quality-measure-engine 0.1.0

data/schema/result.json

@@ -0,0 +1,28 @@
+{
+  "name": "Result",
+  "properties": {
+    "initialPopulation": {
+      "type": "integer",
+      "description": "Individuals for whom the measure is intended."
+    },
+    "denominator": {
+      "type": "integer",
+      "description": "Individuals who should meet the measure. Sometimes equivalent to the initial population."
+    },
+    "numerator": {
+      "type": "array",
+      "description": "Individuals who do meet the measure.",
+      "items": {
+        "type": "integer"
+      }
+    },
+    "exclusions": {
+      "type": "array",
+      "description": "Individuals that should be in the denominator but have characteristics that make them inappropriate for the measure.",
+      "optional": true,
+      "items": {
+        "type": "integer"
+      }
+    }
+  }
+}

data/schema/schema.json

@@ -0,0 +1,143 @@
+{"description":"This is the JSON Schema for JSON Schemas.",
+ "type":["object","array"],
+ "items":{
+     "type":"object",
+     "properties":{"$ref":"$.properties"},
+     "description":"When the schema is an array, it indicates that it is enforcing tuple typing. Each item in the instance array must correspond to the item in the schema array"},
+ "properties":{
+     "type":{
+     	"type":["string","array"],
+     	"items":{"$ref":"$.properties.type"},
+	"description":"This is a type definition value. This can be a simple type, or a union type",
+	"enum":["string","object","array","boolean","number","integer","null","any"],
+	"unconstrained":true,
+	"optional":true,
+	"default":"any"},
+     "optional":{
+     	"type":"boolean",
+     	"description":"This indicates that the instance property in the instance object is not required.",
+	"optional":true,
+	"default":false},
+     "properties":{
+     	"type":"object",
+     	"additionalProperties":{"$ref":"$"},
+     	"description":"This is a definition for the properties of an object value",
+     	"optional":true,
+     	"default":{}
+     },
+     "items":{
+     	"type":"object",
+     	"properties":{"$ref":"$.properties"},
+     	"description":"When the value is an array, this indicates the schema to use to validate each item in an array",
+	"optional":true,
+	"default":{}},
+     "additionalProperties":{
+     	"type":["boolean","object"],
+     	"properties":{"$ref":"$.properties"},
+     	"description":"This provides a default property definition for all properties that are not explicitly defined in an object type definition.",
+	"optional":true,
+	"default":{}},
+     "specificity":{
+        "type":"number",
+        "description":"This indicates an order of specificity of properties. If an instance defines another property with a higher specificity than this one, than this instance property is required.",
+	"optional":true,
+        "default":false},
+     "unique":{
+     	"type":"boolean",
+     	"description":"This indicates that the instance property should have unique values. No other property with the same name in the instance object tree should have the same value.",
+	"optional":true,
+	"default":false},
+     "minimum":{
+     	"type":"number",
+	"optional":true,
+     	"description":"This indicates the minimum value for the instance property when the type of the instance value is a number, or it indicates the minimum number of values in an array when an array is the instance value."},
+     "maximum":{
+     	"type":"number",
+	"optional":true,
+     	"description":"This indicates the maximum value for the instance property when the type of the instance value is a number, or it indicates the maximum number of values in an array when an array is the instance value."},
+     "pattern":{
+     	"type":"string",
+     	"format":"regex",
+     	"description":"When the instance value is a string, this provides a regular expression that a instance string value should match in order to be valid.",
+	"optional":true,
+	"default":".*"},
+     "maxLength" :{
+     	"type":"number",
+	"optional":true,
+     	"description":"When the instance value is a string, this indicates maximum length of the string."},
+     "minLength" :{
+     	"type":"number",
+	"optional":true,
+     	"description":"When the instance value is a string, this indicates minimum length of the string."},
+     "maxItems" :{
+     	"type":"number",
+	"optional":true,
+     	"description":"When the instance value is an array, this indicates maximum number of items."},
+     "minItems" :{
+     	"type":"number",
+	"optional":true,
+     	"description":"When the instance value is an array, this indicates minimum number of items."},
+     "enum" : {
+     	"type":"array",
+	"optional":true,
+     	"description":"This provides an enumeration of possible values that are valid for the instance property."},
+     "options" : {
+     	"type":"array",
+     	"items":{
+     	   "properties":{
+     	   	"label":{
+     	   	    "type":"string",
+     	   	    "description":"This is the label for this option",
+     	   	    "optional":true
+     	   	    },
+     	   	"value":{
+     	   	    "description":"This is the value for this option"
+     	   	}
+     	   },
+     	   "description":"This is an option for list of possible values"
+     	},
+	"optional":true,
+     	"description":"This provides a list of suggested options for the instance property."},
+     "readonly":{
+     	"type":"boolean",
+     	"description":"This indicates that the instance property should not be changed (this is only for interaction, it has no effect for standalone validation).",
+	"optional":true,
+	"default":false},
+     "description":{
+     	"type":"string",
+	"optional":true,
+     	"description":"This provides a description of the purpose the instance property. The value can be a string or it can be an object with properties corresponding to various different instance languages (with an optional default property indicating the default description)."},
+     "format":{
+     	"type":"string",
+	"optional":true,
+     	"description":"This indicates what format the data is among some predefined formats which may include:\n\ndate - a string following the ISO format \naddress \nschema - a schema definition object \nperson \npage \nhtml - a string representing HTML"},
+     "default":{
+     	"type":"any",
+	"optional":true,
+     	"description":"This indicates the default for the instance property."},
+     "transient":{
+     	"type":"boolean",
+	"optional":true,
+     	"description":"This indicates that the property will be used for transient/volatile values that should not be persisted.",
+	"default":false},
+     "maxDecimal":{
+     	"type":"integer",
+	"optional":true,
+     	"description":"This indicates the maximum number of decimal places in a floating point number."},
+     "hidden":{
+     	"type":"boolean",
+	"optional":true,
+     	"description":"This indicates whether the property should be hidden in user interfaces."},     	
+     "extends":{
+     	"type":"object",
+     	"properties":{"$ref":"$.properties"},
+     	"description":"This indicates the schema extends the given schema. All instances of this schema must be valid to by the extended schema also.",
+	"optional":true,
+	"default":{}},     	
+     "id":{
+     	"type":["string","number"],
+	"optional":true,
+	"format":"url",
+     	"unique":true}
+   }
+}

data/spec/qme/map/map_reduce_builder_spec.rb

@@ -0,0 +1,64 @@
+MAP_FUNCTION = <<END_OF_MAP_FN
+function () {
+  var value = {i: 0, d: 0, n: 0, e: 0};
+  if (this.birthdate<=-764985600) {
+    value.i++;
+    if (this.measures["0043"].encounter>=1253318400) {
+      value.d++;
+      if (this.measures["0043"].vaccination==true) {
+        value.n++;
+      } else if (false) {
+        value.e++;
+        value.d--;
+      }
+    }
+  }
+  emit(null, value);
+};
+END_OF_MAP_FN
+
+describe QME::MapReduce::Builder do
+  
+  before do
+    raw_measure_json = File.read('measures/0043/0043_NQF_PneumoniaVaccinationStatusForOlderAdults.json')
+    @measure_json = JSON.parse(raw_measure_json)
+    raw_measure_json = File.read('fixtures/complex_measure.json')
+    @complex_measure_json = JSON.parse(raw_measure_json)
+  end
+
+  it 'should extract the measure metadata' do
+    measure = QME::MapReduce::Builder.new(@measure_json, :effective_date=>Time.gm(2010, 9, 19).to_i)
+    measure.id.should eql('0043')
+  end
+  it 'should extract three parameters for measure 0043 (one provided, two calculated)' do
+    time = Time.gm(2010, 9, 19).to_i
+
+    measure = QME::MapReduce::Builder.new(@measure_json, :effective_date=>time)
+    measure.parameters.size.should eql(3)
+    measure.parameters.should have_key(:effective_date)
+    measure.parameters[: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
+  it 'should calculate the calculated dates correctly' do
+    date = Time.gm(2010, 9, 19).to_i
+    measure = QME::MapReduce::Builder.new(@measure_json, :effective_date=>date)
+    measure.parameters[:earliest_encounter].should eql(date-QME::MapReduce::Builder::YEAR_IN_SECONDS)
+  end
+  it 'should produce valid JavaScript expressions for the query components' do
+    date = Time.gm(2010, 9, 19).to_i
+    builder = QME::MapReduce::Builder.new(@measure_json, :effective_date=>date)
+    builder.numerator.should eql('(this.measures["0043"].vaccination==true)')
+    builder.denominator.should eql('(this.measures["0043"].encounter>='+builder.parameters[:earliest_encounter].to_s+')')
+    builder.population.should eql('(this.birthdate<='+builder.parameters[:earliest_birthdate].to_s+')')
+    builder.exception.should eql('(false)')
+    builder.map_function.should eql(MAP_FUNCTION)
+    builder.reduce_function.should eql(QME::MapReduce::Builder::REDUCE_FUNCTION)
+  end
+  it 'should handle logical combinations' do
+    builder = QME::MapReduce::Builder.new(@complex_measure_json, {})
+    builder.population.should eql('((this.measures["0043"].age>17)&&(this.measures["0043"].age<75)&&((this.measures["0043"].sex=="male")||(this.measures["0043"].sex=="female")))')
+  end
+end

data/spec/qme/measures_spec.rb

@@ -0,0 +1,50 @@
+describe QME::MapReduce::Executor do
+
+  before do
+    db_host = nil
+    if ENV['TEST_DB_HOST']
+      db_host = ENV['TEST_DB_HOST']
+    else
+      db_host = 'localhost'
+    end
+    @db = Mongo::Connection.new(db_host, 27017).db('test')
+    @measures = Dir.glob('measures/*')
+  end
+  
+  it 'should produce the expected results for each measure' do
+    print "\n"
+    @measures.each do |dir|
+      # load db with measure and sample patient records
+      files = Dir.glob(File.join(dir,'*.json'))
+      files.size.should eql(1)
+      measure_file = files[0]
+      patient_files = Dir.glob(File.join(dir, 'patients', '*.json'))
+      measure = JSON.parse(File.read(measure_file))
+      measure_id = measure['id']
+      print "Validating measure #{measure_id}"
+      @db.drop_collection('measures')
+      @db.drop_collection('records')
+      measure_collection = @db.create_collection('measures')
+      record_collection = @db.create_collection('records')
+      measure_collection.save(measure)
+      patient_files.each do |patient_file|
+        patient = JSON.parse(File.read(patient_file))
+        record_collection.save(patient)
+      end
+      
+      # load expected results
+      result_file = File.join(dir, 'result', 'result.json')
+      expected = JSON.parse(File.read(result_file))
+      
+      # evaulate measure using Map/Reduce and validate results
+      executor = QME::MapReduce::Executor.new(@db)
+      result = executor.measure_result(measure_id, :effective_date=>Time.gm(2010, 9, 19).to_i)
+      result[:population].should eql(expected['initialPopulation'])
+      result[:numerator].should eql(expected['numerator'])
+      result[:denominator].should eql(expected['denominator'])
+      result[:exceptions].should eql(expected['exclusions'])
+      print " - done\n"
+    end
+  end
+  
+end

data/spec/qme/query/json_document_builder_spec.rb

@@ -0,0 +1,56 @@
+describe QME::Query::JSONDocumentBuilder do
+
+  before do
+    raw_measure_json = File.read('measures/0043/0043_NQF_PneumoniaVaccinationStatusForOlderAdults.json')
+    @measure_json = JSON.parse(raw_measure_json)
+    raw_measure_json = File.read('fixtures/complex_measure.json')
+    @complex_measure_json = JSON.parse(raw_measure_json)
+  end
+
+  it 'should calculate dates for a measure' do
+    jdb = QME::Query::JSONDocumentBuilder.new(@measure_json)
+    jdb.parameters = {:effective_date => 1287685441}
+    jdb.calculate_dates
+    jdb.calculated_dates['earliest_birthdate'].should == -762154559
+  end
+
+  it 'should create a query for a simple measure' do
+    jdb = QME::Query::JSONDocumentBuilder.new(@measure_json, {:effective_date => 1287685441})
+    query_hash = jdb.create_query(@measure_json['denominator'])
+    query_hash.size.should be 1
+    query_hash['measures.0043.encounter'].should_not be_nil
+    query_hash['measures.0043.encounter']['$gte'].should == 1256149441
+  end
+
+  it 'should properly transform a property name' do
+    jdb = QME::Query::JSONDocumentBuilder.new(@measure_json, {:effective_date => 1287685441})
+    jdb.transform_query_property('birthdate').should == 'birthdate'
+    jdb.transform_query_property('foo').should == 'measures.0043.foo'
+  end
+
+  it 'should properly process a query leaf when it is an expression' do
+    jdb = QME::Query::JSONDocumentBuilder.new(@measure_json, {:effective_date => 1287685441})
+    args = {}
+    jdb.process_query({"encounter" => {"_gte" => "@earliest_encounter"}}, args)
+    args.size.should be 1
+    args['measures.0043.encounter'].should_not be_nil
+    args['measures.0043.encounter']['$gte'].should == 1256149441
+  end
+
+  it 'should properly process a query leaf when it is a value' do
+    jdb = QME::Query::JSONDocumentBuilder.new(@measure_json, {:effective_date => 1287685441})
+    args = {}
+    jdb.process_query({"encounter" => 'splat'}, args)
+    args.size.should be 1
+    args['measures.0043.encounter'].should_not be_nil
+    args['measures.0043.encounter'].should == 'splat'
+  end
+
+  it 'should create a query for a complex measure' do
+    jdb = QME::Query::JSONDocumentBuilder.new(@complex_measure_json)
+    query_hash = jdb.create_query(@complex_measure_json['population'])
+    query_hash['measures.0043.age']['$gt'].should == 17
+    query_hash['measures.0043.age']['$lt'].should == 75
+    query_hash['$or'].should have(2).items
+  end
+end

data/spec/schema_spec.rb

@@ -0,0 +1,21 @@
+require 'json'
+
+describe JSON, 'All JSON Schemas' do
+  it 'should conform to JSON Schema' do
+    schema = File.open('schema/schema.json', 'rb'){|f| JSON.parse(f.read)}
+    Dir.glob('schema/*.json').each do |schema_file|
+      if schema_file != 'schema/schema.json' # Don't check the schema itself
+       data = File.open(schema_file, 'rb'){|f| JSON.parse(f.read)}
+       JSON::Schema.validate(data, schema)
+      end
+    end
+  end
+end
+
+describe JSON, 'Result Example' do 
+  it 'should conform to the schema defined' do
+    schema = File.open('schema/result.json', 'rb'){|f| JSON.parse(f.read)}
+    data = File.open('fixtures/result_example.json', 'rb'){|f| JSON.parse(f.read)}
+    JSON::Schema.validate(data, schema)
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,15 @@
+begin
+  # Try to require the preresolved locked set of gems.
+  require File.expand_path('../.bundle/environment', __FILE__)
+rescue LoadError
+  # Fall back on doing an unlocked resolve at runtime.
+  require "rubygems"
+  require "bundler"
+  Bundler.setup
+end
+
+Bundler.require(:default, :test)
+
+PROJECT_ROOT = File.dirname(__FILE__) + '/../'
+
+require PROJECT_ROOT + 'lib/quality_measure_engine'

data/spec/validate_measures_spec.rb

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

metadata

@@ -0,0 +1,221 @@
+--- !ruby/object:Gem::Specification 
+name: quality-measure-engine
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Marc Hadley
+- Andy Gregorowicz
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-10-28 00:00:00 -04:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: mongo
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 1
+        version: "1.1"
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: mongomatic
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        - 5
+        - 8
+        version: 0.5.8
+  type: :runtime
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: therubyracer
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        - 7
+        - 5
+        version: 0.7.5
+  type: :runtime
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: bson_ext
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 1
+        - 1
+        version: 1.1.1
+  type: :runtime
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: jsonschema
+  prerelease: false
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 2
+        - 0
+        - 0
+        version: 2.0.0
+  type: :development
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  prerelease: false
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 2
+        - 0
+        - 0
+        version: 2.0.0
+  type: :development
+  version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: awesome_print
+  prerelease: false
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        - 2
+        - 1
+        version: 0.2.1
+  type: :development
+  version_requirements: *id007
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  prerelease: false
+  requirement: &id008 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 4
+        - 0
+        version: 1.4.0
+  type: :development
+  version_requirements: *id008
+description: A library for extracting quality measure information from HITSP C32's and ASTM CCR's
+email: talk@projectpophealth.org
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README.md
+files: 
+- .gitignore
+- Gemfile
+- Gemfile.lock
+- README.md
+- Rakefile
+- VERSION
+- fixtures/complex_measure.json
+- fixtures/result_example.json
+- lib/patches/v8.rb
+- lib/qme/map/map_reduce_builder.rb
+- lib/qme/map/map_reduce_executor.rb
+- lib/qme/query/json_document_builder.rb
+- lib/quality_measure_engine.rb
+- measures/0032/0032_NQF_Cervical_Cancer_Screening.json
+- measures/0032/patients/denominator1.json
+- measures/0032/patients/denominator2.json
+- measures/0032/patients/numerator1.json
+- measures/0032/patients/population1.json
+- measures/0032/patients/population2.json
+- measures/0032/result/result.json
+- measures/0043/0043_NQF_PneumoniaVaccinationStatusForOlderAdults.json
+- measures/0043/patients/denominator.json
+- measures/0043/patients/numerator.json
+- measures/0043/patients/population.json
+- measures/0043/result/result.json
+- quality-measure-engine.gemspec
+- schema/result.json
+- schema/schema.json
+- spec/qme/map/map_reduce_builder_spec.rb
+- spec/qme/measures_spec.rb
+- spec/qme/query/json_document_builder_spec.rb
+- spec/schema_spec.rb
+- spec/spec_helper.rb
+- spec/validate_measures_spec.rb
+has_rdoc: true
+homepage: http://github.com/pophealth/quality-measure-engine
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: A library for extracting quality measure information from HITSP C32's and ASTM CCR's
+test_files: 
+- spec/qme/map/map_reduce_builder_spec.rb
+- spec/qme/measures_spec.rb
+- spec/qme/query/json_document_builder_spec.rb
+- spec/schema_spec.rb
+- spec/spec_helper.rb
+- spec/validate_measures_spec.rb