Properly support chains in JPA conditional URLs

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

@@ -84,6 +84,7 @@ import ca.uhn.fhir.rest.param.ResourceParameter.Mode;
 import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
 import ca.uhn.fhir.rest.param.TransactionParameter;
+import ca.uhn.fhir.rest.param.UriAndListParam;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.EncodingEnum;
 import ca.uhn.fhir.rest.server.IDynamicSearchResourceProvider;
@@ -630,6 +631,9 @@ public class MethodUtil {
 		case TOKEN:
 			binder = new QueryParameterAndBinder(TokenAndListParam.class, Collections.<Class<? extends IQueryParameterType>> emptyList());
 			break;
+		case URI:
+			binder = new QueryParameterAndBinder(UriAndListParam.class, Collections.<Class<? extends IQueryParameterType>> emptyList());
+			break;
 		}
 
 		return binder.parse(theUnqualifiedParamName, theParameters);

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/ExampleDataUploader.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.cli;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
@@ -28,7 +29,6 @@ import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.EntryRequest;
-import ca.uhn.fhir.model.dstu2.resource.DataElement;
 import ca.uhn.fhir.model.dstu2.resource.SearchParameter;
 import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -61,9 +61,14 @@ public class ExampleDataUploader extends BaseCommand {
 		opt.setRequired(false);
 		options.addOption(opt);
 
-		opt = new Option("t", "target", true, "Base URL for the target server");
+		opt = new Option("t", "target", true, "Base URL for the target server (e.g. \"http://example.com/fhir\")");
 		opt.setRequired(true);
 		options.addOption(opt);
+
+		opt = new Option("l", "limit", true, "Sets a limit to the number of resources the uploader will try to upload");
+		opt.setRequired(false);
+		options.addOption(opt);
+
 		return options;
 	}
 
@@ -76,6 +81,15 @@ public class ExampleDataUploader extends BaseCommand {
 		} else if (targetServer.startsWith("http") == false) {
 			throw new ParseException("Invalid target server specified, must begin with 'http'");
 		}
+		Integer limit = null;
+		String limitString = theCommandLine.getOptionValue('l');
+		if (isNotBlank(limitString)) {
+			try {
+			limit = Integer.parseInt(limitString);
+			} catch (NumberFormatException e) {
+				throw new ParseException("Invalid number for limit (-l) option, must be a number: " + limitString);
+			}
+		}
 
 		FhirContext ctx = FhirContext.forDstu2();
 		String specUrl = "http://hl7.org/fhir/" + specVersion + "/examples-json.zip";
@@ -100,7 +114,13 @@ public class ExampleDataUploader extends BaseCommand {
 
 		Bundle bundle = new Bundle();
 
+		int count = 0;
 		while (true) {
+			count++;
+			if (limit != null && count > limit) {
+				break;
+			}
+			
 			ZipEntry nextEntry = zis.getNextEntry();
 			if (nextEntry == null) {
 				break;

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

@@ -23,8 +23,6 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.io.UnsupportedEncodingException;
-import java.net.URI;
-import java.net.URISyntaxException;
 import java.text.Normalizer;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -93,12 +91,14 @@ import ca.uhn.fhir.jpa.entity.TagDefinition;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
+import ca.uhn.fhir.model.dstu.resource.BaseResource;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
@@ -110,8 +110,13 @@ import ca.uhn.fhir.rest.method.MethodUtil;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
 import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.StringAndListParam;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.UriAndListParam;
+import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.Constants;
-import ca.uhn.fhir.rest.server.EncodingEnum;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -120,9 +125,36 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.util.FhirTerser;
+import net.sourceforge.cobertura.CoverageIgnore;
 
 public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
+	/**
+	 * These are parameters which are supported by {@link BaseHapiFhirResourceDao#searchForIds(Map)}
+	 */
+	protected static final Map<String, Class<? extends IQueryParameterType>> RESOURCE_META_PARAMS;
+	/**
+	 * These are parameters which are supported by {@link BaseHapiFhirResourceDao#searchForIds(Map)}
+	 */
+	protected static final Map<String, Class<? extends IQueryParameterAnd<?>>> RESOURCE_META_AND_PARAMS;
+
+	static {
+		Map<String, Class<? extends IQueryParameterType>> resourceMetaParams = new HashMap<String, Class<? extends IQueryParameterType>>();
+		Map<String, Class<? extends IQueryParameterAnd<?>>> resourceMetaAndParams = new HashMap<String, Class<? extends IQueryParameterAnd<?>>>();
+		resourceMetaParams.put(BaseResource.SP_RES_ID, StringParam.class);
+		resourceMetaAndParams.put(BaseResource.SP_RES_ID, StringAndListParam.class);
+		resourceMetaParams.put(BaseResource.SP_RES_LANGUAGE, StringParam.class);
+		resourceMetaAndParams.put(BaseResource.SP_RES_LANGUAGE, StringAndListParam.class);
+		resourceMetaParams.put(Constants.PARAM_TAG, TokenParam.class);
+		resourceMetaAndParams.put(Constants.PARAM_TAG, TokenAndListParam.class);
+		resourceMetaParams.put(Constants.PARAM_PROFILE, UriParam.class);
+		resourceMetaAndParams.put(Constants.PARAM_PROFILE, UriAndListParam.class);
+		resourceMetaParams.put(Constants.PARAM_SECURITY, TokenParam.class);
+		resourceMetaAndParams.put(Constants.PARAM_SECURITY, TokenAndListParam.class);
+		RESOURCE_META_PARAMS = Collections.unmodifiableMap(resourceMetaParams);
+		RESOURCE_META_AND_PARAMS = Collections.unmodifiableMap(resourceMetaAndParams);
+	}
+
 	public static final long INDEX_STATUS_INDEXED = Long.valueOf(1L);
 	public static final long INDEX_STATUS_INDEXING_FAILED = Long.valueOf(2L);
 	public static final String NS_JPA_PROFILE = "https://github.com/jamesagnew/hapi-fhir/ns/jpa/profile";
@@ -703,6 +735,30 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return false;
 	}
 
+	@CoverageIgnore
+	protected static IQueryParameterAnd<?> newInstanceAnd(String chain) {
+		IQueryParameterAnd<?> type;
+		Class<? extends IQueryParameterAnd<?>> clazz = RESOURCE_META_AND_PARAMS.get(chain);
+		try {
+			type = clazz.newInstance();
+		} catch (Exception e) {
+			throw new InternalErrorException("Failure creating instance of " + clazz, e);
+		}
+		return type;
+	}
+
+	@CoverageIgnore
+	protected static IQueryParameterType newInstanceType(String chain) {
+		IQueryParameterType type;
+		Class<? extends IQueryParameterType> clazz = RESOURCE_META_PARAMS.get(chain);
+		try {
+			type = clazz.newInstance();
+		} catch (Exception e) {
+			throw new InternalErrorException("Failure creating instance of " + clazz, e);
+		}
+		return type;
+	}
+
 	protected <R extends IResource> Set<Long> processMatchUrl(String theMatchUrl, Class<R> theResourceType) {
 		RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(theResourceType);
 
@@ -745,13 +801,13 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 			String paramName = next.getName();
 			String qualifier = null;
-			for (int i = 0; i < paramMap.size(); i++) {
+			for (int i = 0; i < paramName.length(); i++) {
 				switch (paramName.charAt(i)) {
 				case '.':
 				case ':':
 					qualifier = paramName.substring(i);
 					paramName = paramName.substring(0, i);
-					i = Integer.MAX_VALUE;
+					i = Integer.MAX_VALUE - 1;
 					break;
 				}
 			}
@@ -787,10 +843,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				continue;
 			}
 
-			if (nextParamName.startsWith("_")) {
+			if (RESOURCE_META_PARAMS.containsKey(nextParamName)) {
-				continue;
+				if (isNotBlank(paramList.get(0).getQualifier()) && paramList.get(0).getQualifier().startsWith(".")) {
+					throw new InvalidRequestException("Invalid parameter chain: " + nextParamName + paramList.get(0).getQualifier()); 
 				}
-
+				IQueryParameterAnd<?> type = newInstanceAnd(nextParamName);
+				type.setValuesAsQueryTokens((paramList));
+				paramMap.add(nextParamName, type);
+			} else if (nextParamName.startsWith("_")) {
+				// ignore these since they aren't search params (e.g. _sort)
+			} else {
 				RuntimeSearchParam paramDef = resourceDef.getSearchParam(nextParamName);
 				if (paramDef == null) {
 					throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Resource type " + resourceDef.getName() + " does not have a parameter with name: " + nextParamName);
@@ -799,6 +861,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				IQueryParameterAnd<?> param = MethodUtil.parseQueryParams(paramDef, nextParamName, paramList);
 				paramMap.add(nextParamName, param);
 			}
+		}
 		return paramMap;
 	}
 

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

@@ -656,8 +656,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 					}
 
 					boolean foundChainMatch = false;
-					for (Class<? extends IBaseResource> nextType : resourceTypes) {
-						RuntimeResourceDefinition typeDef = getContext().getResourceDefinition(nextType);
 
 					String chain = ref.getChain();
 					String remainingChain = null;
@@ -667,29 +665,48 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 						chain = chain.substring(0, chainDotIndex);
 					}
 
-						RuntimeSearchParam param = typeDef.getSearchParam(chain);
+					for (Class<? extends IBaseResource> nextType : resourceTypes) {
+						RuntimeResourceDefinition typeDef = getContext().getResourceDefinition(nextType);
+						
+						IFhirResourceDao<?> dao = getDao(nextType);
+						if (dao == null) {
+							ourLog.debug("Don't have a DAO for type {}", nextType.getSimpleName());
+							continue;
+						}
+						
+						int qualifierIndex = chain.indexOf(':');
+						String qualifier = null;
+						if (qualifierIndex != -1) {
+							qualifier = chain.substring(qualifierIndex);
+							chain = chain.substring(0, qualifierIndex);
+						}
+						
+						boolean isMeta = RESOURCE_META_PARAMS.containsKey(chain);
+						RuntimeSearchParam param = null;
+						if (!isMeta) {
+							param = typeDef.getSearchParam(chain);
 							if (param == null) {
 								ourLog.debug("Type {} doesn't have search param {}", nextType.getSimpleName(), param);
 								continue;
 							}
-						IFhirResourceDao<?> dao = getDao(nextType);
-						if (dao == null) {
-							ourLog.debug("Don't have a DAO for type {}", nextType.getSimpleName(), param);
-							continue;
 						}
 
 						IQueryParameterType chainValue;
 						if (remainingChain != null) {
-							if (param.getParamType() != RestSearchParameterTypeEnum.REFERENCE) {
+							if (param == null || param.getParamType() != RestSearchParameterTypeEnum.REFERENCE) {
 								ourLog.debug("Type {} parameter {} is not a reference, can not chain {}", new Object[] { nextType.getSimpleName(), chain, remainingChain });
 								continue;
 							}
 
 							chainValue = new ReferenceParam();
-							chainValue.setValueAsQueryToken(null, resourceId);
+							chainValue.setValueAsQueryToken(qualifier, resourceId);
 							((ReferenceParam) chainValue).setChain(remainingChain);
+						} else if (isMeta) {
+							IQueryParameterType type = newInstanceType(chain);
+							type.setValueAsQueryToken(qualifier, resourceId);
+							chainValue = type;
 						} else {
-							chainValue = toParameterType(param, resourceId);
+							chainValue = toParameterType(param, qualifier, resourceId);
 						}
 
 						foundChainMatch = true;
@@ -729,6 +746,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		return new HashSet<Long>(q.getResultList());
 	}
 
+
 	private Set<Long> addPredicateString(String theParamName, Set<Long> thePids, List<? extends IQueryParameterType> theList) {
 		if (theList == null || theList.isEmpty()) {
 			return thePids;
@@ -783,7 +801,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		} else if (Constants.PARAM_SECURITY.equals(theParamName)) {
 			tagType = TagTypeEnum.SECURITY_LABEL;
 		} else {
-			throw new IllegalArgumentException("Paramname: " + theParamName); // shouldn't happen
+			throw new IllegalArgumentException("Param name: " + theParamName); // shouldn't happen
 		}
 
 		for (List<? extends IQueryParameterType> nextAndParams : theList) {
@@ -1358,7 +1376,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 
 		}
 
-		ourLog.info("Processed delete on {} (matched {} resource(s)) in {}ms", new Object[] {theUrl, resource.size(), w.getMillisAndRestart()});
+		ourLog.info("Processed delete on {} (matched {} resource(s)) in {}ms", new Object[] { theUrl, resource.size(), w.getMillisAndRestart() });
 
 		return new DaoMethodOutcome();
 	}
@@ -2114,16 +2132,16 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 						List<Long> pidsSubList = pids.subList(theFromIndex, theToIndex);
 
 						// Load includes
-						if (theParams.getEverythingMode()==null) {
+						if (theParams.getEverythingMode() == null) {
 							pidsSubList = new ArrayList<Long>(pidsSubList);
 							revIncludedPids.addAll(loadReverseIncludes(pidsSubList, theParams.getIncludes(), false, null));
 						}
 
 						// Execute the query and make sure we return distinct results
-						List<IBaseResource> retVal = new ArrayList<IBaseResource>();
+						List<IBaseResource> resources = new ArrayList<IBaseResource>();
-						loadResourcesByPid(pidsSubList, retVal, revIncludedPids, false);
+						loadResourcesByPid(pidsSubList, resources, revIncludedPids, false);
 
-						return retVal;
+						return resources;
 					}
 
 				});
@@ -2140,13 +2158,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 			}
 		};
 
-		ourLog.info("Processed search for {} on {} in {}ms", new Object[] { myResourceName, theParams, w.getMillisAndRestart() });
+		ourLog.info(" {} on {} in {}ms", new Object[] { myResourceName, theParams, w.getMillisAndRestart() });
 
 		return retVal;
 	}
 
-	private List<Long> processSort(final SearchParameterMap theParams, Set<Long> loadPids) {
+	private List<Long> processSort(final SearchParameterMap theParams, Set<Long> theLoadPids) {
 		final List<Long> pids;
+		Set<Long> loadPids = theLoadPids;
 		if (theParams.getSort() != null && isNotBlank(theParams.getSort().getParamName())) {
 			List<Order> orders = new ArrayList<Order>();
 			List<Predicate> predicates = new ArrayList<Predicate>();
@@ -2220,7 +2239,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 
 		for (Entry<String, List<List<? extends IQueryParameterType>>> nextParamEntry : params.entrySet()) {
 			String nextParamName = nextParamEntry.getKey();
-			if (nextParamName.equals("_id")) {
+			if (nextParamName.equals(BaseResource.SP_RES_ID)) {
 
 				if (nextParamEntry.getValue().isEmpty()) {
 					continue;
@@ -2262,7 +2281,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 					}
 				}
 
-			} else if (nextParamName.equals("_language")) {
+			} else if (nextParamName.equals(BaseResource.SP_RES_LANGUAGE)) {
 
 				pids = addPredicateLanguage(pids, nextParamEntry.getValue());
 
@@ -2413,10 +2432,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 		return qp;
 	}
 
-	private IQueryParameterType toParameterType(RuntimeSearchParam theParam, String theValueAsQueryToken) {
+	private IQueryParameterType toParameterType(RuntimeSearchParam theParam, String theQualifier, String theValueAsQueryToken) {
 		IQueryParameterType qp = toParameterType(theParam);
 
-		qp.setValueAsQueryToken(null, theValueAsQueryToken);
+		qp.setValueAsQueryToken(theQualifier, theValueAsQueryToken); // aaaa
 		return qp;
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2.java

@@ -37,6 +37,7 @@ import org.springframework.beans.factory.annotation.Qualifier;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
@@ -55,16 +56,19 @@ import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.validation.DefaultProfileValidationSupport;
 import ca.uhn.fhir.validation.FhirInstanceValidator;
 import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.IValidationContext;
 import ca.uhn.fhir.validation.IValidationSupport;
+import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ValidationResult;
 import ca.uhn.fhir.validation.ValidationSupportChain;
+import net.sourceforge.cobertura.CoverageIgnore;
 
 public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResourceDao<T> {
 
 	/**
 	 * TODO: set this to required after the next release
 	 */
-	@Autowired(required=false)
+	@Autowired(required = false)
 	@Qualifier("myJpaValidationSupportDstu2")
 	private IValidationSupport myJpaValidationSupport;
 
@@ -122,6 +126,8 @@ public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResou
 		val.setValidationSupport(new ValidationSupportChain(new DefaultProfileValidationSupport(), myJpaValidationSupport));
 		validator.registerValidatorModule(val);
 
+		validator.registerValidatorModule(new IdChecker(theMode));
+
 		ValidationResult result;
 		if (isNotBlank(theRawResource)) {
 			result = validator.validateWithResult(theRawResource);
@@ -139,4 +145,35 @@ public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResou
 
 	}
 
+	private class IdChecker implements IValidatorModule {
+
+		private ValidationModeEnum myMode;
+
+		public IdChecker(ValidationModeEnum theMode) {
+			myMode = theMode;
+		}
+
+		@Override
+		public void validateResource(IValidationContext<IBaseResource> theCtx) {
+			boolean hasId = theCtx.getResource().getIdElement().hasIdPart();
+			if (myMode == ValidationModeEnum.CREATE) {
+				if (hasId) {
+					throw new InvalidRequestException("Resource has an ID - ID must not be populated for a FHIR create");
+				}
+			} else if (myMode == ValidationModeEnum.UPDATE) {
+				if (hasId == false) {
+					throw new InvalidRequestException("Resource has no ID - ID must be populated for a FHIR update");
+				}
+			}
+
+		}
+
+		@CoverageIgnore
+		@Override
+		public void validateBundle(IValidationContext<Bundle> theContext) {
+			throw new UnsupportedOperationException();
+		}
+
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java

@@ -166,6 +166,8 @@ public class FhirResourceDaoSubscriptionDstu2 extends FhirResourceDaoDstu2<Subsc
 
 		mySubscriptionFlaggedResourceDataDao.save(flags);
 
+		ourLog.debug("Updating most recent match for subcription {} to {}", subscription.getId().getIdPart(), new InstantDt(mostRecentMatch));
+		
 		theSubscriptionTable.setMostRecentMatch(mostRecentMatch);
 		myEntityManager.merge(theSubscriptionTable);
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2SubscriptionTest.java

@@ -366,4 +366,83 @@ public class FhirResourceDaoDstu2SubscriptionTest extends BaseJpaDstu2Test {
 
 	}
 
+
+	@Test
+	public void testSubscriptionResourcesAppear2() throws Exception {
+		myDaoConfig.setSubscriptionPollDelay(0);
+
+		String methodName = "testSubscriptionResourcesAppear2";
+		Patient p = new Patient();
+		p.addName().addFamily(methodName);
+		IIdType pId = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+		Observation obs = new Observation();
+		obs.getSubject().setReference(pId);
+		obs.setStatus(ObservationStatusEnum.FINAL);
+		myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+
+		Subscription subs;
+
+		/*
+		 * Create 2 identical subscriptions
+		 */
+
+		subs = new Subscription();
+		subs.getChannel().setType(SubscriptionChannelTypeEnum.WEBSOCKET);
+		subs.setCriteria("Observation?subject=Patient/" + pId.getIdPart());
+		subs.setStatus(SubscriptionStatusEnum.ACTIVE);
+		Long subsId1 = mySubscriptionDao.getSubscriptionTablePidForSubscriptionResource(mySubscriptionDao.create(subs).getId());
+
+		assertNull(mySubscriptionTableDao.findOne(subsId1).getLastClientPoll());
+
+		Thread.sleep(100);
+		ourLog.info("Before: {}", System.currentTimeMillis());
+
+		obs = new Observation();
+		obs.getSubject().setReference(pId);
+		obs.setStatus(ObservationStatusEnum.FINAL);
+		IIdType afterId1 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+
+		obs = new Observation();
+		obs.getSubject().setReference(pId);
+		obs.setStatus(ObservationStatusEnum.FINAL);
+		IIdType afterId2 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+
+		Thread.sleep(100);
+
+		ourLog.info("After: {}", System.currentTimeMillis());
+
+		List<IBaseResource> results;
+		List<IIdType> resultIds;
+
+		mySubscriptionDao.pollForNewUndeliveredResources();
+		assertEquals(2, mySubscriptionFlaggedResourceDataDao.count());
+
+		Thread.sleep(100);
+		
+		mySubscriptionDao.pollForNewUndeliveredResources();
+		assertEquals(2, mySubscriptionFlaggedResourceDataDao.count());
+		
+		Thread.sleep(100);
+		
+		mySubscriptionDao.pollForNewUndeliveredResources();
+		assertEquals(2, mySubscriptionFlaggedResourceDataDao.count());
+
+		Thread.sleep(100);
+		
+		obs = new Observation();
+		obs.getSubject().setReference(pId);
+		obs.setStatus(ObservationStatusEnum.FINAL);
+		myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+
+		mySubscriptionDao.pollForNewUndeliveredResources();
+		assertEquals(3, mySubscriptionFlaggedResourceDataDao.count());
+		
+		Thread.sleep(100);
+		
+		mySubscriptionDao.pollForNewUndeliveredResources();
+		assertEquals(3, mySubscriptionFlaggedResourceDataDao.count());
+	}
+
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2Test.java

@@ -803,6 +803,205 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		assertEquals(id2, gotId);
 	}
 
+	@Test
+	public void testDeleteWithMatchUrlChainedString() {
+		String methodName = "testDeleteWithMatchUrlChainedString";
+
+		Organization org = new Organization();
+		org.setName(methodName);
+		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.getManagingOrganization().setReference(orgId);
+		IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+		ourLog.info("Created patient, got it: {}", id);
+
+		myPatientDao.deleteByUrl("Patient?organization.name=" + methodName);
+
+		assertGone(id);
+	}
+
+	@Test
+	public void testDeleteWithMatchUrlChainedTag() {
+		String methodName = "testDeleteWithMatchUrlChainedString";
+
+		TagList tl = new TagList();
+		tl.addTag("http://foo", "term");
+		
+		Organization org = new Organization();
+		ResourceMetadataKeyEnum.TAG_LIST.put(org, tl);
+		org.setName(methodName);
+		
+		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.getManagingOrganization().setReference(orgId);
+		IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+		ourLog.info("Created patient, got it: {}", id);
+
+		myPatientDao.deleteByUrl("Patient?organization._tag=http://foo|term");
+		assertGone(id);
+		
+		myOrganizationDao.deleteByUrl("Organization?_tag=http://foo|term");
+		try {
+			myOrganizationDao.read(orgId);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			myPatientDao.deleteByUrl("Patient?organization._tag.identifier=http://foo|term");
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid parameter chain: organization._tag.identifier", e.getMessage());
+		}
+
+		try {
+			myOrganizationDao.deleteByUrl("Organization?_tag.identifier=http://foo|term");
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid parameter chain: _tag.identifier", e.getMessage());
+		}
+
+	}
+
+	
+	@Test
+	public void testDeleteWithMatchUrlQualifierMissing() {
+		String methodName = "testDeleteWithMatchUrlChainedProfile";
+
+		/*
+		 * Org 2 has no name
+		 */
+
+		Organization org1 = new Organization();
+		org1.addIdentifier().setValue(methodName);
+		IIdType org1Id = myOrganizationDao.create(org1).getId().toUnqualifiedVersionless();
+
+		Patient p1 = new Patient();
+		p1.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p1.getManagingOrganization().setReference(org1Id);
+		IIdType patId1 = myPatientDao.create(p1).getId().toUnqualifiedVersionless();
+
+		/*
+		 * Org 2 has a name
+		 */
+		
+		Organization org2 = new Organization();
+		org2.setName(methodName);		
+		org2.addIdentifier().setValue(methodName);
+		IIdType org2Id = myOrganizationDao.create(org2).getId().toUnqualifiedVersionless();
+
+		Patient p2 = new Patient();
+		p2.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p2.getManagingOrganization().setReference(org2Id);
+		IIdType patId2 = myPatientDao.create(p2).getId().toUnqualifiedVersionless();
+
+		ourLog.info("Pat ID 1 : {}", patId1);
+		ourLog.info("Org ID 1 : {}", org1Id);
+		ourLog.info("Pat ID 2 : {}", patId2);
+		ourLog.info("Org ID 2 : {}", org2Id);
+		
+		myPatientDao.deleteByUrl("Patient?organization.name:missing=true");
+		assertGone(patId1);
+		assertNotGone(patId2);
+		assertNotGone(org1Id);
+		assertNotGone(org2Id);
+		
+		myOrganizationDao.deleteByUrl("Organization?name:missing=true");
+		assertGone(patId1);
+		assertNotGone(patId2);
+		assertGone(org1Id);
+		assertNotGone(org2Id);
+
+		myPatientDao.deleteByUrl("Patient?organization.name:missing=false");
+		assertGone(patId1);
+		assertGone(patId2);
+		assertGone(org1Id);
+		assertNotGone(org2Id);
+		
+		myOrganizationDao.deleteByUrl("Organization?name:missing=false");
+		assertGone(patId1);
+		assertGone(patId2);
+		assertGone(org1Id);
+		assertGone(org2Id);
+	}
+
+	/**
+	 * This gets called from assertGone too! Careful about exceptions...
+	 */
+	private void assertNotGone(IIdType theId) {
+		if ("Patient".equals(theId.getResourceType())) {
+			myPatientDao.read(theId);
+		} else if ("Organization".equals(theId.getResourceType())){
+			myOrganizationDao.read(theId);
+		} else {
+			fail("No type");
+		}
+	}
+	private void assertGone(IIdType theId) {
+		try {
+			assertNotGone(theId);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+	}
+
+	
+	
+	@Test
+	public void testDeleteWithMatchUrlChainedProfile() {
+		String methodName = "testDeleteWithMatchUrlChainedProfile";
+
+		List<IdDt> profileList = new ArrayList<IdDt>();
+		profileList.add(new IdDt("http://foo"));
+		
+		Organization org = new Organization();
+		ResourceMetadataKeyEnum.PROFILES.put(org, profileList);
+		org.setName(methodName);
+		
+		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.getManagingOrganization().setReference(orgId);
+		IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+		ourLog.info("Created patient, got it: {}", id);
+
+		myPatientDao.deleteByUrl("Patient?organization._profile=http://foo");
+		assertGone(id);
+		
+		myOrganizationDao.deleteByUrl("Organization?_profile=http://foo");
+		try {
+			myOrganizationDao.read(orgId);
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		try {
+			myPatientDao.deleteByUrl("Patient?organization._profile.identifier=http://foo");
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid parameter chain: organization._profile.identifier", e.getMessage());
+		}
+
+		try {
+			myOrganizationDao.deleteByUrl("Organization?_profile.identifier=http://foo");
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid parameter chain: _profile.identifier", e.getMessage());
+		}
+
+	}
+
 	@Test
 	public void testDeleteWithMatchUrl() {
 		String methodName = "testDeleteWithMatchUrl";
@@ -840,8 +1039,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
-
-	
 	@Test
 	public void testHistoryByForcedId() {
 		IIdType idv1;
@@ -1619,6 +1816,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		}
 
 	}
+
 	@Test
 	public void testReadWithDeletedResource() {
 		String methodName = "testReadWithDeletedResource";
@@ -1628,12 +1826,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		IIdType id = myPatientDao.create(patient).getId().toVersionless();
 		myPatientDao.delete(id);
 
-		try {
+		assertGone(id);
-			myPatientDao.read(id);
-			fail();
-		} catch (ResourceGoneException e) {
-			// good
-		}
 
 		patient.setId(id);
 		patient.addAddress().addLine("AAA");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2ValidateTest.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
 import ca.uhn.fhir.rest.server.EncodingEnum;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 
@@ -127,6 +128,70 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
 
 	}
 	
+	@Test
+	public void testValidateForCreate() {
+		String methodName = "testValidateForCreate";
+		
+		Patient pat = new Patient();
+		pat.setId("Patient/123");
+		pat.addName().addFamily(methodName);
+		
+		try {
+			myPatientDao.validate(pat, null, null, null, ValidationModeEnum.CREATE, null);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("ID must not be populated"));
+		}
+
+		pat.setId("");
+		myPatientDao.validate(pat, null, null, null, ValidationModeEnum.CREATE, null);
+
+	}
+	
+	@Test
+	public void testValidateForUpdate() {
+		String methodName = "testValidateForUpdate";
+		
+		Patient pat = new Patient();
+		pat.setId("Patient/123");
+		pat.addName().addFamily(methodName);
+		myPatientDao.validate(pat, null, null, null, ValidationModeEnum.UPDATE, null);
+
+		pat.setId("");
+		
+		try {
+			myPatientDao.validate(pat, null, null, null, ValidationModeEnum.UPDATE, null);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("ID must be populated"));
+		}
+
+	}
+
+	@Test
+	public void testValidateForUpdateWithContained() {
+		String methodName = "testValidateForUpdate";
+		
+		Organization org = new Organization();
+		org.setId("#123");
+		
+		Patient pat = new Patient();
+		pat.setId("Patient/123");
+		pat.addName().addFamily(methodName);
+		myPatientDao.validate(pat, null, null, null, ValidationModeEnum.UPDATE, null);
+
+		pat.setId("");
+		
+		try {
+			myPatientDao.validate(pat, null, null, null, ValidationModeEnum.UPDATE, null);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertThat(e.getMessage(), containsString("ID must be populated"));
+		}
+
+	}
+
+	
 	@Test
 	public void testValidateForDelete() {
 		String methodName = "testValidateForDelete";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2Test.java

@@ -60,9 +60,7 @@ import ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.model.primitive.UriDt;
-import ca.uhn.fhir.rest.api.PreferReturnEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
-import ca.uhn.fhir.rest.client.IGenericClient;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -75,6 +73,13 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu2Test.class);
 
+	@Test
+	public void testTransactionFromBundle6() throws Exception {
+		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle3.xml");
+		String bundle = IOUtils.toString(bundleRes);
+		mySystemDao.transaction(myFhirCtx.newXmlParser().parseResource(Bundle.class, bundle));
+	}
+	
 	@Test
 	public void testRendexing() {
 		Patient p = new Patient();
@@ -292,6 +297,23 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2Test {
 
 	}
 
+	@Test
+	public void testEverythingType() {
+		
+		Bundle request = new Bundle();
+		request.setType(BundleTypeEnum.SEARCH_RESULTS);
+		Patient p = new Patient();
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerbEnum.POST);
+
+		try {
+			mySystemDao.transaction(request);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Unable to process transaction where incoming Bundle.type = searchset", e.getMessage());
+		}
+
+	}
+
 	@Test
 	public void testTransactionBatchWithFailingRead() {
 		String methodName = "testTransactionBatchWithFailingRead";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/QuestionnaireResourceProviderDstu2.java

@@ -0,0 +1,13 @@
+package ca.uhn.fhir.jpa.provider;
+
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.dstu2.resource.Questionnaire;
+
+public class QuestionnaireResourceProviderDstu2 extends JpaResourceProviderDstu1<Questionnaire> {
+
+	@Override
+	public Class<? extends IResource> getResourceType() {
+		return Questionnaire.class;
+	}
+
+}

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

@@ -2006,14 +2006,15 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 		String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(input);
 		ourLog.info(inputStr);
 
-		HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
+		HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate?_pretty=true");
 		post.setEntity(new StringEntity(inputStr, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
 
 		CloseableHttpResponse response = ourHttpClient.execute(post);
 		try {
 			String resp = IOUtils.toString(response.getEntity().getContent());
 			ourLog.info(resp);
-			assertEquals(412, response.getStatusLine().getStatusCode());
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			assertThat(resp, not(containsString("Resource has no id")));
 		} finally {
 			IOUtils.closeQuietly(response.getEntity().getContent());
 			response.close();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu2Test.java

@@ -3,8 +3,14 @@ package ca.uhn.fhir.jpa.provider;
 import static org.junit.Assert.*;
 
 import java.io.InputStream;
+import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
@@ -17,14 +23,14 @@ import org.springframework.context.support.ClassPathXmlApplicationContext;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.BaseJpaTest;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
-import ca.uhn.fhir.jpa.rp.dstu.ObservationResourceProvider;
+import ca.uhn.fhir.jpa.rp.dstu2.ObservationResourceProvider;
-import ca.uhn.fhir.jpa.rp.dstu.OrganizationResourceProvider;
+import ca.uhn.fhir.jpa.rp.dstu2.OrganizationResourceProvider;
-import ca.uhn.fhir.jpa.rp.dstu.PatientResourceProvider;
+import ca.uhn.fhir.jpa.rp.dstu2.PatientResourceProvider;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
-import ca.uhn.fhir.model.dstu.resource.Observation;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
-import ca.uhn.fhir.model.dstu.resource.Organization;
+import ca.uhn.fhir.model.dstu2.resource.Organization;
-import ca.uhn.fhir.model.dstu.resource.Patient;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.dstu.resource.Questionnaire;
+import ca.uhn.fhir.model.dstu2.resource.Questionnaire;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.OperationDefinition;
 import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
@@ -40,7 +46,19 @@ public class SystemProviderDstu2Test  extends BaseJpaTest {
 	private static ClassPathXmlApplicationContext ourAppCtx;
 	private static FhirContext ourCtx;
 	private static IGenericClient ourClient;
+	private static String ourServerBase;
+	private static CloseableHttpClient ourHttpClient;
 
+	@Test
+	public void testEverythingType() throws Exception {
+		HttpGet get = new HttpGet(ourServerBase + "/Patient/$everything");
+		CloseableHttpResponse http = ourHttpClient.execute(get);
+		try {
+			assertEquals(200, http.getStatusLine().getStatusCode());
+		} finally {
+			http.close();
+		}
+	}
 
 	@Test
 	public void testTransactionFromBundle4() throws Exception {
@@ -71,6 +89,20 @@ public class SystemProviderDstu2Test  extends BaseJpaTest {
 		}
 	}
 
+	@Test
+	public void testTransactionFromBundle6() throws Exception {
+		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle3.xml");
+		String bundle = IOUtils.toString(bundleRes);
+		ourClient.transaction().withBundle(bundle).prettyPrint().execute();
+//		try {
+//			fail();
+//		} catch (InvalidRequestException e) {
+//			OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
+//			assertEquals("Invalid placeholder ID found: uri:uuid:bb0cd4bc-1839-4606-8c46-ba3069e69b1d - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'", oo.getIssue().get(0).getDiagnostics());
+//			assertEquals("processing", oo.getIssue().get(0).getCode());
+//		}
+	}
+
 	@Test
 	public void testTransactionFromBundle() throws Exception {
 		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve.xml");
@@ -82,7 +114,7 @@ public class SystemProviderDstu2Test  extends BaseJpaTest {
 	/**
 	 * This is Gramahe's test transaction - it requires some set up in order to work
 	 */
-//	@Test
+	// @Test
 	public void testTransactionFromBundle3() throws Exception {
 
 		InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/grahame-transaction.xml");
@@ -150,7 +182,7 @@ public class SystemProviderDstu2Test  extends BaseJpaTest {
 		patientRp.setDao(patientDao);
 
 		IFhirResourceDao<Questionnaire> questionnaireDao = (IFhirResourceDao<Questionnaire>) ourAppCtx.getBean("myQuestionnaireDaoDstu2", IFhirResourceDao.class);
-		QuestionnaireResourceProvider questionnaireRp = new QuestionnaireResourceProvider();
+		QuestionnaireResourceProviderDstu2 questionnaireRp = new QuestionnaireResourceProviderDstu2();
 		questionnaireRp.setDao(questionnaireDao);
 
 		IFhirResourceDao<Observation> observationDao = (IFhirResourceDao<Observation>) ourAppCtx.getBean("myObservationDaoDstu2", IFhirResourceDao.class);
@@ -173,7 +205,7 @@ public class SystemProviderDstu2Test  extends BaseJpaTest {
 		ServletContextHandler proxyHandler = new ServletContextHandler();
 		proxyHandler.setContextPath("/");
 
-		String serverBase = "http://localhost:" + myPort + "/fhir/context";
+		ourServerBase = "http://localhost:" + myPort + "/fhir/context";
 
 		ServletHolder servletHolder = new ServletHolder();
 		servletHolder.setServlet(restServer);
@@ -185,9 +217,13 @@ public class SystemProviderDstu2Test  extends BaseJpaTest {
 		ourServer.setHandler(proxyHandler);
 		ourServer.start();
 
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourHttpClient = builder.build();
 
 		ourCtx.getRestfulClientFactory().setSocketTimeout(600 * 1000);
-		ourClient = ourCtx.newRestfulGenericClient(serverBase);
+		ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
 		ourClient.setLogRequestAndResponse(true);
 	}
 

hapi-fhir-jpaserver-base/src/test/resources/logback-test.xml

@@ -1,13 +1,20 @@
 <configuration>
 
 	<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+		<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+			<level>DEBUG</level>
+		</filter>
 		<encoder>
 			<pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n
 			</pattern>
 		</encoder>
 	</appender>
 
-	<logger name="org.springframework.web.socket.handler.ExceptionWebSocketHandlerDecorator" additivity="false" info="debug">
+	<logger name="org.springframework.web.socket.handler.ExceptionWebSocketHandlerDecorator" additivity="false" level="debug">
+		<appender-ref ref="STDOUT" />
+	</logger>
+
+	<logger name="ca.uhn.fhir.jpa.dao.FhirResourceDaoSubscriptionDstu2" additivity="false" level="debug">
 		<appender-ref ref="STDOUT" />
 	</logger>
 

hapi-fhir-jpaserver-base/src/test/resources/simone_bundle3.xml

@@ -0,0 +1,241 @@
+<Bundle xmlns="http://hl7.org/fhir">
+	<id value="20151004163829"/>
+	<type value="transaction"/>
+	<entry>
+		<fullUrl value="urn:uuid:87c8e948-e0d2-4b92-74bd-a824a4769ab4"/>
+		<resource>
+			<Patient>
+				<identifier>
+					<use value="usual"/>
+					<type>
+						<coding>
+							<system value="http://hl7.org/fhir/identifier-type"/>
+							<code value="NH"/>
+						</coding>
+					</type>
+					<system value="urn:oid:2.16.840.1.113883.2.1.4.1"/>
+					<value value="123412312345"/>
+					<assigner>
+						<display value="NHS"/>
+					</assigner>
+				</identifier>
+				<identifier>
+					<use value="usual"/>
+					<type>
+						<coding>
+							<system value="http://hl7.org/fhir/identifier-type"/>
+							<code value="MR"/>
+						</coding>
+					</type>
+					<system value="http://www.ghh.org/identifiers"/>
+					<value value="456756756745"/>
+					<assigner>
+						<display value="TCPAS"/>
+					</assigner>
+				</identifier>
+				<name>
+					<use value="official"/>
+					<family value="Connectathon"/>
+					<given value="Ten"/>
+				</name>
+				<telecom>
+					<system value="phone"/>
+					<value value="277543"/>
+					<use value="home"/>
+				</telecom>
+				<gender value="female"/>
+				<birthDate value="2015-05-24"/>
+				<address>
+					<line value="22 Peachtree Road"/>
+					<city value="Whitstable"/>
+					<state value="Kent"/>
+					<country value="CR5 1EL"/>
+				</address>
+				<contact>
+					<relationship>
+						<coding>
+							<system value="http://hl7.org/fhir/patient-contact-relationship"/>
+							<code value="parent"/>
+						</coding>
+					</relationship>
+					<name>
+						<family value="Connectathon"/>
+						<given value="Nine"/>
+					</name>
+				</contact>
+				<contact>
+					<relationship>
+						<coding>
+							<system value="http://hl7.org/fhir/patient-contact-relationship"/>
+						</coding>
+					</relationship>
+					<name>
+						<family value="Connectathon"/>
+						<given value="Eight"/>
+					</name>
+				</contact>
+			</Patient>
+		</resource>
+		<request>
+			<method value="PUT"/>
+			<url value="Patient?identifier=http://www.ghh.org/identifiers|456756756745"/>
+		</request>
+	</entry>
+	<entry>
+		<fullUrl value="urn:uuid:b23ee048-63c1-4373-6194-54adb2f64821"/>
+		<resource>
+			<Encounter>
+				<identifier>
+					<use value="usual"/>
+					<type>
+						<coding>
+							<system value="http://hl7.org/fhir/identifier-type"/>
+							<code value="MR"/>
+						</coding>
+					</type>
+					<system value="http://general-hospital.co.uk/Identifiers"/>
+					<value value="09876876876"/>
+					<assigner>
+						<display value="GENHOS"/>
+					</assigner>
+				</identifier>
+				<status value="in-progress"/>
+				<class value="inpatient"/>
+				<patient>
+					<reference value="urn:uuid:87c8e948-e0d2-4b92-74bd-a824a4769ab4"/>
+					<display value="Connectathon, Ten(*24.05.2015)"/>
+				</patient>
+				<period>
+					<start value="2015-05-02T09:00:00+01:00"/>
+				</period>
+			</Encounter>
+		</resource>
+		<request>
+			<method value="PUT"/>
+			<url value="Encounter?identifier=http://general-hospital.co.uk/Identifiers|09876876876"/>
+		</request>
+	</entry>
+	<entry>
+		<request>
+			<method value="DELETE"/>
+			<url value="AllergyIntolerance?patient.identifier=http://general-hospital.co.uk/Identifiers|123412312345"/>
+		</request>
+	</entry>
+	<entry>
+		<resource>
+			<AllergyIntolerance>
+				<identifier>
+					<system value="http://health-comm.de/identifiers"/>
+					<value value="123412312345-DA-1605"/>
+					<assigner>
+						<display value="CLOVERLEAF"/>
+					</assigner>
+				</identifier>
+				<patient>
+					<reference value="urn:uuid:87c8e948-e0d2-4b92-74bd-a824a4769ab4"/>
+					<display value="Connectathon, Ten(*24.05.2015)"/>
+				</patient>
+				<substance>
+					<coding>
+						<code value="1605"/>
+						<display value="L"/>
+					</coding>
+					<text value="acetaminophen"/>
+				</substance>
+				<category value="medication"/>
+				<reaction>
+					<manifestation>
+						<text value="Muscle Pain"/>
+					</manifestation>
+					<severity value="moderate"/>
+				</reaction>
+				<reaction>
+					<manifestation>
+						<text value="hair loss"/>
+					</manifestation>
+					<severity value="moderate"/>
+				</reaction>
+			</AllergyIntolerance>
+		</resource>
+		<request>
+			<method value="PUT"/>
+			<url value="AllergyIntolerance?identifier=http://health-comm.de/identifiers|123412312345-DA-1605"/>
+		</request>
+	</entry>
+	<entry>
+		<resource>
+			<AllergyIntolerance>
+				<identifier>
+					<system value="http://health-comm.de/identifiers"/>
+					<value value="123412312345-DA-1558"/>
+					<assigner>
+						<display value="CLOVERLEAF"/>
+					</assigner>
+				</identifier>
+				<patient>
+					<reference value="urn:uuid:87c8e948-e0d2-4b92-74bd-a824a4769ab4"/>
+					<display value="Connectathon, Ten(*24.05.2015)"/>
+				</patient>
+				<substance>
+					<coding>
+						<code value="1558"/>
+						<display value="L"/>
+					</coding>
+					<text value="Oxycodone"/>
+				</substance>
+				<category value="medication"/>
+				<reaction>
+					<manifestation>
+						<text value="Muscle Pain"/>
+					</manifestation>
+					<severity value="moderate"/>
+				</reaction>
+				<reaction>
+					<manifestation>
+						<text value="hair loss"/>
+					</manifestation>
+					<severity value="moderate"/>
+				</reaction>
+			</AllergyIntolerance>
+		</resource>
+		<request>
+			<method value="PUT"/>
+			<url value="AllergyIntolerance?identifier=http://health-comm.de/identifiers|123412312345-DA-1558"/>
+		</request>
+	</entry>
+	<entry>
+		<resource>
+			<AllergyIntolerance>
+				<identifier>
+					<system value="http://health-comm.de/identifiers"/>
+					<value value="123412312345-MA-2221"/>
+					<assigner>
+						<display value="CLOVERLEAF"/>
+					</assigner>
+				</identifier>
+				<patient>
+					<reference value="urn:uuid:87c8e948-e0d2-4b92-74bd-a824a4769ab4"/>
+					<display value="Connectathon, Ten(*24.05.2015)"/>
+				</patient>
+				<substance>
+					<coding>
+						<code value="2221"/>
+						<display value="L"/>
+					</coding>
+					<text value="Peanuts"/>
+				</substance>
+				<category value="environment"/>
+				<reaction>
+					<manifestation>
+						<text value="Anaphylactic Shock "/>
+					</manifestation>
+					<severity value="severe"/>
+				</reaction>
+			</AllergyIntolerance>
+		</resource>
+		<request>
+			<method value="PUT"/>
+			<url value="AllergyIntolerance?identifier=http://health-comm.de/identifiers|123412312345-MA-2221"/>
+		</request>
+	</entry>
+</Bundle>

hapi-fhir-jpaserver-example/pom.xml

@@ -169,8 +169,6 @@
 					<configuration>
 						<webApp>
 							<contextPath>/hapi-fhir-jpaserver-example</contextPath>
-						</webApp>
-						<webAppConfig>
 							<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
 						</webAppConfig>
 					</configuration>

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/validation/InstanceValidator.java

@@ -1026,6 +1026,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       return parts.length > 2 && parts[parts.length - 1].equals("resource") && ((parts.length > 2 && parts[parts.length - 3].equals("entry")) || parts[parts.length - 2].equals("entry"));
   }
 
+  private boolean isParametersEntry(String path) {
+	    String[] parts = path.split("\\/");
+	    if (path.startsWith("/f:"))
+	      return parts.length == 4 && parts[parts.length-3].equals("f:Parameters") && parts[parts.length-2].startsWith("f:parameter") && parts[parts.length-1].startsWith("f:resource");
+	    else
+	      return parts.length == 4 && parts[parts.length-3].equals("Parameters") && parts[parts.length-2].startsWith("parameter") && parts[parts.length-1].startsWith("resource");
+	  }
+
   private boolean isPrimitiveType(String type) {
     return type.equalsIgnoreCase("boolean") || type.equalsIgnoreCase("integer") || type.equalsIgnoreCase("string") || type.equalsIgnoreCase("decimal") || type.equalsIgnoreCase("uri")
         || type.equalsIgnoreCase("base64Binary") || type.equalsIgnoreCase("instant") || type.equalsIgnoreCase("date") || type.equalsIgnoreCase("uuid") || type.equalsIgnoreCase("id")
@@ -1790,7 +1798,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
             if (type.equals("Extension")) {
               checkExtension(errors, ei.path, ei.element, ei.definition, profile, localStack);
             } else if (type.equals("Resource")) {
-              validateContains(errors, ei.path, ei.definition, definition, ei.element, localStack, !isBundleEntry(ei.path)); // if
+              validateContains(errors, ei.path, ei.definition, definition, ei.element, localStack, !isBundleEntry(ei.path) && !isParametersEntry(ei.path)); // if
                                                                                                                              // (str.matches(".*([.,/])work\\1$"))
             } else {
               StructureDefinition p = getProfileForType(type);

src/changes/changes.xml

@@ -139,6 +139,13 @@
 				of the narrative section caused an invalid
 				re-encoding when encoding to JSON.
 			</action>
+			<action type="fix">
+				Conditional deletes in JPA did not correctly 
+				process if the condition had a chain or a 
+				qualifier, e.g. "Patient?organization.name" or
+				"Patient.identifier:missing"
+
+			</action>
 		</release>
 		<release version="1.2" date="2015-09-18">
 			<action type="add">