Class: HQMF2::Document

Inherits:
Object
  • Object
show all
Includes:
Utilities
Defined in:
lib/hqmf-parser/2.0/document.rb

Overview

Class representing an HQMF document

Constant Summary collapse

NAMESPACES = 
{'cda' => 'urn:hl7-org:v3', 'xsi' => 'http://www.w3.org/2001/XMLSchema-instance'}

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Utilities

#attr_val, attr_val, #to_xml

Methods included from HQMF::Conversion::Utilities

#build_hash, #check_equality, #json_array, #openstruct_to_json

Constructor Details

#initialize(hqmf_contents) ⇒ Document

Create a new HQMF2::Document instance by parsing at file at the supplied path

Parameters:

  • path (String) —

    the path to the HQMF document



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# File 'lib/hqmf-parser/2.0/document.rb', line 12

def initialize(hqmf_contents)
  @doc = @entry = Document.parse(hqmf_contents)
  @id = attr_val('cda:QualityMeasureDocument/cda:id/@extension')
  @hqmf_set_id = attr_val('cda:QualityMeasureDocument/cda:setId/@extension')
  @hqmf_version_number = attr_val('cda:QualityMeasureDocument/cda:versionNumber/@value').to_i
  measure_period_def = @doc.at_xpath('cda:QualityMeasureDocument/cda:controlVariable/cda:measurePeriod/cda:value', NAMESPACES)
  if measure_period_def
    @measure_period = EffectiveTime.new(measure_period_def)
  end
  
  # Extract measure attributes
  @attributes = @doc.xpath('/cda:QualityMeasureDocument/cda:subjectOf/cda:measureAttribute', NAMESPACES).collect do |attribute|
    id = attribute.at_xpath('./cda:id/@root', NAMESPACES).try(:value)
    code = attribute.at_xpath('./cda:code/@code', NAMESPACES).try(:value)
    name = attribute.at_xpath('./cda:code/cda:displayName/@value', NAMESPACES).try(:value)
    value = attribute.at_xpath('./cda:value/@value', NAMESPACES).try(:value)

    id_obj = nil
    if attribute.at_xpath('./cda:id', NAMESPACES)
      id_obj = HQMF::Identifier.new(attribute.at_xpath('./cda:id/@xsi:type', NAMESPACES).try(:value), id, attribute.at_xpath('./cda:id/@extension', NAMESPACES).try(:value))
    end

    code_obj = nil;
    if attribute.at_xpath('./cda:code', NAMESPACES)
      nullFlavor = attribute.at_xpath('./cda:code/@nullFlavor', NAMESPACES).try(:value)
      oText = attribute.at_xpath('./cda:code/cda:originalText', NAMESPACES) ? attribute.at_xpath('./cda:code/cda:originalText/@value', NAMESPACES).try(:value) : nil
      code_obj = HQMF::Coded.new(attribute.at_xpath('./cda:code/@xsi:type', NAMESPACES).try(:value) || 'CD',
                             attribute.at_xpath('./cda:code/@codeSystem', NAMESPACES).try(:value),
                             code,
                             attribute.at_xpath('./cda:code/@valueSet', NAMESPACES).try(:value),
                             name,
                             nullFlavor,
                             oText)


      # Mapping for nil values to align with 1.0 parsing
      if code == nil
        code = nullFlavor
      end

      if name == nil
        name = oText
      end

    end

    value_obj = nil
    if attribute.at_xpath('./cda:value', NAMESPACES)
      type = attribute.at_xpath('./cda:value/@xsi:type', NAMESPACES).try(:value)
      case type
      when 'II'
        value_obj = HQMF::Identifier.new(type, attribute.at_xpath('./cda:value/@root', NAMESPACES).try(:value), attribute.at_xpath('./cda:value/@extension', NAMESPACES).try(:value))
        if value == nil
          value = attribute.at_xpath('./cda:value/@extension', NAMESPACES).try(:value)
        end
      when 'ED'
        value_obj = HQMF::ED.new(type, value, attribute.at_xpath('./cda:value/@mediaType', NAMESPACES).try(:value))
      when 'CD'
        value_obj = HQMF::Coded.new('CD', attribute.at_xpath('./cda:value/@codeSystem', NAMESPACES).try(:value), attribute.at_xpath('./cda:value/@code', NAMESPACES).try(:value), attribute.at_xpath('./cda:value/@valueSet', NAMESPACES).try(:value), attribute.at_xpath('./cda:value/cda:displayName/@value', NAMESPACES).try(:value))
      else
        value_obj = value.present? ? HQMF::GenericValueContainer.new(type, value) : HQMF::AnyValue.new(type)
      end
    end

    # Handle the cms_id
    if name == "eMeasure Identifier"
       @cms_id = "CMS#{value}v#{@hqmf_version_number}"
    end

    HQMF::Attribute.new(id, code, value, nil, name, id_obj, code_obj, value_obj)
  end
  
  # Extract the data criteria
  @data_criteria = []
  @source_data_criteria = []
  @doc.xpath('cda:QualityMeasureDocument/cda:component/cda:dataCriteriaSection/cda:entry', NAMESPACES).each do |entry|
    criteria = DataCriteria.new(entry)
    if criteria.is_source_data_criteria
      @source_data_criteria << criteria
    else
      @data_criteria << criteria
    end
  end
  
  # Extract the population criteria and population collections
  @populations = []
  @population_criteria = []
  
  population_counters = {}
  ids_by_hqmf_id = {}
  
  @doc.xpath('cda:QualityMeasureDocument/cda:component/cda:populationCriteriaSection', NAMESPACES).each_with_index do |population_def, population_index|
    population = {}

    stratifier_id_def = population_def.at_xpath('cda:templateId/cda:item[@root="'+HQMF::Document::STRATIFIED_POPULATION_TEMPLATE_ID+'"]/@controlInformationRoot', NAMESPACES)
    population['stratification'] = stratifier_id_def.value if stratifier_id_def

    {
      HQMF::PopulationCriteria::IPP => 'initialPopulationCriteria',
      HQMF::PopulationCriteria::DENOM => 'denominatorCriteria',
      HQMF::PopulationCriteria::NUMER => 'numeratorCriteria',
      HQMF::PopulationCriteria::DENEXCEP => 'denominatorExceptionCriteria',
      HQMF::PopulationCriteria::DENEX => 'denominatorExclusionCriteria',
      HQMF::PopulationCriteria::STRAT => 'stratifierCriteria',
      HQMF::PopulationCriteria::MSRPOPL => 'measurePopulationCriteria'
    }.each_pair do |criteria_id, criteria_element_name|
      criteria_def = population_def.at_xpath("cda:component[cda:#{criteria_element_name}]", NAMESPACES)
      
      if criteria_def

        criteria = PopulationCriteria.new(criteria_def, self)
        
        # check to see if we have an identical population criteria.
        # this can happen since the hqmf 2.0 will export a DENOM, NUMER, etc for each population, even if identical.
        # if we have identical, just re-use it rather than creating DENOM_1, NUMER_1, etc.
        identical = @population_criteria.select {|pc| pc.to_model.base_json.to_json == criteria.to_model.base_json.to_json}
        
        if (identical.empty?)
          # this section constructs a human readable id.  The first IPP will be IPP, the second will be IPP_1, etc.  This allows the populations to be
          # more readable.  The alternative would be to have the hqmf ids in the populations, which would work, but is difficult to read the populations.
          if ids_by_hqmf_id["#{criteria.hqmf_id}-#{population['stratification']}"]
            criteria.create_human_readable_id(ids_by_hqmf_id[criteria.hqmf_id])
          else
            if population_counters[criteria_id]
              population_counters[criteria_id] += 1
              criteria.create_human_readable_id("#{criteria_id}_#{population_counters[criteria_id]}")
            else
              population_counters[criteria_id] = 0
              criteria.create_human_readable_id(criteria_id)
            end
            ids_by_hqmf_id["#{criteria.hqmf_id}-#{population['stratification']}"] = criteria.id
          end
        
        
          @population_criteria << criteria
          population[criteria_id] = criteria.id
        else
          population[criteria_id] = identical.first.id
        end
      end
    end


    id_def = population_def.at_xpath('cda:id/@extension', NAMESPACES)
    population['id'] = id_def ? id_def.value : "Population#{population_index}"
    title_def = population_def.at_xpath('cda:title/@value', NAMESPACES)
    population['title'] = title_def ? title_def.value : "Population #{population_index}"
    observation_section = @doc.xpath('cda:QualityMeasureDocument/cda:component/cda:measureObservationsSection', NAMESPACES)
    if !observation_section.empty?
       population['OBSERV'] = 'OBSERV'
    end
    @populations << population
  end


  #look for observation data in separate section but create a population for it if it exists
  observation_section = @doc.xpath('cda:QualityMeasureDocument/cda:component/cda:measureObservationsSection', NAMESPACES)
  if !observation_section.empty?
    observation_section.xpath("cda:definition",NAMESPACES).each do |criteria_def|
      criteria_id = "OBSERV"
      population = {}
      criteria = PopulationCriteria.new(criteria_def, self)
      criteria.type="OBSERV"
      # this section constructs a human readable id.  The first IPP will be IPP, the second will be IPP_1, etc.  This allows the populations to be
      # more readable.  The alternative would be to have the hqmf ids in the populations, which would work, but is difficult to read the populations.
      if ids_by_hqmf_id["#{criteria.hqmf_id}"]
         criteria.create_human_readable_id(ids_by_hqmf_id[criteria.hqmf_id])
      else
        if population_counters[criteria_id]
          population_counters[criteria_id] += 1
          criteria.create_human_readable_id("#{criteria_id}_#{population_counters[criteria_id]}")
        else
          population_counters[criteria_id] = 0
          criteria.create_human_readable_id(criteria_id)
        end
        ids_by_hqmf_id["#{criteria.hqmf_id}"] = criteria.id
      end
      
      @population_criteria << criteria

      population[criteria_id] = criteria.id
      @populations << population
      end 
  end

end

Instance Attribute Details

#attributes ⇒ Object (readonly)

Returns the value of attribute attributes.



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# File 'lib/hqmf-parser/2.0/document.rb', line 8

def attributes
  @attributes
end

#hqmf_set_id ⇒ Object (readonly)

Returns the value of attribute hqmf_set_id.



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# File 'lib/hqmf-parser/2.0/document.rb', line 8

def hqmf_set_id
  @hqmf_set_id
end

#hqmf_version_number ⇒ Object (readonly)

Returns the value of attribute hqmf_version_number.



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# File 'lib/hqmf-parser/2.0/document.rb', line 8

def hqmf_version_number
  @hqmf_version_number
end

#id ⇒ Object (readonly)

Returns the value of attribute id.



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# File 'lib/hqmf-parser/2.0/document.rb', line 8

def id
  @id
end

#measure_period ⇒ Object (readonly)

Returns the value of attribute measure_period.



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# File 'lib/hqmf-parser/2.0/document.rb', line 8

def measure_period
  @measure_period
end

#populations ⇒ Object (readonly)

Returns the value of attribute populations.



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# File 'lib/hqmf-parser/2.0/document.rb', line 8

def populations
  @populations
end

#source_data_criteria ⇒ Object (readonly)

Returns the value of attribute source_data_criteria.



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# File 'lib/hqmf-parser/2.0/document.rb', line 8

def source_data_criteria
  @source_data_criteria
end

Class Method Details

.parse(hqmf_contents) ⇒ Nokogiri::XML::Document

Returns:

  • (Nokogiri::XML::Document) 


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# File 'lib/hqmf-parser/2.0/document.rb', line 240

def self.parse(hqmf_contents)
  doc = hqmf_contents.kind_of?(Nokogiri::XML::Document) ? hqmf_contents : Nokogiri::XML(hqmf_contents)
  doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
  doc
end

Instance Method Details

#all_data_criteria ⇒ Array

Get all the data criteria defined by the measure

Returns:

  • (Array) —

    an array of HQMF2::DataCriteria describing the data elements used by the measure



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# File 'lib/hqmf-parser/2.0/document.rb', line 227

def all_data_criteria
  @data_criteria
end

#all_population_criteria ⇒ Array

Get all the population criteria defined by the measure

Returns:

  • (Array) —

    an array of HQMF2::PopulationCriteria



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# File 'lib/hqmf-parser/2.0/document.rb', line 214

def all_population_criteria
  @population_criteria
end

#data_criteria(id) ⇒ HQMF2::DataCriteria

Get a specific data criteria by id.

Parameters:

  • id (String) —

    the data criteria identifier

Returns:



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# File 'lib/hqmf-parser/2.0/document.rb', line 234

def data_criteria(id)
  find(@data_criteria, :id, id)
end

#description ⇒ String

Get the description of the measure

Returns:

  • (String) —

    the description



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# File 'lib/hqmf-parser/2.0/document.rb', line 207

def description
  description = @doc.at_xpath('cda:QualityMeasureDocument/cda:text/@value', NAMESPACES)
  description==nil ? '' : description.inner_text
end

#population_criteria(id) ⇒ HQMF2::PopulationCriteria

Get a specific population criteria by id.

Parameters:

  • id (String) —

    the population identifier

Returns:



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# File 'lib/hqmf-parser/2.0/document.rb', line 221

def population_criteria(id)
  find(@population_criteria, :id, id)
end

#title ⇒ String

Get the title of the measure

Returns:



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# File 'lib/hqmf-parser/2.0/document.rb', line 201

def title
  @doc.at_xpath('cda:QualityMeasureDocument/cda:title/@value', NAMESPACES).inner_text
end

#to_model ⇒ Object 



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# File 'lib/hqmf-parser/2.0/document.rb', line 246

def to_model

  dcs = all_data_criteria.collect {|dc| dc.to_model}
  pcs = all_population_criteria.collect {|pc| pc.to_model}
  sdc = source_data_criteria.collect{|dc| dc.to_model}
  dcs = update_data_criteria(dcs, sdc)
  HQMF::Document.new(id, id, hqmf_set_id, hqmf_version_number, @cms_id, title, description, pcs, dcs, sdc, attributes, measure_period.to_model, populations)
end

#update_data_criteria(data_criteria, source_data_criteria) ⇒ Object

Update the data criteria to handle variables properly



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# File 'lib/hqmf-parser/2.0/document.rb', line 256

def update_data_criteria(data_criteria, source_data_criteria)
   # step through each criteria and look for groupers (type derived) with one child
   data_criteria.map do |criteria|
     if criteria.type == "derived".to_sym && criteria.children_criteria.length == 1
       source_data_criteria.each do |source_criteria|
         if source_criteria.title == criteria.children_criteria[0]
           criteria.children_criteria = source_criteria.children_criteria
           #if criteria.is_same_type?(source_criteria)
           criteria.update_copy( source_criteria.hard_status, source_criteria.title, source_criteria.description,
                                 source_criteria.derivation_operator, source_criteria.definition )#, occur_letter )
         end
       end
     end
     criteria
   end
end