Merge branch 'master' of https://github.com/jamesagnew/hapi-fhir

hapi-deployable-pom/pom.xml

@@ -1,5 +1,4 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<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/xsd/maven-4.0.0.xsd">
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
@@ -14,6 +13,9 @@
 
 	<name>HAPI FHIR - Deployable Artifact Parent POM</name>
 
+	<dependencies>
+	</dependencies>
+
 	<build>
 		<plugins>
 			<plugin>
@@ -53,7 +55,6 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-project-info-reports-plugin</artifactId>
-				<version>${maven_project_info_plugin_version}</version>
 				<configuration>
 					<skip>true</skip>
 				</configuration>
@@ -61,7 +62,6 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-javadoc-plugin</artifactId>
-				<version>${maven_javadoc_plugin_version}</version>
 				<reportSets>
 					<reportSet>
 						<id>default</id>
@@ -110,7 +110,6 @@
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-source-plugin</artifactId>
-						<version>${maven_source_plugin_version}</version>
 						<executions>
 							<execution>
 								<phase>package</phase>
@@ -123,7 +122,6 @@
 					<plugin>
 						<groupId>org.codehaus.mojo</groupId>
 						<artifactId>license-maven-plugin</artifactId>
-						<version>${maven_license_plugin_version}</version>
 						<executions>
 							<execution>
 								<id>first</id>

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/TemporalPrecisionEnum.java

@@ -46,6 +46,13 @@ public enum TemporalPrecisionEnum {
 			return DateUtils.addDays(theInput, theAmount);
 		}
 	},
+	MINUTE(Calendar.MINUTE) {
+		@Override
+		public Date add(Date theInput, int theAmount) {
+			return DateUtils.addMinutes(theInput, theAmount);
+		}
+		
+	},
 	SECOND(Calendar.SECOND) {
 		@Override
 		public Date add(Date theInput, int theAmount) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/BaseDateTimeDt.java

@@ -68,6 +68,8 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 	private static final FastDateFormat ourHumanDateFormat = FastDateFormat.getDateInstance(FastDateFormat.MEDIUM);
 	private static final Pattern ourYearMonthPattern = Pattern.compile("[0-9]{4}[0-9]{2}");
 	private static final Pattern ourYearPattern = Pattern.compile("[0-9]{4}");
+	private static final FastDateFormat ourYearMonthDayTimeMinsFormat = FastDateFormat.getInstance("yyyy-MM-dd'T'HH:mm");
+	private static final FastDateFormat ourYearMonthDayTimeMinsZoneFormat = FastDateFormat.getInstance("yyyy-MM-dd'T'HH:mmZZ");
 
 	static {
 		ArrayList<FastDateFormat> formatters = new ArrayList<FastDateFormat>();
@@ -185,36 +187,40 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 		if (theValue == null) {
 			return null;
 		} else {
+			GregorianCalendar cal;
+			if (myTimeZoneZulu) {
+				cal = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
+			} else if (myTimeZone != null) {
+				cal = new GregorianCalendar(myTimeZone);
+			} else {
+				cal = new GregorianCalendar();
+			}
+			cal.setTime(theValue);
+
 			switch (myPrecision) {
 			case DAY:
-				return ourYearMonthDayFormat.format(theValue);
+				return ourYearMonthDayFormat.format(cal);
 			case MONTH:
-				return ourYearMonthFormat.format(theValue);
+				return ourYearMonthFormat.format(cal);
 			case YEAR:
-				return ourYearFormat.format(theValue);
+				return ourYearFormat.format(cal);
+			case MINUTE:
+				if (myTimeZoneZulu) {
+					return ourYearMonthDayTimeMinsFormat.format(cal) + "Z";
+				} else {
+					return ourYearMonthDayTimeMinsZoneFormat.format(cal);
+				}
 			case SECOND:
 				if (myTimeZoneZulu) {
-					GregorianCalendar cal = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
-					cal.setTime(theValue);
 					return ourYearMonthDayTimeFormat.format(cal) + "Z";
-				} else if (myTimeZone != null) {
-					GregorianCalendar cal = new GregorianCalendar(myTimeZone);
-					cal.setTime(theValue);
-					return ourYearMonthDayTimeZoneFormat.format(cal);
 				} else {
-					return ourYearMonthDayTimeFormat.format(theValue);
+					return ourYearMonthDayTimeZoneFormat.format(cal);
 				}
 			case MILLI:
 				if (myTimeZoneZulu) {
-					GregorianCalendar cal = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
-					cal.setTime(theValue);
 					return ourYearMonthDayTimeMilliFormat.format(cal) + "Z";
-				} else if (myTimeZone != null) {
-					GregorianCalendar cal = new GregorianCalendar(myTimeZone);
-					cal.setTime(theValue);
-					return ourYearMonthDayTimeMilliZoneFormat.format(cal);
 				} else {
-					return ourYearMonthDayTimeMilliFormat.format(theValue);
+					return ourYearMonthDayTimeMilliZoneFormat.format(cal);
 				}
 			}
 			throw new IllegalStateException("Invalid precision (this is a HAPI bug, shouldn't happen): " + myPrecision);

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/DateDt.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.model.primitive;
 
+import java.util.Calendar;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -21,6 +23,8 @@ package ca.uhn.fhir.model.primitive;
  */
 
 import java.util.Date;
+import java.util.GregorianCalendar;
+import java.util.TimeZone;
 
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@@ -34,6 +38,17 @@ import ca.uhn.fhir.parser.DataFormatException;
  * <li>{@link TemporalPrecisionEnum#MONTH}
  * <li>{@link TemporalPrecisionEnum#DAY}
  * </ul>
+ * 
+ * <p>
+ * <b>Note on using Java Date objects:</b> This type stores the date as a Java Date. Note that
+ * the Java Date has more precision (millisecond precision), and does not store a timezone. As such,
+ * it could potentially cause issues. For example, if a Date contains the number of milliseconds at
+ * midnight in a timezone across the date line from your location, it might refer to a different date than
+ * intended.
+ * </p>
+ * <p>
+ * As such, it is recommended to use the <code>Calendar<code> or <code>int,int,int</code> constructors  
+ * </p>
  */
 @DatatypeDef(name = "date")
 public class DateDt extends BaseDateTimeDt {
@@ -51,7 +66,17 @@ public class DateDt extends BaseDateTimeDt {
 	}
 
 	/**
-	 * Constructor which accepts a date value and uses the {@link #DEFAULT_PRECISION} for this type
+	 * Constructor which accepts a date value and uses the {@link #DEFAULT_PRECISION} for this type.
+	 */
+	public DateDt(Calendar theCalendar) {
+		super(theCalendar.getTime(), DEFAULT_PRECISION);
+		setTimeZone(theCalendar.getTimeZone());
+	}
+
+	/**
+	 * Constructor which accepts a date value and uses the {@link #DEFAULT_PRECISION} for this type.
+	 * <b>Please see the note on timezones</b> on the {@link DateDt class documentation} for considerations
+	 * when using this constructor!
 	 */
 	@SimpleSetter(suffix = "WithDayPrecision")
 	public DateDt(@SimpleSetter.Parameter(name = "theDate") Date theDate) {
@@ -65,6 +90,8 @@ public class DateDt extends BaseDateTimeDt {
 	 * <li>{@link TemporalPrecisionEnum#MONTH}
 	 * <li>{@link TemporalPrecisionEnum#DAY}
 	 * </ul>
+	 * <b>Please see the note on timezones</b> on the {@link DateDt class documentation} for considerations
+	 * when using this constructor!
 	 * 
 	 * @throws DataFormatException
 	 *             If the specified precision is not allowed for this type
@@ -74,6 +101,17 @@ public class DateDt extends BaseDateTimeDt {
 		super(theDate, thePrecision);
 	}
 
+	/**
+	 * Constructor which accepts a date value and uses the {@link #DEFAULT_PRECISION} for this type.
+	 * 
+	 * @param theYear The year, e.g. 2015
+	 * @param theMonth The month, e.g. 0 for January
+	 * @param theDay The day (1 indexed) e.g. 1 for the first day of the month
+	 */
+	public DateDt(int theYear, int theMonth, int theDay) {
+		this(toCalendarZulu(theYear, theMonth, theDay));
+	}
+
 	/**
 	 * Constructor which accepts a date as a string in FHIR format
 	 * 
@@ -84,6 +122,16 @@ public class DateDt extends BaseDateTimeDt {
 		super(theDate);
 	}
 
+	/**
+	 * Returns the default precision for this datatype
+	 * 
+	 * @see #DEFAULT_PRECISION
+	 */
+	@Override
+	protected TemporalPrecisionEnum getDefaultPrecisionForDatatype() {
+		return DEFAULT_PRECISION;
+	}
+
 	@Override
 	boolean isPrecisionAllowed(TemporalPrecisionEnum thePrecision) {
 		switch (thePrecision) {
@@ -96,14 +144,12 @@ public class DateDt extends BaseDateTimeDt {
 		}
 	}
 
-	/**
+	private static GregorianCalendar toCalendarZulu(int theYear, int theMonth, int theDay) {
-	 * Returns the default precision for this datatype
+		GregorianCalendar retVal = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
-	 * 
+		retVal.set(Calendar.YEAR, theYear);
-	 * @see #DEFAULT_PRECISION
+		retVal.set(Calendar.MONTH, theMonth);
-	 */
+		retVal.set(Calendar.DATE, theDay);
-	@Override
+		return retVal;
-	protected TemporalPrecisionEnum getDefaultPrecisionForDatatype() {
-		return DEFAULT_PRECISION;
 	}
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/OperationParameter.java

@@ -23,6 +23,7 @@ package ca.uhn.fhir.rest.method;
 import java.lang.reflect.Method;
 import java.lang.reflect.Modifier;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
@@ -82,8 +83,6 @@ public class OperationParameter implements IParameter {
 		myContext = theCtx;
 	}
 
-
-
 	protected FhirContext getContext() {
 		return myContext;
 	}
@@ -109,7 +108,8 @@ public class OperationParameter implements IParameter {
 	public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
 		if (getContext().getVersion().getVersion().isRi()) {
 			if (IDatatype.class.isAssignableFrom(theParameterType)) {
-				throw new ConfigurationException("Incorrect use of type " + theParameterType.getSimpleName() + " as parameter type for method when context is for version " + getContext().getVersion().getVersion().name() + " in method: " + theMethod.toString());
+				throw new ConfigurationException("Incorrect use of type " + theParameterType.getSimpleName() + " as parameter type for method when context is for version "
+						+ getContext().getVersion().getVersion().name() + " in method: " + theMethod.toString());
 			}
 		}
 
@@ -123,8 +123,7 @@ public class OperationParameter implements IParameter {
 		myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType) || String.class.equals(myParameterType);
 
 		/*
-		 * The parameter can be of type string for validation methods - This is a bit
+		 * The parameter can be of type string for validation methods - This is a bit weird. See ValidateDstu2Test. We should probably clean this up..
-		 * weird. See ValidateDstu2Test. We should probably clean this up..
 		 */
 		if (!myParameterType.equals(IBase.class) && !myParameterType.equals(String.class)) {
 			if (IBaseResource.class.isAssignableFrom(myParameterType) && myParameterType.isInterface()) {
@@ -150,7 +149,8 @@ public class OperationParameter implements IParameter {
 	}
 
 	@Override
-	public void translateClientArgumentIntoQueryArgument(FhirContext theContext, Object theSourceClientArgument, Map<String, List<String>> theTargetQueryArguments, IBaseResource theTargetResource) throws InternalErrorException {
+	public void translateClientArgumentIntoQueryArgument(FhirContext theContext, Object theSourceClientArgument, Map<String, List<String>> theTargetQueryArguments, IBaseResource theTargetResource)
+			throws InternalErrorException {
 		assert theTargetResource != null;
 		Object sourceClientArgument = theSourceClientArgument;
 		if (sourceClientArgument == null) {
@@ -212,42 +212,51 @@ public class OperationParameter implements IParameter {
 				return null;
 			}
 
-			Class<? extends IBaseResource> wantedResourceType = theMethodBinding.getContext().getResourceDefinition("Parameters").getImplementingClass();
+			// Class<? extends IBaseResource> wantedResourceType = theMethodBinding.getContext().getResourceDefinition("Parameters").getImplementingClass();
+			Class<IBaseResource> wantedResourceType = null;
 			IBaseResource requestContents = ResourceParameter.loadResourceFromRequest(theRequest, theMethodBinding, wantedResourceType);
 
 			RuntimeResourceDefinition def = ctx.getResourceDefinition(requestContents);
+			if (def.getName().equals("Parameters")) {
 
-			BaseRuntimeChildDefinition paramChild = def.getChildByName("parameter");
+				BaseRuntimeChildDefinition paramChild = def.getChildByName("parameter");
-			BaseRuntimeElementCompositeDefinition<?> paramChildElem = (BaseRuntimeElementCompositeDefinition<?>) paramChild.getChildByName("parameter");
+				BaseRuntimeElementCompositeDefinition<?> paramChildElem = (BaseRuntimeElementCompositeDefinition<?>) paramChild.getChildByName("parameter");
 
-			RuntimeChildPrimitiveDatatypeDefinition nameChild = (RuntimeChildPrimitiveDatatypeDefinition) paramChildElem.getChildByName("name");
+				RuntimeChildPrimitiveDatatypeDefinition nameChild = (RuntimeChildPrimitiveDatatypeDefinition) paramChildElem.getChildByName("name");
-			BaseRuntimeChildDefinition valueChild = paramChildElem.getChildByName("value[x]");
+				BaseRuntimeChildDefinition valueChild = paramChildElem.getChildByName("value[x]");
-			BaseRuntimeChildDefinition resourceChild = paramChildElem.getChildByName("resource");
+				BaseRuntimeChildDefinition resourceChild = paramChildElem.getChildByName("resource");
 
-			IAccessor paramChildAccessor = paramChild.getAccessor();
+				IAccessor paramChildAccessor = paramChild.getAccessor();
-			List<IBase> values = paramChildAccessor.getValues(requestContents);
+				List<IBase> values = paramChildAccessor.getValues(requestContents);
-			for (IBase nextParameter : values) {
+				for (IBase nextParameter : values) {
-				List<IBase> nextNames = nameChild.getAccessor().getValues(nextParameter);
+					List<IBase> nextNames = nameChild.getAccessor().getValues(nextParameter);
-				if (nextNames != null && nextNames.size() > 0) {
+					if (nextNames != null && nextNames.size() > 0) {
-					IPrimitiveType<?> nextName = (IPrimitiveType<?>) nextNames.get(0);
+						IPrimitiveType<?> nextName = (IPrimitiveType<?>) nextNames.get(0);
-					if (myName.equals(nextName.getValueAsString())) {
+						if (myName.equals(nextName.getValueAsString())) {
 
-						if (myParameterType.isAssignableFrom(nextParameter.getClass())) {
+							if (myParameterType.isAssignableFrom(nextParameter.getClass())) {
-							matchingParamValues.add(nextParameter);
+								matchingParamValues.add(nextParameter);
-						} else {
+							} else {
-							List<IBase> paramValues = valueChild.getAccessor().getValues(nextParameter);
+								List<IBase> paramValues = valueChild.getAccessor().getValues(nextParameter);
-							List<IBase> paramResources = resourceChild.getAccessor().getValues(nextParameter);
+								List<IBase> paramResources = resourceChild.getAccessor().getValues(nextParameter);
-							if (paramValues != null && paramValues.size() > 0) {
+								if (paramValues != null && paramValues.size() > 0) {
-								tryToAddValues(paramValues, matchingParamValues);
+									tryToAddValues(paramValues, matchingParamValues);
-							} else if (paramResources != null && paramResources.size() > 0) {
+								} else if (paramResources != null && paramResources.size() > 0) {
-								tryToAddValues(paramResources, matchingParamValues);
+									tryToAddValues(paramResources, matchingParamValues);
+								}
 							}
-						}
 
+						}
 					}
 				}
-			}
 
+			} else {
+				
+				if (myParameterType.isAssignableFrom(requestContents.getClass())) {
+					tryToAddValues(Arrays.asList((IBase) requestContents), matchingParamValues);
+				}
+
+			}
 		}
 
 		if (matchingParamValues.isEmpty()) {

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

@@ -80,6 +80,12 @@ import ca.uhn.fhir.util.VersionUtil;
 
 public class RestfulServer extends HttpServlet implements IRestfulServer<ServletRequestDetails> {
 
+	/**
+	 * Requests will have an HttpServletRequest attribute set with this name, containing the servlet
+	 * context, in order to avoid a dependency on Servlet-API 3.0+ 
+	 */
+	public static final String SERVLET_CONTEXT_ATTRIBUTE = "ca.uhn.fhir.rest.server.RestfulServer.servlet_context";
+	
 	/**
 	 * Default setting for {@link #setETagSupport(ETagSupportEnum) ETag Support}: {@link ETagSupportEnum#ENABLED}
 	 */
@@ -518,6 +524,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
 		requestDetails.setServletRequest(theRequest);
 		requestDetails.setServletResponse(theResponse);
 		
+		theRequest.setAttribute(SERVLET_CONTEXT_ATTRIBUTE, getServletContext());
+
 		try {
 
 			for (IServerInterceptor next : myInterceptors) {

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

@@ -186,9 +186,11 @@ public class FhirValidator {
 			next.validateBundle(ctx);
 		}
 
-		IBaseOperationOutcome oo = ctx.toResult().toOperationOutcome();
+		if (ctx.toResult().isSuccessful() == false ) {
-		if (oo != null && OperationOutcomeUtil.hasIssues(myContext, oo)) {
+			IBaseOperationOutcome oo = ctx.toResult().toOperationOutcome();
-			throw new ValidationFailureException(myContext, oo);
+			if (oo != null && OperationOutcomeUtil.hasIssues(myContext, oo)) {
+				throw new ValidationFailureException(myContext, oo);
+			}
 		}
 		
 	}

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

@@ -111,6 +111,11 @@ public class ValidationResult {
 			OperationOutcomeUtil.addIssue(myCtx, oo, severity, next.getMessage(), location, ExceptionHandlingInterceptor.PROCESSING);
 		}
 
+		if (myMessages.isEmpty()) {
+			String message = myCtx.getLocalizer().getMessage(ValidationResult.class, "noIssuesDetected");
+			OperationOutcomeUtil.addIssue(myCtx, oo, "information", message, null, "informational");
+		}
+
 		return oo;
 	}
 

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

@@ -38,6 +38,7 @@ ca.uhn.fhir.rest.server.RestfulServer.rootRequest=This is the base URL of FHIR s
 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.noPhlocError=Phloc-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-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderQuestionnaireResponseDstu21.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jpa.provider;
 
+import org.hl7.fhir.dstu21.model.QuestionnaireResponse;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -20,9 +22,7 @@ package ca.uhn.fhir.jpa.provider;
  * #L%
  */
 
-import ca.uhn.fhir.model.dstu2.resource.QuestionnaireResponse;
+public class BaseJpaResourceProviderQuestionnaireResponseDstu21 extends JpaResourceProviderDstu21<QuestionnaireResponse> {
-
-public class BaseJpaResourceProviderQuestionnaireResponseDstu21 extends JpaResourceProviderDstu2<QuestionnaireResponse> {
 
 	// nothing yet
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu21Config.java

@@ -62,6 +62,7 @@ public class TestDstu21Config extends BaseJavaConfigDstu21 {
 		extraProperties.put("hibernate.search.default.directory_provider" ,"filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", "target/lucene_index_dstu21");
 		extraProperties.put("hibernate.search.lucene_version","LUCENE_CURRENT");
+		extraProperties.put("hibernate.search.autoregister_listeners", "true");
 		return extraProperties;
 	}
 

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

@@ -0,0 +1,56 @@
+package ca.uhn.fhir.jpa.config;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Organization;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
+import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.client.IGenericClient;
+import ca.uhn.fhir.rest.client.ServerValidationModeEnum;
+
+public class Tmp {
+
+	public static void main(String[] args) {
+		
+		FhirContext ctx = FhirContext.forDstu2();
+		ctx.getRestfulClientFactory().setSocketTimeout(200000);
+		ctx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+		IGenericClient client = ctx.newRestfulGenericClient("http://localhost:8080/hapi-fhir-jpaserver-example/baseDstu2");
+		
+		Bundle b = new Bundle();
+		b.setType(BundleTypeEnum.TRANSACTION);
+		int resCount = 20;
+		for (int i = 0; i < (resCount / 2); i++) {
+			Organization org = new Organization();
+			org.setId(IdDt.newRandomUuid());
+			org.setName("Random Org " + i);
+			org.addAddress().addLine("Random Org Line 1");
+			org.addIdentifier().setSystem("urn:foo").setValue("some_system" + i);
+			b.addEntry().setResource(org).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Organization");
+			
+			Patient patient = new Patient();
+			patient.setId(IdDt.newRandomUuid());
+			patient.addName().addFamily("Family" + i).addGiven("Gigven " + i);
+			patient.addAddress().addLine("Random Patient Line 1");
+			patient.addIdentifier().setSystem("urn:bar").setValue("some_system" + i);
+			b.addEntry().setResource(patient).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
+		}
+		
+		int total = 0;
+		long start = System.currentTimeMillis();
+		for (int i = 0; i < 300; i++) {
+		client.transaction().withBundle(b).execute();
+		ourLog.info("" + i);
+		total += resCount;
+		}
+		
+		long delay = System.currentTimeMillis() - start;
+		ourLog.info("Wrote {} resources at {}ms / res", total, delay / total);
+		
+		//sync  13:57:14.683 [main] INFO  ca.uhn.fhir.jpa.config.Tmp - Wrote 6000 resources at 7ms / res
+	}
+private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Tmp.class);
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu21/ResourceProviderDstu21Test.java

@@ -57,6 +57,7 @@ import org.hl7.fhir.dstu21.model.Encounter;
 import org.hl7.fhir.dstu21.model.Encounter.EncounterClass;
 import org.hl7.fhir.dstu21.model.Encounter.EncounterLocationComponent;
 import org.hl7.fhir.dstu21.model.Encounter.EncounterState;
+import org.hl7.fhir.dstu21.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.dstu21.model.IdType;
 import org.hl7.fhir.dstu21.model.ImagingStudy;
 import org.hl7.fhir.dstu21.model.InstantType;
@@ -163,7 +164,7 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		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")));
@@ -177,12 +178,11 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 			.execute();
 		//@formatter:on
 
-		actual = toUnqualifiedVersionlessIds((Bundle)response.getParameter().get(0).getResource());
+		actual = toUnqualifiedVersionlessIds((Bundle) response.getParameter().get(0).getResource());
 		assertThat(actual, containsInAnyOrder(ptId1, obsId1, devId1));
 
 	}
 
-	
 	@Test
 	public void testBundleCreate() throws Exception {
 		IGenericClient client = ourClient;
@@ -211,7 +211,6 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		}
 	}
 
-	
 	// private void delete(String theResourceType, String theParamName, String theParamValue) {
 	// Bundle resources;
 	// do {
@@ -297,24 +296,11 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		ourClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
 
 		//@formatter:on
-		Bundle found = ourClient
+		Bundle found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("rpdstu2_testCountParam_01")).count(10).returnBundle(Bundle.class).execute();
-				.search()
-				.forResource(Organization.class)
-				.where(Organization.NAME.matches()
-				.value("rpdstu2_testCountParam_01"))
-				.count(10)
-				.returnBundle(Bundle.class)
-				.execute();
 		assertEquals(100, found.getTotal());
 		assertEquals(10, found.getEntry().size());
 
-		found = ourClient
+		found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("rpdstu2_testCountParam_01")).count(999).returnBundle(Bundle.class).execute();
-				.search()
-				.forResource(Organization.class)
-				.where(Organization.NAME.matches().value("rpdstu2_testCountParam_01"))
-				.count(999)
-				.returnBundle(Bundle.class)
-				.execute();
 		//@formatter:on
 		assertEquals(100, found.getTotal());
 		assertEquals(50, found.getEntry().size());
@@ -602,7 +588,8 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 			//@formatter:on
 			fail();
 		} catch (PreconditionFailedException e) {
-			assertEquals("HTTP 412 Precondition Failed: Failed to DELETE resource with match URL \"Patient?identifier=testDeleteConditionalMultiple\" because this search matched 2 resources", e.getMessage());
+			assertEquals("HTTP 412 Precondition Failed: Failed to DELETE resource with match URL \"Patient?identifier=testDeleteConditionalMultiple\" because this search matched 2 resources",
+					e.getMessage());
 		}
 
 		// Not deleted yet..
@@ -713,8 +700,7 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		}
 
 		/*
-		 * Try it with a raw socket call. The Apache client won't let us use the unescaped "|" in the URL but we want to
+		 * Try it with a raw socket call. The Apache client won't let us use the unescaped "|" in the URL but we want to make sure that works too..
-		 * make sure that works too..
 		 */
 		Socket sock = new Socket();
 		sock.setSoTimeout(3000);
@@ -842,7 +828,7 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		IIdType devId = ourClient.create().resource(dev).execute().getId().toUnqualifiedVersionless();
 
 		Location locParent = new Location();
-		locParent.setName(methodName+"Parent");
+		locParent.setName(methodName + "Parent");
 		IIdType locPId = ourClient.create().resource(locParent).execute().getId().toUnqualifiedVersionless();
 
 		Location locChild = new Location();
@@ -906,7 +892,7 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		IIdType devId = ourClient.create().resource(dev).execute().getId().toUnqualifiedVersionless();
 
 		Location locParent = new Location();
-		locParent.setName(methodName+"Parent");
+		locParent.setName(methodName + "Parent");
 		IIdType locPId = ourClient.create().resource(locParent).execute().getId().toUnqualifiedVersionless();
 
 		Location locChild = new Location();
@@ -1058,8 +1044,6 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 
 	}
 
-	
-	
 	@Test
 	public void testEverythingPatientOperation() throws Exception {
 		String methodName = "testEverythingOperation";
@@ -1110,18 +1094,18 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		String methodName = "testEverythingPatientType";
 
 		Organization o1 = new Organization();
-		o1.setName(methodName+"1");
+		o1.setName(methodName + "1");
 		IIdType o1Id = ourClient.create().resource(o1).execute().getId().toUnqualifiedVersionless();
 		Organization o2 = new Organization();
-		o2.setName(methodName+"2");
+		o2.setName(methodName + "2");
 		IIdType o2Id = ourClient.create().resource(o2).execute().getId().toUnqualifiedVersionless();
 
 		Patient p1 = new Patient();
-		p1.addName().addFamily(methodName+"1");
+		p1.addName().addFamily(methodName + "1");
 		p1.getManagingOrganization().setReferenceElement(o1Id);
 		IIdType p1Id = ourClient.create().resource(p1).execute().getId().toUnqualifiedVersionless();
 		Patient p2 = new Patient();
-		p2.addName().addFamily(methodName+"2");
+		p2.addName().addFamily(methodName + "2");
 		p2.getManagingOrganization().setReferenceElement(o2Id);
 		IIdType p2Id = ourClient.create().resource(p2).execute().getId().toUnqualifiedVersionless();
 
@@ -1133,7 +1117,7 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		IIdType c2Id = ourClient.create().resource(c2).execute().getId().toUnqualifiedVersionless();
 
 		Condition c3 = new Condition();
-		c3.addIdentifier().setValue(methodName+"3");
+		c3.addIdentifier().setValue(methodName + "3");
 		IIdType c3Id = ourClient.create().resource(c3).execute().getId().toUnqualifiedVersionless();
 
 		Parameters output = ourClient.operation().onType(Patient.class).named("everything").withNoParameters(Parameters.class).execute();
@@ -1172,7 +1156,7 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		Thread.sleep(10);
 		long time3 = System.currentTimeMillis();
 
-		// %3E=>   %3C=<
+		// %3E=> %3C=<
 
 		HttpGet get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantType(new Date(time1)).getValueAsString());
 		CloseableHttpResponse response = ourHttpClient.execute(get);
@@ -1188,7 +1172,8 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 			response.close();
 		}
 
-		get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantType(new Date(time2)).getValueAsString() + "&_lastUpdated=%3C" + new InstantType(new Date(time3)).getValueAsString());
+		get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantType(new Date(time2)).getValueAsString() + "&_lastUpdated=%3C"
+				+ new InstantType(new Date(time3)).getValueAsString());
 		response = ourHttpClient.execute(get);
 		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
@@ -1786,12 +1771,12 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		String methodName = "testSearchWithMissing";
 
 		Organization org = new Organization();
-		IIdType deletedIdMissingTrue = (IdType) ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless();
+		IIdType deletedIdMissingTrue = ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless();
 		ourClient.delete().resourceById(deletedIdMissingTrue).execute();
 
 		org = new Organization();
 		org.setName("Help I'm a Bug");
-		IIdType deletedIdMissingFalse = (IdType) ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless();
+		IIdType deletedIdMissingFalse = ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless();
 		ourClient.delete().resourceById(deletedIdMissingFalse).execute();
 
 		List<IBaseResource> resources = new ArrayList<IBaseResource>();
@@ -1805,11 +1790,11 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		org = new Organization();
 		org.addIdentifier().setSystem("urn:system:rpdstu2").setValue(methodName + "01");
 		org.setName(methodName + "name");
-		IIdType orgNotMissing = (IdType) ourClient.create().resource(org).prettyPrint().encodedXml().execute().getId().toUnqualifiedVersionless();
+		IIdType orgNotMissing = ourClient.create().resource(org).prettyPrint().encodedXml().execute().getId().toUnqualifiedVersionless();
 
 		org = new Organization();
 		org.addIdentifier().setSystem("urn:system:rpdstu2").setValue(methodName + "01");
-		IIdType orgMissing = (IdType) ourClient.create().resource(org).prettyPrint().encodedXml().execute().getId().toUnqualifiedVersionless();
+		IIdType orgMissing = ourClient.create().resource(org).prettyPrint().encodedXml().execute().getId().toUnqualifiedVersionless();
 
 		{
 			//@formatter:off
@@ -1817,7 +1802,7 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 					.search()
 					.forResource(Organization.class)
 					.where(Organization.NAME.isMissing(false))
-					.limitTo(100)
+					.count(100)
 					.prettyPrint()
 					.returnBundle(Bundle.class)
 					.execute();
@@ -2214,7 +2199,7 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 	}
 
 	@Test
-	public void testValidateResource() throws IOException {
+	public void testValidateResourceWithNoIdParameters() throws IOException {
 
 		Patient patient = new Patient();
 		patient.addName().addGiven("James");
@@ -2224,8 +2209,6 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 		input.addParameter().setName("resource").setResource(patient);
 
 		String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(input);
-		ourLog.info(inputStr);
-
 		HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate?_pretty=true");
 		post.setEntity(new StringEntity(inputStr, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
 
@@ -2235,6 +2218,61 @@ public class ResourceProviderDstu21Test extends BaseResourceProviderDstu21Test {
 			ourLog.info(resp);
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			assertThat(resp, not(containsString("Resource has no id")));
+			assertThat(resp, containsString("<pre>No issues detected during validation</pre>"));
+			assertThat(resp,
+					stringContainsInOrder("<issue>", "<severity value=\"information\"/>", "<code value=\"informational\"/>", "<diagnostics value=\"No issues detected during validation\"/>", "</issue>"));
+		} finally {
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.close();
+		}
+	}
+
+	@Test
+	public void testValidateResourceWithNoIdRaw() throws IOException {
+
+		Patient patient = new Patient();
+		patient.addName().addGiven("James");
+		patient.setBirthDateElement(new DateType("2011-02-02"));
+
+		String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(patient);
+		HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
+		post.setEntity(new StringEntity(inputStr, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+
+		CloseableHttpResponse response = ourHttpClient.execute(post);
+		try {
+			String resp = IOUtils.toString(response.getEntity().getContent());
+			ourLog.info(resp);
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			assertThat(resp, not(containsString("Resource has no id")));
+			assertThat(resp, containsString("<pre>No issues detected during validation</pre>"));
+			assertThat(resp,
+					stringContainsInOrder("<issue>", "<severity value=\"information\"/>", "<code value=\"informational\"/>", "<diagnostics value=\"No issues detected during validation\"/>", "</issue>"));
+		} finally {
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.close();
+		}
+	}
+
+	@Test
+	public void testValidateResourceBaseWithNoIdRaw() throws IOException {
+
+		Patient patient = new Patient();
+		patient.addName().addGiven("James");
+		patient.setBirthDateElement(new DateType("2011-02-02"));
+		patient.addContact().setGender(AdministrativeGender.MALE);
+
+		String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(patient);
+		HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
+		post.setEntity(new StringEntity(inputStr, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+
+		CloseableHttpResponse response = ourHttpClient.execute(post);
+		try {
+			String resp = IOUtils.toString(response.getEntity().getContent());
+			ourLog.info(resp);
+			assertEquals(412, response.getStatusLine().getStatusCode());
+			assertThat(resp, not(containsString("Resource has no id")));
+			assertThat(resp,
+					stringContainsInOrder(">ERROR<","/f:Patient/f:contact","<pre>SHALL at least contain a contact's details or a reference to an organization</pre>","<issue><severity value=\"error\"/>","<code value=\"processing\"/>","<diagnostics value=\"SHALL at least contain a contact's details or a reference to an organization\"/>","<location value=\"/f:Patient/f:contact\"/>"));
 		} finally {
 			IOUtils.closeQuietly(response.getEntity().getContent());
 			response.close();

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu21.java

@@ -88,6 +88,7 @@ public class FhirServerConfigDstu21 extends BaseJavaConfigDstu21 {
 		extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
 		extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
+//		extraProperties.put("hibernate.search.default.worker.execution", "async");
 		return extraProperties;
 	}
 

hapi-fhir-structures-dstu/pom.xml

@@ -20,9 +20,14 @@
 			<version>1.4-SNAPSHOT</version>
 		</dependency>
 
+		<!-- 
+		The JPA project uses a newer API but we'll try to hold to this version
+		as much as possible. See #283.
+		-->
 		<dependency>
 			<groupId>javax.servlet</groupId>
-			<artifactId>javax.servlet-api</artifactId>
+			<artifactId>servlet-api</artifactId>
+			<version>2.5</version>
 			<scope>provided</scope>
 		</dependency>
 

hapi-fhir-structures-dstu/src/main/java/ca/uhn/fhir/rest/server/provider/ServerConformanceProvider.java

@@ -36,7 +36,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
-import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.dstu.resource.Conformance;
 import ca.uhn.fhir.model.dstu.resource.Conformance.Rest;
 import ca.uhn.fhir.model.dstu.resource.Conformance.RestQuery;
@@ -156,7 +155,7 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 			String resourceName = next.getResourceName();
 			RuntimeResourceDefinition def = myServerConfiguration.getFhirContext().getResourceDefinition(resourceName);
 			resource.getType().setValue(def.getName());
-			ServletContext servletContext  = theRequest == null ? null : theRequest.getServletContext();
+			ServletContext servletContext  = (ServletContext) (theRequest == null ? null : theRequest.getAttribute(RestfulServer.SERVLET_CONTEXT_ATTRIBUTE));
 			String serverBase = myServerConfiguration.getServerAddressStrategy().determineServerBase(servletContext, theRequest);
             resource.getProfile().setReference(new IdDt(def.getResourceProfile(serverBase)));
 

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/validation/ResourceValidatorTest.java

@@ -153,7 +153,7 @@ public class ResourceValidatorTest {
 		
 		assertTrue(result.isSuccessful());
 		assertNotNull(operationOutcome);
-		assertEquals(0, operationOutcome.getIssue().size());
+		assertEquals(1, operationOutcome.getIssue().size());
 	}
 
 	@Test

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

@@ -26,9 +26,15 @@
 			<version>1.4-SNAPSHOT</version>
 			<scope>test</scope>
 		</dependency>
+
+		<!-- 
+		The JPA project uses a newer API but we'll try to hold to this version
+		as much as possible. See #283.
+		-->
 		<dependency>
 			<groupId>javax.servlet</groupId>
-			<artifactId>javax.servlet-api</artifactId>
+			<artifactId>servlet-api</artifactId>
+			<version>2.5</version>
 			<scope>provided</scope>
 		</dependency>
 

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu21/hapi/rest/server/ServerConformanceProvider.java

@@ -85,8 +85,10 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
  * Server FHIR Provider which serves the conformance statement for a RESTful server implementation
  * 
  * <p>
- * Note: This class is safe to extend, but it is important to note that the same instance of {@link Conformance} is always returned unless {@link #setCache(boolean)} is called with a value of
+ * Note: This class is safe to extend, but it is important to note that the same instance of {@link Conformance} is
- * <code>false</code>. This means that if you are adding anything to the returned conformance instance on each call you should call <code>setCache(false)</code> in your provider constructor.
+ * always returned unless {@link #setCache(boolean)} is called with a value of <code>false</code>. This means that if
+ * you are adding anything to the returned conformance instance on each call you should call
+ * <code>setCache(false)</code> in your provider constructor.
  * </p>
  */
 public class ServerConformanceProvider implements IServerConformanceProvider<Conformance> {
@@ -103,20 +105,18 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 	}
 
 	public ServerConformanceProvider(RestulfulServerConfiguration theServerConfiguration) {
-	    this.myServerConfiguration = theServerConfiguration;
+		this.myServerConfiguration = theServerConfiguration;
 	}
 
 	/*
-	 * Add a no-arg constructor and seetter so that the
+	 * Add a no-arg constructor and seetter so that the ServerConfirmanceProvider can be Spring-wired with the
-	 * ServerConfirmanceProvider can be Spring-wired with
+	 * RestfulService avoiding the potential reference cycle that would happen.
-	 * the RestfulService avoiding the potential reference
-	 * cycle that would happen.
 	 */
-	public ServerConformanceProvider () {
+	public ServerConformanceProvider() {
 		super();
 	}
 
-	public void setRestfulServer (RestfulServer theRestfulServer) {
+	public void setRestfulServer(RestfulServer theRestfulServer) {
 		myServerConfiguration = theRestfulServer.createConfiguration();
 	}
 
@@ -167,8 +167,9 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 	}
 
 	/**
-	 * Gets the value of the "publisher" that will be placed in the generated conformance statement. As this is a mandatory element, the value should not be null (although this is not enforced). The
+	 * Gets the value of the "publisher" that will be placed in the generated conformance statement. As this is a
-	 * value defaults to "Not provided" but may be set to null, which will cause this element to be omitted.
+	 * mandatory element, the value should not be null (although this is not enforced). The value defaults to
+	 * "Not provided" but may be set to null, which will cause this element to be omitted.
 	 */
 	public String getPublisher() {
 		return myPublisher;
@@ -186,7 +187,8 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 		retVal.setPublisher(myPublisher);
 		retVal.setDateElement(conformanceDate());
 		retVal.setFhirVersion("1.0.2"); // TODO: pull from model
-		retVal.setAcceptUnknown(UnknownContentCode.EXTENSIONS); // TODO: make this configurable - this is a fairly big effort since the parser
+		retVal.setAcceptUnknown(UnknownContentCode.EXTENSIONS); // TODO: make this configurable - this is a fairly big
+																					// effort since the parser
 		// needs to be modified to actually allow it
 
 		retVal.getImplementation().setDescription(myServerConfiguration.getImplementationDescription());
@@ -211,8 +213,8 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 				String resourceName = nextEntry.getKey();
 				RuntimeResourceDefinition def = myServerConfiguration.getFhirContext().getResourceDefinition(resourceName);
 				resource.getTypeElement().setValue(def.getName());
-	            ServletContext servletContext  = theRequest == null ? null : theRequest.getServletContext();
+				ServletContext servletContext = (ServletContext) (theRequest == null ? null : theRequest.getAttribute(RestfulServer.SERVLET_CONTEXT_ATTRIBUTE));
-	            String serverBase = myServerConfiguration.getServerAddressStrategy().determineServerBase(servletContext, theRequest);
+				String serverBase = myServerConfiguration.getServerAddressStrategy().determineServerBase(servletContext, theRequest);
 				resource.getProfile().setReference((def.getResourceProfile(serverBase)));
 
 				TreeSet<String> includes = new TreeSet<String>();
@@ -441,7 +443,7 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 					if (targetDef != null) {
 						ResourceType code;
 						try {
-						code = ResourceType.fromCode(targetDef.getName());
+							code = ResourceType.fromCode(targetDef.getName());
 						} catch (FHIRException e) {
 							code = null;
 						}
@@ -561,8 +563,9 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 	}
 
 	/**
-	 * Sets the value of the "publisher" that will be placed in the generated conformance statement. As this is a mandatory element, the value should not be null (although this is not enforced). The
+	 * Sets the value of the "publisher" that will be placed in the generated conformance statement. As this is a
-	 * value defaults to "Not provided" but may be set to null, which will cause this element to be omitted.
+	 * mandatory element, the value should not be null (although this is not enforced). The value defaults to
+	 * "Not provided" but may be set to null, which will cause this element to be omitted.
 	 */
 	public void setPublisher(String thePublisher) {
 		myPublisher = thePublisher;

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu21/model/BaseDateTimeType.java

@@ -126,51 +126,43 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
 		if (theValue == null) {
 			return null;
 		} else {
+			GregorianCalendar cal;
+			if (myTimeZoneZulu) {
+				cal = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
+			} else if (myTimeZone != null) {
+				cal = new GregorianCalendar(myTimeZone);
+			} else {
+				cal = new GregorianCalendar();
+			}
+			cal.setTime(theValue);
+
 			switch (myPrecision) {
 			case DAY:
-				return ourYearMonthDayFormat.format(theValue);
+				return ourYearMonthDayFormat.format(cal);
 			case MONTH:
-				return ourYearMonthFormat.format(theValue);
+				return ourYearMonthFormat.format(cal);
 			case YEAR:
-				return ourYearFormat.format(theValue);
+				return ourYearFormat.format(cal);
 			case MINUTE:
 				if (myTimeZoneZulu) {
-					GregorianCalendar cal = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
-					cal.setTime(theValue);
 					return ourYearMonthDayTimeMinsFormat.format(cal) + "Z";
-				} else if (myTimeZone != null) {
-					GregorianCalendar cal = new GregorianCalendar(myTimeZone);
-					cal.setTime(theValue);
-					return (ourYearMonthDayTimeMinsZoneFormat.format(cal));
 				} else {
-					return ourYearMonthDayTimeMinsFormat.format(theValue);
+					return ourYearMonthDayTimeMinsZoneFormat.format(cal);
 				}
 			case SECOND:
 				if (myTimeZoneZulu) {
-					GregorianCalendar cal = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
-					cal.setTime(theValue);
 					return ourYearMonthDayTimeFormat.format(cal) + "Z";
-				} else if (myTimeZone != null) {
-					GregorianCalendar cal = new GregorianCalendar(myTimeZone);
-					cal.setTime(theValue);
-					return (ourYearMonthDayTimeZoneFormat.format(cal));
 				} else {
-					return ourYearMonthDayTimeFormat.format(theValue);
+					return ourYearMonthDayTimeZoneFormat.format(cal);
 				}
 			case MILLI:
 				if (myTimeZoneZulu) {
-					GregorianCalendar cal = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
-					cal.setTime(theValue);
 					return ourYearMonthDayTimeMilliFormat.format(cal) + "Z";
-				} else if (myTimeZone != null) {
-					GregorianCalendar cal = new GregorianCalendar(myTimeZone);
-					cal.setTime(theValue);
-					return (ourYearMonthDayTimeMilliZoneFormat.format(cal));
 				} else {
-					return ourYearMonthDayTimeMilliFormat.format(theValue);
+					return ourYearMonthDayTimeMilliZoneFormat.format(cal);
 				}
 			}
-			throw new IllegalStateException("Invalid precision (this is a bug, shouldn't happen): " + myPrecision);
+			throw new IllegalStateException("Invalid precision (this is a HAPI bug, shouldn't happen): " + myPrecision);
 		}
 	}
 

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu21/model/DateType.java

@@ -29,11 +29,14 @@ POSSIBILITY OF SUCH DAMAGE.
 
 package org.hl7.fhir.dstu21.model;
 
+import java.util.Calendar;
+
 /**
  * Primitive type "date" in FHIR: any day in a gregorian calendar
  */
 
 import java.util.Date;
+import java.util.GregorianCalendar;
 import java.util.TimeZone;
 
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@@ -95,6 +98,33 @@ public class DateType extends BaseDateTimeType {
 		super(theDate);
 	}
 
+	/**
+	 * Constructor which accepts a date value and uses the {@link #DEFAULT_PRECISION} for this type.
+	 */
+	public DateType(Calendar theCalendar) {
+		super(theCalendar.getTime(), DEFAULT_PRECISION);
+		setTimeZone(theCalendar.getTimeZone());
+	}
+
+	/**
+	 * Constructor which accepts a date value and uses the {@link #DEFAULT_PRECISION} for this type.
+	 * 
+	 * @param theYear The year, e.g. 2015
+	 * @param theMonth The month, e.g. 0 for January
+	 * @param theDay The day (1 indexed) e.g. 1 for the first day of the month
+	 */
+	public DateType(int theYear, int theMonth, int theDay) {
+		this(toCalendarZulu(theYear, theMonth, theDay));
+	}
+
+	private static GregorianCalendar toCalendarZulu(int theYear, int theMonth, int theDay) {
+		GregorianCalendar retVal = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
+		retVal.set(Calendar.YEAR, theYear);
+		retVal.set(Calendar.MONTH, theMonth);
+		retVal.set(Calendar.DATE, theDay);
+		return retVal;
+	}
+
 	@Override
 	boolean isPrecisionAllowed(TemporalPrecisionEnum thePrecision) {
 		switch (thePrecision) {

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/model/BaseDateTimeTypeDstu21Test.java

@@ -0,0 +1,105 @@
+package ca.uhn.fhir.model;
+
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.Locale;
+import java.util.TimeZone;
+
+import org.hl7.fhir.dstu21.model.DateTimeType;
+import org.hl7.fhir.dstu21.model.DateType;
+import org.hl7.fhir.dstu21.model.TemporalPrecisionEnum;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class BaseDateTimeTypeDstu21Test {
+	private static Locale ourDefaultLocale;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseDateTimeTypeDstu21Test.class);
+	private SimpleDateFormat myDateInstantParser;
+
+	@Before
+	public void before() {
+		myDateInstantParser = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS");
+	}
+
+	/**
+	 * See HAPI #101 - https://github.com/jamesagnew/hapi-fhir/issues/101
+	 */
+	@Test
+	public void testPrecisionRespectedForSetValue() throws Exception {
+		Calendar cal = Calendar.getInstance();
+		cal.setTime(myDateInstantParser.parse("2012-01-02 22:31:02.333"));
+		cal.setTimeZone(TimeZone.getTimeZone("EST"));
+
+		Date time = cal.getTime();
+
+		DateType date = new DateType();
+		date.setValue(time);
+		assertEquals("2012-01-02", date.getValueAsString());
+	}
+
+	@Test
+	public void testMinutePrecisionEncode() throws Exception {
+		Calendar cal = Calendar.getInstance();
+		cal.setTimeZone(TimeZone.getTimeZone("Europe/Berlin"));
+		cal.set(1990, Calendar.JANUARY, 3, 3, 22, 11);
+		
+		DateTimeType date = new DateTimeType();
+		date.setValue(cal.getTime(), TemporalPrecisionEnum.MINUTE);
+		date.setTimeZone(TimeZone.getTimeZone("EST"));
+		assertEquals("1990-01-02T21:22-05:00", date.getValueAsString());
+
+		date.setTimeZoneZulu(true);
+		assertEquals("1990-01-03T02:22Z", date.getValueAsString());
+	}
+
+	/**
+	 * See HAPI #101 - https://github.com/jamesagnew/hapi-fhir/issues/101
+	 */
+	@Test
+	public void testPrecisionRespectedForSetValueWithPrecision() throws Exception {
+		Calendar cal = Calendar.getInstance();
+		cal.setTime(myDateInstantParser.parse("2012-01-02 22:31:02.333"));
+		cal.setTimeZone(TimeZone.getTimeZone("EST"));
+
+		Date time = cal.getTime();
+
+		DateType date = new DateType();
+		date.setValue(time, TemporalPrecisionEnum.DAY);
+		assertEquals("2012-01-02", date.getValueAsString());
+	}
+
+	@Test
+	public void testToHumanDisplay() {
+		DateTimeType dt = new DateTimeType("2012-01-05T12:00:00-08:00");
+		String human = dt.toHumanDisplay();
+		ourLog.info(human);
+		assertThat(human, containsString("2012"));
+		assertThat(human, containsString("12"));
+	}
+
+	public static void afterClass() {
+		Locale.setDefault(ourDefaultLocale);
+	}
+
+	@BeforeClass
+	public static void beforeClass() {
+		/*
+		 * We cache the default locale, but temporarily set it to a random value during this test. This helps ensure
+		 * that there are no language specific dependencies in the test.
+		 */
+		ourDefaultLocale = Locale.getDefault();
+
+		Locale[] available = { Locale.CANADA, Locale.GERMANY, Locale.TAIWAN };
+		Locale newLocale = available[(int) (Math.random() * available.length)];
+		Locale.setDefault(newLocale);
+
+		ourLog.info("Tests are running in locale: " + newLocale.getDisplayName());
+	}
+
+}

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/model/DateTypeTest.java

@@ -0,0 +1,52 @@
+package ca.uhn.fhir.model;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.Calendar;
+import java.util.TimeZone;
+
+import org.hl7.fhir.dstu21.model.DateType;
+import org.junit.Test;
+
+public class DateTypeTest {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DateTypeTest.class);
+
+	@Test
+	public void testPrecision() {
+
+//		ourLog.info(""+ new TreeSet<String>(Arrays.asList(TimeZone.getAvailableIDs())));
+		
+		final Calendar cal = Calendar.getInstance();
+		cal.setTimeZone(TimeZone.getTimeZone("GMT"));
+		cal.set(1990, Calendar.JANUARY, 1, 0, 0, 0);
+		ourLog.info("Time: {}", cal); // 631152000775
+
+		DateType dateDt = new DateType(cal.getTime());
+		long time = dateDt.getValue().getTime();
+		ourLog.info("Time: {}", time); // 631152000775
+		ourLog.info("Time: {}", dateDt.getValue()); // 631152000775
+
+		dateDt.setTimeZone(TimeZone.getTimeZone("Europe/Berlin"));
+		time = dateDt.getValue().getTime();
+		ourLog.info("Time: {}", time); // 631152000775
+		ourLog.info("Time: {}", dateDt.getValue()); // 631152000775
+
+		String valueAsString = dateDt.getValueAsString();
+		ourLog.info(valueAsString);
+		// is 631152000030
+
+	}
+
+	@Test
+	public void testConstructors() {
+		final Calendar cal = Calendar.getInstance();
+		cal.setTimeZone(TimeZone.getTimeZone("Europe/Berlin"));
+		cal.set(1990, Calendar.JANUARY, 5, 0, 0, 0);
+		DateType dateDt = new DateType(cal);
+		assertEquals("1990-01-05", dateDt.getValueAsString());
+
+		dateDt = new DateType(1990, 0, 5);
+		assertEquals("1990-01-05", dateDt.getValueAsString());
+	}
+	
+}

hapi-fhir-structures-dstu2/pom.xml

@@ -27,9 +27,14 @@
 			<scope>test</scope>
 		</dependency>
 
+		<!-- 
+		The JPA project uses a newer API but we'll try to hold to this version
+		as much as possible. See #283.
+		-->
 		<dependency>
 			<groupId>javax.servlet</groupId>
-			<artifactId>javax.servlet-api</artifactId>
+			<artifactId>servlet-api</artifactId>
+			<version>2.5</version>
 			<scope>provided</scope>
 		</dependency>
 

hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2/ServerConformanceProvider.java

@@ -206,7 +206,7 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 				String resourceName = nextEntry.getKey();
 				RuntimeResourceDefinition def = myServerConfiguration.getFhirContext().getResourceDefinition(resourceName);
 				resource.getTypeElement().setValue(def.getName());
-	            ServletContext servletContext  = theRequest == null ? null : theRequest.getServletContext();
+				ServletContext servletContext  = (ServletContext) (theRequest == null ? null : theRequest.getAttribute(RestfulServer.SERVLET_CONTEXT_ATTRIBUTE));
 	            String serverBase = myServerConfiguration.getServerAddressStrategy().determineServerBase(servletContext, theRequest);
 				resource.getProfile().setReference(new IdDt(def.getResourceProfile(serverBase)));
 

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/model/primitive/BaseDateTimeDtDstu2Test.java

@@ -41,6 +41,21 @@ public class BaseDateTimeDtDstu2Test {
 		assertEquals("2012-01-02", date.getValueAsString());
 	}
 
+	@Test
+	public void testMinutePrecisionEncode() throws Exception {
+		Calendar cal = Calendar.getInstance();
+		cal.setTimeZone(TimeZone.getTimeZone("Europe/Berlin"));
+		cal.set(1990, Calendar.JANUARY, 3, 3, 22, 11);
+		
+		DateTimeDt date = new DateTimeDt();
+		date.setValue(cal.getTime(), TemporalPrecisionEnum.MINUTE);
+		date.setTimeZone(TimeZone.getTimeZone("EST"));
+		assertEquals("1990-01-02T21:22-05:00", date.getValueAsString());
+
+		date.setTimeZoneZulu(true);
+		assertEquals("1990-01-03T02:22Z", date.getValueAsString());
+	}
+
 	/**
 	 * See HAPI #101 - https://github.com/jamesagnew/hapi-fhir/issues/101
 	 */

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/model/primitive/DateDtTest.java

@@ -0,0 +1,55 @@
+package ca.uhn.fhir.model.primitive;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.Arrays;
+import java.util.Calendar;
+import java.util.TimeZone;
+import java.util.TreeSet;
+
+import org.junit.Test;
+
+public class DateDtTest {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DateDtTest.class);
+
+	@Test
+	public void testPrecision() {
+
+//		ourLog.info(""+ new TreeSet<String>(Arrays.asList(TimeZone.getAvailableIDs())));
+		
+		final Calendar cal = Calendar.getInstance();
+		cal.setTimeZone(TimeZone.getTimeZone("GMT"));
+		cal.set(1990, Calendar.JANUARY, 1, 0, 0, 0);
+		ourLog.info("Time: {}", cal); // 631152000775
+
+		DateDt dateDt = new DateDt(cal.getTime());
+		long time = dateDt.getValue().getTime();
+		ourLog.info("Time: {}", time); // 631152000775
+		ourLog.info("Time: {}", dateDt.getValue()); // 631152000775
+
+		dateDt.setTimeZone(TimeZone.getTimeZone("Europe/Berlin"));
+		time = dateDt.getValue().getTime();
+		ourLog.info("Time: {}", time); // 631152000775
+		ourLog.info("Time: {}", dateDt.getValue()); // 631152000775
+
+		String valueAsString = dateDt.getValueAsString();
+		ourLog.info(valueAsString);
+		// is 631152000030
+
+	}
+
+	@Test
+	public void testConstructors() {
+		final Calendar cal = Calendar.getInstance();
+		cal.setTimeZone(TimeZone.getTimeZone("Europe/Berlin"));
+		cal.set(1990, Calendar.JANUARY, 5, 0, 0, 0);
+		DateDt dateDt = new DateDt(cal);
+		assertEquals("1990-01-05", dateDt.getValueAsString());
+
+		dateDt = new DateDt(1990, 0, 5);
+		assertEquals("1990-01-05", dateDt.getValueAsString());
+	}
+	
+	
+	
+}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/ExtensionsDstu2Test.java

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.parser;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.dstu2.resource.Conformance;
+import ca.uhn.fhir.model.dstu2.resource.Conformance.RestSecurity;
+
+public class ExtensionsDstu2Test {
+
+	private static final FhirContext ourCtx = FhirContext.forDstu2();
+	
+	@Test
+	public void testParseExtensions() throws Exception {
+		String input = IOUtils.toString(getClass().getResourceAsStream("/smart-conf.xml"));
+		Conformance conf = (Conformance) ourCtx.newXmlParser().parseResource(input);
+		
+		RestSecurity sec = conf.getRest().get(0).getSecurity();
+		List<ExtensionDt> uris = sec.getUndeclaredExtensionsByUrl("http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris");
+		assertEquals(1, uris.size());
+	}
+	
+}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/validation/ResourceValidatorDstu2Test.java

@@ -132,7 +132,7 @@ public class ResourceValidatorDstu2Test {
 		
 		assertTrue(result.toString(), result.isSuccessful());
 		assertNotNull(operationOutcome);
-		assertEquals(0, operationOutcome.getIssue().size());
+		assertEquals(1, operationOutcome.getIssue().size());
 	}
 
 	@SuppressWarnings("deprecation")

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

@@ -26,13 +26,18 @@
 			<version>1.4-SNAPSHOT</version>
 			<scope>test</scope>
 		</dependency>
+
+		<!-- 
+		The JPA project uses a newer API but we'll try to hold to this version
+		as much as possible. See #283.
+		-->
 		<dependency>
 			<groupId>javax.servlet</groupId>
-			<artifactId>javax.servlet-api</artifactId>
+			<artifactId>servlet-api</artifactId>
+			<version>2.5</version>
 			<scope>provided</scope>
 		</dependency>
 
-
 		<!-- <dependency> <groupId>net.sf.saxon</groupId> <artifactId>saxon</artifactId> 
 			<version>8.7</version> </dependency> -->
 

hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/Controller.java

@@ -109,7 +109,6 @@ public class Controller extends BaseController {
 		return "result";
 	}
 
-	@SuppressWarnings("unchecked")
 	@RequestMapping(value = { "/delete" })
 	public String actionDelete(HttpServletRequest theReq, HomeRequest theRequest, BindingResult theBindingResult, ModelMap theModel) {
 		addCommonParams(theReq, theRequest, theModel);

pom.xml

@@ -248,7 +248,6 @@
 		<hibernate_version>5.0.6.Final</hibernate_version>
 		<hibernate_validator_version>5.2.2.Final</hibernate_validator_version>
 		<maven_assembly_plugin_version>2.5.3</maven_assembly_plugin_version>
-		<maven_failsafe_plugin_version>2.18.1</maven_failsafe_plugin_version>
 		<maven_license_plugin_version>1.8</maven_license_plugin_version>
 		<maven_site_plugin_version>3.4</maven_site_plugin_version>
 		<maven_source_plugin_version>2.4</maven_source_plugin_version>
@@ -731,7 +730,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-failsafe-plugin</artifactId>
-					<version>2.19</version>
+					<version>2.19.1</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
@@ -741,7 +740,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-surefire-plugin</artifactId>
-					<version>2.19</version>
+					<version>2.19.1</version>
 					<configuration>
 						<redirectTestOutputToFile>true</redirectTestOutputToFile>
 						<runOrder>random</runOrder>
@@ -1314,7 +1313,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-report-plugin</artifactId>
-				<version>2.19</version>
+				<version>2.19.1</version>
 				<reportSets>
 					<reportSet>
 						<reports>

src/changes/changes.xml

@@ -139,6 +139,12 @@
 				implementations and wasn't compatible
 				with coming changes to that API.
 			</action>
+			<action type="fix" issue="283">
+				Remove dependency on Servlet-API 3.0+ by using methods available in 2.5 where possible.
+				Note that we continue to use Servlet-API 3.0+ features in some parts of the JPA API, so
+				running in an old serlvet container should be tested well before use. Thanks to Bill Denton
+				for reporting!
+			</action>
 		</release>
 		<release version="1.3" date="2015-11-14">
 			<action type="add">

src/site/xdoc/doc_cli.xml

@@ -35,7 +35,12 @@
 			
 			<subsection name="Troubleshooting">
 				<p>
-					The tool should work correctly on any system that has Java 6 (or newer) installed. If
+					<b>Note on Java version support:</b> The HAPI library is designed to
+					work in Java 6+, but the Command Line Tool required a minimum of Java 8. This
+					is because the Jetty Web Server that is used within the tool has this requirement. 
+				</p>
+				<p>
+					The tool should work correctly on any system that has Java 8 (or newer) installed. If
 					it is not working correctly, first try the following command to test if Java is installed:<br/>
 					<code>$ java -version</code>
 				</p>