hqmf2js 1.1.0 → 1.2.0

data/Gemfile

@@ -8,9 +8,7 @@ group :assets do
   gem 'uglifier'
 end
 
-gem "hquery-patient-api", '~> 1.0.0'
-gem 'hqmf-parser', '~> 1.1.0'
-gem "health-data-standards", '~> 2.2.0'
+gemspec
 
 gem 'nokogiri'
 gem 'sprockets', '~> 2.2.2'

data/Gemfile.lock

@@ -1,3 +1,14 @@
+PATH
+  remote: .
+  specs:
+    hqmf2js (1.2.0)
+      coffee-script (~> 2.2.0)
+      health-data-standards (~> 3.0.1)
+      hquery-patient-api (~> 1.0.1)
+      nokogiri (~> 1.5.5)
+      sprockets (~> 2.2.2)
+      tilt (~> 1.3.3)
+
 GEM
   remote: http://rubygems.org/
   specs:
@@ -49,28 +60,28 @@ GEM
     erubis (2.7.0)
     execjs (1.4.0)
       multi_json (~> 1.0)
-    faraday (0.8.4)
+    faraday (0.8.6)
       multipart-post (~> 1.1)
     google-spreadsheet-ruby (0.1.8)
       nokogiri (>= 1.4.3.1)
       oauth (>= 0.3.6)
       oauth2 (>= 0.5.0)
     hashie (1.2.0)
-    health-data-standards (2.2.0)
+    health-data-standards (3.0.1)
       activesupport (~> 3.2.9)
       builder (~> 3.0.0)
       erubis (~> 2.7.0)
-      mongoid (~> 3.0.14)
+      google-spreadsheet-ruby (= 0.1.8)
+      log4r (~> 1.1.10)
+      mongoid (~> 3.1.0)
       nokogiri (~> 1.5.5)
       rest-client (~> 1.6.7)
-      uuid (~> 2.3.5)
-    hike (1.2.1)
-    hqmf-parser (1.1.0)
-      google-spreadsheet-ruby (= 0.1.8)
       roo (= 1.10.1)
       rubyzip
       spreadsheet (= 0.6.8)
-    hquery-patient-api (1.0.0)
+      uuid (~> 2.3.5)
+    hike (1.2.1)
+    hquery-patient-api (1.0.1)
     httpauth (0.2.0)
     i18n (0.6.1)
     journey (1.0.4)
@@ -86,23 +97,25 @@ GEM
       mime-types (~> 1.16)
       treetop (~> 1.4.8)
     method_source (0.8.1)
-    mime-types (1.19)
+    mime-types (1.20.1)
     minitest (4.3.2)
-    mongoid (3.0.15)
-      activemodel (~> 3.1)
-      moped (~> 1.1)
+    mongoid (3.1.2)
+      activemodel (~> 3.2)
+      moped (~> 1.4.2)
       origin (~> 1.0)
       tzinfo (~> 0.3.22)
-    moped (1.3.1)
-    multi_json (1.4.0)
-    multipart-post (1.1.5)
-    nokogiri (1.5.5)
+    moped (1.4.2)
+    multi_json (1.5.0)
+    multi_xml (0.5.3)
+    multipart-post (1.2.0)
+    nokogiri (1.5.6)
     oauth (0.4.7)
-    oauth2 (0.8.0)
+    oauth2 (0.9.1)
       faraday (~> 0.8)
       httpauth (~> 0.1)
       jwt (~> 0.1.4)
       multi_json (~> 1.0)
+      multi_xml (~> 0.5)
       rack (~> 1.2)
     origin (1.0.11)
     polyglot (0.3.3)
@@ -110,7 +123,7 @@ GEM
       coderay (~> 1.0.5)
       method_source (~> 0.8)
       slop (~> 3.3.1)
-    rack (1.4.1)
+    rack (1.4.4)
     rack-cache (1.2)
       rack (>= 0.4)
     rack-ssl (1.3.2)
@@ -175,7 +188,7 @@ GEM
     uglifier (1.3.0)
       execjs (>= 0.3.0)
       multi_json (~> 1.0, >= 1.0.2)
-    uuid (2.3.6)
+    uuid (2.3.7)
       macaddr (~> 1.0)
     yamler (0.1.0)
 
@@ -187,9 +200,7 @@ DEPENDENCIES
   coffee-rails
   coffee-script
   cover_me (~> 1.2.0)
-  health-data-standards (~> 2.2.0)
-  hqmf-parser (~> 1.1.0)
-  hquery-patient-api (~> 1.0.0)
+  hqmf2js!
   minitest
   nokogiri
   pry

data/app/assets/javascripts/custom_calculations.js.coffee

@@ -1,16 +1,74 @@
 @hqmf.CustomCalc = {}
 
+@hqmf.CustomCalc.ADE_TTR_OBSERV = (patient, hqmfjs) ->
+  inrReadings = DURING(hqmfjs.LaboratoryTestResultInr(patient), hqmfjs.MeasurePeriod(patient));
+  inrReadings = new hqmf.CustomCalc.PercentTTREntries(inrReadings)
+  [inrReadings.calculatePercentTTR()]
+
 class @hqmf.CustomCalc.PercentTTREntries extends hQuery.CodedEntryList
 
   constructor: (events) ->
     super()
-    events = events.sort(dateSortAscending)
-    @push(event) for event in events
     @minInr = 2.0
     @maxInr = 3.0
-    # sort entries ascending
-    # filter duplicates to those closest to 2.5
-    # remove duplicate results on entries
+    @minOutOfRange = 0.8
+    @maxOutOfRange = 10
+    @closestSetpoint = 2.5
+
+    clonedEvents = []
+    clonedEvents.push(new event.constructor(event.json)) for event in events
+
+    # remove entries < 0.8
+    # reset > 10 to be 10
+    # remove duplicate results on entries to those closest to 2.5
+    for entry in clonedEvents
+      currentClosestValue = null
+      for value in entry.values()
+        if value.scalar() > @maxOutOfRange
+          value.json['scalar'] = '10.0'
+        if value.scalar() >= @minOutOfRange && value.scalar() <= @maxOutOfRange
+          currentClosestValue = @closestValueToSetpoint(currentClosestValue, value)
+      
+      passingValues = []
+      passingValues = [currentClosestValue.json] if currentClosestValue?
+      entry.json['values'] = passingValues
+
+    # filter duplicates to those closest to 2.5 on the same day
+    # remove any entries with no values (removed because the value was below 0.8, or no value on source data)
+    entriesByDay = {}
+    for entry in clonedEvents
+      date = entry.timeStamp()
+      key = "#{date.getUTCFullYear()}_#{date.getUTCMonth()}_#{date.getUTCDate()}"
+      entriesByDay[key] = [] unless entriesByDay[key]
+      entriesByDay[key].push(entry) if entry.values().length > 0
+
+    # keep the closest entry to 2.5 when there are multiple entries per day
+    finalEvents = []
+    for key in _.keys(entriesByDay)
+      if (entriesByDay[key].length > 1)
+        currentClosestValue = null
+        selectedEntry = null
+        for entry in entriesByDay[key]
+          currentClosestValue = @closestValueToSetpoint(currentClosestValue, entry.values()[0])
+          if currentClosestValue.scalar() == entry.values()[0].scalar()
+            selectedEntry = entry
+        finalEvents.push(selectedEntry)
+      else
+        finalEvents = finalEvents.concat(entriesByDay[key])
+
+    finalEvents = finalEvents.sort(dateSortAscending)
+
+    @push(event) for event in finalEvents
+
+
+  closestValueToSetpoint: (one, two) ->
+    return two if one == null
+    return one if two == null
+    if (Math.abs(one.scalar() - @closestSetpoint) > Math.abs(two.scalar() - @closestSetpoint))
+      return two
+    else
+      return one
+
 
   calculateDaysInRange: (firstInr, secondInr) ->
 

data/app/assets/javascripts/hqmf_util.js.coffee

@@ -408,26 +408,26 @@ class ANYNonNull
 @ANYNonNull = ANYNonNull
 
 # Returns true if one or more of the supplied values is true
-atLeastOneTrue = (values...) ->
+atLeastOneTrue = (precondition, values...) ->
   trueValues = (value for value in values when value && value.isTrue())
   trueValues.length>0
   hqmf.SpecificsManager.unionAll(new Boolean(trueValues.length>0), values)
 @atLeastOneTrue = atLeastOneTrue
   
 # Returns true if all of the supplied values are true
-allTrue = (values...) ->
+allTrue = (precondition, values...) ->
   trueValues = (value for value in values when value && value.isTrue())
   hqmf.SpecificsManager.intersectAll(new Boolean(trueValues.length>0 && trueValues.length==values.length), values)
 @allTrue = allTrue
   
 # Returns true if one or more of the supplied values is false
-atLeastOneFalse = (values...) ->
+atLeastOneFalse = (precondition, values...) ->
   falseValues = (value for value in values when value.isFalse())
   hqmf.SpecificsManager.intersectAll(new Boolean(falseValues.length>0), values, true)
 @atLeastOneFalse = atLeastOneFalse
   
 # Returns true if all of the supplied values are false
-allFalse = (values...) ->
+allFalse = (precondition, values...) ->
   falseValues = (value for value in values when value.isFalse())
   hqmf.SpecificsManager.unionAll(new Boolean(falseValues.length>0 && falseValues.length==values.length), values, true)
 @allFalse = allFalse
@@ -514,6 +514,8 @@ class CrossProduct extends Array
       @eventLists.push eventList
       for event in eventList
         this.push(event)
+  listCount: -> @eventLists.length
+  childList: (index) -> @eventLists[index]
 
 # Create a CrossProduct of the supplied event lists.
 XPRODUCT = (eventLists...) ->
@@ -545,7 +547,7 @@ getIVL = (eventOrTimeStamp) ->
     ts.date = eventOrTimeStamp
     new IVL_TS(ts, ts)
 @getIVL = getIVL
-    
+
 eventAccessor = {  
   'DURING': 'low',
   'OVERLAP': 'low',
@@ -820,6 +822,37 @@ DATEDIFF = (events, range) ->
   hqmf.SpecificsManager.maintainSpecifics(new Boolean(withinRange('DATEDIFF', getIVL(events[0]), getIVL(events[1]), range)), events)
 @DATEDIFF = DATEDIFF
 
+# Calculate the set of time differences in minutes between pairs of events
+# events - a XPRODUCT of two event lists
+# range - ignored
+# initialSpecificContext - the specific context containing one row per permissible
+# combination of events
+TIMEDIFF = (events, range, initialSpecificContext) ->
+  if events.listCount() != 2
+    throw "TIMEDIFF can only process 2 lists of events"
+  eventList1 = events.childList(0)
+  eventList2 = events.childList(1)
+  eventIndex1 = hqmf.SpecificsManager.getColumnIndex(eventList1.specific_occurrence)
+  eventIndex2 = hqmf.SpecificsManager.getColumnIndex(eventList2.specific_occurrence)
+  eventMap1 = {}
+  eventMap2 = {}
+  for event in eventList1
+    eventMap1[event.id] = event
+  for event in eventList2
+    eventMap2[event.id] = event
+  results = []
+  for row in initialSpecificContext.rows
+    event1 = row.values[eventIndex1]
+    event2 = row.values[eventIndex2]
+    if event1 and event2 and event1 != hqmf.SpecificsManager.any and event2 != hqmf.SpecificsManager.any 
+      # The maps contain the actual events we want to work with since these may contain
+      # time shifted clones of the events in the specificContext, e.g. via adjustBoundsForField
+      shiftedEvent1 = eventMap1[event1.id]
+      shiftedEvent2 = eventMap2[event2.id]
+      if shiftedEvent1 and shiftedEvent2
+        results.push(shiftedEvent1.asTS().difference(shiftedEvent2.asTS(), 'min'))
+  results
+@TIMEDIFF = TIMEDIFF
 
 @OidDictionary = {};
 

data/app/assets/javascripts/logging_utils.js.coffee

@@ -1,7 +1,11 @@
 class @Logger
   @logger: []
+  @rationale: {}
   @info: (string) ->
     @logger.push("#{Logger.indent()}#{string}")
+  @record: (id, result) ->
+    if result? and typeof(result.isTrue) == 'function'
+      @rationale[id] = result.isTrue()
   @enabled: true
   @initialized: false
   @indentCount = 0
@@ -40,12 +44,17 @@ class @Logger
 
 @enableMeasureLogging = (hqmfjs) ->
   _.each(_.functions(hqmfjs), (method) ->
-    hqmfjs[method] = _.wrap(hqmfjs[method], (func, patient) ->
+    hqmfjs[method] = _.wrap(hqmfjs[method], (func) ->
+
+      args = Array.prototype.slice.call(arguments,1)
+
       Logger.info("#{method}:")
       Logger.indentCount++
-      result = func(patient)
+      result = func.apply(this, args)
+
       Logger.indentCount--
       Logger.info("#{method} -> #{Logger.asBoolean(result)}")
+      Logger.record(method,result)
       return result;
     );
   );
@@ -73,12 +82,6 @@ class @Logger
     );
     
     hQuery.CodedEntryList.prototype.match = _.wrap(hQuery.CodedEntryList.prototype.match, (func, codeSet, start, end) ->
-      
-      # if (codeSet)
-      #   Logger.info("matching: codeSets(#{_.keys(codeSet).join(",")}), #{start}, #{end}")
-      # else
-      #   Logger.info("matching: WARNING: CODE SETS ARE NULL, #{start}, #{end}")
-        
       func = _.bind(func, this, codeSet,start,end)
       result = func(codeSet,start,end)
       Logger.info("matched -> #{Logger.stringify(result)}")
@@ -98,6 +101,7 @@ class @Logger
       result = func.apply(this, args)
       Logger.indentCount--
       Logger.info("atLeastOneTrue -> #{result}")
+      Logger.record("precondition_#{args[0]}",result)
       result
     )
     
@@ -108,6 +112,7 @@ class @Logger
       result = func.apply(this, args)
       Logger.indentCount--
       Logger.info("allTrue -> #{result}")
+      Logger.record("precondition_#{args[0]}",result)
       result
     )
 
@@ -118,6 +123,7 @@ class @Logger
       result = func.apply(this, args)
       Logger.indentCount--
       Logger.info("allFalse -> #{result}")
+      Logger.record("precondition_#{args[0]}",result)
       result
     )
 
@@ -128,6 +134,7 @@ class @Logger
       result = func.apply(this, args)
       Logger.indentCount--
       Logger.info("atLeastOneFalse -> #{result}")
+      Logger.record("precondition_#{args[0]}",result)
       result
     )
     

data/app/assets/javascripts/patient_api_extension.js.coffee

@@ -13,6 +13,10 @@ hQuery.CodedEntry::asIVL_TS = ->
   tsHigh = new TS()
   tsHigh.date = this.endDate() || this.date() || null
   new IVL_TS(tsLow, tsHigh)
+hQuery.CodedEntry::asTS = ->
+  ts = new TS()
+  ts.date = this.timeStamp()
+  ts
 
 hQuery.CodedEntry::respondTo = (functionName) ->
   typeof(@[functionName]) == "function"

data/hqmf2js.gemspec

@@ -7,13 +7,15 @@ Gem::Specification.new do |s|
   s.email = "hquery-talk@googlegroups.com"
   s.homepage = "http://github.com/hquery/hqmf2js"
   s.authors = ["Marc Hadley", "Andre Quina", "Andy Gregorowicz"]
-  s.version = '1.1.0'
+  s.version = '1.2.0'
   
   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', '~> 3.0.1'
+  s.add_dependency 'hquery-patient-api', '~> 1.0.1'
 
   s.files = s.files = `git ls-files`.split("\n")
 end

data/lib/generator/codes_to_json.rb

@@ -16,9 +16,9 @@ module HQMF2JS
         translation = {}
         value_sets.each do |value_set|
           code_sets = {}
-          value_set["code_sets"].each do |code_set|
-            code_sets[code_set["code_set"]] ||= []
-            code_sets[code_set["code_set"]].concat(code_set["codes"])
+          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)
           end
           
           translation[value_set["oid"]] = code_sets
@@ -35,6 +35,7 @@ module HQMF2JS
       #   <ValueSet id="2.16.840.1.113883.3.464.1.14" displayName="birth date">
       #     <ConceptList xml:lang="en-US">
       #       <Concept code="00110" codeSystemName="HL7" displayName="Date/Time of birth (TS)"
+      
       #         codeSystemVersion="3"/>
       #      </ConceptList>
       #   </ValueSet>
@@ -78,4 +79,4 @@ module HQMF2JS
       
     end
   end
-end
+end

data/lib/generator/data_criteria.js.erb

@@ -6,7 +6,7 @@ var <%=  js_name(criteria) %> = <%= js_for_value(criteria.value) %>;
 
 // Data critera
 <%- all_criteria.select {|c| c.type != :variable}.each do |criteria| -%>
-hqmfjs.<%= js_name(criteria) %> = function(patient) {
+hqmfjs.<%= js_name(criteria) %> = function(patient, initialSpecificContext) {
   <%- if criteria.type == :characteristic and !criteria.property.nil? -%>
 <%= js_for_characteristic(criteria) %>
   <%- else -%>
@@ -37,7 +37,7 @@ hqmfjs.<%= js_name(criteria) %> = function(patient) {
     <%- 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 %>);
+  events = <%= subset_operator.type %>(events<%= ", #{js_for_bounds(subset_operator.value)}" if subset_operator.value %>, initialSpecificContext);
       <%- end # each operator -%>
     <%- end # subset operators -%>
   return events;

data/lib/generator/derived_data.js.erb

@@ -1,5 +1,5 @@
   var events = <%= criteria.derivation_operator %>(
     <%- criteria.children_criteria.each_with_index do |child, index| -%>
-    <%= "hqmfjs.#{child}(patient)" %><%= "," if index<criteria.children_criteria.length-1 %>
+    <%= "hqmfjs.#{child}(patient, initialSpecificContext)" %><%= "," if index<criteria.children_criteria.length-1 %>
     <%- end -%>
   );

data/lib/generator/js.rb

@@ -138,8 +138,8 @@ module HQMF2JS
       end
       
       # Returns the JavaScript generated for a HQMF::Precondition
-      def js_for_precondition(precondition, indent)
-        HQMF2JS::Generator.render_template('precondition', {'doc' => doc, 'precondition' => precondition, 'indent' => indent})
+      def js_for_precondition(precondition, indent, context=false)
+        HQMF2JS::Generator.render_template('precondition', {'doc' => doc, 'precondition' => precondition, 'indent' => indent, 'context' => context})
       end
       
       def patient_api_method(criteria)
@@ -202,6 +202,7 @@ module HQMF2JS
         #{js_for(population[HQMF::PopulationCriteria::DENEXCEP], HQMF::PopulationCriteria::DENEXCEP)}
         // CV
         #{js_for(population[HQMF::PopulationCriteria::MSRPOPL], HQMF::PopulationCriteria::MSRPOPL)}
+        #{js_for(population[HQMF::PopulationCriteria::OBSERV], HQMF::PopulationCriteria::OBSERV)}
         "
       end
       
@@ -224,7 +225,11 @@ module HQMF2JS
         type ||= criteria_code
         criteria = @doc.population_criteria(criteria_code)
         if criteria && criteria.preconditions && criteria.preconditions.length > 0
-          HQMF2JS::Generator.render_template('population_criteria', {'doc' => @doc, 'criteria' => criteria, 'type'=>type})
+          if type==HQMF::PopulationCriteria::OBSERV
+            HQMF2JS::Generator.render_template('observation_criteria', {'doc' => @doc, 'criteria' => criteria, 'type'=>type})
+          else
+            HQMF2JS::Generator.render_template('population_criteria', {'doc' => @doc, 'criteria' => criteria, 'type'=>type})
+          end
         else
           "hqmfjs.#{type} = function(patient) { return new Boolean(#{when_not_found}); }"
         end

data/lib/generator/measure_period.js.erb

@@ -13,6 +13,7 @@ hqmfjs.MeasurePeriod = function(patient) {
 }
 if (typeof effective_date === 'number') {
   MeasurePeriod.high.date = new Date(1000*effective_date);
-  MeasurePeriod.low.date = new Date(1000*effective_date);
+  // add one minute before pulling off the year.  This turns 12-31-2012 23:59 into 1-1-2013 00:00 => 1-1-2012 00:00
+  MeasurePeriod.low.date = new Date(1000*(effective_date+60));
   MeasurePeriod.low.date.setFullYear(MeasurePeriod.low.date.getFullYear()-1);
 }

data/lib/generator/observation_criteria.js.erb

@@ -0,0 +1,4 @@
+hqmfjs.<%= type %> = function(patient, initialSpecificContext) {
+  return <%= js_for_precondition(criteria.preconditions()[0], 0, true) -%>;
+};
+

data/lib/generator/population_criteria.js.erb

@@ -1,4 +1,4 @@
-hqmfjs.<%= type %> = function(patient) {
-  return <%= js_for_precondition(criteria, 0) -%>;
+hqmfjs.<%= type %> = function(patient, initialSpecificContext) {
+  return <%= js_for_precondition(criteria, 0, true) -%>;
 };
 

data/lib/generator/precondition.js.erb

@@ -1,14 +1,16 @@
 <%- if precondition.conjunction? -%>
 <%- if indent>0 -%>
-<%= "\n#{'  '*(indent+1)}#{conjunction_code_for(precondition)}(" -%>
+<%= "\n#{'  '*(indent+1)}#{conjunction_code_for(precondition)}('#{precondition.id}'," -%>
 <%- else -%>
-<%= "#{conjunction_code_for(precondition)}(" -%>
+<%= "#{conjunction_code_for(precondition)}('#{precondition.id}'," -%>
 <%- end -%>
 <%- precondition.preconditions.each_with_index do |child, index| -%>
-<%= "#{'  '*(indent+1)}#{js_for_precondition(child, indent+1)}" -%>
+<%= "#{'  '*(indent+1)}#{js_for_precondition(child, indent+1, context)}" -%>
 <%= "," if index < precondition.preconditions.length-1 -%>
 <%- end -%>
 <%= "\n#{'  '*(indent+1)})" -%>
+<%- elsif context -%>
+<%= " hqmfjs.#{js_name(precondition.reference)}(patient, initialSpecificContext)" -%>
 <%- else -%>
 <%= "\n#{'  '*(indent+1)}hqmfjs.#{js_name(precondition.reference)}(patient)" -%>
 <%- end -%>

data/lib/tasks/convert.rake

@@ -29,15 +29,19 @@ namespace :hqmf do
       f.write("// #########################\n\n")
            
       f.write("// INITIAL PATIENT POPULATION\n")
-      f.write(gen.js_for('IPP'))
-      f.write("// DENOMINATOR\n")
-      f.write(gen.js_for('DENOM'))
-      f.write("// NUMERATOR\n")
-      f.write(gen.js_for('NUMER'))
-      f.write("// EXCLUSIONS\n")
-      f.write(gen.js_for('EXCL'))
-      f.write("// DENOMINATOR EXCEPTIONS\n")
-      f.write(gen.js_for('DENEXCEP'))
+      f.write(gen.js_for(HQMF::PopulationCriteria::IPP))
+      f.write("\n// DENOMINATOR\n")
+      f.write(gen.js_for(HQMF::PopulationCriteria::DENOM))
+      f.write("\n// NUMERATOR\n")
+      f.write(gen.js_for(HQMF::PopulationCriteria::NUMER))
+      f.write("\n// EXCLUSIONS\n")
+      f.write(gen.js_for(HQMF::PopulationCriteria::DENEX))
+      f.write("\n// DENOMINATOR EXCEPTIONS\n")
+      f.write(gen.js_for(HQMF::PopulationCriteria::DENEXCEP))
+      f.write("\n// MSRPOPL\n")
+      f.write(gen.js_for(HQMF::PopulationCriteria::MSRPOPL))
+      f.write("\n// OBSERV\n")
+      f.write(gen.js_for(HQMF::PopulationCriteria::OBSERV))
     end
     
     puts "wrote javascript to: #{out_file}"

data/test/fixtures/json/59New.json

@@ -893,7 +893,7 @@
                 {
                     "type": "SUMMARY",
                     "value": {
-                        "type": "IVL_INT",
+                        "type": "IVL_PQ",
                         "low": {
                             "type": "PQ",
                             "value": "2",
@@ -1118,7 +1118,7 @@
                 {
                     "type": "COUNT",
                     "value": {
-                        "type": "IVL_INT",
+                        "type": "IVL_PQ",
                         "low": {
                             "type": "PQ",
                             "value": "3",
@@ -1145,7 +1145,7 @@
                 {
                     "type": "COUNT",
                     "value": {
-                        "type": "IVL_INT",
+                        "type": "IVL_PQ",
                         "low": {
                             "type": "PQ",
                             "value": "5",

data/test/fixtures/patients/larry_vanderman.json

@@ -107,7 +107,7 @@
         "end_time": 1291166000,
         "code": {
           "code": "bar",
-          "codeSystem": "SNOMED-CT"
+          "code_system": "SNOMED-CT"
         }
       }, 
       "end_time": 1291266000

data/test/unit/custom_calculations_test.rb

@@ -34,6 +34,42 @@ class CustomCalculationsTest < Test::Unit::TestCase
       inr_b9 = new hQuery.CodedEntry({time:#{Time.gm(2010,10,31).to_i}, values:[{scalar:'1.8'}]})
       
       list2 = new hqmf.CustomCalc.PercentTTREntries([inr_b1,inr_b2,inr_b3,inr_b4,inr_b5,inr_b6,inr_b7,inr_b8,inr_b9])
+
+      inr_c1 = new hQuery.CodedEntry({time:#{Time.gm(2010,1,5).to_i}, values:[{scalar:'2.8'}]})
+      inr_c2 = new hQuery.CodedEntry({time:#{Time.gm(2010,1,18).to_i}, values:[{scalar:'3.5'}]})
+      inr_c3 = new hQuery.CodedEntry({time:#{Time.gm(2010,2,2).to_i}, values:[{scalar:'3.4'}]})
+      inr_c4 = new hQuery.CodedEntry({time:#{Time.gm(2010,2,15).to_i}, values:[{scalar:'3.9'}]})
+      inr_c5 = new hQuery.CodedEntry({time:#{Time.gm(2010,3,10).to_i}, values:[{scalar:'1.7'}]})
+      inr_c6 = new hQuery.CodedEntry({time:#{Time.gm(2010,3,24).to_i}, values:[{scalar:'2.3'}]})
+      inr_c7 = new hQuery.CodedEntry({time:#{Time.gm(2010,4,12).to_i}, values:[{scalar:'2.4'}]})
+      inr_c8 = new hQuery.CodedEntry({time:#{Time.gm(2010,5,13).to_i}, values:[{scalar:'3.2'}]})
+      inr_c9 = new hQuery.CodedEntry({time:#{Time.gm(2010,5,27).to_i}, values:[{scalar:'3.5'}]})
+      inr_c10 = new hQuery.CodedEntry({time:#{Time.gm(2010,6,10).to_i}, values:[{scalar:'3.5'}]})
+      inr_c11 = new hQuery.CodedEntry({time:#{Time.gm(2010,6,24).to_i}, values:[{scalar:'3.4'}]})
+      inr_c12 = new hQuery.CodedEntry({time:#{Time.gm(2010,7,8).to_i}, values:[{scalar:'2.1'}]})
+      inr_c13 = new hQuery.CodedEntry({time:#{Time.gm(2010,7,22).to_i}, values:[{scalar:'2.6'}]})
+      
+      list3 = new hqmf.CustomCalc.PercentTTREntries([inr_c10,inr_c2,inr_c6,inr_c9,inr_c5,inr_c3,inr_c7,inr_c8,inr_c4,inr_c1,inr_c11,inr_c12,inr_c13])
+
+      inr_c1 = new hQuery.CodedEntry({time:#{Time.gm(2010,1,5).to_i}, values:[{scalar:'2.8'}]})
+      inr_c2 = new hQuery.CodedEntry({time:#{Time.gm(2010,1,18).to_i}, values:[{scalar:'3.5'}]})
+      inr_c3 = new hQuery.CodedEntry({time:#{Time.gm(2010,2,2).to_i}, values:[{scalar:'3.4'}]})
+      inr_c4 = new hQuery.CodedEntry({time:#{Time.gm(2010,2,2).to_i}, values:[{scalar:'2.1'}]})
+      inr_c5 = new hQuery.CodedEntry({time:#{Time.gm(2010,2,15).to_i}, values:[{scalar:'3.9'}]})
+      inr_c6 = new hQuery.CodedEntry({time:#{Time.gm(2010,3,10).to_i}, values:[{scalar:'1.7'}]})
+      inr_c7 = new hQuery.CodedEntry({time:#{Time.gm(2010,3,11).to_i}, values:[{scalar:'0.7'}]})
+      inr_c8 = new hQuery.CodedEntry({time:#{Time.gm(2010,3,24).to_i}, values:[{scalar:'2.9'},{scalar:'2.3'}]})
+      inr_c9 = new hQuery.CodedEntry({time:#{Time.gm(2010,4,12).to_i}, values:[{scalar:'2.4'}]})
+      inr_c10 = new hQuery.CodedEntry({time:#{Time.gm(2010,5,13).to_i}, values:[{scalar:'3.2'}]})
+      inr_c11 = new hQuery.CodedEntry({time:#{Time.gm(2010,5,13).to_i}, values:[{scalar:'3.6'}]})
+      inr_c12 = new hQuery.CodedEntry({time:#{Time.gm(2010,5,27).to_i}, values:[{scalar:'13.5'}]})
+      inr_c13 = new hQuery.CodedEntry({time:#{Time.gm(2010,6,10).to_i}, values:[{scalar:'3.5'}]})
+      inr_c14 = new hQuery.CodedEntry({time:#{Time.gm(2010,6,24).to_i}, values:[{scalar:'3.4'}]})
+      inr_c15 = new hQuery.CodedEntry({time:#{Time.gm(2010,7,8).to_i}, values:[{scalar:'12.1'}]})
+      inr_c16 = new hQuery.CodedEntry({time:#{Time.gm(2010,7,22).to_i}, values:[{scalar:'2.6'}, {scalar:'2.1'}]})
+      
+      list4 = new hqmf.CustomCalc.PercentTTREntries([inr_c9,inr_c8,inr_c3,inr_c14,inr_c10,inr_c6,inr_c7,inr_c2,inr_c1,inr_c5,inr_c11,inr_c12,inr_c13,inr_c4,inr_c15,inr_c16])
+
     "
     @context.eval(test_initialize_js)
     
@@ -69,6 +105,36 @@ class CustomCalculationsTest < Test::Unit::TestCase
   def test_calculate_percent_ttr
     assert @context.eval("Math.abs(list.calculatePercentTTR() - 43.99552468) < .001")
   end
+
+  def test_calculate_ttr_testdeck_record
+    assert @context.eval("Math.abs(list2.calculateTTR() - 203.66666666) < .001")
+  end
+
+  def test_calculate_percent_ttr_testdeck_record
+    assert @context.eval("Math.abs(list2.calculatePercentTTR() - 95.6181533646322) < .001")
+  end
   
+  def test_calculate_ttr_out_of_order
+    assert @context.eval("Math.abs(list3.calculateTTR() - 87.11113886) < .001")
+  end
+
+  def test_calculate_percent_ttr_out_of_order
+    assert @context.eval("Math.abs(list3.calculatePercentTTR() - 43.99552468) < .001")
+  end
+
+  def test_cleanup_of_inr_values
+
+    cleaned_inrs = [2.8, 3.5, 2.1, 3.9, 1.7, 2.3, 2.4, 3.2, 10.0, 3.5, 3.4, 10.0, 2.6]
+
+    assert @context.eval("list4.length == #{cleaned_inrs.size}")
+    cleaned_inrs.each_with_index do |inr,index|
+      assert @context.eval("list4[#{index}].values()[0].scalar() == #{inr}")
+    end
+
+    assert @context.eval("Math.abs(list4.calculateTTR() - 80.3184450684) < .001")
+    assert @context.eval("Math.abs(list4.calculatePercentTTR() - 40.56487124668) < .001")
+
+  end
+
   
 end

data/test/unit/library_function_test.rb

@@ -17,31 +17,31 @@ class LibraryFunctionTest < Test::Unit::TestCase
   end
   
   def test_all_true
-    @context.eval('allTrue(new Boolean(false),new Boolean(false),new Boolean(false)).isTrue()').must_equal false
-    @context.eval('allTrue(new Boolean(false),new Boolean(true),new Boolean(false)).isTrue()').must_equal false
-    @context.eval('allTrue(new Boolean(true),new Boolean(true),new Boolean(true)).isTrue()').must_equal true
-    @context.eval('allTrue().isTrue()').must_equal false
+    @context.eval('allTrue(1,new Boolean(false),new Boolean(false),new Boolean(false)).isTrue()').must_equal false
+    @context.eval('allTrue(1,new Boolean(false),new Boolean(true),new Boolean(false)).isTrue()').must_equal false
+    @context.eval('allTrue(1,new Boolean(true),new Boolean(true),new Boolean(true)).isTrue()').must_equal true
+    @context.eval('allTrue(1).isTrue()').must_equal false
   end
   
   def test_at_least_one_true
-    @context.eval('atLeastOneTrue(new Boolean(true),new Boolean(false),new Boolean(false)).isTrue()').must_equal true
-    @context.eval('atLeastOneTrue(new Boolean(true),new Boolean(true),new Boolean(true)).isTrue()').must_equal true
-    @context.eval('atLeastOneTrue(new Boolean(false),new Boolean(false),new Boolean(false)).isTrue()').must_equal false
-    @context.eval('atLeastOneTrue().isTrue()').must_equal false
+    @context.eval('atLeastOneTrue(1,new Boolean(true),new Boolean(false),new Boolean(false)).isTrue()').must_equal true
+    @context.eval('atLeastOneTrue(1,new Boolean(true),new Boolean(true),new Boolean(true)).isTrue()').must_equal true
+    @context.eval('atLeastOneTrue(1,new Boolean(false),new Boolean(false),new Boolean(false)).isTrue()').must_equal false
+    @context.eval('atLeastOneTrue(1).isTrue()').must_equal false
   end
   
   def test_all_false
-    @context.eval('allFalse(new Boolean(false),new Boolean(false),new Boolean(false)).isTrue()').must_equal true
-    @context.eval('allFalse(new Boolean(false),new Boolean(true),new Boolean(false)).isTrue()').must_equal false
-    @context.eval('allFalse(new Boolean(true),new Boolean(true),new Boolean(true)).isTrue()').must_equal false
-    @context.eval('allFalse().isTrue()').must_equal false
+    @context.eval('allFalse(1,new Boolean(false),new Boolean(false),new Boolean(false)).isTrue()').must_equal true
+    @context.eval('allFalse(1,new Boolean(false),new Boolean(true),new Boolean(false)).isTrue()').must_equal false
+    @context.eval('allFalse(1,new Boolean(true),new Boolean(true),new Boolean(true)).isTrue()').must_equal false
+    @context.eval('allFalse(1).isTrue()').must_equal false
   end
   
   def test_at_least_one_false
-    @context.eval('atLeastOneFalse(new Boolean(true),new Boolean(false),new Boolean(false)).isTrue()').must_equal true
-    @context.eval('atLeastOneFalse(new Boolean(true),new Boolean(true),new Boolean(true)).isTrue()').must_equal false
-    @context.eval('atLeastOneFalse(new Boolean(false),new Boolean(false),new Boolean(false)).isTrue()').must_equal true
-    @context.eval('atLeastOneFalse().isTrue()').must_equal false
+    @context.eval('atLeastOneFalse(1,new Boolean(true),new Boolean(false),new Boolean(false)).isTrue()').must_equal true
+    @context.eval('atLeastOneFalse(1,new Boolean(true),new Boolean(true),new Boolean(true)).isTrue()').must_equal false
+    @context.eval('atLeastOneFalse(1,new Boolean(false),new Boolean(false),new Boolean(false)).isTrue()').must_equal true
+    @context.eval('atLeastOneFalse(1).isTrue()').must_equal false
   end
   
   def test_patient_extensions

data/test/unit/specifics_test.rb

@@ -202,6 +202,29 @@ class SpecificsTest < Test::Unit::TestCase
     
   end
   
+  def test_specifics_timediff
+    init_rows = "
+      var row1 = new Row('OccurrenceAEncounter',{'OccurrenceAEncounter':{'id':1},'OccurrenceBEncounter':{'id':20}});
+      var row2 = new Row('OccurrenceAEncounter',{'OccurrenceAEncounter':{'id':2},'OccurrenceBEncounter':{'id':20}});
+      var row3 = new Row('OccurrenceAEncounter',{'OccurrenceAEncounter':{'id':3},'OccurrenceBEncounter':{'id':30}});
+      
+      var specific = new hqmf.SpecificOccurrence([row1,row2,row3]);
+      
+      var ts1 = new TS('20100101100000');
+      var ts2 = new TS('20100101101000');
+      
+      var events1 = [{'id': 1, 'asTS': function() {return ts1;}}];
+      events1.specific_occurrence = 'OccurrenceAEncounter';
+      var events2 = [{'id': 20, 'asTS': function() {return ts2;}},{'id': 30, 'asTS': function() {return ts2;}}];
+      events2.specific_occurrence = 'OccurrenceBEncounter';
+      var timediffs = TIMEDIFF(XPRODUCT(events1, events2), null, specific);
+    "
+    
+    @context.eval(init_rows)
+    @context.eval("timediffs.length").must_equal 1
+    @context.eval("timediffs[0]").must_equal 10
+  end
+  
   def test_specifics_event_counting
     
     init_rows = "

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: hqmf2js
 version: !ruby/object:Gem::Version
-  version: 1.1.0
+  version: 1.2.0
   prerelease: 
 platform: ruby
 authors:
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-19 00:00:00.000000000 Z
+date: 2013-02-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -93,6 +93,38 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: 1.1.0
+- !ruby/object:Gem::Dependency
+  name: health-data-standards
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.0.1
+- !ruby/object:Gem::Dependency
+  name: hquery-patient-api
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.1
 description: A library for converting HQMF files to executable JavaScript suitable
   for use with the hQuery Gateway
 email: hquery-talk@googlegroups.com
@@ -124,6 +156,7 @@ files:
 - lib/generator/derived_data.js.erb
 - lib/generator/js.rb
 - lib/generator/measure_period.js.erb
+- lib/generator/observation_criteria.js.erb
 - lib/generator/patient_data.js.erb
 - lib/generator/population_criteria.js.erb
 - lib/generator/precondition.js.erb