hqmf-parser 1.0.3 → 1.0.4

data/Gemfile

@@ -7,7 +7,7 @@ gem 'nokogiri'
 gem 'rubyzip'
 
 #gem "health-data-standards", :git => 'http://github.com/projectcypress/health-data-standards.git', :branch => 'develop'
-gem "health-data-standards", '~> 2.1.2'
+gem "health-data-standards", '~> 2.1.3'
 gem "bson_ext"
 
 # below are gems required for excel spreadsheet processing

data/lib/hqmf-generator/hqmf-generator.rb

@@ -278,7 +278,7 @@ module HQMF2
           'denominator'
         when HQMF::PopulationCriteria::NUMER
           'numerator'
-        when HQMF::PopulationCriteria::EXCEP
+        when HQMF::PopulationCriteria::DENEXCEP
           'denominatorException'
         when HQMF::PopulationCriteria::DENEX
           'denominatorExclusion'

data/lib/hqmf-model/document.rb

@@ -40,7 +40,7 @@ module HQMF
           HQMF::PopulationCriteria::IPP => HQMF::PopulationCriteria::IPP,
           HQMF::PopulationCriteria::DENOM => HQMF::PopulationCriteria::DENOM,
           HQMF::PopulationCriteria::NUMER => HQMF::PopulationCriteria::NUMER,
-          HQMF::PopulationCriteria::EXCEP => HQMF::PopulationCriteria::EXCEP,
+          HQMF::PopulationCriteria::DENEXCEP => HQMF::PopulationCriteria::DENEXCEP,
           HQMF::PopulationCriteria::DENEX => HQMF::PopulationCriteria::DENEX
         }
       ]

data/lib/hqmf-model/population_criteria.rb

@@ -10,10 +10,11 @@ module HQMF
     IPP = 'IPP'
     DENOM = 'DENOM'
     NUMER = 'NUMER'
-    EXCEP = 'EXCEP'
+    DENEXCEP = 'DENEXCEP'
     DENEX = 'DENEX'
+    MSRPOPL = 'MSRPOPL'
     
-    ALL_POPULATION_CODES = [IPP, DENOM, NUMER, EXCEP, DENEX]
+    ALL_POPULATION_CODES = [IPP, DENOM, NUMER, DENEXCEP, DENEX, MSRPOPL]
     
     # Create a new population criteria
     # @param [String] id
@@ -64,7 +65,7 @@ module HQMF
       case @type
       when IPP, DENOM, NUMER
         HQMF::Precondition::ALL_TRUE
-      when EXCEP, DENEX, EXCEP
+      when DENEXCEP, DENEX
         HQMF::Precondition::AT_LEAST_ONE_TRUE
       else
         raise "Unknown population type [#{@type}]"

data/lib/hqmf-parser/1.0/population_criteria.rb

@@ -24,7 +24,7 @@ module HQMF1
     end
     
     # Get the code for the population criteria
-    # @return [String] the code (e.g. IPP, DEMON, NUMER, DENEX, EXCEP)
+    # @return [String] the code (e.g. IPP, DEMON, NUMER, DENEX, DENEXCEP)
     def code
       value = attr_val('cda:observation/cda:value/@code')
       # exclusion population criteria has id of DENOM with actionNegationInd of true
@@ -32,10 +32,6 @@ module HQMF1
       if attr_val('cda:observation/@actionNegationInd')=='true'
         value = HQMF::PopulationCriteria::DENEX
       end
-      # replace measure population with NUMER.  MSRPOPL is used in continuous variable calculations.
-      value = HQMF::PopulationCriteria::NUMER if value == 'MSRPOPL'
-      # replace DENEXCEP with EXCEP.  DENEXCEP is used by the MAT instead of EXCEP as required by HQMF V2 and QRDA.
-      value = HQMF::PopulationCriteria::EXCEP if value == 'DENEXCEP'
       value.upcase
     end
     

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

@@ -57,7 +57,7 @@ module HQMF2
           HQMF::PopulationCriteria::IPP => 'patientPopulationCriteria',
           HQMF::PopulationCriteria::DENOM => 'denominatorCriteria',
           HQMF::PopulationCriteria::NUMER => 'numeratorCriteria',
-          HQMF::PopulationCriteria::EXCEP => 'denominatorExceptionCriteria',
+          HQMF::PopulationCriteria::DENEXCEP => 'denominatorExceptionCriteria',
           HQMF::PopulationCriteria::DENEX => 'denominatorExclusionCriteria'
         }.each_pair do |criteria_id, criteria_element_name|
           criteria_def = population_def.at_xpath("cda:component[cda:#{criteria_element_name}]", NAMESPACES)

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

@@ -36,7 +36,7 @@ module HQMF2
       case @type
       when HQMF::PopulationCriteria::IPP, HQMF::PopulationCriteria::DENOM, HQMF::PopulationCriteria::NUMER
         HQMF::Precondition::ALL_TRUE
-      when HQMF::PopulationCriteria::EXCEP, HQMF::PopulationCriteria::DENEX
+      when HQMF::PopulationCriteria::DENEXCEP, HQMF::PopulationCriteria::DENEX
         HQMF::Precondition::AT_LEAST_ONE_TRUE
       else
         raise "Unknown population type [#{@type}]"

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

@@ -22,10 +22,6 @@ module HQMF
     # the restrictions added may be different for the numerator, denominator, different IPP_1, IPP_2, etc.
     def duplicate_data_criteria(data_criteria, parent_id)
       
-      # if this is a specific occurrence, then we do not want to duplicate it.
-      # we may need to duplicate it for a population however.
-      # return data_criteria if (specific_occurrences[data_criteria.id]) 
-      
       if (data_criteria.is_a? HQMF::Converter::SimpleDataCriteria and data_criteria.precondition_id == parent_id)
         new_data_criteria = data_criteria
       else
@@ -176,6 +172,12 @@ module HQMF
       specific_occurrence = criteria[:specific_occurrence]
       specific_occurrence_const = criteria[:specific_occurrence_const]
       
+      # specific occurrences do not properly set the description, so we want to add the definition and status
+      if (specific_occurrence)
+        _status = ", #{status.titleize}" if status
+        description = "#{definition.titleize}#{_status}: #{description}" 
+      end
+      
       value = nil # value is filled out by backfill_patient_characteristics for things like gender and by REFR restrictions
       effective_time = nil # filled out by temporal reference code
       temporal_references = # filled out by operator code

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

@@ -169,7 +169,7 @@ module HQMF
         
       oid_fields = document.all_data_criteria.select {|dc| dc.field_values != nil}
       if oid_fields.size > 0
-        referenced_oids = (oid_fields.map{|dc| dc.field_values.map {|key,field| puts "field: #{key} is nil" unless field; field.code_list_id if field != nil and field.type == 'CD'}}).flatten.compact.uniq
+        referenced_oids = (oid_fields.map{|dc| dc.field_values.map {|key,field| puts "field: #{key} is nil" unless field || key.match(/DATETIME/); field.code_list_id if field != nil and field.type == 'CD'}}).flatten.compact.uniq
         referenced_oids.each do |oid|
           value_set = codes[oid]
           puts "\tFIELDS (#{document.id},#{document.title}): referenced OID could not be found #{oid}" unless value_set

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

@@ -25,8 +25,9 @@ module HQMF
       ipps = @population_criteria_by_id.select {|key, value| value.type == HQMF::PopulationCriteria::IPP}
       denoms = @population_criteria_by_id.select {|key, value| value.type == HQMF::PopulationCriteria::DENOM}
       nums = @population_criteria_by_id.select {|key, value| value.type == HQMF::PopulationCriteria::NUMER}
+      msrpopls = @population_criteria_by_id.select {|key, value| value.type == HQMF::PopulationCriteria::MSRPOPL}
       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::EXCEP}
+      denexcs = @population_criteria_by_id.select {|key, value| value.type == HQMF::PopulationCriteria::DENEXCEP}
       
       if (ipps.size<=1 and denoms.size<=1 and nums.size<=1 and excls.size<=1 and denexcs.size<=1 )
         @sub_measures << 
@@ -34,7 +35,7 @@ module HQMF
             HQMF::PopulationCriteria::IPP => HQMF::PopulationCriteria::IPP,
             HQMF::PopulationCriteria::DENOM => HQMF::PopulationCriteria::DENOM,
             HQMF::PopulationCriteria::NUMER => HQMF::PopulationCriteria::NUMER,
-            HQMF::PopulationCriteria::EXCEP => HQMF::PopulationCriteria::EXCEP,
+            HQMF::PopulationCriteria::DENEXCEP => HQMF::PopulationCriteria::DENEXCEP,
             HQMF::PopulationCriteria::DENEX => HQMF::PopulationCriteria::DENEX
           }
       else
@@ -42,10 +43,13 @@ module HQMF
         nums.each do |num_id, num|
           @sub_measures << {HQMF::PopulationCriteria::NUMER => num.id}
         end
+        msrpopls.each do |popl_id, popl|
+          @sub_measures << {HQMF::PopulationCriteria::MSRPOPL => popl.id}
+        end
         apply_to_submeasures(@sub_measures, HQMF::PopulationCriteria::DENOM, denoms.values)
         apply_to_submeasures(@sub_measures, HQMF::PopulationCriteria::IPP, ipps.values)
         apply_to_submeasures(@sub_measures, HQMF::PopulationCriteria::DENEX, excls.values)
-        apply_to_submeasures(@sub_measures, HQMF::PopulationCriteria::EXCEP, denexcs.values)
+        apply_to_submeasures(@sub_measures, HQMF::PopulationCriteria::DENEXCEP, denexcs.values)
         
         keep = []
         @sub_measures.each do |sub|

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

@@ -7,9 +7,7 @@ module HQMF
       attr_accessor :precondition_id
 
       def self.from_data_criteria(data_criteria)
-        description = get_description(data_criteria)
-        
-        HQMF::Converter::SimpleDataCriteria.new(data_criteria.id, data_criteria.title, data_criteria.display_name, description, data_criteria.code_list_id, 
+        HQMF::Converter::SimpleDataCriteria.new(data_criteria.id, data_criteria.title, data_criteria.display_name, data_criteria.description, data_criteria.code_list_id, 
           data_criteria.children_criteria, data_criteria.derivation_operator, data_criteria.definition,data_criteria.status, data_criteria.value, data_criteria.field_values, 
           data_criteria.effective_time, data_criteria.inline_code_list,data_criteria.negation,data_criteria.negation_code_list_id,data_criteria.temporal_references, data_criteria.subset_operators, data_criteria.specific_occurrence,data_criteria.specific_occurrence_const)
       end
@@ -21,13 +19,6 @@ module HQMF
         @id = "#{@id}_precondition_#{precondtion_id}"
       end
       
-      def self.get_description(data_criteria)
-        description = data_criteria.description
-        status = ", #{data_criteria.status.titleize}" if data_criteria.status
-        description = "#{data_criteria.definition.titleize}#{status}: #{data_criteria.description}" if (data_criteria.description.downcase.match /#{data_criteria.definition.titleize.downcase}/).nil? and (data_criteria.description.downcase.match /#{data_criteria.status}/).nil?
-        description
-      end
-      
     end
   end
   

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: hqmf-parser
 version: !ruby/object:Gem::Version
-  version: 1.0.3
+  version: 1.0.4
   prerelease: 
 platform: ruby
 authors:
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-01 00:00:00.000000000 Z
+date: 2012-11-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rubyzip
@@ -119,8 +119,6 @@ files:
 - lib/hqmf-parser/converter/pass1/simple_restriction.rb
 - lib/hqmf-parser/converter/pass2/comparison_converter.rb
 - lib/hqmf-parser/converter/pass2/operator_converter.rb
-- lib/hqmf-parser/converter/pass3/specific_occurrence_converter.rb
-- lib/hqmf-parser/converter/pass3/specific_occurrence_converter_bak.rb
 - lib/hqmf-parser/parser.rb
 - lib/hqmf-parser/value_sets/value_set_parser.rb
 - lib/hqmf-parser.rb

data/lib/hqmf-parser/converter/pass3/specific_occurrence_converter.rb

@@ -1,86 +0,0 @@
-module HQMF
-  # Class for cleaning up references to specific occurrences in the tree
-  class SpecificOccurrenceConverter
-    
-    def initialize(data_criteria_converter)
-      @data_criteria_converter = data_criteria_converter
-    end
-   
-    def convert_specific_occurrences(population_criteria)
-      population_criteria.each do |population|
-        walk_up_tree(population.preconditions)
-      end
-    end
-    
-    def walk_up_tree(preconditions)
-      preconditions.each do |precondition|
-        if (has_child_comparison(precondition))
-          walk_up_tree(precondition.preconditions)
-        end
-        unless (precondition.comparison?)
-          occurrence_map = get_grouped_occurrences(precondition.preconditions)
-          occurrence_map.each do |key, value|
-            
-            ##
-            ##### figure out negations
-            ##
-            
-            if (precondition.conjunction_code == 'atLeastOneTrue')
-              
-              group = @data_criteria_converter.build_group_data_criteria(value, "#{key}_union", precondition.id, HQMF::DataCriteria::UNION)
-              binding.pry
-            elsif (precondition.conjunction_code == 'allTrue')
-              binding.pry
-            end
-            
-          end
-        end
-      end
-    end
-    
-    def get_grouped_occurrences(preconditions)
-      
-      result = {}
-      preconditions.each do |precondition|
-        if (precondition.preconditions and !precondition.preconditions.empty?)
-          get_grouped_occurrences(precondition.preconditions).each do |key, value|
-            if (result[key])
-              result[key].concat(value)
-            else
-              result[key] = value
-            end
-          end
-        else
-          data_criteria = @data_criteria_converter.v2_data_criteria_by_id[precondition.reference.id]
-          if is_specific_occurrence(data_criteria)
-            binding.pry
-            result[data_criteria.source_data_criteria] ||= []
-            result[data_criteria.source_data_criteria] << data_criteria
-            preconditions.delete(precondition)
-            binding.pry
-          end
-        end
-      end
-      result
-      
-    end
-    
-    def is_specific_occurrence(data_criteria)
-      !data_criteria.specific_occurrence.nil?
-    end
-    
-    def has_child_comparison(node)
-      value = false
-      node.preconditions.each do |precondition|
-        if (precondition.comparison?)
-          value ||= true
-        elsif precondition.has_preconditions?
-          value ||= has_child_comparison(precondition)
-        end
-      end if node.preconditions
-      value
-    end
-    
-    
-  end  
-end

data/lib/hqmf-parser/converter/pass3/specific_occurrence_converter_bak.rb

@@ -1,70 +0,0 @@
-module HQMF
-  # Class for cleaning up references to specific occurrences in the tree
-  class SpecificOccurrenceConverter
-    
-    def initialize(data_criteria_converter)
-      @data_criteria_converter = data_criteria_converter
-    end
-   
-   def convert_specific_occurrences(population_criteria)
-     create_precondition_map(population_criteria)
-     
-     @specific_occurrence_key_mapper = {}
-     
-     specific_occurrences = {}
-     @data_criteria_converter.v2_data_criteria.each do |data_criteria|
-       if (is_specific_occurrence(data_criteria))
-         if (data_criteria.respond_to? :precondition_id and @precondition_map[data_criteria.precondition_id])
-           specific_occurrences[data_criteria.source_data_criteria] ||= []
-           specific_occurrences[data_criteria.source_data_criteria] << data_criteria
-         elsif (data_criteria.children_criteria or data_criteria.subset_operators or data_criteria.temporal_references)
-           binding.pry
-         end
-       end
-     end
-     specific_occurrences.each do |key, occurrences|
-       
-       occurrences.sort! do |left, right|
-         @precondition_map[right.precondition_id].depth <=> @precondition_map[left.precondition_id].depth
-       end
-       
-       occurrences.each_cons(2) do |pair|
-         parent = get_common_parent(@precondition_map[pair[0].precondition_id], @precondition_map[pair[1].precondition_id])
-         binding.pry
-       end
-       
-     end
-   end
-   
-   def get_common_parent(left, right)
-     return left if left == right
-     get_common_parent(@precondition_parent_map[left.id], @precondition_parent_map[right.id])
-   end
-   
-   def create_precondition_map(population_criteria)
-     @precondition_map = {}
-     @precondition_parent_map = {}
-     depth = 0
-     population_criteria.each do |population|
-       recurse_precondition_map(population, depth)
-     end
-   end
-   
-   def recurse_precondition_map(node, depth)
-     node.preconditions.each do |precondition|
-       precondition.depth = depth
-       @precondition_map[precondition.id] = precondition
-       @precondition_parent_map[precondition.id] = node
-       if precondition.has_preconditions?
-         depth += 1
-         recurse_precondition_map(precondition, depth)
-       end
-     end if node.preconditions
-   end
-   
-   def is_specific_occurrence(data_criteria)
-     !data_criteria.specific_occurrence.nil?
-   end
-   
-  end  
-end