bonnie_bundler 2.0.0

data/test/unit/storing_mat_export_package_test.rb

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+require 'test_helper'
+require 'vcr_setup.rb'
+
+class StoringMATExportPackageTest < ActiveSupport::TestCase
+
+  setup do
+    @cql_mat_export = File.new File.join('test', 'fixtures', 'CMS158_v5_4_Artifacts.zip')
+  end
+
+  test "Loading a MAT package, confirming the contents of the MAT package are viewable and stored correctly" do
+    VCR.use_cassette("valid_vsac_response_158") do
+      dump_db
+      user = User.new
+      user.save
+
+      measure_details = { 'episode_of_care'=> false }
+      Measures::CqlLoader.load(@cql_mat_export, user, measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD']).save
+      assert_equal 1, CqlMeasure.all.count
+      measure = CqlMeasure.all.first
+      assert_equal "Test 158", measure.title
+
+      assert_equal 1, CqlMeasurePackage.all.count
+      measure_package = CqlMeasurePackage.all.first
+      assert_equal measure.id, measure_package.measure_id
+
+      Dir.mktmpdir do |dir|
+        # Write the package to a temp directory
+        File.open(File.join(dir, measure.measure_id + '.zip'), 'wb') do |zip_file|
+          # Write the package binary to a zip file.
+          zip_file.write(measure_package.file.data)
+          Zip::ZipFile.open(zip_file.path) do |file|
+            cql_files = file.glob(File.join('**','**.cql')).select {|x| !x.name.starts_with?('__MACOSX') }
+            xml_files = file.glob(File.join('**','**.xml')).select {|x| !x.name.starts_with?('__MACOSX') }
+            json_files = file.glob(File.join('**','**.json')).select {|x| !x.name.starts_with?('__MACOSX') }
+
+            assert_equal 1, cql_files.count
+            assert_equal 2, xml_files.count
+            assert_equal 1, json_files.count
+          end
+        end
+      end
+    end
+  end
+
+end

data/test/unit/value_set_loading_test.rb

@@ -0,0 +1,109 @@
+require 'test_helper'
+require 'vcr_setup.rb'
+
+# Test ensures that the correct vsac requests are made when loading a measure.
+class ValueSetLoadingTest < ActiveSupport::TestCase
+  
+  setup do
+    dump_db
+    @user = User.new
+    @user.save
+  end
+  
+  test 'Loading with IncludeDraft and no Profile or Version' do
+    # Expects that draft and default profile will be used
+    VCR.use_cassette("vs_loading_draft_no_profile_version") do
+      mat_file = File.new File.join("test", "fixtures", "vs_loading", "DocofMeds_v5_1_Artifacts.zip")
+      measure_details = {}
+      measure = Measures::CqlLoader.load(mat_file, @user, measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD'], false, false, true)
+      measure.value_sets.each do |vs|
+        if vs.oid == "2.16.840.1.113883.3.600.1.1834"
+          assert_equal 154, vs.concepts.count
+        end
+      end
+    end
+  end
+
+  test 'Loading with IncludeDraft and a Profile' do
+    # Expects that draft and default profile will be used, and provided Profile will be ignored
+    VCR.use_cassette("vs_loading_draft_profile") do
+      mat_file = File.new File.join("test", "fixtures", "vs_loading", "DocofMeds_v5_1_Artifacts_With_Profiles.zip")
+      measure_details = {}
+      measure = Measures::CqlLoader.load(mat_file, @user, measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD'], false, false, true)
+      measure.value_sets.each do |vs|
+        if vs.oid == "2.16.840.1.113883.3.600.1.1834"
+          assert_equal 154, vs.concepts.count
+        end
+      end
+    end
+
+  end
+
+  test 'Loading with IncludeDraft and a Version' do
+    # Expects that draft and default profile will be used, and provided Version will be ignored
+    VCR.use_cassette("vs_loading_draft_verion") do
+      mat_file = File.new File.join("test", "fixtures", "vs_loading", "DocofMeds_v5_1_Artifacts_Version.zip")
+      measure_details = {}
+      measure = Measures::CqlLoader.load(mat_file, @user, measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD'], false, false, true)
+      measure.value_sets.each do |vs|
+        if vs.oid == "2.16.840.1.113883.3.600.1.1834"
+          assert_equal 154, vs.concepts.count
+        end
+      end
+    end
+  end
+
+  test 'Loading without IncludeDraft and no Profile or Version' do
+    # Expects that default profile will be used
+    VCR.use_cassette("vs_loading_no_profile_version") do
+      mat_file = File.new File.join("test", "fixtures", "vs_loading", "DocofMeds_v5_1_Artifacts.zip")
+      measure_details = {}
+      measure = Measures::CqlLoader.load(mat_file, @user, measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD'], false, false, false)
+      measure.value_sets.each do |vs|
+        if vs.oid == "2.16.840.1.113883.3.600.1.1834"
+          assert_equal 154, vs.concepts.count
+        end
+      end
+    end
+  end
+
+  test 'VSAC Error Exception Handling' do
+    # Expects that default profile will be used
+    VCR.use_cassette("vs_loading_no_profile_version") do
+      mat_file = File.new File.join("test", "fixtures", "vs_loading", "DocofMeds_v5_1_Artifacts.zip")
+      measure_details = {}
+      exception = assert_raise Measures::VSACException do
+        measure = Measures::CqlLoader.load(mat_file, "fake user", measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD'], false, false, false)
+      end
+      assert_equal 'Error Loading Value Sets from VSAC: undefined method `id\' for "fake user":String', exception.message
+    end
+  end
+  
+  test 'Loading without IncludeDraft and a Profile' do
+    # Expects that given profile will be used
+    VCR.use_cassette("vs_loading_profile") do
+      mat_file = File.new File.join("test", "fixtures", "vs_loading", "DocofMeds_v5_1_Artifacts_With_Profiles.zip")
+      measure_details = {}
+      measure = Measures::CqlLoader.load(mat_file, @user, measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD'], false, false, false)
+      measure.value_sets.each do |vs|
+        if vs.oid == "2.16.840.1.113883.3.600.1.1834"
+          assert_equal 152, vs.concepts.count
+        end
+      end
+    end
+  end
+
+  test 'Loading without IncludeDraft and a Version' do
+    # Expects that given version will be used
+    VCR.use_cassette("vs_loading_version") do
+      mat_file = File.new File.join("test", "fixtures", "vs_loading", "DocofMeds_v5_1_Artifacts_Version.zip")
+      measure_details = {}
+      measure = Measures::CqlLoader.load(mat_file, @user, measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD'], false, false, false)
+      measure.value_sets.each do |vs|
+        if vs.oid == "2.16.840.1.113883.3.600.1.1834"
+          assert_equal 148, vs.concepts.count
+        end
+      end
+    end
+  end
+end

data/test/vcr_setup.rb

@@ -0,0 +1,20 @@
+require 'vcr'
+# VCR records HTTP interactions to cassettes that can be replayed during unit tests
+# allowing for faster, more predictible web interactions
+VCR.configure do |c|
+  # This is where the various cassettes will be recorded to
+  c.cassette_library_dir = 'test/fixtures/vcr_cassettes'
+  c.hook_into :webmock
+  
+  # To avoid storing plain text VSAC credentials or requiring the VSAC credentials
+  # be provided at every run of the rake tests, provide the VSAC_USERNAME and VSAC_PASSWORD
+  # whenever you need to record a cassette that requires valid credentials
+  ENV['VSAC_USERNAME'] = "vcrtest" unless ENV['VSAC_USERNAME']
+  ENV['VSAC_PASSWORD'] = "vcrpass" unless ENV['VSAC_PASSWORD']
+
+  # Ensure plain text passwords do not show up during logging
+  c.filter_sensitive_data('<VSAC_USERNAME>') {ENV['VSAC_USERNAME']}
+  c.filter_sensitive_data('<VSAC_PASSWORD>') {ENV['VSAC_PASSWORD']}
+  c.default_cassette_options = {record: :once }
+
+end

metadata

@@ -0,0 +1,258 @@
+--- !ruby/object:Gem::Specification
+name: bonnie_bundler
+version: !ruby/object:Gem::Version
+  version: 2.0.0
+platform: ruby
+authors:
+- The MITRE Corporation
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2017-11-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: health-data-standards
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.0'
+- !ruby/object:Gem::Dependency
+  name: quality-measure-engine
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+- !ruby/object:Gem::Dependency
+  name: hquery-patient-api
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.1'
+- !ruby/object:Gem::Dependency
+  name: simplexml_parser
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: hqmf2js
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.2'
+- !ruby/object:Gem::Dependency
+  name: mongoid
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+- !ruby/object:Gem::Dependency
+  name: rubyzip
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.1
+- !ruby/object:Gem::Dependency
+  name: zip-zip
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+- !ruby/object:Gem::Dependency
+  name: diffy
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+- !ruby/object:Gem::Dependency
+  name: roo
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.13'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.13'
+description: A Gem for creating and managing bonnie bundles
+email: pophealth-talk@googlegroups.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- Gemfile.lock
+- README.md
+- Rakefile
+- bonnie-bundler.gemspec
+- config/initializers/mongo.rb
+- config/measures/measures_2_4_0.yml
+- config/mongoid.yml
+- lib/bonnie_bundler.rb
+- lib/ext/hash.rb
+- lib/ext/railtie.rb
+- lib/ext/valueset.rb
+- lib/measures/cql_to_elm_helper.rb
+- lib/measures/elm_parser.rb
+- lib/measures/loading/base_loader_definition.rb
+- lib/measures/loading/cql_loader.rb
+- lib/measures/loading/exceptions.rb
+- lib/measures/loading/loader.rb
+- lib/measures/loading/value_set_loader.rb
+- lib/measures/logic_extractor.rb
+- lib/measures/mongo_hash_key_wrapper.rb
+- lib/models/cql_measure.rb
+- lib/models/measure.rb
+- test/fixtures/BCS_v5_0_Artifacts.zip
+- test/fixtures/CMS158_v5_4_Artifacts.zip
+- test/fixtures/CMS158_v5_4_Artifacts_Update.zip
+- test/fixtures/DRAFT_CMS2_CQL.zip
+- test/fixtures/bonnienesting01_fixed.zip
+- test/fixtures/vcr_cassettes/mat_5-4_cql_export_vsac_response.yml
+- test/fixtures/vcr_cassettes/multi_library_webcalls.yml
+- test/fixtures/vcr_cassettes/valid_translation_response.yml
+- test/fixtures/vcr_cassettes/valid_vsac_response.yml
+- test/fixtures/vcr_cassettes/valid_vsac_response_158.yml
+- test/fixtures/vcr_cassettes/valid_vsac_response_158_update.yml
+- test/fixtures/vcr_cassettes/valid_vsac_response_includes_draft.yml
+- test/fixtures/vcr_cassettes/vs_loading_draft_no_profile_version.yml
+- test/fixtures/vcr_cassettes/vs_loading_draft_profile.yml
+- test/fixtures/vcr_cassettes/vs_loading_draft_verion.yml
+- test/fixtures/vcr_cassettes/vs_loading_no_profile_version.yml
+- test/fixtures/vcr_cassettes/vs_loading_profile.yml
+- test/fixtures/vcr_cassettes/vs_loading_version.yml
+- test/fixtures/vs_loading/DocofMeds_v5_1_Artifacts.zip
+- test/fixtures/vs_loading/DocofMeds_v5_1_Artifacts_Version.zip
+- test/fixtures/vs_loading/DocofMeds_v5_1_Artifacts_With_Profiles.zip
+- test/simplecov_init.rb
+- test/test_helper.rb
+- test/unit/load_mat_export_test.rb
+- test/unit/measure_complexity_test.rb
+- test/unit/measure_diff_test.rb
+- test/unit/mongo_hash_key_wrapper_test.rb
+- test/unit/storing_mat_export_package_test.rb
+- test/unit/value_set_loading_test.rb
+- test/vcr_setup.rb
+homepage: http://github.com/projecttacoma/bonnie_bundler
+licenses:
+- Apache-2.0
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.14
+signing_key: 
+specification_version: 4
+summary: A Gem for creating and managing bonnie bundles
+test_files: []