9457 Commits

Author SHA1 Message Date
jmarchionatto
4482622602
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>
2023-05-18 16:10:31 -04:00
michaelabuckley
c45809c8ee
Remove _lastUpdated filtering of _revincludes. (#4899)
Remove _lastUpdated filtering of _revincludes.
2023-05-18 17:55:54 +00:00
Tadgh
b1f3df8d93 Merge branch 'rel_6_6' of github.com:hapifhir/hapi-fhir into rel_6_6 2023-05-18 09:39:38 -07:00
Tadgh
2fe54dea0a License 2023-05-18 09:39:36 -07:00
TynerGjs
ea03069a04
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>
2023-05-18 12:31:35 -04:00
Josie
ce952cb993
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>
2023-05-18 10:42:15 -04:00
jmarchionatto
34ebc42a45
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>
2023-05-17 19:19:16 +00:00
longma1
70093b83af
CVE rel 6 6 (#4907)
* cve pom changes

* bump javax.el to jakarta.el

---------

Co-authored-by: Long Ma <long@smilecdr.com>
2023-05-17 11:49:39 -06:00
Tadgh
dba51a3b23
lowers log level to remove bootup noise (#4908) 2023-05-17 08:45:26 -07:00
TipzCM
a304565a0e
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>
2023-05-17 13:15:56 +00:00
Ken Stevens
94ef289830
backport subscription topic bean cleanup (#4904) 2023-05-17 02:47:49 +00:00
longma1
91b7dbc710
cve pom changes (#4898)
Co-authored-by: Long Ma <long@smilecdr.com>
2023-05-16 13:23:01 -07:00
Tadgh
7aa4fbce8a
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>
2023-05-16 08:47:42 -07:00
jmarchionatto
757320c431
Remove default implementation intended only for interim backwards compatibility (#4894)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-05-16 11:33:43 -04:00
michaelabuckley
835d6d2d89
Throw 404 when requesting $export of non-existent Group or Patient (#4890) 2023-05-15 17:54:49 -04:00
michaelabuckley
75e28ba6a6
Fix batch job (bulk export) processed record count (#4879)
* Remove racy stats recalc.
2023-05-15 20:05:28 +00:00
jmarchionatto
680dcc06a1
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>
2023-05-15 14:19:26 -04:00
TipzCM
2973b6595c
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>
2023-05-15 13:30:08 +00:00
Ken Stevens
cf8935e4ea
disable wars (#4877)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-14 18:54:02 -04:00
Luke deGruchy
30eea1b140
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.
2023-05-12 21:58:37 +00:00
jmarchionatto
681a21c398
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>
2023-05-12 21:57:18 +00:00
longma1
e8cc02ff99
added warn message and test (#4848)
* added warn message and test

* code review fixes

---------

Co-authored-by: Long Ma <long@smilecdr.com>
2023-05-12 18:25:28 +00:00
Luke deGruchy
f464113633
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.
2023-05-12 12:10:04 -04:00
Tadgh
1891a196ab Move image file 2023-05-11 20:32:33 -07:00
Tadgh
c3ccfb3976 fix link 2023-05-11 20:19:37 -07:00
TipzCM
99f58f5902
fixing patient everything operator (#4845)
* fixing patient everything operator

* review fix

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-05-11 22:48:32 +00:00
StevenXLi
22c9a18ad4
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>
2023-05-11 15:26:37 -04:00
chalmarm
9d9df271d7
Add documentation for $care-gaps operation. (#4862)
* Add documentation for -gaps.

* addressing the comments.

---------

Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
2023-05-11 09:16:05 -07:00
Brenin Rhodes
37bfbf0ad5
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
2023-05-11 06:55:14 -06:00
Sam Gunter
d63dc073e5
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>
2023-05-10 11:37:48 -04:00
TipzCM
5fa92dc04c
fixing test (#4835)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-05-08 14:57:09 +00:00
Tadgh
ab070ef632 Remove superfluous migration 2023-05-07 10:04:38 -07:00
Tadgh
5212009f73 Create correct version enum 2023-05-06 18:00:50 -07:00
Ken Stevens
a8e823afee fix migration issue (#4830)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-06 09:32:26 -07:00
Tadgh
609bc53897 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>
2023-05-06 09:30:40 -07:00
JP
f97da3b201
Update the changelog for 4697 to be more descriptive (#4827)
* Update the changelog for 4697 to be more descriptive

* Futher tweaks of the changelog
2023-05-05 21:15:55 +00:00
longma1
9af24adc3c
added version to mdm golden resource tag (#4820)
Co-authored-by: Long Ma <long@smilecdr.com>
2023-05-05 16:41:52 +00:00
chalmarm
b33263d469
Opening the care-gaps endpoint for GET. (#4823)
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
2023-05-05 13:51:18 +00:00
Brenin Rhodes
2821201d42
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>
2023-05-04 23:10:47 +00:00
James Agnew
5855ea9036
Fix migrator error on Oracle (#4814)
* Fix Oracle SQL error

* Add changelog
2023-05-04 05:44:08 -04:00
Ken Stevens
71edea38f9
fix ITs (#4809)
* fix RestHookTestR5IT

* fix intermittent

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-03 14:22:20 -04:00
Tadgh
55305ad1e1 Force Verify tests 2023-05-02 17:56:31 -07:00
Luke deGruchy
79c96dc1bb
Port changes to master from release branch 6_4 (#4785)
* 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 (#4779)
Post review batch2 cleanup.

Review fixes and cleanup from #4647

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 (#4788) 2023-04-28 19:30:51 +00:00
James Agnew
69a79e39a1
Subscription retriggering enhancements (#4758)
* 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 (#4763)
* 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 (#4727)
* 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 (#4770)
* 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

---------

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 (#4767)
* 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

---------

Co-authored-by: David Chen <david.chen@smilecdr.com>
2023-04-27 21:35:27 -06:00