Commit Graph

1608 Commits

Author SHA1 Message Date
TynerGjs bc0ee995a2
Resolve MDM query links operation score field imprecise value (#5332)
* - Fixed precision error and rounded to 4 decimal places
- Removed the vector field from the return value of mdmlink toJSON
- modified tests for the above changes.

* changed to use BigDecimal instead of Precision to round score

* reformatted file
2023-09-25 10:44:36 -04:00
Tadgh 10d9d9628c
Binary storage prefix during update (#5334)
* wip

* Changelog

* Fix tests
2023-09-23 00:55:23 +00:00
Justin McKelvy 6a0b2794eb
5089 cr measure refactor (#5324)
* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

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

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* _source search parameter needs to support modifiers (#5095)

_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers

* Fix HFQL docs (#5151)

* repository measure refactor

* undo bundle edit, add config

* embedded library true

* undo post of bundle

* clear library cache on test

* fix sumbit-data test

* missing packages from cql

* fix test data and test cases for repository api

* 3.0.0 clinical reasoning uplift

* r4 cql execution provider and tests

* fix submitdata provider config

* wip cql tests

* debugging cql op wip

* wip debugging cql

* update tests for $cql, fix class names

* prep for Pre6 uplift

* spotless checks and test fixes

* bump to 3.0.0-PRE6

* cleanup

* fix version

* cleanup

* fix exlusions in pom

* add in cache invalidation config

* search converter bug and test for repository

* update searchconverter

* version bump, add changelog

* remove term config, move IDaoRegistryUser class

* Break out dstu3 providers and move config to version folders

* CVE-2023-26119

* remove * imports

* code review updates

---------

Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
2023-09-22 16:51:36 -07:00
TipzCM 0049319751
updating partition interceptor to allow multiple patient ids (#5326)
* updating partition interceptor to allow multiple patient ids

* spotless

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-09-22 17:23:43 +00:00
James Agnew 2b7ebbcb27
Make display name validation configurable (#5321)
* Test fixes

* Build cleanup

* Initial test passing

* Test fixes

* Tests all seem to be working

* Make display validation level configurable

* Should be all working

* Add changelog

* Add to changelog

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-09-19 22:25:33 +00:00
dotasek 9f9aeb980c
Bump core version to 6.1.2 (#5317)
* WIP Fix compile errors

* Fix compile errors 2

* Fix test fails due to new Validation messages

* Ignore validation issues

Ignore two validation issues:

Two 'side is inherently a collection' warnings are now thrown for the following expressions:

NamingSystem nsd-1 uniqueId.type = 'uuid'
Observation obs-7 code != component.code

There is also a general error ignored because the StructureDefinition for StructureDefinition is actually for FHIR 3.0.1, and contains an invalid expression in constraint sdf-9. This is remedied in the expression used in 3.0.2, but a full update of all profile structure definitions is out of scope for this PR.

* Fix property name

* Add changelog
2023-09-19 11:26:20 -07:00
TynerGjs 8d4f07c56e
Resolve 5262 adding new parameter strictmatch to the mdm history link operation 1 (#5282)
* implemented the strictMatch parameter, added corresponding test

* implemented the strictMatch parameter, added corresponding test

* updated mdm link history documentation
created changelog

* reverted previous changes. Made the default behaviour of history link as AND instead of OR

* optimized imports

* modified changelog

* modified tests
2023-09-19 16:15:47 +00:00
dotasek 7eb3150644
Update DSTU 3 Validation resources (#5320)
* Update resources with FHIR 3.0.1

* Minimize profiles

* Minimize valuesets

* Restore minimizer

* Changelog

* Remove FIXME, improve specificity of comments
2023-09-19 08:56:01 -07:00
Tadgh 49a28efd53
5290 - Feature Request - Implement toggle to prevent conditional updates from invalidating match criteria. (#5291)
* Test skeleton, TODO IMPLEMENTER added all over the place

* Add test and TODO IMPLEMENTER

* Add jpa storage property to allow preventing conditional updates to invalidate match criteria

* spotless

* Implement review suggestions

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-09-19 10:01:33 -04:00
Etienne Poirier 67e421649b
Reindex operation fails when operation is executed on a specific partition (#5311)
* adding initial test.

* adding solution

* adding changeLog.

* satisfying spotless check.

* fixing changelog

* addressing code review comments.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-09-18 09:08:45 -04:00
longma1 43e45db85a
Rel 6 6 2 mb (#5315)
* Force Verify tests

* fix ITs (#4809)

* fix RestHookTestR5IT

* fix intermittent

---------

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

* Fix migrator error on Oracle (#4814)

* Fix Oracle SQL error

* Add changelog

* 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>

* Opening the care-gaps endpoint for GET. (#4823)

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

* added version to mdm golden resource tag (#4820)

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

* Update the changelog for 4697 to be more descriptive (#4827)

* Update the changelog for 4697 to be more descriptive

* Futher tweaks of the changelog

* 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>

* fix migration issue (#4830)

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

* Create correct version enum

* Remove superfluous migration

* fixing test (#4835)

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

* 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>

* 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

* Add documentation for $care-gaps operation. (#4862)

* 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 (#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>

* fixing patient everything operator (#4845)

* 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 (#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.

* added warn message and test (#4848)

* 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 (#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>

* 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.

* disable wars (#4877)

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

* 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>

* 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>

* Fix batch job (bulk export) processed record count (#4879)

* Remove racy stats recalc.

* Throw 404 when requesting $export of non-existent Group or Patient (#4890)

* Remove default implementation intended only for interim backwards compatibility (#4894)

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

* 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>

* cve pom changes (#4898)

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

* backport subscription topic bean cleanup (#4904)

* 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>

* lowers log level to remove bootup noise (#4908)

* CVE rel 6 6 (#4907)

* 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 (#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>

* 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>

* 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>

* License

* Remove _lastUpdated filtering of _revincludes. (#4899)

Remove _lastUpdated filtering of _revincludes.

* 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>

* 4873 empty fhirid causes missing resource (#4874)

* 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 (#4919)

Use hash_identity for canonical join

* License

* Version bump

* Temp disable

* Make this dependency provided

* Updating version to: 6.6.1 post release.

* Bump snakeyaml

* Bump jackson to be compatible with new snakeyaml

* Bump deps (#4926)

* resolve CVEs, add new notes

* Updating version to: 6.6.2 post release.

* #5023 Unexpected usage of awssdk StringUtils in hapi 6.6 jpa migration (#5024)

task

Replace usage of awssdk

* added docs

* mssql test fixes

* Updating version to: 6.6.3 post release.

* fix up random errors when merging back

* undisable test

* remove mention of 6.6.3 which does not exist

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
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: 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>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Thomas Papke <web@thopap.de>
2023-09-15 13:36:48 -07:00
volodymyr-korzh f94295d46c
Transaction with conditional delete and update on the same resource should not fail (#5318)
* Transaction with conditional delete and update on the same resource should not fail - test

* Transaction with conditional delete and update on the same resource should not fail - implementation

* Transaction with conditional delete and update on the same resource should not fail - added changelog

* Transaction with conditional delete and update on the same resource should not fail - fixes
2023-09-15 13:14:18 -07:00
StevenXLi 8b7c9f1453
5307 search for medicationrequests with medication contained does not return correct results (#5308)
* added failing test

* implemented solution

* added changelog

* code review changes

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-09-14 11:54:55 -04:00
James Agnew de341a5bb7
Don't preserve history mode (#5306)
* No history mode

* Spotless

* Version history

* Fix changelog

* Address review comment
2023-09-14 12:42:24 +00:00
Tadgh d4a57fc123
Fix version names (#5309) 2023-09-14 08:06:18 -04:00
michaelabuckley e20382c4c8
Fix for `userSelected` and `version`. (#5310)
Fix `userSelected` and `version` in tags and security labels to DSTU2 and security labels in JPA storage.
2023-09-14 00:27:37 +00:00
longma1 0c42229985
Rel 6 8 2 mb (#5299)
* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

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

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* _source search parameter needs to support modifiers (#5095)

_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers

* Fix HFQL docs (#5151)

* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)

* Initial failing test.

* Solution with changelog.

* fixing format.

* Addressing comment from code review.

* fixing failing test.

---------

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

* documentation update (#5154)

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

* Fix hsql jdbc driver deps (#5168)

Avoid non-included classes in jdbc driver dependencies.

* $delete-expunge over 10k resources will now delete all resources (#5144)

* First commit with very rough fix and unit test.

* Refinements to ResourceIdListStep and Batch2DaoSvcImpl.  Make LoadIdsStepTest pass.   Enhance Batch2DaoSvcImplTest.

* Spotless

* Fix checkstyle errors.

* Fix test failures.

* Minor refactoring.  New unit test.  Finalize changelist.

* Spotless fix.

* Delete now useless code from unit test.

* Delete more useless code.

* Test pre-commit hook

* More spotless fixes.

* Address most code review feedback.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Fix the noUrl case by passing an unlimited Pegeable instead.  Effectively stop using page size for most databases.

* Deprecate the old method and have it call the new one by default.

* updating documentation (#5170)

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

* _source search parameter modifiers for Subscription matching (#5159)

* _source search parameter modifiers for Subscription matching - test, implementation and changelog

* Removal of meta tags during updates do not trigger subscription (#5181)

* Initial failing test.

* adding solution;
fixing documentation;

* spotless apply

* adding changelog

* modifying current test

---------

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

* Issue 5173 get gateway everything doesnt return all patients (#5174)

* Failing test

* Also set offset and count in base DAO override

* Changelog

* Fix for specific case where count has been set in parameters

* spotless

* Improve checks

---------

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

* Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175)

* First commit with failing unit test and small tweaks.

* Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead.  Add more detailed unit testing.

* Tweaks to logic and update the changelog.  Reverse all changes to TermReadSvcImpl.

* Revert PackageResourceParsingSvc to release branch baseline.

* Accept code reviewer suggestion to change changelog description.

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

---------

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

* Fix link

* Remove target slf4j version

* dont use new API for a bit (#5191)

* Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193)

DropIdGeneratorTask.

* Dqm performance bug update and provider loader fix (#5180)

* update tests, move properties, update operation loader

* update wip

* remove test

* fixing tests, adding config

* update config and provider loader

* fix bundles

* fix cache settings on tests

* version bump and change log

* version bump

* fix formatting

* CVE-2022-45868

* wip cve change

* cve h2 add back in

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>

* bulkExportReuse with POST and GET (#5161)

* string manipulation

* Code to ensure bulkExportReuse works with POST and GET requests

* Added formatting changes

* Fixed tests that were not working

* Formatting

* Code clean up

* fixing test failures

* fixing test failures

* Removed arrOfParams to now utilize ObjectMapper

* Removing stack trace and adding an exception

* Fixed test issue

* formatting

* formatting

* Resolving code review comments

* Reduce size of subscription max results (#5194)

* Reduce MAX_SUBSCRIPTION_RESULTS to 10000

* Add changelog

* 5037 goldenresource remains when target resource deleted (#5038)

* draft test and fix

* remove unused fields

* remove unused fields

* remove unused fields

* draft test + solution for possible match case

* combine sql statement + more error checking

* add test case for possible duplicate

* add config for autodeleting grs

* refactoring, adding support for mongo, docs

* refactoring + fixing mongo queries

* add changelogs

* fix both way link removal

* clean up test comments

* rename method

* remove unnecessary bean

* merge master/resolve conflicts

* mvn spotless

* address comment

* changes to avoid version bumping

* spotless

* change error code

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* dont use new API for a bit (#5190)

* licenses

* Fixing terminology upload with large file. (#5204)

* create initial test

* adding fix;
adding changelog;

* fixing format.

---------

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

* up version to 6.8.0 from snapshot

* fix up some duplicate deps for skipping

* Force deployment of other projects

* make dummy java class to pass sonatype checks

* make dummy java class to pass sonatype checks

* Cheeky test removal

* Another test removal

* Updating version to: 6.8.1 post release.

* adding back in tests for release pipelines

* Fix bad version insert

* Bump to core library version 6.0.22.2 (#5261)

* Bump to core library version 6.0.22.2

* Bump HAPI to 6.8.1-SNAPSHOT, core library version to 6.0.22.2

* up version to 6.8.1

* Prevent remote deployment

* Updating version to: 6.8.2 post release.

* Re-add deploy plugin skip

* re-add version

* Bump core library version to 6.0.22.2

* Bump HAPI to 6.8.2-SNAPSHOT

* Fix up version enum

* Version bump

* Updating version to: 6.8.3 post release.

* mvn spotless:apply

---------

Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
2023-09-13 14:21:38 -07:00
James Agnew 7ecc0e66c8
Fix timeout in large $everything operation (#5298)
* Fixes

* Changelog

* Spotless

* Compress data file

* Remove fixme

* Fix imports

* Test fix

* Compile fix

* Apply spotless

* Address review comments
2023-09-13 21:08:00 +00:00
James Agnew 564beb7211
Allow absolute links for refs with an identifier (#5295)
* Allow absolute links for refs with an identifier

* Add changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5295-fix-absolute-refs-with-identifier.yaml

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>

* Remove redundant class

* Review comments

---------

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
2023-09-13 09:55:02 +00:00
TipzCM f97eadadc6
rebuild golden resource from survivorship on link edit (#5250)
* adding rebuilding option for survivorship

* rebuild survivorship resources

* cleanup

* configuring beans

* fixing tests

* cleanup

* spotless

* import fixing

* cleaning up

* fixing tests

* fixing tests

* version bump

* undo change

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-09-12 23:03:24 -04:00
James Agnew 2da8aafad0
Add support for _lanugage SP (#5300)
* Add support for _lanugage SP

* Add changelog

* Formatting fix

* Add to JPA

* Add validator

* Validate language SP

* Assign new code

* Fixes
2023-09-13 00:35:17 +00:00
volodymyr-korzh fe8c6c066e
SearchBuilder should not allow $everything operation to follow links to Group or List resources (#5283)
* SearchBuilder should not allow $everything operation to follow links to Group or List resources - tests

* SearchBuilder should not allow $everything operation to follow links to Group or List resources - implementation

* SearchBuilder should not allow $everything operation to follow links to Group or List resources - spotless check fix and changelog added

* Add a new permission: FHIR_OP_PATIENT_EVERYTHING_ACCESS_ALL for $everything operation - fixes

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

* MongoIncludeSvc should not allow $everything operation to follow links to Group or List resources - fixes

* MongoIncludeSvc should not allow $everything operation to follow links to Group or List resources - fixes

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-09-12 10:39:53 -07:00
James Agnew 03ebabad5b
Several IPS fixes (#5297)
* Several IPS fixes

* One more fix

* Fix

* Fixes

* med fixes

* Null safety
2023-09-12 11:41:33 -04:00
James Agnew 5a88b505d0
Upgrade Thymeleaf (#5239)
* Upgrade Thymeleaf

* Apply spotless

* Version bump

* Test fix
2023-09-09 09:42:29 -04:00
Kevin Dougan SmileCDR b8fcba0d45
Added changelog for 2023. (#5281) 2023-09-08 14:25:35 +00:00
Tadgh 57f6a705a5
Fix NPE in MDM post-mdm-clear on UPDATE operations. (#3851)
* Fix bug, imlpementation, changelog

* wip

* wip

* wip

* Add test

* wip

* wip
2023-09-07 22:51:12 +00:00
James Agnew a676506fc5
Improve terminology validation error messages (#5271)
* Improve terminology validation error messages

* Changelog

* Validation issues

* Test fixes

* Cleanup

* Review comments

* Fix
2023-09-07 08:52:38 -04:00
StevenXLi 3e46f71542
5276 the graphql request results in an http 400 error (#5278)
* fixed issue, added test

* added change logs

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-09-06 20:34:37 +00:00
Kevin Dougan SmileCDR 650fbe541c
Fixed HFQL Section name. (#5279) 2023-09-06 20:34:20 +00:00
jdar8 d563b97ad8
5242 mdm clear doesn't expunge redirected golden resource (#5245)
* fix + test

* changelog

* spotless

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-09-06 11:43:14 -04:00
Emre Dincturk 862c0487f6
5259 sorted tags, security labels and profiles (#5260)
* 5259 sorted tags, security labels and profiles

* fixed typos and augmented a test case for sorter
2023-09-01 11:12:26 -07:00
TynerGjs 33be707238
Added RequestDetails as part of the parameters to cleaning up possible matches to enable interceptors to MdmStorageInterceptor.cleanUpPossibleMatches (#5257)
access it
2023-09-01 10:22:43 -07:00
Tadgh 5f5b3db4a1
Fix, test changelog (#5266) 2023-08-31 14:58:28 -04:00
Nathan Doef cc283b7732
Respect response status code set in MethodOutcome of a Resource provider (#5267)
* failing test

* fix

* extract response code modifying resource provider for testing

* comment

* remove TestResponseCodeModifyingPatientProvider
2023-08-31 14:08:45 -04:00
jdar8 f38df4b91a
doc change (#5248)
Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-08-30 16:10:54 -07:00
StevenXLi cd0f6d16cd
5246 bulk export merge steps (#5247)
* added failing test

* added the new step, replace existing steps

* added changelog

* fixed check style

* changed the error code

* added back the bean definition for ExpandResourcesStep, to keep test from erroring

* code review fix

* fixed placement

* mirrored the implementation in the test

* added null check

* code review change

* style fix

* missed reverts

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-08-30 12:58:47 -07:00
LalithE 293f02ad7c
Fix to Bulk Export Enabled Disrupts Custom Resource Addition (#5255)
* Required change to fix bug editing test case currently

* Solution and unit test

* Adding changelogs

* adding coverage for registerCustomTypes

* Fixing test cases, using same context for two tests messed it up
2023-08-29 17:16:01 -06:00
Etienne Poirier fb3e141c4d
Messages submitted to the subscription pipeline are lost when submission fails. (#4733)
* One more fix for #4467

* Enabling massIngestionMode causes incomplete resource deletion (#4476)

* Adding initial test.

* Adding fix and subsequent test.

* Adding changelog.

---------

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

* Provide the capability to request that the name of the subscription matching channel be unqualified (#4464)

* Adding initial test.

* Adding initial solution implementation.

* Adding change log and code clean up.

* addressing comments from 1st code review.

---------

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

* Change visibility of migration method (#4471)

* change migration visibility

* add empty migration method for 640

---------

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484)

* First commit:  Make SubscriptionValidatingInterceptor aware of which Pointcut is being called.  In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED.   Fix resulting compile errors in various unit tests.

* Fix/enhance unit tests.  Mark methods as deprecated instead of deleting them.  Add proper error code.  Complete changelog.

* Remove erroneous TODOs and tweak the validation logic.

* Enhance unit tests and fix changelog.

* Reindex batch job fails when processing deleted resources. (#4482)

* adding changelog.

* Providing solution and adding changelog.

* Adding new test.

---------

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

* cleaning up checkstyle files (#4470)

* cleaning up checkstyle files

* One more fix for #4467 (#4469)

* added exlusions for files at base project level so checkstyle doesn't error out

* duplicate error code from merge

* changing lifecycle goal for all module checkstyle check

* moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code

* wip

* trying to figure out why pipeline cannot copy files

* removing modules that don't actually need to be built.

* I messed up the version

---------

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

* Bump core to 5.6.881 (#4496)

* Bump core to 5.6.881-SNAPSHOT

* Work on fixing tests

* Work on fixing tests 2

* Bump to core release

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>

* Issue 4486 mdm inconsistent possible match score values (#4487)

* Extract method for readability

* Save always normalized score values in POSSIBLE_MATCH links.

* Avoid setting properties to null values. Adjust test.

* Simplify fix

* Fix test. Add RangeTestHelper.

---------

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

* Revert "cleaning up checkstyle files (#4470)"

This reverts commit efae3b5d5f.

* core version fix

* Loosen rules for id helper

* initial test implementation/changes and solution wiring.

* adding support for jpa/mongo abstraction.

* refact completed.  need to start implementing scheduling of subscription re-submission with the scheduler service.

* post release, merging in master.

* wip: commit before merging in branch master.

* wip: resuming work on the issue.

* wip: before merging in master.

* wip: partial implementation of mongo support.

* wip: more work to support partial implementation on mongo.

* Test implementation

* providing method getMessageKeyOrDefault();

* providing changelog

* preping codereview.

* wip: passing tests

* wip: finally solving the Meta issue.

* wip: adjusting interfaces

* Adding IT and

* IT test;
fixing rollback issue.

* removing non required logging

* fixing merge conflict

* Preparing for code review.

* Preparing for code review.

* Compiling code after merging in master.

* Fixing checkstyle failure.

* Modifications towards getting all tests to pass.

* addressing comments from code review.

* compiling code after switching target merge branch to rel_pub_2023_05

* compiling code after switching target merge branch to rel_6_6

* Addressing comments made in design meeting.  wip.

* Addressing comments made in design meeting. finally completed.
and last 2 comments addressed.

* removing non required override

* reverting changes as they are not required.

* Modified test and implementation.

* implementation of a SynchronousSubscriptionMatcherInterceptor to submit modifiedResources to the subscription pipeline for testing only.

* fix tests by modifying the matchingInterceptor to call pointcut when processing

* fixing more tests.

* WIP to pass all tests in jpaserer-4504-a-resource-submitted-to-the-subscription-pipeline-is-lost-when-the-pipeline-encounters-an-issue

* fixing circular dependency

* Adding import dependency to class TestSubscriptionSubmitterConfig to allow submission of messages with the SynchronousSubscriptionMatcherInterceptor.

* bumping version 6.7.7-SNAPSHOT

* bumping HAPI version to 6.7.7-SNAPSHOT

* fixing tests failure caused by asynch deliver of resourceModifiedMsg to the processing pipeline.

* passing all tests.

* unbumping to 6.7.7

* compiling after merging in master.

* creating a custom hapi version

* providing an synchronous subscription matcher interceptor for testing.

* updating pom version to generate artifacts.

* fixing tests, WIP/0

* fixing tests, WIP/1

* fixing tests, WIP/2

* Matching entity annotation with migration task declarations.

* Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage.

* Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage.

* Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc].

* Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc] again.

* Removing creation of new transaction to inflate PersistedRresourceModifiedMessages since it is already executing in a transaction.

* bumping to version 6.7.14-ASYNC-SNAPSHOT for pipeline.

* bumping hapi version to 6.7.14-ASYNC-SNAPSHOT for pipeline.

* Formatter changes.

* add generic

* add generic

* Addressing code review comments.

* Adding file asynch_subscription_610.md to docs/upgrades

* changing poms to 6.9.2-SNAPSHOT before merging in master.

* compiling after merging in master.

* Lowering logging level to debug.

* Bumping to 6.9.3-SNAPSHOT

* Bumping hapi version to 6.9.4-SNAPSHOT

* Adding update documentation.

* Modifying update file following review.

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: dotasek <dotasek.dev@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-08-28 12:47:53 -04:00
jdar8 6a7340a879
5231 MDM Link History gives 404 after MDM clear and submit (#5232)
* fix + tests

* remove comments

* docs + changelog

* spotless

* edit changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-08-25 15:59:44 -04:00
TipzCM 318b68ee0c
5192 include in search empty page results (#5211)
Fixing paging with _include query parameter
2023-08-24 16:36:31 +00:00
Emre Dincturk 8d39e3466c
cast errorcount to string for batchjob failure message (#5230) (#5233)
Co-authored-by: Emre Dincturk <emre.dincturk@smilecdr.com>
2023-08-24 10:41:01 -04:00
Ken Stevens deeffe2253
fix some race conditions (#5220)
* fix memory leak

* race condition fixes and change log

* race condition fixes and change log
2023-08-21 17:27:44 +00:00
Ken Stevens b9155721a7
fix batch2 npe when no results returned (#5219)
* fix npe error

* spotless

* spotless
2023-08-20 00:37:16 +00:00
James Agnew 1e45506526
Improve ID filtering (#5215)
* Improve ID filtering

* Formatting

* Add license header

* Address review comments
2023-08-18 16:30:00 +00:00
VK-SMILECDR 3512f82a6d
fix the issue (#5214) 2023-08-17 18:01:50 +00:00
TipzCM fdfda37f73
5198 fixing searching everything op (#5201)
* fixing searches

* fixing paging in master

* cleanup

* Fixing the tests

* fixing tests

* fixing test

* cleanup

* fixing

* removing unneeded class

* adding a changelog and cleaning some final details

* code styles

* cleaning up imports

* review notes

* formatting

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-08-17 15:42:06 +00:00
Tadgh a10856e091
GM1 Mergeback (#5203)
* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

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

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* Rename file to force IT mode

* _source search parameter needs to support modifiers (#5095)

_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers

* Fix HFQL docs (#5151)

* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)

* Initial failing test.

* Solution with changelog.

* fixing format.

* Addressing comment from code review.

* fixing failing test.

---------

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

* documentation update (#5154)

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

* Fix hsql jdbc driver deps (#5168)

Avoid non-included classes in jdbc driver dependencies.

* $delete-expunge over 10k resources will now delete all resources (#5144)

* First commit with very rough fix and unit test.

* Refinements to ResourceIdListStep and Batch2DaoSvcImpl.  Make LoadIdsStepTest pass.   Enhance Batch2DaoSvcImplTest.

* Spotless

* Fix checkstyle errors.

* Fix test failures.

* Minor refactoring.  New unit test.  Finalize changelist.

* Spotless fix.

* Delete now useless code from unit test.

* Delete more useless code.

* Test pre-commit hook

* More spotless fixes.

* Address most code review feedback.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Fix the noUrl case by passing an unlimited Pegeable instead.  Effectively stop using page size for most databases.

* Deprecate the old method and have it call the new one by default.

* updating documentation (#5170)

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

* _source search parameter modifiers for Subscription matching (#5159)

* _source search parameter modifiers for Subscription matching - test, implementation and changelog

* Removal of meta tags during updates do not trigger subscription (#5181)

* Initial failing test.

* adding solution;
fixing documentation;

* spotless apply

* adding changelog

* modifying current test

---------

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

* Issue 5173 get gateway everything doesnt return all patients (#5174)

* Failing test

* Also set offset and count in base DAO override

* Changelog

* Fix for specific case where count has been set in parameters

* spotless

* Improve checks

---------

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

* Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175)

* First commit with failing unit test and small tweaks.

* Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead.  Add more detailed unit testing.

* Tweaks to logic and update the changelog.  Reverse all changes to TermReadSvcImpl.

* Revert PackageResourceParsingSvc to release branch baseline.

* Accept code reviewer suggestion to change changelog description.

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

---------

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

* Fix link

* Remove target slf4j version

* dont use new API for a bit (#5191)

* Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193)

DropIdGeneratorTask.

* Dqm performance bug update and provider loader fix (#5180)

* update tests, move properties, update operation loader

* update wip

* remove test

* fixing tests, adding config

* update config and provider loader

* fix bundles

* fix cache settings on tests

* version bump and change log

* version bump

* fix formatting

* CVE-2022-45868

* wip cve change

* cve h2 add back in

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>

* bulkExportReuse with POST and GET (#5161)

* string manipulation

* Code to ensure bulkExportReuse works with POST and GET requests

* Added formatting changes

* Fixed tests that were not working

* Formatting

* Code clean up

* fixing test failures

* fixing test failures

* Removed arrOfParams to now utilize ObjectMapper

* Removing stack trace and adding an exception

* Fixed test issue

* formatting

* formatting

* Resolving code review comments

* Reduce size of subscription max results (#5194)

* Reduce MAX_SUBSCRIPTION_RESULTS to 10000

* Add changelog

* 5037 goldenresource remains when target resource deleted (#5038)

* draft test and fix

* remove unused fields

* remove unused fields

* remove unused fields

* draft test + solution for possible match case

* combine sql statement + more error checking

* add test case for possible duplicate

* add config for autodeleting grs

* refactoring, adding support for mongo, docs

* refactoring + fixing mongo queries

* add changelogs

* fix both way link removal

* clean up test comments

* rename method

* remove unnecessary bean

* merge master/resolve conflicts

* mvn spotless

* address comment

* changes to avoid version bumping

* spotless

* change error code

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* dont use new API for a bit (#5190)

* licenses

* wip

* Fix API usage

* wip

* Version bump

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
2023-08-15 12:32:10 -07:00
TynerGjs f2087d2ccc
added validateExpungeEnabled() call to type-level expunge, moved two … (#5197)
* added validateExpungeEnabled() call to type-level expunge, moved two overloading method so that they are next to each other

* added test for expunge
enabled expunge for testExpungeAllVersionsWithTagsDeletesRow in FhirResourceDaoR4QueryCountTest

* added changelog

* optimized tests and changelogs
2023-08-14 10:04:07 -04:00
jdar8 de9a747666
MDM operation to return total number of Possible Duplicates (#5130)
* addition, test, changelog

* update changelog

* address review comment + add test for coverage

* remove unnecessary space + changes

* mvn spotless

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-08-04 16:24:01 -04:00
TipzCM a48c602f71
adding pointcuts for mdm operations (#5116)
* adding pointcuts for mdm operations

* adding changelog

* cleanup

* cleaning up

* formatting

* review fixes

* formatting

* more cleanup

* cleanup

* moving changelog

* fixing a bug

* cleanup

* formatting

* version bump

* fixing broken merge

* fixing the version

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-08-02 16:38:33 -04:00
TipzCM fd5c2c2862
all updated resources to link to existing resources (#5152)
updating mdm resources will update all links to them as well as any links that it would match after update
2023-08-02 16:29:17 +00:00
Tadgh 5eda18f500
Mergeback of rel_6_8 (#5146)
* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

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

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* Rename file to force IT mode

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-07-30 22:28:26 +00:00
James Agnew 2b91f0a232
Version bump HAPI FHIR and a couple of deps (#5121)
* Version bumps

* Version bump HAPI

* Add enum for next release

* Changelog update

* HAPI version bump
2023-07-28 09:46:01 -04:00
Ken Stevens b376778b99
change mdm interceptor loader to fail when message subscription types… (#5128)
* change mdm interceptor loader to fail when message subscription types aren't enabled.

* cleanup

* cleanup

* fix tests

* cleanup

* spotless

* fix test

* fix test

* changelog

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-07-27 10:39:32 -04:00
Tadgh dcf3240191
Proper version bump (#5135)
* Fix version

* Fix version enum
2023-07-26 18:53:15 +00:00
James Agnew e14bbec83b
IPS Connectathon Fixes (#4834)
* IPS Connectathon Fixes

* Fix changelog

* Cleanup
2023-07-24 19:32:42 +00:00
Tadgh 53ceb7cac4
Bump to nov (#5120)
* bump version, make new folders

* Fix typo in versionenum
2023-07-24 08:49:40 -07:00
James Agnew 6d745b4f2d
Initial HFQL SQL Implementation (#5083)
* FQL tests

* Working so far

* Tests working

* Tests passing

* Work on parser

* Tests passing

* Cleanup

* Working

* Work on parser

* Work

* Working

* Work on tests

* Work on driver

* Work

* Ongoing work

* Rename SEARCH to WHERE

* Work on fhirpath

* Test fixes

* Work on statements

* Build fixes

* Spotless application

* Fix CI

* Build fixes

* Clean up changelogs

* Remove redundant gitignore

* Add docs

* Add docs

* Code cleanup

* Build cleanup

* Fix compile error

* Test fixes

* Test fix

* Test fix

* Work on integration

* Work on design

* Work on UI

* Update hapi-fhir-jpaserver-hfql/src/main/java/ca/uhn/fhir/jpa/fql/jdbc/JdbcDriver.java

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

* Address review comments

* Review comments

* HFQL work

* Cleanup

* CLeanup

* License headers

* Test fixes

* HAPI version bump

* License header update

* Changelog cleanup

* Fixes

* Test fix

* Fix spotless issues

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-07-21 22:51:23 +00:00
TynerGjs f68f3fbb0f
Resolve 5112 unable to expunge deleted codesystem until several minutes later (#5113)
* returned user-friendlier message, implemented unit tests, added changelog

* reformatted file

* added Msg.code to the exception thrown

* added Msg.code in test

* Changed to catch DataIntegrityViolationException only.
2023-07-21 17:08:58 +00:00
James Agnew d31da211b9
Fix openapi for R5 (#5115)
* Fix openapi for R5

* Add changelog
2023-07-21 08:17:13 -07:00
Steve Corbett 66f428d356
5103 - Adjust our handling of space escape characters in URLs (#5104)
* 5103 - Adjust our handling of space escape characters in URLs

* 5103 - Fix formatting

* 5103 - Adjust URL escaping and update test expectations

* 5103 - additional test for values with literal plus signs

* 5103 add changelog for this issue

* 5103 - documentation change to describe proper URL escaping

* 5103 - Minor documentation addition
2023-07-20 14:14:28 -06:00
jdar8 e02468b552
5080 new similarity algorithm to handle numeric normalization (#5082)
* solution

* test

* docs + changelog

* fix formatting

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-07-20 13:20:51 -04:00
LalithE 2fbd3fa272
Lowering the logging severity level from info to debug for specific services (#4948)
* Changed the two files to reduce info level to debug level for select services.

* Adding change log

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-07-20 10:52:11 -04:00
jdar8 675699a177
5092 results ordering for mdm link history is incorrect (#5093)
* update docs to be more specific

* fix ordering when client assigned id doesn't match pid

* remove fix ordering when client assigned id doesn't match pid

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-07-19 16:57:21 -04:00
jmarchionatto cd3c4d2076
Issue 5102 mdm link history ordering is incorrect when client assigned id and pid are different (#5105)
* Failing test

* Add some self-assigned Patient IDs

* Sort after client-selected ID is interpolated into the result

* spotless

* changelog

* Keep DAO level ordering enforced by tests

* Filter out non-client-provider ids from test as they are unpredictable in build pipeline

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-07-19 15:35:51 -04:00
TipzCM cf8c70994f
fixing bug in findcandidatebyexamplesvc (#5101)
* fixing build

* cleanup

* review fix

* review changes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-07-19 08:26:05 -04:00
TipzCM 2401b2339e
fixing a bug with duplicte golden resources being returned (#5085)
* fixing a bug with duplicte golden resources being returned

* review points

* fixing tests

* blah

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-07-13 19:58:27 +00:00
TipzCM 906355dd65
adding block list for mdm (#5059)
* using any/exact enum

* bluck rule evaluation svc

* adding blocklist

* adding documentation

* cleanup

* adding mdm blocking service and code cleanup

* review points

* another review point

* review points

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-07-13 13:59:02 +00:00
Luke deGruchy 43694f378c
Ensure FhirContext loads custom resources in the list of resource names (#5073)
* Fix bug by maintaining a separate list of resource types including the custom resources that will be used to validate the Bundle resources.

* Add custom resource types to resource types list and add conditional logic in ValidationDataInitializerSvcImpl to ensure there is no Exception when parsing a custom resource type.

* Add changelog.

* Remove unnecessary change.

* Address code review feedback.

* Address code review feedback.

* Add one more unit test.

* Bump to 6.7.14-SNAPSHOT.
2023-07-12 14:32:09 +00:00
Tadgh 52f3ef5992
New formatting rules and pre-commit hooks (#5027)
* pre-apply spotless

* New pre-format checkpoint

* Once-over the repository

* Add pre-commit hook

* New github action

* excludes

* Revert "Once-over the repository"

This reverts commit 89334ba8d1.

* Once-over the repo

* do not inherit

* Revert "Once-over the repo"

This reverts commit 31ed8731ad.

* Add baisc license support to spotless

* Move license

* Fix inclusions

* Fix inclusions

* Fix licensing

* license fixes

* Remove dead file that is only a license

* Remove dead class

* remove dead file

* Tighten licensing

* Tighten licensing

* Tighten licensing

* Tighten licensing

* Remove specific package

* Make the precommit hook executable

* Fix ordering

* rollback license

* wip

* Add to deployable pom

* remove file

* Fix location

* Remove dead comment

* wipP

* Fix ratchet

* Fix up error

* Add pre-commit

* precommit fixes

* wip

* wip

* Autoformat

* remove dead pom parts

* replace internal hook with pre-commit

* Fix fetch-depth for checker action

* Remove ratchet and filter

* fix up

* rename

* Add comment check

* rework message

* First once-over of the repo

* wip

* format
2023-07-11 17:36:44 -07:00
Tadgh 1ce2043dcd
Add JPA_PERFTRACE_INFO invocation to Fulltext Searches (#5072)
* Changelog

* basic test

* Api change for fulltext, add test

* Add javadocs

* Refactor to use a simpler method

* Review comments
2023-07-11 20:32:02 +00:00
Brenin Rhodes eb06b473b9
Update version of the Clinical Reasoning module (#5045)
* Update version of the Clinical Reasoning module

* cleanup

* Add changelog

* Update snapshot

* Inc version
2023-07-07 10:05:10 -04:00
Steve Corbett 10af1434fc
Delete expunge fails with identical update timestamps (#5047)
* 4759 - WIP unit test for this issue

* WIP updating unit test for ResourceIdListStep

* WIP candidate fix for ResourceIdListStep batch size problem

* Enhance unit test with ArgumentCaptor.

* WIP Parameterized the ResourceIdListStepTest and added assertions

* Adding changelog for this issue

* Updating changelog message for 5055

* Code formatting and import cleanup

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
2023-07-06 11:59:56 -04:00
JasonRoberts-smile a87321a227
add instantiateBackboneElement method to TerserUtil (#5060)
* add instantiateBackboneElement method to TerserUtil

* changelog
2023-07-05 21:57:19 +00:00
James Agnew a93d06c25f
Restrict bulk export download to specific user (#5052)
* Work

* Bulk export partitioning fixes

* Changelog fixes

* cleanup

* Work on security

* Compile fixes

* Work

* Test fix

* Work

* Add changelog

* License header changes

* Test fix

* Test fix

* Fixes

* Version bump

* Test fix

* Fix accidental change
2023-07-05 12:48:15 -04:00
Ken Stevens 9a6288c363
fix hapi paging regression (#5057)
* fix regression

* change log

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-07-04 18:43:43 +00:00
Yusuf Daniju 39ee86d0fe
fix: typo in 'opposed' (#5051) 2023-07-02 15:48:20 -04:00
Tadgh a73b74869d
5014 only positive ints (#5050)
* limit ints, add test and changelog

* changelog
2023-07-01 17:02:52 +00:00
Luke deGruchy ad71755c2b
Resolve 5029 Token params with system and value longer than maximum length should be created and searched differently (#4998)
* Partial implementation after this has been paused:  Move trimming of value and system from BaseSearchParamExtractor to ResourceIndexedSearchParamToken.  Do not throw Exceptions in TokenPredicateBuilder.  Ensure that the hash computing in the search param token takes the 200+ token value into account.  Other search param tokens are not yet implemented.

* in ResourceIndexedSearchParamToken,changed hardcoded length to constant MAX_LENGTH;
in BaseSearchParamExtractor, added check in createTokenIndexIfNotBlank so that the return value is null if system or value is blank.

* added test for TokenPredicateBuilder to verify that long values exceeds the max length does not cause exception.

added test in FhirSystemDaoR4SearchTest to verify searchParamToken with longer system and value than max length can be created successfully. And hash value will be calculated before truncation

* fixed a logical error in previous commits

* changed existing tests to accommodate for the changes

* modified existing tests

* added changelog

* changed truncation method name and added comments

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

* modified changelog

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

* combined redundant tests

---------

Co-authored-by: tyner <tyner.guo@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-06-30 10:48:33 -04:00
volodymyr-korzh 93a41559b5
Reindex Batch Jobs stuck in QUEUED status after SearchParameter update (#5043)
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - test added

* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix

* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix test

* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - send BatchJobWorkNotification after commit

* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - changelog fix

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

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-06-29 14:29:37 -04:00
James Agnew 6e0651e261
Bulk export partitioning fixes (#5039)
* Work

* Bulk export partitioning fixes

* Changelog fixes

* cleanup

* Compile fixes

* Test fix

* Add JIRA note

* Version bump

* Drop unneeded tag
2023-06-29 08:34:32 -04:00
jmarchionatto ed04dd2498
Issue 5004 make bundleutil also accept name prev for previous links (#5042)
* Add test

* Fix

* Changelog

* Small details to reset build pipe

* Reformat

* Make definition animal-sniffer (check-android-26-compliance) compliant

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-06-28 15:46:54 -04:00
TipzCM ce04e897cf
5033 fk indexing round2 (#5040)
* updated query to find more results and be simpler

* updating query in fhir

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-28 15:37:45 -04:00
jmarchionatto 17eeb07c58
Issue 5032 gateway pagination throws NPE when targets use usehttppostforallsearches true (#5036)
* Allow PageMethodBinding to bind also for POST

* Add changelog

* Adjust test

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-06-28 12:58:51 -04:00
Tadgh 9fb718820d
Complete change, changelog, test (#5035)
* Complete change, changelog, test

* whitespace

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

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

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-06-28 14:14:22 +00:00
StevenXLi 73d6997d21
fixed batch jobs on Postgres (#5022)
* fixed issue

* fixed pipeline issue

* review changes

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-06-23 09:06:38 -04:00
volodymyr-korzh 1f44ac1092
GenericClient POST paging support (#5013)
* GenericClient POST paging support - implementation and test

* GenericClient POST paging support - fixes

* GenericClient POST paging support - fixes

* GenericClient POST paging support - failed tests fix

* GenericClient POST paging support - HAPI version bump
2023-06-22 15:28:47 -04:00
LalithE a59eb1ace3
Partitioning: creating two partitions with the same ID overwrites the first (#5012)
* Added unit test and bug fix to ensure no two partitions with the same ID can be created.

* Added changelogs, and changed the equals operator.

* Made required changes to ensure updating of partition is not affected

* Changed unit test and its location to ensure functionality.

* changing for loop to findById to avoid iteration over all partitions.

* Only allows findById when list is not empty, deals with that edge case.

* Replaced null with isPresent in if statement to fix issues regarding the creation of links on different partitions

* Removed the findAll command within the function. To avoid searching twice.

* Edited the changelogs to properly describe the issue that we have at hand

* Edited the changelogs to properly describe the issue that we have at hand pt 2, wording changes.
2023-06-22 11:23:39 -04:00
TipzCM d7bdabb91b
nickname svc refatoring (#5006)
* nickname svc refatoring

* moving things around

* cleanup

* gitignore

* removing factory

* added changelog

* version bump

* fixing test

* fix test

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-22 08:26:47 -04:00
Tadgh 20a9ad0985
Make Partition ID non-mandatory during partition creation. (#5016)
* closes #5014, fix, changelog, docs

* documentationf fixes

* checkstyle fix
2023-06-21 21:19:12 -04:00
James Agnew ddf3b72f2d
Encode non-resource types (#5003)
* Encode non-resource types

* Add changelog

* Compile fix
2023-06-21 13:02:40 -04:00
jdar8 ee3c59a3bc
4968 mdm throws nonsensical error when updating resources after mdm clear (#4975)
* log specific error message + test

* changelog

* remove draft tests

* remove another comment i left behind

* update issue number in changelog

* update error location

* update error location

* update test

* change to exception

* address review comments: add test with submit and also update change log

* format test nicer

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-06-20 14:41:22 -04:00
Ken Stevens 8eec285611
revinclude order (#5009)
* start building tests

* add test

* merge master

* fix bug

* fix regression

* changelog

* documentation

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-06-20 07:54:20 -04:00
TynerGjs ac9eaf9d89
4959 loadsynchronousupto will affect searchforids when set to small value (#4966)
* Implemented fixes, created test for JPA side

* Added test and getter for test for register listener

* refactored test names to make them more descriptive

* Modified tests

* resolved comments

* created changlog

* changed test to use MAX_MANAGED_PARAM_COUNT, and created the corresponding getter
2023-06-19 09:54:39 -04:00
volodymyr-korzh 6296884583
Error when expanding task code ValueSet resource (#4974)
* Error when expanding task-code ValueSet resource - tests

* Error when expanding task-code ValueSet resource - fix valuesets.xml for R4 and R4B

* Error when expanding task-code ValueSet resource - throw exception in case of Not found CodeSystem

* Error when expanding task-code ValueSet resource - added changelog

* Error when expanding task-code ValueSet resource - fixed changelog

* Error when expanding task-code ValueSet resource - fixes

* Error when expanding task-code ValueSet resource - fixes

* Error when expanding task-code ValueSet resource - fixes and tests

* Error when expanding task-code ValueSet resource - added tests for TermCodeSystemVersionDao methods

* Error when expanding task-code ValueSet resource - added comments to valuesets.xml

* Error when expanding task-code ValueSet resource - test fixes
2023-06-19 09:31:05 -04:00
Tadgh a544a546ec
Raw sql revincludes (#5001)
* start building tests

* add test

* Basic test and fix bug

* remove tests, fix existing test

* fix up tests

* fix up tests

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-06-17 05:52:10 -04:00
TipzCM 65ae1785e8
mdm-clear will now use batch-size parameter (#4985)
* using delete expunge service

* test fixing

* update version

* review points

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-15 20:32:21 -04:00
Luke deGruchy f79ac1992e
First commit: Patch bad implementation of RuleBulkExportImpl to fix … (#4986)
* First commit:  Patch bad implementation of RuleBulkExportImpl to fix this use case.

* Fix changelog.  Fix comments on unit tests.

* Fix TODO with correct issue number.
2023-06-15 15:34:00 +00:00
jmarchionatto 048c1f99bb
issue-4987-searchbundle-parts-are-labeled-by-default-as-include-instead-of-match (#4988)
* Default search mode to MATCH when creating SearchBundleEntryParts

* Add changelog

* Use enum name instead of explicit constant

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Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-06-15 10:03:45 -04:00
TipzCM c87ff96d5c
4976 adding indexes to foreign keys (#4980)
* adding test and initial migrations

* indexing and verifying foreign keys

* connection with resources

* fixing migration for oracle

* adding change log

* updates and cleanup

* cleanup

* fixing broken tests

* remove unique constraints

* debug code

* cleanup

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Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-14 13:20:53 +00:00