quality-measure-engine 1.1.5 → 2.0.0

data/test/unit/qme/quality_measure_test.rb

@@ -0,0 +1,14 @@
+require 'test_helper'
+
+class QualityMeasureTest < MiniTest::Unit::TestCase
+  def setup
+    importer = QME::Bundle::Importer.new
+    importer.import(File.new('test/fixtures/bundles/just_measure_0002.zip'), true)
+  end
+
+  def test_getting_all_measures
+    all_measures = QME::QualityMeasure.all
+    assert_equal 1, all_measures.size
+    assert all_measures["2E679CD2-3FEC-4A75-A75A-61403E5EFEE8.json"]
+  end
+end

data/{spec/qme/quality_report_spec.rb → test/unit/qme/quality_report_test.rb}

@@ -1,9 +1,12 @@
-describe QME::QualityReport do
-  before do
-    loader = QME::Database::Loader.new
-    loader.drop_collection('query_cache')
-    loader.drop_collection('patient_cache')
-    loader.get_db['query_cache'].save(
+require 'test_helper'
+
+class QualityReportTest < MiniTest::Unit::TestCase
+  include QME::DatabaseAccess
+  
+  def setup
+    get_db()['query_cache'].drop()
+    get_db()['patient_cache'].drop()
+    get_db()['query_cache'].insert(
       "measure_id" => "test2",
       "sub_id" =>  "b",
       "initialPopulation" => 4,
@@ -12,7 +15,7 @@ describe QME::QualityReport do
       "exclusions" => 1,
       "effective_date" => Time.gm(2010, 9, 19).to_i
     )
-    loader.get_db['patient_cache'].save(
+    get_db()['patient_cache'].insert(
       "value" => {
         "population" => false,
         "denominator" => false,
@@ -40,35 +43,44 @@ describe QME::QualityReport do
       }
     )
   end
-  
-  it "should be able to determine if it has been calculated" do
+
+  def test_calculated
     qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
-    qr.calculated?.should be_true
+    assert qr.calculated?
     
     qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 20).to_i)
-    qr.calculated?.should be_false
+    assert !qr.calculated?
   end
   
-  it "should return the result of a calculated quality measure" do
+  def test_result
     qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
     result = qr.result
     
-    result['numerator'].should == 1
+    assert_equal 1, result['numerator']
   end
   
-  it "should be able to clear all of the quality reports" do
+  def test_destroy_all
     QME::QualityReport.destroy_all
     
     qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
-    qr.calculated?.should be_false
+    assert !qr.calculated?
   end
   
-  it "should be remove results for updated patients" do
+  def test_update_patient_results
     qr = QME::QualityReport.new('test2', 'b', "effective_date" => Time.gm(2010, 9, 19).to_i)
-    qr.calculated?.should be_true
-    qr.patients_cached?.should be_true
+    assert qr.calculated?
+    assert qr.patients_cached?
     QME::QualityReport.update_patient_results("0616911582")
-    qr.calculated?.should be_false
-    qr.patients_cached?.should be_false    
+    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')
+    assert_equal :complete, status
+    status = qr.status("508aeff07042f9f88900000d")
+    assert_equal :queued, status
   end
+
 end

metadata

@@ -1,211 +1,173 @@
 --- !ruby/object:Gem::Specification
 name: quality-measure-engine
 version: !ruby/object:Gem::Version
-  version: 1.1.5
+  version: 2.0.0
   prerelease: 
 platform: ruby
 authors:
 - Marc Hadley
 - Andy Gregorowicz
 - Rob Dingwell
+- Adam Goldstein
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-03 00:00:00.000000000Z
+date: 2012-10-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: mongo
-  requirement: &2153471000 !ruby/object:Gem::Requirement
+  name: moped
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: 1.2.7
   type: :runtime
   prerelease: false
-  version_requirements: *2153471000
-- !ruby/object:Gem::Dependency
-  name: rubyzip
-  requirement: &2153470520 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.4
-  type: :runtime
-  prerelease: false
-  version_requirements: *2153470520
+        version: 1.2.7
 - !ruby/object:Gem::Dependency
-  name: nokogiri
-  requirement: &2153469980 !ruby/object:Gem::Requirement
+  name: mongoid
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.4.4
+        version: 3.0.9
   type: :runtime
   prerelease: false
-  version_requirements: *2153469980
-- !ruby/object:Gem::Dependency
-  name: resque
-  requirement: &2153469500 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.15.0
-  type: :runtime
-  prerelease: false
-  version_requirements: *2153469500
+        version: 3.0.9
 - !ruby/object:Gem::Dependency
-  name: redis
-  requirement: &2153468840 !ruby/object:Gem::Requirement
+  name: rubyzip
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.2.2
+        version: 0.9.9
   type: :runtime
   prerelease: false
-  version_requirements: *2153468840
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.9
 - !ruby/object:Gem::Dependency
-  name: resque-status
-  requirement: &2153463060 !ruby/object:Gem::Requirement
+  name: delayed_job_mongoid
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.2.3
+        version: 2.0.0
   type: :runtime
   prerelease: false
-  version_requirements: *2153463060
-- !ruby/object:Gem::Dependency
-  name: jsonschema
-  requirement: &2153461740 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 2.0.0
-  type: :development
-  prerelease: false
-  version_requirements: *2153461740
 - !ruby/object:Gem::Dependency
-  name: rspec
-  requirement: &2153460480 !ruby/object:Gem::Requirement
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.5.0
+        version: 4.1.0
   type: :development
   prerelease: false
-  version_requirements: *2153460480
-- !ruby/object:Gem::Dependency
-  name: awesome_print
-  requirement: &2153459880 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.3'
-  type: :development
-  prerelease: false
-  version_requirements: *2153459880
+        version: 4.1.0
 - !ruby/object:Gem::Dependency
-  name: roo
-  requirement: &2153458460 !ruby/object:Gem::Requirement
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.9.3
+        version: 0.7.1
   type: :development
   prerelease: false
-  version_requirements: *2153458460
-- !ruby/object:Gem::Dependency
-  name: builder
-  requirement: &2153456780 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 3.0.0
-  type: :development
-  prerelease: false
-  version_requirements: *2153456780
+        version: 0.7.1
 - !ruby/object:Gem::Dependency
-  name: spreadsheet
-  requirement: &2153455880 !ruby/object:Gem::Requirement
+  name: rails
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.6.5.2
+        version: 3.2.8
   type: :development
   prerelease: false
-  version_requirements: *2153455880
-- !ruby/object:Gem::Dependency
-  name: google-spreadsheet-ruby
-  requirement: &2153410360 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.1.2
-  type: :development
-  prerelease: false
-  version_requirements: *2153410360
-description: A library for extracting quality measure information from HITSP C32's
-  and ASTM CCR's
-email: talk@projectpophealth.org
+        version: 3.2.8
+description: A library for running clinical quality measures
+email:
+- talk@projectpophealth.org
 executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- .gitignore
+- .travis.yml
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/qme/bundle/bundle.rb
+- lib/qme/bundle/importer.rb
 - lib/qme/database_access.rb
-- lib/qme/ext/record.rb
-- lib/qme/importer/entry.rb
-- lib/qme/importer/generic_importer.rb
-- lib/qme/importer/measure_properties_generator.rb
-- lib/qme/importer/property_matcher.rb
 - lib/qme/map/map_reduce_builder.rb
 - lib/qme/map/map_reduce_executor.rb
 - lib/qme/map/measure_calculation_job.rb
-- lib/qme/measure/database_loader.rb
-- lib/qme/measure/measure_loader.rb
-- lib/qme/measure/properties_builder.rb
-- lib/qme/measure/properties_converter.rb
 - lib/qme/quality_measure.rb
 - lib/qme/quality_report.rb
-- lib/qme/randomizer/patient_randomization_job.rb
-- lib/qme/randomizer/patient_randomizer.rb
-- lib/qme/randomizer/random_patient_creator.rb
-- lib/qme_test.rb
+- lib/qme/railtie.rb
+- lib/qme/tasks/bundle.rake
+- lib/qme/version.rb
 - lib/quality-measure-engine.rb
-- lib/tasks/fixtures.rake
-- lib/tasks/measure.rake
-- lib/tasks/mongo.rake
-- lib/tasks/patient_random.rake
-- js/map_reduce_utils.js
-- js/underscore_min.js
-- spec/qme/bundle_spec.rb
-- spec/qme/importer/generic_importer_spec.rb
-- spec/qme/importer/measure_properties_generator_spec.rb
-- spec/qme/importer/property_matcher_spec.rb
-- spec/qme/map/map_reduce_builder_spec.rb
-- spec/qme/map/measures_spec.rb
-- spec/qme/map/patient_mapper_spec.rb
-- spec/qme/measure_loader_spec.rb
-- spec/qme/properties_builder_spec.rb
-- spec/qme/quality_report_spec.rb
-- spec/spec_helper.rb
-- spec/validate_measures_spec.rb
-- Gemfile
-- README.md
-- Rakefile
-- VERSION
-homepage: http://github.com/pophealth/quality-measure-engine
+- quality-measure-engine.gemspec
+- test/fixtures/bundles/just_measure_0002.zip
+- test/fixtures/delayed_backend_mongoid_jobs/queued_job.json
+- test/fixtures/measures/measure_metadata.json
+- test/fixtures/records/barry_berry.json
+- test/fixtures/records/billy_jones_ipp.json
+- test/fixtures/records/jane_jones_numerator.json
+- test/fixtures/records/jill_jones_denominator.json
+- test/simplecov_setup.rb
+- test/test_helper.rb
+- test/unit/qme/map/map_reduce_builder_test.rb
+- test/unit/qme/map/map_reduce_executor_test.rb
+- test/unit/qme/map/measure_calculation_job_test.rb
+- test/unit/qme/quality_measure_test.rb
+- test/unit/qme/quality_report_test.rb
+homepage: http://www.projectpophealth.org
 licenses: []
 post_install_message: 
 rdoc_options: []
@@ -225,10 +187,24 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
-summary: A library for extracting quality measure information from HITSP C32's and
-  ASTM CCR's
-test_files: []
+summary: This library can run JavaScript based clinical quality measures on a repository
+  of patients stored in MongoDB
+test_files:
+- test/fixtures/bundles/just_measure_0002.zip
+- test/fixtures/delayed_backend_mongoid_jobs/queued_job.json
+- test/fixtures/measures/measure_metadata.json
+- test/fixtures/records/barry_berry.json
+- test/fixtures/records/billy_jones_ipp.json
+- test/fixtures/records/jane_jones_numerator.json
+- test/fixtures/records/jill_jones_denominator.json
+- test/simplecov_setup.rb
+- test/test_helper.rb
+- test/unit/qme/map/map_reduce_builder_test.rb
+- test/unit/qme/map/map_reduce_executor_test.rb
+- test/unit/qme/map/measure_calculation_job_test.rb
+- test/unit/qme/quality_measure_test.rb
+- test/unit/qme/quality_report_test.rb
 has_rdoc: 

data/VERSION

@@ -1 +0,0 @@
-1.1.0

data/js/map_reduce_utils.js

@@ -1,173 +0,0 @@
-function() {
-// Adds common utility functions to the root JS object. These are then
-// available for use by the map-reduce functions for each measure.
-// lib/qme/mongo_helpers.rb executes this function on a database
-// connection.
-
-  var root = this;
-
-  // Takes an arbitrary number of arrays and single values and returns a flattened
-  // array of all of the elements with any null values removed. For efficiency, if 
-  // called with just a single array then it simply returns that array
-  root.normalize = function() {
-    if (arguments.length==1 && _.isArray(arguments[0]))
-      return arguments[0];
-    return _.compact(_.flatten(arguments));
-  }
-
-  // returns the number of values which fall between the supplied limits
-  // value may be a number or an array of numbers
-  root.inRange = function(value, min, max) {
-    value = normalize(value);
-    var count = 0;
-    for (i=0;i<value.length;i++) {
-      if ((value[i]>=min) && (value[i]<=max))
-        count++;
-    }
-    return count;
-  };
-  
-  // returns the largest member of value that is within the supplied range
-  root.maxInRange = function(value, min, max) {
-    value = normalize(value);
-    var allInRange = _.select(value, function(v) {return v>=min && v<=max;});
-    return _.max(allInRange);
-  }
-  
-  // returns the number of values which are less than the supplied limit
-  // value may be a number or an array of numbers
-  root.lessThan = function(value, max) {
-    value = normalize(value);
-    var matching = _.select(value, function(v) {return v<=max;});
-    return matching.length;
-  };
-  
-  // Returns true if any conditions[i].end is within the specified period,
-  // false otherwise
-  root.conditionResolved = function(conditions, startDate, endDate) {
-    conditions = normalize(conditions);
-    var resolvedWithinPeriod = function(condition) {
-      return (condition.end>=startDate && condition.end<=endDate);
-    };
-    return _.any(conditions, resolvedWithinPeriod);
-  };
-  
-  // Returns the minimum of readings[i].value where readings[i].date is in
-  // the supplied startDate and endDate. If no reading meet this criteria,
-  // returns defaultValue.
-  root.minValueInDateRange = function(readings, startDate, endDate, defaultValue) {
-    readings = normalize(readings);
-    
-    var readingInDateRange = function(reading) {
-      return (reading.date>=startDate && reading.date<=endDate);
-    };
-    
-    var allInDateRange = _.select(readings, readingInDateRange);
-    if (allInDateRange.length==0)
-      return defaultValue;
-    var min = _.min(allInDateRange, function(reading) {return reading.value;});
-    if (min==undefined)
-      return defaultValue;
-    return min.value;
-  };
-  
-  // Returns the most recent readings[i].value where readings[i].date is in
-  // the supplied startDate and endDate. If no reading meet this criteria,
-  // returns defaultValue.
-  root.latestValueInDateRange = function(readings, startDate, endDate, defaultValue) {
-    readings = normalize(readings);
-  
-    var readingInDateRange = function(reading) {
-      return (reading.date>=startDate && reading.date<=endDate);
-    };
-    
-    var allInDateRange = _.select(readings, readingInDateRange);
-    if (allInDateRange.length==0)
-      return defaultValue;
-    var latest = _.max(allInDateRange, function(reading) {return reading.date;});
-    if (latest==undefined)
-      return defaultValue;
-    return latest.value;
-  };
-  
-  // Returns the number of actions that occur within the specified time period of
-  // something. The first two arguments are arrays or single-valued time stamps in
-  // seconds-since-the-epoch, timePeriod is in seconds.
-  root.actionFollowingSomething = function(something, action, timePeriod) {
-    something = normalize(something);
-    action = normalize(action);
-    if (timePeriod===undefined)
-      timePeriod=Infinity;
-    
-    var result = 0;
-    for (i=0; i<something.length; i++) {
-      var timeStamp = something[i];
-      for (j=0; j<action.length;j++) {
-        if (action[j]>=timeStamp && (action[j] <= (timeStamp+timePeriod)))
-          result++;
-      }
-    }
-    
-    return result;
-  }
-    
-  // Returns all members of the values array that fall between min and max inclusive
-  root.selectWithinRange = function(values, min, max) {
-    values = normalize(values);
-    return _.select(values, function(value) { return value<=max && value>=min; });
-  }
-  
-  // calculates the earliest birthdate for a maximum age given a target date.
-  // calculation is inclusive of the full year for the target age
-  // returns: (earliest birthdate that will reach by not exceed the age by the target date)
-  // age: integer in years
-  // effective_date: end of the measurement period, in seconds
-  root.earliestBirthdayForThisAge = function(age, effective_date) {
-    return calculateDateForAge(age, effective_date, true);
-  }
-  // calculates the latest birthdate for a minimum age given a target date 
-  // returns: (latest birthdate that will reach the age by the target date)
-  // age: integer in years
-  // effective_date: end of the measurement period, in seconds
-  root.latestBirthdayForThisAge = function(age, effective_date) {
-    return calculateDateForAge(age, effective_date, false);
-  }
-  // returns birth date for an age value given a specific date
-  // age: integer in years
-  // effective_date: end of the measurement period, in seconds
-  // is_inclusive: boolean for including or excluding age
-  root.calculateDateForAge = function(age, effective_date, is_inclusive) {
-    var earliest_birthdate = new Date(effective_date*1000);
-    var difference = age;
-    if (is_inclusive) difference += 1;
-    earliest_birthdate.setFullYear(earliest_birthdate.getFullYear()-difference);
-    return earliest_birthdate.getTime()/1000;
-  }
-  
-  
-  root.map = function(record, population, denominator, numerator, exclusion) {
-    var value = {population: false, denominator: false, numerator: false, 
-                 exclusions: false, antinumerator: false, patient_id: record._id,
-                 medical_record_id: record.medical_record_number,
-                 first: record.first, last: record.last, gender: record.gender,
-                 birthdate: record.birthdate, test_id: record.test_id,
-                 provider_performances: record.provider_performances,
-                 race: record.race, ethnicity: record.ethnicity, languages: record.languages};
-    if (population()) {
-      value.population = true;
-      if (denominator()) {
-        value.denominator = true;
-        if (numerator()) {
-          value.numerator = true;
-        } else if (exclusion()) {
-          value.exclusions = true;
-          value.denominator = false;
-        } else {
-          value.antinumerator = true;
-        }
-      }
-    }
-    emit(ObjectId(), value);
-  };
-
-}