merge master

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>7.7.8-SNAPSHOT</version>
+		 <version>7.7.9-SNAPSHOT</version>
 
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/DefaultProfileValidationSupportBundleStrategy.java

@@ -150,9 +150,15 @@ private void initializeResourceLists() {
 	@Override
 	public List<IBaseResource> fetchAllConformanceResources() {
 		ArrayList<IBaseResource> retVal = new ArrayList<>();
-		retVal.addAll(myCodeSystems.values());
-		retVal.addAll(myStructureDefinitions.values());
-		retVal.addAll(myValueSets.values());
+		if (myCodeSystems != null) {
+			retVal.addAll(myCodeSystems.values());
+		}
+		if (myStructureDefinitions != null) {
+			retVal.addAll(myStructureDefinitions.values());
+		}
+		if (myValueSets != null) {
+			retVal.addAll(myValueSets.values());
+		}
 		return retVal;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/ValidationSupportContext.java

@@ -30,7 +30,7 @@ public class ValidationSupportContext {
 	private final Set<String> myCurrentlyGeneratingSnapshots = new HashSet<>();
 
 	public ValidationSupportContext(IValidationSupport theRootValidationSupport) {
-		Validate.notNull(theRootValidationSupport, "theRootValidationSupport musty not be null");
+		Validate.notNull(theRootValidationSupport, "theRootValidationSupport must not be null");
 		myRootValidationSupport = theRootValidationSupport;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/IFhirVersion.java

@@ -74,6 +74,17 @@ default IIdType newIdType(String theValue) {
 		return retVal;
 	}
 
+	/**
+	 * Creates a new {@link IIdType} instance for the given version with the given value
+	 *
+	 * @since 8.0.0
+	 */
+	default IIdType newIdType(String theResourceType, String theIdPart) {
+		IIdType retVal = newIdType();
+		retVal.setParts(null, theResourceType, theIdPart, null);
+		return retVal;
+	}
+
 	/**
 	 * Returns an instance of <code>IFhirVersionServer<code> for this version.
 	 * Note that this method may only be called if the <code>hapi-fhir-server</code>

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/HistorySearchDateRangeParam.java

@@ -19,9 +19,22 @@
  */
 package ca.uhn.fhir.rest.param;
 
+import java.util.Collections;
 import java.util.Map;
 
 public class HistorySearchDateRangeParam extends DateRangeParam {
+	/**
+	 * Constructor
+	 *
+	 * @since 8.0.0
+	 */
+	public HistorySearchDateRangeParam() {
+		this(Collections.emptyMap(), new DateRangeParam(), null);
+	}
+
+	/**
+	 * Constructor
+	 */
 	public HistorySearchDateRangeParam(
 			Map<String, String[]> theParameters, DateRangeParam theDateRange, Integer theOffset) {
 		super(theDateRange);

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

@@ -29,7 +29,7 @@ public static String formatFileSize(long theBytes) {
 		if (theBytes <= 0) {
 			return "0 " + UNITS[0];
 		}
-		int digitGroups = (int) (Math.log10(theBytes) / Math.log10(1024));
+		int digitGroups = (int) (Math.log10((double) theBytes) / Math.log10(1024));
 		digitGroups = Math.min(digitGroups, UNITS.length - 1);
 		return new DecimalFormat("###0.#").format(theBytes / Math.pow(1024, digitGroups)) + " " + UNITS[digitGroups];
 	}

hapi-fhir-bom/pom.xml

@@ -4,15 +4,15 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir-bom</artifactId>
-	<version>7.7.8-SNAPSHOT</version>
+	<version>7.7.9-SNAPSHOT</version>
 
 	<packaging>pom</packaging>
 	<name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6409-fix-timezone-issue-for-history-at-query.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 6409
+title: "When performing a `_history` query using the `_at` parameter, the time value
+    is now converted to a zoned-date before being passed to the database. This should
+    avoid conflicts around date changes on some databases.
+    "

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6409-optimize-versioned-tag-loading.yaml

@@ -0,0 +1,7 @@
+---
+type: perf
+issue: 6409
+title: "When searching in versioned tag mode, the JPA server now avoids a redundant
+    lookup of the un-versioned tags, avoiding an extra unnecessary database query
+    in some cases. 
+    "

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6409-stop-using-provenance-table.yaml

@@ -0,0 +1,11 @@
+---
+type: perf
+issue: 6409
+title: "The JPA server will no longer use the HFJ_RES_VER_PROV table to store and index values from
+    the `Resource.meta.source` element. Beginning in HAPI FHIR 6.8.0 (and Smile CDR 2023.08.R01), a
+    new pair of columns have been used to store data for this element, so this change only affects
+    data which was stored in HAPI FHIR prior to version 6.8.0 (released August 2023). If you have
+    FHIR resources which were stored in a JPA server prior to this version, and you use the
+    Resource.meta.source element and/or the `_source` search parameter, you should perform a complete
+    reindex of your server to ensure that data is not lost. See the upgrade notes for more information.
+    "

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6478-transaction-bundle-updates-with-multiple-conditional-urls.yaml

@@ -0,0 +1,8 @@
+---
+type: perf
+issue: 6478
+jira: SMILE-8955
+title: "Transactions with multiple saved search urls will have the saved search urls
+        deleted in a batch, instead of 1 at a time.
+        This is a minor performance update.
+"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6522-cache-cleanup.yaml

@@ -0,0 +1,7 @@
+---
+type: perf
+issue: 6522
+title: "Several memory caches in various parts of the JPA server have been removed in an
+   effort to consolidate caching in this system to two places: The MemoryCacheService, and
+   ValidationSupportChain. This should make management of the system easier."
+

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/upgrade.md

@@ -1,4 +1,20 @@
+# Upgrade Notes
+
+The JPA server stores values for the field `Resource.meta.source` in dedicated columns in its database so that they can be indexes and searched for as needed, using the `_source` Search Parameter.
+
+Prior to HAPI FHIR 6.8.0 (and Smile CDR 2023.08.R01), these values were stored in a dedicated table called `HFJ_RES_VER_PROV`. Beginning in HAPI FHIR 6.8.0 (Smile CDR 2023.08.R01), two new columns were added to the `HFJ_RES_VER`
+table which store the same data and make it available for searches.
+
+As of HAPI FHIR 8.0.0, the legacy table is no longer searched by default. If you do not have Resource.meta.source data stored in HAPI FHIR that was last created/updated prior to version 6.8.0, this change will not affect you and no action needs to be taken.
+
+If you do have such data, you should follow the following steps:
+
+* Enable the JpaStorageSettings setting `setAccessMetaSourceInformationFromProvenanceTable(true)` to configure the server to continue using the legacy table.
+
+* Perform a server resource reindex by invoking the [$reindex Operation (server)](https://smilecdr.com/docs/fhir_repository/search_parameter_reindexing.html#reindex-server) with the `optimizeStorage` parameter set to `ALL_VERSIONS`. 
+
+* When this reindex operation has successfully completed, the setting above can be disabled. Disabling this setting avoids an extra database round-trip when loading data, so this change will have a positive performance impact on your server.
+
 # Fulltext Search with _lastUpdated Filter
 
-Fulltext searches have been updated to support `_lastUpdated` search parameter. A reindexing of Search Parameters
-is required to migrate old data to support the `_lastUpdated` search parameter.
+Fulltext searches have been updated to support `_lastUpdated` search parameter. If you are using Advanced Hibernate Search indexing and wish to use the `_lastUpdated` search parameetr with this feature, a full reindex of your repository is required.

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpa/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.7.8-SNAPSHOT</version>
+		<version>7.7.9-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/cache/ResourceVersionSvcDaoImpl.java

@@ -23,7 +23,9 @@
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
 import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
+import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
@@ -37,6 +39,7 @@
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Optional;
 
 import static org.slf4j.LoggerFactory.getLogger;
@@ -90,20 +93,9 @@ public ResourceVersionMap getVersionMap(
 	public ResourcePersistentIdMap getLatestVersionIdsForResourceIds(
 			RequestPartitionId theRequestPartitionId, List<IIdType> theIds) {
 		ResourcePersistentIdMap idToPID = new ResourcePersistentIdMap();
-		HashMap<String, List<IIdType>> resourceTypeToIds = new HashMap<>();
 
-		for (IIdType id : theIds) {
-			String resourceType = id.getResourceType();
-			if (!resourceTypeToIds.containsKey(resourceType)) {
-				resourceTypeToIds.put(resourceType, new ArrayList<>());
-			}
-			resourceTypeToIds.get(resourceType).add(id);
-		}
-
-		for (List<IIdType> nextIds : resourceTypeToIds.values()) {
-			ResourcePersistentIdMap idAndPID = getIdsOfExistingResources(theRequestPartitionId, nextIds);
-			idToPID.putAll(idAndPID);
-		}
+		ResourcePersistentIdMap idAndPID = getIdsOfExistingResources(theRequestPartitionId, theIds);
+		idToPID.putAll(idAndPID);
 
 		return idToPID;
 	}
@@ -124,14 +116,17 @@ private ResourcePersistentIdMap getIdsOfExistingResources(
 			return retval;
 		}
 
-		List<JpaPid> jpaPids =
-				myIdHelperService.resolveResourcePersistentIdsWithCache(thePartitionId, new ArrayList<>(theIds));
+		Map<IIdType, IResourceLookup<JpaPid>> identities = myIdHelperService.resolveResourceIdentities(
+				thePartitionId,
+				new ArrayList<>(theIds),
+				ResolveIdentityMode.includeDeleted().cacheOk());
 
 		// we'll use this map to fetch pids that require versions
 		HashMap<Long, JpaPid> pidsToVersionToResourcePid = new HashMap<>();
 
 		// fill in our map
-		for (JpaPid pid : jpaPids) {
+		for (IResourceLookup<JpaPid> identity : identities.values()) {
+			JpaPid pid = identity.getPersistentId();
 			if (pid.getVersion() == null) {
 				pidsToVersionToResourcePid.put(pid.getId(), pid);
 			}