Commit Graph

9756 Commits

Author SHA1 Message Date
Tadgh c98c4a4dca
Implement codeowners ()
* Initial run through codeowners

* Remove dead action

* Add consent intercept and auth interceptor
2023-05-24 21:48:55 +00:00
Tadgh d9530a9aff
Bump snake yaml ()
* Bump snakeyaml

* Bump jackson to be compatible with new snakeyaml
2023-05-23 21:39:38 -07:00
Nathan Doef 3b9a9c6193
Oracle Testcontainers and Test Data ()
* OracleEmbeddedDatabase + test data
2023-05-23 18:59:41 -04:00
Nathan Doef 970befad90
Fixes broken Oracle migration () 2023-05-23 17:06:27 -04:00
Tadgh 93a4a7bb33
Bump deps () 2023-05-23 09:53:52 -07:00
Tadgh 32a4ee056c
Bump snake yaml ()
* Bump snakeyaml

* Bump jackson to be compatible with new snakeyaml
2023-05-23 09:32:55 -07:00
dependabot[bot] cfc8b02b93
Bump spring-security-core from 5.7.5 to 5.7.8 in /hapi-fhir-storage-cr ()
Bumps [spring-security-core](https://github.com/spring-projects/spring-security) from 5.7.5 to 5.7.8.
- [Release notes](https://github.com/spring-projects/spring-security/releases)
- [Changelog](https://github.com/spring-projects/spring-security/blob/main/RELEASE.adoc)
- [Commits](https://github.com/spring-projects/spring-security/compare/5.7.5...5.7.8)

---
updated-dependencies:
- dependency-name: org.springframework.security:spring-security-core
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-05-21 22:17:59 +00:00
James Agnew 82ab61f796
Expunge performance tweak ()
* Expunge performance tweak

* Add changelog

* Address review comment
2023-05-21 17:56:31 +00:00
Tadgh 805e80e61f
6.6.0 Mergeback ()
* Force Verify tests

* fix ITs ()

* fix RestHookTestR5IT

* fix intermittent

---------

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

* Fix migrator error on Oracle ()

* Fix Oracle SQL error

* Add changelog

* Update clinical reasoning version ()

* 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. ()

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

* added version to mdm golden resource tag ()

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

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

* Update the changelog for 4697 to be more descriptive

* Futher tweaks of the changelog

* Fixes a bug with tags.  ()

* 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 ()

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

* Create correct version enum

* Remove superfluous migration

* fixing test ()

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

* email subscription, throw NullPointerException ()

* 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 ()

* 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. ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

* version bump for next release  ()

* version bump

* Bump to correctnumber

* Version Enum and folder

* Remove interim from list

* wip

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

* Fix operation on nested type-choices in FhirPatch implementation

* Add credit for 

---------

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

*  fix previous link offset no cache pagination ()

*  Add test reproducing the issue

*  Fix previous link for no cache offset pagination

*  Use unchecked URI parsing

* Credit for 

---------

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 ()

* 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 ()

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

* 4868 fix paging hapi ()

* 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 ()

* 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 ()

* Remove racy stats recalc.

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

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

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

* Rule apply patient export ()

* 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 ()

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

* backport subscription topic bean cleanup ()

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

* 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 ()

* CVE rel 6 6 ()

* 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 ()

* 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 ()

* 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 ()

* 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. ()

Remove _lastUpdated filtering of _revincludes.

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

* 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 ()

* 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 ()

Use hash_identity for canonical join

* License

* Version bump

* Fix failure in test

* Licenses

* Review comments for pipeline

* Dead entry

* other typo

---------

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: longma1 <32119004+longma1@users.noreply.github.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>
2023-05-20 20:38:35 -07:00
James Agnew 307e52f88f
Index name fix ()
* Index name fix

* Build fix

* Test restore

* Revert change
2023-05-20 21:29:56 +00:00
Ken Stevens d932730525
Fixed R5 Subscription deserialization ()
* review feedback

* fixed

* changelog

* test both ways

* add bundle test

* change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state

* fix v2 issues

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-20 00:32:25 +00:00
Ken Stevens a722cc46a9
SubscriptionTopicDispatcher ()
* Extract SubscriptionTopicBundleDispatcher into a separate service for use by custom interceptors that need to dispatch their own notifications

* rename

* changelog

* rename

* review feedback

* Msg.code

* review feedback

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-18 22:46:00 +00:00
David d94627c382
4847 allow filtering batch jobs by status ()
* Add method to get all jobs of a certain status

* add queries

* add tests

* Refactor so extra parameter is not added

* Version bump

* Fix broken test

* Revert accidental change to pom unrelated to version

---------

Co-authored-by: David Chen <david.chen@smilecdr.com>
2023-05-18 14:46:44 -04:00
James Agnew 1c66e57465
Update resource provenance indexing strategy ()
* Add migration

* Update indexes

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

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

* Address review comments

* Test fixes

* Test fixes

* Test fix

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-05-18 13:23:57 -04:00
Ken Stevens 54cec79a65
fix subscription topic beans ()
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-17 10:45:36 -04:00
Ken Stevens 55940bdf27
Add PreviousVersion service with tests ()
* started writing PreviousVersionReader

* started writing PreviousVersionReader

* moar tests

* add partitioning to the test

* switch subscription to use previous version reader

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-16 22:59:47 -04:00
Kevin Dougan SmileCDR 2fd2d95c88
Fixed broken Unit Tester. ()
* Fixed broken Unit Tester.

* Fixed issue with compilation against CDR.

* Fixed an overlay id value in the kotlin pom.xml.
2023-05-15 21:48:29 -04:00
James Agnew 05defb58c5
Server fixes from Connectathon 32 ()
* NPM test cleanup

* fix imports

* Ongoing cleanup

* Rework memory queue

* Reindex cleanup

* Cleanup

* Clean up

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Test fix
2023-05-15 08:28:55 -04:00
James Agnew 483ddca3be
Transaction with delete then update should not fail ()
* Fixed

* Test fixes

* Add test

* Ongoing work

* Work on xactx

* Cleanup

* Changelog cleanup

* Resolve fixme

* Rework broken APIs

* Version bump

* Add license headers

* License header update

* License

* rk on fixes

* Test fixes

* Address review comments

* Test fixes

* Add license headers

* License header
2023-05-15 07:41:40 -04:00
James Agnew 8cf14c8c0e
Dont crash indexing contained references on Bundle ()
* Dont crash indexing contained references on Bundle

* Add changelog
2023-05-14 21:33:32 -04:00
Ken Stevens a308f60e16
relax ()
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-13 22:35:18 -04:00
Ken Stevens 4313dc9958
pointcut exceptions ()
* enforce no exceptions on the invoking thread in PointCutLatch

* comment

* Msg.code

* Catch exceptions outside of await block

* fix migration issue

* Refactor PointcutLatch and add tests

* fix tests

* fix tests

* fix tests

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test!

* fix test!

* fix test

* fix test

* clean up latch error formatting

* fix test

* fix test

* fix test

* fix test

* fix test

* fix tests

* fix test

* fix test

* Remove hapi-fhir-jpaserver-uhnfhirtest from build as it is crashing CI

* fix test

* fix intermittent

* A SNAPSHOT dependency on an upstream module was added to HAPI FHIR, which changed and caused some downstream tests to break.

* fix intermittent

* Add Maven enforcer plugin for CR dependencies

* Make maven enforcer conditional on CI builds

* Remove hapi-fhir-jpaserver-uhnfhirtest from build as it is crashing CI

* improve test logging

* pre-review cleanup

* review feedback

* remove hapi-fhir-base-test-jaxrsserver-kotlin from the build

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-05-11 22:31:38 -04:00
JasonRoberts-smile 0475cb682f
Jr 20230502 fhir patch test coverage ()
* add tests for fhir patch

* extract constants

* extract some methods

* isolate add operation

* isolate delete operation

* isolate replace operation

* isolate move operation

* clean up integer handling

* enumeration creation

* improve variable naming

* code review feedback
2023-05-11 16:40:57 -04:00
Tadgh 9d34e6b248
Credit for ()
* Add credit

* Typo
2023-05-11 18:34:22 +00:00
Nicolai Gjøderum 679b809bf3
Fix: Replace basic field with empty value in TerserUtil ()
* add test proving bug

* fix: handle empty fromValue in TerserUtil.replaceField

* add comment to TerserUtilTest.testReplaceFieldByEmptyValue
2023-05-10 20:09:43 -07:00
JP c052663561
Change to a release version of the Clinical Reasoning dependency. ()
* A SNAPSHOT dependency on an upstream module was added to HAPI FHIR, which changed and caused some downstream tests to break.

* Add Maven enforcer plugin for CR dependencies

* Make maven enforcer conditional on CI builds
2023-05-10 20:25:42 +00:00
Ken Stevens 224b7f6206
SubscriptionTopic part3 ()
* Force Verify tests

* wip

* merge troubleshooting rel_6_6 troubleshooting changes

* fix ITs ()

* fix RestHookTestR5IT

* fix intermittent

---------

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

* post-merge cleanup

* fix test

* fix mock test

* fix wiring

* fix mock test

* fix test

* use IBaseResource.isDeleted()

* fixmes

* cleanup

* change log

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-09 16:29:21 -04:00
Tadgh e3545446eb
Mergeback of release into master branch ()
* Force Verify tests

* fix ITs ()

* fix RestHookTestR5IT

* fix intermittent

---------

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

* Fix migrator error on Oracle ()

* Fix Oracle SQL error

* Add changelog

* Update clinical reasoning version ()

* 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. ()

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

* added version to mdm golden resource tag ()

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

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

* Update the changelog for 4697 to be more descriptive

* Futher tweaks of the changelog

* Fixes a bug with tags.  ()

* 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 ()

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

* Create correct version enum

* Remove superfluous migration

* fixing test ()

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

---------

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: longma1 <32119004+longma1@users.noreply.github.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>
2023-05-09 11:23:02 -07:00
Max Bureck 648d14c52c
Parser: Reporting unexpected repeating element for choice () ()
* Parser: Reporting unexpected repeating element for choice ()

IParserErrorHandler.unexpectedRepeatingElement is now also called for
unexpected repeating elements of type choice, where concrete names
may be different based on the choice's data type.

* setting test-utilities java version to the test version

* added changelog

* added Max to the developer liss

* removed unneeded dependency

---------

Co-authored-by: patrick-werner <pa.f.werner@gmail.com>
2023-05-08 20:42:25 +00:00
Dominique Villard 9ae71aba95
4379: allow interceptor annotation on methods ()
* 4379: allow interceptor annotation on methods

* 4379: document order parameter when annotation set on method

* Credit for 

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-07 12:25:29 +00:00
James Agnew d5184a8a57
Don't generate empty JSON element for comment ()
* Don't generate empty JSON element for comment

* Fixed
2023-05-06 16:05:48 -04:00
Tadgh 93f93d5e41
Add Migration Reviewer Workflow ()
* Add new workflow

* Add some whitespace

* Empty spaces in non-migration file

* wip

* Tidy up workflow
2023-05-06 10:33:17 -07:00
Ken Stevens 17423e4831
fix migration issue ()
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-06 09:13:50 -07:00
Tadgh f0726a32d5
Fixes a bug with tags. ()
* 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>
2023-05-05 19:06:03 +00:00
Kevin Dougan SmileCDR c637cec622
4801 - Added new Index on HFJ_RESOURCE table ()
* 4801 - Added new Index on HFJ_RESOURCE table.

* 4801 - Added new migration task for new Index on HFJ_RESOURCE table.

* Update hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

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

* Applied review changes.

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Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-05-05 17:37:25 +00:00
Brenin Rhodes 87e8a810cd
Merge 4821 back to master ()
* Merge 4821 into master

* Update to PRE3 snapshot
2023-05-05 08:50:53 -07:00
Ken Stevens 350d1a422c
merge release branch to master ()
* Force Verify tests

* fix ITs ()

* fix RestHookTestR5IT

* fix intermittent

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

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Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-03 19:51:43 +00:00
James Agnew a3c33d2a53
Add BasicAuditEventLogging (BALP) Interceptor ()
* Begin work on BALP interceptor

* Work on BALP

* Basic profile

* Work on BALP

* Add BALP

* Work on balp

* Add update and delete

* Work on BALP

* Add logging

* Tests

* Modify test server

* Work on docs

* Add documentation

* Add changelog

* Fix  - Typos in docs

* Test fixes

* Move changelog

* Update hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/interceptor/balp/BalpAuditCaptureInterceptor.java

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

* Resolve PR comments

* Test fixes

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Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-05-03 15:46:22 +00:00
Aleksej Parovysnik f4c0f6e9fc
fix previous link offset no cache pagination ()
*  Add test reproducing the issue

*  Fix previous link for no cache offset pagination

*  Use unchecked URI parsing

* Credit for 

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Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-02 12:49:36 +00:00
Zach Smith 9c1d235f90
Fix operation on nested type-choices in FhirPatch implementation ()
* Fix operation on nested type-choices in FhirPatch implementation

* Add credit for 

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Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-01 09:52:34 +00:00
Tadgh 9a095cc2d7
version bump for next release ()
* version bump

* Bump to correctnumber

* Version Enum and folder

* Remove interim from list

* wip
2023-04-30 15:01:28 -04:00
Luke deGruchy 79c96dc1bb
Port changes to master from release branch 6_4 ()
* Start porting changes to master that were lost from the release branch.

* Add remainder of tag changes from release branch.

* Changelog changes.

* Fix schema migration.

* Remove duplicate lines.

* Update core to 6.0.1.

* Fixes for new core.

* Bump to snapshot 19 to mirror James' changes.

* Fix migration tasks.

* Fix some of the tests due to the core upgrade.

* Fix rest of tests.
2023-04-28 19:56:02 +00:00
michaelabuckley 81854baa02
Batch2 cleanup ()
Post review batch2 cleanup.

Review fixes and cleanup from 

Deleted methods in IJobPersistence unused in prod paths, and replaced their usage in tests.
Lots of docs.
Replace copy-on-write pattern in JobDefinitionRegistry with simple ConcurrentHashMap
Fixed bad mappings from job ERRORED state to external APIs. People think ERRORED is a failed state. ¯\_(ツ)_/¯
Added some spec tests for chunk purging
Deprecated ERRORED. For deleting in 6.8
Lots of plans for 6.8. Too risky for 6.6
2023-04-28 15:44:30 -04:00
James Agnew e2e5ff6bb8
Version bump HAPI FHIR () 2023-04-28 19:30:51 +00:00
James Agnew 69a79e39a1
Subscription retriggering enhancements ()
* Work on forward porting reindex optimize storage

* Subscription retriggering performance enhancements

* Adjust readmes

* Add a test

* Add test

* Cleanup

* Test cleanup

* Add comment

* Add changelogs

* Test fixes

* Test fixes

* Bump size

* Fixes

* Test logging

* Restore forkcount

* Test fix

* Test fix

* Version bump

* Clean up changelogs

* Address review comment
2023-04-28 12:06:38 -04:00
James Agnew 78ff58277a
Make inline resource storage use a better column type ()
* Use text column on postgres

* Add changelog

* Test fix

* Merge
2023-04-28 12:06:27 -04:00
James Agnew e2717bd63a
Bump corelib to FHIR R5 Final ()
* Core bump

* Build build issues

* Bump core

* Cleanup

* Cleanup

* Resolve intermittent

* Work on core

* Add failing test for a check

* Test fixes

* Fixes

* DOn't mangle subscriptions

* Fix

* License headers

* Build fixes

* Version bump

* Compile fixes

* Fix compile issues
2023-04-28 06:28:22 -04:00
longma1 2171ad04a2
3924 mdm match resources across partitions and storing golden resources on a specific partition ()
* added mdm search all partition for golden resource functionality

* added mdm partition setting

* build header fix

* test fixes and added missing side effect of allowing cross partition links on opeartions

* added changelog, also test fixes

* fixed changelog to an actual yaml file

* review fixes,  also simplified tests

* reverted one test because the original test schenario was correct

* added setting clearing in afterEach method so test dont fail while run in maven

* bump to pre-15

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Co-authored-by: Long Ma <long@smilecdr.com>
2023-04-28 02:15:35 -06:00
David 457b39bac1
Fix $mdm clear doesn't expunge golden record resources ()
* Failing test

* Add method to expunge collection of deleted resources

* Failing test passes

* Add changelog

* Version bump

* Forgot to commit change

* Update test

* Check type validity

* Fix broken tests

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Co-authored-by: David Chen <david.chen@smilecdr.com>
2023-04-27 21:35:27 -06:00
JasonRoberts-smile ae1e7400dd
delete operation removes element from list ()
* delete operation removes element from list

* changelog
2023-04-28 00:01:28 +00:00