quality-measure-engine 0.1.2 → 0.2.0

data/.gitignore

@@ -1,6 +0,0 @@
-.bundle
-*.DS_Store
-vendor
-nbproject
-pkg
-.redcar

data/Gemfile.lock

@@ -1,44 +0,0 @@
-GEM
-  remote: http://rubygems.org/
-  specs:
-    awesome_print (0.2.1)
-    bson (1.1)
-    bson_ext (1.1.1)
-    diff-lcs (1.1.2)
-    gemcutter (0.6.1)
-    git (1.2.5)
-    jeweler (1.4.0)
-      gemcutter (>= 0.1.0)
-      git (>= 1.2.5)
-      rubyforge (>= 2.0.0)
-    json_pure (1.4.6)
-    jsonschema (2.0.0)
-    mongo (1.1)
-      bson (>= 1.0.5)
-    rake (0.8.7)
-    rspec (2.0.0)
-      rspec-core (= 2.0.0)
-      rspec-expectations (= 2.0.0)
-      rspec-mocks (= 2.0.0)
-    rspec-core (2.0.0)
-    rspec-expectations (2.0.0)
-      diff-lcs (>= 1.1.2)
-    rspec-mocks (2.0.0)
-      rspec-core (= 2.0.0)
-      rspec-expectations (= 2.0.0)
-    rubyforge (2.0.4)
-      json_pure (>= 1.1.7)
-    therubyracer (0.7.5)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  awesome_print
-  bson_ext
-  jeweler
-  jsonschema
-  mongo
-  rake
-  rspec
-  therubyracer

data/fixtures/complex_measure.json

@@ -1,36 +0,0 @@
-{
-  "id": "0043",
-  "name": "Pneumonia Vaccination Status for Older Adults",
-  "steward": "NCQA",
-  "population": {
-    "and": [
-      {
-        "category": "Patient Characteristic",
-        "title": "Age > 17 before measure period",
-        "query": {"age": {"_gt": 17}}
-      },
-      {
-        "category": "Patient Characteristic",
-        "title": "Age < 75 before measure period",
-        "query": {"age": {"_lt": 75}}
-      },
-      {
-        "or": [
-          {
-            "category": "Patient Characteristic",
-            "title": "Male",
-            "query": {"sex": "male"}
-          },
-          {
-            "category": "Patient Characteristic",
-            "title": "Female",
-            "query": {"sex": "female"}
-          }
-        ]
-      }
-    ]
-  },
-  "denominator": {},
-  "numerator": {},
-  "exception": {}
-}

data/fixtures/result_example.json

@@ -1,6 +0,0 @@
-{
-  "initialPopulation": 50,
-  "denominator": 45,
-  "numerator": [35],
-  "exclusions": [5]
-}

data/lib/patches/v8.rb

@@ -1,20 +0,0 @@
-# Patching V8::Object because it is the entry point for conversions
-# between Ruby and JavaScript types. We are using seconds since the
-# epoch to represent dates. On 32 bit architectures, for recent dates
-# this will be too large for Fixnum and become a Bignum. Ruby Racer
-# worn't properly convert a Bignum to JavaScript, but it will work
-# just fine for a Float. Because of this, we will convert all Bignums
-# passed into a JavaScript context to a Float
-module V8
-  class Object
-    alias :old_index_setter :'[]='
-    
-    def []=(key, value)
-      if value.kind_of?(Bignum)
-        old_index_setter(key, value.to_f)
-      else
-        old_index_setter(key, value)
-      end
-    end
-  end
-end

data/lib/qme/query/json_document_builder.rb

@@ -1,130 +0,0 @@
-module QME
-  module Query
-    class JSONDocumentBuilder
-      attr_accessor :parameters, :calculated_dates
-
-      # Creates the JSONDocumentBuilder. Will calculate dates if parameters
-      # are passed in.
-      def initialize(measure_json, parameters={})
-        @measure_json = measure_json
-        @parameters = parameters
-        @measure_id = measure_json['id']
-
-        if ! parameters.empty?
-          calculate_dates
-        end
-      end
-
-      # Calculates all dates necessary to create a query for this measure
-      # This will be run by the constructor if params were passed in
-      def calculate_dates
-        @calculated_dates = {}
-        
-        ctx = V8::Context.new        
-        @parameters.each_pair do |key, value|
-          ctx[key] = value
-          @calculated_dates[key] = value
-        end
-
-        ctx['year'] = 365 * 24 * 60 * 60 # TODO: Replace this with a js file that has all constants
-
-        @measure_json["calculated_dates"].each_pair do |key, value|
-          @calculated_dates[key] = ctx.eval(value)
-        end
-      end
-
-      def numerator_query
-        create_query(@measure_json['numerator']).merge(denominator_query)
-      end
-      
-      def denominator_query
-        create_query(@measure_json['denominator']).merge(initial_population_query)
-      end
-      
-      def initial_population_query
-        create_query(@measure_json['population'])
-      end
-      
-      def exclusions_query
-        create_query(@measure_json['exception'])
-      end
-
-      # Creates the appropriate JSON document to query MongoDB based on
-      # a measure definition passed in. This method calls itself recursively
-      # to walk the tree and get all possible logical operators available
-      # in a measure definition
-      def create_query(definition_json, args={})
-        if definition_json.has_key?('and')
-          definition_json['and'].each do |operand|
-            create_query(operand, args)
-          end
-        elsif definition_json.has_key?('or')
-          operands = []
-          definition_json['or'].each do |operand|
-            operands << create_query(operand)
-          end
-          if args['$or']
-            args['$ne'] = {'$or' => operands}
-          else
-            args['$or'] = operands
-          end
-        elsif definition_json.has_key?('query')
-          process_query(definition_json['query'], args)
-        end
-
-        args
-      end
-
-      # Called by create_query to process leaf nodes in a measure
-      # definition
-      def process_query(definition_json, args)
-        if definition_json.size > 1
-          raise 'A query should have only one property'
-        end
-
-        query_property = definition_json.keys.first
-        document_key = transform_query_property(query_property)
-        document_value = nil
-        query_value = definition_json[query_property]
-        if query_value.kind_of?(Hash)
-          if query_value.size > 1
-            raise 'A query value should only have one property'
-          end
-
-          document_value = {query_value.keys.first.gsub('_', '$') =>
-                            substitute_variables(query_value.values.first)}
-          if args[document_key]
-            args[document_key].merge!(document_value)
-          else
-            args[document_key] = document_value
-          end
-        else
-          document_value = substitute_variables(query_value)
-          args[document_key] = document_value
-        end
-      end
-      
-      # Takes a query property name and transforms it into
-      # a name of a key in a MongoDB document
-      def transform_query_property(property_name)
-        #TODO What do we do with special case fields - the stuff we are keeping at the patient level?
-        if ['birthdate'].include?(property_name)
-          property_name
-        else
-          "measures.#{@measure_id}.#{property_name}"
-        end
-      end
-
-      # Finds strings that start with "@" and replaces them
-      # with the calculated date
-      def substitute_variables(value)
-        if value.kind_of?(String) && value[0] == '@'
-          variable_name = value[1..-1]
-          @calculated_dates[variable_name]
-        else
-          value
-        end
-      end
-    end
-  end
-end

data/lib/qme/query/json_query_executor.rb

@@ -1,44 +0,0 @@
-module QME
-  module Query
-    class JsonQueryExecutor
-      def initialize(db)
-        @db = db
-      end
-
-      def measure_def(measure_id)
-        measures = @db.collection('measures')
-        measures.find({'id'=> "#{measure_id}"}).to_a[0]
-      end
-
-      def measure_result(measure_id, parameter_values)
-        jdb = JSONDocumentBuilder.new(measure_def(measure_id),
-                                      parameter_values)
-
-        collection = @db.collection('records')
-        result = {}
-        
-        collection.find(jdb.numerator_query) do |cursor|
-          result[:numerator] = cursor.count
-        end
-        
-        collection.find(jdb.denominator_query) do |cursor|
-          result[:denominator] = cursor.count
-        end
-        collection.find(jdb.initial_population_query) do |cursor|
-          result[:population] = cursor.count
-        end
-        
-        exclusions_query = jdb.exclusions_query
-        if exclusions_query.empty?
-          result[:exceptions] = 0
-        else
-          collection.find(exclusions_query) do |cursor|
-            result[:exceptions] = cursor.count
-          end
-        end
-        
-        result
-      end
-    end
-  end
-end

data/measures/0032/0032_NQF_Cervical_Cancer_Screening.json

@@ -1,171 +0,0 @@
-{
-  "id": "0032",
-  "name": "Cervical Cancer Screening",
-  "steward": "NCQA",
-  "parameters": {
-    "effective_date": {
-      "name": "Effective end date for measure",
-      "type": "long"
-    }
-  },
-  "properties": {
-    "birthdate": {
-      "name": "Date of birth",
-      "type": "long",
-      "codes": [
-        {
-          "set": "HL7",
-          "version": "3.0",
-          "values": ["00110"]
-        }
-      ]
-    },
-    "encounter_outpatient": {
-      "name": "Date of outpatient encounter",
-      "type": "long",
-      "codes": [
-        {
-          "set": "CPT",
-          "version": "06/2009",
-          "values": ["99201", "99202", "99203", "99204", "99205", "99211", "99212", "99213", "99214", "99215", "99217", "99218", "99219", "99220", "99241", "99242", "99243", "99244", "99245", "99341", "99342", "99343", "99344", "99345", "99347-99350", "99384", "99385", "99386", "99387", "99394", "99395", "99396", "99397", "99401", "99402", "99403", "99404", "99411", "99412", "99420", "99429", "99455", "99456"]
-        },
-        {
-          "set": "ICD-9-CM",
-          "version": "06/2009",
-          "values": ["V70.0", "V70.3", "V70.5", "V70.6", "V70.8", "V70.9"]
-        }
-      ]
-    },
-    "encounter_obgyn": {
-      "name": "Date of ObGyn encounter",
-      "type": "long",
-      "codes": [
-        {
-          "set": "ICD-9-CM",
-          "version": "06/2009",
-          "values": ["V24", "V25", "V26", "V27", "V28", "V45.5", "V61.5", "V61.6", "V61.7", "V69.2", "V72.3", "V72.4"]
-        }
-      ]
-    },
-    "hysterectomy": {
-      "name": "Hysterectomy performed",
-      "type": "long",
-      "codes": [
-        {
-          "set": "CPT",
-          "version": "06/2009",
-          "values": ["51925", "56308", "58150", "58152", "58200", "58210", "58240", "58260", "58262", "58263", "58267", "58270", "58275", "58280", "58285", "58290", "58291", "58292", "58293", "58294", "58550", "58552", "58553", "58554", "58570", "58571", "58572", "58573", "58951", "58953", "58954", "58956", "59135"]
-        },
-        {
-          "set": "ICD-9-CM",
-          "version": "06/2009",
-          "values": ["618.5", "68.4", "68.41", "68.49", "68.5", "68.51", "68.59", "68.6", "68.61", "68.69", "68.7", "68.71", "68.79", "68.8", "V67.01", "V76.47", "V88.01", "V88.03"]
-        },
-        {
-          "set": "ICD-10-CM",
-          "version": "06/2009",
-          "values": ["N81.81", "Z12.72", "Z90.71", "Z90.710", "Z90.7112"]
-        },
-        {
-          "set": "SNOMED-CT",
-          "version": "07/2009",
-          "values": ["116140006", "116142003", "116143008", "116144002", "236886002", "236888001", "236891001", "27950001", "307771009", "31545000", "35955002", "361222003", "361223008", "414575003", "59750000", "79095000", "86477000", "88144003"]
-        }
-      ]
-    },
-    "pap_test": {
-      "name": "Pap test",
-      "type": "long",
-      "codes": [
-        {
-          "set": "CPT",
-          "version": "06/2009",
-          "values": ["88141", "88142", "88143", "88147", "88148", "88150", "88152", "88153", "88154", "88155", "88164", "88165", "88166", "88167", "88174", "88175"]
-        },
-        {
-          "set": "HCPCS",
-          "version": "06/2009",
-          "values": ["G0123", "G0124", "G0141", "G0143", "G0144", "G0145", "G0147", "G0148", "P3000", "P3001", "Q0091"]
-        },
-        {
-          "set": "ICD-10-CM",
-          "version": "06/2009",
-          "values": ["Z12.4", "Z12.72"]
-        },
-        {
-          "set": "ICD-9-CM",
-          "version": "06/2009",
-          "values": ["91.46", "V72.32"]
-        },
-        {
-          "set": "LOINC",
-          "version": "06/2009",
-          "values": ["10524-7", "18500-9", "19762-4", "19764-0", "19765-7", "19766-5", "19774-9", "33717-0", "47527-7", "47528-5"]
-        },
-        {
-          "set": "SNOMED-CT",
-          "version": "07/2009",
-          "values": ["439958008", "440615002", "440623000"]
-        }
-      ]
-    }
-  },
-  "calculated_dates": {
-    "earliest_birthdate": "effective_date - 64*year",
-    "latest_birthdate": "effective_date - 23*year",
-    "earliest_encounter": "effective_date - 2*year",
-    "earliest_pap": "effective_date - 3*year"
-  },
-  "population": {
-    "and": [
-      {
-        "category": "Patient Characteristic",
-        "title": "Age >= 23 before measure period",
-        "query": {"birthdate": {"_lte": "@latest_birthdate"}}
-      },
-      {
-        "category": "Patient Characteristic",
-        "title": "Age <= 64 before measure period",
-        "query": {"birthdate": {"_gte": "@earliest_birthdate"}}
-      }
-    ]
-  },
-  "denominator": {
-    "and": [
-      {
-        "or": [
-          {
-            "category": "Outpatient Encounter",
-            "title": "Outpatient encounter within last three years",
-            "query": {"encounter_outpatient": {"_gte": "@earliest_encounter"}}
-          },
-          {
-            "category": "ObGyn Encounter",
-            "title": "ObGyn encounter within last three years",
-            "query": {"encounter_obgyn": {"_gte": "@earliest_encounter"}}
-          }
-        ]
-      },
-      {
-        "or": [
-          {
-            "category": "Procedure not performed",
-            "title": "Hysterectomy",
-            "query": {"hysterectomy": null}
-          },
-          {
-            "category": "Procedure performed",
-            "title": "Hysterectomy after effective date",
-            "query": {"hysterectomy": {"_gte": "@effective_date"}}
-          }
-        ]
-      }
-    ]
-  },
-  "numerator": {
-    "category": "Laboratory test result",
-    "title": "Pap test",
-    "query": {"pap_test": {"_gte": "@earliest_pap"}}
-  },
-  "exception": {}
-}