bonnie_bundler 2.2.0 → 3.0.0

data/test/unit/vsac_api_auth_test.rb

@@ -4,10 +4,10 @@ require 'vcr_setup.rb'
 # Tests that ensure VSAC authentication related situations are handled
 class VSACAPIAuthTest < ActiveSupport::TestCase
 
-  test 'valid username and password provided' do
+  test 'valid api_key provided' do
     VCR.use_cassette("vsac_auth_good_credentials") do
       assert_nothing_raised do
-        api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+        api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
         assert_not_nil api.ticket_granting_ticket
         assert_not_nil api.ticket_granting_ticket[:ticket]
         assert_not_nil api.ticket_granting_ticket[:expires]
@@ -15,42 +15,18 @@ class VSACAPIAuthTest < ActiveSupport::TestCase
     end
   end
 
-  test 'invalid username and password provided' do
+  test 'invalid api_key provided' do
     VCR.use_cassette("vsac_auth_bad_credentials") do
       assert_raise Util::VSAC::VSACInvalidCredentialsError do
-        api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: 'baduser', password: 'badpass')
+        api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: 'badapikey')
       end
     end
   end
 
-  test 'empty username and password provided' do
+  test 'empty api_key provided' do
     api = nil
     assert_nothing_raised do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: nil, password: nil)
-    end
-
-    # now attempt to get a valueset
-    assert_raise Util::VSAC::VSACNoCredentialsError do
-      api.get_valueset('2.16.840.1.113762.1.4.1')
-    end
-  end
-
-  test 'provided username but no password' do
-    api = nil
-    assert_nothing_raised do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: "vsacuser")
-    end
-
-    # now attempt to get a valueset
-    assert_raise Util::VSAC::VSACNoCredentialsError do
-      api.get_valueset('2.16.840.1.113762.1.4.1')
-    end
-  end
-
-  test 'provided password but no username' do
-    api = nil
-    assert_nothing_raised do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: "vsacuser")
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: nil)
     end
 
     # now attempt to get a valueset
@@ -62,7 +38,7 @@ class VSACAPIAuthTest < ActiveSupport::TestCase
   test 'valid ticket_granting_ticket provided and used' do
     VCR.use_cassette("vsac_auth_good_credentials_and_simple_call") do
       # first get a ticket_granting_ticket
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       assert_not_nil api.ticket_granting_ticket
 
       reused_ticket_granting_ticket = {

data/test/unit/vsac_api_test.rb

@@ -18,7 +18,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset with version' do
     VCR.use_cassette("vsac_vs_version") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       vs = api.get_valueset("2.16.840.1.113883.3.600.1.1834", version: "MU2 EP Update 2014-07-01")
       assert_not_nil vs
       doc = Nokogiri::XML(vs)
@@ -28,7 +28,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valuest with include_draft no profile' do
     VCR.use_cassette("vsac_vs_include_draft_no_profile") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       assert_raise Util::VSAC::VSACArgumentError do
         api.get_valueset("2.16.840.1.113883.3.600.1.1834", include_draft: true)
       end
@@ -37,7 +37,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset with include_draft specified profile' do
     VCR.use_cassette("vsac_vs_include_draft_with_profile") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       vs = api.get_valueset("2.16.840.1.113762.1.4.1", include_draft: true, profile: "eCQM Update 2018-05-04")
       assert_not_nil vs
       doc = Nokogiri::XML(vs)
@@ -47,7 +47,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset no options' do
     VCR.use_cassette("vsac_vs_no_options") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       vs = api.get_valueset("2.16.840.1.113762.1.4.1")
       assert_not_nil vs
       doc = Nokogiri::XML(vs)
@@ -57,7 +57,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset not found' do
     VCR.use_cassette("vsac_vs_not_found") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       assert_raise Util::VSAC::VSNotFoundError do
         api.get_valueset("bad.oid")
       end
@@ -66,7 +66,7 @@ class VSACApiTest < ActiveSupport::TestCase
 
   test 'get_valueset with release' do
     VCR.use_cassette("vsac_vs_release") do
-      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], username: ENV['VSAC_USERNAME'], password: ENV['VSAC_PASSWORD'])
+      api = Util::VSAC::VSACAPI.new(config: APP_CONFIG['vsac'], api_key: ENV['VSAC_API_KEY'])
       vs = api.get_valueset("2.16.840.1.113762.1.4.1", release: "MU2 EP Update 2014-05-30")
       assert_not_nil vs
       doc = Nokogiri::XML(vs)

data/test/vcr_setup.rb

@@ -5,16 +5,14 @@ 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
+  # be provided at every run of the rake tests, provide the VSAC_API_KEY
   # 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']
+  ENV['VSAC_API_KEY'] = "vcrpass" unless ENV['VSAC_API_KEY']
 
   # 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.filter_sensitive_data('<VSAC_API_KEY>') {URI.escape(ENV['VSAC_API_KEY'])}
   c.default_cassette_options = {record: :once }
 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bonnie_bundler
 version: !ruby/object:Gem::Version
-  version: 2.2.0
+  version: 3.0.0
 platform: ruby
 authors:
 - The MITRE Corporation
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2018-07-13 00:00:00.000000000 Z
+date: 2020-10-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: health-data-standards
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: 4.3.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: 4.3.2
 - !ruby/object:Gem::Dependency
   name: quality-measure-engine
   requirement: !ruby/object:Gem::Requirement
@@ -84,16 +84,22 @@ dependencies:
   name: rails
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: '4.2'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '6.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: '4.2'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '6.0'
 - !ruby/object:Gem::Dependency
   name: mongoid
   requirement: !ruby/object:Gem::Requirement
@@ -162,14 +168,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.13'
+        version: '2.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.13'
+        version: '2.7'
 description: A Gem for creating and managing bonnie bundles
 email: pophealth-talk@googlegroups.com
 executables: []
@@ -178,10 +184,13 @@ extra_rdoc_files: []
 files:
 - ".github/CONTRIBUTING.md"
 - ".github/PULL_REQUEST_TEMPLATE.md"
+- ".github/gitleaks.toml"
+- ".github/workflows/main.yml"
 - ".gitignore"
 - ".travis.yml"
 - Gemfile
 - Gemfile.lock
+- LICENSE.txt
 - README.md
 - Rakefile
 - bonnie-bundler.gemspec
@@ -194,7 +203,6 @@ files:
 - 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
@@ -204,13 +212,24 @@ files:
 - lib/models/cql_measure.rb
 - lib/models/measure.rb
 - lib/util/vsac_api.rb
+- notice.md
 - test/fixtures/BCS_v5_0_Artifacts.zip
 - test/fixtures/CMS134v6.zip
 - test/fixtures/CMS158_v5_4_Artifacts.zip
 - test/fixtures/CMS158_v5_4_Artifacts_Update.zip
+- test/fixtures/CMSAWA_v5_6_Artifacts.zip
+- test/fixtures/CMSAWA_v5_6_Artifacts_missing_component.zip
+- test/fixtures/CMSAWA_v5_6_Artifacts_missing_composite_files.zip
+- test/fixtures/CMSAWA_v5_6_Artifacts_missing_file.zip
 - test/fixtures/DRAFT_CMS2_CQL.zip
 - test/fixtures/PVC2_v5_4_Unused_Support_Libraries.zip
+- test/fixtures/TOB2_v5_5_Artifacts.zip
 - test/fixtures/bonnienesting01_fixed.zip
+- test/fixtures/not_mat_export.zip
+- test/fixtures/vcr_cassettes/load_composite_measure.yml
+- test/fixtures/vcr_cassettes/load_composite_measure_with_missing_component.yml
+- test/fixtures/vcr_cassettes/load_composite_measure_with_missing_composite_files.yml
+- test/fixtures/vcr_cassettes/load_composite_measure_with_missing_file.yml
 - 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
@@ -220,6 +239,7 @@ files:
 - test/fixtures/vcr_cassettes/valid_vsac_response_hospice.yml
 - test/fixtures/vcr_cassettes/valid_vsac_response_includes_draft.yml
 - test/fixtures/vcr_cassettes/valid_vsac_response_pvc_unused_libraries.yml
+- test/fixtures/vcr_cassettes/valid_vsac_response_special_characters.yml
 - test/fixtures/vcr_cassettes/vs_loading_500_response.yml
 - test/fixtures/vcr_cassettes/vs_loading_draft_no_profile_version.yml
 - test/fixtures/vcr_cassettes/vs_loading_draft_profile.yml
@@ -253,7 +273,9 @@ files:
 - test/fixtures/vs_loading/DocofMeds_v5_1_Artifacts_With_Profiles.zip
 - test/simplecov_init.rb
 - test/test_helper.rb
+- test/unit/composite_cql_loader_test.rb
 - test/unit/cql_loader_test.rb
+- test/unit/get_value_sets_from_measure_model_test.rb
 - test/unit/load_mat_export_test.rb
 - test/unit/measure_complexity_test.rb
 - test/unit/measure_diff_test.rb
@@ -268,7 +290,7 @@ homepage: http://github.com/projecttacoma/bonnie_bundler
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -283,9 +305,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.12
-signing_key: 
+rubygems_version: 3.0.8
+signing_key:
 specification_version: 4
 summary: A Gem for creating and managing bonnie bundles
 test_files: []

data/lib/measures/loading/base_loader_definition.rb

@@ -1,61 +0,0 @@
-module Measures
-  # Base Class for the different types of loader formats Bonnie Bundler supports.
-  class BaseLoaderDefinition
-
-    def self.extract(zip_file, entry, out_dir)
-      out_file = File.join(out_dir,Pathname.new(entry.name).basename.to_s)
-      zip_file.extract(entry, out_file)
-      out_file
-    end
-    
-    # Wrapper function that performs checks before extracting all xml files in the given zip 
-    # Returns a hash with the type of xml files present and their paths.
-    # Ex: {:HQMF_XML => '/var/149825825jf/Test111_eMeasure.xml'}
-    def self.extract_xml_files(zip_file, files, output_directory=nil)
-      file_paths_hash = {}
-      if files.count > 0
-        # If no directory is given, create a new temporary directory.
-        if output_directory.nil?
-          # Create a temporary directory to extract all xml files contained in the zip.
-          Dir.mktmpdir do |dir|         
-            file_paths_hash = extract_to_temporary_location(zip_file, files, dir)
-          end
-        # Use the provided directory to extract the files to.
-        else
-          file_paths_hash = extract_to_temporary_location(zip_file, files, output_directory)
-        end
-      end
-      file_paths_hash
-    end      
- 
-    private 
-    
-    # Extracts the xml files from the zip and provides a key value pair for HQMF and ELM xml files.
-    # Currently only checks for HQMF xml, ELM xml and SIMPLE xml. Uses the root node in each of the files.
-    # {file_type => file_path}
-    def self.extract_to_temporary_location(zip_file, files, output_directory)
-      file_paths_hash = {}
-      file_paths_hash[:ELM_XML] = []
-      begin
-        # Iterate over all files passed in, extract file to temporary directory.
-        files.each do |xml_file|
-          if xml_file && xml_file.size > 0
-            xml_file_path = extract(zip_file, xml_file, output_directory)
-            # Open up xml file and read contents.
-            doc = Nokogiri::XML.parse(File.read(xml_file_path))
-            # Check if root node in xml file matches either the HQMF file or ELM file.
-            if doc.root.name == 'QualityMeasureDocument' # Root node for HQMF XML
-              file_paths_hash[:HQMF_XML] = xml_file_path
-            elsif doc.root.name == 'library' # Root node for ELM XML
-              file_paths_hash[:ELM_XML] << xml_file_path
-            end
-          end
-        end     
-      rescue Exception => e
-        raise MeasureLoadingException.new "Error Checking MAT Export: #{e.message}"
-      end
-      file_paths_hash
-    end
-
-  end
-end