Merge pull request #283 from onc-healthit/development

Version 2.5.0

Gemfile.lock

@@ -10,11 +10,11 @@ GEM
       public_suffix (>= 2.0.2, < 4.0)
     aes_key_wrap (1.0.1)
     ast (2.4.0)
-    backports (3.13.0)
+    backports (3.15.0)
     base62-rb (0.3.1)
     bcp47 (0.3.3)
       i18n
-    bcrypt (3.1.12)
+    bcrypt (3.1.13)
     bcrypt-ruby (3.1.5)
       bcrypt (>= 3.1.3)
     bindata (2.4.4)
@@ -80,66 +80,67 @@ GEM
       dm-core (~> 1.2.0)
     do_sqlite3 (0.10.17)
       data_objects (= 0.10.17)
-    docile (1.3.1)
-    domain_name (0.5.20180417)
+    docile (1.3.2)
+    domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
     eventmachine (1.2.7)
     faraday (0.15.4)
       multipart-post (>= 1.2, < 3)
     fastercsv (1.5.5)
-    fhir_client (4.0.0)
+    fhir_client (4.0.2)
       activesupport (>= 3)
       addressable (>= 2.3)
-      fhir_dstu2_models (>= 1.0.9)
-      fhir_models (>= 4.0.0)
-      fhir_stu3_models (>= 3.0.0)
-      nokogiri (>= 1.8.2)
+      fhir_dstu2_models (>= 1.0.10)
+      fhir_models (>= 4.0.1)
+      fhir_stu3_models (>= 3.0.1)
+      nokogiri (>= 1.10.4)
       oauth2 (~> 1.1)
       rack (>= 1.5)
       rest-client (~> 2.0)
       tilt (>= 1.1)
-    fhir_dstu2_models (1.0.9)
+    fhir_dstu2_models (1.0.10)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
-      nokogiri (>= 1.8.5)
-    fhir_models (4.0.0)
+      nokogiri (>= 1.10.4)
+    fhir_models (4.0.1)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
-      nokogiri (>= 1.8.2)
-    fhir_stu3_models (3.0.0)
+      nokogiri (>= 1.10.4)
+    fhir_stu3_models (3.0.1)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
-      nokogiri (>= 1.8.2)
-    hashdiff (0.3.9)
+      nokogiri (>= 1.10.4)
+    hashdiff (1.0.0)
+    http-accept (1.7.0)
     http-cookie (1.0.3)
       domain_name (~> 0.5)
     i18n (1.6.0)
       concurrent-ruby (~> 1.0)
-    jaro_winkler (1.5.2)
+    jaro_winkler (1.5.3)
     json (1.8.6)
-    json-jwt (1.10.0)
+    json-jwt (1.10.2)
       activesupport (>= 4.2)
       aes_key_wrap
       bindata
     json_pure (1.8.6)
-    jwt (2.1.0)
+    jwt (2.2.1)
     kramdown (2.1.0)
     method_source (0.9.2)
     mime-types (3.2.2)
       mime-types-data (~> 3.2015)
     mime-types-data (3.2019.0331)
     mini_portile2 (2.4.0)
     minitest (5.11.3)
-    msgpack (1.2.10)
+    msgpack (1.3.1)
     multi_json (1.13.1)
     multi_xml (0.6.0)
-    multipart-post (2.0.0)
+    multipart-post (2.1.1)
     mustermann (1.0.3)
     netrc (0.11.0)
-    nokogiri (1.10.3)
+    nokogiri (1.10.4)
       mini_portile2 (~> 2.4.0)
     oauth2 (1.4.1)
       faraday (>= 0.8, < 0.16.0)
@@ -148,60 +149,59 @@ GEM
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
     parallel (1.17.0)
-    parser (2.6.2.1)
+    parser (2.6.3.0)
       ast (~> 2.4.0)
     pry (0.12.2)
       coderay (~> 1.1.0)
       method_source (~> 0.9.0)
     pry-byebug (3.7.0)
       byebug (~> 11.0)
       pry (~> 0.10)
-    psych (3.1.0)
-    public_suffix (3.0.3)
+    public_suffix (3.1.1)
     rack (2.0.7)
-    rack-protection (2.0.5)
+    rack-protection (2.0.7)
       rack
     rack-test (1.1.0)
       rack (>= 1.0, < 3)
     rainbow (3.0.0)
-    rake (12.3.2)
+    rake (12.3.3)
     rb-readline (0.5.5)
-    rest-client (2.0.2)
+    rest-client (2.1.0)
+      http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rubocop (0.67.2)
+    rubocop (0.74.0)
       jaro_winkler (~> 1.5.1)
       parallel (~> 1.10)
-      parser (>= 2.5, != 2.5.1.1)
-      psych (>= 3.1.0)
+      parser (>= 2.6)
       rainbow (>= 2.2.2, < 4.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 1.4.0, < 1.6)
-    ruby-progressbar (1.10.0)
-    rubyzip (1.2.2)
+      unicode-display_width (>= 1.4.0, < 1.7)
+    ruby-progressbar (1.10.1)
+    rubyzip (1.2.3)
     safe_yaml (1.0.5)
-    selenium-webdriver (3.141.5926)
+    selenium-webdriver (3.142.3)
       childprocess (>= 0.5, < 2.0)
       rubyzip (~> 1.2, >= 1.2.2)
-    simplecov (0.16.1)
+    simplecov (0.17.0)
       docile (~> 1.1)
       json (>= 1.8, < 3)
       simplecov-html (~> 0.10.0)
     simplecov-html (0.10.2)
-    sinatra (2.0.5)
+    sinatra (2.0.7)
       mustermann (~> 1.0)
       rack (~> 2.0)
-      rack-protection (= 2.0.5)
+      rack-protection (= 2.0.7)
       tilt (~> 2.0)
-    sinatra-contrib (2.0.5)
+    sinatra-contrib (2.0.7)
       backports (>= 2.8.2)
       multi_json
       mustermann (~> 1.0)
-      rack-protection (= 2.0.5)
-      sinatra (= 2.0.5)
-      tilt (>= 1.3, < 3)
-    sqlite3 (1.4.0)
+      rack-protection (= 2.0.7)
+      sinatra (= 2.0.7)
+      tilt (~> 2.0)
+    sqlite3 (1.4.1)
     stringex (1.5.1)
     thin (1.7.2)
       daemons (~> 1.0, >= 1.0.9)
@@ -216,12 +216,12 @@ GEM
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.7.6)
-    unicode-display_width (1.5.0)
+    unicode-display_width (1.6.0)
     uuidtools (2.1.5)
-    webmock (3.5.1)
+    webmock (3.6.2)
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
-      hashdiff
+      hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
   ruby

config.yml

@@ -17,7 +17,7 @@ disable_verify_peer: false
 # When running in a docker container, we have to listen to other than just 'localhost' which is the default
 bind: '0.0.0.0'
 
-# Skip TLS tests
+# Omit TLS tests
 disable_tls_tests: false
 
 # Default scopes

generators/uscore-r4/templates/module.yml.erb

@@ -23,3 +23,4 @@ test_sets:
         sequences:<% sequences.each do |sequence| %>
         - <%=sequence[:classname]%><% end %>
         - R4ProvenanceSequence
+        - USCoreR4ClinicalNotesSequence

lib/app.rb

@@ -21,7 +21,7 @@
 require_relative 'app/endpoint'
 require_relative 'app/utils/secure_random_base62'
 require_relative 'app/sequence_base'
-require_relative 'app/module'
+require_relative 'app/models/module'
 require_relative 'version'
 require_relative 'app/models'
 require_relative 'app/utils/terminology'