Implement the new Gazelle validation API

Fixes #141

docs/changelog.md

@@ -1,3 +1,7 @@
+YYYY/MM/DD Release X.Y.Z
+
+- Implement the new Gazelle validation API [#141](https://github.com/ahdis/matchbox/issues/141)
+
 2024/01/31 Release 3.5.4
 
 - `docker pull europe-west6-docker.pkg.dev/ahdis-ch/ahdis/matchbox:v3.5.4`

matchbox-server/src/main/java/ca/uhn/fhir/jpa/starter/Application.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ch.ahdis.matchbox.spring.MatchboxEventListener;
+import ch.ahdis.matchbox.gazelle.GazelleValidationWs;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
 import org.springframework.boot.SpringApplication;
@@ -26,7 +27,8 @@
 	MdmConfig.class,
 	MatchboxJpaConfig.class,
 	FhirServerConfigR4.class,
-	MatchboxEventListener.class})
+	MatchboxEventListener.class,
+	GazelleValidationWs.class})
 public class Application extends SpringBootServletInitializer {
 
   public static void main(String[] args) {
@@ -48,8 +50,8 @@ protected SpringApplicationBuilder configure(
 
   @Bean
   @Conditional(OnEitherVersion.class)
-  public ServletRegistrationBean hapiServletRegistration(RestfulServer restfulServer) {
-    ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean();
+  public ServletRegistrationBean<RestfulServer> hapiServletRegistration(RestfulServer restfulServer) {
+    ServletRegistrationBean<RestfulServer> servletRegistrationBean = new ServletRegistrationBean<>();
     beanFactory.autowireBean(restfulServer);
     servletRegistrationBean.setServlet(restfulServer);
     servletRegistrationBean.addUrlMappings("/fhir/*");

matchbox-server/src/main/java/ch/ahdis/fhir/hapi/jpa/validation/ValidationProvider.java

@@ -43,6 +43,7 @@
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
 import org.hl7.fhir.r5.model.OperationOutcome;
 import org.hl7.fhir.r5.model.StringType;
+import org.hl7.fhir.r5.utils.EOperationOutcome;
 import org.hl7.fhir.r5.utils.OperationOutcomeUtilities;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
@@ -73,9 +74,6 @@ public class ValidationProvider {
 	@Autowired
 	private FhirContext myContext;
 
-	@Autowired
-	private INpmPackageVersionDao myPackageVersionDao;
-
 //	@Operation(name = "$canonical", manualRequest = true, idempotent = true, returnParameters = {
 //			@OperationParam(name = "return", type = IBase.class, min = 1, max = 1) })
 //	public IBaseResource canonical(HttpServletRequest theRequest) {
@@ -140,7 +138,13 @@ public IBaseResource validate(final HttpServletRequest theRequest) {
 			reload = theRequest.getParameter("reload").equals("true");
 		}
 
-		final String contentString = this.getContentString(theRequest, addedValidationMessages);
+		String contentString = "";
+		try {
+			contentString = new String(theRequest.getInputStream().readAllBytes(), StandardCharsets.UTF_8);
+		} catch (final Exception e) {
+			log.error(e.getMessage(), e);
+		}
+
 		if (contentString.isEmpty()) {
 			return this.getOoForError("No content provided in HTTP body");
 		} else {
@@ -172,10 +176,7 @@ public IBaseResource validate(final HttpServletRequest theRequest) {
 
 		final List<ValidationMessage> messages;
 		try {
-			final var format = encoding == EncodingEnum.XML ? FhirFormat.XML : FhirFormat.JSON;
-			final var stream = new ByteArrayInputStream(contentString.getBytes(StandardCharsets.UTF_8));
-			messages = engine.validate(format, stream, profile);
-
+			messages = doValidate(engine, contentString, encoding, profile);
 		} catch (final Exception e) {
 			sw.endCurrentTask();
 			log.debug("Validation time: {}", sw);
@@ -188,32 +189,6 @@ public IBaseResource validate(final HttpServletRequest theRequest) {
 		return this.getOperationOutcome(sha3Hex, messages, profile, engine, sw.formatTaskDurations(), cliContext);
 	}
 
-	private String getContentString(final HttpServletRequest theRequest,
-											  final List<SingleValidationMessage> addedValidationMessages) {
-		byte[] bytes = null;
-		String contentString = "";
-		try {
-			bytes = IOUtils.toByteArray(theRequest.getInputStream());
-			if (bytes.length > 2 && bytes[0] == -17 && bytes[1] == -69 && bytes[2] == -65) {
-				byte[] dest = new byte[bytes.length - 3];
-				System.arraycopy(bytes, 3, dest, 0, bytes.length - 3);
-				bytes = dest;
-				if (addedValidationMessages != null) {
-					final var m = new SingleValidationMessage();
-					m.setSeverity(ResultSeverityEnum.WARNING);
-					m.setMessage(
-						"Resource content has a UTF-8 BOM marking, skipping BOM, see https://en.wikipedia.org/wiki/Byte_order_mark");
-					m.setLocationCol(0);
-					m.setLocationLine(0);
-					addedValidationMessages.add(m);
-				}
-			}
-			contentString = new String(bytes);
-		} catch (final IOException e) {
-			log.error(e.getMessage(), e);
-		}
-		return contentString;
-	}
 
 	private IBaseResource getOperationOutcome(final String id,
 															final List<ValidationMessage> messages,
@@ -295,4 +270,27 @@ private IBaseResource getOoForError(final @NonNull String message) {
 		issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_SOURCE).setValue(new StringType("ValidationProvider"));
 		return VersionConvertorFactory_40_50.convertResource(oo);
 	}
+
+	public static List<ValidationMessage> doValidate(final MatchboxEngine engine,
+									 String content,
+									 final EncodingEnum encoding,
+									 final String profile) throws EOperationOutcome, IOException {
+		final List<ValidationMessage> messages = new ArrayList<>();
+
+		if (content.startsWith("\uFEFF")) {
+			content = content.replace("\uFEFF", "");
+			final var m = new ValidationMessage();
+			m.setLevel(ValidationMessage.IssueSeverity.WARNING);
+			m.setMessage(
+				"Resource content has a UTF-8 BOM marking, skipping BOM, see https://en.wikipedia.org/wiki/Byte_order_mark");
+			m.setCol(0);
+			m.setLine(0);
+			messages.add(m);
+		}
+
+		final var format = encoding == EncodingEnum.XML ? FhirFormat.XML : FhirFormat.JSON;
+		final var stream = new ByteArrayInputStream(content.getBytes(StandardCharsets.UTF_8));
+		messages.addAll(engine.validate(format, stream, profile));
+		return messages;
+	}
 }