Module: HQMF2::DataCriteriaTypeAndDefinitionExtraction

Included in:
DataCriteria, HQMF2CQL::DataCriteriaTypeAndDefinitionExtraction
Defined in:
lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb

Overview

Extracts the type, and modifies the data criteria, based on the template id or definition

Constant Summary collapse

VARIABLE_TEMPLATE = 
'0.1.2.3.4.5.6.7.8.9.1'
SATISFIES_ANY_TEMPLATE = 
'2.16.840.1.113883.10.20.28.3.108'
SATISFIES_ALL_TEMPLATE = 
'2.16.840.1.113883.10.20.28.3.109'

Instance Method Summary collapse

Instance Method Details

#definition_for_demographic ⇒ Object

Return the definition for a known subset of patient characteristics



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 184

def definition_for_demographic
  demographic_type = attr_val('./cda:observationCriteria/cda:code/@code')
  demographic_translation = {
    '21112-8' => 'patient_characteristic_birthdate',
    '424144002' => 'patient_characteristic_age',
    '263495000' => 'patient_characteristic_gender',
    '102902016' => 'patient_characteristic_languages',
    '125680007' => 'patient_characteristic_marital_status',
    '103579009' => 'patient_characteristic_race'
  }
  if demographic_translation[demographic_type]
    demographic_translation[demographic_type]
  else
    fail "Unknown demographic identifier [#{demographic_type}]"
  end
end

#definition_for_nil_entry ⇒ Object

If there is no entry type, extract the entry type from what it references, and extract additional information for specific occurrences. If there are no outbound references, print an error and mark it as variable.



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 132

def definition_for_nil_entry
  reference = @entry.at_xpath('./*/cda:outboundRelationship/cda:criteriaReference', HQMF2::Document::NAMESPACES)
  ref_id = nil
  unless reference.nil?
    ref_id = "#{HQMF2::Utilities.attr_val(reference, 'cda:id/@extension')}_#{HQMF2::Utilities.attr_val(reference, 'cda:id/@root')}"
  end
  reference_criteria = @data_criteria_references[strip_tokens(ref_id)] unless ref_id.nil?
  if reference_criteria
    # we only want to copy the reference criteria definition, status, and code_list_id if this is this is not a grouping criteria (i.e., there are no children)
    if @children_criteria.blank?
      @definition = reference_criteria.definition
      @status = reference_criteria.status
      if @specific_occurrence
        @title = reference_criteria.title
        @description = reference_criteria.description
        @code_list_id = reference_criteria.code_list_id
      end
    else
      # if this is a grouping data criteria (has children) mark it as derived and only pull title and description from the reference criteria
      @definition = 'derived'
      if @specific_occurrence
        @title = reference_criteria.title
        @description = reference_criteria.description
      end
    end
  else
    puts "MISSING_DC_REF: #{ref_id}" unless @variable
    @definition = 'variable'
  end
end

#extract_definition_from_entry_type(entry_type) ⇒ Object

Given an entry type (which describes the criteria’s purpose) return the appropriate defintino



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 164

def extract_definition_from_entry_type(entry_type)
  case entry_type
  when 'Problem', 'Problems'
    'diagnosis'
  when 'Encounter', 'Encounters'
    'encounter'
  when 'LabResults', 'Results'
    'laboratory_test'
  when 'Procedure', 'Procedures'
    'procedure'
  when 'Demographics'
    definition_for_demographic
  when 'Derived'
    'derived'
  else
    fail "Unknown data criteria template identifier [#{entry_type}]"
  end
end

#extract_definition_from_template_id ⇒ Object

Given a template id, derive (if available) the definition for the template.

The definitions are stored in hqmf-model/data_criteria.json.



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 18

def extract_definition_from_template_id
  found = false

  @template_ids.each do |template_id|
    defs = HQMF::DataCriteria.definition_for_template_id(template_id, 'r2')
    if defs
      @definition = defs['definition']
      @status = defs['status'].length > 0 ? defs['status'] : nil
      found ||= true
    else
      found ||= handle_known_template_id(template_id)
    end
  end

  found
end

#extract_definition_from_template_or_type ⇒ Object 



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 7

def extract_definition_from_template_or_type
  # Try to determine what kind of data criteria we are dealing with
  # First we look for a template id and if we find one just use the definition
  # status and negation associated with that
  # If no template id or not one we recognize then try to determine type from
  # the definition element
  extract_definition_from_type unless extract_definition_from_template_id
end

#extract_definition_from_type ⇒ Object

Extract the definition (sometimes status, sometimes other elements) of the data criteria based on the type



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 57

def extract_definition_from_type
  # If we have a specific occurrence of a variable, pull attributes from the reference.
  # IDEA set this up to be called from dc_specific_and_source_extract, the number of
  #  fields changed by handle_specific_variable_ref may pose an issue.
  extract_information_for_specific_variable if @variable && @specific_occurrence

  if @entry.at_xpath('./cda:grouperCriteria')
    @definition ||= 'derived'
    return
  end
  # See if we can find a match for the entry definition value and status.
  entry_type = attr_val('./*/cda:definition/*/cda:id/@extension')
  handle_entry_type(entry_type)
end

#extract_information_for_specific_variable ⇒ Object

Extracts information from a reference for a specific



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 73

def extract_information_for_specific_variable
  reference = @entry.at_xpath('./*/cda:outboundRelationship/cda:criteriaReference',
                              HQMF2::Document::NAMESPACES)
  if reference
    ref_id = strip_tokens(
      "#{HQMF2::Utilities.attr_val(reference, 'cda:id/@extension')}_#{HQMF2::Utilities.attr_val(reference, 'cda:id/@root')}")
  end
  reference_criteria = @data_criteria_references[ref_id] if ref_id
  # if the reference is derived, pull from the original variable
  if reference_criteria && reference_criteria.definition == 'derived'
    reference_criteria = @data_criteria_references["GROUP_#{ref_id}"]
  end
  return unless reference_criteria
  handle_specific_variable_ref(reference_criteria)
end

#handle_entry_type(entry_type) ⇒ Object

Generate the definition and/or status from the entry type in most cases. If the entry type is nil, and the value is a specific occurrence, more parsing may be necessary.



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 110

def handle_entry_type(entry_type)
  # settings is required to trigger exceptions, which set the definition
  HQMF::DataCriteria.get_settings_for_definition(entry_type, @status)
  @definition = entry_type
rescue
  # if no exact match then try a string match just using entry definition value
  case entry_type
  when 'Medication', 'Medications'
    @definition = 'medication'
    @status = 'active' unless @status
  when 'RX'
    @definition = 'medication'
    @status = 'dispensed' unless @status
  when nil
    definition_for_nil_entry
  else
    @definition = extract_definition_from_entry_type(entry_type)
  end
end

#handle_known_template_id(template_id) ⇒ Object

Given a template id, modify the variables inside this data criteria to reflect the template



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 36

def handle_known_template_id(template_id)
  case template_id
  when VARIABLE_TEMPLATE
    @derivation_operator = HQMF::DataCriteria::INTERSECT if @derivation_operator == HQMF::DataCriteria::XPRODUCT
    @definition ||= 'derived'
    @variable = true
    @negation = false
  when SATISFIES_ANY_TEMPLATE
    @definition = HQMF::DataCriteria::SATISFIES_ANY
    @negation = false
  when SATISFIES_ALL_TEMPLATE
    @definition = HQMF::DataCriteria::SATISFIES_ALL
    @derivation_operator = HQMF::DataCriteria::INTERSECT
    @negation = false
  else
    return false
  end
  true
end

#handle_specific_variable_ref(reference_criteria) ⇒ Object

Apply additional information to a specific occurrence’s elements from the criteria it references.



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# File 'lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb', line 90

def handle_specific_variable_ref(reference_criteria)
  # if there are no referenced children, then it's a variable representing
  # a single data criteria, so just reference it
  if reference_criteria.children_criteria.empty?
    @children_criteria = [reference_criteria.id]
  # otherwise pull all the data criteria info from the reference
  else
    @field_values = reference_criteria.field_values
    @temporal_references = reference_criteria.temporal_references
    @subset_operators = reference_criteria.subset_operators
    @derivation_operator = reference_criteria.derivation_operator
    @definition = reference_criteria.definition
    @description = reference_criteria.description
    @status = reference_criteria.status
    @children_criteria = reference_criteria.children_criteria
  end
end