Commit Graph

9953 Commits

Author SHA1 Message Date
TynerGjs df047a9dea
Resolve 5758-completion-handler-for-reduction-steps-are-not-called-with-the-up-to-date-job-instance-status (#5759)
* updated instance status after run is called.

* added changelog

* version bump
2024-03-06 11:01:42 -05:00
Luke deGruchy 4570c28cb6
Fix _has then chain then _has searches (#5735)
* Add SQL logging:  Attempt to add test.

* Small fix.

* moar tests

* Tweak unit tests to be parameterized.

* Enhance tests and more logging.

* Better tests.  More logging.  More TODOs.

* Better tests.  More logging.  More TODOs.

* Changes

* Changes

* Updates to tests.  More logging and experimental code.

* Introduce fix along with more logging and TODOs and tweaks to tests.

* Cleanup solution.  Get rid of logs and todos.  Rename test class, test methods and clean up unnecessary code.

* Add changelog.

* Implement simpler chain algorithm without conditional logic and leave a long comment explaining why.

* Implement simpler chain algorithm without conditional logic and leave a long comment explaining why.

* Fix comment.

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-03-04 15:52:04 +00:00
Nathan Doef 9ec8882457
Unable to POST a transaction Bundle with nested collection Bundle entries (#5693)
* failing test

* fix

* fix

* improve / fix old tests

* changelog

* cleanup

* comment
2024-03-04 10:50:05 -05:00
TipzCM 370d2c16b1
5746 fixing reducer step (#5753)
* fixing reduction step to fire job completion handler

* unwinding

* fixing changelog

* spotless

* review fixes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-03-04 09:12:31 -05:00
Tadgh 3a1a0418a0
Readd migration (#5747)
* Re-add removed migration

* spotless
2024-02-29 21:07:24 +00:00
longma1 f5cc015ff3
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>
2024-02-27 22:12:23 +00:00
Tadgh 28b8662637
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 17:50:01 +00:00
Luke deGruchy 497b9f2e53
Fix FhirTerser to handle Enumeration correctly (#5726)
* Add test for CDA with binary database blog storage and some logging for the Terser.

* More logging and a new FhirTerser test.

* Add more comments and prove Enumeration is a valid subtype of Type.

* More logging and comments.

* James solution:  Comment out some code.  Spotless.

* Get rid of logging and TODOs.  Use AtomicBoolean for test.

* Try just commenting out the continue; line.

* Integrate changes from ja_20240222_choice_specialization_fix.

* Spotless.

* Changelog and fix for bad import.

* Code review feedback.
2024-02-26 15:10:12 +00:00
Artiom Darie d8f6c10df2
Added content message delivery for SubscriptionWebsocketHandler (#5692)
* Added content message delivery for SubscriptionWebsocketHandler

* 5687: Code clean up and small bug fix on empty payload

* 5687: Provided unit tests for the SubscriptionWebsocketHandler with subscription topic content: id-only, empty and full-resource

* 5687: Apply mvn spotless:apply

* 5687: Code formatting

* Credit for #5692

---------

Co-authored-by: artiom.darie <artiom.darie@adswizz.com>
Co-authored-by: Artiom Darie <5781864-artiom.darie@users.noreply.gitlab.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-02-26 08:54:04 -05:00
jmarchionatto 2c2afd4a83
Hibernate SQL log filtering feature (#5594)
* Hibernate SQL log filtering feature

* changelog

* Add exception msg codes

* Improve test which failed in pipeline

* Join tests to avoid threading issues

* Fix comment

* Add review suggestions

* Add extra documentation including example.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/appendix/logging.md

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

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-02-25 09:09:56 -05:00
longma1 28a1a4d4df
Rel 7 0 mb 2 (#5714)
* 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>

* 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

* 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>

* Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)

* Failing test

* fix

* changelog

* Avoiding Exception being thrown on @EventListener invocation (#5628)

* replaced EventListener annotation with @PreDestroy

* adding changelog

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* simple fix (#5630)

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

* 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

* 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>

* 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

* $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)

* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation

* 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>

* 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.

* 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

---------

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

* Index review fixes (#5649)

* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.

* 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

* Searching for Bundles with read all Bundles permission returns 403 (#5644)

* failing test

* another failing test case

* fix

* changelog

* fix bug

* spotless

* cr

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* 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

* Revert change to other safe version to stop problem with deprecated field

* Rel 7 0 CVE (#5663)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* 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

---------

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

---------

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>

* $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

* 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>

---------

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

* 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

* version bump to 7.0.0

* pipeline fix

* Update java home

* Updating version to: 7.0.1 post release.

* post mergeback cleanup

* bump clinical-reasoning.version to pre17

* test fix

* version bump to 7.1.5-snapshot

---------

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
2024-02-23 11:03:26 -07:00
James Agnew e759bc0958
Make seaech URL cleanup job clustered (#5734)
* Make seaech URL cleanup job clustered

* Add changelog
2024-02-23 11:16:40 -05:00
James Agnew ec525f4457
Apply SearchNarrowingInterceptor to conditional URLs (#5712)
* Fix #5110 - Failure in tx processing

* Test fix

* Work on narrowins

* Add changelog

* Docs cleanup

* Fix compile error

* Rollback incompatible change

* Test fix

* Test fix

* Force update

* Test fixes

* Build fixes

* Bump HTMLUnit

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5712-apply-searchnarrowing-to-conditional-urls.yaml

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

* Address review comments

* Version bump to 7.1.4-SNAPSHOT

* Spotless

* Roll back version

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-02-23 08:42:26 -05:00
dotasek c7f413d6ea
Bump commons compress to 1.26 (#5718)
* Bump commons compress to 1.26

* Use full version name

* Add changes.yaml
2024-02-22 14:02:40 -05:00
pano-smals a5eddc3837
Bugfix: removed reference to public schema in raw sql (#5722)
* Bugfix: removed reference to public schema in raw sql

* Add attribution for #5722

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-02-21 13:57:08 -05:00
James Agnew 3974239c48
Make history pages stable (#5720)
* Make history pages stable

* Add changelog

* Apply spotless
2024-02-21 13:32:59 -05:00
volodymyr-korzh b4155e5d11
Reflected XSS vulnerability in Testpage overlay (#5719)
* HAPI FHIR Testpage potential XSS vulnerability - fix
2024-02-20 15:12:53 -07:00
Martha Mitran e5d410d10b
Refactor and fix functionality dealing with ReadPartitionIdRequestDetails (#5691)
* Throw exception when resourceType of parameter value is invalid when performing FHIR search with non-chained reference

* Fix changelog issue id and spotless warning

* Cleanup unnecessary test

* Validate resourceType only when using relative reference

* Fix test for search using _type parameter

* Refactor and fix functionality dealing with ReadPartitionIdRequestDetails

* Spotless fixes

* Revert some of the refactoring changes to BaseRequestPartitionHelperSvc and fix tests

* Small cleanup

* Missing change

* Small changes

* Fix tests and add a few more

* Spotless fix

* Address code review comments

* Some polishing on the interface annotations and documentation

* Spotless fix

* Fix test

* Fix tests and test method rename

* Ensure SearchParameterMap is not null

---------

Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
2024-02-17 16:16:14 -05:00
Luke deGruchy c8d6e9fb73
Fix validation caching issue with initially unpopulated StructureDefinitions (#5705)
* Solution to caching issue with new tests.

* Fix animal sniffer issue.  Clean up unit tests.  Finalize changelog.  Add TODO referencing change in validation cache behaviour.

* Spotless.

* Fix unit test.

* Code review feedback.
2024-02-15 21:54:24 +00:00
Luke deGruchy bdaedb605b
Return HAPI-2498 if a REST request contains an :identifier modifier (#5696)
* Failing tests and logging.

* Spotless.

* Fix error message for bad modifiers.  Add more tests.

* Spotless.

* Fix conditional logic for detecting modifiers to check for colon (:).

* Finalize tests.  Fix animal sniffer error.  Remove logging code.  Finalize changelog.

* Try again to fix animal sniffer error.

* Null handling on request.
2024-02-14 00:51:37 +00:00
James Agnew 90f1690809
Failure in tx processing (#5703)
* Fix #5110 - Failure in tx processing

* Test fix
2024-02-13 16:48:55 -08:00
Tadgh 2caccc796b
Attribution for 5668 (#5702)
* Attribution

* Attribution
2024-02-13 10:48:08 -08:00
Jens Kristian Villadsen 1deca0756c
Feature/chained location.near search (#5668)
* Added support for chained location search

* Added unit tests

* Assigned new error code

* Reworked according to review
2024-02-12 10:47:50 -08:00
James Agnew 12eb2d6f35
IPS API Refactor (#5682)
* IPS enhancements

* API design complete

* Work on section registry

* Work on external fetch

* IPS rewrite

* Cleanup

* Work

* IPS refactor

* Add changelog

* Changelog updates

* Spotless

* Compile fix

* Address review comments

* Address review comments

* License header

* Revert narrative builder change

* Address review comments

* Addres review comments

* Cleanup
2024-02-11 10:43:56 -05:00
Michael Buckley d71736bf9d
Suspend tx when refreshing version cache (#5671)
* Suspend tx when refreshing version cache
* Undo refactor to reduce merge size
* changelog
* Bump to 7.1.3
* Fix version test
* Unwrap transaction proxy
2024-02-08 14:01:39 -05:00
Luke deGruchy a7eceda5d7
Enforce limit on the number of resources resolved by a deleteByUrl call. (#5689)
* Enforce limit on the number of resources resolved by a deleteByUrl call.

* Add changelog and TODO comment.

* Code review suggestion.
2024-02-08 11:13:21 -05:00
Martha Mitran 43f1e4b2dd
Handle invalid resourceType when performing FHIR search with non-chained reference (#5674)
* Throw exception when resourceType of parameter value is invalid when performing FHIR search with non-chained reference

* Fix changelog issue id and spotless warning

* Cleanup unnecessary test

* Validate resourceType only when using relative reference

* Fix test for search using _type parameter
2024-02-08 11:08:13 -05:00
longma1 993cfcce99
7 0 0 mb (#5678)
* 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>

* 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

* 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>

* Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)

* Failing test

* fix

* changelog

* Avoiding Exception being thrown on @EventListener invocation (#5628)

* replaced EventListener annotation with @PreDestroy

* adding changelog

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* simple fix (#5630)

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

* 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

* 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>

* 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

* $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)

* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation

* 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>

* 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.

* 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

---------

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

* Index review fixes (#5649)

* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.

* 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

* Searching for Bundles with read all Bundles permission returns 403 (#5644)

* failing test

* another failing test case

* fix

* changelog

* fix bug

* spotless

* cr

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660)

* 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

* Rel 7 0 CVE (#5663)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* 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

---------

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

---------

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>

* fix conflict mistake

* removed test assert that is no longer true:

* version bumpb to 7.1.1

* fix version Enum test

---------

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-02-07 22:16:34 -07:00
volodymyr-korzh 8e69170c89
Xml encoded fhir resource created with decimal element that has leading plus sign value couldn't be retrieved or modified (#5670)
* XML encoded FHIR resource created with decimal element that has leading plus sign value couldn't be retrieved or modified - implementation
2024-02-06 18:04:03 -07:00
Tadgh 8c16f57c05
changelog (#5673) 2024-02-06 07:23:51 -05:00
Jens Kristian Villadsen bc955b8539
introduced _list fix (#5664)
* introduced fix

* Add value

* Added backing tests

* Ignore _list as _has is done
2024-02-05 17:26:20 -08:00
Martha Mitran cbd733c340
Refactor `CommonCodeSystemTerminologyService` method `validateCode` (#5631)
* Refactored CommonCodeSystemTerminologyService validateCode method and added more tests
2024-02-02 15:20:43 -07:00
Martha Mitran 250bc7b031
Fix contentType request parameter in UploadTerminologyCommand (#5639) 2024-02-02 13:45:46 -05:00
jmarchionatto 51a6ddad3d
Add setting to make broker not use JacksonMessageConverter (#5611)
* Add setting to make broker not use JacksonMessageConverter

* Add changelog

* Implement suggestions

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-01-26 15:06:20 -05:00
Michael Buckley 949c970cfd
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>
2024-01-22 23:21:27 +00:00
longma1 29fec706de
pom bump, doc add, version enum add (#5616)
Co-authored-by: Long Ma <long@smilecdr.com>
2024-01-22 22:42:54 +00:00
Ken Stevens c207b4949b
fix default partition setting on resource (#5617)
* fix default partition setting on resource

* changelog

* Handle DEFAULT partition in rule checker.

* Fix spotless

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-01-22 22:29:40 +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
James Agnew 5a747051de
Fix CI deploy (#5596) 2024-01-15 23:08:04 +00:00
James Agnew 878e27b06d
HAPI FHIR Dependency Bumps (#5576)
* HAPI FHIR Dependency Bumps

* Hibernate search 6

* Dep bumps

* Bump mockito

* Fix memory leak

* Test cleanup

* Test fix

* Test fixes

* Test fix

* Test fix

* Test fix

* Test fix

* Prepare to try and rework max clauses

* Refactor large VS expansion

* Spotless

* Test fix

* Version bump

* Test fixes

* Bump maven container

* Build fix

* Add license headers

* Version bump

* License headers
2024-01-14 14:15:08 -05:00
volodymyr-korzh 5286829585
New extension for auto versioning references of the resource (#5591)
New extension for auto-versioning references of the resource
2024-01-12 17:00:58 -07:00
Luke deGruchy 763894c28f
Reverse changes from 5493. Ensure MDM expansion is limited by queried partition. Support $everything with MDM expansion and POST (#5585)
* Reverse changes from 5493.  Add a stub changelist.

* Add various changes including stub changelist, beginnings of integration test, pass request details to interceptor, obtain partition ID, and stub code for each partition-aware query.

* Spotless.  Implement methods and SQLs for both golden and source IDs.  Not yet tested.  Add default interface methods.

* Fix HQLs that were referring to incorrect columns.  Rename parameter.  Formatting.

* Fix logic to use single queries by source and golden resource.  Filter by partition IDs in Java instead of in SQL.  Write a new unit test for MdmLinkExpandSvc.

* Spotless.

* Ensure $everything with mdm expansion works on POST as well as GET.  Some cleanup.

* More cleanup.

* Null safety for mdmExpand.

* Spotless.

* Small changes.

* Enhance changelog.

* Delete commented out code.

* First round of code review changes.

* More code review changes.
2024-01-12 13:46:15 -05:00
TipzCM d6128dece0
adding additional data to (bulk data export) parameters (#5541)
* adding additional data to parameters

* checkstyle

* updated consent service

* updating documentation

* working

* updating and cleaning

* some review points

* spotless

* review fixes

* bumping version

* consent interceotpr fixes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2024-01-12 09:49:45 -05:00
James Agnew 01c748163d
Don't contain resources in Bundle with only fullUrl (#5589)
* Don't contain resources in Bundle with only fullUrl

* Add changelog

* Spotless

* Fix RDF issue
2024-01-10 12:32:44 -05:00
Martha Mitran effbc98b30
Fix fhirpath expression evaluation with _fhirpath parameter when resolve() references resources within a Bundle (#5565)
* Fix fhirpath expression evaluation with _fhirpath parameter when resolve() references resources within a Bundle

* Update parameters for getBundleReference method

* Addressing some code review comments

* Spotless fix and update test logic to address code review comment
2024-01-09 13:15:01 -05:00