HAPI FHIR 7.4.5 and Spring 3.2.6

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
-		<version>3.2.2</version>
+		<version>3.2.6</version>
 		<relativePath/> <!-- lookup parent from repository -->
 	</parent>
 	<groupId>uk.nhs.england</groupId>
@@ -17,8 +17,8 @@
 	<properties>
 		<java.version>20</java.version>
 		<kotlin.version>1.9.22</kotlin.version>
-		<fhir.version>7.0.2</fhir.version>
-		<swagger_version>2.2.20</swagger_version>
+		<fhir.version>7.4.5</fhir.version>
+		<swagger_version>2.2.25</swagger_version>
 		<parser_version>2.1.20</parser_version>
 		<jackson_databind_version>2.17.0</jackson_databind_version>
 	</properties>

src/main/kotlin/uk/nhs/england/fhirvalidator/configuration/ValidationConfiguration.kt

@@ -7,12 +7,9 @@ import ca.uhn.fhir.context.support.ValidationSupportContext
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException
 import ca.uhn.fhir.validation.FhirValidator
 import com.fasterxml.jackson.databind.ObjectMapper
-import io.swagger.v3.oas.models.examples.Example
 import mu.KLogging
 import org.hl7.fhir.common.hapi.validation.support.*
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator
-import org.hl7.fhir.r4.model.CapabilityStatement
-import org.hl7.fhir.r4.model.ImplementationGuide
 import org.hl7.fhir.r4.model.StructureDefinition
 import org.hl7.fhir.utilities.json.model.JsonProperty
 import org.hl7.fhir.utilities.npm.NpmPackage
@@ -195,9 +192,7 @@ open class ValidationConfiguration(
     ): uk.nhs.england.fhirvalidator.shared.RemoteTerminologyServiceValidationSupport {
         logger.info("Using remote terminology server at ${terminologyValidationProperties.url}")
         val validationSupport =
-            uk.nhs.england.fhirvalidator.shared.RemoteTerminologyServiceValidationSupport(
-                fhirContext
-            )
+            uk.nhs.england.fhirvalidator.shared.RemoteTerminologyServiceValidationSupport(fhirContext)
         validationSupport.setBaseUrl(terminologyValidationProperties.url)
 
         if (optionalAuthorizedClientManager.isPresent) {

src/main/kotlin/uk/nhs/england/fhirvalidator/provider/ValidateR4Provider.kt

@@ -14,7 +14,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource
 import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext
 import org.hl7.fhir.r4.model.*
 import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent
-import org.hl7.fhir.r4.utils.FHIRPathEngine
 import org.springframework.beans.factory.annotation.Qualifier
 import org.springframework.stereotype.Component
 import uk.nhs.england.fhirvalidator.interceptor.CapabilityStatementApplier
@@ -25,6 +24,9 @@ import uk.nhs.england.fhirvalidator.util.createOperationOutcome
 import java.net.URLDecoder
 import java.nio.charset.StandardCharsets
 import jakarta.servlet.http.HttpServletRequest
+import org.hl7.fhir.r4.fhirpath.FHIRPathEngine
+import org.hl7.fhir.r4.model.Bundle.BundleType
+
 
 @Component
 class ValidateR4Provider (
@@ -52,7 +54,7 @@ class ValidateR4Provider (
         if (expression==null) return returnResult
         var hapiWorkerContext = HapiWorkerContext(fhirContext,supportChain)
         var fhirPathEngine = FHIRPathEngine(hapiWorkerContext)
-       // var expression = "identifier.where(system='https://fhir.nhs.uk/Id/nhs-number').exists().not() or (identifier.where(system='https://fhir.nhs.uk/Id/nhs-number').exists()  and identifier.where(system='https://fhir.nhs.uk/Id/nhs-number').value.matches('^([456789]{1}[0-9]{9})\$'))"
+        // var expression = "identifier.where(system='https://fhir.nhs.uk/Id/nhs-number').exists().not() or (identifier.where(system='https://fhir.nhs.uk/Id/nhs-number').exists()  and identifier.where(system='https://fhir.nhs.uk/Id/nhs-number').value.matches('^([456789]{1}[0-9]{9})\$'))"
         var decode = URLDecoder.decode(expression, StandardCharsets.UTF_8.name())
         System.out.println(expression)
         System.out.println(decode)
@@ -83,18 +85,18 @@ class ValidateR4Provider (
     ): IBaseResource? {
         return resource
     }
-/*
- Move to a STU3 RestfulServer, is asuming input is R4 at present
-    @Operation(name = "\$convertR4", idempotent = true)
-    @Throws(java.lang.Exception::class)
-    fun convertR4(
-        @ResourceParam resource: IBaseResource?
-    ): IBaseResource? {
-        val convertor = VersionConvertor_30_40(BaseAdvisor_30_40())
-        val resourceR3 = resource as Resource
-        return convertor.convertResource(resourceR3)
-    }
-*/
+    /*
+     Move to a STU3 RestfulServer, is asuming input is R4 at present
+        @Operation(name = "\$convertR4", idempotent = true)
+        @Throws(java.lang.Exception::class)
+        fun convertR4(
+            @ResourceParam resource: IBaseResource?
+        ): IBaseResource? {
+            val convertor = VersionConvertor_30_40(BaseAdvisor_30_40())
+            val resourceR3 = resource as Resource
+            return convertor.convertResource(resourceR3)
+        }
+    */
     @Validate
     fun validate(
         servletRequest: HttpServletRequest,
@@ -117,38 +119,56 @@ class ValidateR4Provider (
             operationOutcome = parseAndValidateResource(resource, profile, importProfile)
         }
         val methodOutcome = MethodOutcome()
-        if (operationOutcome != null ) {
-            if (operationOutcome.hasIssue()) {
+        if (operationOutcome.hasIssue()) {
             // Temp workaround for onto validation issues around workflow code
-                for (issue in operationOutcome.issue) {
-                    if (issue.hasDiagnostics() && issue.diagnostics.contains("404")) {
-                        if(// issue.diagnostics.contains("https://fhir.nhs.uk/CodeSystem/Workflow-Code") ||
-                            issue.diagnostics.contains("https://fhir.nhs.uk/CodeSystem/NHSDataModelAndDictionary-treatment-function")) {
-                            issue.severity = OperationOutcome.IssueSeverity.INFORMATION
-                        }
-                        // This is to downgrade onto server issues to information.
-                        if (!issue.diagnostics.contains(".uk") && (issue.diagnostics.contains("A usable code system with URL")
-                            || issue.diagnostics.contains("LOINC is not indexed!"))) {
-                            // This is probably ontology server issue so degrade warning to information
-                            issue.severity = OperationOutcome.IssueSeverity.INFORMATION
-                        }
+            val newIssue = ArrayList<OperationOutcomeIssueComponent>()
+            for (issue in operationOutcome.issue) {
 
+                if (issue.hasLocation()) {
+                    val newLocs = ArrayList<StringType>()
+                    issue.location.forEach { str ->
+                        if (str.value == null || !str.value.startsWith("Line")) newLocs.add(str)
                     }
-                    if (issue.diagnostics.contains("http://unstats.un.org/unsd/")) {
+                    issue.location = newLocs
+                }
+                if (issue.hasDiagnostics() && issue.diagnostics.contains("404")) {
+                    if(// issue.diagnostics.contains("https://fhir.nhs.uk/CodeSystem/Workflow-Code") ||
+                        issue.diagnostics.contains("https://fhir.nhs.uk/CodeSystem/NHSDataModelAndDictionary-treatment-function")) {
                         issue.severity = OperationOutcome.IssueSeverity.INFORMATION
                     }
-                    if (issue.diagnostics.contains("note that the validator cannot judge what is suitable")) {
+                    // This is to downgrade onto server issues to information.
+                    if (!issue.diagnostics.contains(".uk") && (issue.diagnostics.contains("A usable code system with URL")
+                                //    || issue.diagnostics.contains("LOINC is not indexed!")
+                                )) {
+                        // This is probably ontology server issue so degrade warning to information
                         issue.severity = OperationOutcome.IssueSeverity.INFORMATION
                     }
+
+                }
+                if (issue.diagnostics.contains("http://unstats.un.org/unsd/")
+                    || issue.diagnostics.contains("note that the validator cannot judge what is suitable")
+                    || issue.diagnostics.contains("A resource should have narrative for robust management")) {
+                    issue.severity = OperationOutcome.IssueSeverity.INFORMATION
+                }
+                if (//!issue.diagnostics.contains("Validation failed for 'http://loinc.org")
+                //&&
+                    !issue.diagnostics.contains("because \"theCodeSystem\"")
+                    && !issue.diagnostics.contains("but you should check that it's not intended to match a slice")
+                    && !issue.diagnostics.contains("because &quot;theCodeSystem&quot; is null")
+                    && !issue.diagnostics.contains("A resource should have narrative for robust management" )
+                ) {
+                    newIssue.add(issue)
                 }
-            } else {
-                // https://nhsd-jira.digital.nhs.uk/browse/IOPS-829
-                operationOutcome.issue.add(OperationOutcome.OperationOutcomeIssueComponent()
-                    .setCode(OperationOutcome.IssueType.INFORMATIONAL)
-                    .setSeverity(OperationOutcome.IssueSeverity.INFORMATION)
-                    .setDiagnostics("No issues detected during validation"))
             }
+            operationOutcome.issue = newIssue
+        } else {
+            // https://nhsd-jira.digital.nhs.uk/browse/IOPS-829
+            operationOutcome.issue.add(OperationOutcome.OperationOutcomeIssueComponent()
+                .setCode(OperationOutcome.IssueType.INFORMATIONAL)
+                .setSeverity(OperationOutcome.IssueSeverity.INFORMATION)
+                .setDiagnostics("No issues detected during validation"))
         }
+
         methodOutcome.operationOutcome = operationOutcome
         return methodOutcome
     }
@@ -203,11 +223,21 @@ class ValidateR4Provider (
             result = validator.validateWithResult(resource, ValidationOptions().addProfile(profile))
                 .toOperationOutcome() as? OperationOutcome
         } else {
-            capabilityStatementApplier.applyCapabilityStatementProfiles(resource, importProfile)
-            val messageDefinitionErrors = fhirMessage.applyMessageDefinition(resource)
-            if (messageDefinitionErrors != null) {
-                messageDefinitionErrors.issue.forEach{
-                    additionalIssues.add(it)
+            if (resource is Bundle && resource.type.equals(BundleType.DOCUMENT)) {
+                // enforce local profiles in the FHIR document
+                (resource as Bundle).entry.forEach { entry ->
+                    if (entry.hasResource()) {
+                        capabilityStatementApplier.applyCapabilityStatementProfiles(entry.resource, importProfile)
+                    }
+                }
+                capabilityStatementApplier.applyCapabilityStatementProfiles(resource, importProfile)
+            } else {
+                capabilityStatementApplier.applyCapabilityStatementProfiles(resource, importProfile)
+                val messageDefinitionErrors = fhirMessage.applyMessageDefinition(resource)
+                if (messageDefinitionErrors != null) {
+                    messageDefinitionErrors.issue.forEach{
+                        additionalIssues.add(it)
+                    }
                 }
             }
             if (importProfile !== null && importProfile && resource is Bundle) fhirDocumentApplier.applyDocumentDefinition(resource)