FI-2168: 2023 SVAP update (#459)

* add us core 6 resources * update terminology code for us core 6 * add additional VS from vsac * update expected terminology manifest * add us core 6 to g10 options * update suite to include us core 6 * add us core 6 single patient api group * update smart scopes test * update preset for us core 6 * add us core validator urls to .env.development * update restricted and unrestricted access groups for us core 6 * add temporary short id for us core 6 single patient group * update bulk data tests for us core 6 * update smart capabilities check for us core 6 * update bulk data tests for us core 6 * update resource lists * include specimen search tests * note locations which need narrative updates * fix uscdi version * fix clinical result profile in bulk data * fix linting errors * update descriptions * add us core 6 to readme * update wording for us core 6 * handle error so missing short id map doesn't prevent inferno from starting * update short ids * make single patient api titles/short titles consistent * fix linting error * update to 2023AA umls release * add final umls 2023 fixes * use rc version * bump core * use dynamic server url in preset * add 2023 prop file for terminology * bump us core * bump core * fix short ids * add required profiles for us core 6
onc-healthit · Nov 8, 2023 · e6bb966 · e6bb966
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diff --git a/.env.development b/.env.development
@@ -1,4 +1,8 @@
 G10_VALIDATOR_URL=http://localhost/validatorapi
+V311_VALIDATOR_URL=http://localhost/validatorapi
+V400_VALIDATOR_URL=http://localhost/validatorapi
+V501_VALIDATOR_URL=http://localhost/validatorapi
+V610_VALIDATOR_URL=http://localhost/validatorapi
 VALIDATOR_URL=http://localhost/validatorapi
 REDIS_URL=redis://localhost:6379/0
 INFERNO_HOST=http://localhost:4567
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,17 +1,17 @@
 PATH
   remote: .
   specs:
-    onc_certification_g10_test_kit (3.8.1)
+    onc_certification_g10_test_kit (4.0.0.rc1)
       bloomer (~> 1.0.0)
       colorize (~> 0.8.1)
-      inferno_core (= 0.4.18)
+      inferno_core (~> 0.4.20)
       json-jwt (~> 1.15.3)
       mime-types (~> 3.4.0)
       ndjson (~> 1.0.0)
       rubyzip (~> 2.3.2)
       smart_app_launch_test_kit (= 0.3.0)
       tls_test_kit (= 0.2.0)
-      us_core_test_kit (= 0.6.0)
+      us_core_test_kit (= 0.6.1)
 
 GEM
   remote: https://rubygems.org/
@@ -160,8 +160,8 @@ GEM
     i18n (1.14.1)
       concurrent-ruby (~> 1.0)
     ice_nine (0.11.2)
-    inferno_core (0.4.18)
-      activesupport (~> 6.1)
+    inferno_core (0.4.22)
+      activesupport (~> 6.1.7.5)
       base62-rb (= 0.3.1)
       blueprinter (= 0.25.2)
       dotenv (~> 2.7)
@@ -178,7 +178,7 @@ GEM
       oj (= 3.11.0)
       pry
       pry-byebug
-      puma (~> 5.3)
+      puma (~> 5.6.7)
       rake (~> 13.0)
       sequel (~> 5.42.0)
       sidekiq (~> 6.5.6)
@@ -200,9 +200,9 @@ GEM
     method_source (1.0.0)
     mime-types (3.4.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.0808)
-    mini_portile2 (2.8.4)
-    minitest (5.19.0)
+    mime-types-data (3.2023.1003)
+    mini_portile2 (2.8.5)
+    minitest (5.20.0)
     msgpack (1.7.2)
     multi_json (1.15.0)
     multi_xml (0.6.0)
@@ -215,14 +215,14 @@ GEM
     ndjson (1.0.0)
     netrc (0.11.0)
     nio4r (2.5.9)
-    nokogiri (1.15.3)
+    nokogiri (1.15.4)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
-    nokogiri (1.15.3-arm64-darwin)
+    nokogiri (1.15.4-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.15.3-x86_64-darwin)
+    nokogiri (1.15.4-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.15.3-x86_64-linux)
+    nokogiri (1.15.4-x86_64-linux)
       racc (~> 1.4)
     oauth2 (1.4.11)
       faraday (>= 0.17.3, < 3.0)
@@ -245,10 +245,10 @@ GEM
     public_suffix (5.0.3)
     puma (5.6.7)
       nio4r (~> 2.0)
-    racc (1.7.1)
+    racc (1.7.3)
     rack (2.2.8)
     rainbow (3.1.1)
-    rake (13.0.6)
+    rake (13.1.0)
     redis (4.8.1)
     regexp_parser (2.6.1)
     reline (0.3.1)
@@ -259,7 +259,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     rexml (3.2.6)
-    rouge (4.1.3)
+    rouge (4.2.0)
     rspec (3.12.0)
       rspec-core (~> 3.12.0)
       rspec-expectations (~> 3.12.0)
@@ -294,26 +294,26 @@ GEM
       rubyzip (>= 1.3.0)
     rubyzip (2.3.2)
     sequel (5.42.0)
-    sidekiq (6.5.9)
+    sidekiq (6.5.12)
       connection_pool (>= 2.2.5, < 3)
       rack (~> 2.0)
       redis (>= 4.5.0, < 5)
     smart_app_launch_test_kit (0.3.0)
       inferno_core (>= 0.4.2)
       jwt (~> 2.2)
       tls_test_kit (~> 0.2.0)
-    sqlite3 (1.6.5)
+    sqlite3 (1.6.8)
       mini_portile2 (~> 2.8.0)
-    sqlite3 (1.6.5-arm64-darwin)
-    sqlite3 (1.6.5-x86_64-darwin)
-    sqlite3 (1.6.5-x86_64-linux)
+    sqlite3 (1.6.8-arm64-darwin)
+    sqlite3 (1.6.8-x86_64-darwin)
+    sqlite3 (1.6.8-x86_64-linux)
     strings (0.2.1)
       strings-ansi (~> 0.2)
       unicode-display_width (>= 1.5, < 3.0)
       unicode_utils (~> 1.4)
     strings-ansi (0.2.0)
     thor (1.2.2)
-    tilt (2.2.0)
+    tilt (2.3.0)
     tls_test_kit (0.2.0)
       inferno_core (>= 0.4.1)
     tty-color (0.6.0)
@@ -330,16 +330,16 @@ GEM
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.8.2)
-    unicode-display_width (2.4.2)
+    unicode-display_width (2.5.0)
     unicode_utils (1.4.0)
-    us_core_test_kit (0.6.0)
+    us_core_test_kit (0.6.1)
       inferno_core (>= 0.4.2)
       tls_test_kit (~> 0.2.0)
     webmock (3.18.1)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    zeitwerk (2.6.11)
+    zeitwerk (2.6.12)
 
 PLATFORMS
   arm64-darwin-21

diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ series of HTTP requests that mimic a real world client to ensure that the API
 supports an approved version of each of the required standards:
 
 * Health Level 7 (HL7®) Fast Healthcare Interoperability Resources (FHIR®) (v4.0.1)
-* US Core Implementation Guide (v3.1.1, v4.0.0, or v5.0.1)
+* US Core Implementation Guide (v3.1.1, v4.0.0, v5.0.1, or v6.1.0)
 * SMART Application Launch Framework Implementation Guide Release (v1.0.0, or
   v2.0.0)
 * HL7 FHIR Bulk Data Access (Flat FHIR) (v1.0.1, or v2.0.0)

diff --git a/Rakefile b/Rakefile
@@ -29,7 +29,7 @@ Inferno.logger.formatter = proc do |_severity, _datetime, _progname, message|
   "#{message}\n"
 end
 
-default_version = '2022'
+default_version = '2023'
 
 namespace :terminology do |_argv|
   desc 'download and execute UMLS terminology data'

diff --git a/bin/create_umls.sh b/bin/create_umls.sh
@@ -4,7 +4,7 @@ if [ -n "$1" ]
 then
   version="$1"
 else
-  version="2022"
+  version="2023"
 fi
 
 echo "Version: ${version}"

diff --git a/bin/prepare_terminology.sh b/bin/prepare_terminology.sh
@@ -5,7 +5,7 @@ if [ -n "$1" ]
 then
   version="$1"
 else
-  version="2022"
+  version="2023"
 fi
 
 temp_folder="tmp/terminology/${version}"

diff --git a/bin/run_terminology.sh b/bin/run_terminology.sh
@@ -11,12 +11,12 @@ if [ -f /.dockerenv ]; then
   fi
 fi
 
-./bin/prepare_terminology.sh 2022
+./bin/prepare_terminology.sh 2023
 bundle exec rake terminology:create_vs_validators["preferred"]
 echo "$?"
 
 if [ -n "$CLEANUP" ]
 then
-  echo 'Deleting 2022 build files'
-  bundle exec rake terminology:cleanup_precursors["2022"]
+    echo 'Deleting 2023 build files'
+    bundle exec rake terminology:cleanup_precursors["2023"]
 fi
diff --git a/...sets/inferno_reference_server_preset.json → .../inferno_reference_server_preset.json.erb b/...sets/inferno_reference_server_preset.json → .../inferno_reference_server_preset.json.erb
@@ -8,7 +8,7 @@
       "type": "text",
       "title": "Standalone FHIR Endpoint",
       "description": "URL of the FHIR endpoint used by standalone applications",
-      "value": "https://inferno.healthit.gov/reference-server/r4"
+      "value": "<%= ENV.fetch('INFERNO_HOST', 'https://inferno.healthit.gov') %>/reference-server/r4"
     },
     {
       "name": "standalone_client_id",
@@ -62,6 +62,19 @@
           ],
           "value": "launch/patient openid fhirUser offline_access patient/Medication.read patient/AllergyIntolerance.read patient/CarePlan.read patient/CareTeam.read patient/Condition.read patient/Device.read patient/DiagnosticReport.read patient/DocumentReference.read patient/Encounter.read patient/Goal.read patient/Immunization.read patient/Location.read patient/MedicationRequest.read patient/Observation.read patient/Organization.read patient/Patient.read patient/Practitioner.read patient/Procedure.read patient/Provenance.read patient/PractitionerRole.read patient/ServiceRequest.read patient/RelatedPerson.read patient/QuestionnaireResponse.read patient/Media.read"
         },
+        {
+          "options": [
+            {
+              "name": "us_core_version",
+              "value": "us_core_6"
+            },
+            {
+              "name": "smart_app_launch_version",
+              "value": "smart_app_launch_1"
+            }
+          ],
+          "value": "launch/patient openid fhirUser offline_access patient/Medication.read patient/AllergyIntolerance.read patient/CarePlan.read patient/CareTeam.read patient/Condition.read patient/Device.read patient/DiagnosticReport.read patient/DocumentReference.read patient/Encounter.read patient/Goal.read patient/Immunization.read patient/Location.read patient/MedicationRequest.read patient/Observation.read patient/Organization.read patient/Patient.read patient/Practitioner.read patient/Procedure.read patient/Provenance.read patient/PractitionerRole.read patient/ServiceRequest.read patient/RelatedPerson.read patient/QuestionnaireResponse.read patient/Media.read patient/Coverage.read patient/MedicationDispense.read patient/Specimen.read"
+        },
         {
           "options": [
             {
@@ -100,6 +113,19 @@
             }
           ],
           "value": "launch/patient openid fhirUser offline_access patient/Medication.rs patient/AllergyIntolerance.rs patient/CarePlan.rs patient/CareTeam.rs patient/Condition.rs patient/Device.rs patient/DiagnosticReport.rs patient/DocumentReference.rs patient/Encounter.rs patient/Goal.rs patient/Immunization.rs patient/Location.rs patient/MedicationRequest.rs patient/Observation.rs patient/Organization.rs patient/Patient.rs patient/Practitioner.rs patient/Procedure.rs patient/Provenance.rs patient/PractitionerRole.rs patient/ServiceRequest.rs patient/RelatedPerson.rs patient/QuestionnaireResponse.rs patient/Media.rs"
+        },
+        {
+          "options": [
+            {
+              "name": "us_core_version",
+              "value": "us_core_6"
+            },
+            {
+              "name": "smart_app_launch_version",
+              "value": "smart_app_launch_2"
+            }
+          ],
+          "value": "launch/patient openid fhirUser offline_access patient/Medication.rs patient/AllergyIntolerance.rs patient/CarePlan.rs patient/CareTeam.rs patient/Condition.rs patient/Device.rs patient/DiagnosticReport.rs patient/DocumentReference.rs patient/Encounter.rs patient/Goal.rs patient/Immunization.rs patient/Location.rs patient/MedicationRequest.rs patient/Observation.rs patient/Organization.rs patient/Patient.rs patient/Practitioner.rs patient/Procedure.rs patient/Provenance.rs patient/PractitionerRole.rs patient/ServiceRequest.rs patient/RelatedPerson.rs patient/QuestionnaireResponse.rs patient/Media.rs patient/Coverage.rs patient/MedicationDispense.rs patient/Specimen.rs"
         }
       ]
     },
@@ -163,6 +189,19 @@
           ],
           "value": "launch openid fhirUser offline_access user/Medication.read user/AllergyIntolerance.read user/CarePlan.read user/CareTeam.read user/Condition.read user/Device.read user/DiagnosticReport.read user/DocumentReference.read user/Encounter.read user/Goal.read user/Immunization.read user/Location.read user/MedicationRequest.read user/Observation.read user/Organization.read user/Patient.read user/Practitioner.read user/Procedure.read user/Provenance.read user/PractitionerRole.read user/ServiceRequest.read user/RelatedPerson.read user/QuestionnaireResponse.read user/Media.read"
         },
+        {
+          "options": [
+            {
+              "name": "us_core_version",
+              "value": "us_core_6"
+            },
+            {
+              "name": "smart_app_launch_version",
+              "value": "smart_app_launch_1"
+            }
+          ],
+          "value": "launch openid fhirUser offline_access user/Medication.read user/AllergyIntolerance.read user/CarePlan.read user/CareTeam.read user/Condition.read user/Device.read user/DiagnosticReport.read user/DocumentReference.read user/Encounter.read user/Goal.read user/Immunization.read user/Location.read user/MedicationRequest.read user/Observation.read user/Organization.read user/Patient.read user/Practitioner.read user/Procedure.read user/Provenance.read user/PractitionerRole.read user/ServiceRequest.read user/RelatedPerson.read user/QuestionnaireResponse.read user/Media.read user/Coverage.read user/MedicationDispense.read user/ServiceRequest.read user/RelatedPerson.read user/Specimen.read"
+        },
         {
           "options": [
             {
@@ -201,6 +240,19 @@
             }
           ],
           "value": "launch openid fhirUser offline_access user/Medication.rs user/AllergyIntolerance.rs user/CarePlan.rs user/CareTeam.rs user/Condition.rs user/Device.rs user/DiagnosticReport.rs user/DocumentReference.rs user/Encounter.rs user/Goal.rs user/Immunization.rs user/Location.rs user/MedicationRequest.rs user/Observation.rs user/Organization.rs user/Patient.rs user/Practitioner.rs user/Procedure.rs user/Provenance.rs user/PractitionerRole.rs user/ServiceRequest.rs user/RelatedPerson.rs user/QuestionnaireResponse.rs user/Media.rs"
+        },
+        {
+          "options": [
+            {
+              "name": "us_core_version",
+              "value": "us_core_6"
+            },
+            {
+              "name": "smart_app_launch_version",
+              "value": "smart_app_launch_2"
+            }
+          ],
+          "value": "launch openid fhirUser offline_access user/Medication.rs user/AllergyIntolerance.rs user/CarePlan.rs user/CareTeam.rs user/Condition.rs user/Device.rs user/DiagnosticReport.rs user/DocumentReference.rs user/Encounter.rs user/Goal.rs user/Immunization.rs user/Location.rs user/MedicationRequest.rs user/Observation.rs user/Organization.rs user/Patient.rs user/Practitioner.rs user/Procedure.rs user/Provenance.rs user/PractitionerRole.rs user/ServiceRequest.rs user/RelatedPerson.rs user/QuestionnaireResponse.rs user/Media.rs user/Coverage.rs user/MedicationDispense.rs user/ServiceRequest.rs user/RelatedPerson.rs user/Specimen.rs"
         }
       ]
     },
@@ -230,7 +282,7 @@
       "type": "text",
       "title": "Backend Services Token Endpoint",
       "description": "The OAuth 2.0 Token Endpoint used by the Backend Services specification\n                        to provide bearer tokens.",
-      "value": "https://inferno.healthit.gov/reference-server/oauth/token"
+      "value": "<%= ENV.fetch('INFERNO_HOST', 'https://inferno.healthit.gov') %>/reference-server/oauth/token"
     },
     {
       "name": "bulk_client_id",
@@ -290,7 +342,7 @@
       "type": "text",
       "title": "Bulk Data FHIR URL",
       "description": "The URL of the Bulk FHIR server.",
-      "value": "https://inferno.healthit.gov/reference-server/r4"
+      "value": "<%= ENV.fetch('INFERNO_HOST', 'https://inferno.healthit.gov') %>/reference-server/r4"
     },
     {
       "name": "group_id",
@@ -381,6 +433,19 @@
           ],
           "value": "launch/patient openid fhirUser offline_access patient/Medication.read patient/AllergyIntolerance.read patient/CarePlan.read patient/CareTeam.read patient/Condition.read patient/Device.read patient/DiagnosticReport.read patient/DocumentReference.read patient/Encounter.read patient/Goal.read patient/Immunization.read patient/Location.read patient/MedicationRequest.read patient/Observation.read patient/Organization.read patient/Patient.read patient/Practitioner.read patient/Procedure.read patient/Provenance.read patient/PractitionerRole.read patient/ServiceRequest.read patient/RelatedPerson.read patient/QuestionnaireResponse.read patient/Media.read"
         },
+        {
+          "options": [
+            {
+              "name": "us_core_version",
+              "value": "us_core_6"
+            },
+            {
+              "name": "smart_app_launch_version",
+              "value": "smart_app_launch_1"
+            }
+          ],
+          "value": "launch/patient openid fhirUser offline_access patient/Medication.read patient/AllergyIntolerance.read patient/CarePlan.read patient/CareTeam.read patient/Condition.read patient/Device.read patient/DiagnosticReport.read patient/DocumentReference.read patient/Encounter.read patient/Goal.read patient/Immunization.read patient/Location.read patient/MedicationRequest.read patient/Observation.read patient/Organization.read patient/Patient.read patient/Practitioner.read patient/Procedure.read patient/Provenance.read patient/PractitionerRole.read patient/ServiceRequest.read patient/RelatedPerson.read patient/QuestionnaireResponse.read patient/Media.read patient/Coverage.read patient/MedicationDispense.read patient/Specimen.read"
+        },
         {
           "options": [
             {
@@ -419,6 +484,19 @@
             }
           ],
           "value": "launch/patient openid fhirUser offline_access patient/Medication.rs patient/AllergyIntolerance.rs patient/CarePlan.rs patient/CareTeam.rs patient/Condition.rs patient/Device.rs patient/DiagnosticReport.rs patient/DocumentReference.rs patient/Encounter.rs patient/Goal.rs patient/Immunization.rs patient/Location.rs patient/MedicationRequest.rs patient/Observation.rs patient/Organization.rs patient/Patient.rs patient/Practitioner.rs patient/Procedure.rs patient/Provenance.rs patient/PractitionerRole.rs patient/ServiceRequest.rs patient/RelatedPerson.rs patient/QuestionnaireResponse.rs patient/Media.rs"
+        },
+        {
+          "options": [
+            {
+              "name": "us_core_version",
+              "value": "us_core_6"
+            },
+            {
+              "name": "smart_app_launch_version",
+              "value": "smart_app_launch_2"
+            }
+          ],
+          "value": "launch/patient openid fhirUser offline_access patient/Medication.rs patient/AllergyIntolerance.rs patient/CarePlan.rs patient/CareTeam.rs patient/Condition.rs patient/Device.rs patient/DiagnosticReport.rs patient/DocumentReference.rs patient/Encounter.rs patient/Goal.rs patient/Immunization.rs patient/Location.rs patient/MedicationRequest.rs patient/Observation.rs patient/Organization.rs patient/Patient.rs patient/Practitioner.rs patient/Procedure.rs patient/Provenance.rs patient/PractitionerRole.rs patient/ServiceRequest.rs patient/RelatedPerson.rs patient/QuestionnaireResponse.rs patient/Media.rs"
         }
       ]
     },