6.4.0 Mergeback (#4563)

* One more fix for #4467

* Enabling massIngestionMode causes incomplete resource deletion (#4476)

* Adding initial test.

* Adding fix and subsequent test.

* Adding changelog.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Provide the capability to request that the name of the subscription matching channel be unqualified (#4464)

* Adding initial test.

* Adding initial solution implementation.

* Adding change log and code clean up.

* addressing comments from 1st code review.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Change visibility of migration method (#4471)

* change migration visibility

* add empty migration method for 640

---------

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484)

* First commit:  Make SubscriptionValidatingInterceptor aware of which Pointcut is being called.  In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED.   Fix resulting compile errors in various unit tests.

* Fix/enhance unit tests.  Mark methods as deprecated instead of deleting them.  Add proper error code.  Complete changelog.

* Remove erroneous TODOs and tweak the validation logic.

* Enhance unit tests and fix changelog.

* Reindex batch job fails when processing deleted resources. (#4482)

* adding changelog.

* Providing solution and adding changelog.

* Adding new test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* cleaning up checkstyle files (#4470)

* cleaning up checkstyle files

* One more fix for #4467 (#4469)

* added exlusions for files at base project level so checkstyle doesn't error out

* duplicate error code from merge

* changing lifecycle goal for all module checkstyle check

* moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code

* wip

* trying to figure out why pipeline cannot copy files

* removing modules that don't actually need to be built.

* I messed up the version

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>

* Bump core to 5.6.881 (#4496)

* Bump core to 5.6.881-SNAPSHOT

* Work on fixing tests

* Work on fixing tests 2

* Bump to core release

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>

* Issue 4486 mdm inconsistent possible match score values (#4487)

* Extract method for readability

* Save always normalized score values in POSSIBLE_MATCH links.

* Avoid setting properties to null values. Adjust test.

* Simplify fix

* Fix test. Add RangeTestHelper.

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Revert "cleaning up checkstyle files (#4470)"

This reverts commit efae3b5d5f.

* core version fix

* Loosen rules for id helper

* License

* fix batch2 reduction step (#4499)

* fix bug where FINALIZE jobs are not cancellable

* moved reduction step to message hander

* moving reduction step to queue

* addingchangelog

* cleaning up

* review fixes

* review fix'

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* Scheduled batch 2 bulk export job and binary delete (#4492)

* First commit:  Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.

* Refine solution and add a concrete unit test but still work to do.

* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.

* Unit tests complete.  New Msg code for new IJobPersistence.fetchInstances() method.  Cleanup TODOs and add others.

* Finish final touches on implementation.

* Add changelog.

* Various cleanup.

* Code review feedback.

* Small tweak to changelog.

* Last code review tweak.

* Address more code review comments.

* Reverse changes to consider work chunks.  Add a constant for write-to-binary.

* Change bulk import test for valueUri type (#4503)

* change tests

* suggested test change

* CVE resolutions (#4513)

* Bump Postgres for CVE

* Bump jetty

* Verison bump

* Remove comments

* Revrt bump

* Add check in scanner (#4518)

* 4516 create hapi fhir cli command to clear stale lock entries (#4517)

* Initial implementation

* better tests

* Add changelog and docs

* Forgotten files

* Code review comments

* Fix checkstyle

* Unable to Expunge CodeSystem (#4507)

* changes for GL-3943

* changes for GL-3943

---------

Co-authored-by: isaacwen <isaac.wen@smilecdr.com>

* New line::

* Update to documentation regarding narrative generation; (#4521)

Providing changelog;

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* changed what score is set for mdmlinks that created new golden resource (#4514)

* changed what score is set for mdmlinks that created new golden resource

* fix test

---------

Co-authored-by: Long Ma <long@smilecdr.com>

* REVERT: change to operationoutcome.html

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527)

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* added change log

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* fix build (#4530)

* Making narrative_generation.md reference an html snippet (#4531)

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)

* fix + test

* minor fix

* Addressing suggestion

* Minor changes

* 4441 rel 6 4 bad references creation bug (#4519)

* adding a test

* fail in the case of ref enforce on type and on write and autocreate are all true

* update to code

* removing a line

* cleanup

* removing check on urn

* changing just to trigger a build

* adding a comment to the pom

* updating test for better information

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* fixed channel import null pointer exception from null header (#4534)

* retryCount 0 on null header + test + changelog

* suggested changes

* Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535)

This reverts commit 53252b8d15.

* Better error handling for when channel type is not supported (#4538)

Co-authored-by: kylejule <kyle.jule@smilecdr.com>

* Avoid logging message payloads that contain sensitive data (#4537)

Don't log payloads - they may contain sensitive data.

* Bulk Export Bug With Many Resources and Low Max File Size (#4506)

* failing test

* fix + changelog

* tweak

* add method to IJobPersistence to use a Stream

* tweak

* tweak

* decrease test time

* clean up

* code review comments

* version bump

* Increase timeout limit to match BulkExportUseCaseTest

* shorten test

* maintenance pass

* add logging

* Revert "add logging"

This reverts commit b0453fd953.

* Revert "maintenance pass"

This reverts commit bbc7418d51.

* test

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* shorten tests

* logging

* move test location

* fixes a regression caused my change in hapi-fhir

* timeout

* Revert "fixes a regression caused my change in hapi-fhir"

This reverts commit 4b58013149.

* testing

* Revert "testing"

This reverts commit aafc95c2f3.

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* bump ver

* License updates'

* Remove checkstyle

* Verison bump

* Move migrations

* semicolon

* Downgrade dep'

* Updating version to: 6.4.1 post release.

* Add javadocs and sources to our serviceloaders

* Reset version

* Change parent

* Remove bumped version

* License fixes, new parent

* Updating version to: 6.4.1 post release.

* Fix bad creation of versionenum

* re-add checkstyle

* respect move-up into storage settings from jpastoragesettings

* remove duplicate test

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: dotasek <dotasek.dev@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com>
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>

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

@@ -114,6 +114,7 @@ public enum VersionEnum {
 	// Dev Build
 	V6_3_0,
 	V6_4_0,
+	V6_4_1,
 	V6_5_0,
 	V6_6_0
 	;

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/submit/interceptor/SubscriptionValidatingInterceptorTest.java

@@ -8,6 +8,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer;
+import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.hl7.fhir.r4.model.Subscription;
 import org.junit.jupiter.api.BeforeEach;

hapi-fhir-serviceloaders/hapi-fhir-caching-api/src/main/java/ca/uhn/fhir/sl/cache/Cache.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching API
+ * %%
+ * Copyright (C) 2014 - 2023 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 java.util.Map;
 import java.util.concurrent.ExecutionException;
 import java.util.function.Function;

hapi-fhir-serviceloaders/hapi-fhir-caching-api/src/main/java/ca/uhn/fhir/sl/cache/CacheFactory.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching API
+ * %%
+ * Copyright (C) 2014 - 2023 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 java.util.Iterator;

hapi-fhir-serviceloaders/hapi-fhir-caching-api/src/main/java/ca/uhn/fhir/sl/cache/CacheLoader.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching API
+ * %%
+ * Copyright (C) 2014 - 2023 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%
+ */
+
 public interface CacheLoader<K, V> {
     V load(K var1) throws Exception;
 }

hapi-fhir-serviceloaders/hapi-fhir-caching-api/src/main/java/ca/uhn/fhir/sl/cache/CacheProvider.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching API
+ * %%
+ * Copyright (C) 2014 - 2023 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%
+ */
+
 public interface CacheProvider<K,V> {
     Cache create(long timeoutMillis);
 

hapi-fhir-serviceloaders/hapi-fhir-caching-api/src/main/java/ca/uhn/fhir/sl/cache/LoadingCache.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching API
+ * %%
+ * Copyright (C) 2014 - 2023 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 java.util.Map;
 import java.util.concurrent.CompletableFuture;
 

hapi-fhir-serviceloaders/hapi-fhir-caching-caffeine/src/main/java/ca/uhn/fhir/sl/cache/caffeine/CacheDelegator.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache.caffeine;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching Caffeine
+ * %%
+ * Copyright (C) 2014 - 2023 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 java.util.Map;
 import java.util.function.Function;
 

hapi-fhir-serviceloaders/hapi-fhir-caching-caffeine/src/main/java/ca/uhn/fhir/sl/cache/caffeine/CacheProvider.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache.caffeine;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching Caffeine
+ * %%
+ * Copyright (C) 2014 - 2023 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 java.util.concurrent.TimeUnit;
 
 import com.github.benmanes.caffeine.cache.Caffeine;

hapi-fhir-serviceloaders/hapi-fhir-caching-caffeine/src/main/java/ca/uhn/fhir/sl/cache/caffeine/LoadingCacheDelegator.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache.caffeine;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching Caffeine
+ * %%
+ * Copyright (C) 2014 - 2023 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 java.util.Map;
 
 import ca.uhn.fhir.sl.cache.LoadingCache;

hapi-fhir-serviceloaders/hapi-fhir-caching-guava/src/main/java/ca/uhn/fhir/sl/cache/guava/CacheDelegator.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache.guava;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching Guava
+ * %%
+ * Copyright (C) 2014 - 2023 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 java.util.Map;
 import java.util.concurrent.ExecutionException;
 import java.util.function.Function;

hapi-fhir-serviceloaders/hapi-fhir-caching-guava/src/main/java/ca/uhn/fhir/sl/cache/guava/CacheProvider.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache.guava;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching Guava
+ * %%
+ * Copyright (C) 2014 - 2023 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 java.util.concurrent.TimeUnit;
 
 import com.google.common.cache.CacheBuilder;

hapi-fhir-serviceloaders/hapi-fhir-caching-guava/src/main/java/ca/uhn/fhir/sl/cache/guava/LoadingCacheDelegator.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.sl.cache.guava;
 
+/*-
+ * #%L
+ * HAPI FHIR - ServiceLoaders - Caching Guava
+ * %%
+ * Copyright (C) 2014 - 2023 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 java.util.Map;
 import java.util.concurrent.ExecutionException;
 

hapi-fhir-serviceloaders/pom.xml

@@ -3,10 +3,10 @@
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
-		<artifactId>hapi-fhir</artifactId>
+		<artifactId>hapi-deployable-pom</artifactId>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<version>6.5.2-SNAPSHOT</version>
-		<relativePath>../pom.xml</relativePath>
+		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
 	<artifactId>hapi-fhir-serviceloaders</artifactId>

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/JpaStorageSettings.java

@@ -312,6 +312,11 @@ public class JpaStorageSettings extends StorageSettings {
 	 */
 	private boolean myJobFastTrackingEnabled = false;
 
+	/**
+	 * Since 6.4.0
+	 */
+
+
 	/**
 	 * Constructor
 	 */
@@ -2332,6 +2337,7 @@ public class JpaStorageSettings extends StorageSettings {
 		myJobFastTrackingEnabled = theJobFastTrackingEnabled;
 	}
 
+
 	public enum StoreMetaSourceInformationEnum {
 		NONE(false, false),
 		SOURCE_URI(true, false),

pom.xml

@@ -1336,7 +1336,7 @@
 			<dependency>
 				<groupId>org.springdoc</groupId>
 				<artifactId>springdoc-openapi-ui</artifactId>
-				<version>1.6.14</version>
+				<version>1.5.13</version>
 			</dependency>
 			<dependency>
 				<groupId>net.sourceforge.htmlunit</groupId>