Class: Measures::CqlLoader

Inherits:
Object
  • Object
show all
Defined in:
lib/measures/loading/cql_loader.rb

Overview

Utility class for loading CQL measure definitions into the database from the MAT export zip

Class Method Summary collapse

Class Method Details

.composite_measure?(measure_dir) ⇒ Boolean

Returns true if ths uploaded measure zip file is a composite measure

Returns:

  • (Boolean) 


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# File 'lib/measures/loading/cql_loader.rb', line 5

def self.composite_measure?(measure_dir)
  # Look through all xml files at current directory level and find QDM 
  files = Dir.glob("#{measure_dir}/**.xml").select 
  begin
    # Iterate over all files passed in, extract file to temporary directory.
    files.each do |xml_file|
      if xml_file && xml_file.size > 0
        # Open up xml file and read contents.
        doc = Nokogiri::XML.parse(File.read(xml_file))
        # Check if root node in xml file matches either the HQMF file or ELM file.
        if doc.root.name == 'QualityMeasureDocument' # Root node for HQMF XML
          # Xpath to determine if it is a composite or not
          doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
          return !doc.at_xpath('//cda:measureAttribute[cda:code[@code="MSRTYPE"]][cda:value[@code="COMPOSITE"]]').nil?
        end
      end
    end     
  rescue Exception => e
    raise MeasureLoadingException.new "Error Checking MAT Export: #{e.message}"
  end
  false
end

.create_component_measures(current_directory, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket) ⇒ Object

Creates a composite’s component measures



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# File 'lib/measures/loading/cql_loader.rb', line 170

def self.create_component_measures(current_directory, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket)
  component_measures = []
  Dir.glob("#{current_directory}/*").sort.each do |file|
    if File.directory?(file)
      component_measures << create_measure(file, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket)
    end
  end
  component_measures
end

.create_measure(measure_dir, user, measure_details, vsac_options, vsac_ticket_granting_ticket, component_elms = nil) ⇒ Object

Creates and returns a measure



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# File 'lib/measures/loading/cql_loader.rb', line 181

def self.create_measure(measure_dir, user, measure_details, vsac_options, vsac_ticket_granting_ticket, component_elms=nil)
  measure = nil

  # Grabs the cql file contents, the elm_xml contents, elm_json contents and the hqmf file path
  files = get_files_from_directory(measure_dir)

  # Load hqmf into HQMF Parser
  hqmf_model = Measures::Loader.parse_hqmf_model(files[:HQMF_XML_PATH])

  # Get main measure from hqmf parser
  main_cql_library = hqmf_model.cql_measure_library

  cql_artifacts = process_cql(files, main_cql_library, user, vsac_options, vsac_ticket_granting_ticket, hqmf_model.hqmf_set_id, component_elms)

  # Create CQL Measure
  hqmf_model.backfill_patient_characteristics_with_codes(cql_artifacts[:all_codes_and_code_names])
  json = hqmf_model.to_json
  json.convert_keys_to_strings

  # Set the code list ids of data criteria and source data criteria that use direct reference codes to GUIDS.
  json['source_data_criteria'], json['data_criteria'] = set_data_criteria_code_list_ids(json, cql_artifacts)

  # Create CQL Measure
  measure_details["composite"] = composite_measure?(measure_dir)
  measure = Measures::Loader.load_hqmf_cql_model_json(json, user, cql_artifacts[:all_value_set_oids], main_cql_library, cql_artifacts[:cql_definition_dependency_structure],
                                                      cql_artifacts[:elms], cql_artifacts[:elm_annotations], files[:CQL], measure_details, cql_artifacts[:value_set_oid_version_objects])
  measure
end

.extract_measures(measure_zip, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket) ⇒ Object

Returns an array of measures Single measure returned into the array if it is a non-composite measure



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# File 'lib/measures/loading/cql_loader.rb', line 120

def self.extract_measures(measure_zip, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket)
  measure = nil
  component_measures = []
  # Unzip measure contents while retaining the directory structure
  Dir.mktmpdir do |tmp_dir|
    current_directory = unzip_measure_contents(measure_zip, tmp_dir)
    if !valid_measure_contents?(current_directory, true)
      raise MeasureLoadingException.new("Zip file was not a MAT package.")
    end
    component_elms = {}
    component_elms[:ELM_JSON] = []

    # If it is a composite measure, load in each of the components
    # Components must be loaded first so their elms can be passed onto the composite
    if composite_measure?(current_directory)
      component_measures = create_component_measures(current_directory, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket)
      component_measures.each do |component_measure|
        component_elms[:ELM_JSON].push(*component_measure.elm)
      end
    end

    # Load in regular/composite measure measure
    begin
      measure = create_measure(current_directory, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket, component_elms)
    rescue => e
      component_measures.each { |component| component.delete }
      raise e
    end

    # Create, associate and save the measure package.
    measure_package = CqlMeasurePackage.new(file: BSON::Binary.new(measure_zip.read()))
    measure.package = measure_package
    measure.package.save 

    component_measures.each do |component_measure|
      # Update the components' hqmf_set_id, formatted as follows:
      #   <composite_hqmf_set_id>&<component_hqmf_set_id>
      component_measure.hqmf_set_id = measure.hqmf_set_id + '&' + component_measure.hqmf_set_id
      component_measure.component = true;
      # Associate the component with the composite
      measure.component_hqmf_set_ids.push(component_measure.hqmf_set_id)
    end
  end # End of temporary directory usage 

  # Put measure (and component measures) into an array to return
  measures = component_measures << measure
  return measures
end

.generate_single_code_references(elms, all_codes_and_code_names, user) ⇒ Object

Add single code references by finding the codes from the elm and creating new ValueSet objects With a generated GUID as a fake oid.



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# File 'lib/measures/loading/cql_loader.rb', line 412

def self.generate_single_code_references(elms, all_codes_and_code_names, user)
  single_code_references = []
  # Add all single code references from each elm file
  elms.each do | elm |
    # Check if elm has single reference code.
    if elm['library'] && elm['library']['codes'] && elm['library']['codes']['def']
      # Loops over all single codes and saves them as fake valuesets.
      elm['library']['codes']['def'].each do |code_reference|
        code_sets = {}

        # look up the referenced code system
        code_system_def = elm['library']['codeSystems']['def'].find { |code_sys| code_sys['name'] == code_reference['codeSystem']['name'] }

        code_system_name = code_system_def['id']
        code_system_version = code_system_def['version']

        code_sets[code_system_name] ||= []
        code_sets[code_system_name] << code_reference['id']
        # Generate a unique number as our fake "oid" based on parameters that identify the DRC
        code_hash = "drc-" + Digest::SHA2.hexdigest("#{code_system_name} #{code_reference['id']} #{code_reference['name']} #{code_system_version}")            # Keep a list of generated_guids and a hash of guids with code system names and codes.
        single_code_references << { guid: code_hash, code_system_name: code_system_name, code: code_reference['id'] }
        all_codes_and_code_names[code_hash] = code_sets
        # code_hashs are unique hashes, there's no sense in adding duplicates to the ValueSet collection
        if !HealthDataStandards::SVS::ValueSet.all().where(oid: code_hash, user_id: user.id).first()
          # Create a new "ValueSet" and "Concept" object and save.
          valueSet = HealthDataStandards::SVS::ValueSet.new({oid: code_hash, display_name: code_reference['name'], version: '' ,concepts: [], user_id: user.id})
          concept = HealthDataStandards::SVS::Concept.new({code: code_reference['id'], code_system_name: code_system_name, code_system_version: code_system_version, display_name: code_reference['name']})
          valueSet.concepts << concept
          valueSet.save!
        end
      end
    end
  end
  # Returns a list of single code objects and a complete list of code systems and codes for all valuesets on the measure.
  return single_code_references, all_codes_and_code_names
end

.get_files_from_directory(dir) ⇒ Object 



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# File 'lib/measures/loading/cql_loader.rb', line 210

def self.get_files_from_directory(dir)
  cql_paths = Dir.glob(File.join("#{dir}/**.cql")).sort
  xml_paths = Dir.glob(File.join("#{dir}/**.xml")).sort
  elm_json_paths = Dir.glob(File.join("#{dir}/**.json")).sort
  
  begin
    cql_contents = []
    cql_paths.each do |cql_path|
      cql_contents << open(cql_path).read
    end

    elm_json = []
    elm_json_paths.each do |elm_json_path|
      elm_json << open(elm_json_path).read
    end
    
    xml_file_hash = retrieve_elm_and_hqmf(xml_paths)
    elm_xml_paths = xml_file_hash[:ELM_XML]
    elm_xml = []
    elm_xml_paths.each do |elm_xml_path|
      elm_xml << open(elm_xml_path).read
    end

    files = { :HQMF_XML_PATH => xml_file_hash[:HQMF_XML],
              :ELM_JSON => elm_json,
              :CQL => cql_contents,
              :ELM_XML => elm_xml }
    return files
  rescue Exception => e
    raise MeasureLoadingException.new "Error Parsing Measure Logic: #{e.message}"
  end
end

.get_value_set_oid_version_objects(value_sets, single_code_references) ⇒ Object

Returns a list of objects that include the valueset oids and their versions



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# File 'lib/measures/loading/cql_loader.rb', line 359

def self.get_value_set_oid_version_objects(value_sets, single_code_references)
  # [LDC] need to make this an array of objects instead of a hash because Mongo is
  # dumb and *let's you* have dots in keys on object creation but *doesn't let you*
  # have dots in keys on object update or retrieve....
  value_set_oid_version_objects = []
  value_sets.each do |vs|
    value_set_oid_version_objects << {:oid => vs.oid, :version => vs.version}
  end
  single_code_references.each do |single_code|
    # Only add unique Direct Reference Codes to the object
    unless value_set_oid_version_objects.include?({:oid => single_code[:guid], :version => ""})
      value_set_oid_version_objects << {:oid => single_code[:guid], :version => ""}
    end
  end
  # Return a list of unique objects only
  value_set_oid_version_objects
end

.mat_cql_export?(zip_file) ⇒ Boolean

Verifies that the zip file contains a valid measure Works for both regular & composite measures

Returns:

  • (Boolean) 


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# File 'lib/measures/loading/cql_loader.rb', line 30

def self.mat_cql_export?(zip_file)
  # Extract contents of zip file while retaining the directory structure
  original = Dir.pwd
  Dir.mktmpdir do |tmp_dir|
    current_directory = unzip_measure_contents(zip_file, tmp_dir)
    # Check if measure contents are valid
    return valid_measure_contents?(current_directory, true)
  end
end

.modify_value_set_versions(elms) ⇒ Object

Adjusting value set version data. If version is profile, set the version to nil



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# File 'lib/measures/loading/cql_loader.rb', line 394

def self.modify_value_set_versions(elms)
  elms.each do |elm|
    if elm['library']['valueSets'] && elm['library']['valueSets']['def']
      elm['library']['valueSets']['def'].each do |value_set|
        # If value set has a version and it starts with 'urn:hl7:profile:' then set to nil
        if value_set['version'] && value_set['version'].include?('urn:hl7:profile:')
          value_set['profile'] = URI.decode(value_set['version'].split('urn:hl7:profile:').last)
          value_set['version'] = nil
        # If value has a version and it starts with 'urn:hl7:version:' then strip that and keep the actual version value.
        elsif value_set['version'] && value_set['version'].include?('urn:hl7:version:')
          value_set['version'] = URI.decode(value_set['version'].split('urn:hl7:version:').last)
        end
      end
    end
  end
end

.process_cql(files, main_cql_library, user, vsac_options, vsac_ticket_granting_ticket, measure_id = nil, component_elms = nil) ⇒ Object

Manages all of the CQL processing that is not related to the HQMF.



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# File 'lib/measures/loading/cql_loader.rb', line 267

def self.process_cql(files, main_cql_library, user, vsac_options, vsac_ticket_granting_ticket, measure_id=nil, component_elms=nil)
  elm_strings = files[:ELM_JSON]
  # Removes 'urn:oid:' from ELM for Bonnie and Parse the JSON
  elm_strings.each { |elm_string| elm_string.gsub! 'urn:oid:', '' }
  elms = elm_strings.map{ |elm| JSON.parse(elm, :max_nesting=>1000)}
  elm_annotations = parse_elm_annotations(files[:ELM_XML])

  if (!component_elms.nil?)
    elms.push(*component_elms[:ELM_JSON]) 
  end
  # Hash of define statements to which define statements they use.
  cql_definition_dependency_structure = populate_cql_definition_dependency_structure(main_cql_library, elms)
  begin
    # Go back for the library statements
    cql_definition_dependency_structure = populate_used_library_dependencies(cql_definition_dependency_structure, main_cql_library, elms)
    # Add unused libraries to structure and set the value to empty hash
    cql_definition_dependency_structure = populate_unused_included_libraries(cql_definition_dependency_structure, elms)
  rescue => e
    raise MeasureLoadingException.new("Measure package missing a library or component.")
  end

  # fix up statement names in cql_statement_dependencies to not use periods <<WRAP 1>>
  # this is matched with an UNWRAP in MeasuresController in the bonnie project
  Measures::MongoHashKeyWrapper::wrapKeys cql_definition_dependency_structure

  # Depening on the value of the value set version, change it to null, strip out a substring or leave it alone.
  modify_value_set_versions(elms)

  # Grab the value sets from the elm
  elm_value_sets = []
  elms.each do | elm |
    # Confirm the library has value sets
    if elm['library'] && elm['library']['valueSets'] && elm['library']['valueSets']['def']
      elm['library']['valueSets']['def'].each do |value_set|
        elm_value_sets << {oid: value_set['id'], version: value_set['version'], profile: value_set['profile']}
      end
    end
  end
  # Get Value Sets
  value_set_models = []
  # Only load value sets from VSAC if there is a ticket_granting_ticket.
  if !vsac_ticket_granting_ticket.nil?
    value_set_models =  Measures::ValueSetLoader.load_value_sets_from_vsac(elm_value_sets, vsac_options, vsac_ticket_granting_ticket, user, measure_id)
  else
    # No vsac credentials were provided grab the valueset and valueset versions from the 'value_set_oid_version_object' on the existing measure
    db_measure = CqlMeasure.by_user(user).where(hqmf_set_id: measure_id).first
    unless db_measure.nil?
      measure_value_set_version_map = db_measure.value_set_oid_version_objects
      measure_value_set_version_map.each do |value_set|
        query_params = {user_id: user.id, oid: value_set['oid'], version: value_set['version']}
        value_set = HealthDataStandards::SVS::ValueSet.where(query_params).first()
        if value_set
          value_set_models << value_set
        else
          raise MeasureLoadingException.new "Value Set not found in database: #{query_params}"
        end
      end
    end
  end

  # Get code systems and codes for all value sets in the elm.
  all_codes_and_code_names = HQMF2JS::Generator::CodesToJson.from_value_sets(value_set_models)
  # Replace code system oids with friendly names
  # TODO: preferred solution would be to continue using OIDs in the ELM and enable Bonnie to supply those OIDs
  #   to the calculation engine in patient data and value sets.
  replace_codesystem_oids_with_names(elms)

  # Generate single reference code objects and a complete list of code systems and codes for the measure.
  single_code_references, all_codes_and_code_names = generate_single_code_references(elms, all_codes_and_code_names, user)

  # Add our new fake oids to measure value sets.
  all_value_set_oids = value_set_models.collect{|vs| vs.oid}
  single_code_references.each do |single_code|
    # Only add unique Direct Reference Codes
    unless all_value_set_oids.include?(single_code[:guid])
      all_value_set_oids << single_code[:guid]
    end
  end

  # Add a list of value set oids and their versions
  value_set_oid_version_objects = get_value_set_oid_version_objects(value_set_models, single_code_references)

  cql_artifacts = {:elms => elms,
                   :elm_annotations => elm_annotations,
                   :cql_definition_dependency_structure => cql_definition_dependency_structure,
                   :all_value_set_oids => all_value_set_oids,
                   :value_set_oid_version_objects => value_set_oid_version_objects,
                   :single_code_references => single_code_references,
                   :all_codes_and_code_names => all_codes_and_code_names}
end

.replace_codesystem_oids_with_names(elms) ⇒ Object

Replace all the code system ids that are oids with the friendly name of the code system TODO: preferred solution would be to continue using OIDs in the ELM and enable Bonnie to supply those OIDs

to the calculation engine in patient data and value sets.



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# File 'lib/measures/loading/cql_loader.rb', line 380

def self.replace_codesystem_oids_with_names(elms)
  elms.each do |elm|
    # Only do replacement if there are any code systems in this library.
    if elm['library'].has_key?('codeSystems')
      elm['library']['codeSystems']['def'].each do |code_system|
        code_name = HealthDataStandards::Util::CodeSystemHelper.code_system_for(code_system['id'])
        # if the helper returns "Unknown" then keep what was there
        code_system['id'] = code_name unless code_name == "Unknown"
      end
    end
  end
end

.retrieve_elm_and_hqmf(files) ⇒ Object

Takes in array of xml files and returns hash with keys HQMF_XML and ELM_XML



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# File 'lib/measures/loading/cql_loader.rb', line 244

def self.retrieve_elm_and_hqmf(files)
  file_paths_hash = {}
  file_paths_hash[:ELM_XML] = []
  begin
    files.each do |xml_file_path|
      if xml_file_path && xml_file_path.size > 0
        # Open up xml file and read contents.
        doc = Nokogiri::XML.parse(File.read(xml_file_path))
        # Check if root node in xml file matches either the HQMF file or ELM file.
        if doc.root.name == 'QualityMeasureDocument' # Root node for HQMF XML
          file_paths_hash[:HQMF_XML] = xml_file_path
        elsif doc.root.name == 'library' # Root node for ELM XML
          file_paths_hash[:ELM_XML] << xml_file_path
        end
      end
    end     
  rescue Exception => e
    raise MeasureLoadingException.new "Error Checking MAT Export: #{e.message}"
  end
  file_paths_hash
end

.set_data_criteria_code_list_ids(json, cql_artifacts) ⇒ Object 



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# File 'lib/measures/loading/cql_loader.rb', line 93

def self.set_data_criteria_code_list_ids(json, cql_artifacts)
  # Loop over data criteria to search for data criteria that is using a single reference code.
  # Once found set the Data Criteria's 'code_list_id' to our fake oid. Do the same for source data criteria.
  json['data_criteria'].each do |data_criteria_name, data_criteria|
    unless data_criteria['code_list_id']
      if data_criteria['inline_code_list']
        # Check to see if inline_code_list contains the correct code_system and code for a direct reference code.
        data_criteria['inline_code_list'].each do |code_system, code_list|
          # Loop over all single code reference objects.
          cql_artifacts[:single_code_references].each do |single_code_object|
            # If Data Criteria contains a matching code system, check if the correct code exists in the data critera values.
            # If both values match, set the Data Criteria's 'code_list_id' to the single_code_object_guid.
            if code_system == single_code_object[:code_system_name] && code_list.include?(single_code_object[:code])
              data_criteria['code_list_id'] = single_code_object[:guid]
              # Modify the matching source data criteria
              json['source_data_criteria'][data_criteria_name + "_source"]['code_list_id'] = single_code_object[:guid]
            end
          end
        end
      end
    end
  end
  return json['source_data_criteria'], json['data_criteria']
end

.unzip_measure_contents(zip_file, tmp_dir) ⇒ Object

Returns the base directory of the measure



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# File 'lib/measures/loading/cql_loader.rb', line 41

def self.unzip_measure_contents(zip_file, tmp_dir)
  Zip::ZipFile.open(zip_file.path) do |zip_file|
    zip_file.each do |f|
      f_path = File.join(tmp_dir, f.name)
      FileUtils.mkdir_p(File.dirname(f_path))
      f.extract(f_path)
    end
  end
  current_directory = tmp_dir
  # Detect if the zip file contents were stored into a single directory
  if Dir.glob("#{current_directory}/*").count < 3
    # If there is a single folder containing the zip file contents, step into it (ignore __MACOSX file if it exists)
    Dir.glob("#{current_directory}/*").select.each do |file|
      if !file.end_with?('__MACOSX') && File.directory?(file)
        current_directory = file
        break
      end
    end
  end
  return current_directory
end

.valid_measure_contents?(measure_dir, check_components = false) ⇒ Boolean

Verifies contents of the given measure are valid (works for regular, composite and component measures)

Returns:

  • (Boolean) 


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# File 'lib/measures/loading/cql_loader.rb', line 64

def self.valid_measure_contents?(measure_dir, check_components = false)
  # If composite measure given, check components
  if check_components
    Dir.glob("#{measure_dir}/*").each do |file|
      if File.directory?(file)
        if !valid_measure_contents?(file)
          return false
        end
      end
    end
  end

  # Grab all cql, elm & human readable docs from measure
  cql_entry = Dir.glob(File.join(measure_dir,'**.cql')).select {|x| !File.basename(x).starts_with?('__MACOSX') }.first
  elm_json = Dir.glob(File.join(measure_dir,'**.json')).select {|x| !File.basename(x).starts_with?('__MACOSX') }.first
  human_readable_entry = Dir.glob(File.join(measure_dir,'**.html')).select {|x| !File.basename(x).starts_with?('__MACOSX') }.first

  # Grab all xml files in the measure.
  xml_files = Dir.glob(File.join(measure_dir,'**.xml')).select {|x| !File.basename(x).starts_with?('__MACOSX') }

  # Find key value pair for HQMF and ELM xml files.
  if xml_files.count > 0
    xml_files_hash = retrieve_elm_and_hqmf(xml_files)
    !cql_entry.nil? && !elm_json.nil? && !human_readable_entry.nil? && !xml_files_hash[:HQMF_XML].nil? && !xml_files_hash[:ELM_XML].nil?
  else
    false
  end
end