Draft: REFV-207: Upgrade to HAPI 8.8.1

.github/workflows/build.yml

@@ -0,0 +1,48 @@
+name: CI Build
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    permissions:
+      contents: read          # checkout
+      actions: read           # needed for upload‑artifact
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Setup Java
+        uses: actions/setup-java@v5
+        with:
+          distribution: 'temurin'
+          java-version: '21'
+          cache: 'maven'
+
+      - name: Build with Maven
+        run: mvn clean install -DskipTests --no-transfer-progress
+
+      - name: Run Tests
+        run: |
+          mvn verify \
+            -Dsurefire.reportFormat=xml \
+            --no-transfer-progress
+
+      - name: Upload JUnit reports
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: junit-reports
+          path: target/surefire-reports/*.xml
+
+      - name: Upload JaCoCo coverage
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: jacoco-report
+          path: target/site/jacoco/**

cli/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>referencevalidator</artifactId>
         <groupId>de.gematik.refv</groupId>
-        <version>2.15.0</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
     <properties>
         <integrationtest.folder>${basedir}/target/test-classes/pluginloader-integration-test</integrationtest.folder>
@@ -107,10 +107,6 @@
             <groupId>info.picocli</groupId>
             <artifactId>picocli</artifactId>
         </dependency>
-        <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>

commons/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>referencevalidator</artifactId>
         <groupId>de.gematik.refv</groupId>
-        <version>2.15.0</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -61,5 +61,13 @@
                 </exclusion>
             </exclusions>
         </dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-caching-caffeine</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+        </dependency>
     </dependencies>
 </project>

commons/src/main/java/de/gematik/refv/commons/Profile.java

@@ -48,9 +48,9 @@ public static Profile parse(String canonical) {
     String[] splittedString = canonical.split("\\|");
     if (splittedString.length < 2) {
       return new Profile(canonical, splittedString[0], null);
-    } else {
-      return new Profile(canonical, splittedString[0], splittedString[1]);
     }
+
+    return new Profile(canonical, splittedString[0], splittedString[1]);
   }
 
   @Override

commons/src/main/java/de/gematik/refv/commons/configuration/ValidationModuleConfiguration.java

@@ -129,12 +129,12 @@ public Profile findFirstSupportedProfileWithExistingConfiguration(List<String> p
         profiles.stream()
             .map(Profile::parse)
             .filter(profile -> getSupportedProfileConfiguration(profile).isPresent())
-            .collect(Collectors.toList());
+            .toList();
     if (supportedProfilesFound.isEmpty()) return null;
     if (supportedProfilesFound.size() > 1)
       log.warn(
           "Multiple supported profiles found. Selecting the first one for further processing: {}",
-          supportedProfilesFound.get(0));
-    return supportedProfilesFound.get(0);
+          supportedProfilesFound.getFirst());
+    return supportedProfilesFound.getFirst();
   }
 }

commons/src/main/java/de/gematik/refv/commons/validation/BundleValidationModule.java

@@ -51,9 +51,10 @@ class BundleValidationModule implements IValidatorModule {
   @Override
   public void validateResource(IValidationContext<IBaseResource> iValidationContext) {
     var resource = iValidationContext.getResource();
-    if (!(resource instanceof Bundle)) return;
+    if (!(resource instanceof Bundle bundle)) {
+      return;
+    }
 
-    var bundle = (Bundle) resource;
     var i = 0;
     for (var entry : bundle.getEntry()) {
       String fullUrl = entry.getFullUrl();

commons/src/main/java/de/gematik/refv/commons/validation/GenericValidator.java

@@ -103,15 +103,15 @@ public ValidationResult validate(
     ValidationResult result;
     var configuration = resourceProvider.getConfiguration();
 
-    if (!validateEncoding(resourceBody, configuration, validationOptions))
+    if (!validateEncoding(resourceBody, configuration, validationOptions)) {
       result =
           ValidationResult.createInstance(
               ResultSeverityEnum.ERROR,
               ERR_REFV_WRONG_ENCODING,
               String.format(
                   "Wrong instance encoding. Allowed encodings: %s",
                   String.join(",", getAcceptedEncodings(configuration, validationOptions))));
-    else {
+    } else {
 
       List<String> allReferencedProfilesInResource =
           referencedProfileLocator.getAllReferencedProfilesInResource(resourceBody);
@@ -131,21 +131,23 @@ && noneReferencedProfileMatches(
           var userDefinedProfile =
               validationOptions
                   .getProfiles()
-                  .get(0); // Only one user defined profile is supported at the moment
+                  .getFirst(); // Only one user defined profile is supported at the moment
           log.warn("Profile for validation has been passed by user: " + userDefinedProfile);
           profileForValidation =
               configuration.findFirstSupportedProfileWithExistingConfiguration(
                   List.of(userDefinedProfile));
-        } else if (!allReferencedProfilesInResource.isEmpty())
+        } else if (!allReferencedProfilesInResource.isEmpty()) {
           profileForValidation =
               configuration.findFirstSupportedProfileWithExistingConfiguration(
                   allReferencedProfilesInResource);
-        else
+        } else {
           throw new IllegalArgumentException(
               "FHIR resources without a referenced profile are currently unsupported. Please provide a profile parameter or a profile in the resource meta.profile element.");
+        }
 
-        if (profileForValidation == null)
+        if (profileForValidation == null) {
           throw new UnsupportedProfileException(allReferencedProfilesInResource);
+        }
 
         result =
             validateResource(
@@ -179,11 +181,12 @@ private ValidationResult validateResource(
 
     var profileConfigurationOptional =
         configuration.getSupportedProfileConfiguration(profileForValidation);
-    if (profileConfigurationOptional.isEmpty())
+    if (profileConfigurationOptional.isEmpty()) {
       // Profile is listed among supported profiles, but there are no dependency lists defined -->
       // corrupted module configuration
       throw new IllegalStateException(
           String.format("Could not retrieve profile configuration for %s", profileForValidation));
+    }
 
     ProfileConfiguration profileConfiguration = profileConfigurationOptional.get();
 
@@ -296,15 +299,19 @@ private boolean validateEncoding(
       de.gematik.refv.commons.validation.ValidationOptions validationOptions) {
     List<String> acceptedEncodings = getAcceptedEncodings(configuration, validationOptions);
 
-    if (acceptedEncodings.isEmpty()) return true;
+    if (acceptedEncodings.isEmpty()) {
+      return true;
+    }
 
     EncodingEnum encoding = EncodingEnum.detectEncodingNoDefault(resourceBody);
 
-    if (acceptedEncodings.contains(Constants.FORMAT_XML) && encoding == EncodingEnum.XML)
+    if (acceptedEncodings.contains(Constants.FORMAT_XML) && encoding == EncodingEnum.XML) {
       return true;
+    }
 
-    if (acceptedEncodings.contains(Constants.FORMAT_JSON) && encoding == EncodingEnum.JSON)
+    if (acceptedEncodings.contains(Constants.FORMAT_JSON) && encoding == EncodingEnum.JSON) {
       return true;
+    }
 
     log.warn("Unknown resource encoding: {}", encoding);
     return false;

commons/src/main/java/de/gematik/refv/commons/validation/HapiFhirValidatorFactory.java

@@ -34,7 +34,6 @@
 import java.util.Collection;
 import lombok.NonNull;
 import lombok.SneakyThrows;
-import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
@@ -66,7 +65,10 @@ private FhirValidator createHapiFhirValidator(
       ValidationModuleConfiguration configuration, ValidationSupportChain validationSupportChain) {
     FhirInstanceValidator hapiValidatorModule = new FhirInstanceValidator(validationSupportChain);
     hapiValidatorModule.setErrorForUnknownProfiles(configuration.isErrorOnUnknownProfile());
-    hapiValidatorModule.setNoExtensibleWarnings(true);
+    hapiValidatorModule.setNoExtensibleWarnings(
+        Boolean.parseBoolean(System.getenv().getOrDefault("DISABLE_EXTENSIBLE_WARNINGS", "true")));
+    hapiValidatorModule.setNoTerminologyChecks(
+        Boolean.parseBoolean(System.getenv().getOrDefault("DISABLE_TERMINOLOGY_CHECKS", "false")));
     hapiValidatorModule.setAnyExtensionsAllowed(configuration.isAnyExtensionsAllowed());
     FhirValidator fhirValidator = fhirContext.newValidator();
     fhirValidator.registerValidatorModule(hapiValidatorModule);
@@ -91,12 +93,9 @@ private ValidationSupportChain createValidationSupportChain(
     return new ValidationSupportChain(
         new UcumValidationSupport(fhirContext, configuration.getUcumValidationSeverityLevel()),
         new SnapshotGeneratingValidationSupport(fhirContext),
-        new CachingValidationSupport(
-            new IgnoreCodeSystemValidationSupport(
-                fhirContext, configuration.getIgnoredCodeSystems())),
-        new CachingValidationSupport(
-            new IgnoreValueSetValidationSupport(fhirContext, configuration.getIgnoredValueSets())),
-        new CachingValidationSupport(validationSupport),
+        new IgnoreCodeSystemValidationSupport(fhirContext, configuration.getIgnoredCodeSystems()),
+        new IgnoreValueSetValidationSupport(fhirContext, configuration.getIgnoredValueSets()),
+        validationSupport,
         new PipedCanonicalCoreResourcesValidationSupport(fhirContext));
   }
 }

commons/src/main/java/de/gematik/refv/commons/validation/ReferencedProfileLocator.java

@@ -66,7 +66,9 @@ public List<String> getAllReferencedProfilesInResource(String resourceBody) {
       } catch (IOException e) {
         throw new IllegalArgumentException("Could not parse resource", e);
       }
-    } else allProfilesInResource = locateInXml(resourceBody);
+    } else {
+      allProfilesInResource = locateInXml(resourceBody);
+    }
 
     return allProfilesInResource;
   }
@@ -80,7 +82,9 @@ private List<String> locateInXml(String resource) throws IllegalArgumentExceptio
       while (xmlEventReader.hasNext()) {
         XMLEvent event = xmlEventReader.nextEvent();
 
-        if (event instanceof DTD) throw new SecurityException("DTD is not allowed");
+        if (event instanceof DTD) {
+          throw new SecurityException("DTD is not allowed");
+        }
 
         if (event.isStartElement()) {
           treeLevel++;
@@ -151,7 +155,9 @@ private void parseXmlEventsForProfiles(XMLEventReader xmlEventReader, List<Strin
     while (xmlEventReader.hasNext()) {
       event = xmlEventReader.nextEvent();
       if (event.isEndElement()
-          && event.asEndElement().getName().getLocalPart().equalsIgnoreCase("meta")) break;
+          && event.asEndElement().getName().getLocalPart().equalsIgnoreCase("meta")) {
+        break;
+      }
       if (event.isStartElement()) {
         nextTag = event.asStartElement();
         if (nextTag.getName().getLocalPart().equalsIgnoreCase(PROFILE_STRING)
@@ -171,9 +177,11 @@ private List<String> locateInJson(String resource) throws IOException {
       int treeLevel = 0;
       var token = jsonParser.nextToken();
       while (jsonParser.hasCurrentToken()) {
-        if (token.isStructStart()) treeLevel++;
-        else if (token.isStructEnd()) treeLevel--;
-        else {
+        if (token.isStructStart()) {
+          treeLevel++;
+        } else if (token.isStructEnd()) {
+          treeLevel--;
+        } else {
           if (treeLevel <= 2) {
             String fieldName = jsonParser.currentName();
             if ("meta".equals(fieldName)) {

commons/src/main/java/de/gematik/refv/commons/validation/ValidationResultOutputFilter.java

@@ -30,7 +30,9 @@
 class ValidationResultOutputFilter {
   public ValidationResult apply(
       ValidationResult result, ValidationMessagesFilter validationMessagesFilter) {
-    if (validationMessagesFilter == ValidationMessagesFilter.KEEP_ALL) return result;
+    if (validationMessagesFilter == ValidationMessagesFilter.KEEP_ALL) {
+      return result;
+    }
 
     if (validationMessagesFilter == ValidationMessagesFilter.KEEP_ERRORS_AND_WARNINGS_ONLY) {
       var filteredMessages =

commons/src/main/java/de/gematik/refv/commons/validation/support/PipedCanonicalCoreResourcesValidationSupport.java

@@ -42,14 +42,19 @@ public PipedCanonicalCoreResourcesValidationSupport(FhirContext ctx) {
   @Override
   public IBaseResource fetchStructureDefinition(String theUrl) {
     Profile p = Profile.parse(theUrl);
-    if (p.getVersion() == null) return null;
+    if (p.getVersion() == null) {
+      return null;
+    }
 
     IValidationSupport support = ctx.getValidationSupport();
     IBaseResource resource = support.fetchStructureDefinition(p.getBaseCanonical());
-    if (resource == null) return null;
+    if (resource == null) {
+      return null;
+    }
 
-    if (Strings.CS.equals(((StructureDefinition) resource).getVersion(), p.getVersion()))
+    if (Strings.CS.equals(((StructureDefinition) resource).getVersion(), p.getVersion())) {
       return resource;
+    }
 
     return null;
   }

commons/src/main/java/de/gematik/refv/commons/validation/support/UcumValidationSupport.java

@@ -41,13 +41,14 @@
 @Slf4j
 public class UcumValidationSupport implements IValidationSupport {
 
-  private FhirContext fhirContext;
+  private final FhirContext fhirContext;
 
-  private IssueSeverity issueSeverity;
+  private final IssueSeverity issueSeverity;
 
   public UcumValidationSupport(FhirContext theFhirContext, IssueSeverity issueSeverity) {
     this.fhirContext = theFhirContext;
-    this.issueSeverity = issueSeverity;
+    this.issueSeverity = issueSeverity != null ? issueSeverity : IssueSeverity.ERROR;
+    ;
   }
 
   @Override
@@ -113,8 +114,9 @@ public CodeValidationResult validateCode(
       String theValueSetUrl) {
     LookupCodeResult lookupResult =
         lookupCode(theValidationSupportContext, theCodeSystem, theCode, null);
-    if (lookupResult.isFound())
+    if (lookupResult != null && lookupResult.isFound()) {
       return new CodeValidationResult().setCode(theCode).setDisplay(lookupResult.getCodeDisplay());
+    }
 
     // The presence of only the following two attributes is important to make sure the code
     // validation will result in a Warning or an Error

commons/src/main/resources/logback.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration>
+
+<configuration>
+    <import class="ch.qos.logback.classic.encoder.PatternLayoutEncoder"/>
+    <import class="ch.qos.logback.core.ConsoleAppender"/>
+
+    <appender name="Console" class="ConsoleAppender">
+        <encoder class="PatternLayoutEncoder">
+            <pattern>[%d{ISO8601}] [%p] [%t] [%c] %m%n</pattern>
+        </encoder>
+    </appender>
+
+    <variable name="ROOT_LOG_LEVEL" value="${ROOT_LOG_LEVEL:-INFO}"/>
+    <root level="${ROOT_LOG_LEVEL}">
+        <appender-ref ref="Console"/>
+    </root>
+</configuration>