cqm-validators 3.0.0 → 4.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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-SHA1:
-  metadata.gz: b6ac5efe9cf0f9d3b494df3e1232e4b344588f5a
-  data.tar.gz: 1af92994e5886b95b087fef53b906b6cb57be40b
+SHA256:
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+  data.tar.gz: 7642850c6daf117dec474a52256801b1263ef0aeb78abcdf6d2bcb8378230431
 SHA512:
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-  data.tar.gz: 33bc96b5f3291ca1bb9ef6e87c9f4a76ee7989f79e5a9c7645f6056aeffda672ab53f85c2f2653c6fa9f901cb7d5a73c1bd58d783e1971fa9e240214841bb747
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+  data.tar.gz: 8a1b7f742eb7107ab9ea3b0caa59935f0c8f47e084ce62262b206902464221f09aa45b62132effe697c17ef5231cc4fee07b6561d4b644bc352bec0d83af9566

data/.github/workflows/ci.yml

@@ -0,0 +1,35 @@
+name: Continuous Integration
+on:
+  pull_request:
+    branches:
+      - master
+      - cqm_validators_2_x
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        ruby-version: [2.6, 2.5]
+        mongodb-version: [4.0.18, 4.4]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Use Ruby ${{ matrix.ruby-version }}
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: ${{ matrix.ruby-version }}
+    - name: Install dependencies
+      run: bundle install
+    - name: Start MongoDB
+      uses: supercharge/mongodb-github-action@1.3.0
+      with:
+        mongodb-version: ${{ matrix.mongodb-version }}
+    - name: Run overcommit
+      run: |
+        bundle exec overcommit --sign
+        bundle exec overcommit --run
+    - name: Run tests
+      run: bundle exec rake test

data/.overcommit.yml

@@ -7,6 +7,8 @@ PreCommit:
     exclude: ['test/fixtures/**/*', 'lib/schema/**/*', 'lib/schematron/iso-schematron-xslt1/**/*', 'lib/schematron/iso-schematron-xslt2/**/*', 'lib/schematron/qrda/**/*']
   AuthorName:
     enabled: false
+  AuthorEmail:
+    enabled: false
 CommitMsg:
   RussianNovel:
     enabled: true

data/.rubocop.yml

@@ -1,5 +1,5 @@
 AllCops:
-  TargetRubyVersion: 2.6
+  TargetRubyVersion: 2.4
   Exclude:
     - bin/*
 Style/Documentation:
@@ -56,6 +56,8 @@ Metrics/CyclomaticComplexity:
   Max: 10
 Metrics/PerceivedComplexity:
   Max: 10
+  Exclude:
+    - 'lib/reported_result_extractor.rb'
 Naming/MethodParameterName:
   Enabled: false
 Style/DateTime:

data/.simplecov

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 SimpleCov.start do
   merge_timeout 3600
 end

data/Gemfile

@@ -9,6 +9,6 @@ gemspec development_group: :test
 
 group :test do
   gem 'codecov', require: false
-  gem 'cqm-models', git: 'https://github.com/projecttacoma/cqm-models.git', branch: 'master'
+  gem 'cqm-models', '~> 3.0'
   gem 'simplecov', require: false
 end

data/README.md

@@ -25,6 +25,7 @@ Starting with version **2.0.0** released on 6/20/19, cqm-validators versioning h
   | X | QRDA Cat 1 | QRDA Cat 3 |
   | --- | --- | --- |
   | 2 | R1 STU5.1 | R1 STU2.1 |
+  | 3 | R1 STU5.2 | R1 STU2.1 |
 
 * **Y** indicates major changes (incompatible API changes)
 

data/cqm_validators.gemspec

@@ -22,7 +22,9 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ['lib']
 
-  spec.add_dependency 'nokogiri', '~>1.10'
+  spec.required_ruby_version = '>= 2.4.0'
+
+  spec.add_dependency 'nokogiri', '>= 1.8.5', '< 1.13.0'
 
   spec.add_development_dependency 'bundler'
   spec.add_development_dependency 'byebug'
@@ -30,6 +32,6 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency 'minitest-reporters'
   spec.add_development_dependency 'mongoid'
   spec.add_development_dependency 'overcommit'
-  spec.add_development_dependency 'rake', '~> 10.0'
-  spec.add_development_dependency 'rubocop', '~> 0.60'
+  spec.add_development_dependency 'rake', '>= 12.3.3'
+  spec.add_development_dependency 'rubocop', '~> 0.93'
 end

data/lib/cqm_validators/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module CqmValidators
-  VERSION = '3.0.0'
+  VERSION = '4.0.0'
 end

data/lib/measure_validator.rb

@@ -12,7 +12,7 @@ module CqmValidators
       @errors = []
       @doc = get_document(file)
       @doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
-      measure_ids = CQM::Measure.all.map(&:hqmf_id)
+      measure_ids = CQM::Measure.pluck(:hqmf_id)
       doc_measure_ids = @doc.xpath(measure_selector).map(&:value).map(&:upcase)
       # list of all of the set ids in the QRDA
       doc_neutral_ids = @doc.xpath(neutral_measure_selector).map(&:value).map(&:upcase).sort

data/lib/performance_rate_validator.rb

@@ -35,10 +35,13 @@ module CqmValidators
       denexcep = 0
       denom = 0
       numer = 0
+      numex = 0
       denex = reported_result['DENEX'] unless reported_result['DENEX'].nil?
       denexcep = reported_result['DENEXCEP'] unless reported_result['DENEXCEP'].nil?
       denom = reported_result['DENOM'] unless reported_result['DENOM'].nil?
       numer = reported_result['NUMER'] unless reported_result['NUMER'].nil?
+      numex = reported_result['NUMEX'] unless reported_result['NUMEX'].nil?
+      numer -= numex
       denom = denom - denex - denexcep
       pr = if denom.zero?
              'NA'

data/lib/reported_result_extractor.rb

@@ -8,7 +8,7 @@ module CqmValidators
     # returns nil if nothing matching is found
     # returns a hash with the values of the populations filled out along with the population_ids added to the result
 
-    ALL_POPULATION_CODES = %w[IPP DENOM NUMER NUMEX DENEX DENEXCEP MSRPOPL MSRPOPLEX OBSERV].freeze
+    ALL_POPULATION_CODES = %w[IPP DENOM NUMER NUMEX DENEX DENEXCEP MSRPOPL MSRPOPLEX].freeze
 
     def extract_results_by_ids(measure, poulation_set_id, doc, stratification_id = nil)
       results = nil
@@ -36,21 +36,14 @@ module CqmValidators
     end
 
     def get_measure_components(n, population_set, stratification_id)
-      results = { supplemental_data: {} }
+      # observations are a hash of population/value. For example {"DENOM"=>108.0, "NUMER"=>2}
+      results = { supplemental_data: {}, observations: {} }
       stratification = stratification_id ? population_set.stratifications.where(stratification_id: stratification_id).first.hqmf_id : nil
       ALL_POPULATION_CODES.each do |pop_code|
-        next unless population_set.populations[pop_code] || pop_code == 'OBSERV'
+        next unless population_set.populations[pop_code]
 
-        val = nil
-        sup = nil
-        if pop_code == 'OBSERV'
-          next unless population_set.populations['MSRPOPL']
-
-          msrpopl = population_set.populations['MSRPOPL']['hqmf_id']
-          val, sup = extract_cv_value(n, population_set.observations.first.hqmf_id, msrpopl, stratification)
-        else
-          val, sup, pr = extract_component_value(n, pop_code, population_set.populations[pop_code]['hqmf_id'], stratification)
-        end
+        get_observed_values(results, n, pop_code, population_set, stratification)
+        val, sup, pr = extract_component_value(n, pop_code, population_set.populations[pop_code]['hqmf_id'], stratification)
         unless val.nil?
           results[pop_code] = val
           results[:supplemental_data][pop_code] = sup
@@ -60,8 +53,19 @@ module CqmValidators
       results
     end
 
-    def extract_cv_value(node, id, msrpopl, strata = nil)
-      xpath_observation = %( cda:component/cda:observation[./cda:value[@code = "MSRPOPL"] and ./cda:reference/cda:externalObservation/cda:id[#{translate('@root')}='#{msrpopl.upcase}']])
+    def get_observed_values(results, n, pop_code, population_set, stratification)
+      statement_name = population_set.populations[pop_code]['statement_name']
+      # look to see if there is an observation that corresponds to the specific statement_name
+      statement_observation = population_set.observations.select { |obs| obs.observation_parameter.statement_name == statement_name }
+      # return unless an observation is found
+      unless statement_observation.empty?
+        hqmf_id = population_set.populations[pop_code]['hqmf_id']
+        results[:observations][pop_code] = extract_cv_value(n, statement_observation.first.hqmf_id, hqmf_id, pop_code, stratification)
+      end
+    end
+
+    def extract_cv_value(node, id, msrpopl, pop_code, strata = nil)
+      xpath_observation = %( cda:component/cda:observation[./cda:value[@code = "#{pop_code}"] and ./cda:reference/cda:externalObservation/cda:id[#{translate('@root')}='#{msrpopl.upcase}']])
       cv = node.at_xpath(xpath_observation)
       return nil unless cv
 
@@ -73,7 +77,7 @@ module CqmValidators
       else
         val = get_cv_value(cv, id)
       end
-      [val, (strata.nil? ? extract_supplemental_data(cv) : nil)]
+      val
     end
 
     def extract_component_value(node, code, id, strata = nil)