Issue 3530 terserutil contained failure (#3532)

* License headers

* begin with failing test

* fixed

* changelog

* add jira tag

* review feedback

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

@@ -180,7 +180,7 @@ public final class TerserUtil {
 				continue;
 			}
 
-			IBase newFieldValue = newElement(childDefinition, theFromFieldValue, null);
+			IBase newFieldValue = newElement(terser, childDefinition, theFromFieldValue, null);
 			terser.cloneInto(theFromFieldValue, newFieldValue, true);
 
 			try {
@@ -316,7 +316,8 @@ public final class TerserUtil {
 
 	/**
 	 * Clears the specified field on the resource provided
-	 *  @param theFhirContext Context holding resource definition
+	 *
+	 * @param theFhirContext Context holding resource definition
 	 * @param theResource
 	 * @param theFieldName
 	 */
@@ -529,19 +530,28 @@ public final class TerserUtil {
 	 * Creates a new element taking into consideration elements with choice that are not directly retrievable by element
 	 * name
 	 *
+	 *
+	 * @param theFhirTerser
 	 * @param theChildDefinition  Child to create a new instance for
 	 * @param theFromFieldValue   The base parent field
 	 * @param theConstructorParam Optional constructor param
 	 * @return Returns the new element with the given value if configured
 	 */
-	private static IBase newElement(BaseRuntimeChildDefinition theChildDefinition, IBase theFromFieldValue, Object theConstructorParam) {
+	private static IBase newElement(FhirTerser theFhirTerser, BaseRuntimeChildDefinition theChildDefinition, IBase theFromFieldValue, Object theConstructorParam) {
 		BaseRuntimeElementDefinition runtimeElementDefinition;
 		if (theChildDefinition instanceof RuntimeChildChoiceDefinition) {
 			runtimeElementDefinition = theChildDefinition.getChildElementDefinitionByDatatype(theFromFieldValue.getClass());
 		} else {
 			runtimeElementDefinition = theChildDefinition.getChildByName(theChildDefinition.getElementName());
 		}
-		return (theConstructorParam == null) ? runtimeElementDefinition.newInstance() : runtimeElementDefinition.newInstance(theConstructorParam);
+		if ("contained".equals(runtimeElementDefinition.getName())) {
+			IBaseResource sourceResource = (IBaseResource) theFromFieldValue;
+			return theFhirTerser.clone(sourceResource);
+		} else if (theConstructorParam == null) {
+			return runtimeElementDefinition.newInstance();
+		} else {
+			return runtimeElementDefinition.newInstance(theConstructorParam);
+		}
 	}
 
 	private static void mergeFields(FhirTerser theTerser, IBaseResource theTo, BaseRuntimeChildDefinition childDefinition, List<IBase> theFromFieldValues, List<IBase> theToFieldValues) {
@@ -550,7 +560,7 @@ public final class TerserUtil {
 				continue;
 			}
 
-			IBase newFieldValue = newElement(childDefinition, theFromFieldValue, null);
+			IBase newFieldValue = newElement(theTerser, childDefinition, theFromFieldValue, null);
 			if (theFromFieldValue instanceof IPrimitiveType) {
 				try {
 					Method copyMethod = getMethod(theFromFieldValue, "copy");

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3530-mdm-contained.yaml

@@ -0,0 +1,4 @@
+type: fix
+issue: 3530
+jira: SMILE-4109
+title: "TerserUtil.mergeAllFields() threw an exception when cloning contained resources.  This has been corrected."

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/util/MdmPartitionHelper.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.mdm.util;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Master Data Management
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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 ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.mdm.util.MessageHelper;

hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/BaseDataSink.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.batch2.impl;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Batch2 Task Processor
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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 ca.uhn.fhir.batch2.api.IJobDataSink;
 import ca.uhn.fhir.model.api.IModelJson;
 import org.slf4j.Logger;

hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/BatchJobSender.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.batch2.impl;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Batch2 Task Processor
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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 ca.uhn.fhir.batch2.model.JobWorkNotification;
 import ca.uhn.fhir.batch2.model.JobWorkNotificationJsonMessage;
 import ca.uhn.fhir.jpa.subscription.channel.api.IChannelProducer;

hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/BatchWorkChunk.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.batch2.impl;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Batch2 Task Processor
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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 org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 

hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/FinalStepDataSink.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.batch2.impl;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Batch2 Task Processor
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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 ca.uhn.fhir.batch2.api.JobExecutionFailedException;
 import ca.uhn.fhir.batch2.api.VoidModel;
 import ca.uhn.fhir.batch2.model.WorkChunkData;

hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobDataSink.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.batch2.impl;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Batch2 Task Processor
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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 ca.uhn.fhir.batch2.api.IJobPersistence;
 import ca.uhn.fhir.batch2.model.JobDefinitionStep;
 import ca.uhn.fhir.batch2.model.JobWorkNotification;

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/binstore/FilesystemBinaryStorageSvcImpl.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.binstore;
 
 /*-
  * #%L
- * HAPI FHIR JPA Server
+ * HAPI FHIR Storage api
  * %%
  * Copyright (C) 2014 - 2022 Smile CDR, Inc.
  * %%
@@ -20,10 +20,10 @@ package ca.uhn.fhir.jpa.binstore;
  * #L%
  */
 
-import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.context.ConfigurationException;
-import ca.uhn.fhir.jpa.binary.svc.BaseBinaryStorageSvcImpl;
+import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.binary.api.StoredDetails;
+import ca.uhn.fhir.jpa.binary.svc.BaseBinaryStorageSvcImpl;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -41,7 +41,16 @@ import org.slf4j.LoggerFactory;
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import javax.annotation.PostConstruct;
-import java.io.*;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.Reader;
 import java.util.Date;
 
 public class FilesystemBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl {

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/binstore/MemoryBinaryStorageSvcImpl.java

@@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.binstore;
 
 /*-
  * #%L
- * HAPI FHIR JPA Server
+ * HAPI FHIR Storage api
  * %%
  * Copyright (C) 2014 - 2022 Smile CDR, Inc.
  * %%
@@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.binstore;
  * #L%
  */
 
-import ca.uhn.fhir.jpa.binary.svc.BaseBinaryStorageSvcImpl;
 import ca.uhn.fhir.jpa.binary.api.IBinaryStorageSvc;
 import ca.uhn.fhir.jpa.binary.api.StoredDetails;
+import ca.uhn.fhir.jpa.binary.svc.BaseBinaryStorageSvcImpl;
 import com.google.common.hash.HashingInputStream;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.CountingInputStream;

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

@@ -9,6 +9,7 @@ import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.HumanName;
 import org.hl7.fhir.r4.model.Identifier;
+import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.PrimitiveType;
 import org.junit.jupiter.api.Test;
@@ -17,78 +18,99 @@ import java.util.Date;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.hasSize;
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 class TerserUtilTest {
 
 	private FhirContext ourFhirContext = FhirContext.forR4();
-	private static final String SAMPLE_PERSON = "{\n" +
+	private static final String SAMPLE_PERSON =
-		"        \"resourceType\": \"Patient\",\n" +
+		"""
-		"        \"extension\": [\n" +
+			{
-		"          {\n" +
+			      "resourceType": "Patient",
-		"            \"url\": \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race\",\n" +
+			      "extension": [
-		"            \"valueCoding\": {\n" +
+			        {
-		"              \"system\": \"MyInternalRace\",\n" +
+			          "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
-		"              \"code\": \"X\",\n" +
+			          "valueCoding": {
-		"              \"display\": \"Eks\"\n" +
+			            "system": "MyInternalRace",
-		"            }\n" +
+			            "code": "X",
-		"          },\n" +
+			            "display": "Eks"
-		"          {\n" +
+			          }
-		"            \"url\": \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity'\",\n" +
+			        },
-		"            \"valueCoding\": {\n" +
+			        {
-		"              \"system\": \"MyInternalEthnicity\",\n" +
+			          "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity'",
-		"              \"display\": \"NNN\"\n" +
+			          "valueCoding": {
-		"            }\n" +
+			            "system": "MyInternalEthnicity",
-		"          }\n" +
+			            "display": "NNN"
-		"        ],\n" +
+			          }
-		"        \"identifier\": [\n" +
+			        }
-		"          {\n" +
+			      ],
-		"            \"system\": \"http://example.org/member_id\",\n" +
+			      "identifier": [
-		"            \"value\": \"123123\"\n" +
+			        {
-		"          },\n" +
+			          "system": "http://example.org/member_id",
-		"          {\n" +
+			          "value": "123123"
-		"            \"system\": \"http://example.org/medicaid_id\",\n" +
+			        },
-		"            \"value\": \"12312323123Z\"\n" +
+			        {
-		"          },\n" +
+			          "system": "http://example.org/medicaid_id",
-		"          {\n" +
+			          "value": "12312323123Z"
-		"            \"system\": \"http://example.org/CDNS_id\",\n" +
+			        },
-		"            \"value\": \"123123123E\"\n" +
+			        {
-		"          },\n" +
+			          "system": "http://example.org/CDNS_id",
-		"          {\n" +
+			          "value": "123123123E"
-		"            \"system\": \"http://example.org/SSN\"\n" +
+			        },
-		"          }\n" +
+			        {
-		"        ],\n" +
+			          "system": "http://example.org/SSN"
-		"        \"active\": true,\n" +
+			        }
-		"        \"name\": [\n" +
+			      ],
-		"          {\n" +
+			      "active": true,
-		"            \"family\": \"TestFamily\",\n" +
+			      "name": [
-		"            \"given\": [\n" +
+			        {
-		"              \"Given\"\n" +
+			          "family": "TestFamily",
-		"            ]\n" +
+			          "given": [
-		"          }\n" +
+			            "Given"
-		"        ],\n" +
+			          ]
-		"        \"telecom\": [\n" +
+			        }
-		"          {\n" +
+			      ],
-		"            \"system\": \"email\",\n" +
+			      "telecom": [
-		"            \"value\": \"email@email.io\"\n" +
+			        {
-		"          },\n" +
+			          "system": "email",
-		"          {\n" +
+			          "value": "email@email.io"
-		"            \"system\": \"phone\",\n" +
+			        },
-		"            \"value\": \"123123231\"\n" +
+			        {
-		"          },\n" +
+			          "system": "phone",
-		"          {\n" +
+			          "value": "123123231"
-		"            \"system\": \"phone\",\n" +
+			        },
-		"            \"value\": \"1231232312\"\n" +
+			        {
-		"          },\n" +
+			          "system": "phone",
-		"          {\n" +
+			          "value": "1231232312"
-		"            \"system\": \"phone\",\n" +
+			        },
-		"            \"value\": \"1231232314\"\n" +
+			        {
-		"          }\n" +
+			          "system": "phone",
-		"        ],\n" +
+			          "value": "1231232314"
-		"        \"gender\": \"male\",\n" +
+			        }
-		"        \"birthDate\": \"1900-01-01\",\n" +
+			      ],
-		"        \"deceasedBoolean\": true\n" +
+			      "gender": "male",
-		"      }";
+			      "birthDate": "1900-01-01",
+			      "deceasedBoolean": true,
+			       "contained": [
+			              {
+			                  "id": "1",
+			                  "identifier": [
+			                      {
+			                          "system": "urn:hssc:srhs:contact:organizationId",
+			                          "value": "1000"
+			                      }
+			                  ],
+			                  "name": "BUILDERS FIRST SOURCE",
+			                  "resourceType": "Organization"
+			              }
+			          ]
+			    }
+				""";
 
 	@Test
 	void testCloneEidIntoResource() {
@@ -130,6 +152,20 @@ class TerserUtilTest {
 		assertEquals(2, p2.getExtension().size());
 	}
 
+	@Test
+	void testCloneContainedResource() {
+		Patient p1 = ourFhirContext.newJsonParser().parseResource(Patient.class, SAMPLE_PERSON);
+
+		Patient p2 = new Patient();
+		TerserUtil.mergeAllFields(ourFhirContext, p1, p2);
+
+		Organization org1 = (Organization) p1.getContained().get(0);
+		Organization org2 = (Organization) p2.getContained().get(0);
+		assertNotEquals(org1, org2);
+		assertEquals("BUILDERS FIRST SOURCE", org1.getName());
+		assertEquals("BUILDERS FIRST SOURCE", org2.getName());
+	}
+
 	@Test
 	void testCloneEidIntoResourceViaHelper() {
 		TerserUtilHelper p1Helper = TerserUtilHelper.newHelper(ourFhirContext, "Patient");

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/LogbackLevelOverrideExtension.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.test.utilities;
 
+/*-
+ * #%L
+ * HAPI FHIR Test Utilities
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * 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 ch.qos.logback.classic.Level;
 import ch.qos.logback.classic.Logger;
 import org.junit.jupiter.api.extension.AfterEachCallback;