Merge 49d64c1633 into fb7571185a

hapi-fhir-android/.gitignore

@@ -0,0 +1 @@
+

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ValidateCommand.java

@@ -35,6 +35,7 @@ import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.text.WordUtils;
 import org.fusesource.jansi.Ansi.Color;
+import org.hl7.fhir.common.hapi.validation.support.NpmPackageValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 
@@ -86,6 +87,8 @@ public class ValidateCommand extends BaseCommand {
 				"igpack",
 				true,
 				"If specified, provides the filename of an IGPack file to include in validation");
+		addOptionalOption(
+				retVal, null, "oneCode", false, "Validate allowing one coding to satisfy CodeableConcept binding");
 		addOptionalOption(retVal, "x", "xsd", false, "Validate using Schemas");
 		addOptionalOption(retVal, "s", "sch", false, "Validate using Schematrons");
 		addOptionalOption(retVal, "e", "encoding", "encoding", "File encoding (default is UTF-8)");
@@ -149,20 +152,23 @@ public class ValidateCommand extends BaseCommand {
 		}
 
 		if (theCommandLine.hasOption("p")) {
+			ValidationSupportChain validationSupportChain;
 			switch (ctx.getVersion().getVersion()) {
 				case DSTU2: {
 					FhirInstanceValidator instanceValidator;
-					ValidationSupportChain validationSupportChain =
+					validationSupportChain =
 							ValidationSupportChainCreator.getValidationSupportChainDstu2(ctx, theCommandLine);
+					validationSupportChain.oneCodingIsSufficient = true;
 					instanceValidator = new FhirInstanceValidator(validationSupportChain);
 					val.registerValidatorModule(instanceValidator);
 					break;
 				}
 				case DSTU3:
 				case R4: {
+					ourLog.info("Adding FHIR R4 validation support chain");
 					FhirInstanceValidator instanceValidator = new FhirInstanceValidator(ctx);
 					val.registerValidatorModule(instanceValidator);
-					ValidationSupportChain validationSupportChain =
+					validationSupportChain =
 							ValidationSupportChainCreator.getValidationSupportChainR4(ctx, theCommandLine);
 					instanceValidator.setValidationSupport(validationSupportChain);
 					break;
@@ -171,6 +177,25 @@ public class ValidateCommand extends BaseCommand {
 					throw new ParseException(
 							Msg.code(1620) + "Profile validation (-p) is not supported for this FHIR version");
 			}
+
+			// Do we allow CodeableConcepts to be satisfied by only one coding?
+			// Useful when we are using additionalBindings.
+			validationSupportChain.oneCodingIsSufficient = theCommandLine.hasOption("oneCode");
+
+			// If they want to do profile validation - there might be a whole IG to load...
+			if (theCommandLine.hasOption("igpack")) {
+				String igPack = theCommandLine.getOptionValue("igpack");
+				ourLog.info("Loading IG Package from {} to the validation support chain", igPack);
+				try {
+					NpmPackageValidationSupport npmPackageSupport = new NpmPackageValidationSupport(ctx);
+					npmPackageSupport.loadPackageFromFile(igPack);
+					validationSupportChain.addValidationSupport(0, npmPackageSupport);
+				} catch (IOException iox) {
+					throw new ParseException(
+							Msg.code(1620) + "IGpack validation (--igpack) failed: " + iox.getMessage());
+				}
+				ourLog.info("Completed loading IG Package from {}", igPack);
+			}
 		}
 
 		val.setValidateAgainstStandardSchema(theCommandLine.hasOption("x"));

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ValidationSupportChainCreator.java

@@ -23,6 +23,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
 import ca.uhn.fhir.i18n.Msg;
 import org.apache.commons.cli.CommandLine;
+import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
 import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.LocalFileValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
@@ -52,7 +53,7 @@ public class ValidationSupportChainCreator {
 		if (commandLine.hasOption("r")) {
 			chain.addValidationSupport(new LoadingValidationSupportDstu3());
 		}
-
+		chain.addValidationSupport(new CommonCodeSystemsTerminologyService(ctx));
 		return chain;
 	}
 

hapi-fhir-jpaserver-mdm/pom.xml

@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>jakarta.servlet</groupId>
 			<artifactId>jakarta.servlet-api</artifactId>
-			<scope>test</scope>
+			<scope>provided</scope>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/search/reindex/InstanceReindexServiceImplR5Test.java

@@ -81,7 +81,7 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
 
 		IIdType id = createPatient(withFamily("Simpson"), withGiven("Homer"));
 
-		runInTransaction(this::logAllNonUniqueIndexes);
+		runInTransaction((Runnable) this::logAllNonUniqueIndexes);
 
 		Parameters outcome = (Parameters) mySvc.reindexDryRun(new SystemRequestDetails(), id, null);
 		ourLog.info("Output:{}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));

hapi-fhir-server-mdm/pom.xml

@@ -133,7 +133,11 @@
 			<version>${project.version}</version>
 			<scope>test</scope>
 		</dependency>
-
+		<dependency>
+			<groupId>jakarta.servlet</groupId>
+			<artifactId>jakarta.servlet-api</artifactId>
+			<scope>provided</scope>
+		</dependency>
     </dependencies>
 
 	<build>

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/NpmPackageValidationSupport.java

@@ -3,13 +3,14 @@ package org.hl7.fhir.common.hapi.validation.support;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.parser.LenientErrorHandler;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.ClasspathUtil;
 import jakarta.annotation.Nonnull;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 
+import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
@@ -31,11 +32,16 @@ public class NpmPackageValidationSupport extends PrePopulatedValidationSupport {
 		super(theFhirContext);
 	}
 
+	@Override
+	public String getName() {
+		return getFhirContext().getVersion().getVersion() + " NPM Package Validation Support";
+	}
+
 	/**
 	 * Load an NPM package using a classpath specification, e.g. <code>/path/to/resource/my_package.tgz</code>. The
 	 * classpath spec can optionally be prefixed with the string <code>classpath:</code>
 	 *
-	 * @throws InternalErrorException If the classpath file can't be found
+	 * @throws IOException If the classpath file can't be found
 	 */
 	public void loadPackageFromClasspath(String theClasspath) throws IOException {
 		try (InputStream is = ClasspathUtil.loadResourceAsStream(theClasspath)) {
@@ -47,6 +53,21 @@ public class NpmPackageValidationSupport extends PrePopulatedValidationSupport {
 		}
 	}
 
+	/**
+	 * Load an NPM package from the filesystem  e.g. <code>my_package.tgz</code>.
+	 *
+	 * @throws IOException If the package file can't be found
+	 */
+	public void loadPackageFromFile(String theFile) throws IOException {
+		File inFile = new File(theFile);
+		InputStream is = new FileInputStream(inFile);
+		NpmPackage pkg = NpmPackage.fromPackage(is);
+		if (pkg.getFolders().containsKey("package")) {
+			loadResourcesFromPackage(pkg);
+			loadBinariesFromPackage(pkg);
+		}
+	}
+
 	private void loadResourcesFromPackage(NpmPackage thePackage) {
 		NpmPackage.NpmPackageFolder packageFolder = thePackage.getFolders().get("package");
 

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java

@@ -371,12 +371,13 @@ public class ValidationSupportChain implements IValidationSupport {
 				if (retVal != null) {
 					if (ourLog.isDebugEnabled()) {
 						ourLog.debug(
-								"Code {}|{} '{}' in ValueSet {} validated by {}",
+								"Code {}|{} '{}' in ValueSet {} validated by {} result: {}",
 								theCodeSystem,
 								theCode,
 								theDisplay,
 								theValueSetUrl,
-								next.getName());
+								next.getName(),
+								retVal.getMessage() != null ? retVal.getMessage() : "Success");
 					}
 					return retVal;
 				}
@@ -401,12 +402,13 @@ public class ValidationSupportChain implements IValidationSupport {
 				if (retVal != null) {
 					if (ourLog.isDebugEnabled()) {
 						ourLog.debug(
-								"Code {}|{} '{}' in ValueSet {} validated by {}",
+								"Code {}|{} '{}' in ValueSet {} validated by {} result: {}",
 								theCodeSystem,
 								theCode,
 								theDisplay,
 								theValueSet.getIdElement(),
-								next.getName());
+								next.getName(),
+								retVal.getMessage() != null ? retVal.getMessage() : "Success");
 					}
 					return retVal;
 				}
@@ -445,4 +447,18 @@ public class ValidationSupportChain implements IValidationSupport {
 		}
 		return null;
 	}
+	/**
+	 * See VersionSpecificWorkerContextWrapper#validateCode in hapi-fhir-validation.
+	 * <p>
+	 * If true, validation for codings will return a positive result if AT LEAST ONE coding is valid.
+	 * If false, validation for codings will return a positive result if there is ALL codings are valid.
+	 * </p>
+	 * @return if the application has configured validation to use logical AND, as opposed to logical OR, which is the default
+	 */
+	public boolean oneCodingIsSufficient = false; // default value from parent Interface (it's the wrong way round !!!)
+
+	@Override
+	public boolean isEnabledValidationForCodingsLogicalAnd() { // should be named ....LogicalAny
+		return oneCodingIsSufficient;
+	}
 }

pom.xml

@@ -1050,9 +1050,9 @@
 
 		<!-- Site properties -->
 		<fontawesomeVersion>5.4.1</fontawesomeVersion>
-		<maven.compiler.source>11</maven.compiler.source>
+		<maven.compiler.source>17</maven.compiler.source>
-		<maven.compiler.target>11</maven.compiler.target>
+		<maven.compiler.target>17</maven.compiler.target>
-		<maven.compiler.release>11</maven.compiler.release>
+		<maven.compiler.release>17</maven.compiler.release>
 		<maven.compiler.testSource>17</maven.compiler.testSource>
 		<maven.compiler.testTarget>17</maven.compiler.testTarget>
 		<maven.compiler.testRelease>17</maven.compiler.testRelease>
@@ -3299,4 +3299,3 @@
 		</profile>
 	</profiles>
 </project>
-