FI-2460: Support for HL7 validator wrapper (#488)

* FI-2460: Start adding support for HL7 validator wrapper * Add cliContext with fields matching original validator settings * switch dockerfile to use ubuntu jammy instead of alpine * rework dockerfile to fetch release jar instead of completely rebuilding * add new env vars for HL7 validator, restore env vars for inferno validator * FI-2532: Add feature flag to toggle using HL7 validator wrapper (#497) * FI-2532: add feature flag to switch between inferno validator and hl7 validator wrapper * standardize name * default hl7 validator to false and comment out its services * use new inferno-resource-validator docker image, remove custom dockerfile * Fix HL7 validator wrapper version at 1.0.51 * Set env var so validator sessions never expire
onc-healthit · Apr 8, 2024 · 785e875 · 785e875
1 parent b0ef029
commit 785e875
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Showing 15 changed files with 382 additions and 62 deletions.
diff --git a/.env b/.env
@@ -1,7 +1,15 @@
 JS_HOST=""
 G10_VALIDATOR_URL=http://validator_service:4567
+G10_FHIR_RESOURCE_VALIDATOR_URL=http://hl7_validator_service:3500
 REDIS_URL=redis://redis:6379/0
 
+USE_HL7_RESOURCE_VALIDATOR=false
+# To use the HL7 validator wrapper instead of the inferno validator wrapper, set the above to true,
+# and uncomment the relevant settings in the following files:
+#  - docker-compose.yml -- "hl7_validator_service" section at the bottom
+#  - docker-compose.background.yml -- "hl7_validator_service" section at the bottom
+#  - nginx.background.conf -- "location /hl7validatorapi/" section at the bottom
+
 # Full path to a custom JWKS json file, will use lib/onc_certification_g10_test_kit/bulk_data_jwks.json if left blank
 # G10_BULK_DATA_JWKS=
 

diff --git a/.env.production b/.env.production
@@ -1,4 +1,6 @@
 REDIS_URL=redis://redis:6379/0
 G10_VALIDATOR_URL=http://validator_service:4567
 VALIDATOR_URL=http://validator_service:4567
+G10_FHIR_RESOURCE_VALIDATOR_URL=http://hl7_validator_service:3500
+FHIR_RESOURCE_VALIDATOR_URL=http://hl7_validator_service:3500
 INFERNO_HOST=http://localhost
diff --git a/config/nginx.background.conf b/config/nginx.background.conf
@@ -82,5 +82,24 @@ http {
 
       proxy_pass http://validator_service:4567/;
     }
+
+
+# To enable the HL7 Validator Wrapper, both the section below and
+# the section in docker-compose.background.yml need to be uncommented
+#    location /hl7validatorapi/ {
+#      proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+#      proxy_set_header Host $http_host;
+#      proxy_set_header X-Forwarded-Proto $scheme;
+#      proxy_set_header X-Forwarded-Port $server_port;
+#      proxy_redirect off;
+#      proxy_set_header Connection '';
+#      proxy_http_version 1.1;
+#      chunked_transfer_encoding off;
+#      proxy_buffering off;
+#      proxy_cache off;
+#      proxy_read_timeout 600s;
+#
+#      proxy_pass http://hl7_validator_service:3500/;
+#    }
   }
 }
diff --git a/docker-compose.background.yml b/docker-compose.background.yml
@@ -28,3 +28,14 @@ services:
     volumes:
       - ./data/redis:/data
     command: redis-server --appendonly yes
+  # hl7_validator_service:
+  #   image: infernocommunity/inferno-resource-validator:1.0.51
+  #   environment:
+  #     # Defines how long validator sessions last if unused, in minutes:
+  #     # Negative values mean sessions never expire, 0 means sessions immediately expire
+  #     SESSION_CACHE_DURATION: -1
+  #   volumes:
+  #     - ./lib/onc_certification_g10_test_kit/igs:/home/igs
+  #     # To let the service share your local FHIR package cache,
+  #     # uncomment the below line
+  #     # - ~/.fhir:/home/ktor/.fhir
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -6,6 +6,7 @@ services:
     volumes:
       - ./data:/opt/inferno/data
     depends_on:
+    #  - hl7_validator_service
       - validator_service
   worker:
     build:
@@ -33,3 +34,7 @@ services:
     extends:
       file: docker-compose.background.yml
       service: redis
+  # hl7_validator_service:
+  #   extends:
+  #     file: docker-compose.background.yml
+  #     service: hl7_validator_service
diff --git a/lib/onc_certification_g10_test_kit.rb b/lib/onc_certification_g10_test_kit.rb
@@ -63,23 +63,39 @@ class G10CertificationSuite < Inferno::TestSuite
     ].freeze
 
     ERROR_FILTERS = [
-      /\A\S+: \S+: Unknown Code/,
+      /\A\S+: \S+: Unknown [Cc]ode/,
       /\A\S+: \S+: None of the codings provided are in the value set/,
       /\A\S+: \S+: The code provided \(\S*\) is not in the value set/,
       /\A\S+: \S+: The Coding provided \(\S*\) is not in the value set/,
       /\A\S+: \S+: The Coding provided \(\S*\) was not found in the value set/,
-      /\A\S+: \S+: A definition for CodeSystem '.*' could not be found, so the code cannot be validated/
+      /\A\S+: \S+: A definition for CodeSystem '.*' could not be found, so the code cannot be validated/,
+      /\A\S+: \S+: URL value '.*' does not resolve/,
+      /\A\S+: \S+: .*\[No server available\]/  # Catch-all for certain errors when TX server is disabled
     ].freeze
 
-    [
-      G10Options::US_CORE_3_REQUIREMENT,
-      G10Options::US_CORE_4_REQUIREMENT,
-      G10Options::US_CORE_5_REQUIREMENT,
-      G10Options::US_CORE_6_REQUIREMENT
+    def self.setup_validator(us_core_version_requirement) # rubocop:disable Metrics/CyclomaticComplexity
+      validator_method = if Feature.use_hl7_resource_validator?
+                           method(:fhir_resource_validator)
+                         else
+                           method(:validator)
+                         end
+
+      validator_method.call :default, required_suite_options: us_core_version_requirement do
+        if Feature.use_hl7_resource_validator?
+          url ENV.fetch('G10_FHIR_RESOURCE_VALIDATOR_URL', 'http://hl7_validator_service:3500')
+
+          cli_context do
+            txServer nil
+            displayWarnings true
+            disableDefaultResourceFetcher true
+          end
 
-    ].each do |us_core_version_requirement|
-      validator :default, required_suite_options: us_core_version_requirement do
-        url ENV.fetch('G10_VALIDATOR_URL', 'http://validator_service:4567')
+          us_core_version_num = G10Options::US_CORE_VERSION_NUMBERS[us_core_version_requirement[:us_core_version]]
+
+          igs("hl7.fhir.us.core##{us_core_version_num}")
+        else
+          url ENV.fetch('G10_VALIDATOR_URL', 'http://validator_service:4567')
+        end
 
         us_core_message_filters =
           case (us_core_version_requirement[:us_core_version])
@@ -148,6 +164,16 @@ class G10CertificationSuite < Inferno::TestSuite
       end
     end
 
+    [
+      G10Options::US_CORE_3_REQUIREMENT,
+      G10Options::US_CORE_4_REQUIREMENT,
+      G10Options::US_CORE_5_REQUIREMENT,
+      G10Options::US_CORE_6_REQUIREMENT
+
+    ].each do |us_core_version_requirement|
+      setup_validator(us_core_version_requirement)
+    end
+
     def self.jwks_json
       bulk_data_jwks = JSON.parse(File.read(
                                     ENV.fetch('G10_BULK_DATA_JWKS',

diff --git a/lib/onc_certification_g10_test_kit/configuration_checker.rb b/lib/onc_certification_g10_test_kit/configuration_checker.rb
@@ -3,6 +3,7 @@
 module ONCCertificationG10TestKit
   class ConfigurationChecker
     EXPECTED_VALIDATOR_VERSION = '2.3.2'.freeze
+    EXPECTED_HL7_VALIDATOR_VERSION = '"6.3.0"'.freeze
 
     def configuration_messages
       validator_version_message + terminology_messages + version_message
@@ -21,24 +22,31 @@ def validator_url
     end
 
     def validator_version_message
-      response = Faraday.get "#{validator_url}/version"
+      if Feature.use_hl7_resource_validator?
+        expected_validator_version = EXPECTED_HL7_VALIDATOR_VERSION
+        validator_version_url = "#{validator_url}/validator/version"
+      else
+        expected_validator_version = EXPECTED_VALIDATOR_VERSION
+        validator_version_url = "#{validator_url}/version"
+      end
 
+      response = Faraday.get validator_version_url
       if response.body.starts_with? '{'
         version_json = JSON.parse(response.body)
         version = version_json['inferno-framework/fhir-validator-wrapper']
       else
         version = response.body
       end
 
-      if version == EXPECTED_VALIDATOR_VERSION
+      if version == expected_validator_version
         [{
           type: 'info',
-          message: "FHIR validator is the expected version `#{EXPECTED_VALIDATOR_VERSION}`"
+          message: "FHIR validator is the expected version `#{expected_validator_version}`"
         }]
       else
         [{
           type: 'error',
-          message: "Expected FHIR validator version `#{EXPECTED_VALIDATOR_VERSION}`, but found `#{version}`"
+          message: "Expected FHIR validator version `#{expected_validator_version}`, but found `#{version}`"
         }]
       end
     rescue JSON::ParserError => e

diff --git a/lib/onc_certification_g10_test_kit/feature.rb b/lib/onc_certification_g10_test_kit/feature.rb
@@ -1,10 +1,9 @@
 module ONCCertificationG10TestKit
   module Feature
-    class << self # rubocop:disable Lint/EmptyClass
-      # This is how you can define feature flags to be used in the g10 test kit
-      # def us_core_v4?
-      #   ENV.fetch('US_CORE_4_ENABLED', 'false')&.casecmp?('true')
-      # end
+    class << self
+      def use_hl7_resource_validator?
+        ENV.fetch('USE_HL7_RESOURCE_VALIDATOR', 'false')&.casecmp?('true')
+      end
     end
   end
 end
diff --git a/lib/onc_certification_g10_test_kit/g10_options.rb b/lib/onc_certification_g10_test_kit/g10_options.rb
@@ -5,6 +5,13 @@ module G10Options
     US_CORE_5 = 'us_core_5'.freeze
     US_CORE_6 = 'us_core_6'.freeze
 
+    US_CORE_VERSION_NUMBERS = {
+      US_CORE_3 => '3.1.1',
+      US_CORE_4 => '4.0.0',
+      US_CORE_5 => '5.0.1',
+      US_CORE_6 => '6.1.0'
+    }.freeze
+
     BULK_DATA_1 = 'multi_patient_api_stu1'.freeze
     BULK_DATA_2 = 'multi_patient_api_stu2'.freeze
 

diff --git a/spec/fixtures/ValidationResponse-code-invalid-1.json b/spec/fixtures/ValidationResponse-code-invalid-1.json
@@ -0,0 +1,42 @@
+{
+    "outcomes": [
+        {
+            "fileInfo": {
+                "fileName": "manually_entered_file.json",
+                "fileContent": "{\n  \"resourceType\": \"Immunization\",\n  \"subpotentReason\": [{\n    \"coding\": [{\n      \"system\": \"http://terminology.hl7.org/CodeSystem/immunization-subpotent-reason\",\n      \"code\": \"partialdose\"\n    }]\n  }]\n}",
+                "fileType": "json"
+            },
+            "issues": [
+                {
+                    "source": "TerminologyEngine",
+                    "server": null,
+                    "line": 3,
+                    "col": 4,
+                    "location": "Immunization.subpotentReason[0].coding[0].code",
+                    "message": "Unknown code 'partialdose' in the CodeSystem 'http://terminology.hl7.org/CodeSystem/immunization-subpotent-reason' version '1.0.0'",
+                    "messageId": null,
+                    "type": "CODEINVALID",
+                    "level": "ERROR",
+                    "html": "Unknown code 'partialdose' in the CodeSystem 'http://terminology.hl7.org/CodeSystem/immunization-subpotent-reason' version '1.0.0'",
+                    "locationLink": null,
+                    "txLink": null,
+                    "sliceHtml": null,
+                    "sliceText": null,
+                    "slicingHint": false,
+                    "signpost": false,
+                    "criticalSignpost": false,
+                    "ruleDate": null,
+                    "matched": false,
+                    "ignorableError": false,
+                    "invId": null,
+                    "comment": null,
+                    "sliceInfo": null,
+                    "error": true,
+                    "display": "ERROR: Immunization.subpotentReason[0].coding[0].code: Unknown code 'partialdose' in the CodeSystem 'http://terminology.hl7.org/CodeSystem/immunization-subpotent-reason' version '1.0.0'"
+                }
+            ]
+        }
+    ],
+    "sessionId": "f4af8f4f-15d0-44f3-8401-dc9f9014aeaf",
+    "validationTimes": {}
+}
diff --git a/spec/fixtures/ValidationResponse-code-invalid-2.json b/spec/fixtures/ValidationResponse-code-invalid-2.json
@@ -0,0 +1,40 @@
+{
+  "outcomes" : [ {
+    "fileInfo" : {
+      "fileName" : "manually_entered_file.json",
+      "fileContent" : "{\n  \"resourceType\": \"AllergyIntolerance\",\n  \"clinicalStatus\": {\n    \"coding\": [\n      {\n        \"system\": \"http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical\",\n        \"code\": \"actives\",\n        \"display\": \"Active\"\n      }\n    ]\n  }\n}",
+      "fileType" : "json"
+    },
+    "issues" : [ 
+    {
+      "source" : "TerminologyEngine",
+      "server" : null,
+      "line" : 3,
+      "col" : 4,
+      "location" : "AllergyIntolerance.clinicalStatus",
+      "message" : "None of the codings provided are in the value set 'AllergyIntolerance Clinical Status Codes' (http://hl7.org/fhir/ValueSet/allergyintolerance-clinical|4.0.1), and a coding from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical#actives)",
+      "messageId" : "Terminology_TX_NoValid_1_CC",
+      "type" : "CODEINVALID",
+      "level" : "ERROR",
+      "html" : "None of the codings provided are in the value set 'AllergyIntolerance Clinical Status Codes' (http://hl7.org/fhir/ValueSet/allergyintolerance-clinical|4.0.1), and a coding from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical#actives)",
+      "locationLink" : null,
+      "txLink" : null,
+      "sliceHtml" : null,
+      "sliceText" : null,
+      "slicingHint" : false,
+      "signpost" : false,
+      "criticalSignpost" : false,
+      "ruleDate" : null,
+      "matched" : false,
+      "ignorableError" : false,
+      "invId" : null,
+      "comment" : null,
+      "sliceInfo" : null,
+      "display" : "ERROR: AllergyIntolerance.clinicalStatus: None of the codings provided are in the value set 'AllergyIntolerance Clinical Status Codes' (http://hl7.org/fhir/ValueSet/allergyintolerance-clinical|4.0.1), and a coding from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical#actives)",
+      "error" : true
+    }
+  ]
+  } ],
+  "sessionId" : "7c0cb248-4dd9-4063-9ed9-03623bbe221a",
+  "validationTimes" : { }
+}
diff --git a/spec/fixtures/ValidationResponse-code-invalid-3.json b/spec/fixtures/ValidationResponse-code-invalid-3.json
@@ -0,0 +1,38 @@
+{
+  "outcomes" : [ {
+    "fileInfo" : {
+      "fileName" : "manually_entered_file.json",
+      "fileContent" : "{\n      \"resourceType\": \"Patient\",\n      \n      \"extension\": [ {\n        \"url\": \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race\",\n        \"extension\": [ {\n          \"url\": \"ombCategory\",\n          \"valueCoding\": {\n            \"system\": \"urn:oid:2.16.840.1.113883.6.238\",\n            \"code\": \"2299-0\",\n            \"display\": \"Asian\"\n          }\n        }, {\n          \"url\": \"text\",\n          \"valueString\": \"Asian\"\n        } ]\n      }, \n      {\n        \"url\": \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity\",\n        \"extension\": [ {\n          \"url\": \"ombCategory\",\n          \"valueCoding\": {\n            \"system\": \"urn:oid:2.16.840.1.113883.6.238\",\n            \"code\": \"2186-5\",\n            \"display\": \"Not Hispanic or Latino\"\n          }\n        }, {\n          \"url\": \"text\",\n          \"valueString\": \"Not Hispanic or Latino\"\n        } ]\n      }\n   ]\n}",
+      "fileType" : "json"
+    },
+    "issues" : [{
+      "source" : "TerminologyEngine",
+      "server" : null,
+      "line" : 8,
+      "col" : 12,
+      "location" : "Patient.extension[0].extension[0].value.ofType(Coding)",
+      "message" : "The Coding provided (urn:oid:2.16.840.1.113883.6.238#2106-3) is not in the value set http://hl7.org/fhir/us/core/ValueSet/omb-race-category, and a code is required from this value set. (error message = Not in value set http://hl7.org/fhir/us/core/ValueSet/omb-race-category)",
+      "messageId" : "Terminology_TX_Confirm_4a",
+      "type" : "CODEINVALID",
+      "level" : "ERROR",
+      "html" : "The Coding provided (urn:oid:2.16.840.1.113883.6.238#2106-3) is not in the value set http://hl7.org/fhir/us/core/ValueSet/omb-race-category, and a code is required from this value set. (error message = Not in value set http://hl7.org/fhir/us/core/ValueSet/omb-race-category)",
+      "locationLink" : null,
+      "txLink" : null,
+      "sliceHtml" : null,
+      "sliceText" : null,
+      "slicingHint" : false,
+      "signpost" : false,
+      "criticalSignpost" : false,
+      "ruleDate" : null,
+      "matched" : false,
+      "ignorableError" : false,
+      "invId" : null,
+      "comment" : null,
+      "sliceInfo" : null,
+      "display" : "ERROR: Patient.extension[0].extension[0].value.ofType(Coding): The Coding provided (urn:oid:2.16.840.1.113883.6.238#2106-3) is not in the value set http://hl7.org/fhir/us/core/ValueSet/omb-race-category, and a code is required from this value set. (error message = Not in value set http://hl7.org/fhir/us/core/ValueSet/omb-race-category)",
+      "error" : true
+    }]
+  } ],
+  "sessionId" : "7c0cb248-4dd9-4063-9ed9-03623bbe221a",
+  "validationTimes" : { }
+}
diff --git a/spec/fixtures/ValidationResponse-no-name.json b/spec/fixtures/ValidationResponse-no-name.json
@@ -0,0 +1,38 @@
+{
+        "outcomes" : [ {
+          "fileInfo" : {
+            "fileName" : "manually_entered_file.json",
+            "fileContent" : "{ \"resourceType\": \"Patient\" }",
+            "fileType" : "json"
+          },
+          "issues" : [{
+            "source" : "InstanceValidator",
+            "server" : null,
+            "line" : 1,
+            "col" : 30,
+            "location" : "Patient",
+            "message" : "Patient.name: minimum required = 1, but only found 0 (from http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient|3.1.1)",
+            "messageId" : "Validation_VAL_Profile_Minimum",
+            "type" : "STRUCTURE",
+            "level" : "ERROR",
+            "html" : "Patient.name: minimum required = 1, but only found 0 (from http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient|3.1.1)",
+            "locationLink" : null,
+            "txLink" : null,
+            "sliceHtml" : null,
+            "sliceText" : null,
+            "slicingHint" : false,
+            "signpost" : false,
+            "criticalSignpost" : false,
+            "ruleDate" : null,
+            "matched" : false,
+            "ignorableError" : false,
+            "invId" : null,
+            "comment" : null,
+            "sliceInfo" : null,
+            "display" : "ERROR: Patient: Patient.name: minimum required = 1, but only found 0 (from http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient|3.1.1)",
+            "error" : true
+          } ]
+        } ],
+        "sessionId" : "4d9d2dc3-5df1-461f-a4d6-bfc2788a1933",
+        "validationTimes" : { }
+      }