hqmf2js 1.0.0

data/test/unit/codes_to_json_test.rb

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+require_relative '../test_helper'
+
+class CodesToJsonTest < Test::Unit::TestCase
+  
+  def setup
+  end
+
+
+  def test_parsing_from_xml
+    
+    codes_file_path = File.expand_path("../../fixtures/codes/codes.xml", __FILE__)
+    # Parse the code systems that are mapped to the OIDs we support
+    codes_json = HQMF2JS::Generator::CodesToJson.hash_to_js(HQMF2JS::Generator::CodesToJson.from_xml(codes_file_path))
+    
+    @context = get_js_context("var dictionary = #{codes_json}")
+    
+    @context.eval("dictionary").entries.length.must_equal 18
+    @context.eval("dictionary['2.16.840.1.113883.3.464.1.42']").entries.first[0].must_equal "CPT"
+    @context.eval("dictionary['2.16.840.1.113883.3.464.1.42']").entries.first[1].length.must_equal 19
+    
+  end
+
+  def test_parsing_from_xls
+    
+    codes_file_path = File.expand_path("../../fixtures/codes/codes.xls", __FILE__)
+    # Parse the code systems that are mapped to the OIDs we support
+    codes_json = HQMF2JS::Generator::CodesToJson.hash_to_js(HQMF2JS::Generator::CodesToJson.from_xls(codes_file_path))
+
+    @context = get_js_context("var dictionary = #{codes_json}")
+    @context.eval("dictionary").entries.length.must_equal 12
+    @context.eval("dictionary['2.16.840.1.113883.3.464.0001.430']").entries.first[0].must_equal "RxNorm"
+    @context.eval("dictionary['2.16.840.1.113883.3.464.0001.430']").entries.first[1].length.must_equal 25
+    
+  end
+  
+
+
+end

data/test/unit/effective_date_test.rb

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+require_relative '../test_helper'
+
+class EffectiveDateTest < Test::Unit::TestCase
+  def setup
+    # Open a path to all of our fixtures
+    hqmf_contents = File.open("test/fixtures/NQF59New.xml").read
+    
+    doc = HQMF::Parser.parse(hqmf_contents, HQMF::Parser::HQMF_VERSION_2)
+    
+    # First compile the CoffeeScript that enables our converted HQMF JavaScript
+    ctx = Sprockets::Environment.new(File.expand_path("../../..", __FILE__))
+    Tilt::CoffeeScriptTemplate.default_bare = true 
+    ctx.append_path "app/assets/javascripts"
+    hqmf_utils = HQMF2JS::Generator::JS.library_functions
+    
+    # Convert the HQMF document included as a fixture into JavaScript
+    @converter = HQMF2JS::Generator::JS.new(doc)
+    converted_hqmf = "var effective_date = 1277870400; // June 30th 2010
+      #{@converter.js_for_data_criteria}
+      #{@converter.js_for('IPP')}
+      #{@converter.js_for('DENOM')}
+      #{@converter.js_for('NUMER')}
+      #{@converter.js_for('EXCEP')}
+      #{@converter.js_for('DUMMY')}"
+
+    # Now we can wrap and compile all of our code as one little JavaScript context for all of the tests below
+    if RUBY_PLATFORM=='java'
+      @context = Rhino::Context.new
+    else
+      @context = V8::Context.new
+    end
+    @context.eval("#{hqmf_utils}
+      #{converted_hqmf}")
+  end
+  
+  def test_override_hqmf_measure_period
+    # Measure variables
+    assert_equal 2009, @context.eval("MeasurePeriod.low.asDate().getFullYear()")
+    assert_equal 5, @context.eval("MeasurePeriod.low.asDate().getMonth()")
+    assert_equal 2010, @context.eval("MeasurePeriod.high.asDate().getFullYear()")
+    assert_equal 5, @context.eval("MeasurePeriod.high.asDate().getMonth()")
+    assert_equal 2009, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().low.asDate().getFullYear()")
+    assert_equal 5, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().low.asDate().getMonth()")
+    assert_equal 2010, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().high.asDate().getFullYear()")
+    assert_equal 5, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().high.asDate().getMonth()")
+  end
+
+end

data/test/unit/hqmf_from_json_javascript_test.rb

@@ -0,0 +1,108 @@
+require_relative '../test_helper'
+
+class HqmfFromJsonJavascriptTest < Test::Unit::TestCase
+  def setup
+    json_measure = File.open("test/fixtures/json/59New.json").read
+    measure_hash = JSON.parse(json_measure)
+
+    doc = HQMF::Document.from_json(measure_hash)
+    
+    codes_file_path = File.expand_path("../../fixtures/codes/codes.xml", __FILE__)
+    # This patient is identified from Cypress as in the denominator and numerator for NQF59
+    numerator_patient_json = File.read('test/fixtures/patients/larry_vanderman.json')
+    
+    # First compile the CoffeeScript that enables our converted HQMF JavaScript
+    hqmf_utils = compile_coffee_script
+    
+    # Parse the code systems that are mapped to the OIDs we support
+    @codes_hash = HQMF2JS::Generator::CodesToJson.from_xml(codes_file_path)
+    codes_json = HQMF2JS::Generator::CodesToJson.hash_to_js(@codes_hash)
+    
+    # Convert the HQMF document included as a fixture into JavaScript
+    @converter = HQMF2JS::Generator::JS.new(doc)
+    converted_hqmf = "#{@converter.js_for_data_criteria}
+      #{@converter.js_for('IPP')}
+      #{@converter.js_for('DENOM')}
+      #{@converter.js_for('NUMER')}
+      #{@converter.js_for('EXCEP')}
+      #{@converter.js_for('DUMMY')}"
+
+    initialize_javascript_context(hqmf_utils, codes_json, converted_hqmf)
+  end
+
+  def test_converted_hqmf
+    # Unspecified time bounds should be nil
+    assert_equal nil, @context.eval("numeratorPatient.encounters()[0].asIVL_TS().low.asDate()")
+    assert_equal 2010, @context.eval("numeratorPatient.encounters()[0].asIVL_TS().high.asDate().getFullYear()")
+
+    # Measure variables
+    assert_equal 2011, @context.eval("MeasurePeriod.low.asDate().getFullYear()")
+    assert_equal 0, @context.eval("MeasurePeriod.low.asDate().getMonth()")
+    assert_equal 2011, @context.eval("MeasurePeriod.high.asDate().getFullYear()")
+    assert_equal 11, @context.eval("MeasurePeriod.high.asDate().getMonth()")
+    assert_equal 2011, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().low.asDate().getFullYear()")
+    assert_equal 0, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().low.asDate().getMonth()")
+    assert_equal 2011, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().high.asDate().getFullYear()")
+    assert_equal 11, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().high.asDate().getMonth()")
+  
+    # Age functions - Fixture is 37.1
+    assert @context.eval("hqmfjs.ageBetween17and64(numeratorPatient).isTrue()")
+    assert @context.eval("hqmfjs.ageBetween30and39(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween17and21(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween22and29(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween40and49(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween50and59(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween60and64(numeratorPatient).isTrue()")
+    
+    # Birthdate function
+    assert_equal 1, @context.eval("hqmfjs.birthdateThirtyYearsBeforeMeasurementPeriod(numeratorPatient)").count
+    assert_equal 0, @context.eval("hqmfjs.birthdateFiftyYearsBeforeMeasurementPeriod(numeratorPatient)").count
+
+    # Gender functions - Fixture is male
+    assert @context.eval("hqmfjs.genderMale(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.genderFemale(numeratorPatient).isTrue()")
+    
+    # Be sure the actual mechanic of code lists being returned works correctly - Using HasDiabetes as an example
+    results = @context.eval("hqmfjs.HasDiabetes(numeratorPatient)[0]")['json']
+    assert_equal 3, results['codes'].count
+    assert_equal '250', results['codes']['ICD-9-CM'].first
+    assert_equal 1270094400, results['time']
+    
+    # Encounters
+    assert_equal 0, @context.eval("hqmfjs.EDorInpatientEncounter(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.AmbulatoryEncounter(numeratorPatient).length")
+    
+    # Conditions
+    assert_equal 1, @context.eval("hqmfjs.HasDiabetes(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.HasGestationalDiabetes(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.HasPolycysticOvaries(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.HasSteroidInducedDiabetes(numeratorPatient).length")
+    
+    # Results
+    assert_equal 2, @context.eval("hqmfjs.HbA1C(numeratorPatient).length")
+    
+    # Medications
+    assert_equal 1, @context.eval("hqmfjs.DiabetesMedAdministered(numeratorPatient).length")
+    assert_equal 1, @context.eval("hqmfjs.DiabetesMedAdministeredFor7Days(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.DiabetesMedAdministeredFor9Days(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.DiabetesMedIntended(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.DiabetesMedSupplied(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.DiabetesMedOrdered(numeratorPatient).length")
+    
+    # Standard population health query buckets
+    assert @context.eval("hqmfjs.IPP(numeratorPatient).isTrue()")
+    assert @context.eval("hqmfjs.DENOM(numeratorPatient).isTrue()")
+    assert @context.eval("hqmfjs.NUMER(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.EXCEP(numeratorPatient).isTrue()")
+    
+    # COUNTing
+    assert @context.eval("hqmfjs.moreThanTwoHbA1CTests(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.moreThanFourHbA1CTests(numeratorPatient).isTrue()")
+
+    # UNIONing
+    assert_equal 1, @context.eval("hqmfjs.anyDiabetes(numeratorPatient).length")
+
+    # XPRODUCTing
+    assert_equal 1, @context.eval("hqmfjs.allDiabetes(numeratorPatient).length")
+  end
+end

data/test/unit/hqmf_javascript_test.rb

@@ -0,0 +1,175 @@
+require_relative '../test_helper'
+
+class HqmfJavascriptTest < Test::Unit::TestCase
+  def setup
+    # Open a path to all of our fixtures
+    hqmf_contents = File.open("test/fixtures/NQF59New.xml").read
+    
+    doc = HQMF::Parser.parse(hqmf_contents, HQMF::Parser::HQMF_VERSION_2)
+    
+    codes_file_path = File.expand_path("../../fixtures/codes/codes.xml", __FILE__)
+    # This patient is identified from Cypress as in the denominator and numerator for NQF59
+    numerator_patient_json = File.read('test/fixtures/patients/larry_vanderman.json')
+    
+    # First compile the CoffeeScript that enables our converted HQMF JavaScript
+    hqmf_utils = compile_coffee_script
+    
+    # Parse the code systems that are mapped to the OIDs we support
+    @codes_hash = HQMF2JS::Generator::CodesToJson.from_xml(codes_file_path)
+    codes_json = HQMF2JS::Generator::CodesToJson.hash_to_js(@codes_hash)
+    
+    # Convert the HQMF document included as a fixture into JavaScript
+    @converter = HQMF2JS::Generator::JS.new(doc)
+    converted_hqmf = "#{@converter.js_for_data_criteria}
+      #{@converter.js_for('IPP')}
+      #{@converter.js_for('DENOM')}
+      #{@converter.js_for('NUMER')}
+      #{@converter.js_for('EXCEP')}
+      #{@converter.js_for('DUMMY')}"
+
+    initialize_javascript_context(hqmf_utils, codes_json, converted_hqmf)
+  end
+  
+  def test_codes
+    # Make sure we're recalling entries correctly
+    assert_equal 1, @context.eval('OidDictionary["2.16.840.1.113883.3.464.1.14"]').count
+    assert_equal "00110", @context.eval('OidDictionary["2.16.840.1.113883.3.464.1.14"]["HL7"][0]')
+    
+    # OIDs that are matched to multiple code systems should also work correctly
+    # The list of supported OIDs will eventually be long, so this won't be an exhaustive test, just want to be sure the functionality is right
+    assert_equal 3, @context.eval('OidDictionary["2.16.840.1.113883.3.464.1.72"]').count
+    assert_equal 2, @context.eval('OidDictionary["2.16.840.1.113883.3.464.1.72"]["CPT"]').count
+    assert_equal 3, @context.eval('OidDictionary["2.16.840.1.113883.3.464.1.72"]["LOINC"]').count
+    assert_equal 9, @context.eval('OidDictionary["2.16.840.1.113883.3.464.1.72"]["SNOMED-CT"]').count
+  end
+  
+  def test_to_js_method
+    value = @converter.to_js(0,@codes_hash)
+    local_context = V8::Context.new
+    patient_api = File.open('test/fixtures/patient_api.js').read
+    hqmf_utils = HQMF2JS::Generator::JS.library_functions
+    local_context.eval("#{patient_api}
+                        #{hqmf_utils}
+                        #{value}")
+                        
+    local_context.eval('typeof hqmfjs != undefined').must_equal true
+    local_context.eval('typeof OidDictionary != undefined').must_equal true
+    local_context.eval('typeof hqmfjs.IPP != undefined').must_equal true
+    local_context.eval('typeof hqmfjs.NUMER != undefined').must_equal true
+    local_context.eval('typeof hqmfjs.DENOM != undefined').must_equal true
+  end
+  
+  def test_converted_hqmf
+    # Unspecified time bounds should be nil
+    assert_equal nil, @context.eval("numeratorPatient.encounters()[0].asIVL_TS().low.asDate()")
+    assert_equal 2010, @context.eval("numeratorPatient.encounters()[0].asIVL_TS().high.asDate().getFullYear()")
+
+    # Measure variables
+    assert_equal 2011, @context.eval("MeasurePeriod.low.asDate().getFullYear()")
+    assert_equal 0, @context.eval("MeasurePeriod.low.asDate().getMonth()")
+    assert_equal 2011, @context.eval("MeasurePeriod.high.asDate().getFullYear()")
+    assert_equal 11, @context.eval("MeasurePeriod.high.asDate().getMonth()")
+    assert_equal 2011, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().low.asDate().getFullYear()")
+    assert_equal 0, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().low.asDate().getMonth()")
+    assert_equal 2011, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().high.asDate().getFullYear()")
+    assert_equal 11, @context.eval("hqmfjs.MeasurePeriod()[0].asIVL_TS().high.asDate().getMonth()")
+  
+    # Age functions - Fixture is 37.1
+    assert @context.eval("hqmfjs.ageBetween17and64(numeratorPatient).isTrue()")
+    assert @context.eval("hqmfjs.ageBetween30and39(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween17and21(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween22and29(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween40and49(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween50and59(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.ageBetween60and64(numeratorPatient).isTrue()")
+    
+    # Birthdate function
+    assert_equal 1, @context.eval("hqmfjs.birthdateThirtyYearsBeforeMeasurementPeriod(numeratorPatient)").count
+    assert_equal 0, @context.eval("hqmfjs.birthdateFiftyYearsBeforeMeasurementPeriod(numeratorPatient)").count
+
+    # Gender functions - Fixture is male
+    assert @context.eval("hqmfjs.genderMale(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.genderFemale(numeratorPatient).isTrue()")
+    
+    # Be sure the actual mechanic of code lists being returned works correctly - Using HasDiabetes as an example
+    results = @context.eval("hqmfjs.HasDiabetes(numeratorPatient)[0]")['json']
+    assert_equal 3, results['codes'].count
+    assert_equal '250', results['codes']['ICD-9-CM'].first
+    assert_equal 1270094400, results['time']
+    
+    # Encounters
+    assert_equal 0, @context.eval("hqmfjs.EDorInpatientEncounter(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.AmbulatoryEncounter(numeratorPatient).length")
+    
+    # Conditions
+    assert_equal 1, @context.eval("hqmfjs.HasDiabetes(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.HasGestationalDiabetes(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.HasPolycysticOvaries(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.HasSteroidInducedDiabetes(numeratorPatient).length")
+    
+    # Results
+    assert_equal 2, @context.eval("hqmfjs.HbA1C(numeratorPatient).length")
+    
+    # Medications
+    assert_equal 1, @context.eval("hqmfjs.DiabetesMedAdministered(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.DiabetesMedIntended(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.DiabetesMedSupplied(numeratorPatient).length")
+    assert_equal 0, @context.eval("hqmfjs.DiabetesMedOrdered(numeratorPatient).length")
+    
+    # Standard population health query buckets
+    assert @context.eval("hqmfjs.IPP(numeratorPatient).isTrue()")
+    assert @context.eval("hqmfjs.DENOM(numeratorPatient).isTrue()")
+    assert @context.eval("hqmfjs.NUMER(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.EXCEP(numeratorPatient).isTrue()")
+    
+    # COUNTing
+    assert @context.eval("hqmfjs.moreThanTwoHbA1CTests(numeratorPatient).isTrue()")
+    assert !@context.eval("hqmfjs.moreThanFourHbA1CTests(numeratorPatient).isTrue()")
+
+    # UNIONing
+    assert_equal 1, @context.eval("hqmfjs.anyDiabetes(numeratorPatient).length")
+
+    # XPRODUCTing
+    assert_equal 1, @context.eval("hqmfjs.allDiabetes(numeratorPatient).length")
+  end
+  
+  def test_converted_utils
+    # Filter events by value - HbA1C as an example
+    events = 'numeratorPatient.results().match(getCodes("2.16.840.1.113883.3.464.1.72"))'
+    assert_equal 2, @context.eval("filterEventsByValue(#{events}, new IVL_PQ(new PQ(9, '%'), null))").count
+    assert_equal 0, @context.eval("filterEventsByValue(#{events}, new IVL_PQ(new PQ(10, '%'), null))").count
+    
+    # getCode
+    assert_equal 1, @context.eval('getCodes("2.16.840.1.113883.3.464.1.14")').count
+    assert_equal "00110", @context.eval('getCodes("2.16.840.1.113883.3.464.1.14")["HL7"][0]')
+  end
+  
+  def test_map_reduce_generation
+    hqmf_contents = File.open("test/fixtures/NQF59New.xml").read
+    doc = HQMF::Parser.parse(hqmf_contents, HQMF::Parser::HQMF_VERSION_2)
+    
+    map_reduce = HQMF2JS::Converter.generate_map_reduce(doc)
+    
+    # Extremely loose testing here. Just want to be sure for now that we're getting results of some kind.
+    # We'll test for validity over on the hQuery Gateway side of things.
+    assert map_reduce[:map].include? 'map'
+    assert map_reduce[:reduce].include? 'reduce'
+    # Check functions to include actual HQMF converted function, HQMF utility function, and OID dictionary
+    assert map_reduce[:functions].include? 'IPP'
+    assert map_reduce[:functions].include? 'atLeastOneTrue'
+    assert map_reduce[:functions].include? 'OidDictionary'
+  end
+  
+  
+  def test_missing_id
+    
+    context = HQMF2JS::Generator::ErbContext.new({})
+    criteria = HQMF::DataCriteria.new(nil,nil,nil,nil,nil,nil,nil,'patient_characteristic',nil,nil,nil,nil,nil,nil,nil,nil,nil,nil,nil)
+    
+    exception = assert_raise RuntimeError do
+      n = context.js_name(criteria)
+    end
+    assert exception.message.match(/^No identifier for .*/)
+  end  
+
+end