Move PATCH to hapi-fhir-storage (#3763)

* Not the final version

* Support PATCH operation

* minor modifications

* minor modifications

* Final version

* Final version

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

@@ -80,9 +80,9 @@ ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.forcedIdConstraintFailure=The
 ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor.externalizedBinaryStorageExtensionFoundInRequestBody=Illegal extension found in request payload - URL "{0}" and value "{1}"
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"
-ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
+ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlMultipleMatches=Invalid match URL "{0}" - Multiple resources match this search
-ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationWithMultipleMatchFailure=Failed to {0} resource with match URL "{1}" because this search matched {2} resources
+ca.uhn.fhir.jpa.dao.BaseStorageDao.transactionOperationWithMultipleMatchFailure=Failed to {0} resource with match URL "{1}" because this search matched {2} resources
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedNoId=Failed to {0} resource in transaction because no ID was provided
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedUnknownId=Failed to {0} resource in transaction because no resource could be found with ID {1}
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.uniqueIndexConflictFailure=Can not create resource of type {0} as it would create a duplicate unique index matching query: {1} (existing index belongs to {2}, new unique index created by {3})

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3762-support-patch-operation-for-mongodb.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 3762
+jira: SMILE-4451
+title: "JPA server patch operation has been moved to the hapi-fhir-storage project, for reuse in other backends."

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

@@ -266,7 +266,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		if (isNotBlank(theIfNoneExist)) {
 			Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theIfNoneExist, myResourceType, theTransactionDetails, theRequest);
 			if (match.size() > 1) {
-				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theIfNoneExist, match.size());
+				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theIfNoneExist, match.size());
 				throw new PreconditionFailedException(Msg.code(958) + msg);
 			} else if (match.size() == 1) {
 				ResourcePersistentId pid = match.iterator().next();
@@ -650,7 +650,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		if (resourceIds.size() > 1) {
 			if (!getConfig().isAllowMultipleDelete()) {
-				throw new PreconditionFailedException(Msg.code(962) + getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "DELETE", theUrl, resourceIds.size()));
+				throw new PreconditionFailedException(Msg.code(962) + getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "DELETE", theUrl, resourceIds.size()));
 			}
 		}
 
@@ -1124,13 +1124,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 			Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theConditionalUrl, myResourceType, theTransactionDetails, theRequest);
 			if (match.size() > 1) {
-				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "PATCH", theConditionalUrl, match.size());
+				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "PATCH", theConditionalUrl, match.size());
 				throw new PreconditionFailedException(Msg.code(972) + msg);
 			} else if (match.size() == 1) {
 				ResourcePersistentId pid = match.iterator().next();
 				entityToUpdate = myEntityManager.find(ResourceTable.class, pid.getId());
 			} else {
-				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "invalidMatchUrlNoMatches", theConditionalUrl);
+				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "invalidMatchUrlNoMatches", theConditionalUrl);
 				throw new ResourceNotFoundException(Msg.code(973) + msg);
 			}
 
@@ -1731,7 +1731,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		if (isNotBlank(theMatchUrl)) {
 			Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theTransactionDetails, theRequest, theResource);
 			if (match.size() > 1) {
-				String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "UPDATE", theMatchUrl, match.size());
+				String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "UPDATE", theMatchUrl, match.size());
 				throw new PreconditionFailedException(Msg.code(988) + msg);
 			} else if (match.size() == 1) {
 				ResourcePersistentId pid = match.iterator().next();

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

@@ -29,6 +29,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.dao.BaseStorageDao;
 import ca.uhn.fhir.jpa.dao.MatchResourceUrlService;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedComboStringUniqueDao;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
@@ -342,7 +343,7 @@ public class SearchParamWithInlineReferencesExtractor {
 				String resourceTypeString = nextIdText.substring(0, nextIdText.indexOf('?')).replace("/", "");
 				RuntimeResourceDefinition matchResourceDef = myContext.getResourceDefinition(resourceTypeString);
 				if (matchResourceDef == null) {
-					String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlInvalidResourceType", nextId.getValue(), resourceTypeString);
+					String msg = myContext.getLocalizer().getMessage(BaseStorageDao.class, "invalidMatchUrlInvalidResourceType", nextId.getValue(), resourceTypeString);
 					throw new InvalidRequestException(Msg.code(1090) + msg);
 				}
 				Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
@@ -360,7 +361,7 @@ public class SearchParamWithInlineReferencesExtractor {
 						theTransactionDetails.addResolvedMatchUrl(nextIdText, match);
 						myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, nextIdText, match);
 					} else {
-						String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlNoMatches", nextId.getValue());
+						String msg = myContext.getLocalizer().getMessage(BaseStorageDao.class, "invalidMatchUrlNoMatches", nextId.getValue());
 						throw new ResourceNotFoundException(Msg.code(1091) + msg);
 					}
 

hapi-fhir-storage/pom.xml

@@ -143,6 +143,14 @@
 			<artifactId>spring-test</artifactId>
 			<scope>test</scope>
 		</dependency>
+        <dependency>
+            <groupId>com.github.dnault</groupId>
+            <artifactId>xml-patch</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>io.dogote</groupId>
+            <artifactId>json-patch</artifactId>
+        </dependency>
 
 	</dependencies>
 	<build>

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/patch/JsonPatchUtils.java

@@ -50,7 +50,7 @@ public class JsonPatchUtils {
 
 		final JsonPatch patch;
 		try {
-			com.fasterxml.jackson.core.JsonParser parser = factory.createParser(thePatchBody);
+			JsonParser parser = factory.createParser(thePatchBody);
 			JsonNode jsonPatchNode = mapper.readTree(parser);
 			patch = JsonPatch.fromJson(jsonPatchNode);