health-data-standards 3.4.6 → 3.5.0

data/lib/hqmf-parser/2.0/population_criteria.rb

@@ -5,16 +5,28 @@ module HQMF2
   
     include HQMF2::Utilities
     
-    attr_reader :preconditions, :id, :hqmf_id, :title, :type
-    
+    attr_reader :preconditions, :id, :hqmf_id, :title, :aggregator, :comments
+    #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')
+      @hqmf_id = attr_val('./*/cda:id/@extension') || attr_val('./*/cda:typeId/@extension')
       @title = attr_val('./*/cda:code/cda:displayName/@value') 
       @type = attr_val('./*/cda:code/@code')
+      @aggregator = nil
+      @comments = @entry.xpath("./*/cda:text/cda:xml/cda:qdmUserComments/cda:item/text()", HQMF2::Document::NAMESPACES)
+                        .map{ |v| v.content }
+      obs_test = attr_val('./cda:measureObservationDefinition/@classCode')
+      if !@title && obs_test.to_s == "OBS"
+          @title = attr_val('../cda:code/cda:displayName/@value')
+          @aggregator = attr_val('./cda:measureObservationDefinition/cda:methodCode/cda:item/@code')
+      end
+      if(!@hqmf_id) # The id extension is not required, if it's not provided use the code
+        @hqmf_id = @type
+      end
       @preconditions = @entry.xpath('./*/cda:precondition[not(@nullFlavor)]', HQMF2::Document::NAMESPACES).collect do |precondition|
         Precondition.new(precondition, @doc)
       end
@@ -34,7 +46,7 @@ module HQMF2
     # @return [String] conjunction code
     def conjunction_code
       case @type
-      when HQMF::PopulationCriteria::IPP, HQMF::PopulationCriteria::DENOM, HQMF::PopulationCriteria::NUMER
+      when HQMF::PopulationCriteria::IPP, HQMF::PopulationCriteria::DENOM, HQMF::PopulationCriteria::NUMER,HQMF::PopulationCriteria::MSRPOPL
         HQMF::Precondition::ALL_TRUE
       when HQMF::PopulationCriteria::DENEXCEP, HQMF::PopulationCriteria::DENEX
         HQMF::Precondition::AT_LEAST_ONE_TRUE
@@ -45,9 +57,9 @@ module HQMF2
     
     def to_model
       mps = preconditions.collect {|p| p.to_model}
-      HQMF::PopulationCriteria.new(id, hqmf_id, type, mps, title)
+      HQMF::PopulationCriteria.new(id, hqmf_id, type, mps, title, aggregator, comments)
     end
 
   end
   
-end
+end

data/lib/hqmf-parser/2.0/precondition.rb

@@ -13,6 +13,9 @@ module HQMF2
         Precondition.new(precondition, @doc)
       end
       reference_def = @entry.at_xpath('./*/cda:id', HQMF2::Document::NAMESPACES)
+      if !reference_def
+        reference_def = @entry.at_xpath('./cda:join/cda:templateId/cda:item', HQMF2::Document::NAMESPACES)
+      end
       if reference_def
         @reference = Reference.new(reference_def)
       end
@@ -41,4 +44,4 @@ module HQMF2
     end
   end
     
-end
+end

data/lib/hqmf-parser/2.0/types.rb

@@ -20,20 +20,16 @@ module HQMF2
     
     attr_reader :type, :unit, :value
     
-    def initialize(entry, default_type='PQ')
+    def initialize(entry, default_type='PQ', force_inclusive=false)
       @entry = entry
       @type = attr_val('./@xsi:type') || default_type
       @unit = attr_val('./@unit')
       @value = attr_val('./@value')
+      @force_inclusive = force_inclusive
     end
     
     def inclusive?
-      case attr_val('./@inclusive')
-      when 'false'
-        false
-      else
-        true
-      end
+      attr_val("../@#{@entry.name}Closed") == 'true' || @force_inclusive
     end
     
     def derived?
@@ -67,9 +63,9 @@ module HQMF2
       @type = type
       @entry = entry
       if @entry
-        @low = optional_value('./cda:low', default_bounds_type)
-        @high = optional_value('./cda:high', default_bounds_type)
-        @width = optional_value('./cda:width', 'PQ')
+        @low = optional_value("#{default_element_name}/cda:low", default_bounds_type)
+        @high = optional_value("#{default_element_name}/cda:high", default_bounds_type)
+        @width = optional_value("#{default_element_name}/cda:width", 'PQ')
       end
     end
     
@@ -81,7 +77,11 @@ module HQMF2
       lm = low ? low.to_model : nil
       hm = high ? high.to_model : nil
       wm = width ? width.to_model : nil
-      HQMF::Range.new(type, lm, hm, wm)
+      model_type = type
+      if @entry.at_xpath('./cda:uncertainRange', HQMF2::Document::NAMESPACES)
+        model_type = 'IVL_PQ'
+      end
+      HQMF::Range.new(model_type, lm, hm, wm)
     end
     
     private
@@ -94,6 +94,17 @@ module HQMF2
         nil
       end
     end
+
+    def default_element_name
+      case type
+      when 'IVL_PQ'
+        '.'
+      when 'IVL_TS'
+        'cda:phase'
+      else
+        'cda:uncertainRange'
+      end
+    end
     
     def default_bounds_type
       case type
@@ -141,7 +152,7 @@ module HQMF2
     end
 
     def title
-      attr_val('./@displayName')
+      attr_val('./*/@value')
     end
 
     def value
@@ -171,8 +182,18 @@ module HQMF2
       @entry = entry
       @type = attr_val('./cda:subsetCode/@code')
       value_def = @entry.at_xpath('./*/cda:repeatNumber', HQMF2::Document::NAMESPACES)
+      if !value_def
+        value_def = @entry.at_xpath('./*/cda:value', HQMF2::Document::NAMESPACES)
+      end
       if value_def
-        @value = HQMF2::Range.new(value_def, 'IVL_INT')
+        value_type = value_def.at_xpath('./@xsi:type', HQMF2::Document::NAMESPACES)
+        if String.try_convert(value_type) ==  "ANY"
+          @value = HQMF2::AnyValue.new()
+        end
+      end
+
+      if value_def && !@value
+        @value = HQMF2::Range.new(value_def, 'IVL_PQ')
       end
     end
 
@@ -193,7 +214,7 @@ module HQMF2
       @reference = Reference.new(@entry.at_xpath('./*/cda:id', HQMF2::Document::NAMESPACES))
       range_def = @entry.at_xpath('./cda:pauseQuantity', HQMF2::Document::NAMESPACES)
       if range_def
-        @range = HQMF2::Range.new(range_def, 'IVL_PQ')
+        @range = HQMF2::Range.new(range_def, 'PQ')
       end
     end
     
@@ -220,4 +241,4 @@ module HQMF2
     end
   end
   
-end
+end

data/lib/hqmf-parser/converter/pass1/document_converter.rb

@@ -9,9 +9,9 @@ module HQMF
       title = json[:title]
       description = json[:description]
       
+      # TODO: Investigate why we never use json[:attributes]
       metadata = json[:metadata]
       metadata.keys.each {|key| metadata[key.to_s] = metadata[key]; metadata.delete(key.to_sym)}
-      
       id = metadata["NQF_ID_NUMBER"][:value] if metadata["NQF_ID_NUMBER"]
       emeasure_id = metadata['EMEASURE_IDENTIFIER'][:value] if metadata['EMEASURE_IDENTIFIER']
       attributes = parse_attributes(metadata)
@@ -45,73 +45,21 @@ module HQMF
       
       doc = HQMF::Document.new(id, hqmf_id, hqmf_set_id, hqmf_version_number, cms_id, title, description, population_criteria, data_criteria, source_data_criteria, attributes, measure_period, populations)
        
-      backfill_patient_characteristics_with_codes(doc, codes)
-      
-      HQMF::DocumentConverter.validate(doc, codes)
+      HQMF::DocumentConverter.validate(doc, codes) if codes
       
       doc
       
     end
    
     private
-    
+
     def self.parse_attributes(metadata)
       attributes = []
       metadata.keys.each do |key|
-        attribute_hash = metadata[key]
-        code = attribute_hash[:code]
-        value = attribute_hash[:value]
-        unit = attribute_hash[:unit]
-        name = attribute_hash[:name]
-        attributes << HQMF::Attribute.new(key,code,value,unit,name)
+        attributes << HQMF::Attribute.from_json(metadata[key])
       end
       attributes
     end
-    
-
-    # patient characteristics data criteria such as GENDER require looking at the codes to determine if the 
-    # measure is interested in Males or Females.  This process is awkward, and thus is done as a separate
-    # step after the document has been converted.
-    def self.backfill_patient_characteristics_with_codes(doc, codes)
-      
-      [].concat(doc.all_data_criteria).concat(doc.source_data_criteria).each do |data_criteria|
-        if (data_criteria.type == :characteristic and !data_criteria.property.nil?)
-          if (codes)
-            value_set = codes[data_criteria.code_list_id]
-            puts "\tno value set for unknown patient characteristic: #{data_criteria.id}" unless value_set
-          else
-            puts "\tno code set to back fill: #{data_criteria.title}"
-            next
-          end
-          
-          if (data_criteria.property == :gender)
-            key = value_set.keys[0]
-            data_criteria.value = HQMF::Coded.new('CD','Administrative Sex',value_set[key].first)
-          else
-            data_criteria.inline_code_list = value_set
-          end
-          
-        elsif (data_criteria.type == :characteristic)
-          if (codes)
-            value_set = codes[data_criteria.code_list_id]
-            if (value_set)
-              # this is looking for a birthdate characteristic that is set as a generic characteristic but points to a loinc code set
-              if (value_set['LOINC'] and value_set['LOINC'].first == '21112-8')
-                data_criteria.definition = 'patient_characteristic_birthdate'
-              end
-              # this is looking for a gender characteristic that is set as a generic characteristic
-              gender_key = (value_set.keys.select {|set| set == 'Administrative Sex' || set == 'AdministrativeSex'}).first
-              if (gender_key and ['M','F'].include? value_set[gender_key].first)
-                data_criteria.definition = 'patient_characteristic_gender'
-                data_criteria.value = HQMF::Coded.new('CD','Gender',value_set[gender_key].first)
-              end
-            end
-          end
-
-        end
-      end
-    end
-    
 
     def self.parse_measure_period(json)
       

data/lib/hqmf-parser/converter/pass1/population_criteria_converter.rb

@@ -29,6 +29,8 @@ module HQMF
       observs = @population_criteria_by_id.select {|key, value| value.type == HQMF::PopulationCriteria::OBSERV}
       excls = @population_criteria_by_id.select {|key, value| value.type == HQMF::PopulationCriteria::DENEX}
       denexcs = @population_criteria_by_id.select {|key, value| value.type == HQMF::PopulationCriteria::DENEXCEP}
+
+      stratifications = @population_criteria_by_id.values.select {|value| value.type == HQMF::PopulationCriteria::STRAT}
       
       if (ipps.size<=1 and denoms.size<=1 and nums.size<=1 and excls.size<=1 and denexcs.size<=1 and msrpopls.size<=1 and observs.size<=1 )
         sub_measure = {}
@@ -70,22 +72,38 @@ module HQMF
               reference = @population_criteria_by_id[reference_id] if reference_id
               if (reference)
                 criteria = @population_criteria_by_key[sub[reference.type]]
-                value['stratification'] = criteria.stratification_id if criteria.stratification_id
-                value = nil if (sub[reference.type] != reference.id and criteria.stratification_id.nil?)
+                value = nil if (sub[reference.type] != reference.id)
               end
             end
           end
           keep << value if (value)
         end
         
-        keep.each_with_index do |sub, i|
+        @sub_measures = keep
+        
+      end
+
+      # add stratifications if we have them
+      if (stratifications.size > 0)
+        strat_subs = []
+        @sub_measures.each do |sub|
+          stratifications.each do |stratification|
+            new_sub = sub.dup
+            new_sub[HQMF::PopulationCriteria::STRAT] = stratification.id
+            new_sub['stratification'] = stratification.hqmf_id
+            strat_subs << new_sub
+          end
+        end
+        @sub_measures.concat strat_subs
+      end
+
+      if (@sub_measures.length > 1)
+        @sub_measures.each_with_index do |sub, i|
           sub['title'] = "Population #{i+1}"
           sub['id'] = "Population#{i+1}"
         end
-        
-        @sub_measures = keep
-        
       end
+
     end
     
     # source are things like exceptions or exclusions, target are IPP, or denom
@@ -151,8 +169,6 @@ module HQMF
       title = population_criteria[:title]
 
       criteria = HQMF::Converter::SimplePopulationCriteria.new(key, hqmf_id, type, preconditions, title)
-      # mark the 2.0 simple population criteria as a stratification... this allows us to create the cartesian product for this in the populations
-      criteria.stratification_id = population_criteria[:stratification_id]
       
       @population_criteria_by_id[id] = criteria
       @population_reference[key] = reference

data/lib/hqmf-parser/converter/pass1/precondition_extractor.rb

@@ -47,15 +47,19 @@ module HQMF
       # if we reference the measurement period, then we want to check if the reference is to the start or end of the measurement period
       # if we SBS of the END of the measurement period, we want to convert that to SBE of the measurement period
       if target_id == HQMF::Document::MEASURE_PERIOD_ID
-        references_start = {'SBS'=>'SBE','SAS'=>'SAE','EBS'=>'EBE','EAS'=>'EAE'}
-        references_end = {'EBE'=>'EBS','EAE'=>'EAS','SBE'=>'SBS','SAE'=>'SAS'}
+        references_start = {'SBS'=>'SBE','SAS'=>'SAE','EBS'=>'EBE','EAS'=>'EAE','SCW'=>'SCWE'}
+        references_end = {'EBE'=>'EBS','EAE'=>'EAS','SBE'=>'SBS','SAE'=>'SAS','ECW'=>'ECWS'}
         if data_criteria_converter.measure_period_v1_keys[:measure_start] == restriction[:target_id] and references_end[type]
           # before or after the END of the measurement period START.  Convert to before or after the START of the measurement period.
           # SAE of MPS => SAS of MP
+          # ends concurrent with measurement period START. Convert to concurrent with START of measurement period.
+          # ECW of MPS => ECWS
           type = references_end[type]
         elsif data_criteria_converter.measure_period_v1_keys[:measure_end] == restriction[:target_id] and references_start[type]
           # before or after the START of the measurement period END.  Convert to before or after the END of the measurement period.
           # SBS of MPE => SBE of MP
+          # starts concurrent with measurement period END. Convert to concurrent with END of measurement period.
+          # SCW of MPE => SCWE
           type = references_start[type]
         end
       end
@@ -132,6 +136,15 @@ module HQMF
         container = HQMF::Converter::SimpleRestriction.new(operator, nil, [comparison_precondition])
       else
         container = HQMF::Converter::SimpleRestriction.new(operator, target_id)
+        # handle transitive restrictions... this is where we are adding a field to a target of a timing restriction
+        if (restrictions && !restrictions.empty? && children.nil?)
+          children = []
+          restrictions.each do |child|
+            comparison_precondition = HQMF::Converter::SimplePrecondition.new(nil,[child],HQMF::Reference.new(target_id),nil, false)
+            comparison_precondition.klass = HQMF::Converter::SimplePrecondition::COMPARISON
+            children << comparison_precondition
+          end
+        end
         container.preconditions = children
       end
       

data/lib/hqmf-parser/converter/pass2/comparison_converter.rb

@@ -62,7 +62,7 @@ module HQMF
                   restriction.converted=true
                 when 'SUBJ'
                   new_data_criteria.field_values ||= {}
-                  new_data_criteria.field_values[operator.field_value_key] = operator.value
+                  new_data_criteria.field_values[operator.field_value_key] = operator.value || HQMF::AnyValue.new
                   restriction.converted=true
                 else
                   puts "\tOperator is unknown: #{operator.type}"

data/lib/hqmf-parser/parser.rb

@@ -4,49 +4,72 @@ module HQMF
     HQMF_VERSION_1 = "1.0"
     HQMF_VERSION_2 = "2.0"
     
-    def self.parse(hqmf_contents, version, codes = nil)
-      
-      HQMF::Counter.instance.reset()
-      case version
-        when HQMF_VERSION_1
-          puts("\tCodes not passed in, cannot backfill properties like gender") unless codes
-          HQMF::DocumentConverter.convert(HQMF1::Document.new(hqmf_contents).to_json, codes)
-        when HQMF_VERSION_2
-          HQMF2::Document.new(hqmf_contents).to_model
-        else
-          raise "Unsupported HQMF version specified: #{version}"
+    class V2Parser
+      def initialize
       end
+
+      def parse(xml_contents, codes=nil)
+        HQMF::Counter.instance.reset()
+        HQMF2::Document.new(xml_contents).to_model
+      end
+
+      def parse_fileds(xml_contents)
+        result = {}
+        doc = HQMF2::Document.parse(xml_contents)
+        type = doc.at_xpath('/cda:QualityMeasureDocument/cda:code/@code').value
+        if type == '57024-2'
+          id = doc.at_xpath('cda:QualityMeasureDocument/cda:id/@extension', HQMF2::Document::NAMESPACES).value.upcase
+          set_id = doc.at_xpath('cda:QualityMeasureDocument/cda:setId/@extension').value.upcase
+          version_number = doc.at_xpath('cda:QualityMeasureDocument/cda:versionNumber/@value').value.to_i
+          title = doc.at_xpath('cda:QualityMeasureDocument/cda:title/@value').inner_text
+          description = doc.at_xpath('cda:QualityMeasureDocument/cda:text/@value').inner_text
+          result=  {'id' => id, 'set_id' => set_id, 'version' => version_number, 'title' => title, 'description' => description}
+        end
+        result
+      end
+
+      def version
+        HQMF_VERSION_2
+      end
+
+      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?
+      end
+
     end
-    
-    def self.parse_fields(hqmf_contents, version)
-      result = {}
-      case version
-        when HQMF_VERSION_1
-          doc = HQMF1::Document.parse(hqmf_contents)
-          type = doc.at_xpath('//cda:code/@code').value
-          if type == '57024-2'
-            id = doc.at_xpath('//cda:id/@root').value.upcase
-            set_id = doc.at_xpath('//cda:setId/@root').value.upcase
-            version_number = doc.at_xpath('//cda:versionNumber/@value').value.to_i
-            title = doc.at_xpath('cda:QualityMeasureDocument/cda:title').inner_text
-            description = doc.at_xpath('cda:QualityMeasureDocument/cda:text').inner_text
-            result = {'id' => id, 'set_id' => set_id, 'version' => version_number, 'title' => title, 'description' => description}
-          end
-        when HQMF_VERSION_2
-          doc = HQMF2::Document.parse(hqmf_contents)
-          type = doc.at_xpath('cda:QualityMeasureDocument/cda:code/@code').value
-          if type == '57024-2'
-            id = doc.at_xpath('cda:QualityMeasureDocument/cda:id/@extension', HQMF2::Document::NAMESPACES).value.upcase
-            set_id = doc.at_xpath('cda:QualityMeasureDocument/cda:setId/@extension').value.upcase
-            version_number = doc.at_xpath('cda:QualityMeasureDocument/cda:versionNumber/@value').value.to_i
-            title = doc.at_xpath('cda:QualityMeasureDocument/cda:title/@value').inner_text
-            description = doc.at_xpath('cda:QualityMeasureDocument/cda:text/@value').inner_text
-            result = {'id' => id, 'set_id' => set_id, 'version' => version_number, 'title' => title, 'description' => description}
-          end
-        else
-          raise "Unsupported HQMF version specified: #{version}"
-      end
-      result
+
+    class V1Parser
+
+      def parse(xml_contents, codes=nil)
+        HQMF::Counter.instance.reset()
+        HQMF::DocumentConverter.convert(HQMF1::Document.new(xml_contents).to_json, codes)
+      end
+
+      def version
+        HQMF_VERSION_1
+      end
+
+      def parse_fields(xml_contents)
+        doc = HQMF1::Document.parse(xml_contents)
+        type = doc.at_xpath('//cda:code/@code').value
+        result = {}
+        if type == '57024-2'
+          id = doc.at_xpath('//cda:id/@root').value.upcase
+          set_id = doc.at_xpath('//cda:setId/@root').value.upcase
+          version_number = doc.at_xpath('//cda:versionNumber/@value').value.to_i
+          title = doc.at_xpath('cda:QualityMeasureDocument/cda:title').inner_text
+          description = doc.at_xpath('cda:QualityMeasureDocument/cda:text').inner_text
+          result = {'id' => id, 'set_id' => set_id, 'version' => version_number, 'title' => title, 'description' => description}
+        end
+        result
+      end
+
+      def self.valid?(xml_contents)
+        doc = HQMF1::Document.parse(xml_contents)
+        !doc.at_xpath("/cda:QualityMeasureDocument/cda:typeId[@root='2.16.840.1.113883.1.3' and @extension='POQM_HD000001']").nil?
+      end
+
     end
 
   end