Rel 6 6 2 mb (#5315)

* Force Verify tests

* fix ITs (#4809)

* fix RestHookTestR5IT

* fix intermittent

---------

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

* Fix migrator error on Oracle (#4814)

* Fix Oracle SQL error

* Add changelog

* Update clinical reasoning version (#4816)

* Update clinical reasoning version

* Update version

* Update version

* Clean-up and more wireup of evaluationSettings

* Add changelog

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>

* Opening the care-gaps endpoint for GET. (#4823)

Co-authored-by: Chalma Maadaadi <chalma@alphora.com>

* added version to mdm golden resource tag (#4820)

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

* Update the changelog for 4697 to be more descriptive (#4827)

* Update the changelog for 4697 to be more descriptive

* Futher tweaks of the changelog

* Fixes a bug with tags.  (#4813)

* Test, fix

* Drop constraint, add migration

* Add changelog

* Fix userSelected null vs false

* Fix merge

* Fix up checkstyle whining

* One more failure

* Fix test

* wip

* changelog clarity

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

* change index

---------

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

* fix migration issue (#4830)

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

* Create correct version enum

* Remove superfluous migration

* fixing test (#4835)

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

* email subscription, throw NullPointerException (#4790)

* fix bug

* Favoring constructor initialization to autowiring.

* enhancing test.

* Making class LoggingEmailSender available outside of the hapi-fhir-japserver-uhnfhirtest module.

* Passing all tests.

* adding changelog.

* Bumping version to 6.5.20-SNAPSHOT

* addressing code review comment.

---------

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

* Add docs for CR operations (#4855)

* Add docs for CR operations

* Correct changelog and javadoc for $package

* Add documentation for $apply parameters

* Add additional documentation for $package

* Cleanup

* Cleanup

* Cleanup

* Address review comments

* Add documentation for $care-gaps operation. (#4862)

* Add documentation for -gaps.

* addressing the comments.

---------

Co-authored-by: Chalma Maadaadi <chalma@alphora.com>

* 4853 validation does not error when display is not the same as the display defined in the codesystem 2 (#4854)

* added failing test

* implemented the solution

* changed test name

* added change log

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4853-validation-does-not-error-when-display-is-not-the-same-as-the-display-defined-in-the-codesystem-2.yaml

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

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>

* fixing patient everything operator (#4845)

* fixing patient everything operator

* review fix

---------

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

* fix link

* Move image file

* Bundle resources containing over 100 references to the same Organization will fail with HAPI-2207 (#4871)

* Add failing unit test.

* Fix JpaId Long equality comparison to use ! equals() instead of !=, which fails for different instances of the same Long value.

* Add changelog.

* added warn message and test (#4848)

* added warn message and test

* code review fixes

---------

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

* Issue 4804 full table scan on mpi link during mdm clear (#4805)

* version bump for next release  (#4793)

* version bump

* Bump to correctnumber

* Version Enum and folder

* Remove interim from list

* wip

* Fix operation on nested type-choices in FhirPatch implementation (#4783)

* Fix operation on nested type-choices in FhirPatch implementation

* Add credit for #4783

---------

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

* #4468 fix previous link offset no cache pagination (#4489)

* #4468 Add test reproducing the issue

* #4468 Fix previous link for no cache offset pagination

* #4468 Use unchecked URI parsing

* Credit for #4489

---------

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

* Changelog and data generating test

* Add MdmLink index

* Avoid double link deletion

* Use ThreadLocal safely

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Fix erroneous batch 2 $export 75% complete count when the job is COMPLETE (#4859)

* Add failing unit test.

* Add conditional logic to the InstanceProgress progress percentage to disregard the incomplete count if this is called from the reduction step.  This is to get around a race condition in which a work chunk is QUEUED and not yet complete when the reduction step calculates the progress.

* Add final.

* Add changelog.

* disable wars (#4877)

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

* 4868 fix paging hapi (#4870)

* fixing some offset and adding a test

* fixing the offset paging

* Removing duplicate

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>

* 4875-binary-access-write-doest-trigger-STORAGE-BINARY-ASSIGN-BLOB-ID-PREFIX-pointcut (#4876)

* Add failing test

* Add failing test

* Fix and changelog

* Pass content type parameter

* Back to auto wiring the context

* Invoke interceptor only when getting blobId, not also when storing it

* Avoid breaking implementers

* Address review comment

* Add new exception Msg code

* Fix broken test

---------

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

* Fix batch job (bulk export) processed record count (#4879)

* Remove racy stats recalc.

* Throw 404 when requesting $export of non-existent Group or Patient (#4890)

* Remove default implementation intended only for interim backwards compatibility (#4894)

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

* Rule apply patient export (#4893)

* Test, fix, and changelog

* Better partition resolution

* Add checks based on rule applier

* Fix ordering failure due to hash set

* Allow empty auth interceptor

* Fix up operation type on invocation

* Add more tests, make hack implementation for patient instance level operation

* Tighten test name

* Changelog

* Default method

* remove dead method

* Remove dead autowire

---------

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

* cve pom changes (#4898)

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

* backport subscription topic bean cleanup (#4904)

* 4891 bulk export do not recurse unasked for resources (#4895)

* updating tests

* fixing bulk export to not fetch resources not requested

* cleanup

* cleanup

* more warning suppressing

* adding error code

* blah

* fix test

* review fixes

---------

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

* lowers log level to remove bootup noise (#4908)

* CVE rel 6 6 (#4907)

* cve pom changes

* bump javax.el to jakarta.el

---------

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

* Issue 4905 post binary failure invoking interceptor for pointcuts storage preshow resources (#4906)

* Initial failing test

* Avoid applying binary blob id prefix multiple times

* Remove recently introduced method not needed anymore

---------

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

* Enhance LogbackCaptureTestExtension (#4869)

* repro bug with test, fix bug

* ken informed me he resolved this bug on master, so i'm switching to use his solution

* disable wars

* review feedback

* review feedback

* review feedback again

---------

Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Resolve 4863 from release branch searchparametercanonicalizer does not account for search parameters for custom resources types when converting dstu23 into runtimesearchparam (#4887)

* Modified canonicalizeSearchParameterDstu2 and 3, now correctly detect search parameters for custom resources

* Canonicalizers now correctly handle search parameters for custom resources

* created changelog

* Modification based on comments:
- remove Resource from target field when there are custom resource types
- fixed changelog typo
- removed unnecessary variable providesMembershipInCompartments

* Added tests for the SearchParameterCanonicalizer to test if base and target of RuntimeSearchParam is set as expected for DSTU2, DSTU3, R4, R4B, and R5 resources

* Fixed typo and removed commented code

* re-ordered init methods

* Update changelog

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* modifications following first code review.

---------

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

* License

* Remove _lastUpdated filtering of _revincludes. (#4899)

Remove _lastUpdated filtering of _revincludes.

* 4910-dm-migration-error-for-oracle-19c (#4916)

* Remove all_constraints references which break in oracle 19c

* Add changelog

---------

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

* 4873 empty fhirid causes missing resource (#4874)

* add check for empty fhirid string and add test

* add test for populateid

* changelog

* version bump

* version bump

* reverse version bump

* Back to 6.5.21-SNAPSHOT.

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>

* Fix include canonical url performance (#4919)

Use hash_identity for canonical join

* License

* Version bump

* Temp disable

* Make this dependency provided

* Updating version to: 6.6.1 post release.

* Bump snakeyaml

* Bump jackson to be compatible with new snakeyaml

* Bump deps (#4926)

* resolve CVEs, add new notes

* Updating version to: 6.6.2 post release.

* #5023 Unexpected usage of awssdk StringUtils in hapi 6.6 jpa migration (#5024)

task

Replace usage of awssdk

* added docs

* mssql test fixes

* Updating version to: 6.6.3 post release.

* fix up random errors when merging back

* undisable test

* remove mention of 6.6.3 which does not exist

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Sam Gunter <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Josie <80289977+pepsiofficial@users.noreply.github.com>
Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Thomas Papke <web@thopap.de>

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

@@ -117,6 +117,8 @@ public enum VersionEnum {
 	V6_4_2,
 	V6_5_0,
 	V6_6_0,
+	V6_6_1,
+	V6_6_2,
 	V6_7_0,
 	V6_8_0,
 	V6_8_1,

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_1/upgrade.md

@@ -0,0 +1 @@
+This release resolves several CVEs. 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_1/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2023-05-28"
+codename: "Xenon"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_2/upgrade.md

@@ -0,0 +1 @@
+This release resolves several CVEs. 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_2/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2023-07-04"
+codename: "Xenon"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5023-fix-usage-of-awssdk-string-utils.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5023
+backport: 6.6.2
+title: "Jpa migration task used awssdk StringUtils rather than apache commons string utils. Thanks to @Thopap for the contribution"