Replace phloc with ph for #775 (#930)

* Replace phloc with ph

* Enable schematron tests

* Make HAPI-FHIR ph-schematron on OSGI

* Work on getting tests passing

* Another test fix

* Fix up transaction handling for DSTU2

* Add changelog

* Avoid double transaction

* Dont use readonly

* One more test fix

* Update to snapshow build

* Resolve a circular dependency

* Try to fix tests

* Solve recurring NPE in DSTU2 tests

* Fix one more test

* Test fix

* More test threading fixes

* One more attempt to get tests passing

* Refactoring for tests

* Refactoring for tests

example-projects/hapi-fhir-jpaserver-cds-example/pom.xml

@@ -181,8 +181,8 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>

example-projects/hapi-fhir-jpaserver-cds-example/src/main/java/ca/uhn/fhir/jpa/cds/example/FhirServerConfig.java

@@ -60,7 +60,7 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(dataSource());
 		retVal.setJpaProperties(jpaProperties());

example-projects/hapi-fhir-jpaserver-dynamic/pom.xml

@@ -11,7 +11,7 @@
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
 		<version>3.4.0-SNAPSHOT</version>
-	   <relativePath>../pom.xml</relativePath>
+	   <relativePath>../../pom.xml</relativePath>
 	</parent>
 
 	<artifactId>hapi-fhir-jpaserver-dynamic</artifactId>
@@ -198,8 +198,8 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>

hapi-deployable-pom/pom.xml

@@ -100,8 +100,8 @@
 							<artifactId>javax.mail-api</artifactId>
 						</dependency>
 						<dependency>
-							<groupId>com.phloc</groupId>
+							<groupId>com.helger</groupId>
-							<artifactId>phloc-commons</artifactId>
+							<artifactId>ph-schematron</artifactId>
 						</dependency>
 						<dependency>
 							<groupId>commons-logging</groupId>
@@ -140,6 +140,7 @@
 						<ignoredResourcePattern>changelog.txt</ignoredResourcePattern>
 						<ignoredResource>javac.bat</ignoredResource>
 						<ignoredResource>about.html</ignoredResource>
+						<ignoredResource>changelog.xml</ignoredResource>
 					</ignoredResourcePatterns>
 				</configuration>
 			</plugin>

hapi-fhir-base/pom.xml

@@ -45,27 +45,14 @@
 
 		<!-- Only required for Schematron Validator Support -->
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<optional>true</optional>
-			<exclusions><!--
-				<exclusion>
-					<artifactId>Saxon-HE</artifactId>
-					<groupId>net.sf.saxon</groupId>
-				</exclusion>-->
-			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 			<optional>true</optional>
-			<exclusions>
-				<exclusion>
-					<!-- Guava brings in a newer replacement for this dependency called com.google.code.findbugs:jsr305 -->
-					<groupId>com.google.code.findbugs</groupId>
-					<artifactId>annotations</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 
 		<!-- <dependency> <groupId>xerces</groupId> <artifactId>xercesImpl</artifactId> 

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

@@ -42,9 +42,9 @@ import ca.uhn.fhir.validation.schematron.SchematronProvider;
  */
 public class FhirValidator {
 
-	private static final String I18N_KEY_NO_PHLOC_ERROR = FhirValidator.class.getName() + ".noPhlocError";
+	private static final String I18N_KEY_NO_PH_ERROR = FhirValidator.class.getName() + ".noPhError";
 
-	private static volatile Boolean ourPhlocPresentOnClasspath;
+	private static volatile Boolean ourPhPresentOnClasspath;
 	private final FhirContext myContext;
 	private List<IValidatorModule> myValidators = new ArrayList<IValidatorModule>();
 
@@ -54,8 +54,8 @@ public class FhirValidator {
 	public FhirValidator(FhirContext theFhirContext) {
 		myContext = theFhirContext;
 
-		if (ourPhlocPresentOnClasspath == null) {
+		if (ourPhPresentOnClasspath == null) {
-			ourPhlocPresentOnClasspath = SchematronProvider.isSchematronAvailable(theFhirContext);
+			ourPhPresentOnClasspath = SchematronProvider.isSchematronAvailable(theFhirContext);
 		}
 	}
 
@@ -96,9 +96,10 @@ public class FhirValidator {
 	 * Should the validator validate the resource against the base schema (the schema provided with the FHIR distribution itself)
 	 */
 	public synchronized boolean isValidateAgainstStandardSchematron() {
-		if (!ourPhlocPresentOnClasspath) {
+		if (!ourPhPresentOnClasspath) {
-			return false; 	// No need to ask since we dont have Phloc. Also Class.forname will complain
+			// No need to ask since we dont have Ph-Schematron. Also Class.forname will complain
-							// about missing phloc import.
+			// about missing ph-schematron import.
+			return false;
 		}
 		Class<? extends IValidatorModule> cls = SchematronProvider.getSchematronValidatorClass();
 		return haveValidatorOfType(cls);
@@ -135,8 +136,11 @@ public class FhirValidator {
 	 * @return Returns a referens to <code>this<code> for method chaining
 	 */
 	public synchronized FhirValidator setValidateAgainstStandardSchematron(boolean theValidateAgainstStandardSchematron) {
-		if (theValidateAgainstStandardSchematron && !ourPhlocPresentOnClasspath) {
+		if (theValidateAgainstStandardSchematron && !ourPhPresentOnClasspath) {
-			throw new IllegalArgumentException(myContext.getLocalizer().getMessage(I18N_KEY_NO_PHLOC_ERROR));
+			throw new IllegalArgumentException(myContext.getLocalizer().getMessage(I18N_KEY_NO_PH_ERROR));
+		}
+		if (!theValidateAgainstStandardSchematron && !ourPhPresentOnClasspath) {
+			return this;
 		}
 		Class<? extends IValidatorModule> cls = SchematronProvider.getSchematronValidatorClass();
 		IValidatorModule instance = SchematronProvider.getSchematronValidatorInstance(myContext);
@@ -163,7 +167,7 @@ public class FhirValidator {
 	private void applyDefaultValidators() {
 		if (myValidators.isEmpty()) {
 			setValidateAgainstStandardSchema(true);
-			if (ourPhlocPresentOnClasspath) {
+			if (ourPhPresentOnClasspath) {
 				setValidateAgainstStandardSchematron(true);
 			}
 		}

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

@@ -20,28 +20,28 @@ package ca.uhn.fhir.validation.schematron;
  * #L%
  */
 
-import java.io.InputStream;
-import java.io.StringReader;
-import java.util.*;
-
-import javax.xml.transform.stream.StreamSource;
-
-import org.apache.commons.io.IOUtils;
-import org.hl7.fhir.instance.model.api.IBaseBundle;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.oclc.purl.dsdl.svrl.SchematronOutputType;
-
-import com.phloc.commons.error.IResourceError;
-import com.phloc.commons.error.IResourceErrorGroup;
-import com.phloc.schematron.ISchematronResource;
-import com.phloc.schematron.SchematronHelper;
-import com.phloc.schematron.xslt.SchematronResourceSCH;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.validation.*;
+import com.helger.commons.error.IError;
+import com.helger.commons.error.list.IErrorList;
+import com.helger.schematron.ISchematronResource;
+import com.helger.schematron.SchematronHelper;
+import com.helger.schematron.xslt.SchematronResourceSCH;
+import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.oclc.purl.dsdl.svrl.SchematronOutputType;
+
+import javax.xml.transform.stream.StreamSource;
+import java.io.InputStream;
+import java.io.StringReader;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
 
 /**
  * This class is only used using reflection from {@link SchematronProvider} in order
@@ -81,27 +81,21 @@ public class SchematronBaseValidator implements IValidatorModule {
 			return;
 		}
 
-		IResourceErrorGroup errors = SchematronHelper.convertToResourceErrorGroup(results, theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName());
+		IErrorList errors = SchematronHelper.convertToErrorList(results, theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName());
 
 		if (errors.getAllErrors().containsOnlySuccess()) {
 			return;
 		}
 
-		for (IResourceError next : errors.getAllErrors().getAllResourceErrors()) {
+		for (IError next : errors) {
 			ResultSeverityEnum severity;
-			switch (next.getErrorLevel()) {
+			if (next.isFailure()) {
-			case ERROR:
 				severity = ResultSeverityEnum.ERROR;
-				break;
+			} else if (next.isError()) {
-			case FATAL_ERROR:
 				severity = ResultSeverityEnum.FATAL;
-				break;
+			} else if (next.isNoError()) {
-			case WARN:
 				severity = ResultSeverityEnum.WARNING;
-				break;
+			} else {
-			case INFO:
-			case SUCCESS:
-			default:
 				continue;
 			}
 
@@ -109,9 +103,9 @@ public class SchematronBaseValidator implements IValidatorModule {
 
 			SingleValidationMessage message = new SingleValidationMessage();
 			message.setMessage(details);
-			message.setLocationLine(next.getLocation().getLineNumber());
+			message.setLocationLine(next.getErrorLocation().getLineNumber());
-			message.setLocationCol(next.getLocation().getColumnNumber());
+			message.setLocationCol(next.getErrorLocation().getColumnNumber());
-			message.setLocationString(next.getLocation().getAsString());
+			message.setLocationString(next.getErrorLocation().getAsString());
 			message.setSeverity(severity);
 			theCtx.addValidationMessage(message);
 		}

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

@@ -30,16 +30,16 @@ import ca.uhn.fhir.validation.IValidatorModule;
 public class SchematronProvider {
 
 
-	private static final String I18N_KEY_NO_PHLOC_WARNING = FhirValidator.class.getName() + ".noPhlocWarningOnStartup";
+	private static final String I18N_KEY_NO_PH_WARNING = FhirValidator.class.getName() + ".noPhWarningOnStartup";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirValidator.class);
 	
 	@CoverageIgnore
 	public static boolean isSchematronAvailable(FhirContext theFhirContext) {
 		try {
-			Class.forName("com.phloc.schematron.ISchematronResource");
+			Class.forName("com.helger.schematron.ISchematronResource");
 			return true;
 		} catch (ClassNotFoundException e) {
-			ourLog.info(theFhirContext.getLocalizer().getMessage(I18N_KEY_NO_PHLOC_WARNING));
+			ourLog.info(theFhirContext.getLocalizer().getMessage(I18N_KEY_NO_PH_WARNING));
 			return false;
 		}
 	}

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -51,8 +51,8 @@ ca.uhn.fhir.rest.server.RestfulServer.unknownMethod=Invalid request: The FHIR en
 ca.uhn.fhir.rest.server.RestfulServer.rootRequest=This is the base URL of FHIR server. Unable to handle this request, as it does not contain a resource type or operation name.
 ca.uhn.fhir.rest.server.RestfulServer.rootRequest.multitenant=This is the base URL of a multitenant FHIR server. Unable to handle this request, as it does not contain a tenant ID.
 ca.uhn.fhir.validation.ValidationContext.unableToDetermineEncoding=Unable to determine encoding (e.g. XML / JSON) on validation input. Is this a valid FHIR resource body? 
-ca.uhn.fhir.validation.FhirValidator.noPhlocWarningOnStartup=Phloc-schematron library not found on classpath, will not attempt to perform schematron validation
+ca.uhn.fhir.validation.FhirValidator.noPhWarningOnStartup=Ph-schematron library not found on classpath, will not attempt to perform schematron validation
-ca.uhn.fhir.validation.FhirValidator.noPhlocError=Phloc-schematron library not found on classpath, can not enable perform schematron validation
+ca.uhn.fhir.validation.FhirValidator.noPhError=Ph-schematron library not found on classpath, can not enable perform schematron validation
 ca.uhn.fhir.validation.ValidationResult.noIssuesDetected=No issues detected during validation
 
 # JPA Messages

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -173,8 +173,8 @@
 		</dependency>
 
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>
@@ -183,8 +183,8 @@
 			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 		</dependency>
 
 		<!--
@@ -196,14 +196,11 @@
 			<artifactId>jaxb-api</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>com.sun.xml.bind</groupId>
+			<groupId>org.glassfish.jaxb</groupId>
-			<artifactId>jaxb-core</artifactId>
+			<artifactId>jaxb-runtime</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>com.sun.xml.bind</groupId>
-			<artifactId>jaxb-impl</artifactId>
 		</dependency>
 
+
 		<dependency>
 			<groupId>org.fusesource.jansi</groupId>
 			<artifactId>jansi</artifactId>

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

@@ -24,7 +24,7 @@ import ca.uhn.fhir.util.VersionUtil;
 import ch.qos.logback.classic.LoggerContext;
 import ch.qos.logback.classic.joran.JoranConfigurator;
 import ch.qos.logback.core.joran.spi.JoranException;
-import com.phloc.commons.io.file.FileUtils;
+import com.helger.commons.io.file.FileHelper;
 import org.apache.commons.cli.*;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.text.WordUtils;
@@ -60,7 +60,7 @@ public abstract class BaseApp {
 		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): " + FileUtils.getFileSizeDisplay(Runtime.getRuntime().maxMemory(), 1));
+		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("------------------------------------------------------------");
 	}
@@ -233,10 +233,10 @@ public abstract class BaseApp {
 			} else {
 				System.exit(1);
 			}
-		} catch (Exception e) {
+		} catch (Throwable t) {
-			ourLog.error("Error during execution: ", e);
+			ourLog.error("Error during execution: ", t);
 			if ("true".equals(System.getProperty("test"))) {
-				throw new CommandFailureException("Error: " + e.toString(), e);
+				throw new CommandFailureException("Error: " + t.toString(), t);
 			} else {
 				System.exit(1);
 			}

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

@@ -30,7 +30,7 @@ public class CommandFailureException extends Error {
 		super(theMessage);
 	}
 
-	public CommandFailureException(String theString, Exception theCause) {
+	public CommandFailureException(String theString, Throwable theCause) {
 		super(theString, theCause);
 	}
 

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

@@ -27,8 +27,8 @@ import ca.uhn.fhir.parser.LenientErrorHandler;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.SingleValidationMessage;
 import ca.uhn.fhir.validation.ValidationResult;
+import com.helger.commons.io.file.FileHelper;
 import com.google.common.base.Charsets;
-import com.phloc.commons.io.file.FileUtils;
 import org.apache.commons.cli.*;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.text.WordUtils;
@@ -80,6 +80,7 @@ public class ValidateCommand extends BaseCommand {
 		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)");
+
     return retVal;
 	}
 
@@ -119,7 +120,7 @@ public class ValidateCommand extends BaseCommand {
 			} catch (IOException e) {
 				throw new CommandFailureException(e);
 			}
-			ourLog.info("Fully read - Size is {}", FileUtils.getFileSizeDisplay(contents.length()));
+			ourLog.info("Fully read - Size is {}", FileHelper.getFileSizeDisplay(contents.length()));
 		}
 
 		ca.uhn.fhir.rest.api.EncodingEnum enc = ca.uhn.fhir.rest.api.EncodingEnum.detectEncodingNoDefault(defaultString(contents));

hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml

@@ -132,8 +132,8 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>

hapi-fhir-dist/pom.xml

@@ -217,8 +217,8 @@
 					<artifactId>thymeleaf</artifactId>
 				</dependency>
 				<dependency>
-					<groupId>com.phloc</groupId>
+					<groupId>com.helger</groupId>
-					<artifactId>phloc-schematron</artifactId>
+					<artifactId>ph-schematron</artifactId>
 					<exclusions>
 						<exclusion>
 							<artifactId>Saxon-HE</artifactId>
@@ -227,8 +227,8 @@
 					</exclusions>
 				</dependency>
 				<dependency>
-					<groupId>com.phloc</groupId>
+					<groupId>com.helger</groupId>
-					<artifactId>phloc-commons</artifactId>
+					<artifactId>ph-commons</artifactId>
 				</dependency>
 				<dependency>
 					<groupId>org.springframework</groupId>

hapi-fhir-jacoco/pom.xml

@@ -78,8 +78,8 @@
 		</dependency>
 
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>
@@ -88,8 +88,8 @@
 			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.thymeleaf</groupId>

hapi-fhir-jpaserver-base/pom.xml

@@ -123,11 +123,6 @@
 			<artifactId>logback-classic</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.thymeleaf</groupId>
-			<artifactId>thymeleaf</artifactId>
-			<scope>test</scope>
-		</dependency>
 		<dependency>
 			<groupId>net.ttddyy</groupId>
 			<artifactId>datasource-proxy</artifactId>
@@ -146,8 +141,8 @@
 		</dependency>
 
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<scope>test</scope>
 			<exclusions>
 				<exclusion>
@@ -157,8 +152,8 @@
 			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 			<scope>test</scope>
 		</dependency>
 
@@ -468,6 +463,11 @@
 			<artifactId>greenmail-spring</artifactId>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-collections4</artifactId>
+			<scope>test</scope>
+		</dependency>
 
 		<dependency>
 			<groupId>com.github.ben-manes.caffeine</groupId>
@@ -566,19 +566,9 @@
 					as JDK9 no longer includes them by default
 					-->
 					<dependency>
-						<groupId>javax.xml.bind</groupId>
+						<groupId>org.glassfish.jaxb</groupId>
-						<artifactId>jaxb-api</artifactId>
+						<artifactId>jaxb-runtime</artifactId>
-						<version>${jaxb_api_version}</version>
+						<version>${jaxb_runtime_version}</version>
-					</dependency>
-					<dependency>
-						<groupId>com.sun.xml.bind</groupId>
-						<artifactId>jaxb-core</artifactId>
-						<version>${jaxb_core_version}</version>
-					</dependency>
-					<dependency>
-						<groupId>com.sun.xml.bind</groupId>
-						<artifactId>jaxb-impl</artifactId>
-						<version>${jaxb_core_version}</version>
 					</dependency>
 				</dependencies>
 			</plugin>

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

@@ -73,7 +73,10 @@ import org.hl7.fhir.r4.model.BaseResource;
 import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.CanonicalType;
 import org.hl7.fhir.r4.model.Reference;
+import org.springframework.beans.BeansException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Slice;
@@ -100,7 +103,7 @@ import static org.apache.commons.lang3.StringUtils.*;
 
 @SuppressWarnings("WeakerAccess")
 @Repository
-public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
+public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao, ApplicationContextAware {
 
 	public static final long INDEX_STATUS_INDEXED = 1L;
 	public static final long INDEX_STATUS_INDEXING_FAILED = 2L;
@@ -186,9 +189,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	@Autowired
 	private PlatformTransactionManager myPlatformTransactionManager;
 	@Autowired
-	private List<IFhirResourceDao<?>> myResourceDaos;
-	private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> myResourceTypeToDao;
-	@Autowired
 	private ISearchDao mySearchDao;
 	@Autowired
 	private ISearchParamExtractor mySearchParamExtractor;
@@ -200,6 +200,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	private ISearchResultDao mySearchResultDao;
 	@Autowired
 	private IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
+	private ApplicationContext myApplicationContext;
+	private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> myResourceTypeToDao;
 
 	protected void clearRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
 		if (theRequestDetails != null) {
@@ -695,6 +697,29 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return retVal;
 	}
 
+
+	@SuppressWarnings("unchecked")
+	public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
+		if (myResourceTypeToDao == null) {
+			Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> theResourceTypeToDao = new HashMap<>();
+			Map<String, IFhirResourceDao> daos = myApplicationContext.getBeansOfType(IFhirResourceDao.class, false, false);
+			for (IFhirResourceDao<?> next : daos.values()) {
+				theResourceTypeToDao.put(next.getResourceType(), next);
+			}
+
+			if (this instanceof IFhirResourceDao<?>) {
+				IFhirResourceDao<?> thiz = (IFhirResourceDao<?>) this;
+				theResourceTypeToDao.put(thiz.getResourceType(), thiz);
+			}
+
+			myResourceTypeToDao = theResourceTypeToDao;
+		}
+
+		IFhirResourceDao<R> dao = (IFhirResourceDao<R>) myResourceTypeToDao.get(theType);
+		return dao;
+	}
+
+
 	protected Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource) {
 		return mySearchParamExtractor.extractSearchParamCoords(theEntity, theResource);
 	}
@@ -896,6 +921,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return myConfig;
 	}
 
+	@Override
+	public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
+		myApplicationContext = theApplicationContext;
+	}
+
 	public void setConfig(DaoConfig theConfig) {
 		myConfig = theConfig;
 	}
@@ -922,26 +952,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		}
 	}
 
-	@SuppressWarnings("unchecked")
-	public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
-		if (myResourceTypeToDao == null) {
-			Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> theResourceTypeToDao = new HashMap<>();
-			for (IFhirResourceDao<?> next : myResourceDaos) {
-				theResourceTypeToDao.put(next.getResourceType(), next);
-			}
-
-			if (this instanceof IFhirResourceDao<?>) {
-				IFhirResourceDao<?> thiz = (IFhirResourceDao<?>) this;
-				theResourceTypeToDao.put(thiz.getResourceType(), thiz);
-			}
-
-			myResourceTypeToDao = theResourceTypeToDao;
-		}
-
-		IFhirResourceDao<R> dao = (IFhirResourceDao<R>) myResourceTypeToDao.get(theType);
-		return dao;
-	}
-
 	public IResourceIndexedCompositeStringUniqueDao getResourceIndexedCompositeStringUniqueDao() {
 		return myResourceIndexedCompositeStringUniqueDao;
 	}

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

@@ -159,7 +159,7 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 		return doExpunge(null, null, null, theExpungeOptions);
 	}
 
-	@Transactional(propagation = Propagation.REQUIRED, readOnly = true)
+	@Transactional(propagation = Propagation.REQUIRED)
 	@Override
 	public Map<String, Long> getResourceCounts() {
 		Map<String, Long> retVal = new HashMap<>();
@@ -172,7 +172,7 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 		return retVal;
 	}
 
-	@Transactional(propagation = Propagation.SUPPORTS, readOnly = true)
+	@Transactional(propagation = Propagation.SUPPORTS)
 	@Nullable
 	@Override
 	public Map<String, Long> getResourceCountsFromCache() {
@@ -265,7 +265,7 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
 	}
 
 	@Override
-	@Transactional(propagation = Propagation.NOT_SUPPORTED)
+	@Transactional(propagation = Propagation.NEVER)
 	public Integer performReindexingPass(final Integer theCount) {
 		if (!myReindexLock.tryLock()) {
 			return null;

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

@@ -32,7 +32,10 @@ import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.BeansException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
 import org.springframework.scheduling.annotation.Scheduled;
 
 import javax.annotation.PostConstruct;
@@ -40,7 +43,7 @@ import java.util.*;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
-public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implements ISearchParamRegistry {
+public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implements ISearchParamRegistry, ApplicationContextAware {
 
 	private static final int MAX_MANAGED_PARAM_COUNT = 10000;
 	private static final Logger ourLog = LoggerFactory.getLogger(BaseSearchParamRegistry.class);
@@ -49,12 +52,12 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
 	private volatile Map<String, Map<Set<String>, List<JpaRuntimeSearchParam>>> myActiveParamNamesToUniqueSearchParams = Collections.emptyMap();
 	@Autowired
 	private FhirContext myCtx;
-	@Autowired
+	private Collection<IFhirResourceDao<?>> myResourceDaos;
-	private Collection<IFhirResourceDao<?>> myDaos;
 	private volatile Map<String, Map<String, RuntimeSearchParam>> myActiveSearchParams;
 	@Autowired
 	private DaoConfig myDaoConfig;
 	private volatile long myLastRefresh;
+	private ApplicationContext myApplicationContext;
 
 	public BaseSearchParamRegistry() {
 		super();
@@ -212,7 +215,13 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
 	public void postConstruct() {
 		Map<String, Map<String, RuntimeSearchParam>> resourceNameToSearchParams = new HashMap<>();
 
-		for (IFhirResourceDao<?> nextDao : myDaos) {
+		myResourceDaos = new ArrayList<>();
+		Map<String, IFhirResourceDao> daos = myApplicationContext.getBeansOfType(IFhirResourceDao.class, false, false);
+		for (IFhirResourceDao next : daos.values()) {
+			myResourceDaos.add(next);
+		}
+
+		for (IFhirResourceDao<?> nextDao : myResourceDaos) {
 			RuntimeResourceDefinition nextResDef = myCtx.getResourceDefinition(nextDao.getResourceType());
 			String nextResourceName = nextResDef.getName();
 			HashMap<String, RuntimeSearchParam> nameToParam = new HashMap<>();
@@ -321,6 +330,11 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
 		refreshCacheIfNecessary();
 	}
 
+	@Override
+	public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
+		myApplicationContext = theApplicationContext;
+	}
+
 	protected abstract RuntimeSearchParam toRuntimeSp(SP theNextSp);
 
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSearchParameterDstu2.java

@@ -33,6 +33,8 @@ import ca.uhn.fhir.model.primitive.CodeDt;
 import org.apache.commons.lang3.time.DateUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -58,6 +60,7 @@ public class FhirResourceDaoSearchParameterDstu2 extends FhirResourceDaoDstu2<Se
 	 */
 	@Override
 	@Scheduled(fixedDelay = DateUtils.MILLIS_PER_MINUTE)
+	@Transactional(propagation = Propagation.NEVER)
 	public void performReindexingPass() {
 		if (getConfig().isSchedulingDisabled()) {
 			return;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -68,6 +68,7 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionCallback;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.persistence.TypedQuery;
@@ -103,15 +104,20 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 					Bundle subRequestBundle = new Bundle();
 					subRequestBundle.setType(BundleTypeEnum.TRANSACTION);
 					subRequestBundle.addEntry(nextRequestEntry);
-
+					return transaction((ServletRequestDetails) theRequestDetails, subRequestBundle, "Batch sub-request");
-					Bundle subResponseBundle = transaction((ServletRequestDetails) theRequestDetails, subRequestBundle, "Batch sub-request");
-					return subResponseBundle;
 				}
 			};
 
 			BaseServerResponseException caughtEx;
 			try {
-				Bundle nextResponseBundle = txTemplate.execute(callback);
+				Bundle nextResponseBundle;
+				if (nextRequestEntry.getRequest().getMethodElement().getValueAsEnum() == HTTPVerbEnum.GET) {
+					// Don't process GETs in a transaction because they'll
+					// create their own
+					nextResponseBundle = callback.doInTransaction(null);
+				} else {
+					nextResponseBundle = txTemplate.execute(callback);
+				}
 				caughtEx = null;
 
 				Entry subResponseEntry = nextResponseBundle.getEntry().get(0);
@@ -156,13 +162,17 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 			return batch(theRequestDetails, theRequest);
 		}
 
-		if (transactionType == null) {
+		return doTransaction(theRequestDetails, theRequest, theActionName, transactionType);
-			String message = "Transactiion Bundle did not specify valid Bundle.type, assuming " + BundleTypeEnum.TRANSACTION.getCode();
-			ourLog.warn(message);
-			transactionType = BundleTypeEnum.TRANSACTION;
 	}
-		if (transactionType != BundleTypeEnum.TRANSACTION) {
+
-			throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + transactionType.getCode());
+	private Bundle doTransaction(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName, BundleTypeEnum theTransactionType) {
+		if (theTransactionType == null) {
+			String message = "Transaction Bundle did not specify valid Bundle.type, assuming " + BundleTypeEnum.TRANSACTION.getCode();
+			ourLog.warn(message);
+			theTransactionType = BundleTypeEnum.TRANSACTION;
+		}
+		if (theTransactionType != BundleTypeEnum.TRANSACTION) {
+			throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + theTransactionType.getCode());
 		}
 
 		ourLog.info("Beginning {} with {} resources", theActionName, theRequest.getEntry().size());
@@ -186,7 +196,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 		 */
 		Bundle response = new Bundle();
 		List<Entry> getEntries = new ArrayList<Entry>();
-		IdentityHashMap<Entry, Integer> originalRequestOrder = new IdentityHashMap<Bundle.Entry, Integer>();
+		IdentityHashMap<Entry, Integer> originalRequestOrder = new IdentityHashMap<Entry, Integer>();
 		for (int i = 0; i < theRequest.getEntry().size(); i++) {
 			originalRequestOrder.put(theRequest.getEntry().get(i), i);
 			response.addEntry();
@@ -203,225 +213,13 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 		Set<ResourceTable> updatedEntities = new HashSet<>();
 
 		/*
-		 * Loop through the request and process any entries of type
+		 * Handle: GET/PUT/POST
-		 * PUT, POST or DELETE
 		 */
-		for (int i = 0; i < theRequest.getEntry().size(); i++) {
+		TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
-
+		txTemplate.execute(t->{
-			if (i % 100 == 0) {
+			handleTransactionWriteOperations(theRequestDetails, theRequest, theActionName, updateTime, allIds, idSubstitutions, idToPersistedOutcome, response, originalRequestOrder, deletedResources, deleteConflicts, entriesToProcess, nonUpdatedEntities, updatedEntities);
-				ourLog.debug("Processed {} non-GET entries out of {}", i, theRequest.getEntry().size());
+			return null;
-			}
+		});
-
-			Entry nextReqEntry = theRequest.getEntry().get(i);
-			IResource res = nextReqEntry.getResource();
-			IdDt nextResourceId = null;
-			if (res != null) {
-
-				nextResourceId = res.getId();
-
-				if (!nextResourceId.hasIdPart()) {
-					if (isNotBlank(nextReqEntry.getFullUrl())) {
-						nextResourceId = new IdDt(nextReqEntry.getFullUrl());
-					}
-				}
-
-				if (nextResourceId.hasIdPart() && nextResourceId.getIdPart().matches("[a-zA-Z]+\\:.*") && !isPlaceholder(nextResourceId)) {
-					throw new InvalidRequestException("Invalid placeholder ID found: " + nextResourceId.getIdPart() + " - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'");
-				}
-
-				if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !isPlaceholder(nextResourceId)) {
-					nextResourceId = new IdDt(toResourceName(res.getClass()), nextResourceId.getIdPart());
-					res.setId(nextResourceId);
-				}
-
-				/*
-				 * Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
-				 */
-				if (isPlaceholder(nextResourceId)) {
-					if (!allIds.add(nextResourceId)) {
-						throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextResourceId));
-					}
-				} else if (nextResourceId.hasResourceType() && nextResourceId.hasIdPart()) {
-					IdDt nextId = nextResourceId.toUnqualifiedVersionless();
-					if (!allIds.add(nextId)) {
-						throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextId));
-					}
-				}
-
-			}
-
-			HTTPVerbEnum verb = nextReqEntry.getRequest().getMethodElement().getValueAsEnum();
-			if (verb == null) {
-				throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionEntryHasInvalidVerb", nextReqEntry.getRequest().getMethod()));
-			}
-
-			String resourceType = res != null ? getContext().getResourceDefinition(res).getName() : null;
-			Entry nextRespEntry = response.getEntry().get(originalRequestOrder.get(nextReqEntry));
-
-			switch (verb) {
-				case POST: {
-					// CREATE
-					@SuppressWarnings("rawtypes")
-					IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
-					res.setId((String) null);
-					DaoMethodOutcome outcome;
-					outcome = resourceDao.create(res, nextReqEntry.getRequest().getIfNoneExist(), false, theRequestDetails);
-					handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
-					entriesToProcess.put(nextRespEntry, outcome.getEntity());
-					if (outcome.getCreated() == false) {
-						nonUpdatedEntities.add(outcome.getEntity());
-					}
-					break;
-				}
-				case DELETE: {
-					// DELETE
-					String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
-					UrlParts parts = UrlUtil.parseUrl(url);
-					ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> dao = toDao(parts, verb.getCode(), url);
-					int status = Constants.STATUS_HTTP_204_NO_CONTENT;
-					if (parts.getResourceId() != null) {
-						DaoMethodOutcome outcome = dao.delete(new IdDt(parts.getResourceType(), parts.getResourceId()), deleteConflicts, theRequestDetails);
-						if (outcome.getEntity() != null) {
-							deletedResources.add(outcome.getId().toUnqualifiedVersionless());
-							entriesToProcess.put(nextRespEntry, outcome.getEntity());
-						}
-					} else {
-						DeleteMethodOutcome deleteOutcome = dao.deleteByUrl(parts.getResourceType() + '?' + parts.getParams(), deleteConflicts, theRequestDetails);
-						List<ResourceTable> allDeleted = deleteOutcome.getDeletedEntities();
-						for (ResourceTable deleted : allDeleted) {
-							deletedResources.add(deleted.getIdDt().toUnqualifiedVersionless());
-						}
-						if (allDeleted.isEmpty()) {
-							status = Constants.STATUS_HTTP_404_NOT_FOUND;
-						}
-					}
-
-					nextRespEntry.getResponse().setStatus(toStatusString(status));
-					break;
-				}
-				case PUT: {
-					// UPDATE
-					@SuppressWarnings("rawtypes")
-					IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
-
-					DaoMethodOutcome outcome;
-
-					String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
-
-					UrlParts parts = UrlUtil.parseUrl(url);
-					if (isNotBlank(parts.getResourceId())) {
-						res.setId(new IdDt(parts.getResourceType(), parts.getResourceId()));
-						outcome = resourceDao.update(res, null, false, theRequestDetails);
-					} else {
-						res.setId((String) null);
-						outcome = resourceDao.update(res, parts.getResourceType() + '?' + parts.getParams(), false, theRequestDetails);
-					}
-
-					if (outcome.getCreated() == Boolean.FALSE) {
-						updatedEntities.add(outcome.getEntity());
-					}
-
-					handleTransactionCreateOrUpdateOutcome(idSubstitutions, idToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
-					entriesToProcess.put(nextRespEntry, outcome.getEntity());
-					break;
-				}
-				case GET:
-					break;
-			}
-		}
-
-		/*
-		 * Make sure that there are no conflicts from deletions. E.g. we can't delete something
-		 * if something else has a reference to it.. Unless the thing that has a reference to it
-		 * was also deleted as a part of this transaction, which is why we check this now at the
-		 * end.
-		 */
-
-		deleteConflicts.removeIf(next -> deletedResources.contains(next.getTargetId().toVersionless()));
-		validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
-
-		/*
-		 * Perform ID substitutions and then index each resource we have saved
-		 */
-
-		FhirTerser terser = getContext().newTerser();
-		for (DaoMethodOutcome nextOutcome : idToPersistedOutcome.values()) {
-			IResource nextResource = (IResource) nextOutcome.getResource();
-			if (nextResource == null) {
-				continue;
-			}
-
-			// References
-			List<BaseResourceReferenceDt> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class);
-			for (BaseResourceReferenceDt nextRef : allRefs) {
-				IdDt nextId = nextRef.getReference();
-				if (!nextId.hasIdPart()) {
-					continue;
-				}
-				if (idSubstitutions.containsKey(nextId)) {
-					IdDt newId = idSubstitutions.get(nextId);
-					ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
-					nextRef.setReference(newId);
-				} else {
-					ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
-				}
-			}
-
-			// URIs
-			List<UriDt> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, UriDt.class);
-			for (UriDt nextRef : allUris) {
-				if (nextRef instanceof IIdType) {
-					continue; // No substitution on the resource ID itself!
-				}
-				IdDt nextUriString = new IdDt(nextRef.getValueAsString());
-				if (idSubstitutions.containsKey(nextUriString)) {
-					IdDt newId = idSubstitutions.get(nextUriString);
-					ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
-					nextRef.setValue(newId.getValue());
-				} else {
-					ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
-				}
-			}
-
-
-			InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(nextResource);
-			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
-			if (updatedEntities.contains(nextOutcome.getEntity())) {
-				updateInternal(theRequestDetails, nextResource, true, false, theRequestDetails, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource());
-			} else if (!nonUpdatedEntities.contains(nextOutcome.getEntity())) {
-				updateEntity(theRequestDetails, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, updateTime, false, true);
-			}
-		}
-
-		myEntityManager.flush();
-
-		/*
-		 * Double check we didn't allow any duplicates we shouldn't have
-		 */
-		for (Entry nextEntry : theRequest.getEntry()) {
-			if (nextEntry.getRequest().getMethodElement().getValueAsEnum() == HTTPVerbEnum.POST) {
-				String matchUrl = nextEntry.getRequest().getIfNoneExist();
-				if (isNotBlank(matchUrl)) {
-					IFhirResourceDao<?> resourceDao = getDao(nextEntry.getResource().getClass());
-					Set<Long> val = resourceDao.processMatchUrl(matchUrl);
-					if (val.size() > 1) {
-						throw new InvalidRequestException(
-							"Unable to process " + theActionName + " - Request would cause multiple resources to match URL: \"" + matchUrl + "\". Does transaction request contain duplicates?");
-					}
-				}
-			}
-		}
-
-		for (IdDt next : allIds) {
-			IdDt replacement = idSubstitutions.get(next);
-			if (replacement == null) {
-				continue;
-			}
-			if (replacement.equals(next)) {
-				continue;
-			}
-			ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
-		}
 
 		/*
 		 * Loop through the request and process any entries of type GET
@@ -447,7 +245,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 				for (NameValuePair next : parameters) {
 					paramValues.put(next.getName(), next.getValue());
 				}
-				for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
+				for (Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
 					String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
 					requestDetails.addParameter(nextParamEntry.getKey(), nextValue);
 				}
@@ -490,10 +288,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 
 		}
 
-		ourLog.info("Flushing context after {}", theActionName);
+		for (Map.Entry<Entry, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
-		myEntityManager.flush();
-
-		for (java.util.Map.Entry<Entry, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
 			nextEntry.getKey().getResponse().setLocation(nextEntry.getValue().getIdDt().toUnqualified().getValue());
 			nextEntry.getKey().getResponse().setEtag(nextEntry.getValue().getIdDt().getVersionIdPart());
 		}
@@ -507,6 +302,229 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 		return response;
 	}
 
+	private void handleTransactionWriteOperations(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName, Date theUpdateTime, Set<IdDt> theAllIds, Map<IdDt, IdDt> theIdSubstitutions, Map<IdDt, DaoMethodOutcome> theIdToPersistedOutcome, Bundle theResponse, IdentityHashMap<Entry, Integer> theOriginalRequestOrder, List<IIdType> theDeletedResources, List<DeleteConflict> theDeleteConflicts, Map<Entry, ResourceTable> theEntriesToProcess, Set<ResourceTable> theNonUpdatedEntities, Set<ResourceTable> theUpdatedEntities) {
+		/*
+		 * Loop through the request and process any entries of type
+		 * PUT, POST or DELETE
+		 */
+		for (int i = 0; i < theRequest.getEntry().size(); i++) {
+
+			if (i % 100 == 0) {
+				ourLog.debug("Processed {} non-GET entries out of {}", i, theRequest.getEntry().size());
+			}
+
+			Entry nextReqEntry = theRequest.getEntry().get(i);
+			IResource res = nextReqEntry.getResource();
+			IdDt nextResourceId = null;
+			if (res != null) {
+
+				nextResourceId = res.getId();
+
+				if (!nextResourceId.hasIdPart()) {
+					if (isNotBlank(nextReqEntry.getFullUrl())) {
+						nextResourceId = new IdDt(nextReqEntry.getFullUrl());
+					}
+				}
+
+				if (nextResourceId.hasIdPart() && nextResourceId.getIdPart().matches("[a-zA-Z]+\\:.*") && !isPlaceholder(nextResourceId)) {
+					throw new InvalidRequestException("Invalid placeholder ID found: " + nextResourceId.getIdPart() + " - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'");
+				}
+
+				if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !isPlaceholder(nextResourceId)) {
+					nextResourceId = new IdDt(toResourceName(res.getClass()), nextResourceId.getIdPart());
+					res.setId(nextResourceId);
+				}
+
+				/*
+				 * Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
+				 */
+				if (isPlaceholder(nextResourceId)) {
+					if (!theAllIds.add(nextResourceId)) {
+						throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextResourceId));
+					}
+				} else if (nextResourceId.hasResourceType() && nextResourceId.hasIdPart()) {
+					IdDt nextId = nextResourceId.toUnqualifiedVersionless();
+					if (!theAllIds.add(nextId)) {
+						throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextId));
+					}
+				}
+
+			}
+
+			HTTPVerbEnum verb = nextReqEntry.getRequest().getMethodElement().getValueAsEnum();
+			if (verb == null) {
+				throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionEntryHasInvalidVerb", nextReqEntry.getRequest().getMethod()));
+			}
+
+			String resourceType = res != null ? getContext().getResourceDefinition(res).getName() : null;
+			Entry nextRespEntry = theResponse.getEntry().get(theOriginalRequestOrder.get(nextReqEntry));
+
+			switch (verb) {
+				case POST: {
+					// CREATE
+					@SuppressWarnings("rawtypes")
+					IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
+					res.setId((String) null);
+					DaoMethodOutcome outcome;
+					outcome = resourceDao.create(res, nextReqEntry.getRequest().getIfNoneExist(), false, theRequestDetails);
+					handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
+					theEntriesToProcess.put(nextRespEntry, outcome.getEntity());
+					if (outcome.getCreated() == false) {
+						theNonUpdatedEntities.add(outcome.getEntity());
+					}
+					break;
+				}
+				case DELETE: {
+					// DELETE
+					String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
+					UrlParts parts = UrlUtil.parseUrl(url);
+					IFhirResourceDao<? extends IBaseResource> dao = toDao(parts, verb.getCode(), url);
+					int status = Constants.STATUS_HTTP_204_NO_CONTENT;
+					if (parts.getResourceId() != null) {
+						DaoMethodOutcome outcome = dao.delete(new IdDt(parts.getResourceType(), parts.getResourceId()), theDeleteConflicts, theRequestDetails);
+						if (outcome.getEntity() != null) {
+							theDeletedResources.add(outcome.getId().toUnqualifiedVersionless());
+							theEntriesToProcess.put(nextRespEntry, outcome.getEntity());
+						}
+					} else {
+						DeleteMethodOutcome deleteOutcome = dao.deleteByUrl(parts.getResourceType() + '?' + parts.getParams(), theDeleteConflicts, theRequestDetails);
+						List<ResourceTable> allDeleted = deleteOutcome.getDeletedEntities();
+						for (ResourceTable deleted : allDeleted) {
+							theDeletedResources.add(deleted.getIdDt().toUnqualifiedVersionless());
+						}
+						if (allDeleted.isEmpty()) {
+							status = Constants.STATUS_HTTP_404_NOT_FOUND;
+						}
+					}
+
+					nextRespEntry.getResponse().setStatus(toStatusString(status));
+					break;
+				}
+				case PUT: {
+					// UPDATE
+					@SuppressWarnings("rawtypes")
+					IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
+
+					DaoMethodOutcome outcome;
+
+					String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
+
+					UrlParts parts = UrlUtil.parseUrl(url);
+					if (isNotBlank(parts.getResourceId())) {
+						res.setId(new IdDt(parts.getResourceType(), parts.getResourceId()));
+						outcome = resourceDao.update(res, null, false, theRequestDetails);
+					} else {
+						res.setId((String) null);
+						outcome = resourceDao.update(res, parts.getResourceType() + '?' + parts.getParams(), false, theRequestDetails);
+					}
+
+					if (outcome.getCreated() == Boolean.FALSE) {
+						theUpdatedEntities.add(outcome.getEntity());
+					}
+
+					handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res);
+					theEntriesToProcess.put(nextRespEntry, outcome.getEntity());
+					break;
+				}
+				case GET:
+					break;
+			}
+		}
+
+		/*
+		 * Make sure that there are no conflicts from deletions. E.g. we can't delete something
+		 * if something else has a reference to it.. Unless the thing that has a reference to it
+		 * was also deleted as a part of this transaction, which is why we check this now at the
+		 * end.
+		 */
+
+		theDeleteConflicts.removeIf(next -> theDeletedResources.contains(next.getTargetId().toVersionless()));
+		validateDeleteConflictsEmptyOrThrowException(theDeleteConflicts);
+
+		/*
+		 * Perform ID substitutions and then index each resource we have saved
+		 */
+
+		FhirTerser terser = getContext().newTerser();
+		for (DaoMethodOutcome nextOutcome : theIdToPersistedOutcome.values()) {
+			IResource nextResource = (IResource) nextOutcome.getResource();
+			if (nextResource == null) {
+				continue;
+			}
+
+			// References
+			List<BaseResourceReferenceDt> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class);
+			for (BaseResourceReferenceDt nextRef : allRefs) {
+				IdDt nextId = nextRef.getReference();
+				if (!nextId.hasIdPart()) {
+					continue;
+				}
+				if (theIdSubstitutions.containsKey(nextId)) {
+					IdDt newId = theIdSubstitutions.get(nextId);
+					ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
+					nextRef.setReference(newId);
+				} else {
+					ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
+				}
+			}
+
+			// URIs
+			List<UriDt> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, UriDt.class);
+			for (UriDt nextRef : allUris) {
+				if (nextRef instanceof IIdType) {
+					continue; // No substitution on the resource ID itself!
+				}
+				IdDt nextUriString = new IdDt(nextRef.getValueAsString());
+				if (theIdSubstitutions.containsKey(nextUriString)) {
+					IdDt newId = theIdSubstitutions.get(nextUriString);
+					ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
+					nextRef.setValue(newId.getValue());
+				} else {
+					ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
+				}
+			}
+
+
+			InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(nextResource);
+			Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
+			if (theUpdatedEntities.contains(nextOutcome.getEntity())) {
+				updateInternal(theRequestDetails, nextResource, true, false, theRequestDetails, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource());
+			} else if (!theNonUpdatedEntities.contains(nextOutcome.getEntity())) {
+				updateEntity(theRequestDetails, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theUpdateTime, false, true);
+			}
+		}
+
+		myEntityManager.flush();
+
+		/*
+		 * Double check we didn't allow any duplicates we shouldn't have
+		 */
+		for (Entry nextEntry : theRequest.getEntry()) {
+			if (nextEntry.getRequest().getMethodElement().getValueAsEnum() == HTTPVerbEnum.POST) {
+				String matchUrl = nextEntry.getRequest().getIfNoneExist();
+				if (isNotBlank(matchUrl)) {
+					IFhirResourceDao<?> resourceDao = getDao(nextEntry.getResource().getClass());
+					Set<Long> val = resourceDao.processMatchUrl(matchUrl);
+					if (val.size() > 1) {
+						throw new InvalidRequestException(
+							"Unable to process " + theActionName + " - Request would cause multiple resources to match URL: \"" + matchUrl + "\". Does transaction request contain duplicates?");
+					}
+				}
+			}
+		}
+
+		for (IdDt next : theAllIds) {
+			IdDt replacement = theIdSubstitutions.get(next);
+			if (replacement == null) {
+				continue;
+			}
+			if (replacement.equals(next)) {
+				continue;
+			}
+			ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
+		}
+	}
+
 	private String extractTransactionUrlOrThrowException(Entry nextEntry, HTTPVerbEnum verb) {
 		String url = nextEntry.getRequest().getUrl();
 		if (isBlank(url)) {
@@ -595,7 +613,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
 		return retVal;
 	}
 
-	@Transactional(propagation = Propagation.REQUIRED)
+	@Transactional(propagation = Propagation.NEVER)
 	@Override
 	public Bundle transaction(RequestDetails theRequestDetails, Bundle theRequest) {
 		if (theRequestDetails != null) {

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

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.Constants;
@@ -41,6 +42,7 @@ import org.hibernate.search.query.dsl.BooleanJunction;
 import org.hibernate.search.query.dsl.QueryBuilder;
 import org.hl7.fhir.dstu3.model.BaseResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Transactional;
 
 import javax.persistence.EntityManager;
@@ -50,12 +52,15 @@ import java.util.*;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
-public class FulltextSearchSvcImpl extends BaseHapiFhirDao<IBaseResource> implements IFulltextSearchSvc {
+public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FulltextSearchSvcImpl.class);
 
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	private EntityManager myEntityManager;
 
+	@Autowired
+	protected IForcedIdDao myForcedIdDao;
+
 	/**
 	 * Constructor
 	 */

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

@@ -112,8 +112,6 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 
 	TagList getAllResourceTags(RequestDetails theRequestDetails);
 
-	<R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType);
-
 	Class<T> getResourceType();
 
 	TagList getTags(IIdType theResourceId, RequestDetails theRequestDetails);

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

@@ -25,8 +25,6 @@ import ca.uhn.fhir.jpa.util.ExpungeOutcome;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.springframework.transaction.annotation.Propagation;
-import org.springframework.transaction.annotation.Transactional;
 
 import javax.annotation.Nullable;
 import java.util.Date;
@@ -40,12 +38,13 @@ public interface IFhirSystemDao<T, MT> extends IDao {
 
 	ExpungeOutcome expunge(ExpungeOptions theExpungeOptions);
 
+	@SuppressWarnings("unchecked")
 	<R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType);
 
 	Map<String, Long> getResourceCounts();
 
 	/**
-	 *Returns a cached count of resources using a cache that regularly
+	 * Returns a cached count of resources using a cache that regularly
 	 * refreshes in the background. This method will never
 	 */
 	@Nullable

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java

@@ -14,6 +14,8 @@ import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.dstu3.model.*;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 
 import java.util.List;
 
@@ -63,6 +65,7 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
 	 */
 	@Override
 	@Scheduled(fixedDelay = DateUtils.MILLIS_PER_MINUTE)
+	@Transactional(propagation = Propagation.NEVER)
 	public void performReindexingPass() {
 		if (getConfig().isSchedulingDisabled()) {
 			return;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/JpaValidationSupportDstu3.java

@@ -11,9 +11,12 @@ import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.beans.BeansException;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
 
+import javax.annotation.PostConstruct;
 import javax.transaction.Transactional;
 import javax.transaction.Transactional.TxType;
 import java.util.Collections;
@@ -42,34 +45,25 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
  */
 
 @Transactional(value = TxType.REQUIRED)
-public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3 {
+public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3, ApplicationContextAware {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JpaValidationSupportDstu3.class);
 
-	@Autowired
-	@Qualifier("myStructureDefinitionDaoDstu3")
 	private IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
-
-	@Autowired
-	@Qualifier("myValueSetDaoDstu3")
 	private IFhirResourceDao<ValueSet> myValueSetDao;
-
-	@Autowired
-	@Qualifier("myQuestionnaireDaoDstu3")
 	private IFhirResourceDao<Questionnaire> myQuestionnaireDao;
-
-	@Autowired
-	@Qualifier("myCodeSystemDaoDstu3")
 	private IFhirResourceDao<CodeSystem> myCodeSystemDao;
-
 	@Autowired
 	private FhirContext myDstu3Ctx;
+	private ApplicationContext myApplicationContext;
 
+	/**
+	 * Constructor
+	 */
 	public JpaValidationSupportDstu3() {
 		super();
 	}
 
-
 	@Override
 	@Transactional(value = TxType.SUPPORTS)
 	public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
@@ -168,6 +162,19 @@ public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3 {
 		return false;
 	}
 
+	@Override
+	public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
+		myApplicationContext = theApplicationContext;
+	}
+
+	@PostConstruct
+	public void start() {
+		myStructureDefinitionDao = myApplicationContext.getBean("myStructureDefinitionDaoDstu3", IFhirResourceDao.class);
+		myValueSetDao = myApplicationContext.getBean("myValueSetDaoDstu3", IFhirResourceDao.class);
+		myQuestionnaireDao = myApplicationContext.getBean("myQuestionnaireDaoDstu3", IFhirResourceDao.class);
+		myCodeSystemDao = myApplicationContext.getBean("myCodeSystemDaoDstu3", IFhirResourceDao.class);
+	}
+
 	@Override
 	@Transactional(value = TxType.SUPPORTS)
 	public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSearchParameterR4.java

@@ -13,6 +13,8 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.*;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 
 import java.util.List;
 
@@ -57,6 +59,7 @@ public class FhirResourceDaoSearchParameterR4 extends FhirResourceDaoR4<SearchPa
 	 */
 	@Override
 	@Scheduled(fixedDelay = DateUtils.MILLIS_PER_MINUTE)
+	@Transactional(propagation = Propagation.NEVER)
 	public void performReindexingPass() {
 		if (getConfig().isSchedulingDisabled()) {
 			return;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/JpaValidationSupportR4.java

@@ -11,9 +11,12 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
+import org.springframework.beans.BeansException;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
 
+import javax.annotation.PostConstruct;
 import javax.transaction.Transactional;
 import javax.transaction.Transactional.TxType;
 import java.util.Collections;
@@ -40,29 +43,22 @@ import java.util.List;
  */
 
 @Transactional(value = TxType.REQUIRED)
-public class JpaValidationSupportR4 implements IJpaValidationSupportR4 {
+public class JpaValidationSupportR4 implements IJpaValidationSupportR4, ApplicationContextAware {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JpaValidationSupportR4.class);
 
-	@Autowired
-	@Qualifier("myStructureDefinitionDaoR4")
 	private IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
-
-	@Autowired
-	@Qualifier("myValueSetDaoR4")
 	private IFhirResourceDao<ValueSet> myValueSetDao;
-
-	@Autowired
-	@Qualifier("myQuestionnaireDaoR4")
 	private IFhirResourceDao<Questionnaire> myQuestionnaireDao;
-
-	@Autowired
-	@Qualifier("myCodeSystemDaoR4")
 	private IFhirResourceDao<CodeSystem> myCodeSystemDao;
 
 	@Autowired
 	private FhirContext myR4Ctx;
+	private ApplicationContext myApplicationContext;
 
+	/**
+	 * Constructor
+	 */
 	public JpaValidationSupportR4() {
 		super();
 	}
@@ -163,6 +159,19 @@ public class JpaValidationSupportR4 implements IJpaValidationSupportR4 {
 		return false;
 	}
 
+	@Override
+	public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
+		myApplicationContext = theApplicationContext;
+	}
+
+	@PostConstruct
+	public void start() {
+		myStructureDefinitionDao = myApplicationContext.getBean("myStructureDefinitionDaoR4", IFhirResourceDao.class);
+		myValueSetDao = myApplicationContext.getBean("myValueSetDaoR4", IFhirResourceDao.class);
+		myQuestionnaireDao = myApplicationContext.getBean("myQuestionnaireDaoR4", IFhirResourceDao.class);
+		myCodeSystemDao = myApplicationContext.getBean("myCodeSystemDaoR4", IFhirResourceDao.class);
+	}
+
 	@Override
 	@Transactional(value = TxType.SUPPORTS)
 	public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java

@@ -77,7 +77,7 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 	}
 
 	@Override
-	@Transactional(propagation = Propagation.NOT_SUPPORTED)
+	@Transactional(propagation = Propagation.NEVER)
 	public void pollForStaleSearchesAndDeleteThem() {
 		if (!myDaoConfig.isExpireSearchResults()) {
 			return;
@@ -127,7 +127,7 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 	}
 
 	@Scheduled(fixedDelay = DEFAULT_CUTOFF_SLACK)
-	@Transactional(propagation = Propagation.NOT_SUPPORTED)
+	@Transactional(propagation = Propagation.NEVER)
 	@Override
 	public synchronized void schedulePollForStaleSearches() {
 		if (!myDaoConfig.isSchedulingDisabled()) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionDeliverySubscriber.java

@@ -67,7 +67,7 @@ public abstract class BaseSubscriptionDeliverySubscriber extends BaseSubscriptio
 				// can have placeholder IDs in them.
 				IIdType payloadId = msg.getPayloadId(getContext());
 				Class type = getContext().getResourceDefinition(payloadId.getResourceType()).getImplementingClass();
-				IFhirResourceDao dao = getSubscriptionDao().getDao(type);
+				IFhirResourceDao dao = getSubscriptionInterceptor().getDao(type);
 				IBaseResource loadedPayload;
 				try {
 					loadedPayload = dao.read(payloadId);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionInterceptor.java

@@ -28,7 +28,6 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
 import ca.uhn.fhir.jpa.util.JpaConstants;
-import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -37,6 +36,7 @@ import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.interceptor.ServerOperationInterceptorAdapter;
+import ca.uhn.fhir.util.StopWatch;
 import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.concurrent.BasicThreadFactory;
@@ -99,6 +99,7 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
 	@Autowired
 	@Qualifier(BaseConfig.TASK_EXECUTOR_NAME)
 	private AsyncTaskExecutor myAsyncTaskExecutor;
+	private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> myResourceTypeToDao;
 
 	/**
 	 * Constructor
@@ -243,6 +244,26 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
 
 	public abstract Subscription.SubscriptionChannelType getChannelType();
 
+	@SuppressWarnings("unchecked")
+	public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
+		if (myResourceTypeToDao == null) {
+			Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> theResourceTypeToDao = new HashMap<>();
+			for (IFhirResourceDao<?> next : myResourceDaos) {
+				theResourceTypeToDao.put(next.getResourceType(), next);
+			}
+
+			if (this instanceof IFhirResourceDao<?>) {
+				IFhirResourceDao<?> thiz = (IFhirResourceDao<?>) this;
+				theResourceTypeToDao.put(thiz.getResourceType(), thiz);
+			}
+
+			myResourceTypeToDao = theResourceTypeToDao;
+		}
+
+		IFhirResourceDao<R> dao = (IFhirResourceDao<R>) myResourceTypeToDao.get(theType);
+		return dao;
+	}
+
 	public SubscribableChannel getDeliveryChannel() {
 		return myDeliveryChannel;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionCheckingSubscriber.java

@@ -140,7 +140,7 @@ public class SubscriptionCheckingSubscriber extends BaseSubscriptionSubscriber {
 		RequestDetails req = new ServletSubRequestDetails();
 		req.setSubRequest(true);
 
-		IFhirResourceDao<? extends IBaseResource> responseDao = getSubscriptionDao().getDao(responseResourceDef.getImplementingClass());
+		IFhirResourceDao<? extends IBaseResource> responseDao = getSubscriptionInterceptor().getDao(responseResourceDef.getImplementingClass());
 		responseCriteriaUrl.setLoadSynchronousUpTo(1);
 
 		IBundleProvider responseResults = responseDao.search(responseCriteriaUrl, req);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/resthook/SubscriptionDeliveringRestHookSubscriber.java

@@ -123,7 +123,7 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDe
 		IBaseResource payloadResource = theMsg.getPayload(getContext());
 
 		if (theSubscription.getRestHookDetails().isDeliverLatestVersion()) {
-			IFhirResourceDao dao = getSubscriptionDao().getDao(payloadResource.getClass());
+			IFhirResourceDao dao = getSubscriptionInterceptor().getDao(payloadResource.getClass());
 			try {
 				payloadResource = dao.read(payloadResource.getIdElement().toVersionless());
 			} catch (ResourceGoneException e) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java

@@ -31,7 +31,6 @@ import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 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.util.ObjectUtil;
 import ca.uhn.fhir.util.StopWatch;
@@ -56,7 +55,10 @@ import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ValueSet;
+import org.springframework.beans.BeansException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.scheduling.annotation.Scheduled;
@@ -80,7 +82,7 @@ import java.util.stream.Collectors;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
-public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc {
+public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc, ApplicationContextAware {
 	public static final int DEFAULT_FETCH_SIZE = 250;
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiTerminologySvcImpl.class);
@@ -123,14 +125,11 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	private boolean myProcessDeferred = true;
 	@Autowired
 	private PlatformTransactionManager myTransactionMgr;
-	@Autowired(required = false)
 	private IFhirResourceDaoCodeSystem<?, ?, ?> myCodeSystemResourceDao;
-
 	private Cache<TranslationQuery, List<TermConceptMapGroupElementTarget>> myTranslationCache;
 	private Cache<TranslationQuery, List<TermConceptMapGroupElement>> myTranslationWithReverseCache;
-
-
 	private int myFetchSize = DEFAULT_FETCH_SIZE;
+	private ApplicationContext myApplicationContext;
 
 	private void addCodeIfNotAlreadyAdded(String theCodeSystem, ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, TermConcept theConcept) {
 		if (theAddedCodes.add(theConcept.getCode())) {
@@ -207,6 +206,32 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 				.build();
 	}
 
+	/**
+	 * This method is present only for unit tests, do not call from client code
+	 */
+	@VisibleForTesting
+	public void clearDeferred() {
+		myDeferredValueSets.clear();
+		myDeferredConceptMaps.clear();
+		myDeferredConcepts.clear();
+	}
+
+	/**
+	 * This method is present only for unit tests, do not call from client code
+	 */
+	@VisibleForTesting
+	public void clearTranslationCache() {
+		myTranslationCache.invalidateAll();
+	}
+
+	/**
+	 * This method is present only for unit tests, do not call from client code
+	 */
+	@VisibleForTesting()
+	public void clearTranslationWithReverseCache() {
+		myTranslationWithReverseCache.invalidateAll();
+	}
+
 	protected abstract IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource);
 
 	protected abstract void createOrUpdateConceptMap(ConceptMap theNextConceptMap);
@@ -788,11 +813,21 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 
 	}
 
+	@Override
+	public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
+		myApplicationContext = theApplicationContext;
+	}
+
 	@Override
 	public void setProcessDeferred(boolean theProcessDeferred) {
 		myProcessDeferred = theProcessDeferred;
 	}
 
+	@PostConstruct
+	public void start() {
+		myCodeSystemResourceDao = myApplicationContext.getBean(IFhirResourceDaoCodeSystem.class);
+	}
+
 	@Override
 	@Transactional(propagation = Propagation.REQUIRED)
 	public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, TermCodeSystemVersion theCodeSystemVersion) {
@@ -1258,32 +1293,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 		ourLastResultsFromTranslationWithReverseCache = false;
 	}
 
-	/**
-	 * This method is present only for unit tests, do not call from client code
-	 */
-	@VisibleForTesting
-	public void clearTranslationCache() {
-		myTranslationCache.invalidateAll();
-	}
-
-	/**
-	 * This method is present only for unit tests, do not call from client code
-	 */
-	@VisibleForTesting
-	public void clearDeferred() {
-		myDeferredValueSets.clear();
-		myDeferredConceptMaps.clear();
-		myDeferredConcepts.clear();
-	}
-
-	/**
-	 * This method is present only for unit tests, do not call from client code
-	 */
-	@VisibleForTesting()
-	public void clearTranslationWithReverseCache() {
-		myTranslationWithReverseCache.invalidateAll();
-	}
-
 	/**
 	 * This method is present only for unit tests, do not call from client code
 	 */

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/ConnectionWrapper.java

@@ -252,6 +252,7 @@ public class ConnectionWrapper implements Connection {
 
 	@Override
 	public void setReadOnly(boolean theReadOnly) throws SQLException {
+		ourLog.info("Setting connection as readonly");
 		myWrap.setReadOnly(theReadOnly);
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java

@@ -4,8 +4,11 @@ import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
+import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder;
+import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
-import org.hibernate.jpa.HibernatePersistenceProvider;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Lazy;
@@ -15,11 +18,35 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
+import java.sql.Connection;
+import java.sql.SQLException;
 import java.util.Properties;
+import java.util.concurrent.TimeUnit;
+
+import static org.junit.Assert.*;
 
 @Configuration
 @EnableTransactionManagement()
 public class TestDstu2Config extends BaseJavaConfigDstu2 {
+	private static final Logger ourLog = LoggerFactory.getLogger(TestDstu2Config.class);
+	private static int ourMaxThreads;
+
+	static {
+		/*
+		 * We use a randomized number of maximum threads in order to try
+		 * and catch any potential deadlocks caused by database connection
+		 * starvation
+		 */
+		ourMaxThreads = (int) (Math.random() * 6.0) + 1;
+	}
+
+	private Exception myLastStackTrace;
+	private String myLastStackTraceThreadName;
+
+	@Bean(name="maxDatabaseThreadsForTest")
+	public Integer getMaxThread(){
+		return ourMaxThreads;
+	}
 
 	@Bean()
 	public DaoConfig daoConfig() {
@@ -28,21 +55,73 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 
 	@Bean()
 	public DataSource dataSource() {
-		BasicDataSource retVal = new BasicDataSource();
+		BasicDataSource retVal = new BasicDataSource() {
+
+
+			@Override
+			public Connection getConnection() throws SQLException {
+				ConnectionWrapper retVal;
+				try {
+					retVal = new ConnectionWrapper(super.getConnection());
+				} catch (Exception e) {
+					ourLog.error("Exceeded maximum wait for connection", e);
+					logGetConnectionStackTrace();
+
+//					if ("true".equals(System.getStringProperty("ci"))) {
+					fail("Exceeded maximum wait for connection: " + e.toString());
+//					}
+//					System.exit(1);
+					retVal = null;
+				}
+
+				try {
+					throw new Exception();
+				} catch (Exception e) {
+					myLastStackTrace = e;
+					myLastStackTraceThreadName = Thread.currentThread().getName();
+				}
+
+				return retVal;
+			}
+
+			private void logGetConnectionStackTrace() {
+				StringBuilder b = new StringBuilder();
+				b.append("Last connection request stack trace:");
+				for (StackTraceElement next : myLastStackTrace.getStackTrace()) {
+					b.append("\n   ");
+					b.append(next.getClassName());
+					b.append(".");
+					b.append(next.getMethodName());
+					b.append("(");
+					b.append(next.getFileName());
+					b.append(":");
+					b.append(next.getLineNumber());
+					b.append(")");
+				}
+				ourLog.info(b.toString());
+				ourLog.info("Last connection thread: {}", myLastStackTraceThreadName);
+			}
+
+		};
 		retVal.setDriver(new org.apache.derby.jdbc.EmbeddedDriver());
 		retVal.setUrl("jdbc:derby:memory:myUnitTestDBDstu2;create=true");
+		retVal.setMaxWaitMillis(10000);
 		retVal.setUsername("");
 		retVal.setPassword("");
-		return retVal;
+
-	}
+		retVal.setMaxTotal(ourMaxThreads);
-
+
-	@Bean()
+		DataSource dataSource = ProxyDataSourceBuilder
-	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+			.create(retVal)
-		JpaTransactionManager retVal = new JpaTransactionManager();
+//			.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
-		retVal.setEntityManagerFactory(entityManagerFactory);
+			.logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
-		return retVal;
+			.countQuery(new ThreadQueryCountHolder())
+			.build();
+
+		return dataSource;
 	}
 
+	@Override
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
 		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
@@ -60,7 +139,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		extraProperties.put("hibernate.dialect", "ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect");
 		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "ram");
-		extraProperties.put("hibernate.search.lucene_version","LUCENE_CURRENT");
+		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
 		return extraProperties;
 	}
 
@@ -79,4 +158,11 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		return requestValidator;
 	}
 
+	@Bean()
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+		JpaTransactionManager retVal = new JpaTransactionManager();
+		retVal.setEntityManagerFactory(entityManagerFactory);
+		return retVal;
+	}
+
 }

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

@@ -20,6 +20,10 @@ import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
+import org.hibernate.HibernateException;
+import org.hibernate.Session;
+import org.hibernate.SessionFactory;
+import org.hibernate.jdbc.Work;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
@@ -30,6 +34,8 @@ import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Rule;
 import org.mockito.Mockito;
+import org.springframework.orm.hibernate5.HibernateTransactionManager;
+import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.TransactionStatus;
@@ -38,8 +44,11 @@ import org.springframework.transaction.support.TransactionTemplate;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.sql.Connection;
+import java.sql.SQLException;
 import java.util.*;
 import java.util.concurrent.Callable;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 import static ca.uhn.fhir.util.TestUtil.randomizeLocale;
 import static org.junit.Assert.*;
@@ -64,7 +73,7 @@ public abstract class BaseJpaTest {
 	protected IRequestOperationCallback myRequestOperationCallback = mock(IRequestOperationCallback.class);
 
 	@After
-	public final void afterPerformCleanup() {
+	public void afterPerformCleanup() {
 		BaseHapiFhirResourceDao.setDisableIncrementOnUpdateForUnitTest(false);
 	}
 
@@ -78,6 +87,32 @@ public abstract class BaseJpaTest {
 		when(mySrd.getHeaders(eq(JpaConstants.HEADER_META_SNAPSHOT_MODE))).thenReturn(new ArrayList<>());
 	}
 
+	@After
+	public void afterValidateNoTransaction() {
+		PlatformTransactionManager txManager = getTxManager();
+		if (txManager != null) {
+			JpaTransactionManager hibernateTxManager = (JpaTransactionManager) txManager;
+			SessionFactory sessionFactory = (SessionFactory) hibernateTxManager.getEntityManagerFactory();
+			AtomicBoolean isReadOnly = new AtomicBoolean();
+			Session currentSession;
+			try {
+				currentSession = sessionFactory.getCurrentSession();
+			} catch (HibernateException e) {
+				currentSession = null;
+			}
+			if (currentSession != null) {
+				currentSession.doWork(new Work() {
+
+					public void execute(Connection connection) throws SQLException {
+						isReadOnly.set(connection.isReadOnly());
+					}
+				});
+
+				assertFalse(isReadOnly.get());
+			}
+		}
+	}
+
 	@Before
 	public void beforeRandomizeLocale() {
 		randomizeLocale();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirDaoConcurrencyDstu3Test.java

@@ -1,10 +1,9 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.TestUtil;
-import com.phloc.commons.compare.ReverseComparator;
+import org.apache.commons.collections4.comparators.ReverseComparator;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Bundle.BundleType;

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

@@ -44,11 +44,7 @@ import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.util.AopTestUtils;
 import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.TransactionDefinition;
-import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Transactional;
-import org.springframework.transaction.support.TransactionCallbackWithoutResult;
-import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.persistence.EntityManager;
 import java.io.IOException;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/BaseResourceProviderDstu2Test.java

@@ -49,6 +49,7 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
 	protected static SubscriptionRestHookInterceptor ourRestHookSubscriptionInterceptor;
 	protected static DatabaseBackedPagingProvider ourPagingProvider;
 	protected static PlatformTransactionManager ourTxManager;
+	protected static Integer ourConnectionPoolSize;
 
 	public BaseResourceProviderDstu2Test() {
 		super();
@@ -84,6 +85,7 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
 			ourRestServer.setServerConformanceProvider(confProvider);
 
 			ourPagingProvider = myAppCtx.getBean(DatabaseBackedPagingProvider.class);
+			ourConnectionPoolSize = myAppCtx.getBean("maxDatabaseThreadsForTest", Integer.class);
 			ourRestServer.setPagingProvider(ourPagingProvider);
 
 			Server server = new Server(ourPort);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -1,41 +1,58 @@
 package ca.uhn.fhir.jpa.provider;
 
-import static org.hamcrest.Matchers.*;
-import static org.junit.Assert.*;
-
-import java.io.*;
-import java.net.*;
-import java.nio.charset.StandardCharsets;
-import java.util.*;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.http.client.ClientProtocolException;
-import org.apache.http.client.methods.*;
-import org.apache.http.entity.*;
-import org.hl7.fhir.instance.model.api.IBaseBundle;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.*;
-import org.junit.Test;
-import org.springframework.test.util.AopTestUtils;
-
-import com.google.common.base.Charsets;
-
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
-import ca.uhn.fhir.model.api.*;
+import ca.uhn.fhir.model.api.ExtensionDt;
-import ca.uhn.fhir.model.dstu2.composite.*;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
+import ca.uhn.fhir.model.dstu2.composite.CodingDt;
+import ca.uhn.fhir.model.dstu2.composite.MetaDt;
+import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
+import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu2.resource.*;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.model.dstu2.valueset.*;
 import ca.uhn.fhir.model.primitive.*;
 import ca.uhn.fhir.parser.IParser;
-import ca.uhn.fhir.rest.api.*;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.SummaryEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.param.*;
-import ca.uhn.fhir.rest.server.exceptions.*;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.util.*;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.util.UrlUtil;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.methods.*;
+import org.apache.http.entity.ByteArrayEntity;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.*;
+import org.springframework.test.util.AopTestUtils;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.InetSocketAddress;
+import java.net.Socket;
+import java.net.SocketTimeoutException;
+import java.nio.charset.StandardCharsets;
+import java.util.*;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
 
 public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 
@@ -208,7 +225,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 	 */
 	@Test
 	public void testCreateAndUpdateBinary() throws ClientProtocolException, Exception {
-		byte[] arr = { 1, 21, 74, 123, -44 };
+		byte[] arr = {1, 21, 74, 123, -44};
 		Binary binary = new Binary();
 		binary.setContent(arr);
 		binary.setContentType("dansk");
@@ -934,7 +951,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 		List<IIdType> actual;
 		StringAndListParam param;
 
-		ourLog.info("Pt1:{} Pt2:{} Obs1:{} Obs2:{} Obs3:{}", new Object[] { ptId1.getIdPart(), ptId2.getIdPart(), obsId1.getIdPart(), obsId2.getIdPart(), obsId3.getIdPart() });
+		ourLog.info("Pt1:{} Pt2:{} Obs1:{} Obs2:{} Obs3:{}", new Object[] {ptId1.getIdPart(), ptId2.getIdPart(), obsId1.getIdPart(), obsId2.getIdPart(), obsId3.getIdPart()});
 
 		param = new StringAndListParam();
 		param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
@@ -1471,6 +1488,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 		}
 	}
 
+
 	@Test
 	public void testPagingOverEverythingSet() throws InterruptedException {
 		Patient p = new Patient();
@@ -1488,6 +1506,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 		mySearchCoordinatorSvcRaw.setSyncSizeForUnitTests(10);
 		mySearchCoordinatorSvcRaw.setNeverUseLocalSearchForUnitTests(true);
 
+		StopWatch sw = new StopWatch();
 		ca.uhn.fhir.model.dstu2.resource.Bundle response = ourClient
 			.operation()
 			.onInstance(new IdDt(pid))
@@ -1498,7 +1517,9 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 			.execute();
 
 		assertEquals(10, response.getEntry().size());
-		assertEquals(null, response.getTotalElement().getValueAsString());
+		if (ourConnectionPoolSize > 1) {
+			assertEquals("Total should be null but was " + response.getTotalElement().getValueAsString() + " in " + sw.toString(), null, response.getTotalElement().getValueAsString());
+		}
 		assertThat(response.getLink("next").getUrl(), not(emptyString()));
 
 		// Load page 2
@@ -1993,7 +2014,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 		Bundle found = ourClient
 			.search()
 			.forResource(Patient.class)
-				.where(Patient.IDENTIFIER.exactly().systemAndIdentifier("urn:system:rpdstu2","testSearchWithInclude02"))
+			.where(Patient.IDENTIFIER.exactly().systemAndIdentifier("urn:system:rpdstu2", "testSearchWithInclude02"))
 			.include(Patient.INCLUDE_ORGANIZATION)
 			.prettyPrint()
 			.returnBundle(Bundle.class)
@@ -2295,7 +2316,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 		CloseableHttpResponse resp = ourHttpClient.execute(post);
 		try {
 			assertEquals(200, resp.getStatusLine().getStatusCode());
-			String output= IOUtils.toString(resp.getEntity().getContent());
+			String output = IOUtils.toString(resp.getEntity().getContent());
 			ourLog.info(output);
 		} finally {
 			resp.close();
@@ -2387,7 +2408,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 			response.close();
 		}
 
-		pt.addName().addFamily(methodName+"2");
+		pt.addName().addFamily(methodName + "2");
 		resource = myFhirCtx.newXmlParser().encodeResourceToString(pt);
 		HttpPut put = new HttpPut(ourServerBase + "/Patient?name=" + methodName);
 		put.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java

@@ -11,14 +11,12 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
 import org.hl7.fhir.r4.model.UriType;
-import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.test.util.AopTestUtils;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
@@ -102,7 +100,6 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 			.addTarget()
 			.setCode("34567");
 
-		runInTransaction(() -> {
 		try {
 			runInTransaction(() -> {
 				myConceptMapDao.create(conceptMap);
@@ -111,7 +108,6 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		} catch (UnprocessableEntityException e) {
 			assertEquals("ConceptMap has no value for ConceptMap.url", e.getMessage());
 		}
-		});
 
 	}
 

hapi-fhir-jpaserver-example/pom.xml

@@ -187,8 +187,8 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>

hapi-fhir-jpaserver-examples/hapi-fhir-jpaserver-example-postgres/pom.xml

@@ -138,8 +138,8 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -55,8 +55,8 @@
 		</dependency>
 
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>
@@ -65,8 +65,8 @@
 			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 		</dependency>
 
 		<dependency>

hapi-fhir-osgi-core/pom.xml

@@ -72,8 +72,8 @@
 			<artifactId>thymeleaf</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>
@@ -82,8 +82,8 @@
 			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 		</dependency>
 
 		<dependency>
@@ -197,8 +197,8 @@
 							com.ctc.wstx.api;version="4.4";resolution:=optional,
 							com.ctc.wstx.*;version="4.4";resolution:=optional,
 							com.google.*;resolution:=optional;-remove-attribute:=version,
-							com.phloc.commons;resolution:=optional;-remove-attribute:=version,
+							com.helger.commons;resolution:=optional;-remove-attribute:=version,
-							com.phloc.*;resolution:=optional;-remove-attribute:=version,
+							com.helger.*;resolution:=optional;-remove-attribute:=version,
 							javassist;-remove-attribute:=version,
 							javax.*;-remove-attribute:=version,
 							net.sf.saxon;resolution:=optional,

hapi-fhir-structures-dstu/pom.xml

@@ -68,13 +68,13 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 			<scope>test</scope>
 		</dependency>
 

hapi-fhir-structures-dstu2.1/pom.xml

@@ -130,22 +130,6 @@
 			<artifactId>thymeleaf</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>com.phloc</groupId>
-			<artifactId>phloc-schematron</artifactId>
-			<scope>test</scope>
-			<exclusions><!--
-				<exclusion>
-					<artifactId>Saxon-HE</artifactId>
-					<groupId>net.sf.saxon</groupId>
-				</exclusion>-->
-			</exclusions>
-		</dependency>
-		<dependency>
-			<groupId>com.phloc</groupId>
-			<artifactId>phloc-commons</artifactId>
-			<scope>test</scope>
-		</dependency>
 
 
 		<!-- UNIT TEST DEPENDENCIES -->
@@ -208,6 +192,16 @@
 			<artifactId>spring-web</artifactId>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>com.helger</groupId>
+			<artifactId>ph-schematron</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>com.helger</groupId>
+			<artifactId>ph-commons</artifactId>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<reporting>

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu2_1Test.java

@@ -11,6 +11,7 @@ import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
 import java.util.*;
 
+import com.helger.commons.io.stream.StringInputStream;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.ReaderInputStream;
 import org.apache.http.*;
@@ -29,7 +30,6 @@ import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 
 import com.google.common.base.Charsets;
-import com.phloc.commons.io.streams.StringInputStream;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
@@ -83,7 +83,7 @@ public class GenericClientDstu2_1Test {
 		return body;
 	}
 
-	private ArgumentCaptor<HttpUriRequest> prepareClientForSearchResponse() throws IOException, ClientProtocolException {
+	private ArgumentCaptor<HttpUriRequest> prepareClientForSearchResponse() throws IOException {
 		final String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
 		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
@@ -92,7 +92,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
 			}
 		});
@@ -111,7 +111,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -149,7 +149,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -187,7 +187,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -225,7 +225,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -264,7 +264,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -303,7 +303,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -330,7 +330,7 @@ public class GenericClientDstu2_1Test {
 	}
 
 	@Test
-	public void testPatchInvalid() throws Exception {
+	public void testPatchInvalid() {
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
 
 		try {
@@ -354,7 +354,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
 			}
 		});
@@ -398,7 +398,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -441,7 +441,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -505,7 +505,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -537,14 +537,14 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
 			@Override
-			public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+			public Header[] answer(InvocationOnMock theInvocation) {
 				return new Header[] { new BasicHeader(Constants.HEADER_LOCATION, "http://foo.com/base/Patient/222/_history/3") };
 			}
 		});
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				if (myAnswerCount++ == 0) {
 					return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp0)), Charset.forName("UTF-8"));
 				} else {
@@ -586,14 +586,14 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
 			@Override
-			public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+			public Header[] answer(InvocationOnMock theInvocation) {
 				return new Header[] { new BasicHeader(Constants.HEADER_LOCATION, "http://foo.com/base/Patient/222/_history/3") };
 			}
 		});
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				myAnswerCount++;
 				return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp1)), Charset.forName("UTF-8"));
 			}
@@ -625,7 +625,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -652,7 +652,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -697,7 +697,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -737,7 +737,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -773,7 +773,7 @@ public class GenericClientDstu2_1Test {
 			private int myCount = 0;
 
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				final String respString;
 				if (myCount == 1 || myCount == 2) {
 					ourLog.info("Encoding patient");
@@ -822,7 +822,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				final String respString;
 				if (myAnswerCount >= 1) {
 					ourLog.info("Encoding patient");
@@ -872,7 +872,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				final String respString;
 				if (myAnswerCount >= 1) {
 					ourLog.info("Encoding patient");
@@ -912,7 +912,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
 			@Override
-			public StringInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public StringInputStream answer(InvocationOnMock theInvocation) {
 				return new StringInputStream("HELLO", Charsets.UTF_8);
 			}
 		});
@@ -937,7 +937,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
 			@Override
-			public StringInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public StringInputStream answer(InvocationOnMock theInvocation) {
 				return new StringInputStream("not implemented", Charsets.UTF_8);
 			}
 		});
@@ -968,7 +968,7 @@ public class GenericClientDstu2_1Test {
 				.forResource(Patient.class)
 				.where(Patient.FAMILY.matches().value((String) null))
 				.and(Patient.BIRTHDATE.exactly().day((Date) null))
-				.and(Patient.GENDER.exactly().code((String) null))
+				.and(Patient.GENDER.exactly().code(null))
 				.and(Patient.ORGANIZATION.hasId((String) null))
 				.returnBundle(Bundle.class)
 				.execute();
@@ -1019,7 +1019,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(encoded), Charset.forName("UTF-8"));
 			}
 		});
@@ -1064,7 +1064,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(encoded), Charset.forName("UTF-8"));
 			}
 		});
@@ -1121,7 +1121,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(null);
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -1152,7 +1152,7 @@ public class GenericClientDstu2_1Test {
 		// when(myHttpResponse.getEntity().getContentType()).thenReturn(null);
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -1179,7 +1179,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
 			}
 		});
@@ -1286,7 +1286,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
 			}
 		});
@@ -1405,7 +1405,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
 			}
 		});
@@ -1497,7 +1497,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
 			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public InputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
 			}
 		});
@@ -1564,7 +1564,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -1601,7 +1601,7 @@ public class GenericClientDstu2_1Test {
 	}
 
 	@Test
-	public void testTransactionWithInvalidBody() throws Exception {
+	public void testTransactionWithInvalidBody() {
 		IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
 
 		// Transaction
@@ -1652,7 +1652,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -1691,14 +1691,14 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
 			@Override
-			public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+			public Header[] answer(InvocationOnMock theInvocation) {
 				return new Header[] { new BasicHeader(Constants.HEADER_LOCATION, "http://foo.com/base/Patient/222/_history/3") };
 			}
 		});
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				if (myAnswerCount++ == 0) {
 					return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp0)), Charset.forName("UTF-8"));
 				} else {
@@ -1739,14 +1739,14 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
 			@Override
-			public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+			public Header[] answer(InvocationOnMock theInvocation) {
 				return new Header[] { new BasicHeader(Constants.HEADER_LOCATION, "http://foo.com/base/Patient/222/_history/3") };
 			}
 		});
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				myAnswerCount++;
 				return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp1)), Charset.forName("UTF-8"));
 			}
@@ -1784,7 +1784,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -1821,7 +1821,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -1842,7 +1842,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -1870,14 +1870,14 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
 		when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
 			@Override
-			public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+			public Header[] answer(InvocationOnMock theInvocation) {
 				return new Header[] {};
 			}
 		});
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp0)), Charset.forName("UTF-8"));
 			}
 		});
@@ -1910,7 +1910,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -1948,7 +1948,7 @@ public class GenericClientDstu2_1Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});

hapi-fhir-structures-dstu2/pom.xml

@@ -103,13 +103,13 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<scope>test</scope><!-- <exclusions> <exclusion> <artifactId>Saxon-HE</artifactId> <groupId>net.sf.saxon</groupId> </exclusion> </exclusions> -->
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 			<scope>test</scope>
 		</dependency>
 

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/ResponseHighlightingInterceptorTest.java

@@ -28,7 +28,7 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.PortUtil;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
-import com.phloc.commons.collections.iterate.ArrayEnumeration;
+import com.helger.collection.iterate.ArrayEnumeration;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -130,7 +130,7 @@ public class ResponseHighlightingInterceptorTest {
 		when(req.getHeaders(Constants.HEADER_ACCEPT)).thenAnswer(new Answer<Enumeration<String>>() {
 			@Override
 			public Enumeration<String> answer(InvocationOnMock theInvocation) throws Throwable {
-				return new ArrayEnumeration<String>("text/html,application/xhtml+xml,application/xml;q=0.9");
+				return new ArrayEnumeration<>("text/html,application/xhtml+xml,application/xml;q=0.9");
 			}
 		});
 		when(req.getHeader(Constants.HEADER_ORIGIN)).thenAnswer(new Answer<String>() {

hapi-fhir-structures-dstu3/pom.xml

@@ -217,13 +217,13 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 			<scope>test</scope>
 		</dependency>
 

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu3Test.java

@@ -11,6 +11,7 @@ import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
 import java.util.*;
 
+import com.helger.commons.io.stream.StringInputStream;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.ReaderInputStream;
 import org.apache.http.*;
@@ -29,7 +30,6 @@ import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 
 import com.google.common.base.Charsets;
-import com.phloc.commons.io.streams.StringInputStream;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;

hapi-fhir-structures-hl7org-dstu2/pom.xml

@@ -122,8 +122,8 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<scope>test</scope>
 			<exclusions>
 				<exclusion>
@@ -133,8 +133,8 @@
 			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 			<scope>test</scope>
 		</dependency>
 

hapi-fhir-structures-r4/pom.xml

@@ -125,13 +125,13 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 			<scope>test</scope>
 		</dependency>
 
@@ -192,11 +192,6 @@
 			<artifactId>spring-web</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-context</artifactId>
-			<scope>test</scope>
-		</dependency>
 	</dependencies>
 
 	<reporting>

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/client/GenericClientR4Test.java

@@ -17,6 +17,7 @@ import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
 import java.util.*;
 
+import com.helger.commons.io.stream.StringInputStream;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.ReaderInputStream;
 import org.apache.http.*;
@@ -36,7 +37,6 @@ import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 
 import com.google.common.base.Charsets;
-import com.phloc.commons.io.streams.StringInputStream;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
@@ -93,7 +93,7 @@ public class GenericClientR4Test {
     return body;
   }
 
-  private ArgumentCaptor<HttpUriRequest> prepareClientForSearchResponse() throws IOException, ClientProtocolException {
+  private ArgumentCaptor<HttpUriRequest> prepareClientForSearchResponse() throws IOException {
     final String msg = "{\"resourceType\":\"Bundle\",\"id\":null,\"base\":\"http://localhost:57931/fhir/contextDev\",\"total\":1,\"link\":[{\"relation\":\"self\",\"url\":\"http://localhost:57931/fhir/contextDev/Patient?identifier=urn%3AMultiFhirVersionTest%7CtestSubmitPatient01&_format=json\"}],\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"id\":\"1\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2014-12-20T18:41:29.706-05:00\"},\"identifier\":[{\"system\":\"urn:MultiFhirVersionTest\",\"value\":\"testSubmitPatient01\"}]}}]}";
 
     ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
@@ -102,7 +102,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
       }
     });
@@ -143,7 +143,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
       }
     });
@@ -187,7 +187,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -234,7 +234,7 @@ public class GenericClientR4Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -278,7 +278,7 @@ public class GenericClientR4Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -322,7 +322,7 @@ public class GenericClientR4Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -366,7 +366,7 @@ public class GenericClientR4Test {
 		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
 		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 			@Override
-			public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+			public ReaderInputStream answer(InvocationOnMock theInvocation) {
 				return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
 			}
 		});
@@ -408,7 +408,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -472,7 +472,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -504,14 +504,14 @@ public class GenericClientR4Test {
     when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
     when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
       @Override
-      public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+      public Header[] answer(InvocationOnMock theInvocation) {
         return new Header[] { new BasicHeader(Constants.HEADER_LOCATION, "http://foo.com/base/Patient/222/_history/3") };
       }
     });
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         if (myAnswerCount++ == 0) {
           return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp0)), Charset.forName("UTF-8"));
         } else {
@@ -553,14 +553,14 @@ public class GenericClientR4Test {
     when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
     when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
       @Override
-      public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+      public Header[] answer(InvocationOnMock theInvocation) {
         return new Header[] { new BasicHeader(Constants.HEADER_LOCATION, "http://foo.com/base/Patient/222/_history/3") };
       }
     });
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         myAnswerCount++;
         return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp1)), Charset.forName("UTF-8"));
       }
@@ -592,7 +592,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -619,7 +619,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -664,7 +664,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -704,7 +704,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -740,7 +740,7 @@ public class GenericClientR4Test {
       private int myCount = 0;
 
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         final String respString;
         if (myCount == 1 || myCount == 2) {
           ourLog.info("Encoding patient");
@@ -788,7 +788,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
 
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         final String respString;
         if (myAnswerCount >= 1) {
           ourLog.info("Encoding patient");
@@ -828,7 +828,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
       @Override
-      public StringInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public StringInputStream answer(InvocationOnMock theInvocation) {
         return new StringInputStream("HELLO", Charsets.UTF_8);
       }
     });
@@ -853,7 +853,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
       @Override
-      public StringInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public StringInputStream answer(InvocationOnMock theInvocation) {
         return new StringInputStream("not implemented", Charsets.UTF_8);
       }
     });
@@ -884,7 +884,7 @@ public class GenericClientR4Test {
         .forResource(Patient.class)
         .where(Patient.FAMILY.matches().value((String) null))
         .and(Patient.BIRTHDATE.exactly().day((Date) null))
-        .and(Patient.GENDER.exactly().code((String) null))
+        .and(Patient.GENDER.exactly().code(null))
         .and(Patient.ORGANIZATION.hasId((String) null))
         .returnBundle(Bundle.class)
         .execute();
@@ -915,7 +915,7 @@ public class GenericClientR4Test {
   }
 
   @Test
-  public void testPatchInvalid() throws Exception {
+  public void testPatchInvalid() {
     IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
 
     try {
@@ -941,7 +941,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -980,7 +980,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -1019,7 +1019,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -1057,7 +1057,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -1095,7 +1095,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -1133,7 +1133,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -1180,7 +1180,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON_NEW + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(encoded), Charset.forName("UTF-8"));
       }
     });
@@ -1225,7 +1225,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(encoded), Charset.forName("UTF-8"));
       }
     });
@@ -1282,7 +1282,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(null);
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -1313,7 +1313,7 @@ public class GenericClientR4Test {
     // when(myHttpResponse.getEntity().getContentType()).thenReturn(null);
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -1331,7 +1331,7 @@ public class GenericClientR4Test {
   }
 
   @Test
-  public void testRevIncludeRecursive() throws ClientProtocolException, IOException {
+  public void testRevIncludeRecursive() throws IOException {
     ArgumentCaptor<HttpUriRequest> capt = prepareClientForSearchResponse();
 
     IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
@@ -1361,7 +1361,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
       }
     });
@@ -1468,7 +1468,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
       }
     });
@@ -1578,7 +1578,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
       }
     });
@@ -1670,7 +1670,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
       }
     });
@@ -1756,7 +1756,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).then(new Answer<InputStream>() {
       @Override
-      public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public InputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(msg), Charset.forName("UTF-8"));
       }
     });
@@ -1793,7 +1793,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -1830,7 +1830,7 @@ public class GenericClientR4Test {
   }
 
   @Test
-  public void testTransactionWithInvalidBody() throws Exception {
+  public void testTransactionWithInvalidBody() {
     IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
 
     // Transaction
@@ -1881,7 +1881,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -1920,14 +1920,14 @@ public class GenericClientR4Test {
     when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
     when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
       @Override
-      public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+      public Header[] answer(InvocationOnMock theInvocation) {
         return new Header[] { new BasicHeader(Constants.HEADER_LOCATION, "http://foo.com/base/Patient/222/_history/3") };
       }
     });
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         if (myAnswerCount++ == 0) {
           return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp0)), Charset.forName("UTF-8"));
         } else {
@@ -1968,14 +1968,14 @@ public class GenericClientR4Test {
     when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
     when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
       @Override
-      public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+      public Header[] answer(InvocationOnMock theInvocation) {
         return new Header[] { new BasicHeader(Constants.HEADER_LOCATION, "http://foo.com/base/Patient/222/_history/3") };
       }
     });
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         myAnswerCount++;
         return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp1)), Charset.forName("UTF-8"));
       }
@@ -2013,7 +2013,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -2050,7 +2050,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -2071,7 +2071,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -2099,14 +2099,14 @@ public class GenericClientR4Test {
     when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
     when(myHttpResponse.getAllHeaders()).thenAnswer(new Answer<Header[]>() {
       @Override
-      public Header[] answer(InvocationOnMock theInvocation) throws Throwable {
+      public Header[] answer(InvocationOnMock theInvocation) {
         return new Header[] {};
       }
     });
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(p.encodeResourceToString(resp0)), Charset.forName("UTF-8"));
       }
     });
@@ -2139,7 +2139,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });
@@ -2177,7 +2177,7 @@ public class GenericClientR4Test {
     when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
     when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
       @Override
-      public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
+      public ReaderInputStream answer(InvocationOnMock theInvocation) {
         return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
       }
     });

hapi-fhir-tutorial/skeleton-project/pom.xml

@@ -65,8 +65,8 @@
 		Schematron resource validation. Otherwise, they may be omitted. 
 		-->
 		<dependency>
-		    <groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-		    <artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<exclusions>
 				<exclusion>
 					<artifactId>Saxon-HE</artifactId>
@@ -75,8 +75,8 @@
 			</exclusions>
 		</dependency>
 		<dependency>
-		    <groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-		    <artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 		    <version>4.3.3</version>
 		</dependency>
 

hapi-fhir-validation/pom.xml

@@ -173,13 +173,13 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-schematron</artifactId>
+			<artifactId>ph-schematron</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>com.phloc</groupId>
+			<groupId>com.helger</groupId>
-			<artifactId>phloc-commons</artifactId>
+			<artifactId>ph-commons</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>

osgi/hapi-fhir-karaf-features/src/main/resources/features.xml

@@ -89,9 +89,14 @@
 		<bundle dependency='true'>
 			mvn:org.apache.servicemix.bundles/org.apache.servicemix.bundles.xmlresolver/${servicemix_xmlresolver_version}
 		</bundle>
+		<bundle dependency="true">mvn:org.apache.aries.spifly/org.apache.aries.spifly.dynamic.bundle/${aries_spifly_version}</bundle>
 		<bundle dependency='true'>mvn:com.google.code.findbugs/jsr305/${jsr305_version}</bundle>
-		<bundle>mvn:com.phloc/phloc-schematron/${phloc_schematron_version}</bundle>
+		<bundle dependency='true'>mvn:com.helger/ph-commons/${ph_commons_version}</bundle>
-		<bundle>mvn:com.phloc/phloc-commons/${phloc_commons_version}</bundle>
+		<bundle dependency='true'>mvn:com.helger/ph-collection/${ph_commons_version}</bundle>
+		<bundle dependency='true'>mvn:com.helger/ph-xml/${ph_commons_version}</bundle>
+		<bundle dependency='true'>mvn:org.apache.servicemix.bundles/org.apache.servicemix.bundles.jaxb-impl/${jaxb_bundle_version}</bundle>
+		<bundle dependency='true'>mvn:com.helger/ph-jaxb/${ph_commons_version}</bundle>
+		<bundle dependency='true'>mvn:com.helger/ph-schematron/${ph_schematron_version}</bundle>
 	</feature>
 
 	<feature name='hapi-fhir-validation' version='${project.version}' start-level='50'>

osgi/hapi-fhir-karaf-integration-tests/pom.xml

@@ -14,7 +14,7 @@
   See the License for the specific language governing permissions and
   limitations under the License.
 -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
    <modelVersion>4.0.0</modelVersion>
 
 	<parent>
@@ -98,6 +98,7 @@
 			<version>${project.version}</version>
 		</dependency>
 
+
       <!-- karaf test -->
       <dependency>
          <groupId>org.ops4j.pax.exam</groupId>
@@ -122,6 +123,12 @@
          <version>${apache_karaf_version}</version>
          <scope>test</scope>
          <type>tar.gz</type>
+			<exclusions>
+				<exclusion>
+					<groupId>org.ops4j.pax.logging</groupId>
+					<artifactId>pax-logging-api</artifactId>
+				</exclusion>
+			</exclusions>
       </dependency>
       <dependency>
          <groupId>org.apache.karaf.shell</groupId>

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/ValidationConstants.java

@@ -0,0 +1,7 @@
+package ca.uhn.fhir.tests.integration.karaf;
+
+public class ValidationConstants {
+
+	public static final boolean SCHEMATRON_ENABLED = true;
+
+}

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu2/Dstu2ResourceValidatorDstu2Test.java

@@ -26,6 +26,7 @@ import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.parser.StrictErrorHandler;
+import ca.uhn.fhir.tests.integration.karaf.ValidationConstants;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.SchemaBaseValidator;
 import ca.uhn.fhir.validation.ValidationFailureException;
@@ -85,7 +86,7 @@ public class Dstu2ResourceValidatorDstu2Test {
 	private FhirValidator createFhirValidator() {
 		FhirValidator val = ourCtx.newValidator();
 		val.setValidateAgainstStandardSchema(true);
-		val.setValidateAgainstStandardSchematron(true);
+		val.setValidateAgainstStandardSchematron(ValidationConstants.SCHEMATRON_ENABLED);
 		return val;
 	}
 
@@ -156,7 +157,9 @@ public class Dstu2ResourceValidatorDstu2Test {
 
 		FhirValidator val = ourCtx.newValidator();
 		val.setValidateAgainstStandardSchema(true);
-		val.setValidateAgainstStandardSchematron(false);
+		if (ValidationConstants.SCHEMATRON_ENABLED) {
+			val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		}
 
 		val.validate(p);
 
@@ -246,7 +249,9 @@ public class Dstu2ResourceValidatorDstu2Test {
 
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		if (ValidationConstants.SCHEMATRON_ENABLED) {
 			val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		}
 
 		ValidationResult result = val.validateWithResult(messageString);
 
@@ -299,7 +304,9 @@ public class Dstu2ResourceValidatorDstu2Test {
 
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		if (ValidationConstants.SCHEMATRON_ENABLED) {
 			val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		}
 
 		ValidationResult result = val.validateWithResult(messageString);
 

osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/ResourceValidatorDstu3FeatureTest.java

@@ -6,19 +6,12 @@ import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.parser.StrictErrorHandler;
+import ca.uhn.fhir.tests.integration.karaf.ValidationConstants;
 import ca.uhn.fhir.validation.*;
 import ca.uhn.fhir.validation.schematron.SchematronBaseValidator;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.Validate;
 import org.hamcrest.core.StringContains;
-import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
-import org.hl7.fhir.dstu3.context.IWorkerContext;
-import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
-import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
 import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
 import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.ops4j.pax.exam.Configuration;
@@ -33,14 +26,10 @@ import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
 
-import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.HAPI_FHIR_VALIDATION_DSTU3;
+import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.*;
-import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.KARAF;
-import static ca.uhn.fhir.tests.integration.karaf.PaxExamOptions.WRAP;
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
-import static org.ops4j.pax.exam.CoreOptions.mavenBundle;
+import static org.ops4j.pax.exam.CoreOptions.*;
-import static org.ops4j.pax.exam.CoreOptions.options;
-import static org.ops4j.pax.exam.CoreOptions.when;
 import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.debugConfiguration;
 
 /**
@@ -145,7 +134,9 @@ public class ResourceValidatorDstu3FeatureTest {
 
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		if (ValidationConstants.SCHEMATRON_ENABLED) {
 			val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		}
 		val.registerValidatorModule(new FhirInstanceValidator());
 
 		ValidationResult output = val.validateWithResult(p);
@@ -162,7 +153,9 @@ public class ResourceValidatorDstu3FeatureTest {
 
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		if (ValidationConstants.SCHEMATRON_ENABLED) {
 			val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		}
 		val.registerValidatorModule(new FhirInstanceValidator());
 
 		ValidationResult output = val.validateWithResult(p);
@@ -232,7 +225,9 @@ public class ResourceValidatorDstu3FeatureTest {
 
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		if (ValidationConstants.SCHEMATRON_ENABLED) {
 			val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		}
 		val.registerValidatorModule(new FhirInstanceValidator());
 
 		ValidationResult result = val.validateWithResult(q);
@@ -273,7 +268,9 @@ public class ResourceValidatorDstu3FeatureTest {
 
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		if (ValidationConstants.SCHEMATRON_ENABLED) {
 			val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		}
 		val.registerValidatorModule(new FhirInstanceValidator());
 
 		ValidationResult result = val.validateWithResult(encoded);
@@ -321,7 +318,9 @@ public class ResourceValidatorDstu3FeatureTest {
 
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		if (ValidationConstants.SCHEMATRON_ENABLED) {
 			val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		}
 		val.registerValidatorModule(new FhirInstanceValidator());
 
 		ValidationResult result = val.validateWithResult(messageString);
@@ -374,7 +373,9 @@ public class ResourceValidatorDstu3FeatureTest {
 
 		FhirValidator val = ourCtx.newValidator();
 		val.registerValidatorModule(new SchemaBaseValidator(ourCtx));
+		if (ValidationConstants.SCHEMATRON_ENABLED) {
 			val.registerValidatorModule(new SchematronBaseValidator(ourCtx));
+		}
 		val.registerValidatorModule(new FhirInstanceValidator());
 
 		ValidationResult result = val.validateWithResult(messageString);

pom.xml

@@ -51,7 +51,20 @@
 		<repository>
 			<id>jitpack.io</id>
 			<url>https://jitpack.io</url>
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
 		</repository>
+		<!--
+		Snapshots should generally not be needed
+		<repository>
+			<id>oss-snapshot</id>
+			<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
+			<snapshots>
+				<enabled>true</enabled>
+			</snapshots>
+		</repository>
+		-->
 	</repositories>
 
 	<description>
@@ -444,16 +457,17 @@
 
 		<!-- Dependency Versions -->
 		<apache_karaf_version>4.1.4</apache_karaf_version>
+		<aries_spifly_version>1.0.10</aries_spifly_version>
 		<caffeine_version>2.6.2</caffeine_version>
 		<commons_codec_version>1.10</commons_codec_version>
 		<commons_io_version>2.5</commons_io_version>
 		<commons_lang3_version>3.6</commons_lang3_version>
-		<derby_version>10.14.1.0</derby_version>
+		<derby_version>10.14.2.0</derby_version>
 		<error_prone_annotations_version>2.0.18</error_prone_annotations_version>
 		<guava_version>23.0</guava_version>
 		<gson_version>2.8.1</gson_version>
 		<jaxb_api_version>2.3.0</jaxb_api_version>
-		<jaxb_core_version>2.3.0</jaxb_core_version>
+		<jaxb_runtime_version>2.3.0</jaxb_runtime_version>
 		<jersey_version>2.25.1</jersey_version>
 		<jetty_version>9.4.8.v20171121</jetty_version>
 		<jsr305_version>3.0.2</jsr305_version>
@@ -464,11 +478,12 @@
 		<hibernate_search_version>5.7.1.Final</hibernate_search_version>
 		<httpcore_version>4.4.6</httpcore_version>
 		<httpclient_version>4.5.3</httpclient_version>
+		<jaxb_bundle_version>2.2.11_1</jaxb_bundle_version>
 		<lucene_version>5.5.4</lucene_version>
 		<maven_assembly_plugin_version>2.5.3</maven_assembly_plugin_version>
 		<maven_license_plugin_version>1.8</maven_license_plugin_version>
-		<phloc_schematron_version>2.7.1</phloc_schematron_version>
+		<ph_schematron_version>5.0.4</ph_schematron_version>
-		<phloc_commons_version>4.4.11</phloc_commons_version>
+		<ph_commons_version>9.1.1</ph_commons_version>
 		<servicemix_saxon_version>9.5.1-5_1</servicemix_saxon_version>
 		<servicemix_xmlresolver_version>1.2_5</servicemix_xmlresolver_version>
 		<spring_version>5.0.3.RELEASE</spring_version>
@@ -572,14 +587,14 @@
 				<version>23.0</version>
 			</dependency>
 			<dependency>
-				<groupId>com.phloc</groupId>
+				<groupId>com.helger</groupId>
-				<artifactId>phloc-schematron</artifactId>
+				<artifactId>ph-schematron</artifactId>
-				<version>${phloc_schematron_version}</version>
+				<version>${ph_schematron_version}</version>
 			</dependency>
 			<dependency>
-				<groupId>com.phloc</groupId>
+				<groupId>com.helger</groupId>
-				<artifactId>phloc-commons</artifactId>
+				<artifactId>ph-commons</artifactId>
-				<version>${phloc_commons_version}</version>
+				<version>${ph_commons_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>com.squareup.okhttp3</groupId>
@@ -601,6 +616,11 @@
 				<artifactId>commons-codec</artifactId>
 				<version>${commons_codec_version}</version>
 			</dependency>
+			<dependency>
+				<groupId>org.apache.commons</groupId>
+				<artifactId>commons-collections4</artifactId>
+				<version>4.1</version>
+			</dependency>
 			<dependency>
 				<groupId>org.apache.commons</groupId>
 				<artifactId>commons-compress</artifactId>
@@ -658,16 +678,6 @@
 				<artifactId>gson</artifactId>
 				<version>${gson_version}</version>
 			</dependency>
-			<dependency>
-				<groupId>com.sun.xml.bind</groupId>
-				<artifactId>jaxb-core</artifactId>
-				<version>${jaxb_core_version}</version>
-			</dependency>
-			<dependency>
-				<groupId>com.sun.xml.bind</groupId>
-				<artifactId>jaxb-impl</artifactId>
-				<version>${jaxb_core_version}</version>
-			</dependency>
 			<dependency>
 				<groupId>javax.mail</groupId>
 				<artifactId>javax.mail-api</artifactId>
@@ -952,6 +962,11 @@
 				<artifactId>javax.json</artifactId>
 				<version>1.0.4</version>
 			</dependency>
+			<dependency>
+				<groupId>org.glassfish.jaxb</groupId>
+				<artifactId>jaxb-runtime</artifactId>
+				<version>${jaxb_runtime_version}</version>
+			</dependency>
 			<dependency>
 				<groupId>org.glassfish.jersey.core</groupId>
 				<artifactId>jersey-server</artifactId>
@@ -1182,6 +1197,11 @@
 					<artifactId>maven-antrun-plugin</artifactId>
 					<version>1.8</version>
 				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-clean-plugin</artifactId>
+					<version>3.1.0</version>
+				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-compiler-plugin</artifactId>
@@ -1251,7 +1271,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-failsafe-plugin</artifactId>
-					<version>2.19.1</version>
+					<version>2.20</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
@@ -1278,7 +1298,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-surefire-plugin</artifactId>
-					<version>2.20.1</version>
+					<version>2.21.0</version>
 					<configuration>
 						<redirectTestOutputToFile>true</redirectTestOutputToFile>
 						<runOrder>random</runOrder>
@@ -1509,14 +1529,20 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-enforcer-plugin</artifactId>
+				<version>1.4.1</version>
 				<executions>
 					<execution>
 						<id>enforce-java</id>
 						<goals>
 							<goal>enforce</goal>
 						</goals>
+					</execution>
+				</executions>
 						<configuration>
 							<rules>
+								<requireMavenVersion>
+									<version>3.5</version>
+								</requireMavenVersion>
 								<requireJavaVersion>
 									<version>[1.8,)</version>
 									<message>
@@ -1525,8 +1551,6 @@
 								</requireJavaVersion>
 							</rules>
 						</configuration>
-					</execution>
-				</executions>
 			</plugin>
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>

src/changes/changes.xml

@@ -162,6 +162,11 @@
 				an unspecified error was thrown by the JPA server. An HTTP 409
 				(Conflict) with an informative error message is now thrown.
 			</action>
+			<action type="fix">
+				A bug in the JPA server's DSTU2 transaction processing routine caused it
+				to occasionally consume two database connections, which could lead to deadlocks
+				under heavy load. This has been fixed.
+			</action>
 		</release>
 		<release version="3.3.0" date="2018-03-29">
 			<action type="add">

src/site/xdoc/doc_cli.xml

@@ -33,6 +33,17 @@
 				<img src="./images/hapi-fhir-cli.png" alt="Basic screen shot" style="margin-left: 40px;"/>
 			</subsection>
 
+			<subsection name="Download and Installation - Mac/OSX">
+
+				<p>
+					hapi-fhir-cli is available as a <a href="https://brew.sh/">Homebrew</a> package
+					for Mac. It can be installed using the following command:
+				</p>
+				<code>brew install hapi-fhir-cli</code>
+
+
+			</subsection>
+
 			<subsection name="Troubleshooting">
 				<p>
 					<b>Note on Java version support:</b> The HAPI library is designed to

src/site/xdoc/doc_validation.xml

@@ -142,7 +142,7 @@
 
 				<p>
 					In order to use HAPI's Schematron support, a libaray called
-					<a href="https://code.google.com/p/phloc-schematron/">Phloc-Schematron</a>
+					<a href="https://github.com/phax/ph-schematron">Ph-Schematron</a>
 					is used, so this library must be added to your classpath (or Maven POM file, Gradle
 					file, etc.)
 					Note that this library is specified as an optional dependency

src/site/xdoc/download.xml.vm

@@ -541,13 +541,14 @@ System.setProperty("javax.xml.stream.XMLEventFactory", "com.ctc.wstx.stax.WstxEv
 
 			</subsection>
 
-			<subsection name="Phloc-Schematron">
+			<subsection name="Ph-Schematron">
 
 				<p>
 					If you are using the
 					<a href="./doc_validation.html">Schematron Validatioon</a>
-					module, you will also need to include the Phloc library on your
+					module, you will also need to include the Ph-Schematron library on your
-					classpath.
+					classpath. (Note that prior to HAPI FHIR 3.4.0 we used Phloc-Schamtron
+					instead, but that lirary has been discontinued)
 				</p>
 				<p>
 					If you are using Maven, this library is not added by default (it is
@@ -556,16 +557,15 @@ System.setProperty("javax.xml.stream.XMLEventFactory", "com.ctc.wstx.stax.WstxEv
 					dependencies to your project POM.xml
 				</p>
 				<source><![CDATA[<dependency>
-    <groupId>com.phloc</groupId>
+	<groupId>com.helger</groupId>
-    <artifactId>phloc-schematron</artifactId>
+	<artifactId>ph-schematron</artifactId>
-    <version>${phloc_schematron_version}</version>
+	<version>${ph_schematron_version}</version>
 </dependency>
 <dependency>
-    <groupId>com.phloc</groupId>
+	<groupId>com.helger</groupId>
-    <artifactId>phloc-commons</artifactId>
+	<artifactId>ph-commons</artifactId>
-    <version>${phloc_commons_version}</version>
+	<version>${ph_commons_version}</version>
 </dependency>]]></source>
-
 			</subsection>
 
 

tests/hapi-fhir-base-test-mindeps-server/src/test/java/ca/uhn/fhir/testmindeps/ValidatorTest.java

@@ -26,7 +26,7 @@ public class ValidatorTest {
 			assertEquals("This parser is for FHIR version DSTU2 - Can not encode a structure for version DSTU3", e.getMessage());
 		}
 
-		// Phloc is not onthe classpath
+		// Ph-Schematron is not onthe classpath
 		assertTrue(val.isValidateAgainstStandardSchema());
 		assertFalse(val.isValidateAgainstStandardSchematron());
 
@@ -34,7 +34,7 @@ public class ValidatorTest {
 			val.setValidateAgainstStandardSchematron(true);
 			fail();
 		} catch (IllegalArgumentException e) {
-			assertEquals("Phloc-schematron library not found on classpath, can not enable perform schematron validation", e.getMessage());
+			assertEquals("Ph-schematron library not found on classpath, can not enable perform schematron validation", e.getMessage());
 		}
 
 	}