quality-measure-engine 2.2.0 → 2.3.0

data/test/fixtures/measures/0142.json

@@ -1,4 +1,5 @@
 {
+  
   "id": "8A4D92B2-3887-5DF3-0139-0D01C6626E46",
   "nqf_id": "0142",
   "hqmf_id": "8A4D92B2-3887-5DF3-0139-0D01C6626E46",

data/test/fixtures/measures/0495a.json

@@ -1,4 +1,5 @@
 {
+  
   "id": "8A4D92B2-3887-5DF3-0139-0C4E41594C98",
   "nqf_id": "0495",
   "hqmf_id": "8A4D92B2-3887-5DF3-0139-0C4E41594C98",

data/test/fixtures/measures/0495b.json

@@ -1,4 +1,5 @@
 {
+  
   "id": "8A4D92B2-3887-5DF3-0139-0C4E41594C98",
   "nqf_id": "0495",
   "hqmf_id": "8A4D92B2-3887-5DF3-0139-0C4E41594C98",

data/test/fixtures/measures/measure_metadata.json

@@ -1,4 +1,5 @@
 {
+  
   "id": "0043",
   "name": "Pneumonia Vaccination Status for Older Adults",
   "description": "Patients more than 65 years old who received a pneumococcal vaccine.",

data/test/test_helper.rb

@@ -9,6 +9,22 @@ Mongoid.configure do |config|
 end
 
 class MiniTest::Unit::TestCase
+
+  def load_system_js
+     Mongoid.default_session['system.js'].drop
+    Dir.glob(File.join(File.dirname(__FILE__), 'fixtures', "library_functions", '*.js')).each do |json_fixture_file|
+      name = File.basename(json_fixture_file,".*")
+      fn = "function () {\n #{File.read(json_fixture_file)} \n }"
+      Mongoid.default_session['system.js'].find('_id' => name).upsert(
+        {
+          "_id" => name,
+          "value" => Moped::BSON::Code.new(fn)
+        }
+      )
+    end
+ 
+  end
+
   # Add more helper methods to be used by all tests here...
   
   def collection_fixtures(db, collection, *id_attributes)

data/test/unit/qme/map/map_reduce_builder_test.rb

@@ -6,6 +6,7 @@ class MapReduceBuilderTest < MiniTest::Unit::TestCase
   def setup
     raw_measure_json = File.read(File.join('test', 'fixtures', 'measures', 'measure_metadata.json'))
     @measure_json = JSON.parse(raw_measure_json)
+     load_system_js
   end
 
   def test_extracting_measure_metadata

data/test/unit/qme/map/map_reduce_executor_test.rb

@@ -4,10 +4,13 @@ class MapReduceExecutorTest < MiniTest::Unit::TestCase
   include QME::DatabaseAccess
 
   def setup
-    importer = QME::Bundle::Importer.new
-    importer.import(File.new('test/fixtures/bundles/just_measure_0002.zip'), true, nil)
 
+    get_db['query_cache'].drop()
+    get_db['patient_cache'].drop()
+    collection_fixtures(get_db(), 'measures')
     collection_fixtures(get_db(), 'records', '_id')
+    collection_fixtures(get_db(), 'bundles')
+    load_system_js
   end
 
   def test_map_records_into_measure_groups

data/test/unit/qme/map/measure_calculation_job_test.rb

@@ -4,10 +4,12 @@ class MapCalculationJobTest < MiniTest::Unit::TestCase
   include QME::DatabaseAccess
 
   def setup
-    importer = QME::Bundle::Importer.new
-    importer.import(File.new('test/fixtures/bundles/just_measure_0002.zip'),  true, nil)
-
+    get_db['query_cache'].drop()
+    get_db['patient_cache'].drop()
+    collection_fixtures(get_db(), 'measures')
     collection_fixtures(get_db(), 'records', '_id')
+    collection_fixtures(get_db(), 'bundles')
+    load_system_js
 
     Delayed::Worker.delay_jobs = false
   end

data/test/unit/qme/quality_measure_test.rb

@@ -1,14 +1,17 @@
 require 'test_helper'
 
 class QualityMeasureTest < MiniTest::Unit::TestCase
+	include QME::DatabaseAccess
   def setup
-    importer = QME::Bundle::Importer.new
-    importer.import(File.new('test/fixtures/bundles/just_measure_0002.zip'), true,nil)
+
+    collection_fixtures(get_db(), 'measures')
+    collection_fixtures(get_db(), 'bundles')
+    load_system_js
   end
 
   def test_getting_all_measures
     all_measures = QME::QualityMeasure.all
-    assert_equal 1, all_measures.size
+    assert_equal 5, all_measures.size
     assert all_measures["2E679CD2-3FEC-4A75-A75A-61403E5EFEE8.json"]
   end
 end

data/test/unit/qme/quality_report_test.rb

@@ -4,6 +4,8 @@ class QualityReportTest < MiniTest::Unit::TestCase
   include QME::DatabaseAccess
   
   def setup
+    load_system_js
+   collection_fixtures(get_db(), 'bundles')
     get_db()['query_cache'].drop()
     get_db()['patient_cache'].drop()
     get_db()['query_cache'].insert(

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quality-measure-engine
 version: !ruby/object:Gem::Version
-  version: 2.2.0
+  version: 2.3.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,10 +9,11 @@ authors:
 - Andy Gregorowicz
 - Rob Dingwell
 - Adam Goldstein
+- Andre Quina
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-19 00:00:00.000000000 Z
+date: 2013-02-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: moped
@@ -21,7 +22,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.2.7
+        version: 1.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -29,7 +30,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.2.7
+        version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: mongoid
   requirement: !ruby/object:Gem::Requirement
@@ -37,7 +38,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 3.0.9
+        version: '3.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -45,7 +46,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 3.0.9
+        version: '3.0'
 - !ruby/object:Gem::Dependency
   name: rubyzip
   requirement: !ruby/object:Gem::Requirement
@@ -172,24 +173,28 @@ files:
 - LICENSE.txt
 - README.md
 - Rakefile
-- lib/qme/bundle/bundle.rb
 - lib/qme/bundle/eh_measure_sheet.rb
 - lib/qme/bundle/eh_patient_importer.rb
-- lib/qme/bundle/importer.rb
 - lib/qme/database_access.rb
+- lib/qme/map/cv_aggregator.rb
 - lib/qme/map/map_reduce_builder.rb
 - lib/qme/map/map_reduce_executor.rb
 - lib/qme/map/measure_calculation_job.rb
 - lib/qme/quality_measure.rb
 - lib/qme/quality_report.rb
 - lib/qme/railtie.rb
-- lib/qme/tasks/bundle.rake
 - lib/qme/version.rb
 - lib/quality-measure-engine.rb
 - quality-measure-engine.gemspec
+- test/fixtures/bundles/bundle.json
 - test/fixtures/bundles/just_measure_0002.zip
+- test/fixtures/bundles/measures_0003_0002.zip
 - test/fixtures/delayed_backend_mongoid_jobs/queued_job.json
 - test/fixtures/eh_patient_sheets/results_matrix_eh.xlsx
+- test/fixtures/library_functions/hqmf_utils.js
+- test/fixtures/library_functions/map_reduce_utils.js
+- test/fixtures/library_functions/underscore_min.js
+- test/fixtures/measures/0002.json
 - test/fixtures/measures/0142.json
 - test/fixtures/measures/0495a.json
 - test/fixtures/measures/0495b.json
@@ -233,9 +238,15 @@ specification_version: 3
 summary: This library can run JavaScript based clinical quality measures on a repository
   of patients stored in MongoDB
 test_files:
+- test/fixtures/bundles/bundle.json
 - test/fixtures/bundles/just_measure_0002.zip
+- test/fixtures/bundles/measures_0003_0002.zip
 - test/fixtures/delayed_backend_mongoid_jobs/queued_job.json
 - test/fixtures/eh_patient_sheets/results_matrix_eh.xlsx
+- test/fixtures/library_functions/hqmf_utils.js
+- test/fixtures/library_functions/map_reduce_utils.js
+- test/fixtures/library_functions/underscore_min.js
+- test/fixtures/measures/0002.json
 - test/fixtures/measures/0142.json
 - test/fixtures/measures/0495a.json
 - test/fixtures/measures/0495b.json

data/lib/qme/bundle/bundle.rb

@@ -1,51 +0,0 @@
-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
-    
-    def self.unpack_bundle_contents(zip, type = nil)
-      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"
-          if type.nil? || entry.name.match(Regexp.new("/#{type}/")) 
-            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[:results][Bundle.entry_key(entry.name,"json")] = zipfile.read(entry.name) if entry.name.match /^results.*\.json/
-          end
-          bundle_contents[:extensions][Bundle.entry_key(entry.name,"js")] = zipfile.read(entry.name) if entry.name.match /^library_functions.*\.js/
-
-        end
-      end
-      bundle_contents
-    end
-  end
-end

data/lib/qme/bundle/importer.rb

@@ -1,63 +0,0 @@
-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 [String] Type of measures to import, either 'ep', 'eh' or nil for all
-      # @param [Boolean] keep_existing If true, delete all current collections related to patients and measures.
-      def import(zip,  delete_existing, type=nil)
-        Bundle.drop_collections(@db) if delete_existing
-        
-        # Unpack content from the bundle.
-        bundle_contents = QME::Bundle.unpack_bundle_contents(zip, type)
-
-        # 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
-        
-        bundle_contents
-      end
-    end
-  end
-end

data/lib/qme/tasks/bundle.rake

@@ -1,95 +0,0 @@
-require 'quality-measure-engine'
-
-db_name = ENV['DB_NAME'] || 'test'
-
-namespace :bundle do
-  desc 'Import a quality bundle into the database.'
-  task :import, [:bundle_path,  :delete_existing, :type] => [:environment] do |task, args|
-    raise "The path to the measures zip file must be specified" unless args.bundle_path
-
-    bundle = File.open(args.bundle_path)    
-    importer = QME::Bundle::Importer.new(db_name)
-    bundle_contents = importer.import(bundle,  args.delete_existing == "true", args.type)
-    
-    puts "Successfully imported bundle at: #{args.bundle_path}"
-    puts "\t Imported into environment: #{Rails.env.upcase}" if defined? Rails 
-    puts "\t Loaded #{args.type || "all"} measures"
-    puts "\t Measures Loaded: #{bundle_contents[:measures].count}"
-    puts "\t Test Patients Loaded: #{bundle_contents[:patients].count}"
-    puts "\t Extensions Loaded: #{bundle_contents[:extensions].count}"
-  end
-  
-  # this task is most likely temporary.  Once Bonnie can handle both EP and EH measures together, this would no longer be required.
-  desc 'Merge two bundles into one.'
-  task :merge, [:bundle_one,:bundle_two] do |t, args|
-    raise "Two bundle zip file paths to be merged must be specified" unless args.bundle_one && args.bundle_two
-    
-    tmpdir = Dir.mktmpdir
-    ['measures','patients','library_functions','results', 'sources'].each do |dir|
-      
-      FileUtils.mkdir_p(File.join(tmpdir, 'output', dir))
-      
-    end
-      
-    begin
-      
-      ({'one'=>args.bundle_one,'two'=>args.bundle_two}).each do |key, source|
-        Zip::ZipFile.open(source) do |zip_file|
-          zip_file.each do |f|
-            f_path=File.join(tmpdir, key, f.name)
-            FileUtils.mkdir_p(File.dirname(f_path))
-            zip_file.extract(f, f_path) unless File.exist?(f_path)
-          end
-        end
-      end
-      
-      
-      ['measures','patients','library_functions', 'sources'].each do |dir|
-        ['one','two'].each do |key|
-          FileUtils.mv(Dir.glob(File.join(tmpdir,key,dir,'*')), File.join(tmpdir,'output',dir))
-        end
-      end
-      
-      Dir.glob(File.join(tmpdir,'one','results','*.json')).each do |result_path_one|
-        json_one = JSON.parse(File.new(result_path_one).read)
-        result_filename = Pathname.new(result_path_one).basename.to_s
-        json_two = JSON.parse(File.new(File.join(tmpdir,'two','results',result_filename)).read)
-        File.open(File.join(tmpdir,'output','results',result_filename), 'w') {|f| f.write(JSON.pretty_generate(json_one + json_two)) }
-      end
-      
-      json_one = JSON.parse(File.new(File.join(tmpdir,'one','bundle.json')).read)
-      json_two = JSON.parse(File.new(File.join(tmpdir,'two','bundle.json')).read)
-      json_out = {}
-
-      ['title','effective_date','version','license','exported'].each do |key|
-        json_out[key] = json_one[key]
-      end
-
-      ['measures','patients','extensions'].each do |key|
-        json_out[key] = (json_one[key] + json_two[key]).uniq
-      end
-      
-      version = json_out['version']
-
-      File.open(File.join(tmpdir,'output','bundle.json'), 'w') {|f| f.write(JSON.pretty_generate(json_out)) }
-      date_string = Time.now.strftime("%Y-%m-%d")
-
-      out_zip = File.join('tmp','bundles',"bundle-merged-#{date_string}-#{version}.zip")
-      FileUtils.remove_entry_secure out_zip if File.exists?(out_zip)
-      Zip::ZipFile.open(out_zip, 'w') do |zipfile|
-        path = File.join(tmpdir,'output')
-        Dir[File.join(path,'**','**')].each do |file|
-          zipfile.add(file.sub(path+'/',''),file)
-        end
-      end
-      
-      puts "wrote merged bundle to: #{out_zip}"
-
-    ensure
-      FileUtils.remove_entry_secure tmpdir
-    end
-    
-  
-  end
-  
-end