Rel 6 8 2 mb (#5299)

* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

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

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* _source search parameter needs to support modifiers (#5095)

_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers

* Fix HFQL docs (#5151)

* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)

* Initial failing test.

* Solution with changelog.

* fixing format.

* Addressing comment from code review.

* fixing failing test.

---------

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

* documentation update (#5154)

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Fix hsql jdbc driver deps (#5168)

Avoid non-included classes in jdbc driver dependencies.

* $delete-expunge over 10k resources will now delete all resources (#5144)

* First commit with very rough fix and unit test.

* Refinements to ResourceIdListStep and Batch2DaoSvcImpl.  Make LoadIdsStepTest pass.   Enhance Batch2DaoSvcImplTest.

* Spotless

* Fix checkstyle errors.

* Fix test failures.

* Minor refactoring.  New unit test.  Finalize changelist.

* Spotless fix.

* Delete now useless code from unit test.

* Delete more useless code.

* Test pre-commit hook

* More spotless fixes.

* Address most code review feedback.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Fix the noUrl case by passing an unlimited Pegeable instead.  Effectively stop using page size for most databases.

* Deprecate the old method and have it call the new one by default.

* updating documentation (#5170)

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* _source search parameter modifiers for Subscription matching (#5159)

* _source search parameter modifiers for Subscription matching - test, implementation and changelog

* Removal of meta tags during updates do not trigger subscription (#5181)

* Initial failing test.

* adding solution;
fixing documentation;

* spotless apply

* adding changelog

* modifying current test

---------

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

* Issue 5173 get gateway everything doesnt return all patients (#5174)

* Failing test

* Also set offset and count in base DAO override

* Changelog

* Fix for specific case where count has been set in parameters

* spotless

* Improve checks

---------

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

* Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175)

* First commit with failing unit test and small tweaks.

* Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead.  Add more detailed unit testing.

* Tweaks to logic and update the changelog.  Reverse all changes to TermReadSvcImpl.

* Revert PackageResourceParsingSvc to release branch baseline.

* Accept code reviewer suggestion to change changelog description.

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Fix link

* Remove target slf4j version

* dont use new API for a bit (#5191)

* Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193)

DropIdGeneratorTask.

* Dqm performance bug update and provider loader fix (#5180)

* update tests, move properties, update operation loader

* update wip

* remove test

* fixing tests, adding config

* update config and provider loader

* fix bundles

* fix cache settings on tests

* version bump and change log

* version bump

* fix formatting

* CVE-2022-45868

* wip cve change

* cve h2 add back in

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>

* bulkExportReuse with POST and GET (#5161)

* string manipulation

* Code to ensure bulkExportReuse works with POST and GET requests

* Added formatting changes

* Fixed tests that were not working

* Formatting

* Code clean up

* fixing test failures

* fixing test failures

* Removed arrOfParams to now utilize ObjectMapper

* Removing stack trace and adding an exception

* Fixed test issue

* formatting

* formatting

* Resolving code review comments

* Reduce size of subscription max results (#5194)

* Reduce MAX_SUBSCRIPTION_RESULTS to 10000

* Add changelog

* 5037 goldenresource remains when target resource deleted (#5038)

* draft test and fix

* remove unused fields

* remove unused fields

* remove unused fields

* draft test + solution for possible match case

* combine sql statement + more error checking

* add test case for possible duplicate

* add config for autodeleting grs

* refactoring, adding support for mongo, docs

* refactoring + fixing mongo queries

* add changelogs

* fix both way link removal

* clean up test comments

* rename method

* remove unnecessary bean

* merge master/resolve conflicts

* mvn spotless

* address comment

* changes to avoid version bumping

* spotless

* change error code

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* dont use new API for a bit (#5190)

* licenses

* Fixing terminology upload with large file. (#5204)

* create initial test

* adding fix;
adding changelog;

* fixing format.

---------

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

* up version to 6.8.0 from snapshot

* fix up some duplicate deps for skipping

* Force deployment of other projects

* make dummy java class to pass sonatype checks

* make dummy java class to pass sonatype checks

* Cheeky test removal

* Another test removal

* Updating version to: 6.8.1 post release.

* adding back in tests for release pipelines

* Fix bad version insert

* Bump to core library version 6.0.22.2 (#5261)

* Bump to core library version 6.0.22.2

* Bump HAPI to 6.8.1-SNAPSHOT, core library version to 6.0.22.2

* up version to 6.8.1

* Prevent remote deployment

* Updating version to: 6.8.2 post release.

* Re-add deploy plugin skip

* re-add version

* Bump core library version to 6.0.22.2

* Bump HAPI to 6.8.2-SNAPSHOT

* Fix up version enum

* Version bump

* Updating version to: 6.8.3 post release.

* mvn spotless:apply

---------

Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/jackson/JacksonStructure.java

@@ -28,6 +28,7 @@ import ca.uhn.fhir.parser.json.BaseJsonLikeWriter;
 import ca.uhn.fhir.parser.json.JsonLikeStructure;
 import com.fasterxml.jackson.core.JsonGenerator;
 import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.StreamReadConstraints;
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -388,6 +389,15 @@ public class JacksonStructure implements JsonLikeStructure {
 		retVal = retVal.disable(JsonGenerator.Feature.AUTO_CLOSE_TARGET);
 		retVal = retVal.disable(JsonParser.Feature.AUTO_CLOSE_SOURCE);
 		retVal = retVal.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
+
+		retVal.getFactory().setStreamReadConstraints(createStreamReadConstraints());
+
 		return retVal;
 	}
+
+	private static StreamReadConstraints createStreamReadConstraints() {
+		return StreamReadConstraints.builder()
+				.maxStringLength(Integer.MAX_VALUE)
+				.build();
+	}
 }

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

@@ -119,7 +119,8 @@ public enum VersionEnum {
 	V6_6_0,
 	V6_7_0,
 	V6_8_0,
-
+	V6_8_1,
+	V6_8_2,
 	V6_9_0,
 
 	V7_0_0;

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5205-uploading-large-vocabulary-file-returns-error.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5205
+title: "Previously, uploading a large vocabulary file (like Loinc) through the upload-external-code-system command would
+return an error.  The issue has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_1/upgrade.md

@@ -0,0 +1 @@
+Note: this release has been decommissioned, and you should not be using it. Please upgrade to a newer version.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_1/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2023-08-31"
+codename: "Yucatán"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_2/upgrade.md

@@ -0,0 +1 @@
+Note: this release has been decommissioned, and you should not be using it. Please upgrade to a newer version.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_2/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2023-09-05"
+codename: "Yucatán"

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

@@ -10,9 +10,13 @@ import ca.uhn.fhir.parser.json.BaseJsonLikeWriter;
 import ca.uhn.fhir.parser.json.JsonLikeStructure;
 import ca.uhn.fhir.parser.json.jackson.JacksonStructure;
 import ca.uhn.fhir.parser.view.ExtPatient;
+import ca.uhn.fhir.util.AttachmentUtil;
+import ca.uhn.fhir.util.ParametersUtil;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.ICompositeType;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.Patient;
@@ -21,6 +25,7 @@ import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Test;
 
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.Reader;
 import java.io.StringReader;
 import java.io.Writer;
@@ -63,6 +68,22 @@ public class JsonLikeParserTest {
 		assertEquals(parsed.getClass().getName(), resource.getClass().getName(), "reparsed resource classes not equal");
 	}
 
+	@Test
+	public void testJacksonStructureCanLoadLoincTerminogy() throws IOException {
+		// given
+		IBaseParameters inputParametersForLoinc = getUploadTerminologyCommandInputParametersForLoinc();
+		String s = ourCtx.newJsonParser().encodeResourceToString(inputParametersForLoinc);
+		StringReader stringReader = new StringReader(s);
+
+		// when
+		JsonLikeStructure jsonLikeStructure = new JacksonStructure();
+		jsonLikeStructure.load(stringReader);
+
+		// then
+		assertNotNull(jsonLikeStructure.getRootObject());
+
+	}
+
 	/**
 	 * Test JSON-Like writer using custom stream writer
 	 * 
@@ -151,14 +172,34 @@ public class JsonLikeParserTest {
 
 		assertEquals(0, va.getExtension().size());
 	}
-	
+
+	private IBaseParameters getUploadTerminologyCommandInputParametersForLoinc() throws IOException {
+		IBaseParameters inputParameters = ParametersUtil.newInstance(ourCtx);
+		ParametersUtil.addParameterToParametersUri(
+			ourCtx, inputParameters, "system", "http://loinc.org");
+
+		try(InputStream inputStream = JsonLikeParserTest.class.getResourceAsStream("/Loinc_2.72.zip")) {
+
+			ICompositeType attachment = AttachmentUtil.newInstance(ourCtx);
+			AttachmentUtil.setContentType(ourCtx, attachment, "application/zip");
+			AttachmentUtil.setUrl(ourCtx, attachment, "Loinc_2.72.zip");
+
+			AttachmentUtil.setData(ourCtx, attachment, IOUtils.toByteArray(inputStream));
+
+			ParametersUtil.addParameterToParameters(
+				ourCtx, inputParameters, "file", attachment);
+
+		}
+
+		return inputParameters;
+
+	}
+
 	@AfterAll
 	public static void afterClassClearContext() {
 		TestUtil.randomizeLocaleAndTimezone();
 	}
-	
+
-	
-	
 	public static class JsonLikeMapWriter extends BaseJsonLikeWriter {
 
 		private Map<String,Object> target;

pom.xml

@@ -897,7 +897,7 @@
 	</licenses>
 
 	<properties>
-		<fhir_core_version>6.0.22</fhir_core_version>
+		<fhir_core_version>6.0.22.2</fhir_core_version>
 		<spotless_version>2.37.0</spotless_version>
 		<ucum_version>1.0.3</ucum_version>
 		<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>

tests/hapi-fhir-base-test-jaxrsserver-kotlin/src/main/java/Sample.java

@@ -0,0 +1,4 @@
+/**
+ * This class exists to satisfy Sonatype.
+ */
+public class Sample {}