Added ability to modify URLs in BundleUtil

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java

@@ -32,6 +32,7 @@ import ca.uhn.fhir.model.primitive.XhtmlDt;
 import ca.uhn.fhir.parser.json.JsonLikeValue.ScalarType;
 import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
 import ca.uhn.fhir.util.*;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.tuple.Pair;

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

@@ -0,0 +1,28 @@
+package ca.uhn.fhir.util.bundle;
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.ParametersUtil;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
+class BundleEntryMutator {
+	private final IBase myEntry;
+	private final BaseRuntimeChildDefinition myRequestChildDef;
+	private final BaseRuntimeElementCompositeDefinition<?> myRequestChildContentsDef;
+
+	BundleEntryMutator(IBase theEntry, BaseRuntimeChildDefinition theRequestChildDef, BaseRuntimeElementCompositeDefinition<?> theRequestChildContentsDef) {
+		myEntry = theEntry;
+		myRequestChildDef = theRequestChildDef;
+		myRequestChildContentsDef = theRequestChildContentsDef;
+	}
+
+	void setRequestUrl(FhirContext theFhirContext, String theRequestUrl) {
+		BaseRuntimeChildDefinition requestUrlChildDef = myRequestChildContentsDef.getChildByName("url");
+		IPrimitiveType<?> url = ParametersUtil.createUri(theFhirContext, theRequestUrl);
+		for (IBase nextRequest : myRequestChildDef.getAccessor().getValues(myEntry)) {
+			requestUrlChildDef.getMutator().addValue(nextRequest, url);
+		}
+	}
+}

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

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.util.bundle;
+
+import ca.uhn.fhir.rest.api.RequestTypeEnum;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+public class BundleEntryParts {
+	private final RequestTypeEnum myRequestType;
+	private final IBaseResource myResource;
+	private final String myUrl;
+	private final String myConditionalUrl;
+
+	BundleEntryParts(RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource, String theConditionalUrl) {
+		super();
+		myRequestType = theRequestType;
+		myUrl = theUrl;
+		myResource = theResource;
+		myConditionalUrl = theConditionalUrl;
+	}
+
+	public RequestTypeEnum getRequestType() {
+		return myRequestType;
+	}
+
+	public IBaseResource getResource() {
+		return myResource;
+	}
+
+	public String getConditionalUrl() {
+		return myConditionalUrl;
+	}
+
+	public String getUrl() {
+		return myUrl;
+	}
+}

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

@@ -1,9 +1,6 @@
-package ca.uhn.fhir.util;
+package ca.uhn.fhir.util.bundle;
 
-import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.*;
-import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.rest.api.RequestTypeEnum;
 import org.apache.commons.lang3.tuple.Pair;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -14,6 +11,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
+import java.util.function.Consumer;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
@@ -42,37 +40,6 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  */
 public class BundleUtil {
 
-	public static class BundleEntryParts {
-		private final RequestTypeEnum myRequestType;
-		private final IBaseResource myResource;
-		private final String myUrl;
-		private final String myConditionalUrl;
-
-		BundleEntryParts(RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource, String theConditionalUrl) {
-			super();
-			myRequestType = theRequestType;
-			myUrl = theUrl;
-			myResource = theResource;
-			myConditionalUrl = theConditionalUrl;
-		}
-
-		public RequestTypeEnum getRequestType() {
-			return myRequestType;
-		}
-
-		public IBaseResource getResource() {
-			return myResource;
-		}
-
-		public String getConditionalUrl() {
-			return myConditionalUrl;
-		}
-
-		public String getUrl() {
-			return myUrl;
-		}
-	}
-
 	/**
 	 * @return Returns <code>null</code> if the link isn't found or has no value
 	 */
@@ -185,20 +152,26 @@ public class BundleUtil {
 	 * Extract all of the resources from a given bundle
 	 */
 	public static List<BundleEntryParts> toListOfEntries(FhirContext theContext, IBaseBundle theBundle) {
-		List<BundleEntryParts> retVal = new ArrayList<>();
 
-		RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
+		EntryListAccumulator entryListAccumulator = new EntryListAccumulator();
-		BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
+		processEntries(theContext, theBundle, entryListAccumulator);
-		List<IBase> entries = entryChild.getAccessor().getValues(theBundle);
+		return entryListAccumulator.getList();
+	}
 
-		BaseRuntimeElementCompositeDefinition<?> entryChildElem = (BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
 
-		BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
+	public static void processEntries(FhirContext theContext, IBaseBundle theBundle, Consumer<ModifiableBundleEntry> theProcessor) {
-		BaseRuntimeChildDefinition requestChild = entryChildElem.getChildByName("request");
+		RuntimeResourceDefinition bundleDef = theContext.getResourceDefinition(theBundle);
-		BaseRuntimeElementCompositeDefinition<?> requestElem = (BaseRuntimeElementCompositeDefinition<?>) requestChild.getChildByName("request");
+		BaseRuntimeChildDefinition entryChildDef = bundleDef.getChildByName("entry");
-		BaseRuntimeChildDefinition requestUrlChild = requestElem.getChildByName("url");
+		List<IBase> entries = entryChildDef.getAccessor().getValues(theBundle);
-		BaseRuntimeChildDefinition requestIfNoneExistChild = requestElem.getChildByName("ifNoneExist");
+
-		BaseRuntimeChildDefinition methodChild = requestElem.getChildByName("method");
+		BaseRuntimeElementCompositeDefinition<?> entryChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) entryChildDef.getChildByName("entry");
+
+		BaseRuntimeChildDefinition resourceChildDef = entryChildContentsDef.getChildByName("resource");
+		BaseRuntimeChildDefinition requestChildDef = entryChildContentsDef.getChildByName("request");
+		BaseRuntimeElementCompositeDefinition<?> requestChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) requestChildDef.getChildByName("request");
+		BaseRuntimeChildDefinition requestUrlChildDef = requestChildContentsDef.getChildByName("url");
+		BaseRuntimeChildDefinition requestIfNoneExistChildDef = requestChildContentsDef.getChildByName("ifNoneExist");
+		BaseRuntimeChildDefinition methodChildDef = requestChildContentsDef.getChildByName("method");
 
 		for (IBase nextEntry : entries) {
 			IBaseResource resource = null;
@@ -206,15 +179,15 @@ public class BundleUtil {
 			RequestTypeEnum requestType = null;
 			String conditionalUrl = null;
 
-			for (IBase next : resourceChild.getAccessor().getValues(nextEntry)) {
+			for (IBase nextResource : resourceChildDef.getAccessor().getValues(nextEntry)) {
-				resource = (IBaseResource) next;
+				resource = (IBaseResource) nextResource;
 			}
-			for (IBase nextRequest : requestChild.getAccessor().getValues(nextEntry)) {
+			for (IBase nextRequest : requestChildDef.getAccessor().getValues(nextEntry)) {
-				for (IBase nextUrl : requestUrlChild.getAccessor().getValues(nextRequest)) {
+				for (IBase nextUrl : requestUrlChildDef.getAccessor().getValues(nextRequest)) {
 					url = ((IPrimitiveType<?>) nextUrl).getValueAsString();
 				}
-				for (IBase nextUrl : methodChild.getAccessor().getValues(nextRequest)) {
+				for (IBase nextMethod : methodChildDef.getAccessor().getValues(nextRequest)) {
-					String methodString = ((IPrimitiveType<?>) nextUrl).getValueAsString();
+					String methodString = ((IPrimitiveType<?>) nextMethod).getValueAsString();
 					if (isNotBlank(methodString)) {
 						requestType = RequestTypeEnum.valueOf(methodString);
 					}
@@ -227,7 +200,7 @@ public class BundleUtil {
 							conditionalUrl = url != null && url.contains("?") ? url : null;
 							break;
 						case POST:
-							List<IBase> ifNoneExistReps = requestIfNoneExistChild.getAccessor().getValues(nextRequest);
+							List<IBase> ifNoneExistReps = requestIfNoneExistChildDef.getAccessor().getValues(nextRequest);
 							if (ifNoneExistReps.size() > 0) {
 								IPrimitiveType<?> ifNoneExist = (IPrimitiveType<?>) ifNoneExistReps.get(0);
 								conditionalUrl = ifNoneExist.getValueAsString();
@@ -241,11 +214,10 @@ public class BundleUtil {
 			 * All 3 might be null - That's ok because we still want to know the
 			 * order in the original bundle.
 			 */
-			retVal.add(new BundleEntryParts(requestType, url, resource, conditionalUrl));
+			BundleEntryMutator mutator = new BundleEntryMutator(nextEntry, requestChildDef, requestChildContentsDef);
+			ModifiableBundleEntry entry = new ModifiableBundleEntry(new BundleEntryParts(requestType, url, resource, conditionalUrl), mutator);
+			theProcessor.accept(entry);
 		}
-
-
-		return retVal;
 	}
 
 	/**
@@ -278,4 +250,6 @@ public class BundleUtil {
 		}
 		return retVal;
 	}
+
+
 }

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

@@ -0,0 +1,18 @@
+package ca.uhn.fhir.util.bundle;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.function.Consumer;
+
+class EntryListAccumulator implements Consumer<ModifiableBundleEntry> {
+	private final List<BundleEntryParts> myList = new ArrayList<>();
+
+	@Override
+	public void accept(ModifiableBundleEntry theModifiableBundleEntry) {
+		myList.add(theModifiableBundleEntry.getBundleEntryParts());
+	}
+
+	public List<BundleEntryParts> getList() {
+		return myList;
+	}
+}

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

@@ -0,0 +1,32 @@
+package ca.uhn.fhir.util.bundle;
+
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.ParametersUtil;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
+public class ModifiableBundleEntry {
+	private final BundleEntryParts myBundleEntryParts;
+	private final BundleEntryMutator myBundleEntryMutator;
+
+	ModifiableBundleEntry(BundleEntryParts theBundleEntryParts, BundleEntryMutator theBundleEntryMutator) {
+		myBundleEntryParts = theBundleEntryParts;
+		myBundleEntryMutator = theBundleEntryMutator;
+	}
+
+	BundleEntryParts getBundleEntryParts() {
+		return myBundleEntryParts;
+	}
+
+	void setRequestUrl(FhirContext theFhirContext, String theRequestUrl) {
+		myBundleEntryMutator.setRequestUrl(theFhirContext, theRequestUrl);
+	}
+
+	String getRequestUrl() {
+		return myBundleEntryParts.getUrl();
+	}
+
+
+}

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

@@ -23,7 +23,7 @@ package ca.uhn.fhir.validation.schematron;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.validation.*;
 import com.helger.commons.error.IError;
 import com.helger.commons.error.list.IErrorList;

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

@@ -35,7 +35,7 @@ import ca.uhn.fhir.rest.api.IVersionSpecificBundleFactory;
 import ca.uhn.fhir.rest.client.apache.GZipContentInterceptor;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.ValidationResult;

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/BaseResourceReturningMethodBinding.java

@@ -22,7 +22,6 @@ package ca.uhn.fhir.rest.client.method;
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.Reader;
 import java.lang.reflect.Method;
 import java.lang.reflect.Modifier;
 import java.util.*;
@@ -37,7 +36,7 @@ import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.client.exceptions.InvalidResponseException;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.ReflectionUtil;
 
 public abstract class BaseResourceReturningMethodBinding extends BaseMethodBinding<Object> {

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

@@ -8,7 +8,7 @@ import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.EncodingEnum;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ch.qos.logback.classic.LoggerContext;
 import ch.qos.logback.core.joran.util.ConfigurationWatchListUtil;
 import org.apache.commons.io.FileUtils;

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

@@ -25,7 +25,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.test.utilities.LoggingRule;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;

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

@@ -126,7 +126,7 @@ import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;

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

@@ -16,7 +16,7 @@ import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.TestUtil;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ConsentInterceptorResourceProviderR4Test.java

@@ -10,7 +10,7 @@ import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.interceptor.consent.*;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
 import com.google.common.collect.Lists;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java

@@ -19,7 +19,7 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import com.google.common.base.Charsets;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionsR4Test.java

@@ -11,7 +11,7 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.test.utilities.JettyUtil;
 import com.google.common.collect.Lists;
 import net.ttddyy.dsproxy.QueryCount;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionsR5Test.java

@@ -12,7 +12,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.test.utilities.JettyUtil;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import com.google.common.collect.Lists;
 import net.ttddyy.dsproxy.QueryCount;
 import net.ttddyy.dsproxy.listener.SingleQueryCountHolder;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/z/ResourceMinimizerMojo.java

@@ -8,7 +8,7 @@ import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.EncodingEnum;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ch.qos.logback.classic.LoggerContext;
 import ch.qos.logback.core.joran.util.ConfigurationWatchListUtil;
 import org.apache.commons.io.FileUtils;

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/module/standalone/FhirClientSearchParamProvider.java

@@ -29,7 +29,7 @@ import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.server.SimpleBundleProvider;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.slf4j.Logger;

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/module/standalone/FhirClientSubscriptionProvider.java

@@ -29,7 +29,7 @@ import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.server.SimpleBundleProvider;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.beans.factory.annotation.Autowired;

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleImplOp.java

@@ -11,8 +11,8 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizationInterceptor.Verdict;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
-import ca.uhn.fhir.util.BundleUtil.BundleEntryParts;
+import ca.uhn.fhir.util.bundle.BundleEntryParts;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.annotations.VisibleForTesting;

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/SearchNarrowingInterceptor.java

@@ -23,15 +23,21 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.interceptor.api.Hook;
+import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.ParameterUtil;
 import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
-import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
+import ca.uhn.fhir.util.bundle.BundleEntryParts;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import org.apache.commons.collections4.ListUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
@@ -60,7 +66,8 @@ import java.util.*;
  *
  * @see AuthorizationInterceptor
  */
-public abstract class SearchNarrowingInterceptor extends InterceptorAdapter {
+public class SearchNarrowingInterceptor {
+	private static final Logger ourLog = LoggerFactory.getLogger(SearchNarrowingInterceptor.class);
 
 	/**
 	 * Subclasses should override this method to supply the set of compartments that
@@ -79,10 +86,8 @@ public abstract class SearchNarrowingInterceptor extends InterceptorAdapter {
 		return null;
 	}
 
-
+	@Hook(Pointcut.SERVER_INCOMING_REQUEST_POST_PROCESSED)
-	@Override
 	public boolean incomingRequestPostProcessed(RequestDetails theRequestDetails, HttpServletRequest theRequest, HttpServletResponse theResponse) throws AuthenticationException {
-
 		// We don't support this operation type yet
 		Validate.isTrue(theRequestDetails.getRestOperationType() != RestOperationTypeEnum.SEARCH_SYSTEM);
 
@@ -171,6 +176,24 @@ public abstract class SearchNarrowingInterceptor extends InterceptorAdapter {
 		return true;
 	}
 
+	@Hook(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED)
+	public void incomingRequestPreHandled(RequestDetails theRequestDetails, HttpServletRequest theRequest, HttpServletResponse theResponse) throws AuthenticationException {
+		if (theRequestDetails.getRestOperationType() != RestOperationTypeEnum.TRANSACTION) {
+			return;
+		}
+		incomingRequestPostProcessedBundle(theRequestDetails, theRequest, theResponse);
+	}
+
+	private void incomingRequestPostProcessedBundle(RequestDetails theRequestDetails, HttpServletRequest theRequest, HttpServletResponse theResponse) {
+		IBaseBundle bundle = (IBaseBundle) theRequestDetails.getResource();
+		FhirContext ctx = theRequestDetails.getFhirContext();
+		List<BundleEntryParts> entries = BundleUtil.toListOfEntries(ctx, bundle);
+		for (BundleEntryParts entry : entries) {
+			bundle.setUserData("test", "bark");
+		}
+		theRequestDetails.setResource(bundle);
+	}
+
 	private void processResourcesOrCompartments(RequestDetails theRequestDetails, RuntimeResourceDefinition theResDef, HashMap<String, List<String>> theParameterToOrValues, Collection<String> theResourcesOrCompartments, boolean theAreCompartments) {
 		String lastCompartmentName = null;
 		String lastSearchParamName = null;

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/consent/ConsentInterceptor.java

@@ -34,7 +34,7 @@ import ca.uhn.fhir.rest.api.server.ResponseDetails;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
 import ca.uhn.fhir.rest.server.util.ICachedSearchDetails;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.IModelVisitor2;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.*;

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

@@ -28,7 +28,7 @@ import ca.uhn.fhir.rest.annotation.TransactionParam;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/IncludeDstu2Test.java

@@ -17,7 +17,7 @@ import ca.uhn.fhir.rest.annotation.RequiredParam;
 import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.test.utilities.JettyUtil;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.ElementUtil;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/IncludeTest.java

@@ -13,7 +13,7 @@ import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.test.utilities.JettyUtil;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.ElementUtil;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/SearchSearchServerR4Test.java

@@ -15,6 +15,7 @@ import java.util.concurrent.TimeUnit;
 
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.test.utilities.JettyUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.*;
 import org.apache.http.client.entity.UrlEncodedFormEntity;

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/interceptor/auth/AuthorizationInterceptorR4Test.java

@@ -40,6 +40,8 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.*;
 import org.junit.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/interceptor/auth/SearchNarrowingInterceptorTest.java

@@ -5,6 +5,8 @@ import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.annotation.OptionalParam;
 import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.annotation.Transaction;
+import ca.uhn.fhir.rest.annotation.TransactionParam;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
@@ -22,9 +24,7 @@ import org.eclipse.jetty.servlet.ServletHolder;
 import org.hamcrest.Matchers;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Resource;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -39,8 +39,11 @@ import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
 
 import ca.uhn.fhir.test.utilities.JettyUtil;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class SearchNarrowingInterceptorTest {
+	private static final Logger ourLog = LoggerFactory.getLogger(SearchNarrowingInterceptorTest.class);
 
 	private static String ourLastHitMethod;
 	private static FhirContext ourCtx;
@@ -104,6 +107,31 @@ public class SearchNarrowingInterceptorTest {
 		assertThat(toStrings(ourLastPatientParam), Matchers.contains("Patient/123,Patient/456"));
 	}
 
+	@Test
+	public void testNarrowObservationsByPatientContext_ClientRequestedBundleNoParams() {
+
+		ourNextCompartmentList = new AuthorizedList().addCompartments("Patient/123", "Patient/456");
+
+		Bundle bundle = new Bundle();
+		bundle.setType(Bundle.BundleType.TRANSACTION);
+		bundle.addEntry().getRequest().setMethod(Bundle.HTTPVerb.GET).setUrl("Observation");
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
+
+		ourClient
+			.transaction()
+			.withBundle(bundle)
+			.execute();
+
+		assertEquals("Observation.search", ourLastHitMethod);
+		assertNull(ourLastIdParam);
+		assertNull(ourLastCodeParam);
+		assertNull(ourLastSubjectParam);
+		assertNull(ourLastPerformerParam);
+		assertThat(toStrings(ourLastPatientParam), Matchers.contains("Patient/123,Patient/456"));
+	}
+
+
+
 	/**
 	 * Should not make any changes
 	 */
@@ -274,6 +302,14 @@ public class SearchNarrowingInterceptorTest {
 
 	}
 
+	public static class DummySystemProvider {
+		@Transaction
+		public Bundle transaction(@TransactionParam Bundle theInput) {
+			return theInput;
+		}
+
+	}
+
 	private static class MySearchNarrowingInterceptor extends SearchNarrowingInterceptor {
 		@Override
 		protected AuthorizedList buildAuthorizedList(RequestDetails theRequestDetails) {
@@ -298,10 +334,12 @@ public class SearchNarrowingInterceptorTest {
 
 		DummyPatientResourceProvider patProvider = new DummyPatientResourceProvider();
 		DummyObservationResourceProvider obsProv = new DummyObservationResourceProvider();
+		DummySystemProvider systemProv = new DummySystemProvider();
 
 		ServletHandler proxyHandler = new ServletHandler();
 		RestfulServer ourServlet = new RestfulServer(ourCtx);
 		ourServlet.setFhirContext(ourCtx);
+		ourServlet.registerProviders(systemProv);
 		ourServlet.setResourceProviders(patProvider, obsProv);
 		ourServlet.setPagingProvider(new FifoMemoryPagingProvider(100));
 		ourServlet.registerInterceptor(new MySearchNarrowingInterceptor());

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/bundle/BundleUtilTest.java

@@ -1,13 +1,18 @@
-package ca.uhn.fhir.util;
+package ca.uhn.fhir.util.bundle;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
+import ca.uhn.fhir.util.bundle.ModifiableBundleEntry;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.AfterClass;
-import org.junit.Assert;
 import org.junit.Test;
 
 import java.util.List;
+import java.util.function.Consumer;
+
+import static org.junit.Assert.assertEquals;
 
 public class BundleUtilTest {
 
@@ -18,27 +23,27 @@ public class BundleUtilTest {
 		Bundle b = new Bundle();
 		b.getLinkOrCreate("prev").setUrl("http://bar");
 		b.getLinkOrCreate("next").setUrl("http://foo");
-		Assert.assertEquals("http://foo", BundleUtil.getLinkUrlOfType(ourCtx, b, "next"));
+		assertEquals("http://foo", BundleUtil.getLinkUrlOfType(ourCtx, b, "next"));
 	}
 
 	@Test
 	public void testGetLinkDoesntExist() {
 		Bundle b = new Bundle();
 		b.getLinkOrCreate("prev").setUrl("http://bar");
-		Assert.assertEquals(null, BundleUtil.getLinkUrlOfType(ourCtx, b, "next"));
+		assertEquals(null, BundleUtil.getLinkUrlOfType(ourCtx, b, "next"));
 	}
 
 	@Test
 	public void testGetTotal() {
 		Bundle b = new Bundle();
 		b.setTotal(999);
-		Assert.assertEquals(999, BundleUtil.getTotal(ourCtx, b).intValue());
+		assertEquals(999, BundleUtil.getTotal(ourCtx, b).intValue());
 	}
 
 	@Test
 	public void testGetTotalNull() {
 		Bundle b = new Bundle();
-		Assert.assertEquals(null, BundleUtil.getTotal(ourCtx, b));
+		assertEquals(null, BundleUtil.getTotal(ourCtx, b));
 	}
 
 	@Test
@@ -48,9 +53,18 @@ public class BundleUtilTest {
 			bundle.addEntry(new Bundle.BundleEntryComponent().setResource(new Patient()));
 		}
 		List<Patient> list = BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Patient.class);
-		Assert.assertEquals(5, list.size());
+		assertEquals(5, list.size());
 	}
 
+	@Test
+	public void testProcessEntries() {
+		Bundle bundle = new Bundle();
+		bundle.setType(Bundle.BundleType.TRANSACTION);
+		bundle.addEntry().getRequest().setMethod(Bundle.HTTPVerb.GET).setUrl("Observation");
+		Consumer<ModifiableBundleEntry> consumer = e -> e.setRequestUrl(ourCtx, e.getRequestUrl() + "?foo=bar");
+		BundleUtil.processEntries(ourCtx, bundle, consumer);
+		assertEquals("Observation?foo=bar", bundle.getEntryFirstRep().getRequest().getUrl());
+	}
 
 	@AfterClass
 	public static void afterClassClearContext() {

hapi-fhir-structures-r5/src/test/java/ca/uhn/fhir/rest/client/GenericClientTest.java

@@ -10,7 +10,7 @@ import ca.uhn.fhir.rest.client.impl.BaseClient;
 import ca.uhn.fhir.rest.client.impl.GenericClient;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.util.BundleUtil;
+import ca.uhn.fhir.util.bundle.BundleUtil;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
@@ -43,7 +43,6 @@ import org.mockito.stubbing.Answer;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringReader;
-import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
 import java.util.Arrays;
 

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ResourceMinimizerMojo.java

@@ -6,8 +6,7 @@ import java.util.Collection;
 
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
-import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
+import ca.uhn.fhir.util.bundle.BundleUtil;
-import ca.uhn.fhir.util.BundleUtil;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;