cqm-validators 0.1.1 → 3.0.1

checksums.yaml

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

@@ -0,0 +1,23 @@
+Pull requests into cqm-validators 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.
+- [ ] Internal ticket for this PR:
+- [ ] Internal ticket links to this PR
+- [ ] Code diff has been done and been reviewed
+- [ ] Tests are included and test edge cases
+- [ ] Tests have been run locally and pass
+
+**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
+
+**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

data/.gitignore

@@ -4,4 +4,6 @@ test/xsd
 tmp
 .DS_Store
 .idea
-.rvmrc
+.rvmrc
+Gemfile.lock
+.byebug_history

data/.overcommit.yml

@@ -0,0 +1,18 @@
+PreCommit:
+  RuboCop:
+    enabled: true
+    on_warn: 'fail'
+  HardTabs:
+    enabled: true
+    exclude: ['test/fixtures/**/*', 'lib/schema/**/*', 'lib/schematron/iso-schematron-xslt1/**/*', 'lib/schematron/iso-schematron-xslt2/**/*', 'lib/schematron/qrda/**/*']
+  AuthorName:
+    enabled: false
+CommitMsg:
+  RussianNovel:
+    enabled: true
+  HardTabs:
+    enabled: true
+  TextWidth:
+    enabled: false
+  CapitalizedSubject:
+    enabled: false

data/.rubocop.yml

@@ -0,0 +1,74 @@
+AllCops:
+  TargetRubyVersion: 2.5
+  Exclude:
+    - bin/*
+Style/Documentation:
+  Enabled: false
+# TODO: remove this exception when java_processor.rb is fixed to rescue StandardError
+Style/HashEachMethods:
+  Enabled: false
+Style/HashTransformKeys:
+  Enabled: false
+Style/HashTransformValues:
+  Enabled: false
+Lint/RescueException:
+  Exclude:
+    - 'lib/schematron/java_processor.rb'
+Metrics/AbcSize:
+  # The ABC size is a calculated magnitude, so this number can be a Fixnum or
+  # a Float.
+  Max: 32
+  Exclude:
+    - 'test/**/*.rb'
+    # TODO: remove exclusions below this line as ABC Size is fixed
+    - 'lib/performance_rate_validator.rb'
+Metrics/BlockLength:
+  Exclude:
+    - 'test/factories/*'
+Metrics/ClassLength:
+  Max: 120
+  Exclude:
+    - 'test/**/*'
+    # TODO: remove exclusions below this line as Class length is fixed
+    - 'lib/qrda_qdm_template_validator.rb'
+Layout/LineLength:
+  Max: 150
+  Exclude:
+    - 'test/**/*'
+    # TODO: remove exclusions below this line as line length is fixed
+    - 'lib/reported_result_extractor.rb'
+    - 'lib/data_validator.rb'
+    - 'lib/measure_validator.rb'
+Metrics/MethodLength:
+  CountComments: false  # count full line comments?
+  Max: 20
+  Exclude:
+    - 'test/**/*'
+    # TODO: remove exclusions below this line as method length is fixed
+    - 'lib/reported_result_extractor.rb'
+Metrics/ModuleLength:
+  Max: 110
+  Exclude:
+    # TODO: remove exclusions below this line as module length is fixed
+    - 'lib/reported_result_extractor.rb'
+# Avoid complex methods.
+Metrics/CyclomaticComplexity:
+  Max: 10
+Metrics/PerceivedComplexity:
+  Max: 10
+  Exclude:
+    - 'lib/reported_result_extractor.rb'
+Naming/MethodParameterName:
+  Enabled: false
+Style/DateTime:
+  Enabled: false
+Style/GuardClause:
+  MinBodyLength: 100
+  Exclude:
+    # TODO: remove exclusions below this line as ABC Size is fixed
+    - 'lib/performance_rate_validator.rb'
+Style/MixinUsage:
+  Exclude:
+    - 'test/test_helper.rb'
+Style/RescueStandardError:
+  Enabled: false

data/.simplecov

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+SimpleCov.start do
+  merge_timeout 3600
+end
+
+if ENV['CI'] == 'true'
+  require 'codecov'
+  SimpleCov.formatter = SimpleCov::Formatter::Codecov
+else
+  SimpleCov.formatter = SimpleCov::Formatter::HTMLFormatter
+end

data/.travis.yml

@@ -0,0 +1,20 @@
+language: ruby
+rvm:
+  - 2.6
+  - 2.5
+cache:
+  - bundler
+sudo: required
+services:
+  - mongodb
+branches:
+  only:
+  - master
+  - cqm_validators_2_x
+before_script:
+  - git config --global user.email "travis@travis.ci"
+  - git config --global user.name "Travis CI"
+script:
+  - bundle exec overcommit --sign
+  - bundle exec overcommit --run
+  - travis_retry bundle exec rake test

data/Gemfile

@@ -1,6 +1,14 @@
-source "https://rubygems.org"
+# frozen_string_literal: true
 
-git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+source 'https://rubygems.org'
+
+git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }
 
 # Specify your gem's dependencies in cqm_validators.gemspec
-gemspec
+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 'simplecov', require: false
+end

data/README.md

@@ -1,11 +1,11 @@
-This is a validation library that is used by Cypress for QRDA validation.
+This is a library that is used by Cypress for QRDA validation. It contains Schematron validators, schema validators, and validators for QRDA-specific features (measure IDs, performance rates, result extraction, etc).
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/cqm_validators.
+Bug reports and pull requests are welcome on GitHub at https://github.com/projecttacoma/cqm_validators.
 
 Environment
 ===========
 
-This project currently uses Ruby 2.0.0, Ruby 2.1.1, Ruby 2.2.1, and JRuby 1.7.11 and is built using [Bundler](http://gembundler.com/). To get all of the dependencies for the project, first install bundler:
+This project currently uses Ruby 2.3, Ruby 2.4, Ruby 2.5 and Ruby 2.6 and is built using [Bundler](http://gembundler.com/). To get all of the dependencies for the project, first install bundler:
 
     gem install bundler
 
@@ -13,9 +13,26 @@ Then run bundler to grab all of the necessary gems:
 
     bundle install
 
-The Quality Measure engine relies on a MongoDB [MongoDB](http://www.mongodb.org/) running a minimum of version 2.4.* or higher.  To get and install Mongo refer to:
 
-    http://www.mongodb.org/display/DOCS/Quickstart
+
+Versioning
+==========
+
+Starting with version **2.0.0** released on 6/20/19, cqm-validators versioning has the format **X.Y.Z**, where:
+
+* **X** maps to a version of QRDA. See the table below to see the existing mapping to QRDA versions.
+
+  | 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)
+
+* **Z** indicates minor changes (added functionality in a backwards-compatible manner) and patch changes (backwards-compatible bug fixes)
+
+For the versions available, see [tags on this repository](https://github.com/projecttacoma/cqm-validators/tags).
+
 
 Project Practices
 =================
@@ -37,4 +54,4 @@ Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
-limitations under the License.
+limitations under the License.

data/Rakefile

@@ -1,10 +1,12 @@
-require "bundler/gem_tasks"
-require "rake/testtask"
+# frozen_string_literal: true
+
+require 'bundler/gem_tasks'
+require 'rake/testtask'
 
 Rake::TestTask.new(:test) do |t|
-  t.libs << "test"
-  t.libs << "lib"
-  t.test_files = FileList["test/**/*_test.rb"]
+  t.libs << 'test'
+  t.libs << 'lib'
+  t.test_files = FileList['test/**/*_test.rb']
 end
 
-task :default => :test
+task default: :test

data/config/mongoid.yml

@@ -0,0 +1,6 @@
+test:
+  clients:
+    default:
+      database: cqmv_test
+      hosts:
+        - <%= ENV['TEST_DB_HOST'] || '127.0.0.1' %>:27017

data/cqm_validators.gemspec

@@ -1,28 +1,37 @@
+# frozen_string_literal: true
 
-lib = File.expand_path("../lib", __FILE__)
+lib = File.expand_path('lib', __dir__)
 $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
-require "cqm_validators/version"
+require 'cqm_validators/version'
 
 Gem::Specification.new do |spec|
-  spec.name          = "cqm-validators"
+  spec.name          = 'cqm-validators'
   spec.version       = CqmValidators::VERSION
-  spec.authors       = ["Laura", "Michael O'Keefe"]
-  spec.email         = ["laclark@mitre.org", 'mokeefe@mitre.org']
+  spec.authors       = ['Laura', "Michael O'Keefe"]
+  spec.email         = ['laclark@mitre.org', 'mokeefe@mitre.org']
   spec.license       = 'Apache-2.0'
 
-  spec.summary       = "new cqm validator library"
-  spec.description   = "new cqm validator library"
-  spec.homepage      = "https://github.com/projecttacoma/cqm-validators"
+  spec.summary       = 'new cqm validator library'
+  spec.description   = 'new cqm validator library'
+  spec.homepage      = 'https://github.com/projecttacoma/cqm-validators'
 
   spec.files         = `git ls-files -z`.split("\x0").reject do |f|
     f.match(%r{^(test|spec|features)/})
   end
-  spec.bindir        = "exe"
+  spec.bindir        = 'exe'
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
-  spec.require_paths = ["lib"]
+  spec.require_paths = ['lib']
 
-  spec.add_dependency "nokogiri", "~>1.10.3"
-  spec.add_development_dependency "bundler", "~> 1.16"
-  spec.add_development_dependency "rake", "~> 10.0"
-  spec.add_development_dependency "minitest", "~> 5.0"
+  spec.required_ruby_version = '>= 2.5.0'
+
+  spec.add_dependency 'nokogiri', '~>1.10'
+
+  spec.add_development_dependency 'bundler'
+  spec.add_development_dependency 'byebug'
+  spec.add_development_dependency 'minitest', '~> 5.0'
+  spec.add_development_dependency 'minitest-reporters'
+  spec.add_development_dependency 'mongoid'
+  spec.add_development_dependency 'overcommit'
+  spec.add_development_dependency 'rake', '>= 12.3.3'
+  spec.add_development_dependency 'rubocop', '~> 0.93'
 end

data/lib/base_validator.rb

@@ -1,22 +1,22 @@
+# frozen_string_literal: true
+
 module CqmValidators
-      module BaseValidator
-  
-        def build_error(msg, loc, file_name)
-          ValidationError.new(message: msg, location: loc, file_name: file_name, validator: @name)
-        end
-  
-        def get_document(input)
-          doc = case input
-          when File
-            input.read
-          when Nokogiri::XML::Document
-            return input
-          else
-            input
-          end
-          Nokogiri::XML(doc.to_s) { |conf| conf.strict.nonet.noblanks } #grumble, grumble nokogiri java @SS 
-        end
-      end
-  
+  module BaseValidator
+    def build_error(msg, loc, file_name)
+      ValidationError.new(message: msg, location: loc, file_name: file_name, validator: @name)
+    end
+
+    def get_document(input)
+      doc = case input
+            when File
+              input.rewind
+              input.read
+            when Nokogiri::XML::Document
+              return input
+            else
+              input
+            end
+      Nokogiri::XML(doc.to_s) { |conf| conf.strict.nonet.noblanks } # grumble, grumble nokogiri java @SS
+    end
+  end
 end
-  

data/lib/cqm_validators.rb

@@ -1,4 +1,6 @@
-require "cqm_validators/version"
+# frozen_string_literal: true
+
+require 'cqm_validators/version'
 require 'reported_result_extractor'
 require 'base_validator'
 require 'data_validator'
@@ -8,7 +10,7 @@ require 'qrda_qdm_template_validator'
 require 'schema_validator'
 require 'schematron_validator'
 require 'validators'
-require "schematron/c_processor"
+require 'schematron/c_processor'
 
 module CqmValidators
   # Your code goes here...

data/lib/cqm_validators/version.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module CqmValidators
-  VERSION = "0.1.1"
+  VERSION = '3.0.1'
 end

data/lib/data_validator.rb

@@ -1,82 +1,77 @@
+# frozen_string_literal: true
+
 module CqmValidators
-      class DataValidator
-        include BaseValidator
-  
-        HL7_QRDA_OIDS = ["2.16.840.1.113883.3.221.5",
-                         "2.16.840.1.113883.3.88.12.3221.8.7",
-                         "2.16.840.1.113883.3.88.12.3221.8.9",
-                         "2.16.840.1.113883.1.11.12839",
-                         "2.16.840.1.113883.3.88.12.3221.8.11",
-                         "2.16.840.1.113883.3.88.12.3221.6.2",
-                         "2.16.840.1.113883.11.20.9.40",
-                         "2.16.840.1.113883.11.20.9.23",
-                         "2.16.840.1.113883.3.88.12.3221.7.4",
-                         "2.16.840.1.113883.11.20.9.18",
-                         "2.16.840.1.113883.11.20.9.22",
-                         "2.16.840.1.113883.1.11.16866",
-                         "2.16.840.1.113883.1.11.20275",
-                         "2.16.840.1.113883.11.20.9.34",
-                         "2.16.840.1.113883.3.88.12.3221.7.2",
-                         "2.16.840.1.113883.3.88.12.80.17",
-                         "2.16.840.1.113883.3.88.12.80.22",
-                         "2.16.840.1.113883.3.88.12.80.64",
-                         "2.16.840.1.113883.3.88.12.3221.6.8",
-                         "2.16.840.1.113883.1.11.78",
-                         "2.16.840.1.113883.11.20.9.25",
-                         "2.16.840.1.113883.11.20.9.39",
-                         "2.16.840.1.113883.3.88.12.80.32",
-                         "2.16.840.1.113883.11.20.9.21",
-                         "2.16.840.1.113883.3.88.12.80.68",
-                         "2.16.840.1.113883.1.11.20.12",
-                         "2.16.840.1.113883.11.20.9.24",
-                         "2.16.840.1.113883.11.20.9.41",
-                         "2.16.840.1.113883.1.11.16926",
-                         "2.16.840.1.113883.1.11.12212",
-                         "2.16.840.1.113883.1.11.19185",
-                         "2.16.840.1.113883.1.11.14914",
-                         "2.16.840.1.114222.4.11.837",
-                         "2.16.840.1.113883.1.11.19563",
-                         "2.16.840.1.113883.1.11.11526",
-                         "2.16.840.1.113883.11.20.9.20",
-                         "2.16.840.1.113883.3.88.12.80.2",
-                         "2.16.840.1.113883.3.88.12.80.63",
-                         "2.16.840.1.113883.1.11.12249",
-                         "2.16.840.1.113883.1.11.1",
-                         "2.16.840.1.113883.1.11.12199",
-                         "2.16.840.1.113883.11.20.9.33",
-                         "2.16.840.1.114222.4.11.1066",
-                         "2.16.840.1.113883.1.11.19579"]
-  
-        def initialize(bundle, measure_ids)
-          @bundle = bundle
-          measures = @bundle.measures.in(hqmf_id: measure_ids)
-  
-          @oids = measures.collect{|m| m.oids}.flatten.uniq + HL7_QRDA_OIDS
+  class DataValidator
+    include BaseValidator
+
+    HL7_QRDA_OIDS = ['2.16.840.1.113883.3.221.5',
+                     '2.16.840.1.113883.3.88.12.3221.8.7',
+                     '2.16.840.1.113883.3.88.12.3221.8.9',
+                     '2.16.840.1.113883.1.11.12839',
+                     '2.16.840.1.113883.3.88.12.3221.8.11',
+                     '2.16.840.1.113883.3.88.12.3221.6.2',
+                     '2.16.840.1.113883.11.20.9.40',
+                     '2.16.840.1.113883.11.20.9.23',
+                     '2.16.840.1.113883.3.88.12.3221.7.4',
+                     '2.16.840.1.113883.11.20.9.18',
+                     '2.16.840.1.113883.11.20.9.22',
+                     '2.16.840.1.113883.1.11.16866',
+                     '2.16.840.1.113883.1.11.20275',
+                     '2.16.840.1.113883.11.20.9.34',
+                     '2.16.840.1.113883.3.88.12.3221.7.2',
+                     '2.16.840.1.113883.3.88.12.80.17',
+                     '2.16.840.1.113883.3.88.12.80.22',
+                     '2.16.840.1.113883.3.88.12.80.64',
+                     '2.16.840.1.113883.3.88.12.3221.6.8',
+                     '2.16.840.1.113883.1.11.78',
+                     '2.16.840.1.113883.11.20.9.25',
+                     '2.16.840.1.113883.11.20.9.39',
+                     '2.16.840.1.113883.3.88.12.80.32',
+                     '2.16.840.1.113883.11.20.9.21',
+                     '2.16.840.1.113883.3.88.12.80.68',
+                     '2.16.840.1.113883.1.11.20.12',
+                     '2.16.840.1.113883.11.20.9.24',
+                     '2.16.840.1.113883.11.20.9.41',
+                     '2.16.840.1.113883.1.11.16926',
+                     '2.16.840.1.113883.1.11.12212',
+                     '2.16.840.1.113883.1.11.19185',
+                     '2.16.840.1.113883.1.11.14914',
+                     '2.16.840.1.114222.4.11.837',
+                     '2.16.840.1.113883.1.11.19563',
+                     '2.16.840.1.113883.1.11.11526',
+                     '2.16.840.1.113883.11.20.9.20',
+                     '2.16.840.1.113883.3.88.12.80.2',
+                     '2.16.840.1.113883.3.88.12.80.63',
+                     '2.16.840.1.113883.1.11.12249',
+                     '2.16.840.1.113883.1.11.1',
+                     '2.16.840.1.113883.1.11.12199',
+                     '2.16.840.1.113883.11.20.9.33',
+                     '2.16.840.1.114222.4.11.1066',
+                     '2.16.840.1.113883.1.11.19579'].freeze
+
+    def initialize(measure_ids)
+      measures = CQM::Measure.find(measure_ids)
+      @value_set_ids = measures.collect { |m| m.value_sets.map(&:_id) }.flatten.uniq
+    end
+
+    def validate(file, options = {})
+      doc = get_document(file)
+
+      doc.xpath('//*[@sdtc:valueSet]').each_with_object([]) do |node, errors|
+        oid = node.at_xpath('@sdtc:valueSet')
+        vs = CQM::ValueSet.where('oid' => oid, '_id' => { '$in' => @value_set_ids }).first
+        next unless vs
+
+        code = node.at_xpath('@code')
+        code_system_oid = node.at_xpath('@codeSystem')
+        null_flavor = node.at_xpath('@nullFlavor')
+        next unless vs.concepts.where(code: code, code_system_oid: code_system_oid).count.zero?
+
+        unless null_flavor
+          errors << build_error("The code #{code} in codeSystem #{code_system_oid} cannot be found in the declared valueset #{oid}",
+                                node.path, options[:file_name])
         end
-  
-        def validate(file, options={})
-          doc = get_document(file)
-  
-          doc.xpath("//*[@sdtc:valueSet]").inject([]) do |errors, node|
-            oid = node.at_xpath("@sdtc:valueSet")
-            vs = @bundle.value_sets.where({"oid" => oid}).first
-            code = node.at_xpath("@code")
-            code_system = node.at_xpath("@codeSystem")
-            null_flavor = node.at_xpath("@nullFlavor")
-            if !vs
-              errors << build_error("The valueset #{oid} declared in the document cannot be found", node.path, options[:file_name])
-            elsif !@oids.include?(oid.value)
-              errors << build_error("File appears to contain data criteria outside that required by the measures. Valuesets in file not in measures tested #{oid}'",
-                          node.path, options[:file_name])
-            elsif vs.concepts.where({"code" => code, "code_system"=>code_system}).count() == 0
-              if !null_flavor
-                errors << build_error("The code #{code} in codeSystem #{code_system} cannot be found in the declared valueset #{oid}",
-                  node.path, options[:file_name])
-              end
-            end
-            errors
-          end
-        end
-  
       end
-end
+    end
+  end
+end