stand-alone validator working, workaround for icd10-gm, ops, pzn

Added a "code ok" validation support impl that assumes that codes from
http://fhir.de/CodeSystem/bfarm/icd-10-gm,
http://fhir.de/CodeSystem/dimdi/icd-10-gm,
http://fhir.de/CodeSystem/bfarm/ops,
http://fhir.de/CodeSystem/dimdi/ops, http://fhir.de/CodeSystem/ifa/pzn
are always valid, this workaround is fine if the codes are later checked
against an expanded ValueSet.

Fixed copy-dependencies build step for stand-alone validator

codex-process-data-transfer/pom.xml

@@ -178,10 +178,10 @@
 								hapi-fhir-base,hapi-fhir-client,hapi-fhir-converter,hapi-fhir-structures-r4,hapi-fhir-structures-r5,hapi-fhir-validation,hapi-fhir-validation-resources-r4,
 								hapi-fhir-validation-resources-r5,org.hl7.fhir.convertors,org.hl7.fhir.dstu2,org.hl7.fhir.dstu2016may,org.hl7.fhir.dstu3,org.hl7.fhir.r4,org.hl7.fhir.r5,org.hl7.fhir.utilities,
 								org.hl7.fhir.validation,jackson-annotations,jackson-core,jackson-databind,jackson-module-jaxb-annotations,caffeine,guava,
-								commons-codec,commons-io,crypto-utils,log4j2-utils,jakarta.activation,jakarta.annotation-api,jakarta.ws.rs-api,jakarta.xml.bind-api,commons-compress,commons-lang3,commons-text,
-								httpclient,httpcore,log4j-api,log4j-core,log4j-slf4j-impl,bcpkix-jdk15on,bcprov-jdk15on,bcutil-jdk15on,ucum,hk2-api,hk2-locator,hk2-utils,osgi-resource-locator,
-								aopalliance-repackaged,jakarta.inject,jersey-apache-connector,jersey-client,jersey-common,jersey-entity-filtering,jersey-hk2,jersey-media-jaxb,jersey-media-json-jackson,
-								dsf-bpe-process-base,dsf-fhir-rest-adapter,dsf-fhir-validation,dsf-openehr-model,jcl-over-slf4j,
+								commons-codec,commons-io,crypto-utils,jakarta.activation,jakarta.annotation-api,jakarta.ws.rs-api,jakarta.xml.bind-api,commons-compress,commons-lang3,commons-text,
+								httpclient,httpcore,log4j-api,log4j-core,log4j-slf4j2-impl,bcpkix-jdk18on,bcprov-jdk18on,bcutil-jdk18on,ucum,hk2-api,hk2-locator,hk2-utils,osgi-resource-locator,
+								aopalliance-repackaged,jakarta.inject-api,jersey-apache-connector,jersey-client,jersey-common,jersey-entity-filtering,jersey-hk2,jersey-media-jaxb,jersey-media-json-jackson,
+								dsf-bpe-process-api-v1,dsf-fhir-auth,dsf-fhir-rest-adapter,dsf-fhir-validation,dsf-openehr-model,jcl-over-slf4j,
 								slf4j-api,spring-aop,spring-beans,spring-context,spring-core,spring-expression,spring-jcl,thymeleaf,unbescape,xpp3,xpp3_xpath
 							</includeArtifactIds>
 						</configuration>

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ValidationConfig.java

@@ -29,6 +29,8 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.BundleValidatorFactory;
@@ -52,7 +54,6 @@
 import de.rwh.utils.crypto.CertificateHelper;
 import de.rwh.utils.crypto.io.CertificateReader;
 import de.rwh.utils.crypto.io.PemIo;
-import dev.dsf.bpe.v1.ProcessPluginApi;
 import dev.dsf.bpe.v1.documentation.ProcessDocumentation;
 import dev.dsf.fhir.validation.SnapshotGenerator;
 import dev.dsf.fhir.validation.ValueSetExpander;
@@ -218,8 +219,13 @@ public static enum TerminologyServerConnectionTestStatus
 	@Value("${java.io.tmpdir}")
 	private String systemTempFolder;
 
+	// not using process plugin api to enable reuse of this config class in stand-alone validator
+	@Autowired
+	private FhirContext fhirContext;
+
+	// not using process plugin api to enable reuse of this config class in stand-alone validator
 	@Autowired
-	private ProcessPluginApi api;
+	private ObjectMapper objectMapper;
 
 
 	@Bean
@@ -230,9 +236,9 @@ public ValidationPackageManager validationPackageManager()
 		EnumSet<BindingStrength> bindingStrengths = EnumSet.copyOf(
 				valueSetExpansionBindingStrengths.stream().map(BindingStrength::fromCode).collect(Collectors.toList()));
 
-		return new ValidationPackageManagerImpl(validationPackageClient(), valueSetExpansionClient(),
-				api.getObjectMapper(), api.getFhirContext(), internalSnapshotGeneratorFactory(),
-				internalValueSetExpanderFactory(), noDownload, bindingStrengths);
+		return new ValidationPackageManagerImpl(validationPackageClient(), valueSetExpansionClient(), objectMapper,
+				fhirContext, internalSnapshotGeneratorFactory(), internalValueSetExpanderFactory(), noDownload,
+				bindingStrengths);
 	}
 
 	private StructureDefinitionModifier createStructureDefinitionModifier(String className)
@@ -368,7 +374,7 @@ else if (clientCertificateFile == null && clientCertificatePrivateKeyFile == nul
 	@Bean
 	public ValidationPackageClient validationPackageClient()
 	{
-		return new ValidationPackageClientWithFileSystemCache(packageCacheFolder(), api.getObjectMapper(),
+		return new ValidationPackageClientWithFileSystemCache(packageCacheFolder(), objectMapper,
 				validationPackageClientJersey());
 	}
 
@@ -410,7 +416,7 @@ public ValueSetExpansionClient valueSetExpansionClient()
 		List<ValueSetModifier> modifiers = valueSetModifierClasses.stream().map(this::createValueSetModifier)
 				.collect(Collectors.toList());
 
-		return new ValueSetExpansionClientWithFileSystemCache(valueSetCacheFolder(), api.getFhirContext(),
+		return new ValueSetExpansionClientWithFileSystemCache(valueSetCacheFolder(), fhirContext,
 				new ValueSetExpansionClientWithModifiers(valueSetExpansionClientJersey(), modifiers));
 	}
 
@@ -464,8 +470,7 @@ private ValueSetExpansionClient valueSetExpansionClientJersey()
 				valueSetExpansionClientBasicAuthUsername, valueSetExpansionClientBasicAuthPassword,
 				valueSetExpansionClientProxySchemeHostPort, valueSetExpansionClientProxyUsername,
 				valueSetExpansionClientProxyPassword, valueSetExpansionClientConnectTimeout,
-				valueSetExpansionClientReadTimeout, valueSetExpansionClientVerbose, api.getObjectMapper(),
-				api.getFhirContext());
+				valueSetExpansionClientReadTimeout, valueSetExpansionClientVerbose, objectMapper, fhirContext);
 	}
 
 	public TerminologyServerConnectionTestStatus testConnectionToTerminologyServer()
@@ -524,7 +529,8 @@ public BundleValidatorFactory bundleValidatorFactory()
 				validationPackageIdentifiers());
 	}
 
-	private List<ValidationPackageIdentifier> validationPackageIdentifiers()
+	@Bean
+	public List<ValidationPackageIdentifier> validationPackageIdentifiers()
 	{
 		if (validationPackages == null || validationPackages.isEmpty())
 			throw new IllegalArgumentException("Validation packages not specified");

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/NonValidatingValidationSupport.java

@@ -0,0 +1,61 @@
+package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.support.ConceptValidationOptions;
+import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValidationSupportContext;
+
+public class NonValidatingValidationSupport implements IValidationSupport
+{
+	private static final Logger logger = LoggerFactory.getLogger(NonValidatingValidationSupport.class);
+
+	private final FhirContext fhirContext;
+	private final List<String> notValidatedCodeSystemSystems = new ArrayList<>();
+
+	public NonValidatingValidationSupport(FhirContext fhirContext, String... notValidatedCodeSystemSystems)
+	{
+		this(fhirContext, Arrays.asList(notValidatedCodeSystemSystems));
+	}
+
+	public NonValidatingValidationSupport(FhirContext fhirContext, Collection<String> notValidatedCodeSystemSystems)
+	{
+		this.fhirContext = fhirContext;
+
+		if (notValidatedCodeSystemSystems != null)
+			this.notValidatedCodeSystemSystems.addAll(notValidatedCodeSystemSystems);
+	}
+
+	@Override
+	public FhirContext getFhirContext()
+	{
+		return fhirContext;
+	}
+
+	@Override
+	public CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext,
+			ConceptValidationOptions theOptions, String system, String code, String display, String valueSetUrl)
+	{
+		if (notValidatedCodeSystemSystems.contains(system))
+		{
+			logger.warn("Not validating code {} from system {} for valueSet {}", code, system, valueSetUrl);
+			return new CodeValidationResult().setCode(code).setCodeSystemName(system).setDisplay(display);
+		}
+
+		else
+			return null;
+	}
+
+	@Override
+	public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String system)
+	{
+		return notValidatedCodeSystemSystems.contains(system);
+	}
+}

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationMain.java

@@ -3,7 +3,9 @@
 import java.io.InputStream;
 import java.nio.file.Files;
 import java.nio.file.Paths;
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.List;
 import java.util.Locale;
 import java.util.Objects;
 import java.util.stream.Stream;
@@ -23,6 +25,11 @@
 import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.core.env.EnumerablePropertySource;
 
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+import com.fasterxml.jackson.databind.MapperFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.json.JsonMapper;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.i18n.HapiLocalizer;
 import ca.uhn.fhir.parser.IParser;
@@ -70,7 +77,7 @@ public static class TestConfig
 		private ValidationPackageManager packageManager;
 
 		@Autowired
-		private ValidationPackageIdentifier validationPackage;
+		private List<ValidationPackageIdentifier> validationPackageIdentifiers;
 
 		@Autowired
 		private ValueSetExpansionClient valueSetExpansionClient;
@@ -79,7 +86,15 @@ public static class TestConfig
 		private ConfigurableEnvironment environment;
 
 		@Bean
-		public FhirContext fhirContext()
+		public ObjectMapper getObjectMapper()
+		{
+			return JsonMapper.builder().serializationInclusion(Include.NON_NULL)
+					.serializationInclusion(Include.NON_EMPTY).disable(MapperFeature.AUTO_DETECT_CREATORS)
+					.disable(MapperFeature.AUTO_DETECT_FIELDS).disable(MapperFeature.AUTO_DETECT_SETTERS).build();
+		}
+
+		@Bean
+		public FhirContext getFhirContext()
 		{
 			FhirContext context = FhirContext.forR4();
 			HapiLocalizer localizer = new HapiLocalizer()
@@ -97,14 +112,15 @@ public Locale getLocale()
 		@Bean
 		public ValidationMain validatorMain()
 		{
-			return new ValidationMain(environment, fhirContext(), packageManager, validationPackage, output,
-					outputPretty, valueSetExpansionClient);
+			return new ValidationMain(environment, getFhirContext(), packageManager, validationPackageIdentifiers,
+					output, outputPretty, valueSetExpansionClient);
 		}
 	}
 
 	public static enum Output
 	{
 		JSON, XML
+
 	}
 
 	public static void main(String[] args)
@@ -137,19 +153,20 @@ public static void main(String[] args)
 	private final ConfigurableEnvironment environment;
 	private final FhirContext fhirContext;
 	private final ValidationPackageManager packageManager;
-	private final ValidationPackageIdentifier validationPackage;
+	private final List<ValidationPackageIdentifier> validationPackageIdentifiers = new ArrayList<>();
 	private final Output output;
 	private final boolean outputPretty;
 	private final ValueSetExpansionClient valueSetExpansionClient;
 
 	public ValidationMain(ConfigurableEnvironment environment, FhirContext fhirContext,
-			ValidationPackageManager packageManager, ValidationPackageIdentifier validationPackage, Output output,
-			boolean outputPretty, ValueSetExpansionClient valueSetExpansionClient)
+			ValidationPackageManager packageManager, List<ValidationPackageIdentifier> validationPackageIdentifiers,
+			Output output, boolean outputPretty, ValueSetExpansionClient valueSetExpansionClient)
 	{
 		this.environment = environment;
 		this.fhirContext = fhirContext;
 		this.packageManager = packageManager;
-		this.validationPackage = validationPackage;
+		if (validationPackageIdentifiers != null)
+			this.validationPackageIdentifiers.addAll(validationPackageIdentifiers);
 		this.output = output;
 		this.outputPretty = outputPretty;
 		this.valueSetExpansionClient = valueSetExpansionClient;
@@ -161,18 +178,16 @@ public void afterPropertiesSet() throws Exception
 		Objects.requireNonNull(environment, "environment");
 		Objects.requireNonNull(fhirContext, "fhirContext");
 		Objects.requireNonNull(packageManager, "packageManager");
-		Objects.requireNonNull(validationPackage, "validationPackage");
 		Objects.requireNonNull(output, "output");
 		Objects.requireNonNull(valueSetExpansionClient, "valueSetExpansionClient");
 	}
 
 	public void validate(String[] files)
 	{
-		logger.info("Using validation package {}", validationPackage);
+		logger.info("Using validation packages {}", validationPackageIdentifiers);
 		getAllNumProperties().forEach(c -> logger.debug("Config: {}", c));
 
-		BundleValidator validator = packageManager.createBundleValidator(validationPackage.getName(),
-				validationPackage.getVersion());
+		BundleValidator validator = packageManager.createBundleValidator(validationPackageIdentifiers);
 
 		Arrays.stream(files).map(this::read).filter(r -> r != null).forEach(r ->
 		{

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageManager.java

@@ -148,4 +148,16 @@ default BundleValidator createBundleValidator(String name, String version)
 	 * @return {@link BundleValidator} for the specified FHIR package
 	 */
 	BundleValidator createBundleValidator(ValidationPackageIdentifier identifier);
+
+	/**
+	 * Downloads the given FHIR packages and all its dependencies. Will try to generate snapshots for all
+	 * {@link StructureDefinition}s of the specified (root) package and its dependencies, will try to expand all
+	 * {@link ValueSet}s with binding strength {@link BindingStrength#EXTENSIBLE}, {@link BindingStrength#PREFERRED} or
+	 * {@link BindingStrength#REQUIRED} used by the {@link StructureDefinition} of the specified (root) package or their
+	 * dependencies, before returning a {@link IValidationSupport}.
+	 *
+	 * @param identifiers
+	 * @return {@link BundleValidator} for the specified FHIR packages
+	 */
+	BundleValidator createBundleValidator(List<ValidationPackageIdentifier> identifiers);
 }

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageManagerImpl.java

@@ -170,6 +170,17 @@ public BundleValidator createBundleValidator(IValidationSupport validationSuppor
 		return validator;
 	}
 
+	@Override
+	public BundleValidator createBundleValidator(List<ValidationPackageIdentifier> identifiers)
+	{
+		Objects.requireNonNull(identifiers, "identifiers");
+
+		List<ValidationPackageWithDepedencies> packageWithDependencies = downloadPackagesWithDependencies(identifiers);
+		IValidationSupport validationSupport = expandValueSetsAndGenerateStructureDefinitionSnapshots(
+				packageWithDependencies);
+		return createBundleValidator(validationSupport, packageWithDependencies);
+	}
+
 	@Override
 	public BundleValidator createBundleValidator(ValidationPackageIdentifier identifier)
 	{
@@ -409,7 +420,11 @@ private ValidationSupportChain createSupportChain(FhirContext context,
 						getAll(ValidationPackageWithDepedencies::getAllStructureDefinitions, packagesWithDependencies),
 						getAll(ValidationPackageWithDepedencies::getAllCodeSystems, packagesWithDependencies),
 						getAll(ValidationPackageWithDepedencies::getAllValueSets, packagesWithDependencies)),
-				new DefaultProfileValidationSupport(context), new QuietCommonCodeSystemsTerminologyService(context));
+				new DefaultProfileValidationSupport(context), new QuietCommonCodeSystemsTerminologyService(context),
+				// TODO remove NonValidatingValidationSupport
+				new NonValidatingValidationSupport(context, "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
+						"http://fhir.de/CodeSystem/dimdi/icd-10-gm", "http://fhir.de/CodeSystem/bfarm/ops",
+						"http://fhir.de/CodeSystem/dimdi/ops", "http://fhir.de/CodeSystem/ifa/pzn"));
 	}
 
 	private <V> List<V> getAll(Function<ValidationPackageWithDepedencies, List<V>> mapper,