quality-measure-engine 0.1.0 → 0.1.1

data/Gemfile

@@ -1,7 +1,6 @@
 source :gemcutter
 
 gem 'mongo'
-gem 'mongomatic'
 gem 'bson_ext'
 gem 'rake'
 gem 'therubyracer', :require => 'v8'

data/Gemfile.lock

@@ -1,7 +1,6 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activesupport (3.0.1)
     awesome_print (0.2.1)
     bson (1.1)
     bson_ext (1.1.1)
@@ -16,10 +15,6 @@ GEM
     jsonschema (2.0.0)
     mongo (1.1)
       bson (>= 1.0.5)
-    mongomatic (0.5.8)
-      activesupport (>= 2.3.5)
-      bson (= 1.1)
-      mongo (= 1.1)
     rake (0.8.7)
     rspec (2.0.0)
       rspec-core (= 2.0.0)
@@ -44,7 +39,6 @@ DEPENDENCIES
   jeweler
   jsonschema
   mongo
-  mongomatic
   rake
   rspec
   therubyracer

data/Rakefile

@@ -15,12 +15,42 @@ Jeweler::Tasks.new do |gem|
   gem.authors = ["Marc Hadley", "Andy Gregorowicz"]
   
   gem.add_dependency 'mongo', '~> 1.1'
-  gem.add_dependency 'mongomatic', '~> 0.5.8'
   gem.add_dependency 'therubyracer', '~> 0.7.5'
-  gem.add_dependency 'bson_ext', '~> 1.1.1'
   
   gem.add_development_dependency "jsonschema", "~> 2.0.0"
   gem.add_development_dependency "rspec", "~> 2.0.0"
   gem.add_development_dependency "awesome_print", "~> 0.2.1"
   gem.add_development_dependency "jeweler", "~> 1.4.0"
 end
+
+desc 'Load all the measures and sample patient files into the database'
+task :loaddb do
+  require './spec/spec_helper'
+  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')
+  
+  db.drop_collection('measures')
+  db.drop_collection('records')
+
+  measures = Dir.glob('measures/*')
+  measures.each do |dir|
+    # load db with measure and sample patient records
+    files = Dir.glob(File.join(dir,'*.json'))
+    measure_file = files[0]
+    patient_files = Dir.glob(File.join(dir, 'patients', '*.json'))
+    measure = JSON.parse(File.read(measure_file))
+    measure_id = measure['id']
+    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
+  end
+end

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/lib/qme/query/json_document_builder.rb

@@ -18,14 +18,16 @@ module QME
       # 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
-        ctx = V8::Context.new
+        @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
 
-        @calculated_dates = {}
         @measure_json["calculated_dates"].each_pair do |key, value|
           @calculated_dates[key] = ctx.eval(value)
         end
@@ -61,7 +63,11 @@ module QME
           definition_json['or'].each do |operand|
             operands << create_query(operand)
           end
-          args['$or'] = operands
+          if args['$or']
+            args['$ne'] = {'$or' => operands}
+          else
+            args['$or'] = operands
+          end
         elsif definition_json.has_key?('query')
           process_query(definition_json['query'], args)
         end

data/lib/qme/query/json_query_executor.rb

@@ -0,0 +1,44 @@
+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/lib/{quality_measure_engine.rb → quality-measure-engine.rb}

@@ -5,7 +5,7 @@ require LIB + '/patches/v8'
 require LIB + '/qme/map/map_reduce_builder'
 require LIB + '/qme/map/map_reduce_executor'
 require LIB + '/qme/query/json_document_builder'
-
+require LIB + '/qme/query/json_query_executor'
 
 require 'json'
 require 'mongo'

data/measures/0032/0032_NQF_Cervical_Cancer_Screening.json

@@ -149,8 +149,8 @@
       {
         "or": [
           {
-            "category": "Procedure performed",
-            "title": "No hysterectomy",
+            "category": "Procedure not performed",
+            "title": "Hysterectomy",
             "query": {"hysterectomy": null}
           },
           {
@@ -163,8 +163,8 @@
     ]
   },
   "numerator": {
-    "category": "Medication Administered",
-    "title": "Pneumococcal vaccination",
+    "category": "Laboratory test result",
+    "title": "Pap test",
     "query": {"pap_test": {"_gte": "@earliest_pap"}}
   },
   "exception": {}

data/quality-measure-engine.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{quality-measure-engine}
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Marc Hadley", "Andy Gregorowicz"]
-  s.date = %q{2010-10-28}
+  s.date = %q{2010-10-29}
   s.description = %q{A library for extracting quality measure information from HITSP C32's and ASTM CCR's}
   s.email = %q{talk@projectpophealth.org}
   s.extra_rdoc_files = [
@@ -28,7 +28,8 @@ Gem::Specification.new do |s|
      "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",
+     "lib/qme/query/json_query_executor.rb",
+     "lib/quality-measure-engine.rb",
      "measures/0032/0032_NQF_Cervical_Cancer_Screening.json",
      "measures/0032/patients/denominator1.json",
      "measures/0032/patients/denominator2.json",
@@ -71,18 +72,14 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<mongo>, ["~> 1.1"])
-      s.add_runtime_dependency(%q<mongomatic>, ["~> 0.5.8"])
       s.add_runtime_dependency(%q<therubyracer>, ["~> 0.7.5"])
-      s.add_runtime_dependency(%q<bson_ext>, ["~> 1.1.1"])
       s.add_development_dependency(%q<jsonschema>, ["~> 2.0.0"])
       s.add_development_dependency(%q<rspec>, ["~> 2.0.0"])
       s.add_development_dependency(%q<awesome_print>, ["~> 0.2.1"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.4.0"])
     else
       s.add_dependency(%q<mongo>, ["~> 1.1"])
-      s.add_dependency(%q<mongomatic>, ["~> 0.5.8"])
       s.add_dependency(%q<therubyracer>, ["~> 0.7.5"])
-      s.add_dependency(%q<bson_ext>, ["~> 1.1.1"])
       s.add_dependency(%q<jsonschema>, ["~> 2.0.0"])
       s.add_dependency(%q<rspec>, ["~> 2.0.0"])
       s.add_dependency(%q<awesome_print>, ["~> 0.2.1"])
@@ -90,9 +87,7 @@ Gem::Specification.new do |s|
     end
   else
     s.add_dependency(%q<mongo>, ["~> 1.1"])
-    s.add_dependency(%q<mongomatic>, ["~> 0.5.8"])
     s.add_dependency(%q<therubyracer>, ["~> 0.7.5"])
-    s.add_dependency(%q<bson_ext>, ["~> 1.1.1"])
     s.add_dependency(%q<jsonschema>, ["~> 2.0.0"])
     s.add_dependency(%q<rspec>, ["~> 2.0.0"])
     s.add_dependency(%q<awesome_print>, ["~> 0.2.1"])

data/spec/spec_helper.rb

@@ -12,4 +12,4 @@ Bundler.require(:default, :test)
 
 PROJECT_ROOT = File.dirname(__FILE__) + '/../'
 
-require PROJECT_ROOT + 'lib/quality_measure_engine'
+require PROJECT_ROOT + 'lib/quality-measure-engine'

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 0
-  version: 0.1.0
+  - 1
+  version: 0.1.1
 platform: ruby
 authors: 
 - Marc Hadley
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-10-28 00:00:00 -04:00
+date: 2010-10-29 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -32,25 +32,10 @@ dependencies:
         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 
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -61,26 +46,11 @@ dependencies:
         - 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
+  version_requirements: *id002
 - !ruby/object:Gem::Dependency 
   name: jsonschema
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -91,11 +61,11 @@ dependencies:
         - 0
         version: 2.0.0
   type: :development
-  version_requirements: *id005
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: rspec
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -106,11 +76,11 @@ dependencies:
         - 0
         version: 2.0.0
   type: :development
-  version_requirements: *id006
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: awesome_print
   prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -121,11 +91,11 @@ dependencies:
         - 1
         version: 0.2.1
   type: :development
-  version_requirements: *id007
+  version_requirements: *id005
 - !ruby/object:Gem::Dependency 
   name: jeweler
   prerelease: false
-  requirement: &id008 !ruby/object:Gem::Requirement 
+  requirement: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -136,7 +106,7 @@ dependencies:
         - 0
         version: 1.4.0
   type: :development
-  version_requirements: *id008
+  version_requirements: *id006
 description: A library for extracting quality measure information from HITSP C32's and ASTM CCR's
 email: talk@projectpophealth.org
 executables: []
@@ -158,7 +128,8 @@ files:
 - 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
+- lib/qme/query/json_query_executor.rb
+- lib/quality-measure-engine.rb
 - measures/0032/0032_NQF_Cervical_Cancer_Screening.json
 - measures/0032/patients/denominator1.json
 - measures/0032/patients/denominator2.json