Commit Graph

9566 Commits

Author SHA1 Message Date
Kevin Dougan SmileCDR 6bd7f7a0e1
PackageInstallerSvcImpl Says R4 is NOT Compatible with R4B (#4396)
* 4395 - Make PackageInstallerSvcImpl equate FHIR version R4 with R4B.
2023-01-04 19:34:16 +00:00
alackerbauer 8d4514ce36
#4401 updated to latest ImmunizationStatusRoutine logic and test data (#4402)
Co-authored-by: Anna <anna.lin@smilecdr.com>
2023-01-04 17:16:54 +00:00
Ken Stevens b44334055a
fix build (#4393) 2022-12-24 11:40:34 -04:00
Vitor Pamplona f5133dd59c
Android compatibility checks (#4070)
* Adding plugin to investigate compatibility with Android APIs:
Run with:
- mvn animal-sniffer:check

* No need to declare woodstox here

* Moving the Android check to the Plugin Management and activating it in all projects being used on the platform: base + android + converter + structures + validation.

* Removing `List.of` and `Optional.isEmpty` for Android compatibility.

* Moving animal-sniffer to the CI profile.

* Adding Android check to structures-r4b as well

* Removing Xml-apis from Xerces to see if CI passes.

* Activating Android check in the client lib

* Moving Xerces to the base-lib, the only place needed for Animal Sniffer

* Applying Xerces as a dependency only on CI

* Removing xml-apis from shexjava
2022-12-23 14:23:36 -05:00
Tadgh f32bc8f67a
Add test and implementation to fix potential NPE in pre-show resources (#4388)
* Add test and implementation to fix potential NPE in pre-show resources

* add test

* WIP getting identical test scenario

* More robust solution

* Finalize Code

* Add changelog, move a bunch of changelogs

* Remove not needed test

* Minor refactor and reporting
2022-12-22 22:53:07 +00:00
Dimitri04 4637ea3ac3
update mdm documentation (#4322)
* update mdm documentation

* fixed typos

Co-authored-by: Dimitri Barker <dimitri.barker@smilecdr.com>
2022-12-22 14:56:07 -05:00
Qingyixia 51797c3c1e
Group bulk export _since parameter issue (#4389)
* Test + fix

* javadoc
2022-12-22 13:19:07 -05:00
Luke deGruchy e4ad370314
Remove duplicate dependency (MemberMatcherR4Helper) from JpaConfig that was present in both JpaConfig and JpaR4Config. (#4390)
* Remove duplicate dependency (MemberMatcherR4Helper) from JpaConfig that was present in both JpaConfig and JpaR4Config.

* Add back @Import for JpaConfig to JpaDstu2Config to resolve DSTU2 unit test issue in jpaserver-starter.
2022-12-22 13:12:30 -05:00
karneet1212 cfa6c13262
Add resource type as a parameter for $mdm-query-links (#4372)
* Added Solution + test

* Removed old methods

* fixed issues

* Added refactoring

* Deprecated methods on the interfaces

* Remove todo

* Documentation

* Changelog

* Changelog

* Changelog

* Changes made based on comments

* Changes made based on comments

* Clean up

* hapi bumping to version 6.3.6-SNAPSHOT

* hapi bumping to version 6.3.6-SNAPSHOT
2022-12-22 09:54:32 -05:00
Luke deGruchy 6e8db3626d
Add Device to the list of resource types considered for group bulk export async (#4384)
* Add Device to the list of resource types considered for group bulk export async. New unit test for bulk export.

* Add changelog.
2022-12-20 16:33:25 -05:00
James Agnew 0d5f8da93f
API improvements for MegaScale (#4112)
* Start work on sharded DB

* Work on migrating

* Work

* Ongoing work

* Ongoing work

* Work

* Work

* Ongoing work

* Work

* Work

* Test fix

* Test fix

* Work

* Compile fix

* Test cleanup

* Test fix

* Resolve fixmes

* Resolve fixme

* Resolve compile errors

* Compile fix

* Fixes

* Work

* Add note for later

* Test fix

* Test fixes

* Build fix

* Test fixes

* Fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fixes

* Fixes

* Remove dead code in pom

* More test cleanup

* Docs fix

* Changes

* Fix

* Fixes

* Resolve merge conflicts

* Build update

* Merge build fixes

* Version bump

* Address review comments

* Review comments

* Review comments

* Test fixes

* Test fix

* Cleanup
2022-12-20 12:05:15 -05:00
Kevin Dougan SmileCDR 155b579093
4000 - Added some comments to the various loincupload.properties files to clarify that the Hierarchy filename was changed for v2.73. (#4382) 2022-12-20 09:06:15 -05:00
Luke deGruchy fd94e16ee0
Enable or disable support for JSON fhir_comments depending on the release. Move HapiFhirStorageResponseCode.json to the module in which it's used (#4374)
* First draft of disabling JsonParser "fhir_comment" code.  Unit test assertion that JSON is not generated with "fhir_comment" in the resulting resource String.

* Surround fhir_comments logic with conditional logic.  Set this to false while awaiting final word from stakeholders.  Add unit tests for STU3 and STU2 proving that fhir_comments do not get generated.

* Add conditional logic for JsonParser and fhir_comments and adjust unit tests accordingly.  Also, move the HapiFhirStorageResponseCode.json file to the same module as DefaultProfileValidationSupport, namely, the code that actually reads it.

* Add changelog.

* Add missing change to JsonParser that I thought I had pushed.   Fix changelog.  Fix unit tests assertions to be clearer.

* JsonParser:  Cache value of isSupportsFhirComment.

* Support version DSTU2_1 as well and add a new unit test.

* Fix pipeline unit test failures.
2022-12-19 12:31:21 -05:00
michaelabuckley 81e313b02e
Log capture test helper cleanup (#4378)
* Only log PHI at debug or lower, even in tests.
* Log capture test helper cleanup
2022-12-19 14:47:51 +00:00
KGJ-software 58c6c86d56
3877 more tests (#4368)
* add tests

* add tests

* clean up test file

* device test

* Added more tests

* Clean up tests

Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2022-12-15 14:08:39 -05:00
karneet1212 0035677563
Add Payload Search Mode To Message Channel (#4325)
* Added possible solution - needs to be refined

* Small changes

* Refactoring

* Refactoring + Test

* Changelog

* Small edits to changelog

* Small changes

* Changes made based on comments

* Clean up

* Changes made based on comments

* Changes made based on comments

Co-authored-by: qingyixia <cherry.xia@smilecdr.com>
2022-12-15 09:46:10 -05:00
Nathan Doef 7b86eda8a9
Refactor Common SearchParameter Functionality (#4321)
* refactor checkpoint

* clean up

* add method to find runtime search param by id

* new search param cache tests

* extract SearchParameter validation functionality

* create common interface for combo searchparameters

* Remove ResourceTable from extractor interface

* clean up

* move SearchParameterDaoValidator

* resolve code review comments

* remove reflection

* change log

* bump version to 6.3.4-SNAPSHOT

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-12-15 06:46:45 -05:00
StevenXLi 29ebb950e8
4360 bulk export questionnaireresponses should get picked when author is not empty (#4361)
* added failing test

* implemented solution

* added more tests

* added changelog

* changed the implementation, now extended to get all the patient based search params for a given resource instead of 2 in a fixed list of resources

* added test for patient bulk export for resources not in patient compartment, fixed implementation to pass test

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-12-14 18:43:11 -05:00
Nathan Doef 360f32f3e4
fix index migration error (#4365)
* fix index migration error

* add exception to duplicateNameValidationExceptionList

* - change index name to match convention
- drop old index h2 automatically created

* Revert "- change index name to match convention"

This reverts commit 59f35a1891.

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-12-14 12:40:53 -05:00
Luke deGruchy 01b1074808
Fix MDM update link on resources with an old version. (#4362)
* Add a failing unit test if we update a link after the MDM version had been bumped.

* Fix bug with new MdmLinkFactory method:  newMdmLinkVersionless().  Call this new method from MdmLinkDaoSvc.getLinkByGoldenResourceAndSourceResource() only.   Think about other use cases for versionless MDM links.

* Replace all read uses of MdmLinkFactory with newMdmLinkVersionless().  Add detailed documentation about why to do this.

* Add changelog.  Reverse wildcard change.
2022-12-14 08:47:44 -08:00
Kevin Dougan SmileCDR c03129f545
4337 - Added a new Index on the HFJ_SEARCH_INCLUDE Table on (#4339)
* 4337 - Added a new Index on the HFJ_SEARCH_INCLUDE Table on SEARCH_PID Column. Also, added a migration task for the Index.

* 4337 - Renamed the new DB Index to keep it to 30 chars.
2022-12-12 16:00:11 -05:00
Vitor Pamplona d70c7bba8c
Upgrading Jackson to 2.14.1 (#4308) 2022-12-12 08:19:03 -08:00
jmarchionatto 8307264330
Add score to MDM links which match multiple candidates (#4329)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-12-12 10:09:49 -05:00
Tadgh daaa92fdbc
4350 ap sa and eb prefixes are not handled correctly (#4358)
* Add test and implementation

* Add changelog
2022-12-11 18:19:54 -05:00
James Agnew 7747ebae41
Combine postconstruct methods (#4330)
* Combine postconstruct methods

* Add changelog
2022-12-11 18:02:04 +00:00
JasonRoberts-smile 3b987d6961
move deleteExpunge up in the hierarchy (#4357) 2022-12-10 14:25:43 -05:00
JP 7e6196ade0
Add missing artifacts to hapi-fhir-bom project. (#4355)
Sort bom file alphabetically to make it easier to maintain.
Resolves #4354
2022-12-09 22:02:21 +00:00
JasonRoberts-smile 9c388279a6
allow mongo implementation of IDeleteExpungeSvc (#4352) 2022-12-09 13:23:46 -05:00
VK-SMILECDR c6733b1111
system property cleanup; added missing tests; (#4342) 2022-12-09 09:43:04 -05:00
kateryna-mironova 017cc4e29c
4244 - Deprecate usages of ResourcePersitentId in jpa (#4245)
* init rev

* id to jpa and mongo id

* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods

* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods

* fixed conflicts, pulled from master

* fixed code for passing tests successfully

* changed PersistentId to Jpa in MdmSearchInterceptor

* added the todo comments with questions

* added one more question

* renamed TODO questions

* first pass at converting to generic ResourcePersistentId

* fix test

* fix test

* fix test

* make ResourcePersistentId abstract

* Generic type MdmLink

* Final TODOs

* Final TODOs

* cleanup

* fix test

* fix id to string

* fix cyclic package dep

* add <?> to Base so we can extract interface

* Revert "add <?> to Base so we can extract interface"

This reverts commit a806f3d2bc.

* switch to interface

* javadoc

* replace base with interface

* fix test

* add generic template to mdmdao

* remove unneccessary JpaPid casts

* remove unneccessary JpaPid casts

* remove unneccessary JpaPid casts

* remove unneccessary MongoPid casts

* fix test

* fix regression

* fix compile issues arising from merging master

* fix beans

* bump version to 6.3.3-SNAPSHOT

* change logs

* review feedback

* review feedback

* fixme

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-12-09 09:30:51 -05:00
Nathan Doef d639a2a86d
meta.versionId Incremented After Update Operation With No Changes (DSTU 3) (#4349)
* Tests for R4 (passing) and DSTU3 (failing)

* Fix

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-12-08 20:26:49 -08:00
KGJ-software b8760cc022
add tests (#4340)
* add tests

* add tests

* clean up test file

* device test

Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2022-12-08 16:06:37 -08:00
granadaCoder 16b97bc6e7
Issue 4310 Fix. Add "distinct" and "sorted" to "Server knows how to handle" error message: (#4311)
* Add "distinct" and "sorted" to "Server knows how to handle" error message.

* Add code comments.  No functional changed.

* Add credit for #4311

Co-authored-by: shollid3 <sloan.h.holliday@optum.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-12-08 16:59:53 -05:00
jmarchionatto c7d991c345
Disallow matching a resource to more than one golden record (#4344)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-12-08 12:26:05 -05:00
Ken Stevens f4ce765122
IndexedSearchParamExtractor regression returned wrong number of links pre-persistence (#4341)
* fixed the issue

* change log

* fix regression

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-12-08 05:22:51 +00:00
StevenXLi 0e59665711
4312 add support for member identifier parameter return from $member match operation (#4314)
* added failing test

* implemented solution

* added change log

* removed special character in change log file name

* added check for member identifier of type MB

* changed msg code to latest

* fixed test for updated msg code

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-12-07 15:55:53 -05:00
dotasek 403016f846
Bump core version to 5.6.84 (#4326)
* WIP. Basic adjustment of r5 IWorkerContext to core refactor

* Replace FIXME with UnsupportedOperationException

* use fetchResource(class_, uri) instead of UnsupportedOperationException

* Fix breaking tests related to fetchResource

* Fix breaking validation test

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2022-12-07 11:26:33 -05:00
Etienne Poirier f13b247c74
4324 excessive amount of time required to update large group resources (#4332)
* Initial test.

* Solution implementation with test adjustment.

* Adding changelog.

* Modifications following first code review.

* Moving changelog to 6.4.0

* Further reductions in query counts

* Fix for broken test

* Test fix

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2022-12-07 15:27:33 +00:00
Mark Iantorno 3556e0fdf8
update to docker installer tool for azure broke docker in the latest version, pinning the version to previous one (#4335) 2022-12-06 18:32:42 -05:00
Ken Stevens 070e97cb01
3907 fix mdm pom dependency (#4331)
* fix import

* fix dependency

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-12-06 09:54:17 -05:00
JasonRoberts-smile 248e48072c
check for existence of issues with a given severity (#4328) 2022-12-06 09:14:59 -05:00
Tadgh 6ae1672599
Change folder name, add versionenum (#4320) 2022-12-05 19:46:52 +00:00
Luke deGruchy 869d9996b1
Move partition ID up from ResourceModifiedMessage to BaseResourceModifiedMessage (#4313)
* Move partition ID up from ResourceModifiedMessage to BaseResourceModifiedMessage.

* Add a changelog.  Add a new constructor that contains partition ID to ResourceOperationMessage.   Add partition ID to the toString() for BaseResourceModifiedMessage.  Tweak constructors of all classes to make sure ResourceModifiedMessage always sets default partition IDs, but BaseResourceModifiedMessage and ResourceOperationMessage do not.

* Reverse an accidental whitespace change.

* Small code review fixes including removing comments and updating changelog description.

* Restore whitespace to what it was on master.

* Fix YAML error.
2022-12-05 09:21:30 -05:00
TipzCM 08ca687c72
4287 fix mdm golden resource merging (#4290)
* fixed goldenresourcemergersvcimpl to allow merging GoldenResource into SourceResource in PossibleDuplicate links

* added changelog

* adding some notations

* working on tests

* updated test to use new convention as demo

* updated to allow creating patints too

* updating more tests

* updated all tests to use new notation

* updates the tests

* adding more test support

* fix merge directions

* fixed duplicate merging in

* updates

* cleanup

* cleanup

* fix changelog

* changing how tests work

* test cleanup

* added a comment

* fixing build

* fix for multimap

* fixing tests

* minor change

* addressed 2 points

* review fixes

* remove one change

* adding todo

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2022-12-05 09:04:51 -05:00
James Agnew 312128754b
Allow forced id for conceptmap translation (#4304)
* Allow forced id for conceptmap translation

* Test fixes

* Test fix

* Conversion cleanup

* Test fixes

* Test fixes

* Build fixes

* Build fix

* Test fixes

* Test fixes
2022-11-30 05:31:26 -05:00
James Agnew 50ca94eded
Improve JPA response messages (#4293)
* Improve JPA response messages

* FIxes

* Test fixes

* Test fixes

* Ongoing testing

* Work on messages

* Work on messages

* Add valueset

* Add response code enum

* Version bump

* Undo bump

* Improve changelog

* Test fixes

* Add javadocs

* Version bump HAPI

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Account for review changes

* Test fix

* Docs fix

* Work on API

* Improve SqlQuery api
2022-11-28 07:52:12 -05:00
James Agnew c3697a5f87
JPA Cleanup (#4278)
* JPA cleanup

* Test fixes

* Cleanup

* Resolve fixme

* Fix bad changelog entry

* A bit of documentation reworking

* Version bump

* POM bump

* Avoid timeout

* Build fix

* HTMLUnit bump
2022-11-24 14:32:56 -05:00
Nathan Doef 028c3ed5c1
Fix Expunge Deleted Resources Race Condition (#4285)
* failing test

* fix race condition

* change log

* refactor

* clean up

* remove ExpungeOptions hard limit enforcement

* nitpick

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2022-11-22 12:48:06 -05:00
James Agnew 9eeb1545a1
Avoid race condition in ServiceLoader (#4295)
* Avoid race condition in ServiceLoader

* Changelog
2022-11-22 07:48:54 -05:00
karneet1212 62c630c546
bundle not throwing an error when multiple matches were found (#4283)
* Added test + condition to throw error

* changelog

* changes made based on comments
2022-11-21 10:08:10 -05:00