quality-measure-engine 0.1.2 → 0.2.0

data/lib/qme_test.rb

@@ -0,0 +1,13 @@
+require 'rspec/core/rake_task'
+Dir[File.join(File.dirname(__FILE__),'tasks/*.rake')].sort.each do |ext|
+  load ext
+end
+
+RSpec::Core::RakeTask.new do |t|
+  t.rspec_opts = ["-c", "-f progress", "-r #{File.join(File.dirname(__FILE__),'../spec/spec_helper.rb')}"]
+  t.pattern = "#{File.join(File.dirname(__FILE__),'../spec/**/*measures_spec.rb')}"
+end
+
+RSpec::Core::RakeTask.new do |t|
+  t.rspec_opts = ["-c", "-f progress", "-r #{File.join(File.dirname(__FILE__),'../spec/spec_helper.rb')}"]
+end

data/lib/quality-measure-engine.rb

@@ -2,12 +2,28 @@ Bundler.require(:default)
 
 LIB = File.dirname(__FILE__)
 
-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 LIB + '/qme/randomizer/patient_randomizer'
+
+require 'singleton'
+
+require LIB + '/qme/importer/entry'
+require LIB + '/qme/importer/property_matcher'
+require LIB + '/qme/importer/patient_importer'
+require LIB + '/qme/importer/code_system_helper'
+require LIB + '/qme/importer/hl7_helper'
+
+require LIB + '/qme/importer/section_importer'
+require LIB + '/qme/importer/generic_importer'
+
+require LIB + '/qme/mongo_helpers'
 
 require 'json'
 require 'mongo'
+require 'nokogiri'
+
+require LIB + '/qme/measure/measure_loader'
+require LIB + '/qme/measure/database_loader'
+

data/lib/tasks/measure.rake

@@ -0,0 +1,76 @@
+path = File.dirname(__FILE__)
+path = path.index('lib') == 0 ? "./#{path}" : path
+require 'json'
+require 'zlib'
+gem 'rubyzip'
+require 'zip/zip'
+require 'zip/zipfilesystem'
+
+
+require File.join(path,'../quality-measure-engine')
+
+
+measures_dir = ENV['MEASURE_DIR'] || 'measures'
+puts "Loading measures from #{measures_dir}"
+
+bundle_dir = ENV['BUNDLE_DIR'] || './'
+namespace :measures do
+  
+  desc 'Build all measures to tmp directory'
+  task :build do
+    dest_dir = File.join('.', 'tmp')
+    Dir.mkdir(dest_dir) if !Dir.exist?(dest_dir)
+    Dir.glob(File.join(measures_dir, '*')).each do |measure_dir|
+      measures = QME::Measure::Loader.load_measure(measure_dir)
+      measures.each do |measure|
+        id = measure['id']
+        sub_id = measure['sub_id']
+        json = JSON.pretty_generate(measure)
+        file_name = File.join(dest_dir, "#{id}#{sub_id}.json")
+        file = File.new(file_name,  "w")
+        file.write(json)
+        file.close
+      end
+    end
+  end
+  
+  
+  
+  desc "run the map_test tool"
+  task :map_tool do
+    require File.join(path,"../../map_test/map_test.rb")
+  end
+  
+  
+  desc "bundle measures into a compressed file for deployment"
+  task :bundle do
+    
+      md = File.join(bundle_dir,measures_dir)
+      js = File.join(bundle_dir,'js')
+      bf = File.join(bundle_dir,'bundle.js')
+      
+      tmp = './tmp'
+      bundle_tmp = File.join(tmp,'bundle')
+      
+      md.sub!(%r[/$],'')
+      FileUtils.rm bundle_tmp, :force=>true
+      FileUtils.mkdir_p(bundle_tmp)
+      archive = File.join(tmp,'bundle.zip')
+      FileUtils.rm archive, :force=>true
+     
+       Zip::ZipFile.open(archive, 'w') do |zipfile|
+          Dir["#{md}/**/**"].reject{|f|f==archive}.each do |file|
+           zipfile.add(file.sub(bundle_dir,''),file)
+          end
+                
+          Dir["#{js}/**/**"].reject{|f|f==archive}.each do |file|
+             zipfile.add(file.sub(bundle_dir,''),file)
+          end
+           
+         if File.exists?(bf)
+           zipfile.add(bf.sub(bundle_dir,''),bf)
+         end
+       end
+  end
+
+end

data/lib/tasks/mongo.rake

@@ -0,0 +1,74 @@
+path = File.dirname(__FILE__)
+path = path.index('lib') == 0 ? "./#{path}" : path
+require 'mongo'
+require 'json'
+require File.join(path,'../quality-measure-engine')
+
+measures_dir = ENV['MEASURE_DIR'] || 'measures'
+bundle_dir = ENV['BUNDLE_DIR'] || '.'
+fixtures_dir = ENV['FIXTURE_DIR'] || File.join('fixtures', 'measures')
+db_name = ENV['DB_NAME'] || 'test'
+loader = QME::Database::Loader.new(db_name)
+
+namespace :mongo do
+
+  desc 'Removed cached measure results'
+  task :drop_cache do
+    loader.drop_collection('query_cache')
+  end
+  
+  desc 'Remove the patient records collection'
+  task :drop_records => :drop_cache do
+    loader.drop_collection('records')
+  end
+
+  desc 'Remove the measures and bundles collection'
+  task :drop_bundle => :drop_measures  do
+    loader.drop_collection('bundles')
+  end
+  
+  desc 'Remove the measures collection'
+  task :drop_measures => :drop_cache do
+    loader.drop_collection('measures')
+  end
+  
+  desc 'Remove all measures and reload'
+  task :reload_measures => :drop_measures do
+    Dir.glob(File.join(measures_dir, '*')).each do |measure_dir|
+      loader.save_measure(measure_dir, 'measures')
+    end
+  end
+  
+  desc 'Remove all patient records and reload'
+  task :reload_records => :drop_records do
+    load_files(loader, File.join(fixtures_dir,'*','patients','*.json'), 'records')
+  end
+
+  desc 'Remove all patient records and reload'
+  task :reload_bundle => [:drop_bundle] do
+   loader.save_bundle(bundle_dir,'bundles')
+  end
+  
+  desc 'Clear database and road each measure and its sample patient files'
+  task :reload => [:reload_records, :reload_measures]
+  
+  desc 'Seed the query cache by calculating the results for all measures'
+  task :seed_cache, [:year, :month, :day] do |t, args|
+    year = args.year.to_i>0 ? args.year.to_i : 2010
+    month = args.month.to_i>0 ? args.month.to_i : 9
+    day = args.day.to_i>0 ? args.day.to_i : 19
+    map = QME::MapReduce::Executor.new(loader.get_db)
+    map.all_measures.each_value do |measure_def|
+      result = map.measure_result(measure_def['id'], measure_def['sub_id'], :effective_date=>Time.gm(year, month, day).to_i)
+      puts "#{measure_def['id']}#{measure_def['sub_id']}: p#{result[:population]}, d#{result[:denominator]}, n#{result[:numerator]}, e#{result[:exclusions]}"
+    end
+  end
+  
+  def load_files(loader, file_pattern, collection_name)
+    Dir.glob(file_pattern).each do |file|
+      json = JSON.parse(File.read(file))
+      loader.save(collection_name, json)
+    end
+  end
+  
+end

data/lib/tasks/patient_random.rake

@@ -0,0 +1,46 @@
+path = File.dirname(__FILE__)
+path = path.index('lib') == 0 ? "./#{path}" : path
+require 'mongo'
+require 'json'
+require File.join(path,'../quality-measure-engine')
+
+patient_template_dir = ENV['PATIENT_TEMPLATE_DIR'] || File.join('fixtures', 'patient_templates')
+db_name = ENV['DB_NAME'] || 'test'
+loader = QME::Database::Loader.new(db_name)
+
+namespace :patient do
+
+  desc 'Generate n (default 10) random patient records and save them in the database'
+  task :random, [:n] => ['mongo:drop_records', 'mongo:reload_measures'] do |t, args|
+    n = args.n.to_i>0 ? args.n.to_i : 1
+    
+    templates = []
+    Dir.glob(File.join(patient_template_dir, '*.json.erb')).each do |file|
+      templates << File.read(file)
+    end
+    
+    if templates.length<1
+      puts "No patient templates in #{patient_template_dir}"
+      return
+    end
+    
+    map = QME::MapReduce::Executor.new(loader.get_db)
+    processed_measures = {}
+    map.all_measures.each_value do |measure_def|
+      measure_id = measure_def['id']
+      if !processed_measures[measure_id]
+        QME::Importer::PatientImporter.instance.add_measure(measure_id, QME::Importer::GenericImporter.new(measure_def))
+        processed_measures[measure_id]=true
+      end
+    end
+
+    n.times do
+      template = templates[rand(templates.length)]
+      generator = QME::Randomizer::Patient.new(template)
+      json = JSON.parse(generator.get())
+      patient_record = QME::Importer::PatientImporter.instance.parse_hash(json)
+      loader.save('records', patient_record)
+    end
+  end
+    
+end

metadata

@@ -1,192 +1,146 @@
 --- !ruby/object:Gem::Specification 
 name: quality-measure-engine
 version: !ruby/object:Gem::Version 
-  prerelease: false
-  segments: 
-  - 0
-  - 1
-  - 2
-  version: 0.1.2
+  prerelease: 
+  version: 0.2.0
 platform: ruby
 authors: 
-- Marc Hadley
-- Andy Gregorowicz
+  - Marc Hadley
+  - Andy Gregorowicz
+  - Rob Dingwell
 autorequire: 
 bindir: bin
 cert_chain: []
 
-date: 2010-11-01 00:00:00 -04:00
+date: 2011-02-23 00:00:00 -05:00
 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: therubyracer
-  prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 7
-        - 5
-        version: 0.7.5
-  type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: jsonschema
-  prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 2
-        - 0
-        - 0
-        version: 2.0.0
-  type: :development
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: rspec
-  prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 2
-        - 0
-        - 0
-        version: 2.0.0
-  type: :development
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: awesome_print
-  prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 2
-        - 1
-        version: 0.2.1
-  type: :development
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: jeweler
-  prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 4
-        - 0
-        version: 1.4.0
-  type: :development
-  version_requirements: *id006
+  - !ruby/object:Gem::Dependency 
+    name: mongo
+    prerelease: false
+    requirement: &id001 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ~>
+          - !ruby/object:Gem::Version 
+            version: "1.2"
+    type: :runtime
+    version_requirements: *id001
+  - !ruby/object:Gem::Dependency 
+    name: rubyzip
+    prerelease: false
+    requirement: &id002 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ~>
+          - !ruby/object:Gem::Version 
+            version: 0.9.4
+    type: :runtime
+    version_requirements: *id002
+  - !ruby/object:Gem::Dependency 
+    name: nokogiri
+    prerelease: false
+    requirement: &id003 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ~>
+          - !ruby/object:Gem::Version 
+            version: 1.4.4
+    type: :runtime
+    version_requirements: *id003
+  - !ruby/object:Gem::Dependency 
+    name: jsonschema
+    prerelease: false
+    requirement: &id004 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ~>
+          - !ruby/object:Gem::Version 
+            version: 2.0.0
+    type: :development
+    version_requirements: *id004
+  - !ruby/object:Gem::Dependency 
+    name: rspec
+    prerelease: false
+    requirement: &id005 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ~>
+          - !ruby/object:Gem::Version 
+            version: 2.5.0
+    type: :development
+    version_requirements: *id005
+  - !ruby/object:Gem::Dependency 
+    name: awesome_print
+    prerelease: false
+    requirement: &id006 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ~>
+          - !ruby/object:Gem::Version 
+            version: 0.2.1
+    type: :development
+    version_requirements: *id006
 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
+extra_rdoc_files: []
+
 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/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
-- 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
+  - lib/qme_test.rb
+  - lib/quality-measure-engine.rb
+  - lib/qme/mongo_helpers.rb
+  - lib/qme/importer/code_system_helper.rb
+  - lib/qme/importer/entry.rb
+  - lib/qme/importer/generic_importer.rb
+  - lib/qme/importer/hl7_helper.rb
+  - lib/qme/importer/patient_importer.rb
+  - lib/qme/importer/property_matcher.rb
+  - lib/qme/importer/section_importer.rb
+  - lib/qme/map/map_reduce_builder.rb
+  - lib/qme/map/map_reduce_executor.rb
+  - lib/qme/measure/database_loader.rb
+  - lib/qme/measure/measure_loader.rb
+  - lib/qme/randomizer/patient_randomizer.rb
+  - lib/tasks/measure.rake
+  - lib/tasks/mongo.rake
+  - lib/tasks/patient_random.rake
+  - js/map-reduce-utils.js
+  - js/underscore-min.js
+  - Gemfile
+  - README.md
+  - Rakefile
+  - VERSION
 has_rdoc: true
 homepage: http://github.com/pophealth/quality-measure-engine
 licenses: []
 
 post_install_message: 
-rdoc_options: 
-- --charset=UTF-8
+rdoc_options: []
+
 require_paths: 
-- lib
+  - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.5.0
 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
+test_files: []
+