health-data-standards 3.4.6 → 3.5.0

data/lib/hqmf-model/data_criteria.rb

@@ -9,6 +9,11 @@ module HQMF
     
     XPRODUCT = 'XPRODUCT'
     UNION = 'UNION'
+    INTERSECT = 'INTERSECT'
+
+    SATISFIES_ALL = 'satisfies_all'
+    SATISFIES_ANY = 'satisfies_any'
+    VARIABLE = 'variable'
 
     FIELDS = {'SEVERITY' => {title:'Severity', coded_entry_method: :severity, code: 'SEV', code_system:'2.16.840.1.113883.5.4', template_id: '2.16.840.1.113883.3.560.1.1021.2', field_type: :value},
              'ORDINAL' => {title:'Ordinal', coded_entry_method: :ordinality, code: '117363000', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1012.2', field_type: :value},
@@ -31,7 +36,7 @@ module HQMF
              'INCISION_DATETIME' => {title:'Incision Date/Time', coded_entry_method: :incision_time, code: '34896006', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1007.1', field_type: :timestamp},
              'REMOVAL_DATETIME' => {title:'Removal Date/Time', coded_entry_method: :removal_time, code: '118292001', code_system:'2.16.840.1.113883.6.96', template_id: '2.16.840.1.113883.3.560.1.1032.1', field_type: :timestamp},
              'TRANSFER_TO' => {title:'Transfer To', coded_entry_method: :transfer_to, code: 'TRANSFER_TO', template_id: '2.16.840.1.113883.3.560.1.72', field_type: :value},
-             'TRANSFER_FROM' => {title:'Transfer From', coded_entry_method: :transfer_from, code: 'TRANSFER_FROM', template_id: '2.16.840.1.113883.3.560.1.71', field_type: :value}
+             'TRANSFER_FROM' => {title:'Transfer From', coded_entry_method: :transfer_from, code: 'TRANSFER_FROM', template_id: '2.16.840.1.113883.3.560.1.71', field_type: :value},
              }
              
     VALUE_FIELDS = {'SEV'      => 'SEVERITY',
@@ -51,12 +56,14 @@ module HQMF
                     '91723000'  => 'ANATOMICAL_STRUCTURE',
                     '397898000' => 'STOP_DATETIME',
                     '34896006'  => 'INCISION_DATETIME',
-                    '118292001' =>'REMOVAL_DATETIME'
+                    '118292001' =>'REMOVAL_DATETIME',
+                    'SDLOC_ARRIVAL'   => 'FACILITY_LOCATION_ARRIVAL_DATETIME',
+                    'SDLOC_DEPARTURE' => 'FACILITY_LOCATION_DEPARTURE_DATETIME'
                    }
     
 
-    attr_reader :title, :description, :code_list_id, :children_criteria, :derivation_operator , :specific_occurrence, :specific_occurrence_const, :source_data_criteria
-    attr_accessor :id, :value, :field_values, :effective_time, :status, :temporal_references, :subset_operators, :definition, :inline_code_list, :negation_code_list_id, :negation, :display_name
+    attr_reader :title, :description, :code_list_id, :derivation_operator , :specific_occurrence, :specific_occurrence_const, :source_data_criteria, :variable
+    attr_accessor :id, :value, :field_values, :children_criteria, :effective_time, :status, :temporal_references, :subset_operators, :definition, :inline_code_list, :negation_code_list_id, :negation, :display_name, :comments
   
     # Create a new data criteria instance
     # @param [String] id
@@ -80,7 +87,9 @@ module HQMF
     # @param [String] specific_occurrence
     # @param [String] specific_occurrence_const
     # @param [String] source_data_criteria (id for the source data criteria, important for specific occurrences)
-    def initialize(id, title, display_name, description, code_list_id, children_criteria, derivation_operator, definition, status, value, field_values, effective_time, inline_code_list, negation, negation_code_list_id, temporal_references, subset_operators, specific_occurrence, specific_occurrence_const, source_data_criteria=nil)
+    # @param [String] user comments for the criteria 
+    # @param [Boolean] variable defines if the element is a QDM variable
+    def initialize(id, title, display_name, description, code_list_id, children_criteria, derivation_operator, definition, status, value, field_values, effective_time, inline_code_list, negation, negation_code_list_id, temporal_references, subset_operators, specific_occurrence, specific_occurrence_const, source_data_criteria=nil, comments=nil, variable=false)
 
       status = normalize_status(definition, status)
       @settings = HQMF::DataCriteria.get_settings_for_definition(definition, status)
@@ -105,6 +114,8 @@ module HQMF
       @specific_occurrence = specific_occurrence
       @specific_occurrence_const = specific_occurrence_const
       @source_data_criteria = source_data_criteria || id
+      @comments = comments
+      @variable = variable
     end
     
     # create a new data criteria given a category and sub_category.  A sub category can either be a status or a sub category
@@ -112,13 +123,6 @@ module HQMF
       settings = HQMF::DataCriteria.get_settings_for_definition(category, sub_category)
       HQMF::DataCriteria.new(id, title, nil, description, code_list_id, nil, nil, settings['definition'], settings['status'], nil, nil, nil, nil, negation, negation_code_list_id, nil, nil, nil,nil)
     end
-    
-    def standard_category
-      @settings['standard_category']
-    end
-    def qds_data_type
-      @settings['qds_data_type']
-    end
     def type
       @settings['category'].to_sym
     end
@@ -131,7 +135,13 @@ module HQMF
     def hard_status
       @settings['hard_status']
     end
-    
+    def update_copy(hard_status, title, description, derivation_operator, definition)
+      @settings['hard_status'] = hard_status
+      @title = title
+      @description = description
+      @derivation_operator = derivation_operator
+      @definition = definition
+    end
     def definition=(definition)
       @definition = definition
       @settings = HQMF::DataCriteria.get_settings_for_definition(@definition, @status)
@@ -163,9 +173,16 @@ module HQMF
       specific_occurrence = json['specific_occurrence'] if json['specific_occurrence']
       specific_occurrence_const = json['specific_occurrence_const'] if json['specific_occurrence_const']
       source_data_criteria = json['source_data_criteria'] if json['source_data_criteria']
+      comments = json['comments'] if json['comments']
+      variable = json['variable'] || false
 
       HQMF::DataCriteria.new(id, title, display_name, description, code_list_id, children_criteria, derivation_operator, definition, status, value, field_values,
-                             effective_time, inline_code_list, negation, negation_code_list_id, temporal_references, subset_operators,specific_occurrence,specific_occurrence_const,source_data_criteria)
+                             effective_time, inline_code_list, negation, negation_code_list_id, temporal_references, subset_operators,specific_occurrence,specific_occurrence_const,source_data_criteria, comments, variable)
+    end
+
+    def is_same_type?(criteria)
+       return @definition == criteria.definition && @hard_status == criteria.hard_status && 
+              @negation == criteria.negation && all_code_set_oids.sort == criteria.all_code_set_oids.sort
     end
 
     def to_json
@@ -175,7 +192,7 @@ module HQMF
 
     def base_json
       x = nil
-      json = build_hash(self, [:title,:display_name,:description,:standard_category,:qds_data_type,:code_list_id,:children_criteria, :derivation_operator, :property, :type, :definition, :status, :hard_status, :negation, :negation_code_list_id,:specific_occurrence,:specific_occurrence_const,:source_data_criteria])
+      json = build_hash(self, [:title,:display_name,:description,:code_list_id,:children_criteria, :derivation_operator, :property, :type, :definition, :status, :hard_status, :negation, :negation_code_list_id,:specific_occurrence,:specific_occurrence_const,:source_data_criteria,:variable])
       json[:children_criteria] = @children_criteria unless @children_criteria.nil? || @children_criteria.empty?
       json[:value] = ((@value.is_a? String) ? @value : @value.to_json) if @value
       json[:field_values] = @field_values.inject({}) {|memo,(k,v)| memo[k] = (!v.nil? ? v.to_json : nil); memo} if @field_values
@@ -183,6 +200,7 @@ module HQMF
       json[:inline_code_list] = @inline_code_list if @inline_code_list
       json[:temporal_references] = x if x = json_array(@temporal_references)
       json[:subset_operators] = x if x = json_array(@subset_operators)
+      json[:comments] = @comments if @comments
       json
     end
 
@@ -259,9 +277,15 @@ module HQMF
       
     end
 
+    def self.get_settings_map
+      return @settings_map if @settings_map
+      settings_file = File.expand_path('../data_criteria.json', __FILE__)
+      @settings_map = JSON.parse(File.read(settings_file))
+    end
+
     def self.get_settings_for_definition(definition, status)
       settings_file = File.expand_path('../data_criteria.json', __FILE__)
-      settings_map = JSON.parse(File.read(settings_file))
+      settings_map = get_settings_map
       key = definition + ((status.nil? || status.empty?) ? '' : "_#{status}")
       settings = settings_map[key]
       

data/lib/hqmf-model/document.rb

@@ -122,6 +122,14 @@ module HQMF
     def population_criteria(id)
       find(@population_criteria, :id, id)
     end
+
+    def is_cv?
+      find(@population_criteria, :type, HQMF::PopulationCriteria::MSRPOPL)
+    end
+
+    def find_population_by_type(type)
+      find(@population_criteria, :type, type)
+    end
     
     # Get all the data criteria defined by the measure
     # @return [Array] an array of HQMF::DataCriteria describing the data elements used by the measure
@@ -167,7 +175,14 @@ module HQMF
       end
       used_dc
     end
-    
+
+    # Get specific attributes by code.
+    # @param [String] code the attribute code
+    # @param [String] code_system the attribute code system
+    # @return [Array#Attribute] the matching attributes, raises an Exception if not found
+    def attributes_for_code(code, code_system)
+      @attributes.find_all { |e| e.send(:code) == code && e.send(:code_obj).send(:system) == code_system }
+    end
     
     # Get a specific data criteria by id.
     # @param [String] id the data criteria identifier
@@ -176,10 +191,54 @@ module HQMF
       find(@data_criteria, :id, id)
     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 backfill_patient_characteristics_with_codes(codes)
+      
+      [].concat(self.all_data_criteria).concat(self.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)
+            next if value_set.nil?
+            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
+
     private
     
     def find(collection, attribute, value)
       collection.find {|e| e.send(attribute)==value}
     end
   end
-end
+end

data/lib/hqmf-model/population_criteria.rb

@@ -5,7 +5,7 @@ module HQMF
   
     include HQMF::Conversion::Utilities
 
-    attr_reader :preconditions, :id, :type, :title, :hqmf_id
+    attr_reader :preconditions, :id, :type, :title, :hqmf_id, :comments
     attr_accessor :aggregator
     
     IPP = 'IPP'
@@ -15,21 +15,24 @@ module HQMF
     DENEX = 'DENEX'
     MSRPOPL = 'MSRPOPL'
     OBSERV = 'OBSERV'
+
+    STRAT = 'STRAT'
     
-    ALL_POPULATION_CODES = [IPP, DENOM, DENEX, NUMER, DENEXCEP, MSRPOPL, OBSERV]
+    ALL_POPULATION_CODES = [STRAT, IPP, DENOM, DENEX, NUMER, DENEXCEP, MSRPOPL, OBSERV]
     
     # Create a new population criteria
     # @param [String] id
     # @param [String] hqmf_id
     # @param [Array#Precondition] preconditions 
     # @param [String] title (optional)
-    def initialize(id, hqmf_id, type, preconditions, title='', aggregator=nil)
+    def initialize(id, hqmf_id, type, preconditions, title='', aggregator=nil, comments=nil)
       @id = id
       @hqmf_id = hqmf_id
       @preconditions = preconditions
       @type = type
       @title = title
       @aggregator = aggregator
+      @comments = comments
     end
     
     # Create a new population criteria from a JSON hash keyed off symbols
@@ -41,8 +44,9 @@ module HQMF
       title = json['title']
       hqmf_id = json['hqmf_id']
       aggregator = json['aggregator']
+      comments = json['comments']
       
-      HQMF::PopulationCriteria.new(id, hqmf_id, type, preconditions, title, aggregator)
+      HQMF::PopulationCriteria.new(id, hqmf_id, type, preconditions, title, aggregator, comments)
     end
     
     def to_json
@@ -51,7 +55,7 @@ module HQMF
     
     def base_json
       x = nil
-      json = build_hash(self, [:conjunction?, :type, :title, :hqmf_id, :aggregator])
+      json = build_hash(self, [:conjunction?, :type, :title, :hqmf_id, :aggregator, :comments])
       json[:preconditions] = x if x = json_array(@preconditions)
       json
     end
@@ -68,7 +72,7 @@ module HQMF
     def conjunction_code
       
       case @type
-      when IPP, DENOM, NUMER, MSRPOPL
+      when IPP, STRAT, DENOM, NUMER, MSRPOPL
         HQMF::Precondition::ALL_TRUE
       when DENEXCEP, DENEX
         HQMF::Precondition::AT_LEAST_ONE_TRUE
@@ -93,4 +97,4 @@ module HQMF
     
   end
   
-end
+end

data/lib/hqmf-model/precondition.rb

@@ -62,7 +62,7 @@ module HQMF
       json[:id] = self.id
       json[:reference] = self.reference.id if self.reference
       json[:preconditions] = x if x = json_array(@preconditions)
-      json[:conjunction_code] = self.conjunction_code if self.conjunction_code
+      json[:conjunction_code] = self.conjunction_code if self.conjunction_code && self.preconditions.length > 0
       json[:negation] = self.negation if self.negation
       json
     end

data/lib/hqmf-model/types.rb

@@ -117,7 +117,6 @@ module HQMF
     end
     
     def stringify
-      operator = ""
       if (@high && @low)
         if (@high.value == @low.value and @high.inclusive? and low.inclusive?)
           "#{@low.stringify}"
@@ -155,19 +154,21 @@ module HQMF
   # Represents a HQMF CD value which has a code and codeSystem
   class Coded
     include HQMF::Conversion::Utilities
-    attr_reader :type, :system, :code, :code_list_id, :title
+    attr_reader :type, :system, :code, :code_list_id, :title, :null_flavor, :original_text
     
     # Create a new HQMF::Coded
     # @param [String] type
     # @param [String] system
     # @param [String] code
     # @param [String] code_list_id
-    def initialize(type,system,code,code_list_id=nil,title=nil)
+    def initialize(type,system,code,code_list_id=nil,title=nil,null_flavor=nil,original_text=nil)
       @type = type
       @system = system
       @code = code
       @code_list_id = code_list_id
       @title = title
+      @null_flavor = null_flavor
+      @original_text = original_text
     end
     
     def self.for_code_list(code_list_id,title=nil)
@@ -177,19 +178,26 @@ module HQMF
     def self.for_single_code(system,code,title=nil)
       HQMF::Coded.new('CD',system,code,nil,title)
     end
+
+    def self.for_null_flavor(null_flavor,original_text=nil)
+      HQMF::Coded.new('CD',nil,nil,nil,nil,null_flavor,original_text)
+    end
     
     def self.from_json(json)
+      json = json.with_indifferent_access
       type = json["type"] if json["type"]
       system = json["system"] if json["system"]
       code = json["code"] if json["code"]
       code_list_id = json["code_list_id"] if json["code_list_id"]
       title = json["title"] if json["title"]
+      null_flavor = json["null_flavor"] if json["null_flavor"]
+      original_text = json["original_text"] if json["original_text"]
       
-      HQMF::Coded.new(type,system,code,code_list_id,title)
+      HQMF::Coded.new(type,system,code,code_list_id,title, null_flavor, original_text)
     end
     
     def to_json
-      build_hash(self, [:type,:system,:code,:code_list_id,:title])
+      build_hash(self, [:type,:system,:code,:code_list_id,:title,:null_flavor,:original_text])
     end
     
     def value
@@ -213,7 +221,7 @@ module HQMF
   class TemporalReference
     include HQMF::Conversion::Utilities
     
-    TYPES = ['DURING','SBS','SAS','SBE','SAE','EBS','EAS','EBE','EAE','SDU','EDU','ECW','SCW','CONCURRENT']
+    TYPES = ['DURING','OVERLAP','SBS','SAS','SBE','SAE','EBS','EAS','EBE','EAE','SDU','EDU','ECW','SCW','ECWS','SCWE','SBCW','SBCWE','SACW','SACWE','SBDU','EBCW','EBCWS','EACW','EACWS','EADU','CONCURRENT']
     INVERSION = {'SBS' => 'SAS','EAE' => 'EBE','SAS' => 'SBS','EBE' => 'EAE','SBE' => 'EAS','EAS' => 'SBE','SAE' => 'EBS','EBS' => 'SAE'}
     
     attr_reader :type, :reference, :range
@@ -241,7 +249,6 @@ module HQMF
     
     
     def to_json
-      x = nil
       json = build_hash(self, [:type])
       json[:reference] = @reference.to_json if @reference
       json[:range] = @range.to_json if @range
@@ -272,6 +279,10 @@ module HQMF
       end
     end
     
+    def supports_grouper_criteria?
+      ['FIRST', 'SECOND', 'THIRD', 'FOURTH', 'FIFTH', 'RECENT', 'LAST'].include? @type
+    end
+
     def self.from_json(json)
       type = json["type"] if json["type"]
 
@@ -282,7 +293,6 @@ module HQMF
     
     
     def to_json
-      x = nil
       json = build_hash(self, [:type])
       json[:value] = @value.to_json if @value
       json
@@ -315,5 +325,78 @@ module HQMF
     end
     
   end
+
+  class Identifier
+    include HQMF::Conversion::Utilities
+    attr_accessor :type, :root, :extension
+
+    def initialize(type, root, extension=nil)
+      @type = type || 'II'
+      @root = root
+      @extension = extension
+    end
+
+    def self.from_json(json)
+      json = json.with_indifferent_access
+      HQMF::Identifier.new(json['type'], json['root'], json['extension'])
+    end
+
+    def to_json
+      build_hash(self, [:type, :root, :extension])
+    end
+
+    def ==(other)
+      check_equality(self,other)
+    end
+  end
+
+  # What does ED stand for?
+  # ED has a lot more elements / attributes to represent, but only caring about what I see used...
+  class ED
+    include HQMF::Conversion::Utilities
+    attr_accessor :type, :value, :media_type
+
+    def initialize(type, value, media_type)
+      @type = type || 'ED'
+      @value = value
+      @media_type = media_type
+    end
+
+    def self.from_json(json)
+      json = json.with_indifferent_access
+      HQMF::ED.new(json['type'], json['value'], json['media_type'])
+    end
+
+    def to_json
+      build_hash(self, [:type, :value, :media_type])
+    end
+
+    def ==(other)
+      check_equality(self,other)
+    end
+  end
+
+  class GenericValueContainer
+    include HQMF::Conversion::Utilities
+    attr_accessor :type, :value
+
+    def initialize(type, value)
+      @type = type
+      @value = value
+    end
+
+    def self.from_json(json)
+      json = json.with_indifferent_access
+      HQMF::GenericValueContainer.new(json['type'], json['value'])
+    end
+
+    def to_json
+      build_hash(self, [:type, :value])
+    end
+
+    def ==(other)
+      check_equality(self,other)
+    end
+  end
   
 end