+ base_checks &&= data_criteria.definition == check_criteria.definition # same definition
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+ base_checks &&= data_criteria.status == check_criteria.status # same status
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+ # same children
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+ 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