quality-measure-engine 2.5.3 → 3.0.0.beta.1

data/test/unit/qme/quality_measure_test.rb

@@ -2,52 +2,16 @@ require 'test_helper'
 
 class QualityMeasureTest < MiniTest::Unit::TestCase
 	include QME::DatabaseAccess
-
   def setup
+
     collection_fixtures(get_db(), 'measures')
     collection_fixtures(get_db(), 'bundles')
-    @bundle_id = get_db['bundles'].find.first['_id']
-    get_db['measures'].find({}).update(:$set => {'bundle_id' => @bundle_id})
     load_system_js
   end
 
-  def test_getting_all_measures_without_bundle_id
+  def test_getting_all_measures
     all_measures = QME::QualityMeasure.all
     assert_equal 5, all_measures.size
-
-    assert all_measures["2E679CD2-3FEC-4A75-A75A-61403E5EFEE8.json"]
-  end
-
-  def test_getting_definition_with_bundle_id
-    result = QME::QualityMeasure.all(@bundle_id).to_a.first.last
-    measure = QME::QualityMeasure.new(result['id'], result['sub_id'], @bundle_id)
-    assert measure.definition
-    assert_equal result['id'], measure.definition['id']
-  end
-
-  def test_getting_all_measure_with_bundle_id
-    get_db()['measures']
-    all_measures = QME::QualityMeasure.all(@bundle_id)
-
-    assert_equal 1, all_measures.size
+    assert all_measures.where({"hqmf_id" => "2E679CD2-3FEC-4A75-A75A-61403E5EFEE8"}).first
   end
-
-  def test_getting_measure_subset
-    measure_ids = get_db['measures'].find({}).map { |m| m['id'] }
-    measure_ids.pop
-    measures = QME::QualityMeasure.get_measures(measure_ids)
-    measure_ids2 = measures.map { |m| m['id'] }
-    assert_equal [], measure_ids - measure_ids2
-  end
-
-  def test_getting_sub_measures
-    measures = QME::QualityMeasure.sub_measures("8A4D92B2-3887-5DF3-0139-0C4E41594C98")
-    assert_equal 2, measures.count
-  end
-
-  def test_getting_sub_measure
-    measure = QME::QualityMeasure.get("8A4D92B2-3887-5DF3-0139-0C4E41594C98", 'a')
-    assert measure
-  end
-
 end

data/test/unit/qme/quality_report_test.rb

@@ -11,10 +11,12 @@ class QualityReportTest < MiniTest::Unit::TestCase
     get_db()['query_cache'].insert(
       "measure_id" => "test2",
       "sub_id" =>  "b",
+      "status" =>{"state" => "completed"},
       "initialPopulation" => 4,
+      "result" => {
       QME::QualityReport::NUMERATOR => 1,
       QME::QualityReport::DENOMINATOR => 2,
-      QME::QualityReport::EXCLUSIONS => 1,
+      QME::QualityReport::EXCLUSIONS => 1},
       "effective_date" => Time.gm(2010, 9, 19).to_i
     )
     get_db()['patient_cache'].insert(
@@ -48,15 +50,15 @@ class QualityReportTest < MiniTest::Unit::TestCase
   end
 
   def test_calculated
-    qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
+    qr = QME::QualityReport.find_or_create('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
     assert qr.calculated?
     
-    qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 20).to_i)
+    qr = QME::QualityReport.find_or_create('test2', 'b', "effective_date" => Time.gm(2010, 9, 20).to_i)
     assert !qr.calculated?
   end
   
   def test_result
-    qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
+    qr = QME::QualityReport.find_or_create('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
     result = qr.result
     
     assert_equal 1, result[QME::QualityReport::NUMERATOR]
@@ -65,24 +67,25 @@ class QualityReportTest < MiniTest::Unit::TestCase
   def test_destroy_all
     QME::QualityReport.destroy_all
     
-    qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
+    qr = QME::QualityReport.find_or_create('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
     assert !qr.calculated?
   end
   
   def test_update_patient_results
-    qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
+    qr = QME::QualityReport.find_or_create('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
     assert qr.calculated?
     assert qr.patients_cached?
     QME::QualityReport.update_patient_results("0616911582")
+    qr = QME::QualityReport.find_or_create('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
     assert !qr.calculated?
     assert !qr.patients_cached?
   end
 
   def test_status
-    qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
-    status = qr.status('not really a job id')
+
+    status = QME::MapReduce::MeasureCalculationJob.status('not really a job id')
     assert_equal :complete, status
-    status = qr.status("508aeff07042f9f88900000d")
+    status = QME::MapReduce::MeasureCalculationJob.status("508aeff07042f9f88900000d")
     assert_equal :queued, status
   end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quality-measure-engine
 version: !ruby/object:Gem::Version
-  version: 2.5.3
+  version: 3.0.0.beta.1
 platform: ruby
 authors:
 - Marc Hadley
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-12-09 00:00:00.000000000 Z
+date: 2013-12-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: moped
@@ -154,13 +154,13 @@ files:
 - LICENSE.txt
 - README.md
 - Rakefile
-- lib/qme/bundle/eh_measure_sheet.rb
-- lib/qme/bundle/eh_patient_importer.rb
 - lib/qme/database_access.rb
+- lib/qme/manual_exclusion.rb
 - lib/qme/map/cv_aggregator.rb
 - lib/qme/map/map_reduce_builder.rb
 - lib/qme/map/map_reduce_executor.rb
 - lib/qme/map/measure_calculation_job.rb
+- lib/qme/patient_cache.rb
 - lib/qme/quality_measure.rb
 - lib/qme/quality_report.rb
 - lib/qme/railtie.rb
@@ -184,10 +184,9 @@ files:
 - test/fixtures/records/billy_jones_ipp.json
 - test/fixtures/records/jane_jones_numerator.json
 - test/fixtures/records/jill_jones_denominator.json
+- test/mongoid.yml
 - test/simplecov_setup.rb
 - test/test_helper.rb
-- test/unit/qme/bundle/eh_measure_sheet_test.rb
-- test/unit/qme/bundle/eh_patient_importer_test.rb
 - test/unit/qme/map/cv_aggregator_test.rb
 - test/unit/qme/map/map_reduce_builder_test.rb
 - test/unit/qme/map/map_reduce_executor_test.rb
@@ -208,12 +207,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ! '>'
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.3
+rubygems_version: 2.0.7
 signing_key: 
 specification_version: 4
 summary: This library can run JavaScript based clinical quality measures on a repository
@@ -236,10 +235,9 @@ test_files:
 - test/fixtures/records/billy_jones_ipp.json
 - test/fixtures/records/jane_jones_numerator.json
 - test/fixtures/records/jill_jones_denominator.json
+- test/mongoid.yml
 - test/simplecov_setup.rb
 - test/test_helper.rb
-- test/unit/qme/bundle/eh_measure_sheet_test.rb
-- test/unit/qme/bundle/eh_patient_importer_test.rb
 - test/unit/qme/map/cv_aggregator_test.rb
 - test/unit/qme/map/map_reduce_builder_test.rb
 - test/unit/qme/map/map_reduce_executor_test.rb

data/lib/qme/bundle/eh_measure_sheet.rb

@@ -1,117 +0,0 @@
-module QME
-  module Bundle
-    class EHMeasureSheet
-      attr_reader :query_cache_document, :patient_cache_documents,
-                  :patient_updates
-
-      def initialize(db, sheet, effective_date=nil)
-        @db = db
-        @sheet = sheet
-        @effective_date = effective_date
-        @patient_cache_documents = []
-        @patient_updates = []
-      end
-
-      def parse
-        qc_document = {}
-        measure_info = extract_measure_info
-        qc_document['population_ids'] = measure_info
-        measure_doc = @db['measures'].where('population_ids' => measure_info).first
-        measure_ids = measure_doc.slice('sub_id', 'nqf_id')
-        measure_ids['measure_id'] = measure_doc['hqmf_id']
-        qc_document.merge!(measure_ids)
-        extract_patients(measure_ids)
-
-        qc_document[QME::QualityReport::POPULATION] = extract_data_from_cell("C#{@population_totals_row}")
-        qc_document[QME::QualityReport::CONSIDERED] = @population_totals_row - 3 # header row, blank row and totals row
-        if cv_measure?
-          qc_document[QME::QualityReport::MSRPOPL] = extract_data_from_cell("E#{@population_totals_row}")
-          qc_document[QME::QualityReport::OBSERVATION] = extract_data_from_cell("F#{@population_totals_row}")
-        else
-          qc_document[QME::QualityReport::DENOMINATOR] = extract_data_from_cell("D#{@population_totals_row}")
-          qc_document[QME::QualityReport::NUMERATOR] = extract_data_from_cell("E#{@population_totals_row}")
-          qc_document[QME::QualityReport::ANTINUMERATOR] = qc_document[QME::QualityReport::DENOMINATOR] - qc_document[QME::QualityReport::NUMERATOR]
-          qc_document[QME::QualityReport::EXCLUSIONS] = extract_data_from_cell("F#{@population_totals_row}")
-          qc_document[QME::QualityReport::EXCEPTIONS] = extract_data_from_cell("G#{@population_totals_row}")
-        end
-
-        qc_document['test_id'] = nil
-        qc_document['filters'] = nil
-        qc_document['execution_time'] = 0
-        qc_document['effective_date'] = @effective_date
-
-        @query_cache_document = qc_document
-      end
-
-      def extract_patients(measure_ids)
-        row = 2
-        medical_record_number = extract_data_from_cell("B#{row}")
-        while medical_record_number.present?
-          patient_document = extract_patient(row, medical_record_number.to_s)
-          patient_document.merge!(measure_ids)
-          @patient_cache_documents << {'value' => patient_document}
-          @patient_updates << {'medical_record_number' => medical_record_number.to_s,
-                               'measure_id' => measure_ids['measure_id']}
-          row = row + 1
-          medical_record_number = extract_data_from_cell("B#{row}")
-        end
-
-        @population_totals_row = row + 1
-      end
-
-      def extract_measure_info
-        measure_info = {}
-        measure_info[QME::QualityReport::POPULATION] = extract_data_from_cell('I5')
-        if cv_measure?
-          measure_info[QME::QualityReport::MSRPOPL] = extract_data_from_cell('I10')
-          measure_info[QME::QualityReport::OBSERVATION] = extract_data_from_cell('I11') if extract_data_from_cell('I11').present?
-          measure_info['stratification'] = extract_data_from_cell('I12') if extract_data_from_cell('I12').present?
-        else
-          measure_info['DENOM'] = extract_data_from_cell('I6')
-          measure_info['NUMER'] = extract_data_from_cell('I7')
-          measure_info['DENEXCEP'] = extract_data_from_cell('I8') if extract_data_from_cell('I8').present?
-          measure_info['DENEX'] = extract_data_from_cell('I9') if extract_data_from_cell('I9').present?
-          measure_info['stratification'] = extract_data_from_cell('I12') if extract_data_from_cell('I12').present?
-        end
-
-        measure_info
-      end
-
-      def extract_patient(row, medical_record_number)
-        record = @db['records'].where('medical_record_number' => medical_record_number).first
-        patient_document = record.slice('first', 'last', 'gender', 'birthdate', 'race',
-                                              'ethnicity', 'languages')
-        patient_document['medical_record_id'] = medical_record_number
-        patient_document['patient_id'] = record['_id'].to_s
-        patient_document[QME::QualityReport::POPULATION] = extract_data_from_cell("C#{row}") || 0
-        if cv_measure?
-          patient_document[QME::QualityReport::MSRPOPL] = extract_data_from_cell("E#{row}") || 0
-          patient_document['values'] = [extract_data_from_cell("F#{row}")]
-        else
-          patient_document[QME::QualityReport::DENOMINATOR] = extract_data_from_cell("D#{row}") || 0
-          patient_document[QME::QualityReport::NUMERATOR] = extract_data_from_cell("E#{row}") || 0
-          patient_document[QME::QualityReport::EXCLUSIONS] = extract_data_from_cell("F#{row}") || 0
-          patient_document[QME::QualityReport::EXCEPTIONS] = extract_data_from_cell("G#{row}") || 0
-          patient_document[QME::QualityReport::ANTINUMERATOR] = patient_document[QME::QualityReport::DENOMINATOR] - patient_document[QME::QualityReport::NUMERATOR]
-
-        end
-        patient_document['test_id'] = nil
-        patient_document['effective_date'] = @effective_date
-
-        patient_document
-      end
-
-      def cv_measure?
-        extract_data_from_cell('E1').eql?('MSRPOPL')
-      end
-
-      private
-
-      def extract_data_from_cell(cell_name)
-        row, column = RubyXL::Parser.convert_to_index(cell_name)
-        @sheet.sheet_data[row][column].try(:value)
-      end
-    end
-
-  end
-end

data/lib/qme/bundle/eh_patient_importer.rb

@@ -1,25 +0,0 @@
-module QME
-  module Bundle
-    class EHPatientImporter
-      def self.load(db, spreadsheet, effective_date=nil)
-        spreadsheet.worksheets.each do |worksheet|
-          ms = EHMeasureSheet.new(db, worksheet, effective_date)
-          ms.parse
-          qc_document = ms.query_cache_document
-          db['query_cache'].find({measure_id: qc_document['measure_id'], sub_id: qc_document['sub_id']}).remove
-          db.command(getLastError: 1)
-          db['query_cache'].insert(qc_document)
-          ms.patient_cache_documents.each do |pcd|
-            db['patient_cache'].find({'value.measure_id'=>pcd['value']['measure_id'], 'value.sub_id'=>pcd['value']['sub_id'],'value.medical_record_id'=>pcd['value']['medical_record_id']}).remove
-            db.command(getLastError: 1)
-            db['patient_cache'].insert(pcd)
-          end
-          ms.patient_updates.each do |patient_update|
-            db['records'].find('medical_record_number' => patient_update['medical_record_number']).update(
-                               '$push' => {'measure_ids' => patient_update['measure_id']})
-          end
-        end
-      end
-    end
-  end
-end

data/test/unit/qme/bundle/eh_measure_sheet_test.rb

@@ -1,37 +0,0 @@
-require 'test_helper'
-
-class EHMeasureSheetTest < MiniTest::Unit::TestCase
-  include QME::DatabaseAccess
-
-  def setup
-    collection_fixtures(get_db(), 'measures')
-    collection_fixtures(get_db(), 'records', '_id')
-    @workbook = RubyXL::Parser.parse(File.join('test', 'fixtures', 'eh_patient_sheets', 'results_matrix_eh.xlsx'))
-    sheet = @workbook.worksheets[0]
-    @ms = QME::Bundle::EHMeasureSheet.new(get_db(), sheet, 12345000)
-  end
-
-  def test_extract_measure_info
-    measure_info = @ms.extract_measure_info
-    assert_equal 'EDD90083-3417-4221-B3B9-52C4E5FAFAF4', measure_info['IPP']
-    assert_equal '193A17EC-66B4-4C44-9302-192556C78454', measure_info['DENOM']
-  end
-
-  def test_query_cache_document
-    @ms.parse
-    qcd = @ms.query_cache_document
-    assert_equal '0142', qcd['nqf_id']
-    assert_equal 4, qcd[QME::QualityReport::POPULATION]
-    assert_equal 12345000, qcd['effective_date']
-  end
-
-  def test_patient_cache_documents
-    @ms.parse
-    pcd = @ms.patient_cache_documents.first
-    assert_equal 1, pcd['value'][QME::QualityReport::POPULATION]
-    assert_equal 0, pcd['value'][QME::QualityReport::NUMERATOR]
-    assert_equal 1, pcd['value'][QME::QualityReport::ANTINUMERATOR]
-    assert_equal '1234', pcd['value']['medical_record_id']
-    assert_equal 12345000, pcd['value']['effective_date']
-  end
-end

data/test/unit/qme/bundle/eh_patient_importer_test.rb

@@ -1,20 +0,0 @@
-require 'test_helper'
-
-class EHPatientImporterTest < MiniTest::Unit::TestCase
-  include QME::DatabaseAccess
-
-  def setup
-    get_db['query_cache'].drop()
-    get_db['patient_cache'].drop()
-    collection_fixtures(get_db(), 'measures')
-    collection_fixtures(get_db(), 'records', '_id')
-    @workbook = RubyXL::Parser.parse(File.join('test', 'fixtures', 'eh_patient_sheets', 'results_matrix_eh.xlsx'))    
-  end
-
-  def test_load
-    assert_equal 0, get_db['query_cache'].find().count
-    QME::Bundle::EHPatientImporter.load(get_db, @workbook)
-    assert_equal 3, get_db['query_cache'].find().count
-    assert_equal 12, get_db['patient_cache'].find().count
-  end
-end