bonnie_bundler 2.0.1 → 2.0.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/.github/CONTRIBUTING.md

@@ -0,0 +1,14 @@
+# :clipboard: Bonnie Bundler contribution rules
+1. All tickets relating to a pull request must link to the pull request.
+2. All pull requests must link to their parent tickets.
+3. All pull requests must have accompanying tests. This means:
+    * Automated tests: Automated tests are expected unless they are not feasible. If they are not feasible, this should be explained in the pull request.
+    * A JIRA test should be included if the automated tests are not sufficient
+        - The JIRA test should link to the pull request
+        - The JIRA test should link to the tasks that were resolved by the pull request
+    * A pull request review also includes a review of the accompanying tests tests
+4. All pull requests must pass a calculation regression test to confirm that calculations do not break with these changes
+
+:clipboard: For more details see: https://gitlab.mitre.org/bonnie/internal-documentation/wikis/pull-requests
+
+As a reviewer of a pull request, you are accountable to verifying that the PR contains all items. :punch:

data/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,45 @@
+Pull requests into Bonnie Bundler require the following. Submitter and reviewer should :white_check_mark: when done. For items that are not-applicable, note it's not-applicable ("N/A") and :white_check_mark:.
+
+**Submitter:**
+- [ ] This pull request describes why these changes were made.
+- [ ] This PR is into the correct branch.
+- [ ] JIRA ticket for this PR:
+- [ ] JIRA ticket links to this PR
+- [ ] Code diff has been done and been reviewed (it **does not** contain: additional white space, not applicable code changes, debug statements, etc.)
+- [ ] Tests are included and test edge cases
+- [ ] Tests have been run locally and pass (remember to update Gemfile when applicable)
+- [ ] Code coverage has not gone down and all code touched or added is covered.
+    * In rare situations, this may not be possible or applicable to a PR. In those situations:
+        1. Note why this could not be done or is not applicable here:
+        2. Add TODOs in the code noting that it requires a test
+        3. Add a JIRA task to add the test and link it here:
+- [ ] Automated regression test(s) pass
+
+If JIRA tests were used to supplement or replace automated tests:
+- [ ] JIRA test links:
+- [ ] Justification for using JIRA tests:
+- [ ] JIRA tests have been added to sprint
+
+
+**Reviewer 1:**
+
+Name:
+- [ ] Code is maintainable and reusable, reuses existing code and infrastructure where appropriate, and accomplishes the task’s purpose
+- [ ] The tests appropriately test the new code, including edge cases
+- [ ] You have tried to break the code
+
+If JIRA tests were used to supplement or replace automated tests:
+- [ ] JIRA tests have been run and pass
+- [ ] You agree with the justification for use of JIRA tests or have provided input on why you disagree
+
+
+**Reviewer 2:**
+
+Name:
+- [ ] Code is maintainable and reusable, reuses existing code and infrastructure where appropriate, and accomplishes the task’s purpose
+- [ ] The tests appropriately test the new code, including edge cases
+- [ ] You have tried to break the code
+
+If JIRA tests were used to supplement or replace automated tests:
+- [ ] JIRA tests have been run and pass
+- [ ] You agree with the justification for use of JIRA tests or have provided input on why you disagree

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bonnie_bundler (2.0.1)
+    bonnie_bundler (2.0.2)
       diffy (~> 3.0.0)
       health-data-standards (~> 4.0)
       hqmf2js (~> 1.4)

data/bonnie-bundler.gemspec

@@ -7,7 +7,7 @@ Gem::Specification.new do |s|
   s.email = "pophealth-talk@googlegroups.com"
   s.homepage = "http://github.com/projecttacoma/bonnie_bundler"
   s.authors = ["The MITRE Corporation"]
-  s.version = '2.0.1'
+  s.version = '2.0.2'
   s.license = 'Apache-2.0'
 
   s.add_dependency 'health-data-standards', '~> 4.0'

data/lib/measures/loading/cql_loader.rb

@@ -42,10 +42,26 @@ module Measures
       json = hqmf_model.to_json
       json.convert_keys_to_strings
 
+      # Set the code list ids of data criteria and source data criteria that use direct reference codes to GUIDS.
+      json['source_data_criteria'], json['data_criteria'] = set_data_criteria_code_list_ids(json, cql_artifacts)
+
+      # Create CQL Measure
+      measure = Measures::Loader.load_hqmf_cql_model_json(json, user, cql_artifacts[:all_value_set_oids], main_cql_library, cql_artifacts[:cql_definition_dependency_structure],
+                                                          cql_artifacts[:elms], cql_artifacts[:elm_annotations], files[:CQL], nil, cql_artifacts[:value_set_oid_version_objects])
+      measure['episode_of_care'] = measure_details['episode_of_care']
+      measure['type'] = measure_details['type']
+
+      # Create, associate and save the measure package.
+      measure.package = CqlMeasurePackage.new(file: BSON::Binary.new(zip_file.read()))
+      measure.package.save
+
+      measure
+    end
+
+    def self.set_data_criteria_code_list_ids(json, cql_artifacts)
       # Loop over data criteria to search for data criteria that is using a single reference code.
       # Once found set the Data Criteria's 'code_list_id' to our fake oid. Do the same for source data criteria.
       json['data_criteria'].each do |data_criteria_name, data_criteria|
-        # We do not want to replace an existing code_list_id. Skip.
         unless data_criteria['code_list_id']
           if data_criteria['inline_code_list']
             # Check to see if inline_code_list contains the correct code_system and code for a direct reference code.
@@ -64,18 +80,7 @@ module Measures
           end
         end
       end
-
-      # Create CQL Measure
-      measure = Measures::Loader.load_hqmf_cql_model_json(json, user, cql_artifacts[:all_value_set_oids], main_cql_library, cql_artifacts[:cql_definition_dependency_structure], 
-                                                          cql_artifacts[:elms], cql_artifacts[:elm_annotations], files[:CQL], nil, cql_artifacts[:value_set_oid_version_objects])
-      measure['episode_of_care'] = measure_details['episode_of_care']
-      measure['type'] = measure_details['type']
-
-      # Create, associate and save the measure package.
-      measure.package = CqlMeasurePackage.new(file: BSON::Binary.new(zip_file.read()))
-      measure.package.save
-
-      measure
+      return json['source_data_criteria'], json['data_criteria']
     end
 
     def self.load(file, user, measure_details, vsac_user=nil, vsac_password=nil, overwrite_valuesets=false, cache=false, includeDraft=false, ticket_granting_ticket=nil)
@@ -245,17 +250,18 @@ module Measures
 
             code_sets[code_system_name] ||= []
             code_sets[code_system_name] << code_reference['id']
-            # Generate a unique number as our fake "oid"
-            code_guid = SecureRandom.uuid
-            # Keep a list of generated_guids and a hash of guids with code system names and codes.
-            single_code_references << { guid: code_guid, code_system_name: code_system_name, code: code_reference['id'] }
-
-            all_codes_and_code_names[code_guid] = code_sets
-            # Create a new "ValueSet" and "Concept" object and save.
-            valueSet = HealthDataStandards::SVS::ValueSet.new({oid: code_guid, display_name: code_reference['name'], version: '' ,concepts: [], user_id: user.id})
-            concept = HealthDataStandards::SVS::Concept.new({code: code_reference['id'], code_system_name: code_system_name, code_system_version: code_system_version, display_name: code_reference['name']})
-            valueSet.concepts << concept
-            valueSet.save!
+            # Generate a unique number as our fake "oid" based on parameters that identify the DRC
+            code_hash = "drc-" + Digest::SHA2.hexdigest("#{code_system_name} #{code_reference['id']} #{code_reference['name']} #{code_system_version}")            # Keep a list of generated_guids and a hash of guids with code system names and codes.
+            single_code_references << { guid: code_hash, code_system_name: code_system_name, code: code_reference['id'] }
+            all_codes_and_code_names[code_hash] = code_sets
+            # code_hashs are unique hashes, there's no sense in adding duplicates to the ValueSet collection
+            if !HealthDataStandards::SVS::ValueSet.all().where(oid: code_hash, user_id: user.id).first()
+              # Create a new "ValueSet" and "Concept" object and save.
+              valueSet = HealthDataStandards::SVS::ValueSet.new({oid: code_hash, display_name: code_reference['name'], version: '' ,concepts: [], user_id: user.id})
+              concept = HealthDataStandards::SVS::Concept.new({code: code_reference['id'], code_system_name: code_system_name, code_system_version: code_system_version, display_name: code_reference['name']})
+              valueSet.concepts << concept
+              valueSet.save!
+            end
           end
         end
       end

data/test/unit/cql_loader_test.rb

@@ -24,4 +24,31 @@ class CQLLoaderTest < ActiveSupport::TestCase
       assert_equal [], cql_statement_dependencies['Hospice']['Has Hospice']
     end
   end
+
+
+  test 'Loading a measure with a direct reference code handles the creation of code_list_id hash properly' do
+    direct_reference_mat_export = File.new File.join('test', 'fixtures', 'CMS158_v5_4_Artifacts_Update.zip')
+    VCR.use_cassette('valid_vsac_response_158_update') do
+      dump_db
+      user = User.new
+      user.save
+
+      measure_details = { 'episode_of_care'=> false }
+      Measures::CqlLoader.load(direct_reference_mat_export, user, measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD']).save
+      assert_equal 1, CqlMeasure.all.count
+      measure = CqlMeasure.all.first
+  
+      # Confirm that the source data criteria with the direct reference code is equal to the expected hash
+      assert_equal measure['source_data_criteria']['prefix_5195_3_LaboratoryTestPerformed_70C9F083_14BD_4331_99D7_201F8589059D_source']['code_list_id'], "drc-986ea3d52eddc4927e63b3769b5efbaf38b76b35a9164e447fcde2e4dfd31a0c"
+      assert_equal measure['data_criteria']['prefix_5195_3_LaboratoryTestPerformed_70C9F083_14BD_4331_99D7_201F8589059D']['code_list_id'], "drc-986ea3d52eddc4927e63b3769b5efbaf38b76b35a9164e447fcde2e4dfd31a0c"
+
+      # Re-load the Measure
+      Measures::CqlLoader.load(direct_reference_mat_export, user, measure_details, ENV['VSAC_USERNAME'], ENV['VSAC_PASSWORD']).save
+      assert_equal 2, CqlMeasure.all.count
+      measures = CqlMeasure.all
+      # Confirm that the Direct Reference Code, code_list_id hash has not changed between Uploads.
+      assert_equal measures[0]['source_data_criteria']['prefix_5195_3_LaboratoryTestPerformed_70C9F083_14BD_4331_99D7_201F8589059D_source']['code_list_id'], measures[1]['source_data_criteria']['prefix_5195_3_LaboratoryTestPerformed_70C9F083_14BD_4331_99D7_201F8589059D_source']['code_list_id']
+      assert_equal measures[0]['data_criteria']['prefix_5195_3_LaboratoryTestPerformed_70C9F083_14BD_4331_99D7_201F8589059D']['code_list_id'], measures[1]['data_criteria']['prefix_5195_3_LaboratoryTestPerformed_70C9F083_14BD_4331_99D7_201F8589059D']['code_list_id']
+    end
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bonnie_bundler
 version: !ruby/object:Gem::Version
-  version: 2.0.1
+  version: 2.0.2
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-12-19 00:00:00.000000000 Z
+date: 2018-01-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: health-data-standards
@@ -176,6 +176,8 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- ".github/CONTRIBUTING.md"
+- ".github/PULL_REQUEST_TEMPLATE.md"
 - ".gitignore"
 - ".travis.yml"
 - Gemfile
@@ -254,7 +256,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.12
+rubygems_version: 2.5.2.1
 signing_key: 
 specification_version: 4
 summary: A Gem for creating and managing bonnie bundles