quality-measure-engine 1.1.5 → 2.0.0

data/spec/qme/map/map_reduce_builder_spec.rb

@@ -1,38 +0,0 @@
-describe QME::MapReduce::Builder do
-  
-  before do
-    @loader = QME::Database::Loader.new('test')
-    raw_measure_json = File.read(File.join('fixtures', 'entry', 'sample.json'))
-    @measure_json = JSON.parse(raw_measure_json)
-  end
-
-  it 'should extract the measure metadata' do
-    measure = QME::MapReduce::Builder.new(@loader.get_db, @measure_json, 'effective_date'=>Time.gm(2010, 9, 19).to_i)
-    measure.id.should eql('0043')
-  end
-  it 'should extract one parameter for measure 0043' do
-    time = Time.gm(2010, 9, 19).to_i
-    measure = QME::MapReduce::Builder.new(@loader.get_db, @measure_json, 'effective_date'=>time)
-    measure.params.size.should eql(1)
-    measure.params.should have_key('effective_date')
-    measure.params['effective_date'].should eql(time)
-  end
-  it 'should raise a RuntimeError if not passed all the parameters' do
-    lambda { QME::MapReduce::Builder.new(@measure_json) }.should
-      raise_error(RuntimeError, 'No value supplied for measure parameter: effective_date')
-  end
-end
-
-describe QME::MapReduce::Builder::Context do
-  before do
-    @loader = QME::Database::Loader.new('test')
-  end 
-  
-  it 'should set instance methods from the supplied hash' do
-    vars = {'a'=>10, 'b'=>20}
-    context = QME::MapReduce::Builder::Context.new(@loader.get_db, vars)
-    binding = context.get_binding
-    eval("a",binding).should eql(10)
-    eval("b",binding).should eql(20)
-  end
-end

data/spec/qme/map/measures_spec.rb

@@ -1,38 +0,0 @@
-describe QME::MapReduce::Executor do
-
-  before do
-    @loader = QME::Database::Loader.new('test')
-    if ENV['MEASURE_DIR']
-      @measures = Dir.glob(File.join(ENV['MEASURE_DIR'], '*'))
-    else
-      @measures = Dir.glob(File.join('measures', '*'))
-    end
-
-    # define custom matchers
-    RSpec::Matchers.define :match_population do |population|
-      match do |value|
-        value == population
-      end
-    end
-    RSpec::Matchers.define :match_denominator do |denominator|
-      match do |value|
-        value == denominator
-      end
-    end
-    RSpec::Matchers.define :match_numerator do |numerator|
-      match do |value|
-        value == numerator
-      end
-    end
-    RSpec::Matchers.define :match_exclusions do |exclusions|
-      match do |value|
-        value == exclusions
-      end
-    end
-  end
-  
-  it 'should produce the expected results for each measure' do
-    validate_measures(@measures,@loader)
-  end
-  
-end

data/spec/qme/map/patient_mapper_spec.rb

@@ -1,11 +0,0 @@
-describe QME::MapReduce::Executor do
-
-  before do
-    @loader = QME::Database::Loader.new('test')
-  end
-  
-  it 'should map patients as expected' do
-    validate_patient_mapping(@loader)
-  end
-  
-end

data/spec/qme/measure_loader_spec.rb

@@ -1,12 +0,0 @@
-describe QME::Measure::Loader do
-  before do
-    @measure_def_dir = File.join('fixtures', 'measure_defs', 'sample_single_from_multi_xls')
-  end
-  
-  it 'Should load the sample measure correctly' do
-    measure = QME::Measure::Loader.load_measure(@measure_def_dir)
-    measure = measure[0]
-    measure['measure'].should have_key('eyes')
-    measure['measure'].should have_key('esrd_diagnosis_active')
-  end
-end

data/spec/qme/properties_builder_spec.rb

@@ -1,61 +0,0 @@
-require 'ap'
-
-describe QME::Measure::PropertiesBuilder do
-  before do
-    @json_file = File.join('fixtures', 'measure_props', 'props2.xlsx.json')
-    @properties = JSON.parse(File.read(@json_file))
-  end
-  
-  it 'Should patch the definition' do
-    @properties['N_1810']['value'].should be_nil
-    patched_properties = QME::Measure::PropertiesBuilder.patch_properties(@properties, @json_file)
-    patched_properties['N_1810']['value'].should have_key('type')
-    patched_properties['N_1472']['group_type'].should eql('abstract')
-  end
-  
-  it 'Should group properties' do
-    @properties.values.select { |value| value['standard_concept_id']=='N_c102' }.should_not be_empty
-    patched_properties = QME::Measure::PropertiesBuilder.patch_properties(@properties, @json_file)
-    grouped_properties = QME::Measure::PropertiesBuilder.build_groups(patched_properties)
-    grouped_properties.select { |key| key['standard_concept_id']=='N_c102' }.should be_empty
-    grouped_properties.select { |key| key['standard_concept_id']=='N_c190' }.should_not be_empty
-  end
-  
-  it 'Should create the expected properties' do
-    result = QME::Measure::PropertiesBuilder.build_properties(@properties, @json_file)
-    result['measure'].should have_key('diastolic_blood_pressure_physical_exam_finding')
-    result['measure']['diastolic_blood_pressure_physical_exam_finding'].should have_key('standard_concept')
-    result['measure']['diastolic_blood_pressure_physical_exam_finding']['standard_concept'].should eql('diastolic_blood_pressure')
-    result['measure']['diastolic_blood_pressure_physical_exam_finding'].should have_key('standard_category')
-    result['measure']['diastolic_blood_pressure_physical_exam_finding']['standard_category'].should eql('physical_exam')
-    result['measure']['diastolic_blood_pressure_physical_exam_finding']['items']['type'].should eql('object')
-    result['measure']['diastolic_blood_pressure_physical_exam_finding'].should have_key('codes')
-    result['measure']['diastolic_blood_pressure_physical_exam_finding']['codes'].length.should eql(1)
-    result['measure'].should have_key('encounter_outpatient_encounter')
-    result['measure']['encounter_outpatient_encounter']['items']['type'].should eql('number')
-    result['measure'].should have_key('esrd_diagnosis_active')
-    result['measure']['esrd_diagnosis_active']['standard_category'].should eql('diagnosis_condition_problem')
-    result['measure']['esrd_diagnosis_active']['codes'].length.should eql(3)
-  end
-  
-  it 'Should not create the excluded properties' do
-    result = QME::Measure::PropertiesBuilder.build_properties(@properties, @json_file)
-    result['measure'].select { |key| QME::Measure::PropertiesBuilder::PROPERTIES_TO_IGNORE.include?(key['standard_concept']) }.should be_empty
-  end
-
-  it 'Should expand code ranges for CPT codes' do
-    result = QME::Measure::PropertiesBuilder.extract_code_values("1, 2-5, 6 ", "SNOMED-CT")
-    result.length.should eql(3)
-    result.should include("1")
-    result.should include("2-5")
-    result.should include("6")
-    result = QME::Measure::PropertiesBuilder.extract_code_values("1, 2-5, 6 ", "CPT")
-    result.length.should eql(6)
-    result.should include("1")
-    result.should include("2")
-    result.should include("3")
-    result.should include("4")
-    result.should include("5")
-    result.should include("6")
-  end
-end

data/spec/spec_helper.rb

@@ -1,120 +0,0 @@
-begin
-  require 'cover_me'
-rescue LoadError
-  puts 'cover_me unavailable, running without code coverage measurement'
-end
-require 'bundler/setup'
-
-#require 'pry'
-
-PROJECT_ROOT = File.dirname(__FILE__) + '/../'
-
-require PROJECT_ROOT + 'lib/quality-measure-engine'
-
-Bundler.require(:test)
-ENV['DB_NAME'] = 'test'
-
-def reload_bundle(bundle_dir='.', measure_dir=ENV['MEASURE_DIR'] || 'measures')
-  loader = QME::Database::Loader.new
-  loader.drop_collection('bundles')
-  loader.drop_collection('measures')
-  loader.drop_collection('manual_exclusions')
-  loader.save_bundle(bundle_dir, measure_dir)
-  loader
-end
-
-def validate_measures(measure_dirs, loader)
-
-  reload_bundle
-
-  loader.get_db.collection('manual_exclusions').save({'measure_id'=>'test1', 'medical_record_id'=>'1234567890'})
-  
-  measure_dirs.each do |dir|
-    # check for sample data
-    fixture_dir = File.join('fixtures', 'measures', File.basename(dir))
-    patient_files = Dir.glob(File.join(fixture_dir, 'patients', '*.json'))
-    if patient_files.length==0
-      puts "Skipping #{dir}, no sample data in #{fixture_dir}"
-      next
-    end
-
-    puts "Parsing #{dir}"
-
-    loader.drop_collection('records')
-    loader.drop_collection('query_cache')
-    loader.drop_collection('patient_cache')
-    
-    # load measure from file system
-    # this is innefficient, could just load it from DB as its already stored there
-    measures = QME::Measure::Loader.load_measure(dir)
-    
-    # patients can include an optional test_id population identifier, extract this if present
-    test_id = nil
-    
-    # load db with sample patient records
-    patient_files.each do |patient_file|
-      patient = JSON.parse(File.read(patient_file))
-      test_id ||= patient['test_id']
-      loader.save('records', patient)
-    end
-      
-    # load expected results
-    result_file = File.join('fixtures', 'measures', File.basename(dir), 'result.json')
-    expected = JSON.parse(File.read(result_file))
-    
-    # evaulate measure using Map/Reduce and validate results
-    measures.each do |measure|
-      measure_id = measure['id']
-      sub_id = measure['sub_id']
-      puts "Validating measure #{measure_id}#{sub_id}"
-      executor = QME::MapReduce::Executor.new(measure_id, sub_id,
-        'effective_date'=>Time.gm(2010, 9, 19).to_i,
-        'test_id'=>test_id)
-      executor.map_records_into_measure_groups
-      result = executor.count_records_in_measure_groups
-      if expected['initialPopulation'] == nil
-        # multiple results for multi numerator/denominator measure
-        # loop through list of results to find the matching one
-        expected['results'].each do |expect|
-          if expect['id'].eql?(measure_id) && (sub_id==nil || expect['sub_id'].eql?(sub_id))
-            result['population'].should match_population(expect['initialPopulation'])
-            result['numerator'].should match_numerator(expect['numerator'])
-            result['denominator'].should match_denominator(expect['denominator'])
-            result['exclusions'].should match_exclusions(expect['exclusions'])
-            (result['numerator']+result['antinumerator']).should eql(expect['denominator'])
-            break
-          end
-        end
-      else
-        result['population'].should match_population(expected['initialPopulation'])
-        result['numerator'].should match_numerator(expected['numerator'])
-        result['denominator'].should match_denominator(expected['denominator'])
-        result['exclusions'].should match_exclusions(expected['exclusions'])
-        (result['numerator']+result['antinumerator']).should eql(expected['denominator'])
-      end
-    end
-    puts ' - done'
-  end
-  
-end
-
-def validate_patient_mapping(loader)
-  reload_bundle
-  loader.drop_collection('records')
-  loader.drop_collection('query_cache')
-  loader.drop_collection('patient_cache')
-  
-  patient_file = File.join('fixtures', 'mapping', 'test1_numerator.json')
-  patient = JSON.parse(File.read(patient_file))
-  loader.save('records', patient)
-
-  executor = QME::MapReduce::Executor.new('test1', nil,
-    'effective_date'=>Time.gm(2010, 9, 19).to_i)
-  result = executor.get_patient_result('patient1')
-
-  result['population'].should be(true)
-  result['numerator'].should be(true)
-  result['denominator'].should be(true)
-  result['exclusions'].should be(false)
-  result['antinumerator'].should be(false)
-end

data/spec/validate_measures_spec.rb

@@ -1,21 +0,0 @@
-# Validate the measure specifications and patient samples
-
-require 'json'
-
-describe JSON, 'All measure specifications' do
-  it 'should be valid JSON' do
-    Dir.glob(File.join('measures', '*', '*.json')).each do |measure_file|
-      measure = File.read(measure_file)
-      json = JSON.parse(measure)
-    end
-  end
-end
-
-describe JSON, 'All patient samples' do
-  it 'should be valid JSON' do
-    Dir.glob(File.join('fixtures', 'measures', '*', 'patients', '*.json')).each do |measure_file|
-      measure = File.read(measure_file)
-      json = JSON.parse(measure)
-    end
-  end
-end