Class: CQM::Converter::Utils

Inherits:
Object
  • Object
show all
Defined in:
lib/cqm/converter/utils.rb

Overview

CQM Converter class utilities.

Class Method Summary collapse

Class Method Details

.date_time_adjuster(results) ⇒ Object

Adjust improper date times from the cql_qdm_patientapi.



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# File 'lib/cqm/converter/utils.rb', line 150

def self.date_time_adjuster(results)
  if results.is_a?(Hash) && results.key?('year') && results.key?('minute')
    DateTime.new(results['year'], results['month'], results['day'], results['hour'], results['minute'], results['second'], results['millisecond']).to_s
  elsif results.is_a?(Hash)
    results.each do |key, value|
      results[key] = date_time_adjuster(value)
    end
  elsif results.is_a?(Array)
    results.map! { |result| date_time_adjuster(result) }
  else
    results
  end
end

.fix_infinity_dates(results) ⇒ Object

Remove any ‘infinity’ dates. The cql_qdm_patientapi adds an end time of ‘infinity’ if an event does not have an end time. Remove this when converting back to HDS from QDM.



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# File 'lib/cqm/converter/utils.rb', line 167

def self.fix_infinity_dates(results)
  if results.is_a?(Hash) && results.key?('end_time')
    results.delete('end_time') if results['end_time'].to_s == '253402300799'
  elsif results.is_a?(Hash)
    results.each do |key, value|
      results[key] = fix_infinity_dates(value)
    end
  elsif results.is_a?(Array)
    results.map! { |result| fix_infinity_dates(result) }
  else
    results
  end
end

.gather_qdm_model_attrs ⇒ Object

This helper method looks at the current state of cqm-models, and builds a hash of datatype models and their attributes.



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# File 'lib/cqm/converter/utils.rb', line 31

def self.gather_qdm_model_attrs
  qdm_model_attrs = {}
  QDM.constants.each do |model|
    if QDM.const_get(model).respond_to?('fields')
      qdm_model_attrs[model.to_s] = QDM.const_get(model).fields.keys.map! { |a| a.camelize(:lower) }
    end
    if QDM.const_get(model).respond_to?('embedded_relations')
      qdm_model_attrs[model.to_s].concat(QDM.const_get(model).embedded_relations.keys.map! { |a| a.camelize(:lower) })
    end
  end
  # TODO: These fields are currently not supported. See:
  # https://github.com/projecttacoma/cql_qdm_patientapi/search?q=does+not+currently+support
  qdm_model_attrs['SubstanceAdministered'].delete('frequency')
  qdm_model_attrs['SubstanceOrder'].delete('refills')
  qdm_model_attrs['PatientCharacteristicExpired'].delete('cause')
  qdm_model_attrs['MedicationDispensed'].delete('refills')
  qdm_model_attrs['MedicationDispensed'].delete('frequency')
  qdm_model_attrs['MedicationOrder'].delete('refills')
  qdm_model_attrs['MedicationOrder'].delete('frequency')
  qdm_model_attrs['MedicationActive'].delete('frequency')
  qdm_model_attrs['MedicationAdministered'].delete('frequency')
  qdm_model_attrs['MedicationDischarge'].delete('refills')
  qdm_model_attrs['MedicationDischarge'].delete('frequency')
  qdm_model_attrs
end

.gather_qdm_to_hds_mappings(qdm_model_attrs = nil) ⇒ Object

Parse the cql_qdm_patientapi datatypes to infer how to construct corresponding HDS entries.



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# File 'lib/cqm/converter/utils.rb', line 59

def self.gather_qdm_to_hds_mappings(qdm_model_attrs = nil)
  qdm_model_attrs = gather_qdm_model_attrs if qdm_model_attrs.nil?
  cql_qdm_patientapi_spec = Gem::Specification.find_by_name('cql_qdm_patientapi')
  datatypes = Dir.glob(cql_qdm_patientapi_spec.gem_dir + '/app/assets/javascripts/datatypes/*.coffee')
  # Read in all datatypes
  datatypes_contents = ''
  datatypes.each do |datatype|
    datatypes_contents += File.read(datatype) + "\n"
  end
  datatypes_contents += 'class'
  # Construct the mappings
  qdm_to_hds_mappings = {}
  qdm_model_attrs.each do |datatype, attributes|
    datatype_pattern = /#{datatype} extends CQL_QDM.QDMDatatype.*?class/m
    next unless (dc_class = datatype_pattern.match(datatypes_contents))
    qdm_to_hds_mappings[datatype] = {}
    attributes.each do |attribute|
      attribute_pattern = /@_#{attribute}(Low|High| ).*?@entry.*?$/
      dc_class.to_s.to_enum(:scan, attribute_pattern).map do
        dc_attr = Regexp.last_match
        # Handle possible mixed values.
        if dc_attr.to_s.include? 'Low'
          qdm_to_hds_mappings[datatype][attribute] = {} unless qdm_to_hds_mappings[datatype][attribute]
          qdm_to_hds_mappings[datatype][attribute][:low] = dc_attr.to_s[/@entry.(.*?)(\)|$|\?)/m, 1]
        elsif dc_attr.to_s.include? 'High'
          qdm_to_hds_mappings[datatype][attribute] = {} unless qdm_to_hds_mappings[datatype][attribute]
          qdm_to_hds_mappings[datatype][attribute][:high] = dc_attr.to_s[/@entry.(.*?)(\)|$|\?)/m, 1]
        else
          qdm_to_hds_mappings[datatype][attribute] = dc_attr.to_s[/@entry.(.*?)(\)|$|\?)/m, 1]
        end
      end
    end
  end
  qdm_to_hds_mappings
end

.hds_codes_to_qdm_codes(hds_codes) ⇒ Object

Convert HDS codes structure to QDM codes structure.



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# File 'lib/cqm/converter/utils.rb', line 19

def self.hds_codes_to_qdm_codes(hds_codes)
  qdm_codes = []
  hds_codes.each do |code_system, codes|
    codes.each do |code|
      qdm_codes << { codeSystem: code_system, code: code }
    end
  end
  qdm_codes
end

.hds_to_qdm_js(js_dependencies, record, qdm_model_attrs) ⇒ Object

Builds JavaScript to assist the HDS Record to QDM Patient conversion.



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# File 'lib/cqm/converter/utils.rb', line 96

def self.hds_to_qdm_js(js_dependencies, record, qdm_model_attrs)
  record_json = JSON.parse(record.to_json)
  # Bonnie changes start_date and end_date in the front end before calculation,
  # and this is what is expected by the cql_qdm_patientapi, so make that change
  # before generating the executable JavaScript.
  record_json = record_json.deep_transform_keys { |key| key.to_s == 'start_date' ? 'start_time' : key }
  record_json = record_json.deep_transform_keys { |key| key.to_s == 'end_date' ? 'end_time' : key }
  "    window = {};\n    \#{js_dependencies};\n    function PatientWrapper() {\n    }\n    PatientWrapper.prototype.get = function(attr) {\n      const contents = \#{record_json.to_json};\n      return contents[attr];\n    }\n    cql = window.cql;\n    patient = new CQL_QDM.CQLPatient(new PatientWrapper());\n    raw_datatypes = patient.buildDatatypes();\n    qdm_model_attrs = \#{qdm_model_attrs.to_json};\n    processed_datatypes = {};\n    // Loop over each QDM datatype.\n    Object.keys(raw_datatypes).forEach(function(key) {\n      processed_datatypes[key] = [];\n      // Collect the values of the QDM attributes.\n      raw_datatypes[key].forEach(function(datatype) {\n        results = {};\n        qdm_model_attrs[datatype.constructor.name].forEach(function(method) {\n          // Call the datatype attribute method to get its value.\n          if (datatype[method]) {\n            result = datatype[method]();\n            // Handle CQL execution engine type results.\n            if (result && result['toJSON']) {\n              results[method] = result.toJSON();\n            } else {\n              results[method] = result;\n            }\n          }\n        });\n        // Add codes to result.\n        results['dataElementCodes'] = datatype['getCode']();\n        // Add description to result.\n        results['description'] = datatype['entry']['description'];\n        // Add oid to result.\n        results['hqmfOid'] = datatype['entry']['oid'];\n\n        processed_datatypes[key].push(results);\n      });\n    });\n    return processed_datatypes;\n  JS\nend\n"

.qdm_codes_to_hds_codes(qdm_codes) ⇒ Object

Convert QDM codes structure to HDS codes structure.



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# File 'lib/cqm/converter/utils.rb', line 6

def self.qdm_codes_to_hds_codes(qdm_codes)
  codes = {}
  qdm_codes.each do |qdm_code|
    qdm_code = qdm_code.stringify_keys
    code_system = qdm_code['codeSystem']
    code_system = qdm_code['code_system'] if qdm_code['code_system']
    codes[code_system] = [] unless codes.key? code_system
    codes[code_system] << qdm_code['code'] if qdm_code['code']
  end
  codes
end

.qdm_to_hds_class_type(category) ⇒ Object

Helper method to handle mismatched HDS Class names for QDM things.



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# File 'lib/cqm/converter/utils.rb', line 182

def self.qdm_to_hds_class_type(category)
  if category.to_s.include? 'diagnostic'
    'procedure'
  elsif category.to_s.include? 'physical_exam'
    'procedure'
  elsif category.to_s.include? 'intervention'
    'procedure'
  elsif category.to_s.include? 'device'
    'medical_equipment'
  elsif category.to_s.include? 'laboratory'
    'vital_sign'
  elsif category.to_s.include? 'substance'
    'medication'
  elsif category.to_s.include? 'immunization'
    'medication'
  else
    category
  end
end