Merge remote-tracking branch 'origin/master' into call_access_method

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/SingleValidationMessage.java

@@ -109,15 +109,15 @@ public class SingleValidationMessage {
 	public String toString() {
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
 		if (myLocationCol != null || myLocationLine != null) {
-			b.append("myLocationCol", myLocationCol);
+			b.append("col", myLocationCol);
-			b.append("myLocationRow", myLocationLine);
+			b.append("row", myLocationLine);
 		}
 		if (myLocationString != null) {
-			b.append("myLocationString", myLocationString);
+			b.append("locationString", myLocationString);
 		}
-		b.append("myMessage", myMessage);
+		b.append("message", myMessage);
 		if (mySeverity != null) {
-			b.append("mySeverity", mySeverity.getCode());
+			b.append("severity", mySeverity.getCode());
 		}
 		return b.toString();
 	}

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

@@ -33,6 +33,7 @@ import org.fusesource.jansi.AnsiConsole;
 import org.slf4j.LoggerFactory;
 
 import java.io.PrintWriter;
+import java.lang.management.ManagementFactory;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -52,16 +53,20 @@ public abstract class BaseApp {
 		loggingConfigOff();
 
 		// We don't use qualified names for loggers in CLI
-		ourLog = LoggerFactory.getLogger(App.class.getSimpleName());
+		ourLog = LoggerFactory.getLogger(App.class);
 	}
 
+	private MyShutdownHook myShutdownHook;
+	private boolean myShutdownHookHasNotRun;
+
 	private void logAppHeader() {
 		System.out.flush();
 		System.out.println("------------------------------------------------------------");
 		System.out.println("\ud83d\udd25 " + ansi().bold() + " " + provideProductName() + ansi().boldOff() + " " + provideProductVersion() + " - Command Line Tool");
 		System.out.println("------------------------------------------------------------");
-		System.out.println("Max configured JVM memory (Xmx): " + FileHelper.getFileSizeDisplay(Runtime.getRuntime().maxMemory(), 1));
+		System.out.println("Process ID                      : " + ManagementFactory.getRuntimeMXBean().getName());
-		System.out.println("Detected Java version: " + System.getProperty("java.version"));
+		System.out.println("Max configured JVM memory (Xmx) : " + FileHelper.getFileSizeDisplay(Runtime.getRuntime().maxMemory(), 1));
+		System.out.println("Detected Java version           : " + System.getProperty("java.version"));
 		System.out.println("------------------------------------------------------------");
 	}
 
@@ -197,6 +202,9 @@ public abstract class BaseApp {
 			return;
 		}
 
+		myShutdownHook = new MyShutdownHook(command);
+		Runtime.getRuntime().addShutdownHook(myShutdownHook);
+
 		Options options = command.getOptions();
 		DefaultParser parser = new DefaultParser();
 		CommandLine parsedOptions;
@@ -215,6 +223,9 @@ public abstract class BaseApp {
 			// Actually execute the command
 			command.run(parsedOptions);
 
+			myShutdownHookHasNotRun = true;
+			runCleanupHookAndUnregister();
+
 			if (!"true".equals(System.getProperty("test"))) {
 				System.exit(0);
 			}
@@ -225,9 +236,11 @@ public abstract class BaseApp {
 			System.err.println("  " + ansi().fg(Ansi.Color.RED).bold() + e.getMessage());
 			System.err.println("" + ansi().fg(Ansi.Color.WHITE).boldOff());
 			logCommandUsageNoHeader(command);
+			runCleanupHookAndUnregister();
 			System.exit(1);
 		} catch (CommandFailureException e) {
 			ourLog.error(e.getMessage());
+			runCleanupHookAndUnregister();
 			if ("true".equals(System.getProperty("test"))) {
 				throw e;
 			} else {
@@ -235,12 +248,22 @@ public abstract class BaseApp {
 			}
 		} catch (Throwable t) {
 			ourLog.error("Error during execution: ", t);
+			runCleanupHookAndUnregister();
 			if ("true".equals(System.getProperty("test"))) {
 				throw new CommandFailureException("Error: " + t.toString(), t);
 			} else {
 				System.exit(1);
 			}
 		}
+
+	}
+
+	private void runCleanupHookAndUnregister() {
+		if (myShutdownHookHasNotRun) {
+			Runtime.getRuntime().removeShutdownHook(myShutdownHook);
+			myShutdownHook.run();
+			myShutdownHookHasNotRun = false;
+		}
 	}
 
 	private void validateJavaVersion() {
@@ -275,4 +298,17 @@ public abstract class BaseApp {
 	}
 
 
+	private class MyShutdownHook extends Thread {
+		private final BaseCommand myFinalCommand;
+
+		public MyShutdownHook(BaseCommand theFinalCommand) {
+			myFinalCommand = theFinalCommand;
+		}
+
+		@Override
+		public void run() {
+			ourLog.info(provideProductName() + " is shutting down...");
+			myFinalCommand.cleanup();
+		}
+	}
 }

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

@@ -152,6 +152,13 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 		addOptionalOption(theOptions, VERBOSE_LOGGING_PARAM, VERBOSE_LOGGING_PARAM_LONGOPT, false, VERBOSE_LOGGING_PARAM_DESC);
 	}
 
+	/**
+	 * Subclasses may override if they want, to do any cleanup they need to do.
+	 */
+	public void cleanup() {
+		// nothing
+	}
+
 	@Override
 	public int compareTo(BaseCommand theO) {
 		return getCommandName().compareTo(theO.getCommandName());

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

@@ -29,6 +29,7 @@ import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.time.DateUtils;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.webapp.WebAppContext;
 import org.springframework.web.context.ContextLoader;
@@ -193,9 +194,22 @@ public class RunServerCommand extends BaseCommand {
 		ourLog.info("Web Testing UI : http://localhost:{}/", myPort);
 		ourLog.info("Server Base URL: http://localhost:{}{}", myPort, path);
 
+		// Never quit.. We'll let the user ctrl-C their way out.
+		loopForever();
 
 	}
 
+	@SuppressWarnings("InfiniteLoopStatement")
+	private void loopForever() {
+		while (true) {
+			try {
+				Thread.sleep(DateUtils.MILLIS_PER_MINUTE);
+			} catch (InterruptedException theE) {
+				// ignore
+			}
+		}
+	}
+
 	public static void main(String[] theArgs) {
 
 

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

@@ -23,6 +23,7 @@ package ca.uhn.fhir.cli;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.igpacks.parser.IgPackParserDstu2;
 import ca.uhn.fhir.igpacks.parser.IgPackParserDstu3;
+import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.LenientErrorHandler;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.SingleValidationMessage;
@@ -103,7 +104,7 @@ public class ValidateCommand extends BaseCommand {
 		parseFhirContext(theCommandLine);
 
 		String fileName = theCommandLine.getOptionValue("n");
-		String contents = theCommandLine.getOptionValue("c");
+		String contents = theCommandLine.getOptionValue("d");
 		if (isNotBlank(fileName) && isNotBlank(contents)) {
 			throw new ParseException("Can not supply both a file (-n) and data (-d)");
 		}
@@ -199,7 +200,12 @@ public class ValidateCommand extends BaseCommand {
 		val.setValidateAgainstStandardSchema(theCommandLine.hasOption("x"));
 		val.setValidateAgainstStandardSchematron(theCommandLine.hasOption("s"));
 
-		ValidationResult results = val.validateWithResult(contents);
+		ValidationResult results;
+		try {
+			results = val.validateWithResult(contents);
+		} catch (DataFormatException e) {
+			throw new CommandFailureException(e.getMessage());
+		}
 
 		StringBuilder b = new StringBuilder("Validation results:" + ansi().boldOff());
 		int count = 0;

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

@@ -53,7 +53,6 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class ValidationDataUploader extends BaseCommand {
-	// TODO: Don't use qualified names for loggers in HAPI CLI.
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidationDataUploader.class);
 
 	private ArrayList<IIdType> myExcludes = new ArrayList<>();
@@ -354,9 +353,10 @@ public class ValidationDataUploader extends BaseCommand {
 		ourLog.info("Finished uploading ValueSets");
 
 
-		uploadDstu3Profiles(theCtx, client, "profiles-resources");
+		uploadDstu3Profiles(theCtx, client, "profile/profiles-resources");
-		uploadDstu3Profiles(theCtx, client, "profiles-types");
+		uploadDstu3Profiles(theCtx, client, "profile/profiles-types");
-		uploadDstu3Profiles(theCtx, client, "profiles-others");
+		uploadDstu3Profiles(theCtx, client, "profile/profiles-others");
+		uploadDstu3Profiles(theCtx, client, "extension/extension-definitions");
 
 		ourLog.info("Finished uploading ValueSets");
 
@@ -446,9 +446,10 @@ public class ValidationDataUploader extends BaseCommand {
 		ourLog.info("Finished uploading ValueSets");
 
 
-		uploadR4Profiles(theCtx, client, "profiles-resources");
+		uploadR4Profiles(theCtx, client, "profile/profiles-resources");
-		uploadR4Profiles(theCtx, client, "profiles-types");
+		uploadR4Profiles(theCtx, client, "profile/profiles-types");
-		uploadR4Profiles(theCtx, client, "profiles-others");
+		uploadR4Profiles(theCtx, client, "profile/profiles-others");
+		uploadR4Profiles(theCtx, client, "extension/extension-definitions");
 
 		ourLog.info("Finished uploading ValueSets");
 
@@ -457,14 +458,14 @@ public class ValidationDataUploader extends BaseCommand {
 		ourLog.info("Finished uploading definitions to server (took {} ms)", delay);
 	}
 
-	private void uploadDstu3Profiles(FhirContext ctx, IGenericClient client, String name) throws CommandFailureException {
+	private void uploadDstu3Profiles(FhirContext ctx, IGenericClient client, String theName) throws CommandFailureException {
 		int total;
 		int count;
 		org.hl7.fhir.dstu3.model.Bundle bundle;
-		ourLog.info("Uploading " + name);
+		ourLog.info("Uploading " + theName);
 		String vsContents;
 		try {
-			vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/dstu3/model/profile/" + name + ".xml"), "UTF-8");
+			vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/dstu3/model/" + theName + ".xml"), "UTF-8");
 		} catch (IOException e) {
 			throw new CommandFailureException(e.toString());
 		}
@@ -498,26 +499,26 @@ public class ValidationDataUploader extends BaseCommand {
 				continue;
 			}
 
-			ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[] {name, count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[] {theName, count, total, next.getIdElement().getValue()});
 			client.update().resource(next).execute();
 
 			count++;
 		}
 	}
 
-	private void uploadR4Profiles(FhirContext ctx, IGenericClient client, String name) throws CommandFailureException {
+	private void uploadR4Profiles(FhirContext theContext, IGenericClient theClient, String theName) throws CommandFailureException {
 		int total;
 		int count;
 		org.hl7.fhir.r4.model.Bundle bundle;
-		ourLog.info("Uploading " + name);
+		ourLog.info("Uploading " + theName);
 		String vsContents;
 		try {
-			vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/r4/model/profile/" + name + ".xml"), "UTF-8");
+			vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/r4/model/" + theName + ".xml"), "UTF-8");
 		} catch (IOException e) {
 			throw new CommandFailureException(e.toString());
 		}
 
-		bundle = ctx.newXmlParser().parseResource(org.hl7.fhir.r4.model.Bundle.class, vsContents);
+		bundle = theContext.newXmlParser().parseResource(org.hl7.fhir.r4.model.Bundle.class, vsContents);
 		filterBundle(bundle);
 		total = bundle.getEntry().size();
 		count = 1;
@@ -546,9 +547,9 @@ public class ValidationDataUploader extends BaseCommand {
 				continue;
 			}
 
-			ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[] {name, count, total, next.getIdElement().getValue()});
+			ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[] {theName, count, total, next.getIdElement().getValue()});
 			try {
-				client.update().resource(next).execute();
+				theClient.update().resource(next).execute();
 			} catch (BaseServerResponseException e) {
 				ourLog.warn("Server responded HTTP " + e.getStatusCode() + ": " + e.toString());
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -511,6 +511,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 	@SuppressWarnings("unchecked")
 	protected Set<String> extractResourceLinks(ResourceTable theEntity, IBaseResource theResource, Set<ResourceLink> theLinks, Date theUpdateTime) {
 		HashSet<String> retVal = new HashSet<>();
+		String resourceType = theEntity.getResourceType();
 
 		/*
 		 * For now we don't try to load any of the links in a bundle if it's the actual bundle we're storing..
@@ -580,6 +581,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
 					}
 				} else if (myContext.getElementDefinition((Class<? extends IBase>) nextObject.getClass()).getName().equals("uri")) {
 					continue;
+				} else if (resourceType.equals("Consent") && nextPathAndRef.getPath().equals("Consent.source")) {
+					// Consent#source-identifier has a path that isn't typed - This is a one-off to deal with that
+					continue;
 				} else {
 					if (!multiType) {
 						if (nextSpDef.getName().equals("sourceuri")) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamExtractorDstu3.java

@@ -105,7 +105,8 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 	 */
 	@Override
 	public Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) {
-		HashSet<ResourceIndexedSearchParamDate> retVal = new HashSet<ResourceIndexedSearchParamDate>();
+		HashSet<ResourceIndexedSearchParamDate> retVal = new HashSet<>();
+		String resourceType = theEntity.getResourceType();
 
 		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
 		for (RuntimeSearchParam nextSpDef : searchParams) {
@@ -164,6 +165,9 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 				} else if (nextObject instanceof StringType) {
 					// CarePlan.activitydate can be a string
 					continue;
+				} else if (resourceType.equals("Consent") && nextPath.equals("Consent.source")) {
+					// Consent#source-identifier has a path that isn't typed - This is a one-off to deal with that
+					continue;
 				} else {
 					if (!multiType) {
 						throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4.java

@@ -20,12 +20,28 @@ package ca.uhn.fhir.jpa.dao.r4;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
-
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
-import java.util.*;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
-
+import ca.uhn.fhir.jpa.util.DeleteConflict;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
+import ca.uhn.fhir.rest.api.ValidationModeEnum;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.IValidationContext;
+import ca.uhn.fhir.validation.IValidatorModule;
+import ca.uhn.fhir.validation.ValidationResult;
 import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
@@ -33,20 +49,10 @@ import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import java.util.ArrayList;
-import ca.uhn.fhir.context.RuntimeSearchParam;
+import java.util.List;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+
-import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import ca.uhn.fhir.jpa.entity.ResourceTable;
-import ca.uhn.fhir.jpa.util.DeleteConflict;
-import ca.uhn.fhir.model.api.Include;
-import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
-import ca.uhn.fhir.rest.api.*;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.server.exceptions.*;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
-import ca.uhn.fhir.util.FhirTerser;
-import ca.uhn.fhir.validation.*;
 
 public class FhirResourceDaoR4<T extends IAnyResource> extends BaseHapiFhirResourceDao<T> {
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/SearchParamExtractorR4.java

@@ -468,6 +468,7 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
 				continue;
 			}
 
+			String resourceType = theEntity.getResourceType();
 			String nextPath = nextSpDef.getPath();
 			if (isBlank(nextPath)) {
 				continue;
@@ -478,8 +479,8 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
 				multiType = true;
 			}
 
-			List<String> systems = new ArrayList<String>();
+			List<String> systems = new ArrayList<>();
-			List<String> codes = new ArrayList<String>();
+			List<String> codes = new ArrayList<>();
 
 			for (Object nextObject : extractValues(nextPath, theResource)) {
 
@@ -555,9 +556,15 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
 				} else if (nextObject instanceof LocationPositionComponent) {
 					ourLog.warn("Position search not currently supported, not indexing location");
 					continue;
+				} else if (nextObject instanceof StructureDefinition.StructureDefinitionContextComponent) {
+					ourLog.warn("StructureDefinition context indexing not currently supported"); // TODO: implement this
+					continue;
+				} else if (resourceType.equals("Consent") && nextPath.equals("Consent.source")) {
+					// Consent#source-identifier has a path that isn't typed - This is a one-off to deal with that
+					continue;
 				} else {
 					if (!multiType) {
-						throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());
+						throw new ConfigurationException("Search param " + nextSpDef.getName() + " with path " + nextPath + " is of unexpected datatype: " + nextObject.getClass());
 					} else {
 						continue;
 					}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -160,6 +160,9 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Qualifier("myOrganizationDaoDstu3")
 	protected IFhirResourceDao<Organization> myOrganizationDao;
 	@Autowired
+	@Qualifier("myConsentDaoDstu3")
+	protected IFhirResourceDao<Consent> myConsentDao;
+	@Autowired
 	protected DatabaseBackedPagingProvider myPagingProvider;
 	@Autowired
 	@Qualifier("myPatientDaoDstu3")

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -1,49 +1,53 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import static org.apache.commons.lang3.StringUtils.defaultString;
+import ca.uhn.fhir.jpa.dao.*;
-import static org.hamcrest.Matchers.*;
+import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
-import static org.junit.Assert.*;
+import ca.uhn.fhir.jpa.entity.TagTypeEnum;
-import static org.mockito.Matchers.eq;
+import ca.uhn.fhir.model.api.Include;
-import static org.mockito.Mockito.*;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
-
+import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
-import java.util.*;
+import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
-
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.*;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.*;
+import ca.uhn.fhir.rest.server.exceptions.*;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
+import ca.uhn.fhir.util.TestUtil;
+import com.google.common.collect.Lists;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.RandomStringUtils;
 import org.hamcrest.Matchers;
 import org.hamcrest.core.StringContains;
 import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.Bundle.*;
+import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.dstu3.model.Bundle.BundleType;
+import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
 import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
 import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
 import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
 import org.hl7.fhir.dstu3.model.OperationOutcome.IssueType;
 import org.hl7.fhir.dstu3.model.Quantity.QuantityComparator;
-import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.*;
 import org.mockito.ArgumentCaptor;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import com.google.common.collect.Lists;
+import java.util.*;
 
-import ca.uhn.fhir.jpa.dao.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
-import ca.uhn.fhir.jpa.entity.*;
+import static org.hamcrest.Matchers.contains;
-import ca.uhn.fhir.model.api.Include;
+import static org.hamcrest.Matchers.*;
-import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import static org.junit.Assert.*;
-import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
+import static org.mockito.Matchers.eq;
-import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
+import static org.mockito.Mockito.*;
-import ca.uhn.fhir.rest.api.*;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.param.*;
-import ca.uhn.fhir.rest.server.exceptions.*;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
-import ca.uhn.fhir.util.TestUtil;
 
-@SuppressWarnings({ "unchecked", "deprecation" })
+@SuppressWarnings({"unchecked", "deprecation"})
 public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3Test.class);
@@ -117,7 +121,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
-	
 	private void sortCodings(List<Coding> theSecLabels) {
 		Collections.sort(theSecLabels, new Comparator<Coding>() {
 			@Override
@@ -479,7 +482,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	}
 
-	
 	@Test
 	public void testCreateDifferentTypesWithSameForcedId() {
 		String idName = "forcedId";
@@ -500,7 +502,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		obs = myObservationDao.read(obsId.toUnqualifiedVersionless(), mySrd);
 	}
 
-
 	@Test
 	public void testCreateDuplicateTagsDoesNotCauseDuplicates() {
 		Patient p = new Patient();
@@ -555,22 +556,22 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 	public void testCreateLongString() {
 		//@formatter:off
 		String input = "<NamingSystem>\n" +
-				"        <name value=\"NDF-RT (National Drug File – Reference Terminology)\"/>\n" + 
+			"        <name value=\"NDF-RT (National Drug File – Reference Terminology)\"/>\n" +
-				"        <status value=\"draft\"/>\n" + 
+			"        <status value=\"draft\"/>\n" +
-				"        <kind value=\"codesystem\"/>\n" + 
+			"        <kind value=\"codesystem\"/>\n" +
-				"        <publisher value=\"HL7, Inc\"/>\n" + 
+			"        <publisher value=\"HL7, Inc\"/>\n" +
-				"        <date value=\"2015-08-21\"/>\n" + 
+			"        <date value=\"2015-08-21\"/>\n" +
-				"        <uniqueId>\n" + 
+			"        <uniqueId>\n" +
-				"          <type value=\"uri\"/>\n" + 
+			"          <type value=\"uri\"/>\n" +
-				"          <value value=\"http://hl7.org/fhir/ndfrt\"/>\n" + 
+			"          <value value=\"http://hl7.org/fhir/ndfrt\"/>\n" +
-				"          <preferred value=\"true\"/>\n" + 
+			"          <preferred value=\"true\"/>\n" +
-				"        </uniqueId>\n" + 
+			"        </uniqueId>\n" +
-				"        <uniqueId>\n" + 
+			"        <uniqueId>\n" +
-				"          <type value=\"oid\"/>\n" + 
+			"          <type value=\"oid\"/>\n" +
-				"          <value value=\"2.16.840.1.113883.6.209\"/>\n" + 
+			"          <value value=\"2.16.840.1.113883.6.209\"/>\n" +
-				"          <preferred value=\"false\"/>\n" + 
+			"          <preferred value=\"false\"/>\n" +
-				"        </uniqueId>\n" + 
+			"        </uniqueId>\n" +
-				"      </NamingSystem>";
+			"      </NamingSystem>";
 		//@formatter:on
 
 		NamingSystem res = myFhirCtx.newXmlParser().parseResource(NamingSystem.class, input);
@@ -809,7 +810,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
-
 	@Test
 	public void testCreateWithInvalidReferenceFailsGracefully() {
 		Patient patient = new Patient();
@@ -1088,7 +1088,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 			patient.addIdentifier().setSystem("ZZZZZZZ").setValue("ZZZZZZZZZ");
 			id2b = myPatientDao.update(patient, mySrd).getId();
 		}
-		ourLog.info("ID1:{}   ID2:{}   ID2b:{}", new Object[] { id1, id2, id2b });
+		ourLog.info("ID1:{}   ID2:{}   ID2b:{}", new Object[] {id1, id2, id2b});
 
 		SearchParameterMap params = new SearchParameterMap();
 		params.setLoadSynchronous(true);
@@ -1697,7 +1697,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 			preDates.add(new Date());
 			Thread.sleep(100);
 			patient.setId(id);
-			patient.getName().get(0).getFamilyElement().setValue(methodName + "_i"+i);
+			patient.getName().get(0).getFamilyElement().setValue(methodName + "_i" + i);
 			ids.add(myPatientDao.update(patient, mySrd).getId().toUnqualified().getValue());
 		}
 
@@ -2057,7 +2057,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 		//@formatter:off
 		String inputStr =
-				"{" +
+			"{" +
 				"  \"resourceType\":\"Organization\",\n" +
 				"  \"extension\":[\n" +
 				"     {\n" +
@@ -2131,7 +2131,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		dr01.setSubject(new Reference(patientId01));
 		IIdType drId01 = myDiagnosticReportDao.create(dr01, mySrd).getId();
 
-		ourLog.info("P1[{}] P2[{}] O1[{}] O2[{}] D1[{}]", new Object[] { patientId01, patientId02, obsId01, obsId02, drId01 });
+		ourLog.info("P1[{}] P2[{}] O1[{}] O2[{}] D1[{}]", new Object[] {patientId01, patientId02, obsId01, obsId02, drId01});
 
 		List<Observation> result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam(patientId01.getIdPart())).setLoadSynchronous(true)));
 		assertEquals(1, result.size());
@@ -2141,7 +2141,8 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		assertEquals(1, result.size());
 		assertEquals(obsId02.getIdPart(), result.get(0).getIdElement().getIdPart());
 
-		result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam("999999999999")).setLoadSynchronous(true)));;
+		result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam("999999999999")).setLoadSynchronous(true)));
+		;
 		assertEquals(0, result.size());
 
 	}
@@ -2224,7 +2225,8 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		long id = outcome.getId().getIdPartAsLong();
 
 		TokenParam value = new TokenParam("urn:system", "001testPersistSearchParams");
-		List<Patient> found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_IDENTIFIER, value).setLoadSynchronous(true)));;
+		List<Patient> found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_IDENTIFIER, value).setLoadSynchronous(true)));
+		;
 		assertEquals(1, found.size());
 		assertEquals(id, found.get(0).getIdElement().getIdPartAsLong().longValue());
 
@@ -3535,6 +3537,16 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	}
 
+	/**
+	 * Make sure this can upload successfully (indexer failed at one point)
+	 */
+	@Test
+	public void testUploadConsentWithSourceAttachment() {
+		Consent consent = new Consent();
+		consent.setSource(new Attachment().setUrl("http://foo"));
+		myConsentDao.create(consent);
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();
@@ -3542,7 +3554,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 
 	public static void assertConflictException(ResourceVersionConflictException e) {
 		assertThat(e.getMessage(), matchesPattern(
-				"Unable to delete [a-zA-Z]+/[0-9]+ because at least one resource has a reference to this resource. First reference found was resource [a-zA-Z]+/[0-9]+ in path [a-zA-Z]+.[a-zA-Z]+"));
+			"Unable to delete [a-zA-Z]+/[0-9]+ because at least one resource has a reference to this resource. First reference found was resource [a-zA-Z]+/[0-9]+ in path [a-zA-Z]+.[a-zA-Z]+"));
 	}
 
 	private static List<String> toStringList(List<UriType> theUriType) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -212,6 +212,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	@Qualifier("myStructureDefinitionDaoR4")
 	protected IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
 	@Autowired
+	@Qualifier("myConsentDaoR4")
+	protected IFhirResourceDao<Consent> myConsentDao;
+	@Autowired
 	@Qualifier("mySubscriptionDaoR4")
 	protected IFhirResourceDaoSubscription<Subscription> mySubscriptionDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -21,6 +21,7 @@ import com.google.common.collect.Lists;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.RandomStringUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Validate;
 import org.hamcrest.Matchers;
 import org.hamcrest.core.StringContains;
 import org.hl7.fhir.instance.model.api.IAnyResource;
@@ -3738,6 +3739,26 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	}
 
+	/**
+	 * Make sure this can upload successfully (indexer failed at one point)
+	 */
+	@Test
+	public void testUploadConsentWithSourceAttachment() {
+		Consent consent = new Consent();
+		consent.setSource(new Attachment().setUrl("http://foo"));
+		myConsentDao.create(consent);
+	}
+
+	/**
+	 * Make sure this can upload successfully (indexer failed at one point)
+	 */
+	@Test
+	public void testUploadExtensionStructureDefinition() {
+		StructureDefinition ext = myValidationSupport.fetchStructureDefinition(myFhirCtx, "http://hl7.org/fhir/StructureDefinition/familymemberhistory-type");
+		Validate.notNull(ext);
+		myStructureDefinitionDao.update(ext);
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/FhirTesterConfig.java

@@ -86,7 +86,7 @@ public class FhirTesterConfig {
 				.withName("Health Intersections (DSTU2 FHIR)")
 			.addServer()
 				.withId("spark2")
-				.withFhirVersion(FhirVersionEnum.DSTU2)
+				.withFhirVersion(FhirVersionEnum.DSTU3)
 				.withBaseUrl("http://vonk.furore.com/")
 				.withName("Vonk - Furore (STU3 FHIR)");
 		

hapi-fhir-jpaserver-uhnfhirtest/src/main/resources/logback.xml

@@ -29,7 +29,7 @@
 
 	<appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
 		<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
-			<level>DEBUG</level>
+			<level>INFO</level>
 		</filter>
 		<file>${fhir.logdir}/fhirtest.log</file>
 		<rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java

@@ -19,42 +19,62 @@ package ca.uhn.fhir.rest.server;
  * limitations under the License.
  * #L%
  */
-import static org.apache.commons.lang3.StringUtils.isBlank;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.io.*;
-import java.lang.annotation.Annotation;
-import java.lang.reflect.*;
-import java.util.*;
-import java.util.Map.Entry;
-import java.util.concurrent.locks.Lock;
-import java.util.concurrent.locks.ReentrantLock;
-import java.util.jar.Manifest;
-
-import javax.servlet.ServletException;
-import javax.servlet.UnavailableException;
-import javax.servlet.http.*;
 
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.ProvidedResourceScanner;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.api.AddProfileTagEnum;
+import ca.uhn.fhir.context.api.BundleInclusionRule;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.annotation.Destroy;
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.Initialize;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.RequestTypeEnum;
+import ca.uhn.fhir.rest.api.server.IFhirVersionServer;
+import ca.uhn.fhir.rest.api.server.IRestfulServer;
+import ca.uhn.fhir.rest.api.server.ParseAction;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.RestfulServerUtils.ResponseEncoding;
+import ca.uhn.fhir.rest.server.exceptions.*;
+import ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
+import ca.uhn.fhir.rest.server.method.ConformanceMethodBinding;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.rest.server.tenant.ITenantIdentificationStrategy;
+import ca.uhn.fhir.util.*;
+import com.google.common.collect.Lists;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 
-import ca.uhn.fhir.context.*;
+import javax.servlet.ServletException;
-import ca.uhn.fhir.context.api.AddProfileTagEnum;
+import javax.servlet.UnavailableException;
-import ca.uhn.fhir.context.api.BundleInclusionRule;
+import javax.servlet.http.HttpServlet;
-import ca.uhn.fhir.parser.IParser;
+import javax.servlet.http.HttpServletRequest;
-import ca.uhn.fhir.rest.annotation.*;
+import javax.servlet.http.HttpServletResponse;
-import ca.uhn.fhir.rest.api.*;
+import java.io.Closeable;
-import ca.uhn.fhir.rest.api.server.*;
+import java.io.IOException;
-import ca.uhn.fhir.rest.server.RestfulServerUtils.ResponseEncoding;
+import java.io.InputStream;
-import ca.uhn.fhir.rest.server.exceptions.*;
+import java.io.Writer;
-import ca.uhn.fhir.rest.server.interceptor.*;
+import java.lang.annotation.Annotation;
-import ca.uhn.fhir.rest.server.method.*;
+import java.lang.reflect.Method;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import java.lang.reflect.Modifier;
-import ca.uhn.fhir.util.*;
+import java.util.*;
+import java.util.Map.Entry;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
+import java.util.jar.Manifest;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 @SuppressWarnings("WeakerAccess")
 public class RestfulServer extends HttpServlet implements IRestfulServer<ServletRequestDetails> {
@@ -96,7 +116,9 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	private BaseMethodBinding<?> myServerConformanceMethod;
 	private Object myServerConformanceProvider;
 	private String myServerName = "HAPI FHIR Server";
-	/** This is configurable but by default we just use HAPI version */
+	/**
+	 * This is configurable but by default we just use HAPI version
+	 */
 	private String myServerVersion = VersionUtil.getVersion();
 	private boolean myStarted;
 	private Map<String, IResourceProvider> myTypeToProvider = new HashMap<>();
@@ -121,10 +143,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		myFhirContext = theCtx;
 	}
 
-	private static boolean partIsOperation(String nextString) {
-		return nextString.length() > 0 && (nextString.charAt(0) == '_' || nextString.charAt(0) == '$' || nextString.equals(Constants.URL_TOKEN_METADATA));
-	}
-
 	private void addContentLocationHeaders(RequestDetails theRequest, HttpServletResponse servletResponse, MethodOutcome response, String resourceName) {
 		if (response != null && response.getId() != null) {
 			addLocationHeader(theRequest, servletResponse, response, Constants.HEADER_LOCATION, resourceName);
@@ -140,15 +158,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 * </p>
 	 */
 	public void addHeadersToResponse(HttpServletResponse theHttpResponse) {
-		StringBuilder b = new StringBuilder();
+		String b = createPoweredByHeader();
-		b.append("HAPI FHIR ");
+		theHttpResponse.addHeader("X-Powered-By", b);
-		b.append(VersionUtil.getVersion());
-		b.append(" REST Server (FHIR Server; FHIR ");
-		b.append(myFhirContext.getVersion().getVersion().getFhirVersionString());
-		b.append('/');
-		b.append(myFhirContext.getVersion().getVersion().name());
-		b.append(")");
-		theHttpResponse.addHeader("X-Powered-By", b.toString());
 	}
 
 	private void addLocationHeader(RequestDetails theRequest, HttpServletResponse theResponse, MethodOutcome response, String headerLocation, String resourceName) {
@@ -198,6 +209,33 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		return result;
 	}
 
+	protected List<String> createPoweredByAttributes() {
+		return Lists.newArrayList("FHIR Server", "FHIR " + myFhirContext.getVersion().getVersion().getFhirVersionString() + "/" + myFhirContext.getVersion().getVersion().name());
+	}
+
+	protected String createPoweredByHeader() {
+		StringBuilder b = new StringBuilder();
+		b.append(createPoweredByHeaderProductName());
+		b.append(" ");
+		b.append(VersionUtil.getVersion());
+		b.append(" REST Server (");
+
+		List<String> poweredByAttributes = createPoweredByAttributes();
+		for (ListIterator<String> iter = poweredByAttributes.listIterator(); iter.hasNext(); ) {
+			if (iter.nextIndex() > 0) {
+				b.append("; ");
+			}
+			b.append(iter.next());
+		}
+
+		b.append(")");
+		return b.toString();
+	}
+
+	protected String createPoweredByHeaderProductName() {
+		return "HAPI FHIR";
+	}
+
 	@Override
 	public void destroy() {
 		if (getResourceProviders() != null) {
@@ -253,6 +291,31 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		return resourceMethod;
 	}
 
+	@Override
+	protected void doDelete(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		handleRequest(RequestTypeEnum.DELETE, request, response);
+	}
+
+	@Override
+	protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		handleRequest(RequestTypeEnum.GET, request, response);
+	}
+
+	@Override
+	protected void doOptions(HttpServletRequest theReq, HttpServletResponse theResp) throws ServletException, IOException {
+		handleRequest(RequestTypeEnum.OPTIONS, theReq, theResp);
+	}
+
+	@Override
+	protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		handleRequest(RequestTypeEnum.POST, request, response);
+	}
+
+	@Override
+	protected void doPut(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+		handleRequest(RequestTypeEnum.PUT, request, response);
+	}
+
 	/**
 	 * Count length of URL string, but treating unescaped sequences (e.g. ' ') as their unescaped equivalent (%20)
 	 */
@@ -356,7 +419,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 
 	/**
 	 * @deprecated As of HAPI FHIR 1.5, this property has been moved to
-	 *             {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
+	 * {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
 	 */
 	@Override
 	@Deprecated
@@ -369,10 +432,9 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 * (which is the default), the server will automatically add a profile tag based on
 	 * the class of the resource(s) being returned.
 	 *
-	 * @param theAddProfileTag
+	 * @param theAddProfileTag The behaviour enum (must not be null)
-	 *           The behaviour enum (must not be null)
 	 * @deprecated As of HAPI FHIR 1.5, this property has been moved to
-	 *             {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
+	 * {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
 	 */
 	@Deprecated
 	@CoverageIgnore
@@ -389,8 +451,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	/**
 	 * Set how bundle factory should decide whether referenced resources should be included in bundles
 	 *
-	 * @param theBundleInclusionRule
+	 * @param theBundleInclusionRule - inclusion rule (@see BundleInclusionRule for behaviors)
-	 *           - inclusion rule (@see BundleInclusionRule for behaviors)
 	 */
 	public void setBundleInclusionRule(BundleInclusionRule theBundleInclusionRule) {
 		myBundleInclusionRule = theBundleInclusionRule;
@@ -429,8 +490,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 * Sets (enables/disables) the server support for ETags. Must not be <code>null</code>. Default is
 	 * {@link #DEFAULT_ETAG_SUPPORT}
 	 *
-	 * @param theETagSupport
+	 * @param theETagSupport The ETag support mode
-	 *           The ETag support mode
 	 */
 	public void setETagSupport(ETagSupportEnum theETagSupport) {
 		if (theETagSupport == null) {
@@ -477,8 +537,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	/**
 	 * Sets (or clears) the list of interceptors
 	 *
-	 * @param theList
+	 * @param theList The list of interceptors (may be null)
-	 *           The list of interceptors (may be null)
 	 */
 	public void setInterceptors(IServerInterceptor... theList) {
 		myInterceptors.clear();
@@ -487,19 +546,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		}
 	}
 
-	/**
-	 * Sets (or clears) the list of interceptors
-	 *
-	 * @param theList
-	 *           The list of interceptors (may be null)
-	 */
-	public void setInterceptors(List<IServerInterceptor> theList) {
-		myInterceptors.clear();
-		if (theList != null) {
-			myInterceptors.addAll(theList);
-		}
-	}
-
 	@Override
 	public IPagingProvider getPagingProvider() {
 		return myPagingProvider;
@@ -533,25 +579,13 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		}
 	}
 
-	/**
-	 * Sets the non-resource specific providers which implement method calls on this server.
-	 *
-	 * @see #setResourceProviders(Collection)
-	 */
-	public void setPlainProviders(Object... theProv) {
-		setPlainProviders(Arrays.asList(theProv));
-	}
-
 	/**
 	 * Allows users of RestfulServer to override the getRequestPath method to let them build their custom request path
 	 * implementation
 	 *
-	 * @param requestFullPath
+	 * @param requestFullPath    the full request path
-	 *           the full request path
+	 * @param servletContextPath the servelet context path
-	 * @param servletContextPath
+	 * @param servletPath        the servelet path
-	 *           the servelet context path
-	 * @param servletPath
-	 *           the servelet path
 	 * @return created resource path
 	 */
 	protected String getRequestPath(String requestFullPath, String servletContextPath, String servletPath) {
@@ -579,16 +613,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		}
 	}
 
-	/**
-	 * Sets the resource providers for this server
-	 */
-	public void setResourceProviders(IResourceProvider... theResourceProviders) {
-		myResourceProviders.clear();
-		if (theResourceProviders != null) {
-			myResourceProviders.addAll(Arrays.asList(theResourceProviders));
-		}
-	}
-
 	/**
 	 * Get the server address strategy, which is used to determine what base URL to provide clients to refer to this
 	 * server. Defaults to an instance of {@link IncomingRequestAddressStrategy}
@@ -608,6 +632,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 
 	/**
 	 * Returns the server base URL (with no trailing '/') for a given request
+	 *
 	 * @param theRequest
 	 */
 	public String getServerBaseForRequest(ServletRequestDetails theRequest) {
@@ -656,9 +681,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 * </p>
 	 * Note that this method can only be called before the server is initialized.
 	 *
-	 * @throws IllegalStateException
+	 * @throws IllegalStateException Note that this method can only be called prior to {@link #init() initialization} and will throw an
-	 *            Note that this method can only be called prior to {@link #init() initialization} and will throw an
+	 *                               {@link IllegalStateException} if called after that.
-	 *            {@link IllegalStateException} if called after that.
 	 */
 	public void setServerConformanceProvider(Object theServerConformanceProvider) {
 		if (myStarted) {
@@ -670,9 +694,9 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		// passing the server into the constructor. Having that sort
 		// of cross linkage causes reference cycles in Spring wiring
 		try {
-			Method setRestfulServer = theServerConformanceProvider.getClass().getMethod("setRestfulServer", new Class[] { RestfulServer.class });
+			Method setRestfulServer = theServerConformanceProvider.getClass().getMethod("setRestfulServer", new Class[] {RestfulServer.class});
 			if (setRestfulServer != null) {
-				setRestfulServer.invoke(theServerConformanceProvider, new Object[] { this });
+				setRestfulServer.invoke(theServerConformanceProvider, new Object[] {this});
 			}
 		} catch (Exception e) {
 			ourLog.warn("Error calling IServerConformanceProvider.setRestfulServer", e);
@@ -680,15 +704,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		myServerConformanceProvider = theServerConformanceProvider;
 	}
 
-	/**
-	 * If provided (default is <code>null</code>), the tenant identification
-	 * strategy provides a mechanism for a multitenant server to identify which tenant
-	 * a given request corresponds to.
-	 */
-	public void setTenantIdentificationStrategy(ITenantIdentificationStrategy theTenantIdentificationStrategy) {
-		myTenantIdentificationStrategy = theTenantIdentificationStrategy;
-	}
-
 	/**
 	 * Gets the server's name, as exported in conformance profiles exported by the server. This is informational only,
 	 * but can be helpful to set with something appropriate.
@@ -1029,10 +1044,9 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 * This method may be overridden by subclasses to do perform initialization that needs to be performed prior to the
 	 * server being used.
 	 *
-	 * @throws ServletException
+	 * @throws ServletException If the initialization failed. Note that you should consider throwing {@link UnavailableException}
-	 *            If the initialization failed. Note that you should consider throwing {@link UnavailableException}
+	 *                          (which extends {@link ServletException}), as this is a flag to the servlet container
-	 *            (which extends {@link ServletException}), as this is a flag to the servlet container
+	 *                          that the servlet is not usable.
-	 *            that the servlet is not usable.
 	 */
 	protected void initialize() throws ServletException {
 		// nothing by default
@@ -1056,6 +1070,24 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		}
 	}
 
+	private void invokeInitialize(Object theProvider) {
+		invokeInitialize(theProvider, theProvider.getClass());
+	}
+
+	private void invokeInitialize(Object theProvider, Class<?> clazz) {
+		for (Method m : ReflectionUtil.getDeclaredMethods(clazz)) {
+			Initialize initialize = m.getAnnotation(Initialize.class);
+			if (initialize != null) {
+				invokeInitializeOrDestroyMethod(theProvider, m, "initialize");
+			}
+		}
+
+		Class<?> supertype = clazz.getSuperclass();
+		if (!Object.class.equals(supertype)) {
+			invokeInitialize(theProvider, supertype);
+		}
+	}
+
 	private void invokeInitializeOrDestroyMethod(Object theProvider, Method m, String theMethodDescription) {
 
 		Class<?>[] paramTypes = m.getParameterTypes();
@@ -1078,24 +1110,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		}
 	}
 
-	private void invokeInitialize(Object theProvider) {
-		invokeInitialize(theProvider, theProvider.getClass());
-	}
-
-	private void invokeInitialize(Object theProvider, Class<?> clazz) {
-		for (Method m : ReflectionUtil.getDeclaredMethods(clazz)) {
-			Initialize initialize = m.getAnnotation(Initialize.class);
-			if (initialize != null) {
-				invokeInitializeOrDestroyMethod(theProvider, m, "initialize");
-			}
-		}
-
-		Class<?> supertype = clazz.getSuperclass();
-		if (!Object.class.equals(supertype)) {
-			invokeInitialize(theProvider, supertype);
-		}
-	}
-
 	/**
 	 * Should the server "pretty print" responses by default (requesting clients can always override this default by
 	 * supplying an <code>Accept</code> header in the request, or a <code>_pretty</code>
@@ -1119,8 +1133,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	 * The default is <code>false</code>
 	 * </p>
 	 *
-	 * @param theDefaultPrettyPrint
+	 * @param theDefaultPrettyPrint The default pretty print setting
-	 *           The default pretty print setting
 	 */
 	public void setDefaultPrettyPrint(boolean theDefaultPrettyPrint) {
 		myDefaultPrettyPrint = theDefaultPrettyPrint;
@@ -1174,8 +1187,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 
 	/**
 	 * @deprecated This feature did not work well, and will be removed. Use {@link ResponseHighlighterInterceptor}
-	 *             instead as an interceptor on your server and it will provide more useful syntax
+	 * instead as an interceptor on your server and it will provide more useful syntax
-	 *             highlighting. Deprocated in 1.4
+	 * highlighting. Deprocated in 1.4
 	 */
 	@Deprecated
 	@Override
@@ -1185,8 +1198,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 
 	/**
 	 * @deprecated This feature did not work well, and will be removed. Use {@link ResponseHighlighterInterceptor}
-	 *             instead as an interceptor on your server and it will provide more useful syntax
+	 * instead as an interceptor on your server and it will provide more useful syntax
-	 *             highlighting. Deprocated in 1.4
+	 * highlighting. Deprocated in 1.4
 	 */
 	@Deprecated
 	public void setUseBrowserFriendlyContentTypes(boolean theUseBrowserFriendlyContentTypes) {
@@ -1285,8 +1298,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	/**
 	 * Register a group of providers. These could be Resource Providers, "plain" providers or a mixture of the two.
 	 *
-	 * @param providers
+	 * @param providers a {@code Collection} of providers. The parameter could be null or an empty {@code Collection}
-	 *           a {@code Collection} of providers. The parameter could be null or an empty {@code Collection}
 	 */
 	public void registerProviders(Collection<? extends Object> providers) {
 		myProviderRegistrationMutex.lock();
@@ -1327,7 +1339,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 					String resourceName = getFhirContext().getResourceDefinition(resourceType).getName();
 					if (myTypeToProvider.containsKey(resourceName)) {
 						throw new ConfigurationException("Multiple resource providers return resource type[" + resourceName + "]: First[" + myTypeToProvider.get(resourceName).getClass().getCanonicalName()
-								+ "] and Second[" + rsrcProvider.getClass().getCanonicalName() + "]");
+							+ "] and Second[" + rsrcProvider.getClass().getCanonicalName() + "]");
 					}
 					if (!inInit) {
 						myResourceProviders.add(rsrcProvider);
@@ -1376,7 +1388,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 	/*
 	 * Remove registered RESTful methods for a Provider (and all superclasses) when it is being unregistered
 	 */
-	private void removeResourceMethods(Object theProvider) throws Exception {
+	private void removeResourceMethods(Object theProvider) {
 		ourLog.info("Removing RESTful methods for: {}", theProvider.getClass());
 		Class<?> clazz = theProvider.getClass();
 		Class<?> supertype = clazz.getSuperclass();
@@ -1447,50 +1459,46 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		}
 
 		switch (method) {
-		case DELETE:
+			case DELETE:
-			doDelete(theReq, theResp);
+				doDelete(theReq, theResp);
-			break;
+				break;
-		case GET:
+			case GET:
-			doGet(theReq, theResp);
+				doGet(theReq, theResp);
-			break;
+				break;
-		case OPTIONS:
+			case OPTIONS:
-			doOptions(theReq, theResp);
+				doOptions(theReq, theResp);
-			break;
+				break;
-		case POST:
+			case POST:
-			doPost(theReq, theResp);
+				doPost(theReq, theResp);
-			break;
+				break;
-		case PUT:
+			case PUT:
-			doPut(theReq, theResp);
+				doPut(theReq, theResp);
-			break;
+				break;
-		default:
+			default:
-			handleRequest(method, theReq, theResp);
+				handleRequest(method, theReq, theResp);
-			break;
+				break;
 		}
 	}
 
-	@Override
+	/**
-	protected void doDelete(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+	 * Sets (or clears) the list of interceptors
-		handleRequest(RequestTypeEnum.DELETE, request, response);
+	 *
+	 * @param theList The list of interceptors (may be null)
+	 */
+	public void setInterceptors(List<IServerInterceptor> theList) {
+		myInterceptors.clear();
+		if (theList != null) {
+			myInterceptors.addAll(theList);
+		}
 	}
 
-	@Override
+	/**
-	protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+	 * Sets the non-resource specific providers which implement method calls on this server.
-		handleRequest(RequestTypeEnum.GET, request, response);
+	 *
-	}
+	 * @see #setResourceProviders(Collection)
-
+	 */
-	@Override
+	public void setPlainProviders(Object... theProv) {
-	protected void doOptions(HttpServletRequest theReq, HttpServletResponse theResp) throws ServletException, IOException {
+		setPlainProviders(Arrays.asList(theProv));
-		handleRequest(RequestTypeEnum.OPTIONS, theReq, theResp);
-	}
-
-	@Override
-	protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
-		handleRequest(RequestTypeEnum.POST, request, response);
-	}
-
-	@Override
-	protected void doPut(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
-		handleRequest(RequestTypeEnum.PUT, request, response);
 	}
 
 	/**
@@ -1505,6 +1513,25 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		}
 	}
 
+	/**
+	 * Sets the resource providers for this server
+	 */
+	public void setResourceProviders(IResourceProvider... theResourceProviders) {
+		myResourceProviders.clear();
+		if (theResourceProviders != null) {
+			myResourceProviders.addAll(Arrays.asList(theResourceProviders));
+		}
+	}
+
+	/**
+	 * If provided (default is <code>null</code>), the tenant identification
+	 * strategy provides a mechanism for a multitenant server to identify which tenant
+	 * a given request corresponds to.
+	 */
+	public void setTenantIdentificationStrategy(ITenantIdentificationStrategy theTenantIdentificationStrategy) {
+		myTenantIdentificationStrategy = theTenantIdentificationStrategy;
+	}
+
 	public void unregisterInterceptor(IServerInterceptor theInterceptor) {
 		Validate.notNull(theInterceptor, "Interceptor can not be null");
 		myInterceptors.remove(theInterceptor);
@@ -1567,6 +1594,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		theResponse.getWriter().write(theException.getMessage());
 	}
 
+	private static boolean partIsOperation(String nextString) {
+		return nextString.length() > 0 && (nextString.charAt(0) == '_' || nextString.charAt(0) == '$' || nextString.equals(Constants.URL_TOKEN_METADATA));
+	}
+
 //	/**
 //	 * Returns the read method binding for the given resource type, or
 //	 * returns <code>null</code> if not

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/DefaultProfileValidationSupport.java

@@ -228,6 +228,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
       loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/r4/model/profile/profiles-resources.xml");
       loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/r4/model/profile/profiles-types.xml");
       loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/r4/model/profile/profiles-others.xml");
+      loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/r4/model/extension/extension-definitions.xml");
 
       myStructureDefinitions = structureDefinitions;
     }

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

@@ -38,6 +38,7 @@ import org.mockito.stubbing.Answer;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.*;
+import java.util.stream.Collectors;
 import java.util.zip.GZIPInputStream;
 
 import static org.hamcrest.Matchers.*;
@@ -411,11 +412,8 @@ public class FhirInstanceValidatorR4Test {
 		ourLog.info("Took {} ms -- {}ms / pass", delay, per);
 	}
 
-	/**
-	 * // TODO: reenable
-	 */
 	@Test
-	 @Ignore
+	@Ignore
 	public void testValidateBuiltInProfiles() throws Exception {
 		org.hl7.fhir.r4.model.Bundle bundle;
 		String name = "profiles-resources";
@@ -442,16 +440,23 @@ public class FhirInstanceValidatorR4Test {
 			ourLog.trace(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(next));
 
 			ValidationResult output = myVal.validateWithResult(next);
-			List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
+			List<SingleValidationMessage> results = logResultsAndReturnAll(output);
 
 			// This isn't a validator problem but a definition problem.. it should get fixed at some point and
-			// we can remove this
+			// we can remove this. Tracker #17207 was filed about this
-			if (next.getId().equalsIgnoreCase("http://hl7.org/fhir/OperationDefinition/StructureDefinition-generate")) {
+			// https://gforge.hl7.org/gf/project/fhir/tracker/?action=TrackerItemEdit&tracker_item_id=17207
-				assertEquals(1, errors.size());
+			if (next.getId().equalsIgnoreCase("http://hl7.org/fhir/OperationDefinition/StructureDefinition-snapshot")) {
-				assertEquals("A search type can only be specified for parameters of type string [searchType implies type = 'string']", errors.get(0).getMessage());
+				assertEquals(1, results.size());
+				assertEquals("A search type can only be specified for parameters of type string [searchType.exists() implies type = 'string']", results.get(0).getMessage());
 				continue;
 			}
 
+
+			List<SingleValidationMessage> errors = results
+				.stream()
+				.filter(t -> t.getSeverity() != ResultSeverityEnum.INFORMATION)
+				.collect(Collectors.toList());
+
 			assertThat("Failed to validate " + i.getFullUrl() + " - " + errors, errors, empty());
 		}
 

osgi/hapi-fhir-karaf-features/pom.xml

@@ -185,34 +185,52 @@
 					</execution>
 				</executions>
 			</plugin>
-			<plugin>
-				<groupId>org.apache.karaf.tooling</groupId>
-				<artifactId>karaf-maven-plugin</artifactId>
-				<version>${apache_karaf_version}</version>
-				<configuration>
-					<descriptors>
-						<descriptor>file://${project.build.directory}/classes/${features.file}</descriptor>
-						<descriptor>mvn:org.apache.karaf.features/enterprise/${apache_karaf_version}/xml/features</descriptor>
-					</descriptors>
-					<distribution>org.apache.karaf.features:framework</distribution>
-					<javase>1.8</javase>
-					<framework>
-						<feature>framework</feature>
-					</framework>
-					<features>
-						<feature>hapi-fhir*</feature>
-					</features>
-				</configuration>
-				<executions>
-					<execution>
-						<id>validate</id>
-						<phase>process-resources</phase>
-						<goals>
-							<goal>verify</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
 		</plugins>
 	</build>
+
+	<profiles>
+
+		<!--
+		The karaf verification step doesn't happen by default
+		because it doesn't seem to work on Windows.
+
+		See https://github.com/jamesagnew/hapi-fhir/issues/921
+		-->
+		<profile>
+			<id>DIST</id>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.karaf.tooling</groupId>
+						<artifactId>karaf-maven-plugin</artifactId>
+						<version>${apache_karaf_version}</version>
+						<configuration>
+							<descriptors>
+								<descriptor>file://${project.build.directory}/classes/${features.file}</descriptor>
+								<descriptor>mvn:org.apache.karaf.features/enterprise/${apache_karaf_version}/xml/features</descriptor>
+							</descriptors>
+							<distribution>org.apache.karaf.features:framework</distribution>
+							<javase>1.8</javase>
+							<framework>
+								<feature>framework</feature>
+							</framework>
+							<features>
+								<feature>hapi-fhir*</feature>
+							</features>
+						</configuration>
+						<executions>
+							<execution>
+								<id>validate</id>
+								<phase>process-resources</phase>
+								<goals>
+									<goal>verify</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
+
 </project>

src/changes/changes.xml

@@ -172,6 +172,18 @@
 				invocation at the type level as being at the instance level if the method
 				indicated that the IdParam parameter was optional. This has been fixed.
 			</action>
+			<action type="add">
+				StructureDefinitions for the FHIR standard extensions have been added to the
+				hapi-fhir-validation-resources-XXXX modules. Thanks to Patrick Werner for the
+				pull request! These have also been added to the list of definitions uploaded
+				by the CLI "upload-definitions" command.
+			</action>
+			<action type="fix">
+				A workaround for an invalid search parameter path in the R4 consent
+				resource has been implemented. This path was preventing some Consent
+				resources from successfully being uploaded to the JPA server. Thanks to
+				Anthony Sute for identifying this.
+			</action>
 		</release>
 		<release version="3.3.0" date="2018-03-29">
 			<action type="add">

sync_ri4.sh

@@ -60,3 +60,4 @@ cp ~/workspace/fhir/trunk/build/publish/profiles-*.xml       hapi-fhir-validatio
 cp ~/workspace/fhir/trunk/build/publish/v2-tables.xml        hapi-fhir-validation-resources-r4/src/main/resources/org/hl7/fhir/r4/model/valueset/
 cp ~/workspace/fhir/trunk/build/publish/v3-codesystems.xml   hapi-fhir-validation-resources-r4/src/main/resources/org/hl7/fhir/r4/model/valueset/
 cp ~/workspace/fhir/trunk/build/publish/valuesets.xml        hapi-fhir-validation-resources-r4/src/main/resources/org/hl7/fhir/r4/model/valueset/
+cp ~/workspace/fhir/trunk/build/publish/extension-definitions.xml hapi-fhir-validation-resources-r4/src/main/resources/org/hl7/fhir/r4/model/extension/