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March 24 master mb #5858

Merged
merged 371 commits into from
Apr 18, 2024
Merged

March 24 master mb #5858

merged 371 commits into from
Apr 18, 2024

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longma1
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@longma1 longma1 commented Apr 18, 2024

mergeback from previous backport releases

tadgh and others added 30 commits May 7, 2023 10:04
Co-authored-by: leif stawnyczy <[email protected]>
* 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.

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Co-authored-by: peartree <[email protected]>
* 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 -gaps.

* addressing the comments.

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Co-authored-by: Chalma Maadaadi <[email protected]>
…splay 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 <[email protected]>

---------

Co-authored-by: Steven Li <[email protected]>
Co-authored-by: James Agnew <[email protected]>
* fixing patient everything operator

* review fix

---------

Co-authored-by: leif stawnyczy <[email protected]>
…ion 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

* code review fixes

---------

Co-authored-by: Long Ma <[email protected]>
* 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 <[email protected]>

* #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 <[email protected]>

* Changelog and data generating test

* Add MdmLink index

* Avoid double link deletion

* Use ThreadLocal safely

---------

Co-authored-by: Tadgh <[email protected]>
Co-authored-by: Zach Smith <[email protected]>
Co-authored-by: James Agnew <[email protected]>
Co-authored-by: Aleksej Parovysnik <[email protected]>
Co-authored-by: juan.marchionatto <[email protected]>
…LETE (#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.
Co-authored-by: Ken Stevens <[email protected]>
* fixing some offset and adding a test

* fixing the offset paging

* Removing duplicate

---------

Co-authored-by: leif stawnyczy <[email protected]>
Co-authored-by: Aleksej Parovysnik <[email protected]>
…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 <[email protected]>
* 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 <[email protected]>
Co-authored-by: Long Ma <[email protected]>
* 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 <[email protected]>
* cve pom changes

* bump javax.el to jakarta.el

---------

Co-authored-by: Long Ma <[email protected]>
…rage 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 <[email protected]>
* 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 <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
…t 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 <[email protected]>

* modifications following first code review.

---------

Co-authored-by: Tadgh <[email protected]>
Co-authored-by: peartree <[email protected]>
tadgh and others added 25 commits February 27, 2024 11:54
* Add backport and folder

* Add missing changelog

* Cherry p icking

* Update upgrade.md

* added new version version.yaml

* Provide default update time to batch2 entities (#4630)

* Data migration - default value for batch2 UPDATE_TIME

* fixed changelog, added 6.4.3 changelog folder

* Spotless

---------

Co-authored-by: Kevin Dougan SmileCDR <[email protected]>
Co-authored-by: longma1 <[email protected]>
Co-authored-by: michaelabuckley <[email protected]>
* Added correction to generated resource providers

* add changelog and fix issue that was adding languange SP to version that does not have language as a SP

* actually fix the test

* fix changelog wrong issue number

---------

Co-authored-by: Jens Kristian Villadsen <[email protected]>
Co-authored-by: Long Ma <[email protected]>
* Reducer LOB usage in Batch2 and Search

* Add changelog

* Rework a number of LOB columns

* Test fix

* Test fix

* Column fixes

* Test fix

* Formatting

* Fixes

* patching bad oracle test

* Apply spotless

---------

Co-authored-by: Tadgh <[email protected]>
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@tadgh tadgh merged commit 29cddae into master Apr 18, 2024
61 of 64 checks passed
@tadgh tadgh deleted the march_24_master_mb branch April 18, 2024 22:36
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