Prevent accidental deletion of deeply nested resources in JPA server

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

@@ -1115,7 +1115,7 @@ public abstract class BaseParser implements IParser {
 				}
 			}
 
-			return true;
+			return false;
 		}
 
 		public BaseRuntimeChildDefinition getDef() {

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

@@ -1434,7 +1434,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
 				}
 				BaseRuntimeElementDefinition<?> childDef = extDef.getChildElementDefinitionByDatatype(value.getClass());
 				if (childDef == null) {
-					throw new ConfigurationException("Unable to encode extension, unregognized child element type: " + value.getClass().getCanonicalName());
+					throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
 				}
 				encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, true, false, myParent, false);
 				managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -4301,6 +4301,56 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		}
 	}
 
+	@Test
+	public void testParseAndEncodeExtensionWithValueWithExtension() throws IOException {
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+			"    <extension url=\"https://purl.org/elab/fhir/network/StructureDefinition/1/BirthWeight\">\n" +
+			"       <valueDecimal>\n" +
+			"          <extension url=\"http://www.hl7.org/fhir/extension-data-absent-reason.html\">\n" +
+			"            <valueCoding>\n" +
+			"                <system value=\"http://hl7.org/fhir/ValueSet/birthweight\"/>\n" +
+			"                <code value=\"Underweight\"/>\n" +
+			"                <userSelected value=\"false\"/>\n" +
+			"            </valueCoding>\n" +
+			"          </extension>\n" +
+			"       </valueDecimal>\n" +
+			"    </extension>\n" +
+			"    <identifier>\n" +
+			"       <system value=\"https://purl.org/elab/fhir/network/StructureDefinition/1/EuroPrevallStudySubjects\"/>\n" +
+			"       <value value=\"1\"/>\n" +
+			"    </identifier>\n" +
+			"    <gender value=\"female\"/>\n" +
+			"</Patient>";
+
+		HttpPost post = new HttpPost(ourServerBase + "/Patient");
+		post.setEntity(new StringEntity(input, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+		CloseableHttpResponse response = ourHttpClient.execute(post);
+		IdType id;
+		try {
+			assertEquals(201, response.getStatusLine().getStatusCode());
+			String newIdString = response.getFirstHeader(Constants.HEADER_LOCATION_LC).getValue();
+			assertThat(newIdString, startsWith(ourServerBase + "/Patient/"));
+			id = new IdType(newIdString);
+		} finally {
+			response.close();
+		}
+
+		HttpGet get = new HttpGet(ourServerBase + "/Patient/" + id.getIdPart() + "?_pretty=true");
+		response = ourHttpClient.execute(get);
+		try {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			assertThat(resp, containsString("Underweight"));
+		} finally {
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.close();
+		}
+
+	}
+
+
+
 	@Test
 	public void testValueSetExpandOperation() throws IOException {
 		CodeSystem cs = myFhirCtx.newXmlParser().parseResource(CodeSystem.class, new InputStreamReader(ResourceProviderR4Test.class.getResourceAsStream("/extensional-case-3-cs.xml")));

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.parser;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.util.TestUtil;
+import com.google.common.collect.Sets;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Patient;
 import org.junit.AfterClass;
@@ -110,6 +111,51 @@ public class JsonParserR4Test {
 		return b;
 	}
 
+
+	@Test
+	public void testParseAndEncodeExtensionWithValueWithExtension() {
+		String input = "{\n" +
+			"  \"resourceType\": \"Patient\",\n" +
+			"  \"extension\": [\n" +
+			"    {\n" +
+			"      \"url\": \"https://purl.org/elab/fhir/network/StructureDefinition/1/BirthWeight\",\n" +
+			"      \"_valueDecimal\": {\n" +
+			"        \"extension\": [\n" +
+			"          {\n" +
+			"            \"url\": \"http://www.hl7.org/fhir/extension-data-absent-reason.html\",\n" +
+			"            \"valueCoding\": {\n" +
+			"              \"system\": \"http://hl7.org/fhir/ValueSet/birthweight\",\n" +
+			"              \"code\": \"Underweight\",\n" +
+			"              \"userSelected\": false\n" +
+			"            }\n" +
+			"          }\n" +
+			"        ]\n" +
+			"      }\n" +
+			"    }\n" +
+			"  ],\n" +
+			"  \"identifier\": [\n" +
+			"    {\n" +
+			"      \"system\": \"https://purl.org/elab/fhir/network/StructureDefinition/1/EuroPrevallStudySubjects\",\n" +
+			"      \"value\": \"1\"\n" +
+			"    }\n" +
+			"  ],\n" +
+			"  \"gender\": \"female\"\n" +
+			"}";
+
+		IParser jsonParser = ourCtx.newJsonParser();
+		IParser xmlParser = ourCtx.newXmlParser();
+		jsonParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
+		xmlParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
+
+		Patient parsed = jsonParser.parseResource(Patient.class, input);
+
+		ourLog.info(jsonParser.setPrettyPrint(true).encodeResourceToString(parsed));
+		assertThat(xmlParser.encodeResourceToString(parsed), containsString("Underweight"));
+		assertThat(jsonParser.encodeResourceToString(parsed), containsString("Underweight"));
+
+	}
+
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/XmlParserR4Test.java

@@ -110,6 +110,36 @@ public class XmlParserR4Test {
 		return b;
 	}
 
+	@Test
+	public void testParseAndEncodeExtensionWithValueWithExtension() {
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
+			"    <extension url=\"https://purl.org/elab/fhir/network/StructureDefinition/1/BirthWeight\">\n" +
+			"       <valueDecimal>\n" +
+			"          <extension url=\"http://www.hl7.org/fhir/extension-data-absent-reason.html\">\n" +
+			"            <valueCoding>\n" +
+			"                <system value=\"http://hl7.org/fhir/ValueSet/birthweight\"/>\n" +
+			"                <code value=\"Underweight\"/>\n" +
+			"                <userSelected value=\"false\"/>\n" +
+			"            </valueCoding>\n" +
+			"          </extension>\n" +
+			"       </valueDecimal>\n" +
+			"    </extension>\n" +
+			"    <identifier>\n" +
+			"       <system value=\"https://purl.org/elab/fhir/network/StructureDefinition/1/EuroPrevallStudySubjects\"/>\n" +
+			"       <value value=\"1\"/>\n" +
+			"    </identifier>\n" +
+			"    <gender value=\"female\"/>\n" +
+			"</Patient>";
+
+		Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, input);
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(parsed));
+		assertThat(ourCtx.newXmlParser().encodeResourceToString(parsed), containsString("Underweight"));
+		assertThat(ourCtx.newJsonParser().encodeResourceToString(parsed), containsString("Underweight"));
+
+	}
+
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

src/changes/changes.xml

@@ -212,6 +212,10 @@
 				client requests.
 				Thanks to Clayton Bodendein for the pull request!
 			</action>
+			<action type="fix">
+				An issue was fixed in JPA server where extensions on primitives which
+				are nestedt several layers deep are lost when resources are retrieved
+			</action>
 		</release>
 		<release version="3.0.0" date="2017-09-27">
 			<action type="add">