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Rule apply patient export #4892

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Rule apply patient export #4892

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@tadgh tadgh commented May 15, 2023

  • new bulk rule builder method to handle Patient-Style export.
  • New rule applier logic to handle Patient Instance-level Export.
  • Continue to delegate type level export to another rule, as we resolve the problems in a future release.
  • Add tests
  • Add commented out method which will eventually need to be uncommented.

Overall, this PR is intended to distinguish Patient-Style export from Group-Style export, and run different permission rules.

tadgh and others added 30 commits May 2, 2023 17:56
* fix RestHookTestR5IT

* fix intermittent

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Co-authored-by: Ken Stevens <[email protected]>
* Fix Oracle SQL error

* Add changelog
* Update clinical reasoning version

* Update version

* Update version

* Clean-up and more wireup of evaluationSettings

* Add changelog

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Co-authored-by: Jonathan Percival <[email protected]>
* Update the changelog for 4697 to be more descriptive

* Futher tweaks of the changelog
* 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 <[email protected]>

* change index

---------

Co-authored-by: Michael Buckley <[email protected]>
Co-authored-by: James Agnew <[email protected]>
Co-authored-by: Ken Stevens <[email protected]>
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

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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

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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

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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

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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]>
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