MAT-2647 Update cqm-parsers to QDM 5.6 (#148)

* MAT-2647 Update cqm-parsers to QDM 5.6 * MAT-2647 Update cqm-parsers to QDM 5.6 * added git actions * removed travis.yaml
projecttacoma · May 11, 2021 · 271e231 · 271e231
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commit 271e231
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diff --git a/.github/ci.yml b/.github/ci.yml
@@ -0,0 +1,33 @@
+name: Continuous Integration
+on:
+  pull_request:
+    branches: [master, bonnie_version]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        ruby-version: [2.5, 2.7.2]
+        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 audit
+      run: bundle exec bundle-audit check --update
+    - name: Run tests
+      run: bundle exec rake test
+    - name: Run rubocop
+      run: rubocop
diff --git a/.travis.yml b/.travis.yml
diff --git a/Gemfile b/Gemfile
@@ -4,8 +4,7 @@ gemspec :development_group => :test
 
 gem 'mongoid', '~> 6.4.2'
 
-# gem 'cqm-models', '~> 3.0.0'
-# gem 'cqm-models', git: 'https://github.com/projecttacoma/cqm-models.git', branch: 'MAT-1708'
+gem 'cqm-models', git: 'https://github.com/projecttacoma/cqm-models.git', branch: 'master'
 # gem 'cqm-models', :path => '../cqm-models'
 
 group :development, :test do

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,10 +1,16 @@
+GIT
+  remote: https://github.com/projecttacoma/cqm-models.git
+  revision: c1b6383b0e91bdb968aa16ed390065e3ea47c72c
+  branch: master
+  specs:
+    cqm-models (4.0.0)
+
 PATH
   remote: .
   specs:
     cqm-parsers (0.2.1.1)
       activesupport (~> 5.2.1)
       builder (~> 3.1)
-      cqm-models (~> 3.0.6)
       erubis (~> 2.7.0)
       highline (~> 1.7.0)
       log4r (~> 1.1.10)
@@ -21,123 +27,119 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activemodel (5.2.4.3)
-      activesupport (= 5.2.4.3)
-    activesupport (5.2.4.3)
+    activemodel (5.2.6)
+      activesupport (= 5.2.6)
+    activesupport (5.2.6)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
       tzinfo (~> 1.1)
-    addressable (2.5.2)
-      public_suffix (>= 2.0.2, < 4.0)
+    addressable (2.7.0)
+      public_suffix (>= 2.0.2, < 5.0)
     ansi (1.5.0)
-    ast (2.4.0)
-    awesome_print (1.8.0)
-    bson (4.10.0)
+    ast (2.4.2)
+    awesome_print (1.9.2)
+    bson (4.12.0)
     builder (3.2.4)
-    bundler-audit (0.6.0)
-      bundler (~> 1.2)
-      thor (~> 0.18)
+    bundler-audit (0.8.0)
+      bundler (>= 1.2.0, < 3)
+      thor (~> 1.0)
     byebug (6.0.2)
     cane (2.3.0)
       parallel
-    codecov (0.2.5)
-      colorize
-      json
-      simplecov
-    coderay (1.1.2)
-    colorize (0.8.1)
-    concurrent-ruby (1.1.6)
-    cqm-models (3.0.6)
-    crack (0.4.3)
-      safe_yaml (~> 1.0.0)
-    docile (1.3.1)
+    codecov (0.5.2)
+      simplecov (>= 0.15, < 0.22)
+    coderay (1.1.3)
+    concurrent-ruby (1.1.8)
+    crack (0.4.5)
+      rexml
+    docile (1.3.5)
     erubis (2.7.0)
-    ethon (0.12.0)
-      ffi (>= 1.3.0)
+    ethon (0.14.0)
+      ffi (>= 1.15.0)
     factory_girl (4.1.0)
       activesupport (>= 3.0.0)
-    ffi (1.14.2)
-    hashdiff (0.3.7)
+    ffi (1.15.0)
+    hashdiff (1.0.1)
     highline (1.7.10)
-    i18n (1.8.5)
+    i18n (1.8.10)
       concurrent-ruby (~> 1.0)
-    json (2.3.1)
     log4r (1.1.10)
     log_switch (1.0.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     memoist (0.9.3)
-    method_source (0.8.2)
+    method_source (0.9.2)
     mini_portile2 (2.4.0)
-    minitest (5.14.1)
-    minitest-reporters (1.3.5)
+    minitest (5.14.4)
+    minitest-reporters (1.4.3)
       ansi
       builder
       minitest (>= 5.0)
       ruby-progressbar
-    mongo (2.13.0)
+    mongo (2.14.0)
       bson (>= 4.8.2, < 5.0.0)
-    mongoid (6.4.5)
+    mongoid (6.4.8)
       activemodel (>= 5.1, < 6.0.0)
       mongo (>= 2.5.1, < 3.0.0)
     mongoid-tree (2.1.1)
       mongoid (>= 4.0, < 8)
     mustache (1.1.1)
     nokogiri (1.10.10)
       mini_portile2 (~> 2.4.0)
-    parallel (1.17.0)
-    parser (2.6.2.0)
-      ast (~> 2.4.0)
-    powerpack (0.1.2)
-    pry (0.10.4)
+    parallel (1.20.1)
+    parser (2.7.2.0)
+      ast (~> 2.4.1)
+    powerpack (0.1.3)
+    pry (0.12.2)
       coderay (~> 1.1.0)
-      method_source (~> 0.8.1)
-      slop (~> 3.4)
-    pry-nav (0.2.4)
-      pry (>= 0.9.10, < 0.11.0)
-    public_suffix (3.0.3)
+      method_source (~> 0.9.0)
+    pry-nav (0.3.0)
+      pry (>= 0.9.10, < 0.13.0)
+    public_suffix (4.0.6)
     rainbow (3.0.0)
-    rake (12.3.3)
+    rake (13.0.3)
+    rexml (3.2.5)
     rubocop (0.52.1)
       parallel (~> 1.10)
       parser (>= 2.4.0.2, < 3.0)
       powerpack (~> 0.1)
       rainbow (>= 2.2.2, < 4.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (~> 1.0, >= 1.0.1)
-    ruby-progressbar (1.10.0)
+    ruby-progressbar (1.11.0)
     rubyzip (1.3.0)
-    safe_yaml (1.0.4)
-    simplecov (0.16.1)
+    simplecov (0.21.2)
       docile (~> 1.1)
-      json (>= 1.8, < 3)
-      simplecov-html (~> 0.10.0)
-    simplecov-html (0.10.2)
-    slop (3.6.0)
+      simplecov-html (~> 0.11)
+      simplecov_json_formatter (~> 0.1)
+    simplecov-html (0.12.3)
+    simplecov_json_formatter (0.1.3)
+    sync (0.5.0)
     systemu (2.6.5)
     tailor (1.1.5)
       log_switch (>= 0.3.0)
       term-ansicolor (>= 1.0.5)
       text-table (>= 1.2.2)
-    term-ansicolor (1.6.0)
+    term-ansicolor (1.7.1)
       tins (~> 1.0)
     text-table (1.2.4)
-    thor (0.20.0)
+    thor (1.1.0)
     thread_safe (0.3.6)
-    tins (1.16.3)
+    tins (1.29.0)
+      sync
     typhoeus (1.4.0)
       ethon (>= 0.9.0)
-    tzinfo (1.2.7)
+    tzinfo (1.2.9)
       thread_safe (~> 0.1)
-    unicode-display_width (1.4.0)
+    unicode-display_width (1.7.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
-    vcr (3.0.3)
-    webmock (3.4.2)
+    vcr (6.0.0)
+    webmock (3.12.2)
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
-      hashdiff
+      hashdiff (>= 0.4.0, < 2.0.0)
     zip-zip (0.3)
       rubyzip (>= 1.0.0)
 
@@ -150,6 +152,7 @@ DEPENDENCIES
   byebug (~> 6.0.2)
   cane (~> 2.3.0)
   codecov
+  cqm-models!
   cqm-parsers!
   factory_girl (~> 4.1.0)
   minitest (~> 5.3)

diff --git a/cqm-parsers.gemspec b/cqm-parsers.gemspec
@@ -11,7 +11,7 @@ Gem::Specification.new do |s|
 
   s.version = '0.2.1.1'
 
-  s.add_dependency 'cqm-models', '~> 3.0.6'
+  # s.add_dependency 'cqm-models', '~> 3.0.6'
   s.add_dependency 'mustache'
   s.add_dependency 'erubis', '~> 2.7.0'
   s.add_dependency 'mongoid', '~> 6.4.2'

diff --git a/lib/util/hqmfr2cql_template_oid_map.json b/lib/util/hqmfr2cql_template_oid_map.json
@@ -219,10 +219,6 @@
       "definition":"care_goal",
       "status":"",
       "negation":false},
-  "2.16.840.1.113883.10.20.28.4.13":{
-      "definition":"device",
-      "status":"applied",
-      "negation":false},
   "2.16.840.1.113883.10.20.28.4.11":{
       "definition":"device_adverse_event",
       "status":"",

diff --git a/test/fixtures/measureloading/CMS144_v5_8_Artifacts_20191104.zip b/test/fixtures/measureloading/CMS144_v5_8_Artifacts_20191104.zip
diff --git a/test/fixtures/measureloading/CMS144v610-Artifacts.zip b/test/fixtures/measureloading/CMS144v610-Artifacts.zip
diff --git a/test/unit/hqmf/1.0/document_v1_test.rb b/test/unit/hqmf/1.0/document_v1_test.rb
@@ -32,7 +32,7 @@ def test_attributes
       attr = @doc.attribute('F8D5AD22-F49E-4181-B886-E5B12BEA8966e')
       assert_equal 'MSRED', attr.code
       assert_equal '00001231', attr.value
-      assert_equal nil, attr.unit
+      assert_nil attr.unit
       assert_equal 'Measurement end date', attr.name
 
       attr = @doc.attribute_for_code('MSRTP')
@@ -59,7 +59,7 @@ def test_population_criteria
       assert_equal '64', ipp.preconditions[0].comparison.restrictions[0].range.low.value
       assert_equal 'a', ipp.preconditions[0].comparison.restrictions[0].range.low.unit
       assert_equal true, ipp.preconditions[0].comparison.restrictions[0].range.low.inclusive?
-      assert_equal nil, ipp.preconditions[0].comparison.restrictions[0].range.high
+      assert_nil ipp.preconditions[0].comparison.restrictions[0].range.high
 
       den = @doc.population_criteria_for_code('DENOM')
       assert_equal 1, den.preconditions.length
@@ -72,7 +72,7 @@ def test_population_criteria
       num = @doc.population_criteria_for_code('NUMER')
       assert_equal 1, num.preconditions.length
       assert_equal 'AND', num.preconditions[0].conjunction
-      assert_equal nil, num.preconditions[0].comparison
+      assert_nil num.preconditions[0].comparison
       assert_equal 2, num.preconditions[0].preconditions.length
       assert_equal 1, num.preconditions[0].restrictions.length
       assert_equal 'DURING', num.preconditions[0].restrictions[0].type