Commit Graph

9760 Commits

Author SHA1 Message Date
Emre Dincturk d83e58b465 dummy-change-for-pipeline 2024-02-29 12:59:10 -05:00
Tadgh 9c1e716a44 spotless 2024-02-28 10:54:23 -08:00
Tadgh e15d35f178 Add accidentally removed migration 2024-02-28 10:54:00 -08:00
Long Ma 3fe3eacce7 added docs for 7.0.1 2024-02-28 09:25:37 -07:00
longma1 6a67fa4155 Added correction to generated resource providers (#5743)
* 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 <jenskristianvilladsen@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
2024-02-28 09:23:34 -07:00
Tadgh c30608a55c Rel 6 4 mb update (#5741)
* 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 <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: longma1 <long@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2024-02-27 11:54:54 -07:00
Michael Buckley 8c71fca161 cherry-picked fix for 5671 searchparameter locks 2024-02-27 11:44:43 -07:00
volodymyr-korzh 538acc6fc5 Reflected XSS vulnerability in Testpage overlay (#5719)
* HAPI FHIR Testpage potential XSS vulnerability - fix
2024-02-27 11:39:09 -07:00
James Agnew e71efe5029
Backport 5722 into 7.0.1 (#5729)
* Bugfix: removed reference to public schema in raw sql (#5722)

* Bugfix: removed reference to public schema in raw sql

* Add attribution for #5722

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

* Add backport tag

* Build fix

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Co-authored-by: pano-smals <135063507+pano-smals@users.noreply.github.com>
2024-02-22 16:06:42 -05:00
markiantorno 28d88b1462 Updating version to: 7.0.1 post release. 2024-02-13 02:40:41 +00:00
James Agnew 0c3deda267 Update java home 2024-02-12 17:21:59 -05:00
Long Ma 6d7fd73888 pipeline fix 2024-02-12 15:06:29 -07:00
Long Ma 5c84b67bf9 version bump to 7.0.0 2024-02-12 14:49:57 -07:00
Martha Mitran f556ba485f
Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type. (#5698)
* Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type.

* Spotless fix

* Address code review comments
2024-02-10 00:26:12 +00:00
Tadgh 742105fd99 Merge branch 'rel_7_0' of github.com:hapifhir/hapi-fhir into rel_7_0 2024-02-09 14:51:38 -08:00
Tadgh 978a6788d8 Merge branch 'rel_7_0_cve' into rel_7_0 2024-02-09 14:51:13 -08:00
Justin McKelvy a6c2bef229
5654 measurescorer bug for denominator exception (#5677)
* update measure bundles and tests for enforced populationId specification on Measure group resources

* bump CR version to PRE17

* fix bug in versionEnumTest

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5654-measurescorer-bug.yaml

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

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Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2024-02-08 10:31:56 -08:00
Martha Mitran de0ddcce5b
$poll-export-status operation with PatientIdPartitionInterceptor fails with NullPointerException (#5681)
* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor.

* Fix NPE on -export-status operation with PatientIdPartitionInterceptor
2024-02-07 00:04:49 +00:00
Tadgh ace3fccf31
Descendent fix (#5669)
* Fix "is-a" ValueSet expansion, add "descendent-of" support

* Fixed tests in DSTU3 and R5

* Trigger new build

* Revert "Trigger new build"

This reverts commit 46c672b338.

* fix default partition setting on resource (#5617)

* fix default partition setting on resource

* changelog

* Handle DEFAULT partition in rule checker.

* Fix spotless

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

* pom bump, doc add, version enum add (#5616)

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

* fix default partition setting on resource (#5618)

* fix default partition setting on resource
* Handle DEFAULT partition in rule checker.

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Add setting to make broker not use JacksonMessageConverter (#5611)

* Add setting to make broker not use JacksonMessageConverter

* Add changelog

* Implement suggestions

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

* Fix version

* add changelog, add attribution, remove accidental bring-overs

* add changelog, add attribution, remove accidental bring-overs

* Finish jira section

---------

Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-02-05 22:39:04 +00:00
Tadgh d63d3cab46
Rel 7 0 CVE (#5663)
* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC
2024-02-04 22:45:26 +00:00
Tadgh 285fde397a Revert change to other safe version to stop problem with deprecated field 2024-02-04 13:38:57 -08:00
Tadgh 14a489c2af
Serializing changes for sensitive data (#5655)
* Add new senstiive data serializer

* Add new senstiive data serializer

* Add new senstiive data serializer

* Remove dead comments

* Change up the test

* review comments

* wip

* Tighten tests and push annotation down

* Tighten tests and push annotation down

* Changelog

* Add test

* 7.0.1-SNAPSHOT bump

* Error code

* Add method used by CDR

* add version enum

* Fix test
2024-02-02 17:38:15 -08:00
Tadgh 42d28fee75 Exclude JDBC 2024-02-02 14:45:07 -08:00
Tadgh a66a94d512 Bump spring version 2024-02-02 14:23:42 -08:00
Tadgh 5ebfe9fb19 Bump elastic 2024-02-02 14:21:16 -08:00
Tadgh 992ee040bb Pin parrson 2024-02-02 14:20:42 -08:00
Tadgh 8f249a4ef8 Bump json-path 2024-02-02 14:15:36 -08:00
Martha Mitran 0f3c744f11
Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660) 2024-02-02 10:19:11 -08:00
Nathan Doef 0537ab58db
Searching for Bundles with read all Bundles permission returns 403 (#5644)
* failing test

* another failing test case

* fix

* changelog

* fix bug

* spotless

* cr
2024-02-02 11:12:00 -05:00
Luke deGruchy ec1b8fe7ee
Fix conditional creates without leading '?' (#5646)
* First commit with failing test.

* More tests and logs.

* More logs

* Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl().

* Simplify solution.  Add more tests.

* Changelog.

* javadoc
2024-01-31 22:20:38 +00:00
Michael Buckley 59f7d4a9a3
Index review fixes (#5649)
* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.
2024-01-31 01:04:27 +00:00
jmarchionatto 5ed30f3181
Prevent batch2 job execution to stop for empty chunk when last job st… (#5635)
* Prevent batch2 job execution to stop for empty chunk when last job step is a reduction.
Add output to bulk export result even when empty.

* Fix test

* Unimportant change to force fresh build

* Implement review suggestions

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Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-01-30 22:08:50 +00:00
Luke deGruchy 16aa9fcdf2
Rule evaluation: Allow Bundles with PATCH Parameters (#5641)
* Remove parameters clause.

* Finalize changelog.  Add tests.  Finalize implementation.

* Undo changes to this test.

* Revert all changes to FhirQueryRuleImplTest.  Add new RuleImplOpTest.  Ensure that proper nested Bundle is created for test and other fixes.

* Tweak test.

* Use real rule applier in test and remove all mocks.
2024-01-30 19:23:27 +00:00
JP 94e932c9a5
Fix Measure group id null pointer exception (#5620)
* Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id

* add changelog

---------

Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
2024-01-30 11:18:00 -05:00
volodymyr-korzh 500490761b
$expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)
* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation
2024-01-30 07:17:49 -07:00
Martha Mitran c7fd015195
Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638)
* When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases.

* Minor change to fix test

* Rename changelog file

* Remove TODOs as they're replaced by reported issue

* Revert accidental change added with TODO removal
2024-01-29 13:18:40 -08:00
Luke deGruchy d3876c546f
Oracle: Ensure migrated database still takes large resource text updates (#5629)
* First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration.

* First stab at agreed upon solution.

* Fix error with 4001 by removing unnecessary annotation.

* Spotless and TODO.

* Remove annotation for good and set length to LONG32.

* Fix copyright year.

* Finalize changelog.

* Remove migration changes.  Fix unit test.

* Fix compile error.

* Log output.

* Refactor resource history code into new ResourceHistoryCalculator.

* Spotless.

* Convert record to POJO.

* Restore pre-17 switch statement.

* Finalize new resource history calculator code and tests.

* Spotless.

* Remove logging.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml

Apply code reviewer suggestion

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

* Code review feedback.

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
2024-01-26 16:09:01 +00:00
volodymyr-korzh 224e569317
Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625)
* Incorrect version from versioned_references.auto_at_paths for conditional update - implementation
2024-01-26 08:49:12 -07:00
longma1 1441a90a9f
simple fix (#5630)
Co-authored-by: Long Ma <long@smilecdr.com>
2024-01-25 09:48:29 -07:00
Etienne Poirier ba28ff977f
Avoiding Exception being thrown on @EventListener invocation (#5628)
* replaced EventListener annotation with @PreDestroy

* adding changelog

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Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-01-25 11:18:44 -05:00
Nathan Doef 4b1ac778cc
Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)
* Failing test

* fix

* changelog
2024-01-24 10:35:40 -05:00
Etienne Poirier 47867fc628
5621 deadlock on caffeine cache when creating a resource with conditional create (#5622)
* Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback.

* Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations.

* adding changelog and spotless.

* Fixing typo.

* Addressing comments from code review.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-01-24 07:40:21 -05:00
Tadgh b982abbfbe
Check index existence on raw SQL creation (#5624)
* Add conditional check on index existence before we try again

* Add conditional check on index existence before we try again

* Changelog

* remit

* remit

* debug statements
2024-01-23 17:56:26 -08:00
longma1 a2a0a8a662
pom bump to 7.0.0 (#5615)
* pom bump to 7.0.0

* add version enum

* fixed feb release name

---------

Co-authored-by: Long Ma <long@smilecdr.com>
2024-01-22 22:30:32 +00:00
Michael Buckley 4aa3b97228
Dao support for searching for FHIR ids, and full resources. (#5612)
Move several search transformations inside the resource dao.

Create search for FHIR Ids, and search for Resources entry points.
2024-01-20 05:42:56 +00:00
Tadgh 9438754b72
Fix publish pipeline (#5613)
* wip

* wip

* Swap to corretto

* Try alpine

* create as root

* create as root

* Swap to root

* Hack around non-root

* revert unjammying

* revert

* now use dockerhub

* now use dockerhub

* New file

* remove comment
2024-01-19 23:23:26 +00:00
TynerGjs 6e1a56d520
Resolve 5602 bulk export would fail if type parameter is not provided (#5605)
* default _type to all resource types in the patient compartment for patient type&instance level bulk export

* parametrized test so that it calls both type and instance level

* added change log and spotless check

* resolved code review comments
2024-01-19 15:05:32 -05:00
Michael Buckley 6a370c60cb
Cleanup and some tests (#5609)
Cleanup warnings, and add some missing tests.
2024-01-19 17:42:50 +00:00
Tadgh bb99d3bf9a Sudo the pipeline command 2024-01-19 09:39:10 -08:00
Tadgh 84f0bb4f34
5606 trigger subscription failure (#5607)
* Fix, test, changelog

* Fix, test, changelog

* Add backwards compat

* Add backwards compat

* set all partitions if enabled

* Test fixes
2024-01-18 19:18:10 -08:00