hqmf2js 1.3.0 → 1.4.0

data/hqmf2js.gemspec

@@ -6,17 +6,12 @@ Gem::Specification.new do |s|
   s.description = "A library for converting HQMF files to executable JavaScript suitable for use with the hQuery Gateway"
   s.email = "hquery-talk@googlegroups.com"
   s.homepage = "http://github.com/hquery/hqmf2js"
-  s.authors = ["Marc Hadley", "Andre Quina", "Andy Gregorowicz"]
-  s.version = '1.3.0'
-  
-#  s.add_dependency 'nokogiri', '~> 1.5.5'
-#  s.add_dependency 'tilt', '~> 1.3.3'
-#  s.add_dependency 'coffee-script', '~> 2.2.0'
-#  s.add_dependency 'sprockets', '~> 2.2.2'
-#  s.add_development_dependency "awesome_print", "~> 1.1.0"
-#  s.add_dependency 'health-data-standards', '~> 3.1.1'
-#  s.add_dependency 'hquery-patient-api', '~> 1.0.2'
-
+  s.authors = ["The MITRE Corporation"]
+  s.version = '1.4.0'
+  s.license = 'Apache-2.0'
   s.files = s.files = `git ls-files`.split("\n")
-end
 
+  s.add_dependency "rails", "~> 4.2"
+  s.add_dependency 'health-data-standards', '~> 4.0'
+  s.add_dependency 'hquery-patient-api', '~> 1.1'
+end

data/lib/assets/javascripts/libraries/map_reduce_utils.js

@@ -5,7 +5,12 @@
 
 var root = this;
 
-root.map = function(record, population, denominator, numerator, exclusion, denexcep, msrpopl, observ, occurrenceId, isContinuousVariable) {
+
+root.emitResult = root.emitResult || function(value) {
+  if (value['IPP'] > 0) emit(ObjectId(), value);
+}
+
+root.map = function(record, population, denominator, numerator, exclusion, denexcep, msrpopl, msrpoplex, observ, occurrenceId, isContinuousVariable, stratification, variables, numex) {
   var value = {IPP: 0, patient_id: record._id,
                medical_record_id: record.medical_record_number,
                first: record.first, last: record.last, gender: record.gender,
@@ -14,22 +19,22 @@ root.map = function(record, population, denominator, numerator, exclusion, denex
                race: record.race, ethnicity: record.ethnicity, languages: record.languages,
                payer: extract_payer(record)};
 
+  value.measure_id = hqmfjs.hqmf_id
+  value.sub_id = hqmfjs.sub_id
+  value.nqf_id = hqmfjs.nqf_id
+  value.effective_date = hqmfjs.effective_date;
+  value.test_id = hqmfjs.test_id;
+
   if (isContinuousVariable) {
-    value = calculateCV(record, population, msrpopl, observ, occurrenceId, value)
+    value = calculateCV(record, population, msrpopl, msrpoplex, observ, occurrenceId, value, stratification, variables)
   } else {
-    value = calculate(record, population, denominator, numerator, exclusion, denexcep, occurrenceId, value)
+    value = calculate(record, population, denominator, numerator, exclusion, denexcep, occurrenceId, value, stratification, variables, numex)
   }
 
   if (typeof Logger != 'undefined') {
     value['logger'] = Logger.logger
     value['rationale'] = Logger.rationale
   }
-  
-  value.measure_id = hqmfjs.hqmf_id
-  value.sub_id = hqmfjs.sub_id
-  value.nqf_id = hqmfjs.nqf_id
-  value.effective_date = hqmfjs.effective_date;
-  value.test_id = hqmfjs.test_id;
 
   if (value.provider_performances) {
     var tmp = [];
@@ -44,8 +49,8 @@ root.map = function(record, population, denominator, numerator, exclusion, denex
     value.provider_performances = null;
   }
 
-  //if (value['IPP'] > 0) emit(ObjectId(), value);
-  emit(ObjectId(), value);
+  emitResult(value);
+  //emit(ObjectId(), value);
 };
 
 root.extract_payer = function(record) {
@@ -60,71 +65,153 @@ root.extract_payer = function(record) {
   return payer;
 };
 
-root.calculate = function(record, population, denominator, numerator, exclusion, denexcep, occurrenceId, value) {
-  
+root.calculate = function(record, population, denominator, numerator, exclusion, denexcep, occurrenceId, value, stratification, variables, numex) {
+
   finalSpecifics = {};
-  value = _.extend(value, {DENOM: 0, NUMER: 0, DENEXCEP: 0, DENEX: 0, antinumerator: 0, finalSpecifics: finalSpecifics});
-  
-  var ipp = population();
-  hqmf.SpecificsManager.storeFinal('IPP', ipp, finalSpecifics);
-  if (hqmf.SpecificsManager.validate(ipp)) {
-    value.IPP = hqmf.SpecificsManager.countUnique(occurrenceId, ipp);
-    var denom = hqmf.SpecificsManager.intersectSpecifics(denominator(), ipp, occurrenceId);
-    hqmf.SpecificsManager.storeFinal('DENOM', denom, finalSpecifics);
-    if (hqmf.SpecificsManager.validate(denom)) {
-      
-      value.DENOM = hqmf.SpecificsManager.countUnique(occurrenceId, denom);
-      var exclusions = hqmf.SpecificsManager.intersectSpecifics(exclusion(), denom, occurrenceId);
-      hqmf.SpecificsManager.storeFinal('DENEX', exclusions, finalSpecifics);
-      if (hqmf.SpecificsManager.validate(exclusions)) {
-        value.DENEX = hqmf.SpecificsManager.countUnique(occurrenceId, exclusions);
-        denom = hqmf.SpecificsManager.exclude(occurrenceId, denom, exclusions);
-      }
+  value = _.extend(value, {IPP: 0, DENOM: 0, NUMER: 0, DENEXCEP: 0, DENEX: 0, NUMEX: 0, antinumerator: 0});
 
+  // For the moment, we are doing this to allow for the disabling of storage of finalSpecifics in Mongo.
+  // At some point, it may make more sense to move this to its own variable, rather than using enable_rationale
+  // For example, if Cypress starts running into finalSpecifics size issues.
+  if (Logger.enable_rationale) {
+    value = _.extend(value, {finalSpecifics: finalSpecifics});
+  }
+
+  var strat;
+  var ipp;
+  var validStrat = false;
+  if(stratification) {
+    strat = stratification()
+    hqmf.SpecificsManager.storeFinal('STRAT', strat, finalSpecifics);
+    value.STRAT = hqmf.SpecificsManager.countUnique(occurrenceId, strat);
+    if (hqmf.SpecificsManager.validate(strat)) {
+      ipp = hqmf.SpecificsManager.intersectSpecifics(population(), strat, occurrenceId);
+      validStrat = true;
     }
-    // DENEX is a subset of the denominator, so we should set the specifics before the exclusion
-    // hqmf.SpecificsManager.storeFinal('DENOM', denom, finalSpecifics);
-
-    // we need to check the denominator again to make sure we still have viable candidates after 
-    // exclusions have been removed
-    if (hqmf.SpecificsManager.validate(denom)) {
-      var numer = hqmf.SpecificsManager.intersectSpecifics(numerator(), denom, occurrenceId);
-      hqmf.SpecificsManager.storeFinal('NUMER', numer, finalSpecifics);
-      if (hqmf.SpecificsManager.validate(numer)) {
-        value.NUMER = hqmf.SpecificsManager.countUnique(occurrenceId, numer);
+  } else {
+    ipp = population();
+  }
+
+  if (ipp) {
+    hqmf.SpecificsManager.storeFinal('IPP', ipp, finalSpecifics);
+    if (hqmf.SpecificsManager.validate(ipp)) {
+      value.IPP = hqmf.SpecificsManager.countUnique(occurrenceId, ipp);
+      // if we have a stratification that does not reference an episode of care then we need to take the IPP count
+      if (validStrat && value.STRAT < value.IPP) value.STRAT = value.IPP;
+      var denom = hqmf.SpecificsManager.intersectSpecifics(denominator(), ipp, occurrenceId);
+      hqmf.SpecificsManager.storeFinal('DENOM', denom, finalSpecifics);
+      if (hqmf.SpecificsManager.validate(denom)) {
+
+        value.DENOM = hqmf.SpecificsManager.countUnique(occurrenceId, denom);
+        var exclusions = hqmf.SpecificsManager.intersectSpecifics(exclusion(), denom, occurrenceId);
+        hqmf.SpecificsManager.storeFinal('DENEX', exclusions, finalSpecifics);
+        if (hqmf.SpecificsManager.validate(exclusions)) {
+          value.DENEX = hqmf.SpecificsManager.countUnique(occurrenceId, exclusions);
+          denom = hqmf.SpecificsManager.exclude(occurrenceId, denom, exclusions);
+        }
+
       }
-      
-      var excep = hqmf.SpecificsManager.intersectSpecifics(denexcep(), denom, occurrenceId);
-      hqmf.SpecificsManager.storeFinal('DENEXCEP', excep, finalSpecifics);
-      if (hqmf.SpecificsManager.validate(excep)) {
-        excep = hqmf.SpecificsManager.exclude(occurrenceId, excep, numer);
-        value.DENEXCEP = hqmf.SpecificsManager.countUnique(occurrenceId, excep);
-        denom = hqmf.SpecificsManager.exclude(occurrenceId, denom, excep);
+      // DENEX is a subset of the denominator, so we should set the specifics before the exclusion
+      // hqmf.SpecificsManager.storeFinal('DENOM', denom, finalSpecifics);
+
+      // we need to check the denominator again to make sure we still have viable candidates after
+      // exclusions have been removed
+      if (hqmf.SpecificsManager.validate(denom)) {
+        var numer = hqmf.SpecificsManager.intersectSpecifics(numerator(), denom, occurrenceId);
+        hqmf.SpecificsManager.storeFinal('NUMER', numer, finalSpecifics);
+        if (hqmf.SpecificsManager.validate(numer)) {
+          value.NUMER = hqmf.SpecificsManager.countUnique(occurrenceId, numer);
+          var numeratorExclusions = hqmf.SpecificsManager.intersectSpecifics(numex(), numer, occurrenceId);
+          hqmf.SpecificsManager.storeFinal('NUMEX', numeratorExclusions, finalSpecifics);
+          if (hqmf.SpecificsManager.validate(numeratorExclusions)) {
+            value.NUMEX = hqmf.SpecificsManager.countUnique(occurrenceId, numeratorExclusions);
+            numer = hqmf.SpecificsManager.exclude(occurrenceId, numer, numeratorExclusions);
+          }
+        }
+
+        var excep = hqmf.SpecificsManager.intersectSpecifics(denexcep(), denom, occurrenceId);
+        hqmf.SpecificsManager.storeFinal('DENEXCEP', excep, finalSpecifics);
+        if (hqmf.SpecificsManager.validate(excep)) {
+          excep = hqmf.SpecificsManager.exclude(occurrenceId, excep, numer);
+          value.DENEXCEP = hqmf.SpecificsManager.countUnique(occurrenceId, excep);
+          denom = hqmf.SpecificsManager.exclude(occurrenceId, denom, excep);
+        }
+        value.antinumerator = value.DENOM-value.NUMER;
       }
-      value.antinumerator = value.DENOM-value.NUMER;
+
     }
-      
+  }
+
+  // Adding a separate set of computations for variables. This is because the
+  // logic view displays non-occurrenced variables. However, these are not always
+  // a part of the actual logic computation. This means that they don't get
+  // colored. By adding in a separate set of computations for variables, we
+  // guarantee that they'll be colored.
+  if(variables){
+    variables();
   }
   return value;
 };
 
-root.calculateCV = function(record, population, msrpopl, observ, occurrenceId, value) {
+root.calculateCV = function(record, population, msrpopl, msrpoplex, observ, occurrenceId, value, stratification, variables) {
   finalSpecifics = {};
-  value = _.extend(value, {MSRPOPL: 0, values: [], finalSpecifics: finalSpecifics});
-  
-  var ipp = population()
-  hqmf.SpecificsManager.storeFinal('IPP', ipp, finalSpecifics);
-  if (hqmf.SpecificsManager.validate(ipp)) {
-    value.IPP = hqmf.SpecificsManager.countUnique(occurrenceId, ipp);
-    var measurePopulation = hqmf.SpecificsManager.intersectSpecifics(msrpopl(), ipp, occurrenceId);
-    hqmf.SpecificsManager.storeFinal('MSRPOPL', measurePopulation, finalSpecifics);
-    if (hqmf.SpecificsManager.validate(measurePopulation)) {
-      var observations = observ(measurePopulation.specificContext);
-      value.MSRPOPL = hqmf.SpecificsManager.countUnique(occurrenceId, measurePopulation);
-      value.values = observations;
+  value = _.extend(value, {MSRPOPL: 0, MSRPOPLEX: 0, values: []});
+
+  // For the moment, we are doing this to allow for the disabling of storage of finalSpecifics in Mongo.
+  // At some point, it may make more sense to move this to its own variable, rather than using enable_rationale
+  // For example, if Cypress starts running into finalSpecifics size issues.
+  if (Logger.enable_rationale) {
+    value = _.extend(value, {finalSpecifics: finalSpecifics});
+  }
+
+  var strat;
+  var ipp;
+  var validStrat = false;
+  if(stratification) {
+    strat = stratification()
+    hqmf.SpecificsManager.storeFinal('STRAT', strat, finalSpecifics);
+    value.STRAT = hqmf.SpecificsManager.countUnique(occurrenceId, strat);
+    if (hqmf.SpecificsManager.validate(strat)) {
+      ipp = hqmf.SpecificsManager.intersectSpecifics(population(), strat, occurrenceId);
+      validStrat = true;
+    }
+  } else {
+    ipp = population();
+  }
+
+
+  if (ipp) {
+    hqmf.SpecificsManager.storeFinal('IPP', ipp, finalSpecifics);
+    if (hqmf.SpecificsManager.validate(ipp)) {
+      value.IPP = hqmf.SpecificsManager.countUnique(occurrenceId, ipp);
+      // if we have a stratification that does not reference an episode of care then we need to take the IPP count
+      if (validStrat && value.STRAT < value.IPP) value.STRAT = value.IPP;
+      var measurePopulation = hqmf.SpecificsManager.intersectSpecifics(msrpopl(), ipp, occurrenceId);
+      hqmf.SpecificsManager.storeFinal('MSRPOPL', measurePopulation, finalSpecifics);
+      if (hqmf.SpecificsManager.validate(measurePopulation)) {
+        value.MSRPOPL = hqmf.SpecificsManager.countUnique(occurrenceId, measurePopulation);
+        
+        var measurePopulationExclusions = hqmf.SpecificsManager.intersectSpecifics(msrpoplex(), measurePopulation, occurrenceId);
+        hqmf.SpecificsManager.storeFinal('MSRPOPLEX', measurePopulationExclusions, finalSpecifics);
+        if (hqmf.SpecificsManager.validate(measurePopulationExclusions)) {
+          value.MSRPOPLEX = hqmf.SpecificsManager.countUnique(occurrenceId, measurePopulationExclusions);
+          // Remove from measure population if in measure population exclusion.
+          measurePopulation = hqmf.SpecificsManager.exclude(occurrenceId, measurePopulation, measurePopulationExclusions);
+        }
+
+        var observations = observ(measurePopulation.specificContext);
+        value.values = observations;
+      }
     }
   }
+
+  // Adding a separate set of computations for variables. This is because the
+  // logic view displays non-occurrenced variables. However, these are not always
+  // a part of the actual logic computation. This means that they don't get
+  // colored. By adding in a separate set of computations for variables, we
+  // guarantee that they'll be colored.
+  if(variables){
+    variables();
+  }
   return value;
 };
-
- 

data/lib/generator/characteristic.js.erb

@@ -1,30 +1,41 @@
   var value = patient.<%= criteria.property %>(<%= js_for_date_bound(criteria) if criteria.property == :age %>) || null;
 <%- if criteria.property == :birthtime -%>
-  var events = [value];
+  var events = value ? [value] : [];
   <%- if criteria.temporal_references -%>
     <%- criteria.temporal_references.each do |temporal_reference| -%>
   events = <%= temporal_reference.type %>(events, hqmfjs.<%= temporal_reference.reference.id %>(patient)<%= ", #{js_for_bounds(temporal_reference.range)}" if temporal_reference.range %>);
     <%- end -%>
   <%- end -%>
-  events.specificContext=hqmf.SpecificsManager.identity();
+  <%- if criteria.field_values.present? -%>
+    <%- criteria.field_values.keys.each do |field| -%>
+  events = matchingValue(value, <%= js_for_bounds(criteria.field_values[field]) %>).isTrue() ? events : [];
+    <%- end -%>
+  <%- end -%>
+  events.specificContext=events.specificContext||hqmf.SpecificsManager.identity();
   return events;
- <%- elsif criteria.property == :expired %>
-  var return_value = matchingValue(value, 'true');
-
+<%- elsif criteria.property == :expired -%>
+  var events = value ? [patient.deathdate()] : [];
     <%- if criteria.temporal_references -%>
-  var events = [patient.deathdate()]; 
-        <%- criteria.temporal_references.each do |temporal_reference| -%>
-  return_value = <%= temporal_reference.type %>(events, hqmfjs.<%= temporal_reference.reference.id %>(patient)<%= ", #{js_for_bounds(temporal_reference.range)}" if temporal_reference.range %>);
-        <%- end -%>
+      <%- criteria.temporal_references.each do |temporal_reference| -%>
+  events = <%= temporal_reference.type %>(events, hqmfjs.<%= temporal_reference.reference.id %>(patient)<%= ", #{js_for_bounds(temporal_reference.range)}" if temporal_reference.range %>);
       <%- end -%>
-return_value.specificContext=hqmf.SpecificsManager.identity();
-return return_value  
+    <%- end -%>
+  events.specificContext=events.specificContext||hqmf.SpecificsManager.identity();
+  return events;
 <%- elsif criteria.property == :clinicalTrialParticipant -%>
   matching = matchingValue(value, 'true');
   matching.specificContext=hqmf.SpecificsManager.identity();
   return matching;
+<%- elsif criteria.property == :race || criteria.property == :payer -%>
+  if (value === null) {
+    matching = new Boolean(false);
+  } else {
+    matching = new Boolean(value.includedIn(<%=criteria.inline_code_list.to_json%>));
+  }
+  matching.specificContext=hqmf.SpecificsManager.identity();
+  return matching;
 <%- else -%>
   matching = matchingValue(value, <%= js_for_bounds(criteria.value) %>);
   matching.specificContext=hqmf.SpecificsManager.identity();
   return matching;
-<%- end -%>
+<%- end -%>

data/lib/generator/codes_to_json.rb

@@ -14,7 +14,7 @@ module HQMF2JS
           code_sets = {}
           value_set.concepts.each do |code_set|
             code_sets[code_set.code_system_name] ||= []
-            code_sets[code_set.code_system_name].concat(code_set.code.to_a)
+            code_sets[code_set.code_system_name] << code_set.code
           end
           
           translation[value_set.oid] = code_sets

data/lib/generator/data_criteria.js.erb

@@ -17,15 +17,27 @@ hqmfjs.<%= js_name(criteria) %> = function(patient, initialSpecificContext) {
     <%- end -%>
     <%- if criteria.value -%>
   events = filterEventsByValue(events, <%= js_for_bounds(criteria.value) %>);
+    <%- elsif is_result_criteria(criteria) && !criteria.negation -%>
+  // force a check of results for non-negated result types so that performed does not bleed into results
+  events = filterEventsByValue(events, new ANYNonNull());
     <%- end -%>
     <%- if criteria.field_values.present?
           criteria.field_values.keys.each do |field| -%>
-  events = <%= field_library_method(field) %>(events, "<%= field_method(field) %>", <%= js_for_bounds(criteria.field_values[field]) %>);
+  events = <%= field_library_method(field, criteria.field_values[field]) %>(events, "<%= field_method(field) %>", <%= js_for_bounds(criteria.field_values[field]) %>);
       <%- end -%>
+      <%- if criteria.subset_operators -%>
+  fields = <%= criteria.field_values.keys.map {|field| field_method(field)} %>;
+      <%- end -%>
+    <%- end -%>
+    <%- if ['transfer_from','transfer_to'].include?(criteria.definition) -%>
+  events = denormalizeEventsByTransfer(events, '<%=criteria.definition.camelize(:lower)%>');
+    <%- end -%>
+    <%- if :communications == criteria.type-%>
+  events = filterEventsByCommunicationDirection(events, '<%=criteria.definition%>');
     <%- end -%>
     <%- if criteria.temporal_references and criteria.temporal_references.length > 0 -%>
       <%- criteria.temporal_references.each do |temporal_reference| -%>
-  if (events.length > 0) events = <%= temporal_reference.type %>(events, hqmfjs.<%= temporal_reference.reference.id %>(patient)<%= ", #{js_for_bounds(temporal_reference.range)}" if temporal_reference.range %>);
+  if (events.length > 0 || !Logger.short_circuit) events = <%= temporal_reference.type %>(events, hqmfjs.<%= temporal_reference.reference.id %>(patient)<%= ", #{js_for_bounds(temporal_reference.range)}" if temporal_reference.range %>);
       <%- end -%>
   if (events.length == 0) events.specificContext=hqmf.SpecificsManager.empty();
     <%- else # no temporal refs -%>
@@ -37,7 +49,7 @@ hqmfjs.<%= js_name(criteria) %> = function(patient, initialSpecificContext) {
     <%- end -%>
     <%- if criteria.subset_operators -%>
       <%- criteria.subset_operators.select {|subset_operator| subset_operator.type}.each do |subset_operator| -%>
-  events = <%= subset_operator.type %>(events<%= ", #{js_for_bounds(subset_operator.value)}" if subset_operator.value %>, initialSpecificContext);
+  events = <%= subset_operator.type %>(events<%= if subset_operator.value then ", #{js_for_bounds(subset_operator.value)}"; elsif subset_operator.type == 'DATETIMEDIFF' then ", null"; end  %>, initialSpecificContext<%- if ['SUM','MEDIAN'].include?(subset_operator.type) -%>, fields<%- end -%>);
       <%- end # each operator -%>
     <%- end # subset operators -%>
   return events;

data/lib/generator/derived_data.js.erb

@@ -3,3 +3,8 @@
     <%= "hqmfjs.#{child}(patient, initialSpecificContext)" %><%= "," if index<criteria.children_criteria.length-1 %>
     <%- end -%>
   );
+  <%- if criteria.variable -%>
+  <%- if criteria.specific_occurrence -%>
+  events.specific_occurrence = '<%= criteria.source_data_criteria%>';
+  <%- end -%>
+  <%- end -%>

data/lib/generator/execution.rb

@@ -2,7 +2,7 @@ module HQMF2JS
   module Generator
     class Execution
 
-    
+
       def self.quoted_string_array_or_null(arr)
         if arr
           quoted = arr.map {|e| "\"#{e}\""}
@@ -20,6 +20,7 @@ module HQMF2JS
           var effective_date = <%= effective_date %>;
           var enable_logging = <%= enable_logging %>;
           var enable_rationale = <%= enable_rationale %>;
+          var short_circuit = <%= short_circuit %>;
 
         <% if (!test_id.nil? && test_id.class==Moped::BSON::ObjectId) %>
           var test_id = new ObjectId(\"<%= test_id %>\");
@@ -32,7 +33,7 @@ module HQMF2JS
 
           hqmfjs.effective_date = effective_date;
           hqmfjs.test_id = test_id;
-      
+
           #{logic(hqmf_document, population_index, options)}
         };
         "
@@ -57,19 +58,25 @@ module HQMF2JS
           crosswalk_instrument = "instrumentTrueCrosswalk(hqmfjs);"
         end
 
-        
+
         "
         var patient_api = new hQuery.Patient(patient);
 
         #{gen.to_js(population_index, codes, force_sources)}
-        
+
         var occurrenceId = #{quoted_string_array_or_null(episode_ids)};
 
         hqmfjs.initializeSpecifics(patient_api, hqmfjs)
-        
+
         var population = function() {
           return executeIfAvailable(hqmfjs.#{HQMF::PopulationCriteria::IPP}, patient_api);
         }
+        var stratification = null;
+        if (hqmfjs.#{HQMF::PopulationCriteria::STRAT}) {
+          stratification = function() {
+            return hqmf.SpecificsManager.setIfNull(executeIfAvailable(hqmfjs.#{HQMF::PopulationCriteria::STRAT}, patient_api));
+          }
+        }
         var denominator = function() {
           return executeIfAvailable(hqmfjs.#{HQMF::PopulationCriteria::DENOM}, patient_api);
         }
@@ -82,13 +89,25 @@ module HQMF2JS
         var denexcep = function() {
           return executeIfAvailable(hqmfjs.#{HQMF::PopulationCriteria::DENEXCEP}, patient_api);
         }
+        var numex = function() {
+          return executeIfAvailable(hqmfjs.#{HQMF::PopulationCriteria::NUMEX}, patient_api);
+        }
         var msrpopl = function() {
-          return executeIfAvailable(hqmfjs.#{HQMF::PopulationCriteria::MSRPOPL}, patient_api);
+          #{msrpopl_function(custom_functions, population_index)}
+        }
+        var msrpoplex = function() {
+          return executeIfAvailable(hqmfjs.#{HQMF::PopulationCriteria::MSRPOPLEX}, patient_api);
         }
         var observ = function(specific_context) {
           #{observation_function(custom_functions, population_index)}
         }
-        
+
+        var variables = function() {
+          if (Logger.enable_rationale) {
+            return executeIfAvailable(hqmfjs.VARIABLES, patient_api);
+          }
+        }
+
         var executeIfAvailable = function(optionalFunction, patient_api) {
           if (typeof(optionalFunction)==='function') {
             result = optionalFunction(patient_api);
@@ -105,15 +124,18 @@ module HQMF2JS
           Logger.logger = [];
           Logger.rationale={};
           if (typeof short_circuit == 'undefined') short_circuit = true;
-        
+
           // turn on logging if it is enabled
           if (enable_logging || enable_rationale) {
             injectLogger(hqmfjs, enable_logging, enable_rationale, short_circuit);
-          } 
+          } else {
+            Logger.enable_rationale = false;
+            Logger.short_circuit = short_circuit;
+          }
         }
 
         try {
-          map(patient, population, denominator, numerator, exclusion, denexcep, msrpopl, observ, occurrenceId,#{continuous_variable});
+          map(patient, population, denominator, numerator, exclusion, denexcep, msrpopl, msrpoplex, observ, occurrenceId,#{continuous_variable},stratification, variables, numex);
         } catch(err) {
           print(err.stack);
           throw err;
@@ -139,6 +161,14 @@ module HQMF2JS
 
       end
 
+      def self.msrpopl_function(custom_functions, population_index)
+        if (custom_functions && custom_functions[HQMF::PopulationCriteria::MSRPOPL])
+          "return #{custom_functions[HQMF::PopulationCriteria::MSRPOPL]}(patient_api, hqmfjs)"
+        else
+          "return executeIfAvailable(hqmfjs.#{HQMF::PopulationCriteria::MSRPOPL}, patient_api);"
+        end
+      end
+
     end
   end
-end
+end