Merge remote-tracking branch 'upstream/master'

.travis.yml

@@ -19,7 +19,7 @@ before_script:
   - export MAVEN_SKIP_RC=true
 
 script:
-#  - mvn -e -B clean install && cd hapi-fhir-cobertura && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID clean test jacoco:report coveralls:report
+#  - mvn -e -B clean install && cd hapi-fhir-ra && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID clean test jacoco:report coveralls:report
-  - mvn -e -B clean install && cd hapi-fhir-cobertura && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID -P COBERTURA clean cobertura:cobertura coveralls:report 
+  - mvn -e -B clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report 
 
 

hapi-fhir-base/pom.xml

@@ -138,6 +138,34 @@
 
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<configuration>
+					<classFolders>
+						<classFolder>${basedir}/target/classes</classFolder>
+					</classFolders>
+					<sourceFolders>
+						<sourceFolder>${basedir}/src/main/java</sourceFolder>
+					</sourceFolders>
+					<dumpOnExit>true</dumpOnExit>
+				</configuration>
+				<executions>
+					<execution>
+						<id>default-prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<configuration>
+					<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>

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

@@ -7,6 +7,7 @@ import java.util.Date;
 import java.util.GregorianCalendar;
 import java.util.TimeZone;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.time.DateUtils;
 import org.apache.commons.lang3.time.FastDateFormat;
@@ -16,14 +17,15 @@ import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import ca.uhn.fhir.parser.DataFormatException;
 
 public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
+	static final long NANOS_PER_MILLIS = 1000000L;
+	static final long NANOS_PER_SECOND = 1000000000L;
 
 	private static final FastDateFormat ourHumanDateFormat = FastDateFormat.getDateInstance(FastDateFormat.MEDIUM);
 	private static final FastDateFormat ourHumanDateTimeFormat = FastDateFormat.getDateTimeInstance(FastDateFormat.MEDIUM, FastDateFormat.MEDIUM);
 
 	private String myFractionalSeconds;
-	private TemporalPrecisionEnum myPrecision = TemporalPrecisionEnum.SECOND;
+	private TemporalPrecisionEnum myPrecision = null;
 	private TimeZone myTimeZone;
-
 	private boolean myTimeZoneZulu = false;
 
 	/**
@@ -186,11 +188,13 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 		if (getValue() == null) {
 			return null;
 		}
-		GregorianCalendar cal = new GregorianCalendar();
+		GregorianCalendar cal;
-		cal.setTime(getValue());
 		if (getTimeZone() != null) {
-			cal.setTimeZone(getTimeZone());
+			cal = new GregorianCalendar(getTimeZone());
+		} else {
+			cal = new GregorianCalendar();
 		}
+		cal.setTime(getValue());
 		return cal;
 	}
 
@@ -199,6 +203,9 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 	 */
 	abstract boolean isPrecisionAllowed(TemporalPrecisionEnum thePrecision);
 
+	/**
+	 * Returns true if the timezone is set to GMT-0:00 (Z)
+	 */
 	public boolean isTimeZoneZulu() {
 		return myTimeZoneZulu;
 	}
@@ -213,7 +220,7 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 		Validate.notNull(getValue(), getClass().getSimpleName() + " contains null value");
 		return DateUtils.isSameDay(new Date(), getValue());
 	}
-	
+
 	private void leftPadWithZeros(int theInteger, int theLength, StringBuilder theTarget) {
 		String string = Integer.toString(theInteger);
 		for (int i = string.length(); i < theLength; i++) {
@@ -228,16 +235,16 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 		cal.setTimeZone(TimeZone.getDefault());
 		String value = theValue;
 		boolean fractionalSecondsSet = false;
-		
+
-		if (value.length() > 0 && (value.charAt(0) == ' ' || value.charAt(value.length()-1) == ' ')) {
+		if (value.length() > 0 && (value.charAt(0) == ' ' || value.charAt(value.length() - 1) == ' ')) {
 			value = value.trim();
 		}
-		
+
 		int length = value.length();
 		if (length == 0) {
 			return null;
 		}
-		
+
 		if (length < 4) {
 			throwBadDateFormat(value);
 		}
@@ -325,7 +332,7 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 		if (fractionalSecondsSet == false) {
 			myFractionalSeconds = "";
 		}
-		
+
 		setPrecision(precision);
 		return cal.getTime();
 
@@ -394,12 +401,12 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 
 	/**
 	 * Sets the value for this type using the given Java Date object as the time, and using the default precision for
-	 * this datatype, as well as the local timezone as determined by the local operating
+	 * this datatype (unless the precision is already set), as well as the local timezone as determined by the local operating
 	 * system. Both of these properties may be modified in subsequent calls if neccesary.
 	 */
 	@Override
 	public BaseDateTimeDt setValue(Date theValue) {
-		setValue(theValue, getDefaultPrecisionForDatatype());
+		setValue(theValue, getPrecision());
 		return this;
 	}
 
@@ -415,11 +422,14 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 	 * @throws DataFormatException
 	 */
 	public void setValue(Date theValue, TemporalPrecisionEnum thePrecision) throws DataFormatException {
-		setTimeZone(TimeZone.getDefault());
+		if (getTimeZone() == null) {
+			setTimeZone(TimeZone.getDefault());
+		}
 		myPrecision = thePrecision;
 		myFractionalSeconds = "";
 		if (theValue != null) {
-			myFractionalSeconds = Integer.toString((int) (theValue.getTime() % 1000));
+			String fractionalSeconds = Integer.toString((int) (theValue.getTime() % 1000));
+			myFractionalSeconds = StringUtils.leftPad(fractionalSeconds, 3, '0');
 		}
 		super.setValue(theValue);
 	}
@@ -490,11 +500,195 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
 		}
 	}
 
-	
 	private void validateLengthIsAtLeast(String theValue, int theLength) {
 		if (theValue.length() < theLength) {
 			throwBadDateFormat(theValue);
 		}
 	}
 
+	/**
+	 * Returns the year, e.g. 2015
+	 */
+	public Integer getYear() {
+		return getFieldValue(Calendar.YEAR);
+	}
+
+	/**
+	 * Returns the month with 0-index, e.g. 0=January
+	 */
+	public Integer getMonth() {
+		return getFieldValue(Calendar.MONTH);
+	}
+
+	/**
+	 * Returns the month with 1-index, e.g. 1=the first day of the month
+	 */
+	public Integer getDay() {
+		return getFieldValue(Calendar.DAY_OF_MONTH);
+	}
+
+	/**
+	 * Returns the hour of the day in a 24h clock, e.g. 13=1pm
+	 */
+	public Integer getHour() {
+		return getFieldValue(Calendar.HOUR_OF_DAY);
+	}
+
+	/**
+	 * Returns the minute of the hour in the range 0-59
+	 */
+	public Integer getMinute() {
+		return getFieldValue(Calendar.MINUTE);
+	}
+
+	/**
+	 * Returns the second of the minute in the range 0-59
+	 */
+	public Integer getSecond() {
+		return getFieldValue(Calendar.SECOND);
+	}
+
+	/**
+	 * Returns the milliseconds within the current second.
+	 * <p>
+	 * Note that this method returns the
+	 * same value as {@link #getNanos()} but with less precision.
+	 * </p>
+	 */
+	public Integer getMillis() {
+		return getFieldValue(Calendar.MILLISECOND);
+	}
+
+	/**
+	 * Returns the nanoseconds within the current second
+	 * <p>
+	 * Note that this method returns the
+	 * same value as {@link #getMillis()} but with more precision.
+	 * </p>
+	 */
+	public Long getNanos() {
+		if (isBlank(myFractionalSeconds)) {
+			return null;
+		}
+		String retVal = StringUtils.rightPad(myFractionalSeconds, 9, '0');
+		retVal = retVal.substring(0, 9);
+		return Long.parseLong(retVal);
+	}
+
+	/**
+	 * Sets the year, e.g. 2015
+	 */
+	public BaseDateTimeDt setYear(int theYear) {
+		setFieldValue(Calendar.YEAR, theYear, null, 0, 9999);
+		return this;
+	}
+
+	/**
+	 * Sets the month with 0-index, e.g. 0=January
+	 */
+	public BaseDateTimeDt setMonth(int theMonth) {
+		setFieldValue(Calendar.MONTH, theMonth, null, 0, 11);
+		return this;
+	}
+
+	/**
+	 * Sets the month with 1-index, e.g. 1=the first day of the month
+	 */
+	public BaseDateTimeDt setDay(int theDay) {
+		setFieldValue(Calendar.DAY_OF_MONTH, theDay, null, 0, 31);
+		return this;
+	}
+
+	/**
+	 * Sets the hour of the day in a 24h clock, e.g. 13=1pm
+	 */
+	public BaseDateTimeDt setHour(int theHour) {
+		setFieldValue(Calendar.HOUR_OF_DAY, theHour, null, 0, 23);
+		return this;
+	}
+
+	/**
+	 * Sets the minute of the hour in the range 0-59
+	 */
+	public BaseDateTimeDt setMinute(int theMinute) {
+		setFieldValue(Calendar.MINUTE, theMinute, null, 0, 59);
+		return this;
+	}
+
+	/**
+	 * Sets the second of the minute in the range 0-59
+	 */
+	public BaseDateTimeDt setSecond(int theSecond) {
+		setFieldValue(Calendar.SECOND, theSecond, null, 0, 59);
+		return this;
+	}
+
+	/**
+	 * Sets the milliseconds within the current second.
+	 * <p>
+	 * Note that this method sets the
+	 * same value as {@link #setNanos(long)} but with less precision.
+	 * </p>
+	 */
+	public BaseDateTimeDt setMillis(int theMillis) {
+		setFieldValue(Calendar.MILLISECOND, theMillis, null, 0, 999);
+		return this;
+	}
+
+	/**
+	 * Sets the nanoseconds within the current second
+	 * <p>
+	 * Note that this method sets the
+	 * same value as {@link #setMillis(int)} but with more precision.
+	 * </p>
+	 */
+	public BaseDateTimeDt setNanos(long theNanos) {
+		validateValueInRange(theNanos, 0, NANOS_PER_SECOND-1);
+		String fractionalSeconds = StringUtils.leftPad(Long.toString(theNanos), 9, '0');
+		
+		// Strip trailing 0s
+		for (int i = fractionalSeconds.length(); i > 0; i--) {
+			if (fractionalSeconds.charAt(i-1) != '0') {
+				fractionalSeconds = fractionalSeconds.substring(0, i);
+				break;
+			}
+		}
+		int millis = (int)(theNanos / NANOS_PER_MILLIS);
+		setFieldValue(Calendar.MILLISECOND, millis, fractionalSeconds, 0, 999);
+		return this;
+	}
+
+	private void setFieldValue(int theField, int theValue, String theFractionalSeconds, int theMinimum, int theMaximum) {
+		validateValueInRange(theValue, theMinimum, theMaximum);
+		Calendar cal;
+		if (getValue() == null) {
+			cal = new GregorianCalendar(0, 0, 0);
+		} else {
+			cal = getValueAsCalendar();
+		}
+		if (theField != -1) {
+			cal.set(theField, theValue);
+		}
+		if (theFractionalSeconds != null) {
+			myFractionalSeconds = theFractionalSeconds;
+		} else if (theField == Calendar.MILLISECOND) {
+			myFractionalSeconds = StringUtils.leftPad(Integer.toString(theValue), 3, '0');
+		}
+		super.setValue(cal.getTime());
+	}
+
+	private void validateValueInRange(long theValue, long theMinimum, long theMaximum) {
+		if (theValue < theMinimum || theValue > theMaximum) {
+			throw new IllegalArgumentException("Value " + theValue + " is not between allowable range: " + theMinimum + " - " + theMaximum);
+		}
+	}
+
+	private Integer getFieldValue(int theField) {
+		if (getValue() == null) {
+			return null;
+		}
+		Calendar cal = getValueAsCalendar();
+		return cal.get(theField);
+	}
+
 }

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

@@ -78,7 +78,7 @@ public class DecimalDt extends BasePrimitive<BigDecimal> implements Comparable<D
 		if (getValue() == null && theObj.getValue() == null) {
 			return 0;
 		}
-		if (getValue() != null && theObj.getValue() == null) {
+		if (getValue() != null && (theObj == null || theObj.getValue() == null)) {
 			return 1;
 		}
 		if (getValue() == null && theObj.getValue() != null) {

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

@@ -185,5 +185,4 @@ public class InstantDt extends BaseDateTimeDt {
 		return DEFAULT_PRECISION;
 	}
 
-
 }

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

@@ -32,22 +32,6 @@ import ca.uhn.fhir.model.api.annotation.SimpleSetter;
 @DatatypeDef(name = "uri")
 public class UriDt extends BasePrimitive<String> {
 
-	/**
-	 * Creates a new UriDt instance which uses the given OID as the content (and prepends "urn:oid:" to the OID string
-	 * in the value of the newly created UriDt, per the FHIR specification).
-	 * 
-	 * @param theOid
-	 *            The OID to use (<code>null</code> is acceptable and will result in a UriDt instance with a
-	 *            <code>null</code> value)
-	 * @return A new UriDt instance
-	 */
-	public static UriDt fromOid(String theOid) {
-		if (theOid == null) {
-			return new UriDt();
-		}
-		return new UriDt("urn:oid:" + theOid);
-	}
-
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UriDt.class);
 
 	/**
@@ -119,18 +103,15 @@ public class UriDt extends BasePrimitive<String> {
 		URI retVal;
 		try {
 			retVal = new URI(theValue).normalize();
-		} catch (URISyntaxException e1) {
+			String urlString = retVal.toString();
-			ourLog.debug("Failed to normalize URL '{}', message was: {}", theValue, e1.toString());
+			if (urlString.endsWith("/") && urlString.length() > 1) {
+				retVal = new URI(urlString.substring(0, urlString.length() - 1));
+			}
+		} catch (URISyntaxException e) {
+			ourLog.debug("Failed to normalize URL '{}', message was: {}", theValue, e.toString());
 			return theValue;
 		}
-		String urlString = retVal.toString();
+
-		if (urlString.endsWith("/") && urlString.length() > 1) {
-			try {
-				retVal = new URI(urlString.substring(0, urlString.length() - 1));
-			} catch (URISyntaxException e) {
-				ourLog.debug("Failed to normalize URL '{}', message was: {}", urlString, e.toString());
-			}
-		}
 		return retVal.toASCIIString();
 	}
 
@@ -139,4 +120,20 @@ public class UriDt extends BasePrimitive<String> {
 		return theValue;
 	}
 
+	/**
+	 * Creates a new UriDt instance which uses the given OID as the content (and prepends "urn:oid:" to the OID string
+	 * in the value of the newly created UriDt, per the FHIR specification).
+	 * 
+	 * @param theOid
+	 *           The OID to use (<code>null</code> is acceptable and will result in a UriDt instance with a
+	 *           <code>null</code> value)
+	 * @return A new UriDt instance
+	 */
+	public static UriDt fromOid(String theOid) {
+		if (theOid == null) {
+			return new UriDt();
+		}
+		return new UriDt("urn:oid:" + theOid);
+	}
+
 }

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

@@ -73,7 +73,7 @@ import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.SummaryEnum;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
 import ca.uhn.fhir.rest.client.BaseHttpClientInvocation;
-import ca.uhn.fhir.rest.method.OperationParameter.IConverter;
+import ca.uhn.fhir.rest.method.OperationParameter.IOperationParamConverter;
 import ca.uhn.fhir.rest.param.CollectionBinder;
 import ca.uhn.fhir.rest.param.DateAndListParam;
 import ca.uhn.fhir.rest.param.NumberAndListParam;
@@ -499,7 +499,7 @@ public class MethodUtil {
 						if (parameterType.equals(ValidationModeEnum.class) == false) {
 							throw new ConfigurationException("Parameter annotated with @" + Validate.class.getSimpleName() + "." + Validate.Mode.class.getSimpleName() + " must be of type " + ValidationModeEnum.class.getName());
 						}
-						param = new OperationParameter(theContext, Constants.EXTOP_VALIDATE, Constants.EXTOP_VALIDATE_MODE, 0, 1).setConverter(new IConverter() {
+						param = new OperationParameter(theContext, Constants.EXTOP_VALIDATE, Constants.EXTOP_VALIDATE_MODE, 0, 1).setConverter(new IOperationParamConverter() {
 							@Override
 							public Object incomingServer(Object theObject) {
 								if (isNotBlank(theObject.toString())) {
@@ -522,7 +522,7 @@ public class MethodUtil {
 						if (parameterType.equals(String.class) == false) {
 							throw new ConfigurationException("Parameter annotated with @" + Validate.class.getSimpleName() + "." + Validate.Profile.class.getSimpleName() + " must be of type " + String.class.getName());
 						}
-						param = new OperationParameter(theContext, Constants.EXTOP_VALIDATE, Constants.EXTOP_VALIDATE_PROFILE, 0, 1).setConverter(new IConverter() {
+						param = new OperationParameter(theContext, Constants.EXTOP_VALIDATE, Constants.EXTOP_VALIDATE_PROFILE, 0, 1).setConverter(new IOperationParamConverter() {
 							@Override
 							public Object incomingServer(Object theObject) {
 								return theObject.toString();

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

@@ -63,6 +63,7 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.ParametersUtil;
+import ca.uhn.fhir.util.ReflectionUtil;
 
 public class OperationParameter implements IParameter {
 
@@ -74,7 +75,7 @@ public class OperationParameter implements IParameter {
 	private boolean myAllowGet;
 
 	private final FhirContext myContext;
-	private IConverter myConverter;
+	private IOperationParamConverter myConverter;
 	@SuppressWarnings("rawtypes")
 	private Class<? extends Collection> myInnerCollectionType;
 	private int myMax;
@@ -203,7 +204,7 @@ public class OperationParameter implements IParameter {
 				mySearchParameterBinding = new SearchParameter(myName, myMin > 0);
 				mySearchParameterBinding.setCompositeTypes(COMPOSITE_TYPES);
 				mySearchParameterBinding.setType(myContext, theParameterType, theInnerCollectionType, theOuterCollectionType);
-				myConverter = new QueryParameterConverter();
+				myConverter = new OperationParamConverter();
 			} else {
 				throw new ConfigurationException("Invalid type for @OperationParam: " + myParameterType.getName());
 			}
@@ -212,7 +213,7 @@ public class OperationParameter implements IParameter {
 
 	}
 
-	public OperationParameter setConverter(IConverter theConverter) {
+	public OperationParameter setConverter(IOperationParamConverter theConverter) {
 		myConverter = theConverter;
 		return this;
 	}
@@ -242,127 +243,9 @@ public class OperationParameter implements IParameter {
 		List<Object> matchingParamValues = new ArrayList<Object>();
 
 		if (theRequest.getRequestType() == RequestTypeEnum.GET) {
-			if (mySearchParameterBinding != null) {
+			translateQueryParametersIntoServerArgumentForGet(theRequest, matchingParamValues);
-
-				List<QualifiedParamList> params = new ArrayList<QualifiedParamList>();
-				String nameWithQualifierColon = myName + ":";
-
-				for (String nextParamName : theRequest.getParameters().keySet()) {
-					String qualifier;
-					if (nextParamName.equals(myName)) {
-						qualifier = null;
-					} else if (nextParamName.startsWith(nameWithQualifierColon)) {
-						qualifier = nextParamName.substring(nextParamName.indexOf(':'));
-					} else {
-						// This is some other parameter, not the one bound by this instance
-						continue;
-					}
-					String[] values = theRequest.getParameters().get(nextParamName);
-					if (values != null) {
-						for (String nextValue : values) {
-							params.add(QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifier, nextValue));
-						}
-					}
-				}
-				if (!params.isEmpty()) {
-					for (QualifiedParamList next : params) {
-						Object values = mySearchParameterBinding.parse(myContext, Collections.singletonList(next));
-						addValueToList(matchingParamValues, values);
-					}
-					
-				}
-
-			} else {
-				String[] paramValues = theRequest.getParameters().get(myName);
-				if (paramValues != null && paramValues.length > 0) {
-					if (myAllowGet) {
-
-						if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
-							List<QualifiedParamList> parameters = new ArrayList<QualifiedParamList>();
-							parameters.add(QualifiedParamList.singleton(paramValues[0]));
-							if (paramValues.length > 1) {
-								parameters.add(QualifiedParamList.singleton(paramValues[1]));
-							}
-							DateRangeParam dateRangeParam = new DateRangeParam();
-							dateRangeParam.setValuesAsQueryTokens(parameters);
-							matchingParamValues.add(dateRangeParam);
-						} else if (String.class.isAssignableFrom(myParameterType)) {
-
-							for (String next : paramValues) {
-								matchingParamValues.add(next);
-							}
-						} else if (ValidationModeEnum.class.equals(myParameterType)) {
-							
-							if (isNotBlank(paramValues[0])) {
-								ValidationModeEnum validationMode = ValidationModeEnum.forCode(paramValues[0]);
-								if (validationMode != null) {
-									matchingParamValues.add(validationMode);
-								} else {
-									throwInvalidMode(paramValues[0]);
-								}
-							}
-							
-						} else {
-							for (String nextValue : paramValues) {
-								FhirContext ctx = theRequest.getServer().getFhirContext();
-								RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
-								IPrimitiveType<?> instance = def.newInstance();
-								instance.setValueAsString(nextValue);
-								matchingParamValues.add(instance);
-							}
-						}
-					} else {
-						HapiLocalizer localizer = theRequest.getServer().getFhirContext().getLocalizer();
-						String msg = localizer.getMessage(OperationParameter.class, "urlParamNotPrimitive", myOperationName, myName);
-						throw new MethodNotAllowedException(msg, RequestTypeEnum.POST);
-					}
-				}
-			}
-			
 		} else {
-
+			translateQueryParametersIntoServerArgumentForPost(theRequest, matchingParamValues);
-			IBaseResource requestContents = (IBaseResource) theRequest.getUserData().get(REQUEST_CONTENTS_USERDATA_KEY);
-			RuntimeResourceDefinition def = myContext.getResourceDefinition(requestContents);
-			if (def.getName().equals("Parameters")) {
-
-				BaseRuntimeChildDefinition paramChild = def.getChildByName("parameter");
-				BaseRuntimeElementCompositeDefinition<?> paramChildElem = (BaseRuntimeElementCompositeDefinition<?>) paramChild.getChildByName("parameter");
-
-				RuntimeChildPrimitiveDatatypeDefinition nameChild = (RuntimeChildPrimitiveDatatypeDefinition) paramChildElem.getChildByName("name");
-				BaseRuntimeChildDefinition valueChild = paramChildElem.getChildByName("value[x]");
-				BaseRuntimeChildDefinition resourceChild = paramChildElem.getChildByName("resource");
-
-				IAccessor paramChildAccessor = paramChild.getAccessor();
-				List<IBase> values = paramChildAccessor.getValues(requestContents);
-				for (IBase nextParameter : values) {
-					List<IBase> nextNames = nameChild.getAccessor().getValues(nextParameter);
-					if (nextNames != null && nextNames.size() > 0) {
-						IPrimitiveType<?> nextName = (IPrimitiveType<?>) nextNames.get(0);
-						if (myName.equals(nextName.getValueAsString())) {
-
-							if (myParameterType.isAssignableFrom(nextParameter.getClass())) {
-								matchingParamValues.add(nextParameter);
-							} else {
-								List<IBase> paramValues = valueChild.getAccessor().getValues(nextParameter);
-								List<IBase> paramResources = resourceChild.getAccessor().getValues(nextParameter);
-								if (paramValues != null && paramValues.size() > 0) {
-									tryToAddValues(paramValues, matchingParamValues);
-								} else if (paramResources != null && paramResources.size() > 0) {
-									tryToAddValues(paramResources, matchingParamValues);
-								}
-							}
-
-						}
-					}
-				}
-
-			} else {
-
-				if (myParameterType.isAssignableFrom(requestContents.getClass())) {
-					tryToAddValues(Arrays.asList((IBase) requestContents), matchingParamValues);
-				}
-
-			}
 		}
 
 		if (matchingParamValues.isEmpty()) {
@@ -373,19 +256,133 @@ public class OperationParameter implements IParameter {
 			return matchingParamValues.get(0);
 		}
 
-		try {
+		Collection<Object> retVal = ReflectionUtil.newInstance(myInnerCollectionType);
-			Collection<Object> retVal = myInnerCollectionType.newInstance();
+		retVal.addAll(matchingParamValues);
-			retVal.addAll(matchingParamValues);
+		return retVal;
-			return retVal;
+	}
-		} catch (InstantiationException e) {
+
-			throw new InternalErrorException("Failed to instantiate " + myInnerCollectionType, e);
+	private void translateQueryParametersIntoServerArgumentForGet(RequestDetails theRequest, List<Object> matchingParamValues) {
-		} catch (IllegalAccessException e) {
+		if (mySearchParameterBinding != null) {
-			throw new InternalErrorException("Failed to instantiate " + myInnerCollectionType, e);
+
+			List<QualifiedParamList> params = new ArrayList<QualifiedParamList>();
+			String nameWithQualifierColon = myName + ":";
+
+			for (String nextParamName : theRequest.getParameters().keySet()) {
+				String qualifier;
+				if (nextParamName.equals(myName)) {
+					qualifier = null;
+				} else if (nextParamName.startsWith(nameWithQualifierColon)) {
+					qualifier = nextParamName.substring(nextParamName.indexOf(':'));
+				} else {
+					// This is some other parameter, not the one bound by this instance
+					continue;
+				}
+				String[] values = theRequest.getParameters().get(nextParamName);
+				if (values != null) {
+					for (String nextValue : values) {
+						params.add(QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifier, nextValue));
+					}
+				}
+			}
+			if (!params.isEmpty()) {
+				for (QualifiedParamList next : params) {
+					Object values = mySearchParameterBinding.parse(myContext, Collections.singletonList(next));
+					addValueToList(matchingParamValues, values);
+				}
+				
+			}
+
+		} else {
+			String[] paramValues = theRequest.getParameters().get(myName);
+			if (paramValues != null && paramValues.length > 0) {
+				if (myAllowGet) {
+
+					if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
+						List<QualifiedParamList> parameters = new ArrayList<QualifiedParamList>();
+						parameters.add(QualifiedParamList.singleton(paramValues[0]));
+						if (paramValues.length > 1) {
+							parameters.add(QualifiedParamList.singleton(paramValues[1]));
+						}
+						DateRangeParam dateRangeParam = new DateRangeParam();
+						dateRangeParam.setValuesAsQueryTokens(parameters);
+						matchingParamValues.add(dateRangeParam);
+					} else if (String.class.isAssignableFrom(myParameterType)) {
+
+						for (String next : paramValues) {
+							matchingParamValues.add(next);
+						}
+					} else if (ValidationModeEnum.class.equals(myParameterType)) {
+						
+						if (isNotBlank(paramValues[0])) {
+							ValidationModeEnum validationMode = ValidationModeEnum.forCode(paramValues[0]);
+							if (validationMode != null) {
+								matchingParamValues.add(validationMode);
+							} else {
+								throwInvalidMode(paramValues[0]);
+							}
+						}
+						
+					} else {
+						for (String nextValue : paramValues) {
+							FhirContext ctx = theRequest.getServer().getFhirContext();
+							RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
+							IPrimitiveType<?> instance = def.newInstance();
+							instance.setValueAsString(nextValue);
+							matchingParamValues.add(instance);
+						}
+					}
+				} else {
+					HapiLocalizer localizer = theRequest.getServer().getFhirContext().getLocalizer();
+					String msg = localizer.getMessage(OperationParameter.class, "urlParamNotPrimitive", myOperationName, myName);
+					throw new MethodNotAllowedException(msg, RequestTypeEnum.POST);
+				}
+			}
 		}
 	}
 
-	public static void throwInvalidMode(String paramValues) {
+	private void translateQueryParametersIntoServerArgumentForPost(RequestDetails theRequest, List<Object> matchingParamValues) {
-		throw new InvalidRequestException("Invalid mode value: \"" + paramValues + "\"");
+		IBaseResource requestContents = (IBaseResource) theRequest.getUserData().get(REQUEST_CONTENTS_USERDATA_KEY);
+		RuntimeResourceDefinition def = myContext.getResourceDefinition(requestContents);
+		if (def.getName().equals("Parameters")) {
+
+			BaseRuntimeChildDefinition paramChild = def.getChildByName("parameter");
+			BaseRuntimeElementCompositeDefinition<?> paramChildElem = (BaseRuntimeElementCompositeDefinition<?>) paramChild.getChildByName("parameter");
+
+			RuntimeChildPrimitiveDatatypeDefinition nameChild = (RuntimeChildPrimitiveDatatypeDefinition) paramChildElem.getChildByName("name");
+			BaseRuntimeChildDefinition valueChild = paramChildElem.getChildByName("value[x]");
+			BaseRuntimeChildDefinition resourceChild = paramChildElem.getChildByName("resource");
+
+			IAccessor paramChildAccessor = paramChild.getAccessor();
+			List<IBase> values = paramChildAccessor.getValues(requestContents);
+			for (IBase nextParameter : values) {
+				List<IBase> nextNames = nameChild.getAccessor().getValues(nextParameter);
+				if (nextNames != null && nextNames.size() > 0) {
+					IPrimitiveType<?> nextName = (IPrimitiveType<?>) nextNames.get(0);
+					if (myName.equals(nextName.getValueAsString())) {
+
+						if (myParameterType.isAssignableFrom(nextParameter.getClass())) {
+							matchingParamValues.add(nextParameter);
+						} else {
+							List<IBase> paramValues = valueChild.getAccessor().getValues(nextParameter);
+							List<IBase> paramResources = resourceChild.getAccessor().getValues(nextParameter);
+							if (paramValues != null && paramValues.size() > 0) {
+								tryToAddValues(paramValues, matchingParamValues);
+							} else if (paramResources != null && paramResources.size() > 0) {
+								tryToAddValues(paramResources, matchingParamValues);
+							}
+						}
+
+					}
+				}
+			}
+
+		} else {
+
+			if (myParameterType.isAssignableFrom(requestContents.getClass())) {
+				tryToAddValues(Arrays.asList((IBase) requestContents), matchingParamValues);
+			}
+
+		}
 	}
 
 	@SuppressWarnings("unchecked")
@@ -419,7 +416,11 @@ public class OperationParameter implements IParameter {
 		}
 	}
 
-	public interface IConverter {
+	public static void throwInvalidMode(String paramValues) {
+		throw new InvalidRequestException("Invalid mode value: \"" + paramValues + "\"");
+	}
+
+	interface IOperationParamConverter {
 
 		Object incomingServer(Object theObject);
 
@@ -427,9 +428,9 @@ public class OperationParameter implements IParameter {
 
 	}
 
-	private class QueryParameterConverter implements IConverter {
+	class OperationParamConverter implements IOperationParamConverter {
 
-		public QueryParameterConverter() {
+		public OperationParamConverter() {
 			Validate.isTrue(mySearchParameterBinding != null);
 		}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java

@@ -29,7 +29,6 @@ import java.util.List;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
-import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -301,7 +300,9 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 	}
 
 	/**
-	 * Sets the range from a pair of dates, inclusive on both ends
+	 * Sets the range from a pair of dates, inclusive on both ends. Note that if
+	 * theLowerBound is after theUpperBound, thie method will automatically reverse
+	 * the order of the arguments in order to create an inclusive range.
 	 * 
 	 * @param theLowerBound
 	 *           A qualified date param representing the lower date bound (optionally may include time), e.g.
@@ -313,8 +314,18 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 	 *           theUpperBound may both be populated, or one may be null, but it is not valid for both to be null.
 	 */
 	public void setRangeFromDatesInclusive(IPrimitiveType<Date> theLowerBound, IPrimitiveType<Date> theUpperBound) {
-		myLowerBound = theLowerBound != null ? new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, theLowerBound) : null;
+		IPrimitiveType<Date> lowerBound = theLowerBound;
-		myUpperBound = theUpperBound != null ? new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, theUpperBound) : null;
+		IPrimitiveType<Date> upperBound = theUpperBound;
+		if (lowerBound != null && lowerBound.getValue() != null && upperBound != null && upperBound.getValue() != null) {
+			if (lowerBound.getValue().after(upperBound.getValue())) {
+				IPrimitiveType<Date> temp = lowerBound;
+				lowerBound = upperBound;
+				upperBound = temp;
+			}
+		}
+		
+		myLowerBound = lowerBound != null ? new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, lowerBound) : null;
+		myUpperBound = upperBound != null ? new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, upperBound) : null;
 		validateAndThrowDataFormatExceptionIfInvalid();
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/NonPrettyPrintWriterWrapper.java

@@ -45,26 +45,31 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
 	}
 
 	@Override
+	@CoverageIgnore
 	public String getPrefix(String theUri) throws XMLStreamException {
 		return myTarget.getPrefix(theUri);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void setPrefix(String thePrefix, String theUri) throws XMLStreamException {
 		myTarget.setPrefix(thePrefix, theUri);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void setDefaultNamespace(String theUri) throws XMLStreamException {
 		myTarget.setDefaultNamespace(theUri);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void setNamespaceContext(NamespaceContext theContext) throws XMLStreamException {
 		myTarget.setNamespaceContext(theContext);
 	}
 
 	@Override
+	@CoverageIgnore
 	public NamespaceContext getNamespaceContext() {
 		return myTarget.getNamespaceContext();
 	}
@@ -94,16 +99,19 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeEmptyElement(String theNamespaceURI, String theLocalName) throws XMLStreamException {
 		myTarget.writeEmptyElement(theNamespaceURI, theLocalName);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeEmptyElement(String thePrefix, String theLocalName, String theNamespaceURI) throws XMLStreamException {
 		myTarget.writeEmptyElement(thePrefix, theLocalName, theNamespaceURI);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeEmptyElement(String theLocalName) throws XMLStreamException {
 		myTarget.writeEmptyElement(theLocalName);
 	}
@@ -127,11 +135,13 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeAttribute(String thePrefix, String theNamespaceURI, String theLocalName, String theValue) throws XMLStreamException {
 		myTarget.writeAttribute(thePrefix, theNamespaceURI, theLocalName, theValue);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeAttribute(String theNamespaceURI, String theLocalName, String theValue) throws XMLStreamException {
 		myTarget.writeAttribute(theNamespaceURI, theLocalName, theValue);
 	}
@@ -152,36 +162,43 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeProcessingInstruction(String theTarget) throws XMLStreamException {
 		myTarget.writeProcessingInstruction(theTarget);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeProcessingInstruction(String theTarget, String theData) throws XMLStreamException {
 		myTarget.writeProcessingInstruction(theTarget, theData);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeCData(String theData) throws XMLStreamException {
 		myTarget.writeCData(theData);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeDTD(String theDtd) throws XMLStreamException {
 		myTarget.writeDTD(theDtd);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeEntityRef(String theName) throws XMLStreamException {
 		myTarget.writeEntityRef(theName);
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeStartDocument() throws XMLStreamException {
 		myTarget.writeStartDocument();
 	}
 
 	@Override
+	@CoverageIgnore
 	public void writeStartDocument(String theVersion) throws XMLStreamException {
 		myTarget.writeStartDocument(theVersion);
 	}
@@ -206,9 +223,7 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
 	}
 
 	static void writeCharacters(char[] theText, int theStart, int theLen, XMLStreamWriter target, int insidePre) throws XMLStreamException {
-		if (theLen == 0) {
+		if (theLen > 0) {
-			return;
-		} else {
 			if (insidePre > 0) {
 				target.writeCharacters(theText, theStart, theLen);
 			} else {
@@ -240,6 +255,7 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
 	}
 
 	@Override
+	@CoverageIgnore
 	public Object getProperty(String theName) throws IllegalArgumentException {
 		return myTarget.getProperty(theName);
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/PortUtil.java

@@ -1,37 +1,19 @@
 package ca.uhn.fhir.util;
 
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2016 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-import java.io.IOException;
 import java.net.ServerSocket;
-import java.util.ArrayList;
-import java.util.List;
 
 /**
  * Provides server ports
  */
+@CoverageIgnore
 public class PortUtil {
 
-	private static List<Integer> ourPorts = new ArrayList<Integer>(); 
+	/*
+	 * Non instantiable
+	 */
+	private PortUtil() {
+		// nothing
+	} 
 	
 	/**
 	 * This is really only used for unit tests but is included in the library so it can be reused across modules. Use with caution.
@@ -41,20 +23,13 @@ public class PortUtil {
 		try {
 			server = new ServerSocket(0);
 			int port = server.getLocalPort();
-			ourPorts.add(port);
 			server.close();
 			Thread.sleep(500);
 			return port;
-		} catch (IOException e) {
+		} catch (Exception e) {
-			throw new Error(e);
-		} catch (InterruptedException e) {
 			throw new Error(e);
 		}
 	}
 
-	public static List<Integer> list() {
-		return ourPorts;
-	}
-
 }
  

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

@@ -61,7 +61,7 @@ public class FhirValidator {
 		myContext = theFhirContext;
 
 		if (ourPhlocPresentOnClasspath == null) {
-			ourPhlocPresentOnClasspath = SchematronProvider.isScematronAvailable(theFhirContext);
+			ourPhlocPresentOnClasspath = SchematronProvider.isSchematronAvailable(theFhirContext);
 		}
 	}
 

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

@@ -23,6 +23,7 @@ package ca.uhn.fhir.validation.schematron;
 import java.lang.reflect.Constructor;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.IValidatorModule;
 
@@ -32,7 +33,8 @@ public class SchematronProvider {
 	private static final String I18N_KEY_NO_PHLOC_WARNING = FhirValidator.class.getName() + ".noPhlocWarningOnStartup";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirValidator.class);
 	
-	public static boolean isScematronAvailable(FhirContext theFhirContext) {
+	@CoverageIgnore
+	public static boolean isSchematronAvailable(FhirContext theFhirContext) {
 		try {
 			Class.forName("com.phloc.schematron.ISchematronResource");
 			return true;
@@ -42,6 +44,8 @@ public class SchematronProvider {
 		}
 	}
 	
+	@SuppressWarnings("unchecked")
+	@CoverageIgnore
 	public static Class<? extends IValidatorModule> getSchematronValidatorClass() {
 		try {
 			return (Class<? extends IValidatorModule>) Class.forName("ca.uhn.fhir.validation.schematron.SchematronBaseValidator");
@@ -50,6 +54,7 @@ public class SchematronProvider {
 		}
 	}
 	
+	@CoverageIgnore
 	public static IValidatorModule getSchematronValidatorInstance(FhirContext myContext) {
 		try {
 			Class<? extends IValidatorModule> cls = getSchematronValidatorClass();

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

@@ -77,5 +77,10 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulUpdate=Successfully update
 ca.uhn.fhir.jpa.dao.SearchBuilder.invalidQuantityPrefix=Unable to handle quantity prefix "{0}" for value: {1}
 ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number prefix "{0}" for value: {1}
 
+ca.uhn.fhir.jpa.provider.BaseJpaProvider.cantCombintAtAndSince=Unable to combine _at and _since parameters for history operation
+
 ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}
-ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!  
+ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
+ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
+
+  

hapi-fhir-jacoco/pom.xml

@@ -0,0 +1,358 @@
+<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">
+	<modelVersion>4.0.0</modelVersion>
+
+	<!-- The parent of this project is the deployable POM. This project isn't deployable, but this keeps it before the root pom in the reactor order when building the site. I don't know why this works... 
+		Need to investigate this. -->
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-deployable-pom</artifactId>
+		<version>1.6-SNAPSHOT</version>
+		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
+	</parent>
+
+	<artifactId>hapi-fhir-jacoco</artifactId>
+	<packaging>jar</packaging>
+
+	<name>HAPI FHIR - JaCoCo Test Coverage</name>
+
+	<dependencies>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-base</artifactId>
+			<version>1.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu</artifactId>
+			<version>1.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu2</artifactId>
+			<version>1.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-dstu3</artifactId>
+			<version>1.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
+			<version>1.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
+			<version>1.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
+			<version>1.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-base</artifactId>
+			<version>1.6-SNAPSHOT</version>
+		</dependency>
+
+		<dependency>
+			<groupId>com.phloc</groupId>
+			<artifactId>phloc-schematron</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.phloc</groupId>
+			<artifactId>phloc-commons</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.thymeleaf</groupId>
+			<artifactId>thymeleaf</artifactId>
+		</dependency>
+
+		<!-- Use an older version of SLF4j just to make sure we compile correctly against old SLF4j - Some people can't upgrade and we have no real need for recent features. -->
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-api</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+		</dependency>
+
+		<!-- Test Database -->
+		<dependency>
+			<groupId>org.apache.derby</groupId>
+			<artifactId>derby</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-dbcp2</artifactId>
+			<scope>test</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>javax.servlet</groupId>
+			<artifactId>javax.servlet-api</artifactId>
+			<scope>provided</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-servlets</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-servlet</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-server</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty</groupId>
+			<artifactId>jetty-util</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>xmlunit</groupId>
+			<artifactId>xmlunit</artifactId>
+			<scope>test</scope>
+		</dependency>
+		
+		<dependency>
+			<groupId>net.sf.json-lib</groupId>
+			<artifactId>json-lib</artifactId>
+			<classifier>jdk15</classifier>
+			<scope>test</scope>
+			<exclusions>
+				<exclusion>
+					<artifactId>commons-logging</artifactId>
+					<groupId>commons-logging</groupId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>net.sf.json-lib</groupId>
+			<artifactId>json-lib</artifactId>
+			<classifier>jdk15-sources</classifier>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>directory-naming</groupId>
+			<artifactId>naming-java</artifactId>
+			<scope>test</scope>
+			<exclusions>
+				<exclusion>
+					<artifactId>commons-logging</artifactId>
+					<groupId>commons-logging</groupId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.ebaysf.web</groupId>
+			<artifactId>cors-filter</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>xmlunit</groupId>
+			<artifactId>xmlunit</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty.websocket</groupId>
+			<artifactId>websocket-api</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty.websocket</groupId>
+			<artifactId>websocket-client</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jetty.websocket</groupId>
+			<artifactId>websocket-server</artifactId>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+
+	<properties>
+	</properties>
+
+	<build>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-site-plugin</artifactId>
+					<configuration>
+						<skipDeploy>true</skipDeploy>
+					</configuration>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+		<plugins>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<executions>
+					<execution>
+						<id>jacoco-merge</id>
+						<goals>
+							<goal>merge</goal>
+						</goals>
+						<phase>install</phase>
+						<configuration>
+							<fileSets>
+								<fileSet implementation="org.apache.maven.shared.model.fileset.FileSet">
+									<directory>${basedir}/..</directory>
+									<includes>
+										<include>hapi-fhir-base/target/jacoco.exec</include>
+										<include>hapi-fhir-structures-dstu/target/jacoco.exec</include>
+										<include>hapi-fhir-structures-dstu2/target/jacoco.exec</include>
+										<include>hapi-fhir-structures-hl7org-dstu2/target/jacoco.exec</include>
+										<include>hapi-fhir-structures-dstu3/target/jacoco.exec</include>
+										<include>hapi-fhir-jpaserver-base/target/jacoco.exec</include>
+									</includes>
+								</fileSet>
+							</fileSets>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.eluder.coveralls</groupId>
+				<artifactId>coveralls-maven-plugin</artifactId>
+				<configuration>
+					<sourceEncoding>UTF-8</sourceEncoding>
+					<serviceName>travis-ci</serviceName>
+					<serviceJobId>${env.TRAVIS_JOB_ID}</serviceJobId>
+					<sourceDirectories>
+						<sourceDirectory>../hapi-fhir-structures-dstu/src/test/java</sourceDirectory>
+						<sourceDirectory>../hapi-fhir-structures-dstu2/src/test/java</sourceDirectory>
+						<sourceDirectory>../hapi-fhir-structures-hl7org-dstu2/src/test/java</sourceDirectory>
+						<sourceDirectory>../hapi-fhir-jpaserver-base/src/test/java</sourceDirectory>
+						<sourceDirectory>../hapi-fhir-base/src/main/java</sourceDirectory>
+						<sourceDirectory>../hapi-fhir-jpaserver-base/src/main/java</sourceDirectory>
+					</sourceDirectories>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>build-helper-maven-plugin</artifactId>
+				<executions>
+					<execution>
+						<id>add-source</id>
+						<phase>generate-sources</phase>
+						<goals>
+							<goal>add-source</goal>
+						</goals>
+						<configuration>
+							<sources>
+								<source>../hapi-fhir-base/src/main/java</source>
+								<source>../hapi-fhir-jpaserver-base/src/main/java</source>
+							</sources>
+						</configuration>
+					</execution>
+					<!-- 
+					<execution>
+						<id>add-test-source</id>
+						<phase>generate-test-sources</phase>
+						<goals>
+							<goal>add-test-source</goal>
+						</goals>
+						<configuration>
+							<sources>
+								<source>../hapi-fhir-structures-dstu/src/test/java</source>
+								<source>../hapi-fhir-structures-dstu2/src/test/java</source>
+								<source>../hapi-fhir-structures-hl7org-dstu2/src/test/java</source>
+								<source>../hapi-fhir-structures-dstu3/src/test/java</source>
+								<source>../hapi-fhir-jpaserver-base/src/test/java</source>
+								<source>../hapi-fhir-base/src/test/java</source>
+							</sources>
+						</configuration>
+					</execution>
+					-->
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-install-plugin</artifactId>
+				<configuration>
+					<skip>true</skip>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-deploy-plugin</artifactId>
+				<configuration>
+					<skip>true</skip>
+				</configuration>
+			</plugin>
+		</plugins>
+		<resources>
+		</resources>
+		<testResources>
+			<testResource>
+				<directory>../hapi-fhir-base/src/test/resources</directory>
+			</testResource>
+			<testResource>
+				<directory>../hapi-fhir-jpaserver-base/src/test/resources</directory>
+			</testResource>
+			<testResource>
+				<directory>../hapi-fhir-structures-dstu/src/test/resources</directory>
+			</testResource>
+			<testResource>
+				<directory>../hapi-fhir-structures-dstu2/src/test/resources</directory>
+			</testResource>
+			<testResource>
+				<directory>../hapi-fhir-structures-hl7org-dstu2/src/test/resources</directory>
+			</testResource>
+			<testResource>
+				<directory>../hapi-fhir-structures-dstu3/src/test/resources</directory>
+			</testResource>
+		</testResources>
+	</build>
+	<reporting>
+		<plugins>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>cobertura-maven-plugin</artifactId>
+				<reportSets>
+					<reportSet>
+						<reports>
+							<report>cobertura</report>
+						</reports>
+						<configuration>
+							<check>
+								<haltOnFailure>true</haltOnFailure>
+							</check>
+						</configuration>
+					</reportSet>
+				</reportSets>
+			</plugin>
+			<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>
+			</plugin>
+		</plugins>
+	</reporting>
+
+</project>

hapi-fhir-jpaserver-base/pom.xml

@@ -335,13 +335,36 @@
 			</plugins>
 		</pluginManagement>
 		<plugins>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<configuration>
+					<classFolders>
+						<classFolder>${basedir}/target/classes</classFolder>
+						<classFolder>${basedir}../hapi-fhir-base/target/classes</classFolder>
+					</classFolders>
+					<sourceFolders>
+						<sourceFolder>${basedir}/src/main/java</sourceFolder>
+						<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
+					</sourceFolders>
+					<dumpOnExit>true</dumpOnExit>
+				</configuration>
+				<executions>
+					<execution>
+						<id>default-prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<!-- These tests all use a shared database, so it's easier if they run in a predictable order -->
 					<runOrder>alphabetical</runOrder>
-					<!--<reuseForks>false</reuseForks>-->
+					<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+					<forkCount>1</forkCount>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java

@@ -28,7 +28,6 @@ import java.util.Collection;
 import java.util.List;
 import java.util.Set;
 
-import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
@@ -56,12 +55,14 @@ import org.hibernate.search.annotations.Field;
 import org.hibernate.search.annotations.Fields;
 import org.hibernate.search.annotations.Indexed;
 import org.hibernate.search.annotations.Store;
+import org.hibernate.search.indexes.interceptor.DontInterceptEntityInterceptor;
 
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
 
 //@formatter:off
 @Entity
-@Indexed()	
+@Indexed(interceptor=DeferConceptIndexingInterceptor.class)	
 @Table(name="TRM_CONCEPT", uniqueConstraints= {
 	@UniqueConstraint(name="IDX_CONCEPT_CS_CODE", columnNames= {"CODESYSTEM_PID", "CODE"})
 }, indexes= {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java

@@ -35,8 +35,6 @@ import javax.persistence.ManyToOne;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
-import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
-
 @Entity
 @Table(name="TRM_CONCEPT_PC_LINK")
 public class TermConceptParentChildLink implements Serializable {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaProvider.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jpa.provider;
 
+import java.util.Date;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -28,9 +30,10 @@ import javax.servlet.http.HttpServletRequest;
 
 import org.apache.commons.lang3.StringUtils;
 import org.jboss.logging.MDC;
-import org.springframework.beans.factory.annotation.Autowired;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 
 public class BaseJpaProvider {
@@ -41,6 +44,9 @@ public class BaseJpaProvider {
 
 	private FhirContext myContext;
 
+	/**
+	 * @param theRequest The servlet request 
+	 */
 	public void endRequest(HttpServletRequest theRequest) {
 		MDC.remove(REMOTE_ADDR);
 		MDC.remove(REMOTE_UA);
@@ -54,10 +60,25 @@ public class BaseJpaProvider {
 		return myContext;
 	}
 
+	protected DateRangeParam processSinceOrAt(Date theSince, DateRangeParam theAt) {
+		boolean haveAt = theAt != null && (theAt.getLowerBoundAsInstant() != null || theAt.getUpperBoundAsInstant() != null);
+		if (haveAt && theSince != null) {
+			String msg = getContext().getLocalizer().getMessage(BaseJpaProvider.class, "cantCombintAtAndSince");
+			throw new InvalidRequestException(msg);
+		}
+		
+		if (haveAt) {
+			return theAt;
+		}
+		
+		return new DateRangeParam(theSince, null);
+	}
+
 	public void setContext(FhirContext theContext) {
 		myContext = theContext;
 	}
 
+	
 	public void startRequest(HttpServletRequest theRequest) {
 		if (theRequest == null) {
 			return;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProvider.java

@@ -65,24 +65,29 @@ public abstract class BaseJpaResourceProvider<T extends IBaseResource> extends B
 			HttpServletRequest theRequest, 
 			@IdParam IIdType theId, 
 			@Since Date theSince, 
-//			@At DateRangeParam theAt, 
+			@At DateRangeParam theAt, 
 			RequestDetails theRequestDetails) {
 	//@formatter:on
 		
 		startRequest(theRequest);
 		try {
-//			DateRangeParam sinceOrAt = processSinceOrAt(theSince)
+			DateRangeParam sinceOrAt = processSinceOrAt(theSince, theAt);
-			return myDao.history(theId, theSince, null, theRequestDetails);
+			return myDao.history(theId, sinceOrAt.getLowerBoundAsInstant(), sinceOrAt.getUpperBoundAsInstant(), theRequestDetails);
 		} finally {
 			endRequest(theRequest);
 		}
 	}
 
 	@History
-	public IBundleProvider getHistoryForResourceType(HttpServletRequest theRequest, @Since Date theDate, RequestDetails theRequestDetails) {
+	public IBundleProvider getHistoryForResourceType(
+			HttpServletRequest theRequest, 
+			@Since Date theSince, 
+			@At DateRangeParam theAt, 
+			RequestDetails theRequestDetails) {
 		startRequest(theRequest);
 		try {
-			return myDao.history(theDate, null, theRequestDetails);
+			DateRangeParam sinceOrAt = processSinceOrAt(theSince, theAt);
+			return myDao.history(sinceOrAt.getLowerBoundAsInstant(), sinceOrAt.getUpperBoundAsInstant(), theRequestDetails);
 		} finally {
 			endRequest(theRequest);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java

@@ -28,10 +28,12 @@ import org.springframework.beans.factory.annotation.Required;
 
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.model.api.TagList;
+import ca.uhn.fhir.rest.annotation.At;
 import ca.uhn.fhir.rest.annotation.GetTags;
 import ca.uhn.fhir.rest.annotation.History;
 import ca.uhn.fhir.rest.annotation.Since;
 import ca.uhn.fhir.rest.method.RequestDetails;
+import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 
 public class BaseJpaSystemProvider<T, MT> extends BaseJpaProvider {
@@ -48,10 +50,11 @@ public class BaseJpaSystemProvider<T, MT> extends BaseJpaProvider {
 	}
 
 	@History
-	public IBundleProvider historyServer(HttpServletRequest theRequest, @Since Date theDate, RequestDetails theRequestDetails) {
+	public IBundleProvider historyServer(HttpServletRequest theRequest, @Since Date theDate, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
 		startRequest(theRequest);
 		try {
-			return myDao.history(theDate, null, theRequestDetails);
+			DateRangeParam range = super.processSinceOrAt(theDate, theAt);
+			return myDao.history(range.getLowerBoundAsInstant(), range.getUpperBoundAsInstant(), theRequestDetails);
 		} finally {
 			endRequest(theRequest);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java

@@ -62,7 +62,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
 		}
 
 		if (moreThanOneTrue(haveId, haveIdentifier, haveValueSet)) {
-			throw new InvalidRequestException("$expand must EITHER be invoked at the type level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.");
+			throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.");
 		}
 		
 		startRequest(theServletRequest);

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

@@ -0,0 +1,9 @@
+package ca.uhn.fhir.jpa.search;
+
+import org.hibernate.search.indexes.interceptor.DontInterceptEntityInterceptor;
+
+public class DeferConceptIndexingInterceptor extends DontInterceptEntityInterceptor
+//implements EntityIndexingInterceptor<TermConcept> 
+{
+	// nothing for now
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java

@@ -15,7 +15,6 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 

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

@@ -40,5 +40,11 @@ public class BaseFhirDaoTest  extends BaseJpaTest {
 		observation.setEffective(period);
 		
 	}
+
+
+	@Override
+	protected FhirContext getContext() {
+		return ourCtx;
+	}
 	
 }

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

@@ -16,6 +16,7 @@ import javax.persistence.EntityManager;
 import org.apache.commons.io.IOUtils;
 import org.hibernate.search.jpa.Search;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
+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.AfterClass;
@@ -26,6 +27,7 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.entity.ForcedId;
 import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;
@@ -55,9 +57,10 @@ import ca.uhn.fhir.rest.method.IRequestOperationCallback;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.TestUtil;
 
-public class BaseJpaTest {
+public abstract class BaseJpaTest {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaTest.class);
 	protected ServletRequestDetails mySrd;
@@ -74,6 +77,32 @@ public class BaseJpaTest {
 		return theSearch.getResources(0, theSearch.size());
 	}
 
+	protected abstract FhirContext getContext();
+	
+	protected List<String> toUnqualifiedVersionlessIdValues(IBaseBundle theFound) {
+		List<String> retVal = new ArrayList<String>();
+
+		List<IBaseResource> res = BundleUtil.toListOfResources(getContext(), theFound);
+		int size = res.size();
+		ourLog.info("Found {} results", size);
+		for (IBaseResource next : res) {
+			retVal.add(next.getIdElement().toUnqualifiedVersionless().getValue());
+		}
+		return retVal;
+	}
+
+	protected List<String> toUnqualifiedIdValues(IBaseBundle theFound) {
+		List<String> retVal = new ArrayList<String>();
+
+		List<IBaseResource> res = BundleUtil.toListOfResources(getContext(), theFound);
+		int size = res.size();
+		ourLog.info("Found {} results", size);
+		for (IBaseResource next : res) {
+			retVal.add(next.getIdElement().toUnqualified().getValue());
+		}
+		return retVal;
+	}
+
 	protected List<IIdType> toUnqualifiedVersionlessIds(Bundle theFound) {
 		List<IIdType> retVal = new ArrayList<IIdType>();
 		for (Entry next : theFound.getEntry()) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu1Test.java

@@ -30,18 +30,22 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 @SuppressWarnings("unused")
-public class FhirResourceDaoDstu1Test  extends BaseJpaTest {
+public class FhirResourceDaoDstu1Test extends BaseJpaTest {
-
+	private static AnnotationConfigApplicationContext ourAppCtx;
+	private static FhirContext ourCtx;
 	private static IFhirResourceDao<Device> ourDeviceDao;
 	private static IFhirResourceDao<DiagnosticReport> ourDiagnosticReportDao;
 	private static IFhirResourceDao<Encounter> ourEncounterDao;
-	private static AnnotationConfigApplicationContext ourAppCtx;
 	private static IFhirResourceDao<Location> ourLocationDao;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu1Test.class);
 	private static IFhirResourceDao<Observation> ourObservationDao;
 	private static IFhirResourceDao<Organization> ourOrganizationDao;
 	private static IFhirResourceDao<Patient> ourPatientDao;
-	private static FhirContext ourCtx;
+
+	@Override
+	protected FhirContext getContext() {
+		return ourCtx;
+	}
 
 	@Test
 	public void testCreateDuplicateIdFails() {
@@ -64,7 +68,7 @@ public class FhirResourceDaoDstu1Test  extends BaseJpaTest {
 			assertThat(e.getMessage(), containsString("Can not create entity with ID[" + methodName + "], a resource with this ID already exists"));
 		}
 	}
-	
+
 	@Test
 	public void testCreateNumericIdFails() {
 		Patient p = new Patient();
@@ -125,6 +129,12 @@ public class FhirResourceDaoDstu1Test  extends BaseJpaTest {
 
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() {
+		ourAppCtx.close();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
 	@SuppressWarnings("unchecked")
 	@BeforeClass
 	public static void beforeClass() {
@@ -139,10 +149,4 @@ public class FhirResourceDaoDstu1Test  extends BaseJpaTest {
 		ourCtx = ourAppCtx.getBean(FhirContext.class);
 	}
 
-	@AfterClass
-	public static void afterClassClearContext() {
-		ourAppCtx.close();
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu1Test.java

@@ -50,30 +50,28 @@ import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.TestUtil;
 
-public class FhirSystemDaoDstu1Test extends BaseJpaTest  {
+public class FhirSystemDaoDstu1Test extends BaseJpaTest {
 
 	private static AnnotationConfigApplicationContext ourCtx;
+	private static EntityManager ourEntityManager;
 	private static FhirContext ourFhirContext;
 	private static IFhirResourceDao<Location> ourLocationDao;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu1Test.class);
 	private static IFhirResourceDao<Observation> ourObservationDao;
 	private static IFhirResourceDao<Patient> ourPatientDao;
 	private static IFhirSystemDao<List<IResource>, MetaDt> ourSystemDao;
-	private static EntityManager ourEntityManager;
 	private static PlatformTransactionManager ourTxManager;
 
-	@AfterClass
-	public static void afterClassClearContext() {
-		ourCtx.close();
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-
 	@Before
 	public void before() {
 		super.purgeDatabase(ourEntityManager, ourTxManager);
 	}
 
+	@Override
+	protected FhirContext getContext() {
+		return ourFhirContext;
+	}
+
 	@Test
 	public void testGetResourceCounts() {
 		Observation obs = new Observation();
@@ -147,7 +145,7 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest  {
 		assertEquals(1, values.size());
 
 	}
-	
+
 	@Test
 	public void testPersistWithSimpleLink() {
 		Patient patient = new Patient();
@@ -378,11 +376,10 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest  {
 
 		String encodeResourceToString = ourFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(response.get(0));
 		ourLog.info(encodeResourceToString);
-		
+
 		assertThat(encodeResourceToString, not(containsString("smsp")));
 	}
 
-
 	/**
 	 * This is the correct way to do this, not {@link #testTransactionWithCidIds()}
 	 */
@@ -479,6 +476,11 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest  {
 
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() {
+		ourCtx.close();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
 
 	@SuppressWarnings("unchecked")
 	@BeforeClass

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -73,31 +73,17 @@ import ca.uhn.fhir.util.TestUtil;
 //@formatter:on
 public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 
-	@AfterClass
-	public static void afterClassClearContext() throws Exception {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-
 	@Autowired
 	protected ApplicationContext myAppCtx;
 	@Autowired
-	protected IFulltextSearchSvc mySearchDao;
-	@Autowired
-	@Qualifier("myConceptMapDaoDstu2")
-	protected IFhirResourceDao<ConceptMap> myConceptMapDao;
-	@Autowired
 	@Qualifier("myAppointmentDaoDstu2")
 	protected IFhirResourceDao<Appointment> myAppointmentDao;
 	@Autowired
 	@Qualifier("myBundleDaoDstu2")
 	protected IFhirResourceDao<Bundle> myBundleDao;
 	@Autowired
-	@Qualifier("myMedicationDaoDstu2")
+	@Qualifier("myConceptMapDaoDstu2")
-	protected IFhirResourceDao<Medication> myMedicationDao;
+	protected IFhirResourceDao<ConceptMap> myConceptMapDao;
-	@Autowired
-	@Qualifier("myMedicationOrderDaoDstu2")
-	protected IFhirResourceDao<MedicationOrder> myMedicationOrderDao;
 	@Autowired
 	protected DaoConfig myDaoConfig;
 	@Autowired
@@ -112,11 +98,9 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myEncounterDaoDstu2")
 	protected IFhirResourceDao<Encounter> myEncounterDao;
-	
+	//	@PersistenceContext()
-//	@PersistenceContext()
 	@Autowired
 	protected EntityManager myEntityManager;
-	
 	@Autowired
 	@Qualifier("myFhirContextDstu2")
 	protected FhirContext myFhirCtx;
@@ -127,6 +111,17 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myLocationDaoDstu2")
 	protected IFhirResourceDao<Location> myLocationDao;
+	
+@Autowired
+	@Qualifier("myMediaDaoDstu2")
+	protected IFhirResourceDao<Media> myMediaDao;
+	
+	@Autowired
+	@Qualifier("myMedicationDaoDstu2")
+	protected IFhirResourceDao<Medication> myMedicationDao;
+	@Autowired
+	@Qualifier("myMedicationOrderDaoDstu2")
+	protected IFhirResourceDao<MedicationOrder> myMedicationOrderDao;
 	@Autowired
 	@Qualifier("myObservationDaoDstu2")
 	protected IFhirResourceDao<Observation> myObservationDao;
@@ -137,9 +132,6 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Qualifier("myPatientDaoDstu2")
 	protected IFhirResourceDaoPatient<Patient> myPatientDao;
 	@Autowired
-	@Qualifier("myMediaDaoDstu2")
-	protected IFhirResourceDao<Media> myMediaDao;
-	@Autowired
 	@Qualifier("myPractitionerDaoDstu2")
 	protected IFhirResourceDao<Practitioner> myPractitionerDao;
 	@Autowired
@@ -152,6 +144,8 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Qualifier("myResourceProvidersDstu2")
 	protected Object myResourceProviders;
 	@Autowired
+	protected IFulltextSearchSvc mySearchDao;
+	@Autowired
 	@Qualifier("myStructureDefinitionDaoDstu2")
 	protected IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
 	@Autowired
@@ -171,21 +165,11 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myValueSetDaoDstu2")
 	protected IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> myValueSetDao;
-
 	@Before
 	public void beforeCreateInterceptor() {
 		myInterceptor = mock(IServerInterceptor.class);
 		myDaoConfig.setInterceptors(myInterceptor);
 	}
-
-	@Before
-	public void beforeResetConfig() {
-		myDaoConfig.setHardSearchLimit(1000);
-		myDaoConfig.setHardTagListLimit(1000);
-		myDaoConfig.setIncludeLimit(2000);
-		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
-	}
-
 	@Before
 	@Transactional
 	public void beforeFlushFT() {
@@ -204,6 +188,19 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 		purgeDatabase(entityManager, myTxManager);
 	}
 
+	@Before
+	public void beforeResetConfig() {
+		myDaoConfig.setHardSearchLimit(1000);
+		myDaoConfig.setHardTagListLimit(1000);
+		myDaoConfig.setIncludeLimit(2000);
+		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
+	}
+
+	@Override
+	protected FhirContext getContext() {
+		return myFhirCtx;
+	}
+
 	protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
 		InputStream stream = FhirResourceDaoDstu2SearchNoFtTest.class.getResourceAsStream(resourceName);
 		if (stream == null) {
@@ -221,4 +218,9 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 		return retVal;
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchFtTest.java

@@ -29,11 +29,10 @@ import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.StringOrListParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.Constants;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
-	
+
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2SearchFtTest.class);
 
 	@AfterClass
@@ -41,7 +40,6 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
-
 	@Test
 	public void testSuggestIgnoresBase64Content() {
 		Patient patient = new Patient();
@@ -52,11 +50,11 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		med.getSubject().setReference(ptId);
 		med.getSubtype().setText("Systolic Blood Pressure");
 		med.getContent().setContentType("LCws");
-		med.getContent().setData(new Base64BinaryDt(new byte[] {44,44,44,44,44,44,44,44}));
+		med.getContent().setData(new Base64BinaryDt(new byte[] { 44, 44, 44, 44, 44, 44, 44, 44 }));
 		med.getContent().setTitle("bbbb syst");
 		myMediaDao.create(med, mySrd);
 		ourLog.info(myFhirCtx.newJsonParser().encodeResourceToString(med));
-		
+
 		List<Suggestion> output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "press");
 		ourLog.info("Found: " + output);
 		assertEquals(2, output.size());
@@ -76,12 +74,12 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		assertEquals("bbbb syst", output.get(1).getTerm());
 		assertEquals("Systolic", output.get(2).getTerm());
 		assertEquals("Systolic Blood Pressure", output.get(3).getTerm());
-		
+
 		output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "LCws");
 		ourLog.info("Found: " + output);
 		assertEquals(0, output.size());
 	}
-	
+
 	@Test
 	public void testSuggest() {
 		Patient patient = new Patient();
@@ -137,7 +135,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		assertEquals(2, output.size());
 		assertEquals("HELLO", output.get(0).getTerm());
 		assertEquals("ZXC HELLO", output.get(1).getTerm());
-		
+
 		output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "Z");
 		ourLog.info("Found: " + output);
 		assertEquals(0, output.size());
@@ -149,8 +147,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		assertEquals("ZXC HELLO", output.get(1).getTerm());
 
 	}
-	
+
-	
 	@Test
 	public void testSearchAndReindex() {
 		Patient patient;
@@ -210,7 +207,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		Device dev1 = new Device();
 		dev1.setManufacturer("Some Manufacturer");
 		IIdType devId1 = myDeviceDao.create(dev1, mySrd).getId().toUnqualifiedVersionless();
-		
+
 		Device dev2 = new Device();
 		dev2.setManufacturer("Some Manufacturer 2");
 		myDeviceDao.create(dev2, mySrd).getId().toUnqualifiedVersionless();
@@ -234,14 +231,14 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		obs3.getCode().addCoding().setCode("CODE3");
 		obs3.setValue(new StringDt("obsvalue3"));
 		IIdType obsId3 = myObservationDao.create(obs3, mySrd).getId().toUnqualifiedVersionless();
-		
+
 		HttpServletRequest request;
 		List<IIdType> actual;
 		request = mock(HttpServletRequest.class);
 		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")));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, param, null, mySrd));
@@ -259,7 +256,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		/*
 		 * Add another match
 		 */
-		
+
 		Observation obs4 = new Observation();
 		obs4.getSubject().setReference(ptId1);
 		obs4.getCode().addCoding().setCode("CODE1");
@@ -275,7 +272,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		/*
 		 * Make one previous match no longer match
 		 */
-		
+
 		obs1 = new Observation();
 		obs1.setId(obsId1);
 		obs1.getSubject().setReference(ptId1);
@@ -289,7 +286,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		assertThat(actual, containsInAnyOrder(ptId1, obsId4));
 
 	}
-	
+
 	@Test
 	public void testEverythingTypeWithContentFilter() {
 		Patient pt1 = new Patient();
@@ -303,7 +300,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		Device dev1 = new Device();
 		dev1.setManufacturer("Some Manufacturer");
 		IIdType devId1 = myDeviceDao.create(dev1, mySrd).getId().toUnqualifiedVersionless();
-		
+
 		Device dev2 = new Device();
 		dev2.setManufacturer("Some Manufacturer 2");
 		IIdType devId2 = myDeviceDao.create(dev2, mySrd).getId().toUnqualifiedVersionless();
@@ -326,14 +323,14 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		obs3.getCode().addCoding().setCode("CODE3");
 		obs3.setValue(new StringDt("obsvalue3"));
 		IIdType obsId3 = myObservationDao.create(obs3, mySrd).getId().toUnqualifiedVersionless();
-		
+
 		HttpServletRequest request;
 		List<IIdType> actual;
 		request = mock(HttpServletRequest.class);
 		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")));
 		actual = toUnqualifiedVersionlessIds(myPatientDao.patientTypeEverything(request, null, null, null, param, null, mySrd));
@@ -346,7 +343,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		/*
 		 * Add another match
 		 */
-		
+
 		Observation obs4 = new Observation();
 		obs4.getSubject().setReference(ptId1);
 		obs4.getCode().addCoding().setCode("CODE1");
@@ -362,7 +359,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		/*
 		 * Make one previous match no longer match
 		 */
-		
+
 		obs1 = new Observation();
 		obs1.setId(obsId1);
 		obs1.getSubject().setReference(ptId1);
@@ -377,10 +374,8 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 
 	}
 
-	
 	/**
-	 * When processing transactions, we do two passes. Make sure we don't update the lucene index twice since that would
+	 * When processing transactions, we do two passes. Make sure we don't update the lucene index twice since that would be inefficient
-	 * be inefficient
 	 */
 	@Test
 	public void testSearchDontReindexForUpdateWithIndexDisabled() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java

@@ -792,19 +792,19 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 		{
 			SearchParameterMap params = new SearchParameterMap();
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, hasItems(id1a, id1b, id2));
+			assertThat(patients, containsInAnyOrder(id1a, id1b, id2));
 		}
 		{
 			SearchParameterMap params = new SearchParameterMap();
 			params.setLastUpdated(new DateRangeParam(beforeAny, null));
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, hasItems(id1a, id1b, id2));
+			assertThat(patients, containsInAnyOrder(id1a, id1b, id2));
 		}
 		{
 			SearchParameterMap params = new SearchParameterMap();
 			params.setLastUpdated(new DateRangeParam(beforeR2, null));
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, hasItems(id2));
+			assertThat(patients, containsInAnyOrder(id2));
 			assertThat(patients, not(hasItems(id1a, id1b)));
 		}
 		{
@@ -812,13 +812,13 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 			params.setLastUpdated(new DateRangeParam(beforeAny, beforeR2));
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
 			assertThat(patients.toString(), patients, not(hasItems(id2)));
-			assertThat(patients.toString(), patients, (hasItems(id1a, id1b)));
+			assertThat(patients.toString(), patients, (containsInAnyOrder(id1a, id1b)));
 		}
 		{
 			SearchParameterMap params = new SearchParameterMap();
 			params.setLastUpdated(new DateRangeParam(null, beforeR2));
 			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, (hasItems(id1a, id1b)));
+			assertThat(patients, (containsInAnyOrder(id1a, id1b)));
 			assertThat(patients, not(hasItems(id2)));
 		}
 	}

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

@@ -106,9 +106,6 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Qualifier("myCarePlanDaoDstu3")
 	protected IFhirResourceDao<CarePlan> myCarePlanDao;
 	@Autowired
-	@Qualifier("myConditionDaoDstu3")
-	protected IFhirResourceDao<Condition> myConditionDao;
-	@Autowired
 	@Qualifier("myCodeSystemDaoDstu3")
 	protected IFhirResourceDao<CodeSystem> myCodeSystemDao;
 	@Autowired
@@ -118,6 +115,9 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Qualifier("myConceptMapDaoDstu3")
 	protected IFhirResourceDao<ConceptMap> myConceptMapDao;
 	@Autowired
+	@Qualifier("myConditionDaoDstu3")
+	protected IFhirResourceDao<Condition> myConditionDao;
+	@Autowired
 	protected DaoConfig myDaoConfig;
 	@Autowired
 	@Qualifier("myDeviceDaoDstu3")
@@ -213,7 +213,6 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myValueSetDaoDstu3")
 	protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
-
 	@After()
 	public void afterGrabCaches() {
 		ourValueSetDao = myValueSetDao;
@@ -251,6 +250,11 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 		myDaoConfig.setIncludeLimit(2000);
 	}
 
+	@Override
+	protected FhirContext getContext() {
+		return myFhirCtx;
+	}
+
 	protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
 		InputStream stream = FhirResourceDaoDstu2SearchNoFtTest.class.getResourceAsStream(resourceName);
 		if (stream == null) {

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

@@ -1491,7 +1491,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		List<Date> preDates = Lists.newArrayList();
 		List<String> ids = Lists.newArrayList();
 		for (int i = 0; i < 10; i++) {
-			Thread.sleep(10);
+			Thread.sleep(100);
 			preDates.add(new Date());
 			patient.setId(id);
 			patient.getName().get(0).getFamily().get(0).setValue(methodName + "_i");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UpdateTest.java

@@ -160,12 +160,13 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 		myPatientDao.create(p, mySrd).getId();
 
 		InstantDt start = InstantDt.withCurrentTime();
+		ourLog.info("First time: {}", start.getValueAsString());
 		Thread.sleep(100);
 		
 		p = new Patient();
 		p.addIdentifier().setSystem("urn:system").setValue(methodName);
 		IIdType id = myPatientDao.create(p, mySrd).getId();
-		ourLog.info("Created patient, got it: {}", id);
+		ourLog.info("Created patient, got ID: {}", id);
 
 		Thread.sleep(100);
 
@@ -174,7 +175,9 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
 		p.addName().addFamily("Hello");
 		p.setId("Patient/" + methodName);
 
-		myPatientDao.update(p, "Patient?_lastUpdated=gt" + start.getValueAsString(), mySrd);
+		String matchUrl = "Patient?_lastUpdated=gt" + start.getValueAsString();
+		ourLog.info("URL is: {}", matchUrl);
+		myPatientDao.update(p, matchUrl, mySrd);
 
 		p = myPatientDao.read(id.toVersionless(), mySrd);
 		assertThat(p.getIdElement().toVersionless().toString(), not(containsString("test")));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu1Test.java

@@ -63,7 +63,6 @@ import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 public class ResourceProviderDstu1Test  extends BaseJpaTest {
@@ -88,6 +87,10 @@ public class ResourceProviderDstu1Test  extends BaseJpaTest {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
+	@Override
+	protected FhirContext getContext() {
+		return ourCtx;
+	}
 
 	// private static JpaConformanceProvider ourConfProvider;
 
@@ -121,11 +124,11 @@ public class ResourceProviderDstu1Test  extends BaseJpaTest {
 		}
 		ourClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
 
-		Bundle found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).limitTo(10).execute();
+		Bundle found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).count(10).execute();
 		assertEquals(100, found.getTotalResults().getValue().intValue());
 		assertEquals(10, found.getEntries().size());
 
-		found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).limitTo(999).execute();
+		found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).count(999).execute();
 		assertEquals(100, found.getTotalResults().getValue().intValue());
 		assertEquals(50, found.getEntries().size());
 

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

@@ -1559,6 +1559,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 	@Test
 	public void testSearchLastUpdatedParamRp() throws InterruptedException {
 		String methodName = "testSearchLastUpdatedParamRp";
+		ourLog.info("Starting " + methodName);
 
 		int sleep = 100;
 		Thread.sleep(sleep);
@@ -1668,8 +1669,10 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 
 	@Test
 	public void testSearchReturnsSearchDate() throws Exception {
+		ourLog.info("Starting testSearchReturnsSearchDate");
+		
 		Date before = new Date();
-		Thread.sleep(1);
+		Thread.sleep(100);
 
 		//@formatter:off
 		ca.uhn.fhir.model.dstu2.resource.Bundle found = ourClient
@@ -1680,7 +1683,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 				.execute();
 		//@formatter:on
 
-		Thread.sleep(1);
+		Thread.sleep(100);
 		Date after = new Date();
 
 		InstantDt updated = ResourceMetadataKeyEnum.UPDATED.get(found);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu1Test.java

@@ -3,7 +3,8 @@ package ca.uhn.fhir.jpa.provider;
 import static org.hamcrest.Matchers.blankOrNullString;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.not;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
 
 import java.io.InputStream;
 
@@ -11,13 +12,10 @@ import org.apache.commons.io.IOUtils;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
-import org.hamcrest.text.IsBlankString;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.springframework.context.annotation.AnnotationConfigApplicationContext;
-import org.springframework.context.support.ClassPathXmlApplicationContext;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.config.TestDstu1Config;
@@ -32,19 +30,22 @@ import ca.uhn.fhir.model.dstu.resource.Observation;
 import ca.uhn.fhir.model.dstu.resource.Organization;
 import ca.uhn.fhir.model.dstu.resource.Patient;
 import ca.uhn.fhir.model.dstu.resource.Questionnaire;
-import ca.uhn.fhir.model.dstu2.resource.Bundle;
-import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.client.IGenericClient;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.util.TestUtil;
 
-public class SystemProviderDstu1Test  extends BaseJpaTest {
+public class SystemProviderDstu1Test extends BaseJpaTest {
 
+	private static AnnotationConfigApplicationContext ourAppCtx;
+	private static IGenericClient ourClient;
+	private static FhirContext ourCtx;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderDstu1Test.class);
 	private static Server ourServer;
-	private static AnnotationConfigApplicationContext ourAppCtx;
+
-	private static FhirContext ourCtx;
+	@Override
-	private static IGenericClient ourClient;
+	protected FhirContext getContext() {
+		return ourCtx;
+	}
 
 	@Test
 	public void testTransactionFromBundle() throws Exception {
@@ -53,7 +54,7 @@ public class SystemProviderDstu1Test  extends BaseJpaTest {
 		String bundle = IOUtils.toString(bundleRes);
 		String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
 		ourLog.info(response);
-		
+
 		ca.uhn.fhir.model.api.Bundle respBundle = ourCtx.newXmlParser().parseBundle(response);
 		assertEquals(3, respBundle.size());
 		for (int i = 1; i < 3; i++) {
@@ -62,10 +63,15 @@ public class SystemProviderDstu1Test  extends BaseJpaTest {
 			assertThat(nextValue, not(blankOrNullString()));
 			assertThat(nextValue, not(containsString("cid")));
 		}
-		
+
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		ourAppCtx.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
-	
-	
 
 	@SuppressWarnings("unchecked")
 	@BeforeClass
@@ -108,22 +114,13 @@ public class SystemProviderDstu1Test  extends BaseJpaTest {
 
 		ourCtx = FhirContext.forDstu1();
 		restServer.setFhirContext(ourCtx);
-		
+
 		ourServer.setHandler(proxyHandler);
 		ourServer.start();
 
-
 		ourCtx.getRestfulClientFactory().setSocketTimeout(600 * 1000);
 		ourClient = ourCtx.newRestfulGenericClient(serverBase);
 		ourClient.setLogRequestAndResponse(true);
 	}
 
-	@AfterClass
-	public static void afterClassClearContext() throws Exception {
-		ourServer.stop();
-		ourAppCtx.stop();
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -7,6 +7,7 @@ import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.hamcrest.Matchers.hasItems;
+import static org.hamcrest.Matchers.hasSize;
 import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.startsWith;
 import static org.hamcrest.Matchers.stringContainsInOrder;
@@ -17,21 +18,17 @@ import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.forwardedUrlPattern;
 
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
-import java.io.UnsupportedEncodingException;
 import java.net.InetSocketAddress;
 import java.net.Socket;
 import java.net.SocketTimeoutException;
 import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Date;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -44,6 +41,7 @@ import org.apache.http.client.methods.HttpPost;
 import org.apache.http.client.methods.HttpPut;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
+import org.hamcrest.Matchers;
 import org.hl7.fhir.dstu3.model.BaseResource;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
@@ -98,27 +96,23 @@ import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
 
-import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import com.google.common.collect.Lists;
-import ca.uhn.fhir.model.api.IQueryParameterType;
+
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.UriDt;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.SummaryEnum;
 import ca.uhn.fhir.rest.client.IGenericClient;
 import ca.uhn.fhir.rest.param.DateRangeParam;
-import ca.uhn.fhir.rest.param.HasParam;
 import ca.uhn.fhir.rest.param.ParamPrefixEnum;
 import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.StringOrListParam;
 import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.Constants;
-import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 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.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
@@ -131,21 +125,11 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
-	protected List<String> toUnqualifiedVersionlessIdValues(IBaseBundle theFound) {
-		List<String> retVal = new ArrayList<String>();
 
-		List<IBaseResource> res = BundleUtil.toListOfResources(myFhirCtx, theFound);
-		int size = res.size();
-		ourLog.info("Found {} results", size);
-		for (IBaseResource next : res) {
-			retVal.add(next.getIdElement().toUnqualifiedVersionless().getValue());
-		}
-		return retVal;
-	}
 
 	@Test
 	public void testHasParameter() throws Exception {
-		IIdType pid0, pid1;
+		IIdType pid0;
 		{
 			Patient patient = new Patient();
 			patient.addIdentifier().setSystem("urn:system").setValue("001");
@@ -156,7 +140,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			Patient patient = new Patient();
 			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("Tester").addGiven("Joe");
-			pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+			myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
 		}
 		{
 			Observation obs = new Observation();
@@ -168,7 +152,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			Device device = new Device();
 			device.addIdentifier().setValue("DEVICEID");
 			IIdType devId = myDeviceDao.create(device, mySrd).getId().toUnqualifiedVersionless();
-			
+
 			Observation obs = new Observation();
 			obs.addIdentifier().setSystem("urn:system").setValue("NOLINK");
 			obs.setDevice(new Reference(devId));
@@ -176,10 +160,56 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		}
 
 		String uri = ourServerBase + "/Patient?_has:Observation:subject:identifier=" + UrlUtil.escape("urn:system|FOO");
-		List<String> ids = searchAndReturnUnqualifiedIdValues(uri);
+		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
 		assertThat(ids, contains(pid0.getValue()));
 	}
-	
+
+	@Test
+	public void testHistoryWithAtParameter() throws Exception {
+		String methodName = "testHistoryWithFromAndTo";
+
+		Patient patient = new Patient();
+		patient.addName().addFamily(methodName);
+		IIdType id = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+
+		List<Date> preDates = Lists.newArrayList();
+		List<String> ids = Lists.newArrayList();
+		for (int i = 0; i < 10; i++) {
+			Thread.sleep(100);
+			preDates.add(new Date());
+			patient.setId(id);
+			patient.getName().get(0).getFamily().get(0).setValue(methodName + "_i");
+			ids.add(myPatientDao.update(patient, mySrd).getId().toUnqualified().getValue());
+		}
+		
+		List<String> idValues;
+
+		idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient/" + id.getIdPart() + "/_history?_at=gt" + toStr(preDates.get(0)) + "&_at=lt" + toStr(preDates.get(3)));
+		assertThat(idValues, contains(ids.get(2), ids.get(1), ids.get(0)));
+
+		idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient/_history?_at=gt" + toStr(preDates.get(0)) + "&_at=lt" + toStr(preDates.get(3)));
+		assertThat(idValues, contains(ids.get(2), ids.get(1), ids.get(0)));
+
+		idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=gt" + toStr(preDates.get(0)) + "&_at=lt" + toStr(preDates.get(3)));
+		assertThat(idValues, contains(ids.get(2), ids.get(1), ids.get(0)));
+		
+		idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=gt2060");
+		assertThat(idValues, empty());
+
+		idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=" + InstantDt.withCurrentTime().getYear());
+		assertThat(idValues, hasSize(10)); // 10 is the page size
+
+		idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=ge" + InstantDt.withCurrentTime().getYear());
+		assertThat(idValues, hasSize(10));
+
+		idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=gt" + InstantDt.withCurrentTime().getYear());
+		assertThat(idValues, hasSize(0));
+	}
+
+	private String toStr(Date theDate) {
+		return new InstantDt(theDate).getValueAsString();
+	}
+
 	@Test
 	public void testHasParameterNoResults() throws Exception {
 
@@ -194,12 +224,11 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		}
 
 	}
-	
+
-	private List<String> searchAndReturnUnqualifiedIdValues(String uri) throws IOException, ClientProtocolException {
+	private List<String> searchAndReturnUnqualifiedVersionlessIdValues(String uri) throws IOException, ClientProtocolException {
 		List<String> ids;
 		HttpGet get = new HttpGet(uri);
-		
+
-		
 		CloseableHttpResponse response = ourHttpClient.execute(get);
 		try {
 			String resp = IOUtils.toString(response.getEntity().getContent());
@@ -212,8 +241,22 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		return ids;
 	}
 
-	
+	private List<String> searchAndReturnUnqualifiedIdValues(String uri) throws IOException, ClientProtocolException {
-	
+		List<String> ids;
+		HttpGet get = new HttpGet(uri);
+
+		CloseableHttpResponse response = ourHttpClient.execute(get);
+		try {
+			String resp = IOUtils.toString(response.getEntity().getContent());
+			ourLog.info(resp);
+			Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, resp);
+			ids = toUnqualifiedIdValues(bundle);
+		} finally {
+			IOUtils.closeQuietly(response);
+		}
+		return ids;
+	}
+
 	/**
 	 * Issue submitted by Bryn
 	 */
@@ -224,7 +267,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		ourClient.create().resource(input).execute().getResource();
 	}
 
-	
 	@Test
 	public void testSearchByExtendedChars() throws Exception {
 		for (int i = 0; i < 10; i++) {
@@ -233,7 +275,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			p.addIdentifier().setValue("ID" + i);
 			myPatientDao.create(p, mySrd);
 		}
-		
+
 		String uri = ourServerBase + "/Patient?name=" + URLEncoder.encode("Jernelöv", "UTF-8") + "&_count=5&_pretty=true";
 		ourLog.info("URI: {}", uri);
 		HttpGet get = new HttpGet(uri);
@@ -242,22 +284,20 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			assertEquals(200, resp.getStatusLine().getStatusCode());
 			String output = IOUtils.toString(resp.getEntity().getContent());
 			ourLog.info(output);
-			
+
 			Bundle b = myFhirCtx.newXmlParser().parseResource(Bundle.class, output);
-			
+
 			assertEquals("http://localhost:" + ourPort + "/fhir/context/Patient?_count=5&_pretty=true&name=Jernel%C3%B6v", b.getLink("self").getUrl());
-			
+
 			Patient p = (Patient) b.getEntry().get(0).getResource();
 			assertEquals("Jernelöv", p.getName().get(0).getFamily().get(0).getValue());
-			
+
 		} finally {
 			IOUtils.closeQuietly(resp.getEntity().getContent());
 		}
-		
+
-		
 	}
-	
+
-	
 	@Override
 	public void before() throws Exception {
 		super.before();
@@ -576,7 +616,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			ourLog.info(responseString);
 			assertEquals(400, response.getStatusLine().getStatusCode());
 			OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, responseString);
-			assertEquals("Can not create resource with ID \"2\", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)", oo.getIssue().get(0).getDiagnostics());
+			assertEquals("Can not create resource with ID \"2\", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)",
+					oo.getIssue().get(0).getDiagnostics());
 
 		} finally {
 			response.getEntity().getContent().close();
@@ -659,7 +700,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			//@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..
@@ -791,8 +833,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		}
 
 		/*
-		 * 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);
@@ -1326,7 +1367,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			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());
@@ -1918,7 +1960,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		Patient patient = new Patient();
 		patient.addIdentifier().setSystem("urn:system").setValue("testSearchTokenParam001");
 		patient.addName().addFamily("Tester").addGiven("testSearchTokenParam1");
-		patient.addCommunication().getLanguage().setText("testSearchTokenParamComText").addCoding().setCode("testSearchTokenParamCode").setSystem("testSearchTokenParamSystem").setDisplay("testSearchTokenParamDisplay");
+		patient.addCommunication().getLanguage().setText("testSearchTokenParamComText").addCoding().setCode("testSearchTokenParamCode").setSystem("testSearchTokenParamSystem")
+				.setDisplay("testSearchTokenParamDisplay");
 		myPatientDao.create(patient, mySrd);
 
 		patient = new Patient();
@@ -2635,7 +2678,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			ourLog.info(responseString);
 			assertEquals(400, response.getStatusLine().getStatusCode());
 			OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, responseString);
-			assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"333\" does not match URL ID of \"2\""));
+			assertThat(oo.getIssue().get(0).getDiagnostics(), containsString(
+					"Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"333\" does not match URL ID of \"2\""));
 		} finally {
 			response.close();
 		}
@@ -2659,7 +2703,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			ourLog.info(resp);
 			assertEquals(412, response.getStatusLine().getStatusCode());
 			assertThat(resp, not(containsString("Resource has no id")));
-			assertThat(resp, stringContainsInOrder(">ERROR<", "[Patient.contact]", "<pre>SHALL at least contain a contact's details or a reference to an organization", "<issue><severity value=\"error\"/>"));
+			assertThat(resp,
+					stringContainsInOrder(">ERROR<", "[Patient.contact]", "<pre>SHALL at least contain a contact's details or a reference to an organization", "<issue><severity value=\"error\"/>"));
 		} finally {
 			IOUtils.closeQuietly(response.getEntity().getContent());
 			response.close();
@@ -2785,7 +2830,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			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>"));
+			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();
@@ -2810,7 +2856,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			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>"));
+			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();
@@ -2831,17 +2878,17 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			String resp = IOUtils.toString(response.getEntity().getContent());
 			ourLog.info(resp);
 			assertEquals(200, response.getStatusLine().getStatusCode());
-			assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">")); 
+			assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
 			assertThat(resp, containsString("<expansion>"));
-			assertThat(resp, containsString("<contains>")); 
+			assertThat(resp, containsString("<contains>"));
 			assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
 			assertThat(resp, containsString("<code value=\"8450-9\"/>"));
-			assertThat(resp, containsString("<display value=\"Systolic blood pressure--expiration\"/>")); 
+			assertThat(resp, containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
 			assertThat(resp, containsString("</contains>"));
 			assertThat(resp, containsString("<contains>"));
 			assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
 			assertThat(resp, containsString("<code value=\"11378-7\"/>"));
-			assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>")); 
+			assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
 			assertThat(resp, containsString("</contains>"));
 			assertThat(resp, containsString("</expansion>"));
 		} finally {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java

@@ -172,7 +172,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 				.execute();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the type level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
+			assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
 		}
 		//@formatter:on
 
@@ -188,7 +188,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 				.execute();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the type level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
+			assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
 		}
 		//@formatter:on
 

hapi-fhir-structures-dstu/pom.xml

@@ -137,6 +137,36 @@
 
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<configuration>
+					<classFolders>
+						<classFolder>${basedir}/target/classes</classFolder>
+						<classFolder>${basedir}/../hapi-fhir-base/target/classes</classFolder>
+					</classFolders>
+					<sourceFolders>
+						<sourceFolder>${basedir}/src/main/java</sourceFolder>
+						<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
+					</sourceFolders>
+					<dumpOnExit>true</dumpOnExit>
+				</configuration>
+				<executions>
+					<execution>
+						<id>default-prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<configuration>
+					<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>ca.uhn.hapi.fhir</groupId>
 				<artifactId>hapi-tinder-plugin</artifactId>

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/param/DateRangeParamTest.java

@@ -46,6 +46,13 @@ public class DateRangeParamTest {
 
 			DateRangeParam range = new DateRangeParam(startDateTime, endDateTime);
 			assertEquals("2009-12-31T19:00:00.000-05:00", range.getValuesAsQueryTokens().get(0).getValueAsString());
+			assertEquals("2009-12-31T19:00:00.001-05:00", range.getValuesAsQueryTokens().get(1).getValueAsString());
+
+			// Now try with arguments reversed (should still create same range)
+			range = new DateRangeParam(endDateTime, startDateTime);
+			assertEquals("2009-12-31T19:00:00.000-05:00", range.getValuesAsQueryTokens().get(0).getValueAsString());
+			assertEquals("2009-12-31T19:00:00.001-05:00", range.getValuesAsQueryTokens().get(1).getValueAsString());
+
 		} finally {
 			TimeZone.setDefault(tz);
 		}

hapi-fhir-structures-dstu2/pom.xml

@@ -146,6 +146,36 @@
 
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<configuration>
+					<classFolders>
+						<classFolder>${basedir}/target/classes</classFolder>
+						<classFolder>${basedir}/../hapi-fhir-base/target/classes</classFolder>
+					</classFolders>
+					<sourceFolders>
+						<sourceFolder>${basedir}/src/main/java</sourceFolder>
+						<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
+					</sourceFolders>
+					<dumpOnExit>true</dumpOnExit>
+				</configuration>
+				<executions>
+					<execution>
+						<id>default-prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<configuration>
+					<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>ca.uhn.hapi.fhir</groupId>
 				<artifactId>hapi-tinder-plugin</artifactId>

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

@@ -32,10 +32,166 @@ public class BaseDateTimeDtDstu2Test {
 	private static FhirContext ourCtx = FhirContext.forDstu2();
 	private static Locale ourDefaultLocale;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseDateTimeDtDstu2Test.class);
-
 	private SimpleDateFormat myDateInstantParser;
-
 	private FastDateFormat myDateInstantZoneParser;
+
+	@Test
+	public void testFromTime() {
+		long millis;
+		InstantDt dt;
+		
+		millis = 1466022208001L;
+		String expected = "2016-06-15T20:23:28.001Z";
+		validate(millis, expected);
+		
+		millis = 1466022208123L;
+		expected = "2016-06-15T20:23:28.123Z";
+		validate(millis, expected);
+
+		millis = 1466022208100L;
+		expected = "2016-06-15T20:23:28.100Z";
+		validate(millis, expected);
+		
+		millis = 1466022208000L;
+		expected = "2016-06-15T20:23:28.000Z";
+		validate(millis, expected);
+		
+	}
+
+
+	private void validate(long millis, String expected) {
+		InstantDt dt;
+		dt = new InstantDt(new Date(millis));
+		dt.setTimeZoneZulu(true);
+		assertEquals(expected, dt.getValueAsString());
+
+		assertEquals(millis % 1000, dt.getMillis().longValue());
+		assertEquals((millis % 1000) * BaseDateTimeDt.NANOS_PER_MILLIS, dt.getNanos().longValue());
+		
+		dt = new InstantDt();
+		dt.setTimeZone(TimeZone.getTimeZone("GMT+0:00"));
+		dt.setValue(new Date(millis));
+		assertEquals(expected.replace("Z", "+00:00"), dt.getValueAsString());
+	}
+	
+
+	@Test
+	public void testSetPartialsYearFromExisting() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		dt.setYear(2016);
+		assertEquals(2016, dt.getYear().intValue());
+		String valueAsString = dt.getValueAsString();
+		ourLog.info(valueAsString);
+		assertEquals("2016-03-11T15:44:13.27564757855254768473697463986328969635-08:00", valueAsString);
+	}
+
+	@Test
+	public void testSetPartialsMonthFromExisting() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		dt.setMonth(3);
+		assertEquals(3, dt.getMonth().intValue());
+		String valueAsString = dt.getValueAsString();
+		ourLog.info(valueAsString);
+		assertEquals("2011-04-11T15:44:13.27564757855254768473697463986328969635-08:00", valueAsString);
+	}
+
+	@Test
+	public void testSetPartialsDayFromExisting() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		dt.setDay(15);
+		assertEquals(15, dt.getDay().intValue());
+		String valueAsString = dt.getValueAsString();
+		ourLog.info(valueAsString);
+		assertEquals("2011-03-15T15:44:13.27564757855254768473697463986328969635-08:00", valueAsString);
+	}
+
+	@Test
+	public void testSetPartialsHourFromExisting() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		dt.setHour(23);
+		assertEquals(23, dt.getHour().intValue());
+		String valueAsString = dt.getValueAsString();
+		ourLog.info(valueAsString);
+		assertEquals("2011-03-11T23:44:13.27564757855254768473697463986328969635-08:00", valueAsString);
+	}
+
+	@Test
+	public void testSetPartialsMinuteFromExisting() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		dt.setMinute(54);
+		assertEquals(54, dt.getMinute().intValue());
+		String valueAsString = dt.getValueAsString();
+		ourLog.info(valueAsString);
+		assertEquals("2011-03-11T15:54:13.27564757855254768473697463986328969635-08:00", valueAsString);
+	}
+
+	@Test
+	public void testSetPartialsSecondFromExisting() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		dt.setSecond(1);
+		assertEquals(1, dt.getSecond().intValue());
+		String valueAsString = dt.getValueAsString();
+		ourLog.info(valueAsString);
+		assertEquals("2011-03-11T15:44:01.27564757855254768473697463986328969635-08:00", valueAsString);
+	}
+
+	@Test
+	public void testSetPartialsMillisFromExisting() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		dt.setMillis(12);
+		assertEquals(12, dt.getMillis().intValue());
+		assertEquals(12 * BaseDateTimeDt.NANOS_PER_MILLIS, dt.getNanos().longValue());
+		String valueAsString = dt.getValueAsString();
+		ourLog.info(valueAsString);
+		assertEquals("2011-03-11T15:44:13.012-08:00", valueAsString);
+	}
+
+	@Test
+	public void testSetPartialsNanosFromExisting() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		dt.setNanos(100000000L);
+		assertEquals(100000000L, dt.getNanos().longValue());
+		assertEquals(100, dt.getMillis().intValue());
+		String valueAsString = dt.getValueAsString();
+		ourLog.info(valueAsString);
+		assertEquals("2011-03-11T15:44:13.100-08:00", valueAsString);
+	}
+
+	@Test
+	public void testSetPartialsInvalid() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		dt.setNanos(0);
+		dt.setNanos(BaseDateTimeDt.NANOS_PER_SECOND - 1);
+		try {
+			dt.setNanos(BaseDateTimeDt.NANOS_PER_SECOND);
+		} catch (IllegalArgumentException e) {
+			assertEquals("Value 1000000000 is not between allowable range: 0 - 999999999", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testGetPartials() {
+		InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
+		assertEquals(2011, dt.getYear().intValue());
+		assertEquals(2, dt.getMonth().intValue());
+		assertEquals(11, dt.getDay().intValue());
+		assertEquals(15, dt.getHour().intValue());
+		assertEquals(44, dt.getMinute().intValue());
+		assertEquals(13, dt.getSecond().intValue());
+		assertEquals(275, dt.getMillis().intValue());
+		assertEquals(275647578L, dt.getNanos().longValue());
+
+		dt = new InstantDt();
+		assertEquals(null, dt.getYear());
+		assertEquals(null, dt.getMonth());
+		assertEquals(null, dt.getDay());
+		assertEquals(null, dt.getHour());
+		assertEquals(null, dt.getMinute());
+		assertEquals(null, dt.getSecond());
+		assertEquals(null, dt.getMillis());
+		assertEquals(null, dt.getNanos());
+	}
+
 	@Before
 	public void before() {
 		myDateInstantParser = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS");
@@ -49,7 +205,7 @@ public class BaseDateTimeDtDstu2Test {
 		dt.setTimeZoneZulu(true);
 		assertEquals("1995-11-15T04:58:08Z", dt.getValueAsString());
 	}
-	
+
 	/**
 	 * Test for #57
 	 */
@@ -194,10 +350,10 @@ public class BaseDateTimeDtDstu2Test {
 	@Test
 	public void testGetValueAsCalendar() {
 		assertNull(new InstantDt().getValueAsCalendar());
-		
+
 		InstantDt dt = new InstantDt("2011-01-03T07:11:22.002-08:00");
 		GregorianCalendar cal = dt.getValueAsCalendar();
-		
+
 		assertEquals(2011, cal.get(Calendar.YEAR));
 		assertEquals(7, cal.get(Calendar.HOUR_OF_DAY));
 		assertEquals(2, cal.get(Calendar.MILLISECOND));

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

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.model.primitive;
+
+import static org.junit.Assert.*;
+
+import java.math.RoundingMode;
+
+import org.junit.Test;
+
+public class DecimalDtTest {
+
+	@Test
+	public void testRoundWithMode() {
+		DecimalDt dt = new DecimalDt("1.66666666");
+		dt.round(3, RoundingMode.FLOOR);
+		assertEquals("1.66", dt.getValueAsString());
+	}
+	
+	@Test
+	public void testGetValue() {
+		DecimalDt dt = new DecimalDt("1.66666666");
+		assertEquals(1, dt.getValueAsInteger());
+		assertEquals("1.66666666", dt.getValueAsNumber().toString());
+		assertEquals("1.66666666", dt.getValueAsString());
+	}
+
+	@Test
+	public void testSetValue() {
+		DecimalDt dt = new DecimalDt();
+		dt.setValueAsInteger(123);
+		assertEquals("123", dt.getValueAsString());
+	}
+
+	@Test
+	public void testRound() {
+		DecimalDt dt = new DecimalDt("1.66666666");
+		dt.round(3);
+		assertEquals("1.67", dt.getValueAsString());
+	}
+	
+	@Test
+	public void testCompareTo() {
+		DecimalDt dt = new DecimalDt("1.66666666");
+		assertEquals(1, dt.compareTo(null));
+		assertEquals(1, dt.compareTo(new DecimalDt()));
+		assertEquals(1, dt.compareTo(new DecimalDt("0.1")));
+		assertEquals(-1, dt.compareTo(new DecimalDt("99")));
+		assertEquals(0, dt.compareTo(new DecimalDt("1.66666666")));
+		assertEquals(0, new DecimalDt().compareTo(new DecimalDt()));
+		assertEquals(-1, new DecimalDt().compareTo(new DecimalDt("1.0")));
+	}
+	
+	
+}

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

@@ -0,0 +1,56 @@
+package ca.uhn.fhir.model.primitive;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class UriDtTest {
+
+	@Test
+	public void testFromOid() {
+		UriDt uri = UriDt.fromOid("0.1.2.3.4");
+		assertEquals("urn:oid:0.1.2.3.4", uri.getValue());
+	}
+	
+	@Test
+	public void testFromOidNull() {
+		UriDt uri = UriDt.fromOid(null);
+		assertEquals(null, uri.getValue());
+	}
+	
+	@Test
+	public void testEqualsObject() {
+		UriDt dt = new UriDt("http://example.com/foo");
+		assertTrue(dt.equals(dt));
+		assertFalse(dt.equals(null));
+		assertFalse(dt.equals(new UriDt()));
+		assertTrue(dt.equals(new UriDt("http://example.com/foo")));
+		assertTrue(dt.equals(new UriDt("http://example.com/foo/")));
+		assertFalse(dt.equals(new UriDt("http://blah.com/foo/")));
+		assertFalse(dt.equals(new StringDt("http://example.com/foo")));
+	}
+
+	@Test
+	public void testEqualsString() {
+		UriDt dt = new UriDt("http://example.com/foo");
+		assertTrue(dt.equals("http://example.com/foo"));
+	}
+
+	@Test
+	public void testHashCode() {
+		UriDt dt = new UriDt("http://example.com/foo");
+		assertEquals(-1671329151, dt.hashCode());
+		
+		dt = new UriDt();
+		assertEquals(31, dt.hashCode());
+
+	}
+
+	@Test
+	public void testSetInvalid() {
+		UriDt dt = new UriDt();
+		dt.setValue("blah : // AA");
+		dt.hashCode();
+	}
+
+}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java

@@ -1040,8 +1040,11 @@ public class XmlParserDstu2Test {
 
 	}
 
+	/**
+	 * Make sure whitespace is preserved for pre tags
+	 */
 	@Test
-	public void testEncodeDivWithPre() {
+	public void testEncodeDivWithPrePrettyPrint() {
 		
 		Patient p = new Patient();
 		p.getText().setDiv("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
@@ -1059,6 +1062,28 @@ public class XmlParserDstu2Test {
 		
 	}
 
+	/**
+	 * Make sure whitespace is preserved for pre tags
+	 */
+	@Test
+	public void testEncodeDivWithPreNonPrettyPrint() {
+		
+		Patient p = new Patient();
+		p.getText().setDiv("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
+		
+		String output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
+		ourLog.info(output);
+		
+		//@formatter:off
+		assertThat(output, stringContainsInOrder(
+			"<text><div",
+			"<p>A P TAG</p><p>",
+			"<pre>line1\nline2\nline3  <b>BOLD</b></pre>"
+		));
+		//@formatter:on
+		
+	}
+
 	@Test
 	public void testEncodeDoesntIncludeUuidId() {
 		Patient p = new Patient();

hapi-fhir-structures-dstu3/pom.xml

@@ -175,13 +175,34 @@
 
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<configuration>
+					<classFolders>
+						<classFolder>${basedir}/target/classes</classFolder>
+						<classFolder>${basedir}/../hapi-fhir-base/target/classes</classFolder>
+					</classFolders>
+					<sourceFolders>
+						<sourceFolder>${basedir}/src/main/java</sourceFolder>
+						<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
+					</sourceFolders>
+					<dumpOnExit>true</dumpOnExit>
+				</configuration>
+				<executions>
+					<execution>
+						<id>default-prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<!--<redirectTestOutputToFile>false</redirectTestOutputToFile>-->
+					<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
-					<runOrder>random</runOrder>
-					<reuseForks>false</reuseForks>
 				</configuration>
 			</plugin>
 			<plugin>

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java

@@ -119,8 +119,31 @@ public class XmlParserDstu3Test {
 		ourCtx.setNarrativeGenerator(null);
 	}
 
+	/**
+	 * Make sure whitespace is preserved for pre tags
+	 */
 	@Test
-	public void testEncodeDivWithPre() {
+	public void testEncodeDivWithPreNonPrettyPrint() {
+		
+		Patient p = new Patient();
+		p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");
+		
+		String output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
+		ourLog.info(output);
+		
+		//@formatter:off
+		assertThat(output, stringContainsInOrder(
+			"<text><div",
+			"<p>A P TAG</p><p>",
+			"<pre>line1\nline2\nline3  <b>BOLD</b></pre>"
+		));
+		//@formatter:on
+		
+	}
+
+	
+	@Test
+	public void testEncodeDivWithPrePrettyPrint() {
 		
 		Patient p = new Patient();
 		p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3  <b>BOLD</b></pre></p></div>");

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

@@ -177,6 +177,36 @@
 
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<configuration>
+					<classFolders>
+						<classFolder>${basedir}/target/classes</classFolder>
+						<classFolder>${basedir}../hapi-fhir-base/target/classes</classFolder>
+					</classFolders>
+					<sourceFolders>
+						<sourceFolder>${basedir}/src/main/java</sourceFolder>
+						<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
+					</sourceFolders>
+					<dumpOnExit>true</dumpOnExit>
+				</configuration>
+				<executions>
+					<execution>
+						<id>default-prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<configuration>
+					<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>

pom.xml

@@ -806,7 +806,6 @@
 						<runOrder>random</runOrder>
 						<argLine>-Dfile.encoding=UTF-8 -Xmx712m</argLine>
 						<forkCount>1</forkCount>
-						<!--<reuseForks>false</reuseForks> -->
 					</configuration>
 				</plugin>
 				<plugin>
@@ -860,6 +859,11 @@
 						</coberturaReports>
 					</configuration>
 				</plugin>
+				<plugin>
+					<groupId>org.jacoco</groupId>
+					<artifactId>jacoco-maven-plugin</artifactId>
+					<version>0.7.7.201606060606</version>
+				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-site-plugin</artifactId>
@@ -1123,7 +1127,8 @@
 								<replace dir="target/site" summary="true">
 									<include name="*.html"/>
 									<replacetoken>\t</replacetoken>
-									<replacevalue>   </replacevalue>
+									<replacevalue>
+									</replacevalue>
 								</replace>
 								<replace dir="target/site" summary="true">
 									<include name="index.html"/>
@@ -1376,6 +1381,8 @@
 		<plugins>
 			<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-checkstyle-plugin</artifactId> <reportSets> <reportSet> <reports><report>checkstyle-aggregate</report></reports> </reportSet> 
 				</reportSets> <configuration> <configLocation>config/sun_checks.xml</configLocation> <includes> hapi-fhir-base/src/main/java/**/*.java </includes> </configuration> </plugin> -->
+			<!-- <plugin> <groupId>org.jacoco</groupId> <artifactId>jacoco-maven-plugin</artifactId> <version>0.7.7.201606060606</version> <reportSets> <reportSet> <reports> <report>report</report> </reports> <configuration> 
+				<dataFileIncludes>${baseDir}/hapi-fhir-base/target/jacoco.exec</dataFileIncludes> </configuration> </reportSet> </reportSets> </plugin> -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-changes-plugin</artifactId>
@@ -1524,7 +1531,6 @@
 			<modules>
 				<module>hapi-deployable-pom</module>
 				<module>hapi-fhir-base</module>
-				<!--<module>hapi-fhir-oauth2</module> -->
 				<module>hapi-fhir-base-test-mindeps-client</module>
 				<module>hapi-fhir-base-test-mindeps-server</module>
 				<module>hapi-tinder-plugin</module>
@@ -1548,6 +1554,7 @@
 				<module>hapi-fhir-dist</module>
 				<module>examples</module>
 				<module>hapi-fhir-base-example-embedded-ws</module>
+				<module>hapi-fhir-jacoco</module>
 			</modules>
 		</profile>
 		<profile>