Incomplete parsing of MAT-generated HQMF 2.1 xml

lib/hqmf-parser/2.0/data_criteria.rb

@@ -9,6 +9,7 @@ class DataCriteria
     attr_reader :derivation_operator, :negation, :negation_code_list_id, :description
     attr_reader :field_values, :source_data_criteria, :specific_occurrence_const
     attr_reader :specific_occurrence, :is_source_data_criteria, :comments
+    attr_reader :id
 
     VARIABLE_TEMPLATE = "0.1.2.3.4.5.6.7.8.9.1"
     SATISFIES_ANY_TEMPLATE = "0.1.2.3.4.5.6.7.8.9.2"
@@ -27,7 +28,7 @@ def initialize(entry)
       @entry = entry
       @local_variable_name = extract_local_variable_name
       @status = attr_val('./*/cda:statusCode/@code')
-      @description = attr_val("./#{CRITERIA_GLOB}/cda:text/@value")
+      @description = attr_val("./#{CRITERIA_GLOB}/cda:text/@value") || attr_val("./#{CRITERIA_GLOB}/cda:title/@value") || attr_val("./#{CRITERIA_GLOB}/cda:id/@extension")
       extract_negation()
       extract_specific_or_source()
       @effective_time = extract_effective_time
@@ -37,10 +38,11 @@ def initialize(entry)
       @subset_operators = extract_subset_operators
       @children_criteria = extract_child_criteria
       @id_xpath = './*/cda:id/@extension'
+      @id = attr_val(@id_xpath)
       @code_list_xpath = './*/cda:code'
       @value_xpath = './*/cda:value'
       @comments = @entry.xpath("./#{CRITERIA_GLOB}/cda:text/cda:xml/cda:qdmUserComments/cda:item/text()", HQMF2::Document::NAMESPACES).map{ |v| v.content }
-      @variable = false
+      @variable = extract_variable
 
       # 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
@@ -94,6 +96,7 @@ def extract_type_from_definition
         return
       end
       # See if we can find a match for the entry definition value and status.
+      # FIXME: Resolve issue with improperly defined data criteria
       entry_type = attr_val('./*/cda:definition/*/cda:id/@extension')
       begin
         settings = HQMF::DataCriteria.get_settings_for_definition(entry_type, @status)
@@ -176,11 +179,12 @@ def to_s
       "DataCriteria#{props.to_s}"
     end
 
+    # TODO: Remove id method if id attribute is sufficient
     # Get the identifier of the criteria, used elsewhere within the document for referencing
     # @return [String] the identifier of this data criteria
-    def id
-      attr_val(@id_xpath)
-    end
+    # def id
+    #   attr_val(@id_xpath)
+    # end
 
     # Get the title of the criteria, provides a human readable description
     # @return [String] the title of this data criteria
@@ -243,6 +247,24 @@ def to_model
         @specific_occurrence_const, @source_data_criteria, @comments, @variable)
     end
 
+    # Return a new DataCriteria instance with only source data criteria attributes set
+    def extract_source_data_criteria
+      DataCriteria.new(@entry).extract_as_source_data_criteria(@source_data_criteria || @id)
+    end
+
+    # Set this data criteria's specific attributes to empty/nil
+    # SHOULD only be called on the source data criteria instance
+    def extract_as_source_data_criteria(id)
+      @field_values = {}
+      @temporal_references = []
+      @subset_operators = []
+      @is_source_data_criteria = true
+      @specific_occurrence = nil
+      @specific_occurrence_const = nil
+      @id = id
+      self
+    end
+
     private
 
     def extract_negation
@@ -389,6 +411,13 @@ def definition_for_demographic
 
     end
 
+    # Determine if this instance is a qdm variable
+    def extract_variable
+      variable = @local_variable_name.start_with? "qdm_var_" unless @local_variable_name.blank?
+      variable ||= @id.start_with? "qdm_var_" unless @id.blank?
+      variable ||= false
+    end
+
   end
 
 end

lib/hqmf-parser/2.0/document.rb

@@ -6,20 +6,20 @@ class Document
     NAMESPACES = {'cda' => 'urn:hl7-org:v3', 'xsi' => 'http://www.w3.org/2001/XMLSchema-instance', 'qdm'=>'urn:hhs-qdm:hqmf-r2-extensions:v1'}
 
     attr_reader :measure_period, :id, :hqmf_set_id, :hqmf_version_number, :populations, :attributes, :source_data_criteria
-      
+
     # Create a new HQMF2::Document instance by parsing at file at the supplied path
     # @param [String] path the path to the HQMF document
     def initialize(hqmf_contents)
       @doc = @entry = Document.parse(hqmf_contents)
       remove_popultaion_preconditions(@doc)
-      @id = attr_val('cda:QualityMeasureDocument/cda:id/@extension')
-      @hqmf_set_id = attr_val('cda:QualityMeasureDocument/cda:setId/@extension')
+      @id = attr_val('cda:QualityMeasureDocument/cda:id/@extension') || attr_val('cda:QualityMeasureDocument/cda:id/@root').upcase
+      @hqmf_set_id = attr_val('cda:QualityMeasureDocument/cda:setId/@extension') || attr_val('cda:QualityMeasureDocument/cda:setId/@root').upcase
       @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)
@@ -75,13 +75,13 @@ def initialize(hqmf_contents)
         end
 
         # Handle the cms_id
-        if name == "eMeasure Identifier"
+        if name.include? "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 = []
@@ -93,14 +93,17 @@ def initialize(hqmf_contents)
           @data_criteria << criteria
         end
       end
-
+
+      # Extract the source data criteria from data criteria
+      @source_data_criteria = @data_criteria.map{|dc| dc.extract_source_data_criteria}.uniq! { |sdc| sdc.id }
+
       # 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 = {}
 
@@ -117,16 +120,16 @@ def initialize(hqmf_contents)
           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.
@@ -142,8 +145,8 @@ def initialize(hqmf_contents)
                 end
                 ids_by_hqmf_id["#{criteria.hqmf_id}-#{population['stratification']}"] = criteria.id
               end
-            
-            
+
+
               @population_criteria << criteria
               population[criteria_id] = criteria.id
             else
@@ -187,63 +190,63 @@ def initialize(hqmf_contents)
             end
             ids_by_hqmf_id["#{criteria.hqmf_id}"] = criteria.id
           end
-          
+
           @population_criteria << criteria
 
           population[criteria_id] = criteria.id
           @populations << population
-          end 
+          end
       end
 
     end
-    
+
     # Get the title of the measure
     # @return [String] the title
     def title
       @doc.at_xpath('cda:QualityMeasureDocument/cda:title/@value', NAMESPACES).inner_text
     end
-    
+
     # Get the description of the measure
     # @return [String] the description
     def description
       description = @doc.at_xpath('cda:QualityMeasureDocument/cda:text/@value', NAMESPACES)
       description==nil ? '' : description.inner_text
     end
-  
+
     # Get all the population criteria defined by the measure
     # @return [Array] an array of HQMF2::PopulationCriteria
     def all_population_criteria
       @population_criteria
     end
-    
+
     # Get a specific population criteria by id.
     # @param [String] id the population identifier
     # @return [HQMF2::PopulationCriteria] the matching criteria, raises an Exception if not found
     def population_criteria(id)
       find(@population_criteria, :id, id)
     end
-    
+
     # Get all the data criteria defined by the measure
     # @return [Array] an array of HQMF2::DataCriteria describing the data elements used by the measure
     def all_data_criteria
       @data_criteria
     end
-    
+
     # Get a specific data criteria by id.
     # @param [String] id the data criteria identifier
     # @return [HQMF2::DataCriteria] the matching data criteria, raises an Exception if not found
     def data_criteria(id)
       find(@data_criteria, :id, id)
     end
-    
+
    # Parse an XML document from the supplied contents
     # @return [Nokogiri::XML::Document]
     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
-    
+
     def to_model
 
       dcs = all_data_criteria.collect {|dc| dc.to_model}
@@ -273,14 +276,15 @@ def update_data_criteria(data_criteria, source_data_criteria)
 
     def remove_popultaion_preconditions(doc)
       #population sections
-      pop_ids = doc.xpath("//cda:populationCriteriaSection/cda:component[@typeCode='COMP']/*/cda:id",NAMESPACES) 
+      pop_ids = doc.xpath("//cda:populationCriteriaSection/cda:component[@typeCode='COMP']/*/cda:id",NAMESPACES)
       #find the population entries and get their ids
       pop_ids.each do |p_id|
         doc.xpath("//cda:precondition[./cda:criteriaReference/cda:id[@extension='#{p_id["extension"]}' and @root='#{p_id["root"]}']]",NAMESPACES).remove
       end
     end
+
     private
-    
+
     def find(collection, attribute, value)
       collection.find {|e| e.send(attribute)==value}
     end

lib/hqmf-parser/2.0/population_criteria.rb

@@ -2,20 +2,21 @@ module HQMF2
   # Represents an HQMF population criteria, also supports all the same methods as
   # HQMF2::Precondition
   class PopulationCriteria
-  
+
     include HQMF2::Utilities
-    
+
     attr_reader :preconditions, :id, :hqmf_id, :title, :aggregator, :comments
-    #need to do this to allow for setting the type to OBSERV for 
+    #need to do this to allow for setting the type to OBSERV for
     attr_accessor :type
     # Create a new population criteria from the supplied HQMF entry
     # @param [Nokogiri::XML::Element] the HQMF entry
     def initialize(entry, doc)
       @doc = doc
       @entry = entry
       @hqmf_id = attr_val('./*/cda:id/@extension') || attr_val('./*/cda:typeId/@extension')
-      @title = attr_val('./*/cda:code/cda:displayName/@value') 
+      @title = attr_val('./*/cda:code/cda:displayName/@value')
       @type = attr_val('./*/cda:code/@code')
+      @type = 'IPP' if @type == 'IPOP'
       @aggregator = nil
       @comments = @entry.xpath("./*/cda:text/cda:xml/cda:qdmUserComments/cda:item/text()", HQMF2::Document::NAMESPACES)
                         .map{ |v| v.content }
@@ -31,11 +32,11 @@ def initialize(entry, doc)
         Precondition.new(precondition, @doc)
       end
     end
-    
+
     def create_human_readable_id(id)
       @id = id
     end
-    
+
     # Return true of this precondition represents a conjunction with nested preconditions
     # or false of this precondition is a reference to a data criteria
     def conjunction?
@@ -54,12 +55,12 @@ def conjunction_code
         raise "Unknown population type [#{@type}]"
       end
     end
-    
+
     def to_model
       mps = preconditions.collect {|p| p.to_model}
       HQMF::PopulationCriteria.new(id, hqmf_id, type, mps, title, aggregator, comments)
     end
 
   end
-  
+
 end

lib/hqmf-parser/parser.rb

@@ -1,9 +1,9 @@
 module HQMF
   class Parser
-    
+
     HQMF_VERSION_1 = "1.0"
     HQMF_VERSION_2 = "2.0"
-    
+
     class V2Parser
       def initialize
       end
@@ -34,7 +34,7 @@ def version
 
       def self.valid?(xml_contents)
          doc = HQMF2::Document.parse(xml_contents)
-        !doc.at_xpath("/cda:QualityMeasureDocument/cda:typeId[@root='2.16.840.1.113883.1.3' and @extension='POQM_MT000001UV03']").nil?
+        !doc.at_xpath("/cda:QualityMeasureDocument/cda:typeId[@root='2.16.840.1.113883.1.3' and @extension='POQM_HD000001UV02']").nil?
       end
 
     end
@@ -73,5 +73,5 @@ def self.valid?(xml_contents)
     end
 
   end
-  
-end
+
+end