Commit Graph

9417 Commits

Author SHA1 Message Date
Tadgh 97d6e30832 Merge branch 'rel_6_4' of github.com:hapifhir/hapi-fhir into rel_6_4 2023-02-25 09:02:14 -08:00
Tadgh 0ada4e7afc ITify 2023-02-25 09:02:06 -08:00
Luke deGruchy 2d4b8d9163
Disable more intermittently failing tests (#4595)
* Disable more intermittently failing tests.

* Disable another intermittently failing tests.
2023-02-25 11:36:29 -05:00
Tadgh d4a5153b55 rename tests to IT 2023-02-24 22:41:13 -08:00
Luke deGruchy d192bcef57
Disable intermittently failing tests. (#4593) 2023-02-24 22:07:53 -05:00
Tadgh 79692dfdfa Tidy metadata 2023-02-24 10:30:19 -08:00
Tadgh 9fe44eeaa6 Fix changelog 2023-02-24 10:13:19 -08:00
Luke deGruchy 9ede6b3b9a
Add model changes to IBaseCoding and related changes (#4587)
* Add IbaseCoding changes, and tinder changes

* Fix up tag definition

* converter addition

* Fix unit test and add changelog.

* Add jira to changelog.

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-02-24 10:12:01 -08:00
Tadgh 4af1a5016c Force pin structs 2023-02-24 10:08:29 -08:00
Tadgh eee61285f3 Exclude pinned core deps 2023-02-24 09:04:39 -08:00
Luke deGruchy b2ebdec183
Address leftover code review feedback from the upgrade to core 5.6.97. (#4585) 2023-02-24 11:32:54 -05:00
Tadgh baa494cd91 Fix up dal test 2023-02-23 19:42:20 -08:00
Luke deGruchy 2c34bf074f
Upgrade core to 5.6.97, make adjustments in hapi-fhir, and ensure that all tests pass (#4579)
* First commit:  Create new branch from the release branch with changes from James' branch.  This probably won't compile as the work is incomplete.

* Second round of changes from integrating James' branch.

* Mark most test failures with TODOs.

* Add whitespace

* Add changes to FhirPathR4 to set FHIRPathEngine to non-strict FP evaluation.

* Fix CreatePackageCommandTest to assert null instead of empty string.  Comments on tests that fail due to the double-quote encoding problem.

* Downgrade to core 5.6.97.

* Fix another test and remove TODOs.

* Fix changelog.

* Clean up some erroneous changes and TODOs.

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-02-23 15:32:13 -08:00
Tadgh bbe437ab86 Add backport info 2023-02-22 16:03:49 -08:00
Justin McKelvy 8698abfbdb typedbundleprovider getallresources override (#4552)
* typedbundleprovider getallresources override

* added test to immunization tests that validates pagination does not result in null pointer if over default queryCount

* moved HapiFhirDal test to its own test class

* removed unused imports

* Update to use JpaStorageSettings

* adding changelog for issue 4551

* fix changelog spacing

* changelog type  to fix

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-02-22 16:02:53 -08:00
Tadgh 6b6f1e2e66 Fix bad creation of versionenum 2023-02-16 23:11:11 -08:00
markiantorno 827bbba1e2 Updating version to: 6.4.1 post release. 2023-02-17 04:29:53 +00:00
Tadgh 71fa4f2cb4 License fixes, new parent 2023-02-16 17:02:14 -08:00
Tadgh 23b7acf04d Remove bumped version 2023-02-16 16:47:36 -08:00
Tadgh 529e47865d Change parent 2023-02-16 16:45:04 -08:00
Tadgh 96855fb943 Reset version 2023-02-16 16:33:56 -08:00
Tadgh 384bea1f60 Merge branch 'rel_6_4' of github.com:hapifhir/hapi-fhir into rel_6_4 2023-02-16 16:33:24 -08:00
Tadgh f08823bfdd Add javadocs and sources to our serviceloaders 2023-02-16 16:33:19 -08:00
markiantorno b2644c1c60 Updating version to: 6.4.1 post release. 2023-02-16 23:33:58 +00:00
Tadgh acfde151b1 Downgrade dep' 2023-02-14 15:24:39 -08:00
Tadgh a0e4c2949e License updates' 2023-02-10 20:51:17 -08:00
Tadgh 9578610e15 bump ver 2023-02-10 20:42:38 -08:00
Nathan Doef 9754a72046
Bulk Export Bug With Many Resources and Low Max File Size (#4506)
* failing test

* fix + changelog

* tweak

* add method to IJobPersistence to use a Stream

* tweak

* tweak

* decrease test time

* clean up

* code review comments

* version bump

* Increase timeout limit to match BulkExportUseCaseTest

* shorten test

* maintenance pass

* add logging

* Revert "add logging"

This reverts commit b0453fd953.

* Revert "maintenance pass"

This reverts commit bbc7418d51.

* test

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* shorten tests

* logging

* move test location

* fixes a regression caused my change in hapi-fhir

* timeout

* Revert "fixes a regression caused my change in hapi-fhir"

This reverts commit 4b58013149.

* testing

* Revert "testing"

This reverts commit aafc95c2f3.

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-02-10 13:14:29 -05:00
michaelabuckley fb0512f78f
Avoid logging message payloads that contain sensitive data (#4537)
Don't log payloads - they may contain sensitive data.
2023-02-10 09:30:55 -05:00
KGJ-software 03ccf3e3d3
Better error handling for when channel type is not supported (#4538)
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2023-02-09 21:49:44 -08:00
Tadgh e99aebd2ca
Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535)
This reverts commit 53252b8d15.
2023-02-09 14:33:53 -08:00
samguntersmilecdr f3847b1d0b
fixed channel import null pointer exception from null header (#4534)
* retryCount 0 on null header + test + changelog

* suggested changes
2023-02-09 11:49:54 -08:00
TipzCM fe078c2884
4441 rel 6 4 bad references creation bug (#4519)
* adding a test

* fail in the case of ref enforce on type and on write and autocreate are all true

* update to code

* removing a line

* cleanup

* removing check on urn

* changing just to trigger a build

* adding a comment to the pom

* updating test for better information

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-02-09 14:48:59 -05:00
Qingyixia 53252b8d15
fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)
* fix + test

* minor fix

* Addressing suggestion

* Minor changes
2023-02-09 10:48:55 -05:00
Etienne Poirier 3d9a318e33
Making narrative_generation.md reference an html snippet (#4531)
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-02-09 09:47:14 -05:00
Nathan Doef b4778f4b24
fix build (#4530) 2023-02-08 19:25:05 -05:00
TipzCM 6b3b954c77
trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527)
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* added change log

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-02-08 16:54:25 -05:00
Tadgh 71ea1b49f2 REVERT: change to operationoutcome.html 2023-02-08 12:04:23 -08:00
longma1 f32157319c
changed what score is set for mdmlinks that created new golden resource (#4514)
* changed what score is set for mdmlinks that created new golden resource

* fix test

---------

Co-authored-by: Long Ma <long@smilecdr.com>
2023-02-08 09:45:59 -07:00
Etienne Poirier 697bd27799
Update to documentation regarding narrative generation; (#4521)
Providing changelog;

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-02-08 08:47:13 -05:00
Tadgh e724040c14 New line:: 2023-02-07 17:22:36 -08:00
Isaac Wen 85ecbf181e
Unable to Expunge CodeSystem (#4507)
* changes for GL-3943

* changes for GL-3943

---------

Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
2023-02-07 15:26:10 -05:00
Tadgh ca21abf0f8
4516 create hapi fhir cli command to clear stale lock entries (#4517)
* Initial implementation

* better tests

* Add changelog and docs

* Forgotten files

* Code review comments

* Fix checkstyle
2023-02-07 11:37:52 -08:00
Tadgh d08995a5e6
Add check in scanner (#4518) 2023-02-07 10:13:29 -08:00
Tadgh e160325af6
CVE resolutions (#4513)
* Bump Postgres for CVE

* Bump jetty

* Verison bump

* Remove comments

* Revrt bump
2023-02-06 13:44:52 -08:00
samguntersmilecdr 33f6ed3d32
Change bulk import test for valueUri type (#4503)
* change tests

* suggested test change
2023-02-06 09:19:21 -08:00
Luke deGruchy 2a963acde2
Scheduled batch 2 bulk export job and binary delete (#4492)
* First commit:  Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.

* Refine solution and add a concrete unit test but still work to do.

* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.

* Unit tests complete.  New Msg code for new IJobPersistence.fetchInstances() method.  Cleanup TODOs and add others.

* Finish final touches on implementation.

* Add changelog.

* Various cleanup.

* Code review feedback.

* Small tweak to changelog.

* Last code review tweak.

* Address more code review comments.

* Reverse changes to consider work chunks.  Add a constant for write-to-binary.
2023-02-06 09:04:04 -05:00
TipzCM 0996124778
fix batch2 reduction step (#4499)
* fix bug where FINALIZE jobs are not cancellable

* moved reduction step to message hander

* moving reduction step to queue

* addingchangelog

* cleaning up

* review fixes

* review fix'

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-02-03 14:00:29 -05:00
Tadgh 7d554d56fd License 2023-02-03 10:25:19 -08:00
Tadgh df83d05fbb Merge branch 'rel_6_4' of github.com:hapifhir/hapi-fhir into rel_6_4 2023-02-02 15:22:28 -08:00