quality-measure-engine 1.1.5 → 2.0.0

data/test/fixtures/records/billy_jones_ipp.json

@@ -0,0 +1,78 @@
+{
+    "_id": "507eb5977042f9362c000001",
+    "birthdate": 1059723000,
+    "conditions": [
+        {
+            "codes": {
+                "ICD-9-CM": [
+                    "034.0"
+                ],
+                "SNOMED-CT": [
+                    "140004.0"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "Condition",
+            "description": "Diagnosis, Active: pharyngitis (Code List: 2.16.840.1.113883.3.464.0001.369)",
+            "start_time": 1295067600,
+            "end_time": 1295067600,
+            "status_code": {
+                "SNOMED-CT": [
+                    "55561003"
+                ],
+                "HL7 ActStatus": [
+                    "active"
+                ]
+            }
+        }
+    ],
+    "description": "",
+    "description_category": "DENOM",
+    "elimination_population": null,
+    "elimination_reason": null,
+    "encounters": [
+        {
+            "codes": {
+                "CPT": [
+                    "99201"
+                ],
+                "ICD-9-CM": [
+                    "V70.0"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "Encounter",
+            "description": "Encounter: Encounter ambulatory including pediatrics (Code List: 2.16.840.1.113883.3.464.0001.231)",
+            "start_time": 1295067600,
+            "end_time": 1295067600
+        }
+    ],
+    "expired": false,
+    "first": "Billy",
+    "gender": "M",
+    "last": "Jones",
+    "measure_period_end": 1325394000000,
+    "measure_period_start": 1293858000000,
+    "medications": [
+        {
+            "codes": {
+                "RxNorm": [
+                    "197450"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "Medication",
+            "description": "Medication, Active: pharyngitis antibiotics (Code List: 2.16.840.1.113883.3.464.0001.373)",
+            "start_time": 1295154000,
+            "end_time": 1295154000,
+            "status_code": {
+                "SNOMED-CT": [
+                    "55561003"
+                ],
+                "HL7 ActStatus": [
+                    "active"
+                ]
+            }
+        }
+    ]
+}

data/test/fixtures/records/jane_jones_numerator.json

@@ -0,0 +1,120 @@
+{
+    "_id": "507ec2077042f9362c00001b",
+    "birthdate": 946715400,
+    "medical_record_number": "12345",
+    "conditions": [
+        {
+            "codes": {
+                "ICD-9-CM": [
+                    "034.0"
+                ],
+                "SNOMED-CT": [
+                    "140004.0"
+                ]
+            },
+            "mood_code": "EVN",
+            "_id": {
+                "$oid": "507ecc2b7042f9362c000061"
+            },
+            "_type": "Condition",
+            "description": "Diagnosis, Active: pharyngitis (Code List: 2.16.840.1.113883.3.464.0001.369)",
+            "start_time": 1293253200,
+            "end_time": 1293253200,
+            "status_code": {
+                "SNOMED-CT": [
+                    "55561003"
+                ],
+                "HL7 ActStatus": [
+                    "active"
+                ]
+            }
+        }
+    ],
+    "description": "",
+    "description_category": "NUMER",
+    "elimination_population": null,
+    "elimination_reason": null,
+    "encounters": [
+        {
+            "codes": {
+                "CPT": [
+                    "99201"
+                ],
+                "ICD-9-CM": [
+                    "V70.0"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "Encounter",
+            "description": "Encounter: Encounter ambulatory including pediatrics (Code List: 2.16.840.1.113883.3.464.0001.231)",
+            "start_time": 1293253200,
+            "end_time": 1293253200
+        }
+    ],
+    "expired": false,
+    "first": "Jane",
+    "gender": "F",
+    "last": "Jones",
+    "measure_period_end": 1325307600000,
+    "measure_period_start": 1293858000000,
+    "medications": [
+        {
+            "codes": {
+                "RxNorm": [
+                    "197450"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "Medication",
+            "description": "Medication, Active: pharyngitis antibiotics (Code List: 2.16.840.1.113883.3.464.0001.373)",
+            "start_time": 1293339600,
+            "end_time": 1293339600,
+            "status_code": {
+                "SNOMED-CT": [
+                    "55561003"
+                ],
+                "HL7 ActStatus": [
+                    "active"
+                ]
+            }
+        }
+    ],
+    "vital_signs": [
+        {
+            "codes": {
+                "CPT": [
+                    "87070"
+                ],
+                "LOINC": [
+                    "11268-0"
+                ],
+                "SNOMED-CT": [
+                    "89634005.0"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "VitalSign",
+            "description": "Laboratory Test, Performed: Group A Streptococcus Test (Code List: 2.16.840.1.113883.3.464.0001.250)",
+            "start_time": 1293166800,
+            "end_time": 1293166800
+        },
+        {
+            "codes": {
+                "CPT": [
+                    "87070"
+                ],
+                "LOINC": [
+                    "11268-0"
+                ],
+                "SNOMED-CT": [
+                    "89634005.0"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "VitalSign",
+            "description": "Laboratory Test, Performed: Group A Streptococcus Test (Code List: 2.16.840.1.113883.3.464.0001.250)",
+            "start_time": 1293339600,
+            "end_time": 1293339600
+        }
+    ]
+}

data/test/fixtures/records/jill_jones_denominator.json

@@ -0,0 +1,78 @@
+{
+    "_id": "507ec1407042f9362c000017",
+    "birthdate": 946715400,
+    "conditions": [
+        {
+            "codes": {
+                "ICD-9-CM": [
+                    "034.0"
+                ],
+                "SNOMED-CT": [
+                    "140004.0"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "Condition",
+            "description": "Diagnosis, Active: pharyngitis (Code List: 2.16.840.1.113883.3.464.0001.369)",
+            "start_time": 1293858000,
+            "end_time": 1293858000,
+            "status_code": {
+                "SNOMED-CT": [
+                    "55561003"
+                ],
+                "HL7 ActStatus": [
+                    "active"
+                ]
+            }
+        }
+    ],
+    "description": "",
+    "description_category": "DENOM",
+    "elimination_population": null,
+    "elimination_reason": null,
+    "encounters": [
+        {
+            "codes": {
+                "CPT": [
+                    "99201"
+                ],
+                "ICD-9-CM": [
+                    "V70.0"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "Encounter",
+            "description": "Encounter: Encounter ambulatory including pediatrics (Code List: 2.16.840.1.113883.3.464.0001.231)",
+            "start_time": 1293858000,
+            "end_time": 1293858000
+        }
+    ],
+    "expired": false,
+    "first": "Jill",
+    "gender": "F",
+    "last": "Jones",
+    "measure_period_end": 1325307600000,
+    "measure_period_start": 1293858000000,
+    "medications": [
+        {
+            "codes": {
+                "RxNorm": [
+                    "197450"
+                ]
+            },
+            "mood_code": "EVN",
+            "_type": "Medication",
+            "description": "Medication, Active: pharyngitis antibiotics (Code List: 2.16.840.1.113883.3.464.0001.373)",
+            "start_time": 1293944400,
+            "end_time": 1293944400,
+            "status_code": {
+                "SNOMED-CT": [
+                    "55561003"
+                ],
+                "HL7 ActStatus": [
+                    "active"
+                ]
+            }
+        }
+    ]
+}

data/test/simplecov_setup.rb

@@ -0,0 +1,18 @@
+require 'simplecov'
+SimpleCov.command_name 'Unit Tests'
+SimpleCov.start do
+  add_filter "test/"
+  add_group "Map Reduce", "lib/qme/map"
+  add_group "Bundles", "lib/qme/bundle"
+end
+
+class SimpleCov::Formatter::QualityFormatter
+  def format(result)
+    SimpleCov::Formatter::HTMLFormatter.new.format(result)
+    File.open("coverage/covered_percent", "w") do |f|
+      f.puts result.source_files.covered_percent.to_f
+    end
+  end
+end
+
+SimpleCov.formatter = SimpleCov::Formatter::QualityFormatter

data/test/test_helper.rb

@@ -0,0 +1,26 @@
+require 'simplecov_setup'
+require 'minitest/autorun'
+require 'quality-measure-engine'
+
+db_host = ENV['TEST_DB_HOST'] || 'localhost'
+
+Mongoid.configure do |config|
+  config.sessions = { default: { hosts: [ "#{db_host}:27017" ], database: 'test' }}
+end
+
+class MiniTest::Unit::TestCase
+  # Add more helper methods to be used by all tests here...
+  
+  def collection_fixtures(db, collection, *id_attributes)
+    db[collection].drop
+    Dir.glob(File.join(File.dirname(__FILE__), 'fixtures', collection, '*.json')).each do |json_fixture_file|
+      #puts "Loading #{json_fixture_file}"
+      fixture_json = JSON.parse(File.read(json_fixture_file))
+      id_attributes.each do |attr|
+        fixture_json[attr] = Moped::BSON::ObjectId.from_string(fixture_json[attr])
+      end
+
+      db[collection].insert(fixture_json)
+    end
+  end
+end

data/test/unit/qme/map/map_reduce_builder_test.rb

@@ -0,0 +1,38 @@
+require 'test_helper'
+
+class MapReduceBuilderTest < MiniTest::Unit::TestCase
+  include QME::DatabaseAccess
+
+  def setup
+    raw_measure_json = File.read(File.join('test', 'fixtures', 'measures', 'measure_metadata.json'))
+    @measure_json = JSON.parse(raw_measure_json)
+  end
+
+  def test_extracting_measure_metadata
+    measure = QME::MapReduce::Builder.new(get_db(), @measure_json, 'effective_date' => Time.gm(2010, 9, 19).to_i)
+    assert_equal '0043', measure.id
+  end
+
+  def test_extracting_parameters
+    time = Time.gm(2010, 9, 19).to_i
+    measure = QME::MapReduce::Builder.new(get_db(), @measure_json, 'effective_date'=>time)
+    assert_equal 1, measure.params.size
+    assert measure.params.keys.include?('effective_date')
+    assert_equal time, measure.params['effective_date']
+  end
+
+  def test_raise_error_when_no_params_provided
+    rte = assert_raises(RuntimeError) do
+      QME::MapReduce::Builder.new(get_db(), @measure_json, {})
+    end
+    assert_equal "No value supplied for measure parameter: effective_date", rte.message
+  end
+
+  def test_context_building
+    vars = {'a'=>10, 'b'=>20}
+    context = QME::MapReduce::Builder::Context.new(get_db(), vars)
+    binding = context.get_binding
+    assert_equal 10, eval("a",binding)
+    assert_equal 20, eval("b",binding)
+  end
+end

data/test/unit/qme/map/map_reduce_executor_test.rb

@@ -0,0 +1,56 @@
+require 'test_helper'
+
+class MapReduceExecutorTest < MiniTest::Unit::TestCase
+  include QME::DatabaseAccess
+
+  def setup
+    importer = QME::Bundle::Importer.new
+    importer.import(File.new('test/fixtures/bundles/just_measure_0002.zip'), true)
+
+    collection_fixtures(get_db(), 'records', '_id')
+  end
+
+  def test_map_records_into_measure_groups
+    executor = QME::MapReduce::Executor.new("2E679CD2-3FEC-4A75-A75A-61403E5EFEE8", nil,
+                                            'effective_date' => Time.gm(2011, 1, 15).to_i)
+    executor.map_records_into_measure_groups
+
+    assert_equal 4, get_db['patient_cache'].find().count
+    assert_equal 3, get_db['patient_cache'].find('value.population' => 1).count
+    assert_equal 1, get_db['patient_cache'].find('value.population' => 0).count
+    assert_equal 2, get_db['patient_cache'].find('value.denominator' => 1).count
+    assert_equal 1, get_db['patient_cache'].find('value.numerator' => 1).count
+  end
+
+  def test_count_records_in_measure_groups
+    executor = QME::MapReduce::Executor.new("2E679CD2-3FEC-4A75-A75A-61403E5EFEE8", nil,
+                                            'effective_date' => Time.gm(2011, 1, 15).to_i)
+    executor.map_records_into_measure_groups
+    executor.count_records_in_measure_groups
+    assert_equal 1, get_db['query_cache'].find().count
+    doc = get_db['query_cache'].find().first
+    assert_equal 3, doc['population']
+    assert_equal 2, doc['denominator']
+    assert_equal 1, doc['numerator']
+  end
+
+  def test_map_record_into_measure_groups
+    executor = QME::MapReduce::Executor.new("2E679CD2-3FEC-4A75-A75A-61403E5EFEE8", nil,
+                                            'effective_date' => Time.gm(2011, 1, 15).to_i)
+    executor.map_record_into_measure_groups("12345")
+
+    assert_equal 1, get_db['patient_cache'].find().count
+    assert_equal 1, get_db['patient_cache'].find('value.population' => 1).count
+    assert_equal 0, get_db['patient_cache'].find('value.population' => 0).count
+    assert_equal 1, get_db['patient_cache'].find('value.denominator' => 1).count
+    assert_equal 1, get_db['patient_cache'].find('value.numerator' => 1).count
+  end
+
+  def test_get_patient_result
+    executor = QME::MapReduce::Executor.new("2E679CD2-3FEC-4A75-A75A-61403E5EFEE8", nil,
+                                            'effective_date' => Time.gm(2011, 1, 15).to_i)
+    result = executor.get_patient_result("12345")
+    assert_equal 0, get_db['patient_cache'].find().count
+    assert result['numerator']
+  end
+end

data/test/unit/qme/map/measure_calculation_job_test.rb

@@ -0,0 +1,22 @@
+require 'test_helper'
+
+class MapCalculationJobTest < MiniTest::Unit::TestCase
+  include QME::DatabaseAccess
+
+  def setup
+    importer = QME::Bundle::Importer.new
+    importer.import(File.new('test/fixtures/bundles/just_measure_0002.zip'), true)
+
+    collection_fixtures(get_db(), 'records', '_id')
+
+    Delayed::Worker.delay_jobs = false
+  end
+
+  def test_perform
+    options = {'measure_id' => "2E679CD2-3FEC-4A75-A75A-61403E5EFEE8",
+               'effective_date' => Time.gm(2011, 1, 15).to_i}
+
+    job = Delayed::Job.enqueue(QME::MapReduce::MeasureCalculationJob.new(options))
+    assert job
+  end
+end