quality-measure-engine 1.1.5 → 2.0.0

data/.gitignore

@@ -0,0 +1,12 @@
+.bundle
+*.DS_Store
+vendor
+nbproject
+pkg
+.redcar
+doc
+.yardoc
+coverage*
+tmp*
+dump.rdb
+

data/.travis.yml

@@ -0,0 +1,16 @@
+language: ruby
+rvm:
+  - 1.9.3
+script: bundle exec rake spec
+services:
+  - mongodb
+notifications:
+  email:
+    recipients:
+      - healthcare-ci@googlegroups.com
+    on_failure: change
+
+branches: 
+  only:
+    - master
+    - develop

data/Gemfile

@@ -1,23 +1,7 @@
-source "http://rubygems.org"
+source 'https://rubygems.org'
 
-gemspec :development_group => :test
+# Specify your gem's dependencies in quality-measure-engine.gemspec
+gemspec
 
-gem 'mongo', '1.5.1'
-gem 'bson_ext', '1.5.1',  :platforms => :mri
-gem 'rake'
-#gem 'pry', :require => true
-#gem 'health-data-standards', :git => 'https://github.com/projectcypress/health-data-standards.git', :branch => 'develop'
-gem 'health-data-standards', '1.0.1'
-
-# does not work with redis 3.0
-gem 'redis', '~> 2.2.2'
-
-group :test do
-  gem 'cover_me', '>= 1.0.0.rc5', :platforms => :ruby_19
-  gem 'sinatra'
-end
-
-group :build do
-  gem 'yard'
-  gem 'kramdown' # needed by yard
-end
+gem 'pry'
+gem 'pry-nav'

data/Gemfile.lock

@@ -0,0 +1,126 @@
+PATH
+  remote: .
+  specs:
+    quality-measure-engine (2.0.0)
+      delayed_job_mongoid (~> 2.0.0)
+      mongoid (~> 3.0.9)
+      moped (~> 1.2.7)
+      rubyzip (~> 0.9.9)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    actionmailer (3.2.8)
+      actionpack (= 3.2.8)
+      mail (~> 2.4.4)
+    actionpack (3.2.8)
+      activemodel (= 3.2.8)
+      activesupport (= 3.2.8)
+      builder (~> 3.0.0)
+      erubis (~> 2.7.0)
+      journey (~> 1.0.4)
+      rack (~> 1.4.0)
+      rack-cache (~> 1.2)
+      rack-test (~> 0.6.1)
+      sprockets (~> 2.1.3)
+    activemodel (3.2.8)
+      activesupport (= 3.2.8)
+      builder (~> 3.0.0)
+    activerecord (3.2.8)
+      activemodel (= 3.2.8)
+      activesupport (= 3.2.8)
+      arel (~> 3.0.2)
+      tzinfo (~> 0.3.29)
+    activeresource (3.2.8)
+      activemodel (= 3.2.8)
+      activesupport (= 3.2.8)
+    activesupport (3.2.8)
+      i18n (~> 0.6)
+      multi_json (~> 1.0)
+    arel (3.0.2)
+    builder (3.0.4)
+    coderay (1.0.8)
+    delayed_job (3.0.3)
+      activesupport (~> 3.0)
+    delayed_job_mongoid (2.0.0)
+      delayed_job (~> 3.0)
+      mongoid (~> 3.0)
+    erubis (2.7.0)
+    hike (1.2.1)
+    i18n (0.6.1)
+    journey (1.0.4)
+    json (1.7.5)
+    mail (2.4.4)
+      i18n (>= 0.4.0)
+      mime-types (~> 1.16)
+      treetop (~> 1.4.8)
+    method_source (0.8.1)
+    mime-types (1.19)
+    minitest (4.1.0)
+    mongoid (3.0.10)
+      activemodel (~> 3.1)
+      moped (~> 1.1)
+      origin (~> 1.0)
+      tzinfo (~> 0.3.22)
+    moped (1.2.7)
+    multi_json (1.3.6)
+    origin (1.0.9)
+    polyglot (0.3.3)
+    pry (0.9.10)
+      coderay (~> 1.0.5)
+      method_source (~> 0.8)
+      slop (~> 3.3.1)
+    pry-nav (0.2.2)
+      pry (~> 0.9.10)
+    rack (1.4.1)
+    rack-cache (1.2)
+      rack (>= 0.4)
+    rack-ssl (1.3.2)
+      rack
+    rack-test (0.6.2)
+      rack (>= 1.0)
+    rails (3.2.8)
+      actionmailer (= 3.2.8)
+      actionpack (= 3.2.8)
+      activerecord (= 3.2.8)
+      activeresource (= 3.2.8)
+      activesupport (= 3.2.8)
+      bundler (~> 1.0)
+      railties (= 3.2.8)
+    railties (3.2.8)
+      actionpack (= 3.2.8)
+      activesupport (= 3.2.8)
+      rack-ssl (~> 1.3.2)
+      rake (>= 0.8.7)
+      rdoc (~> 3.4)
+      thor (>= 0.14.6, < 2.0)
+    rake (0.9.2.2)
+    rdoc (3.12)
+      json (~> 1.4)
+    rubyzip (0.9.9)
+    simplecov (0.7.1)
+      multi_json (~> 1.0)
+      simplecov-html (~> 0.7.1)
+    simplecov-html (0.7.1)
+    slop (3.3.3)
+    sprockets (2.1.3)
+      hike (~> 1.2)
+      rack (~> 1.0)
+      tilt (~> 1.1, != 1.3.0)
+    thor (0.16.0)
+    tilt (1.3.3)
+    treetop (1.4.12)
+      polyglot
+      polyglot (>= 0.3.1)
+    tzinfo (0.3.34)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  minitest (~> 4.1.0)
+  pry
+  pry-nav
+  quality-measure-engine!
+  rails (~> 3.2.8)
+  simplecov (~> 0.7.1)

data/LICENSE.txt

@@ -0,0 +1,13 @@
+Copyright (c) 2012 The MITRE Corporation
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+   http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

data/README.md

@@ -1,14 +1,7 @@
-This project is a library designed to calculate clinical quality measures over a given population. Quality measures are described via JSON and provide the details on what information is needed from a patient record to calculate a quality measure. The logic of the measure is described in JavaScript using the MapReduce algorithmic framework.
-
-Usage
-=====
-
-Extracting Measure Data from a HITSP C32
-----------------------------------------
-
-Each quality measure will need to extract specific information from a HITSP C32 for calculation. First, for each quality measure, a QME::Importer::GenericImporter should be created by passing in the JSON definition of the quality measure.
+Quality Measure Engine
+----------------------
 
-Next, an instance of QME::Importer::PatientImporter should be obtained by calling instance (it follows the singleton pattern). Add the GenericImporters for each desired measure with the add measure method. Finally, you can get a JSON representation of a patient record with the necessary information extracted by calling parse_c32.
+This project is a library designed to calculate clinical quality measures over a given population. Quality measures are described via JSON and provide the details on what information is needed from a patient record to calculate a quality measure. The logic of the measure is described in JavaScript using the MapReduce algorithmic framework.
 
 Calculating Quality Measures
 ----------------------------
@@ -18,7 +11,7 @@ Results of quality measures are represented by QME::QualityReport. This class pr
 Environment
 ===========
 
-This project currently uses Ruby 1.9.2 and is built using [Bundler](http://gembundler.com/). To get all of the dependencies for the project, first install bundler:
+This project currently uses Ruby 1.9.3 and is built using [Bundler](http://gembundler.com/). To get all of the dependencies for the project, first install bundler:
 
     gem install bundler
 
@@ -26,7 +19,7 @@ Then run bundler to grab all of the necessary gems:
 
     bundle install
 
-The Quality Measure engine relies on a MongoDB [MongoDB](http://www.mongodb.org/) running a minimum of version 1.8.* or higher.  To get and install Mongo refer to:
+The Quality Measure engine relies on a MongoDB [MongoDB](http://www.mongodb.org/) running a minimum of version 2.2.* or higher.  To get and install Mongo refer to:
 
     http://www.mongodb.org/display/DOCS/Quickstart
 
@@ -46,44 +39,30 @@ QME::QualityReport will kick off background jobs with Resque. For these jobs to
 Testing
 =======
 
-This project uses [RSpec](http://github.com/rspec/rspec-core) for testing. To run the suite, just enter the following:
-
-    bundle exec rake spec
-
-The coverage of the test suite is monitored with [cover_me](https://github.com/markbates/cover_me) and can be run with:
-
-    bundle exec rake coverage
+This project uses [minitest](https://github.com/seattlerb/minitest) for testing. To run the suite, just enter the following:
 
-Map Reduce Testing
-------------------
+    bundle exec rake test
 
-This project used the [MapReduce](http://www.mongodb.org/display/DOCS/MapReduce) functionality of MongoDB pretty heavily.
-Debugging JavaScript that is to be run inside of MongoDB can be a bit of a chore, so there is a testing tool that can be run
-in your browser to aid in troubleshooting.
+The coverage of the test suite is monitored with [cover_me](https://github.com/markbates/cover_me). You can see the code coverage by looking in the coverage directory after running the test suite
 
-The tool is a very small web application based on the [Sinatra](http://www.sinatrarb.com/) framework. It can be run
-by executing the following command:
-
-    bundle exec ruby map_test/map_test.rb
-
-After running this command, you can open your browser to [http://localhost:4567](http://localhost:4567). This will show you a page
-of measures to choose from. Once you have selected a measure, it will take you to a page where you can choose the map function you
-want to test and the effective date you want to run the function with. Once that is selected, you will arrive at the map test page.
-The map test page provides the ability to load test JSON records from within the project. Once they are loaded, they can be edited
-in the textarea on the page. Finally, if you click the "run" button, it will execute the map function on the record in the text area
-and output the results. Since this is executing in a web browser, you can use the JavaScript debugging utilities provided to set
-breakpoints and inspect variables.
+Project Practices
+=================
 
-Source Code Analysis
---------------------
+Please try to follow our [Coding Style Guides](http://github.com/eedrummer/styleguide). Additionally, we will be using git in a pattern similar to [Vincent Driessen's workflow](http://nvie.com/posts/a-successful-git-branching-model/). While feature branches are encouraged, they are not required to work on the project.
 
-This project uses [metric_fu](http://metric-fu.rubyforge.org/) for source code analysis. Reports can be run with:
+License
+=======
 
-    bundle exec rake metrics:all
+Copyright 2012 The MITRE Corporation
 
-The project is currently configured to run Flay, Flog, Churn, Reek and Roodi
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-Project Practices
-=================
+   http://www.apache.org/licenses/LICENSE-2.0
 
-Please try to follow our [Coding Style Guides](http://github.com/eedrummer/styleguide). Additionally, we will be using git in a pattern similar to [Vincent Driessen's workflow](http://nvie.com/posts/a-successful-git-branching-model/). While feature branches are encouraged, they are not required to work on the project.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

data/Rakefile

@@ -1,31 +1,8 @@
-require 'rspec/core/rake_task'
-require 'yard'
-require 'resque/tasks'
+require "bundler/gem_tasks"
+require 'rake/testtask'
 
-ENV['MEASURE_DIR'] = ENV['MEASURE_DIR'] || File.join('fixtures', 'measure_defs')
-ENV['MEASURE_PROPS'] = ENV['MEASURE_PROPS'] || File.join('fixtures', 'measure_props')
-
-Dir['lib/tasks/*.rake'].sort.each do |ext|
-  load ext
-end
-
-RSpec::Core::RakeTask.new do |t|
-  t.rspec_opts = ["-c", "-f progress", "-r ./spec/spec_helper.rb"]
-  t.pattern = 'spec/**/*_spec.rb'
+Rake::TestTask.new do |t|
+  t.libs << "test"
+  t.test_files = FileList['test/**/*_test.rb']
+  t.verbose = true
 end
-
-YARD::Rake::YardocTask.new
-
-namespace :cover_me do
-  
-  task :report do
-    require 'cover_me'
-    CoverMe.complete!
-  end
-  
-end
-
-task :coverage do
-  Rake::Task['spec'].invoke
-  Rake::Task['cover_me:report'].invoke
-end

data/lib/qme/bundle/bundle.rb

@@ -0,0 +1,34 @@
+module QME
+  module Bundle
+    # Delete a list of collections. By default, this function drops all of collections related to measures and patients.
+    #
+    # @param [Array] collection_names Optionally, an array of collection names to be dropped.
+    def self.drop_collections(db, collection_names=[])
+      collection_names = ["bundles", "records", "measures", "selected_measures", "patient_cache", "query_cache", "system.js"] if collection_names.empty?
+      collection_names.each {|collection| db[collection].drop}
+    end
+
+    # Save a javascript function into Mongo's system.js collection for measure execution.
+    #
+    # @param [String] name The name by which the function will be referred.
+    # @param [String] fn The body of the function being saved.
+    def self.save_system_js_fn(db, name, fn)
+      fn = "function () {\n #{fn} \n }"
+      db['system.js'].find('_id' => name).upsert(
+        {
+          "_id" => name,
+          "value" => Moped::BSON::Code.new(fn)
+        }
+      )
+    end
+
+    # A utility function for finding files in a bundle. Strip a file path of it's extension and just give the filename.
+    #
+    # @param [String] original A file path.
+    # @param [String] extension A file extension.
+    # @return The filename at the end of the original String path with the extension removed. e.g. "/boo/urns.html" -> "urns"
+    def self.entry_key(original, extension)
+      original.split('/').last.gsub(".#{extension}", '')
+    end
+  end
+end

data/lib/qme/bundle/importer.rb

@@ -0,0 +1,69 @@
+module QME
+  module Bundle
+    class Importer
+      include QME::DatabaseAccess
+
+      # Create a new Importer.
+      # @param [String] db_name the name of the database to use
+      def initialize(db_name = nil)
+        determine_connection_information(db_name)
+        @db = get_db
+      end
+
+      # Import a quality bundle into the database. This includes metadata, measures, test patients, supporting JS libraries, and expected results.
+      #
+      # @param [File] zip The bundle zip file.
+      # @param [Boolean] keep_existing If true, delete all current collections related to patients and measures.
+      def import(zip, delete_existing)
+        Bundle.drop_collections(@db) if delete_existing
+        
+        # Unpack content from the bundle.
+        bundle_contents = { bundle: nil, measures: {}, patients: {}, extensions: {}, results: {} }
+        Zip::ZipFile.open(zip.path) do |zipfile|
+          zipfile.entries.each do |entry|
+            bundle_contents[:bundle] = zipfile.read(entry.name) if entry.name.include? "bundle"
+            bundle_contents[:measures][Bundle.entry_key(entry.name, "json")] = zipfile.read(entry.name) if entry.name.match /^measures.*\.json$/
+            bundle_contents[:patients][Bundle.entry_key(entry.name, "json")] = zipfile.read(entry.name) if entry.name.match /^patients.*\.json$/ # Only need to import one of the formats
+            bundle_contents[:extensions][Bundle.entry_key(entry.name,"js")] = zipfile.read(entry.name) if entry.name.match /^library_functions/
+            bundle_contents[:results][Bundle.entry_key(entry.name,"json")] = zipfile.read(entry.name) if entry.name.match /^results/
+          end
+        end
+
+        # Store all JS libraries.
+        bundle_contents[:extensions].each do |key, contents|
+          Bundle.save_system_js_fn(@db, key, contents)
+        end
+
+        # Store the bundle metadata.
+        bundle_id = Moped::BSON::ObjectId.new()
+        bundle = JSON.parse(bundle_contents[:bundle])
+        bundle["_id"] = bundle_id
+        @db['bundles'].insert(bundle)
+        
+        # Store all measures.
+        bundle_contents[:measures].each do |key, contents|
+          measure_id = Moped::BSON::ObjectId.new()
+          measure = JSON.parse(contents, {:max_nesting => 100})
+          measure['_id'] = measure_id
+          measure['bundle'] = bundle_id  
+          @db['measures'].insert(measure)
+        end
+        
+        # Store all patients.
+        bundle_id = Moped::BSON::ObjectId(bundle_id.to_s)
+        bundle_contents[:patients].each do |key, contents|
+          patient = JSON.parse(contents, {:max_nesting => 100})
+          patient['bundle'] = bundle_id
+          Record.new(patient).save
+        end
+        
+        # Store the expected results into the query and patient caches.
+        bundle_contents[:results].each do |name, contents|
+          collection = name == "by_patient" ? "patient_cache" : "query_cache"
+          contents = JSON.parse(contents, {:max_nesting => 100})
+          contents.each {|document| @db[collection].insert(document)}
+        end
+      end
+    end
+  end
+end

data/lib/qme/database_access.rb

@@ -10,22 +10,18 @@ module QME
       @db_host = ENV['TEST_DB_HOST'] || 'localhost'
       @db_port = ENV['TEST_DB_PORT'] ? ENV['TEST_DB_PORT'].to_i : 27017
     end
-    
-    # Directly inject an instance of a database
-    # @param [Mongo::Database] db the database that you would like the object to use
-    def inject_db(db)
-      @db = db
-    end
 
     # Lazily creates a connection to the database and initializes the
     # JavaScript environment
-    # @return [Mongo::Connection]
+    # @return [Moped::Session]
     def get_db
       if @db == nil
-        @db = Mongo::Connection.new(@db_host, @db_port).db(@db_name)
-      end
-      Mongoid.configure do |config|
-        config.master = Mongo::Connection.new(@db_host, @db_port).db(@db_name)
+        if @db_name==nil || @db_host==nil || @db_port==nil
+          determine_connection_information()
+        end
+        
+        @db = Moped::Session.new(["#{@db_host}:#{@db_port}"])
+        @db.use(@db_name)
       end
       
       @db