Commit Graph

9777 Commits

Author SHA1 Message Date
volodymyr-korzh 737238b97d
validate code on remote terminology service returns nullpointerexception (#4958)
* validate-code on remote-terminology service returns NullPointerException - tests

* validate-code on remote-terminology service returns NullPointerException - fixed

* validate-code on remote-terminology service returns NullPointerException - added changelog

* validate-code on remote-terminology service returns NullPointerException - tests readability improvement and fixes

* validate-code on remote-terminology service returns NullPointerException - fixes
2023-06-08 12:47:39 -04:00
TynerGjs fddea8db92
Resolve 4952 PUT requests for resources that don't exist get created in sequential format rather than abiding by the ResourceServerIdStrategy (#4953)
* Test implemented, issue resolved

* fixed a logical bug in the previous change

* modified comment

* added tests for Dstu2&3 resources

* Adding afterEach constructions to reset spring context beans.

* resolved comments

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-06-08 12:38:24 -04:00
volodymyr-korzh e28398fc4c
4888 Add validation for composite SearchParameter components types (#4909)
* Added unit tests for composite SearchParameter validator

* Added validation for composite SearchParameter components

* validation for composite SearchParameter components - fixes

* Modified tests

* fixed string in setDefinition

* validation for composite SearchParameter components - fixed validation and Unit tests

* validation for composite SearchParameter components - added method getActiveSearchParameterByComponentDefinition and unit tests

* validation for composite SearchParameter components - minor fixes

* validation for composite SearchParameter components - remove getActiveSearchParameterByComponentDefinition method

* validation for composite SearchParameter components - optimise import

* validation for composite SearchParameter components - fix changelog

* validation for composite SearchParameter components - improved validation logic

* validation for composite SearchParameter components - improved validation logic (remove unused lines)

* validation for composite SearchParameter components - improved validation logic

* validation for composite SearchParameter components - improved validation logic

* validation for composite SearchParameter components - fixed validation logic

* validation for composite SearchParameter components - added test for uri and number combo search

* validation for composite SearchParameter components - added test for uri and number combo search

* validation for composite SearchParameter components - validation logic fix

* validation for composite SearchParameter components - fixes

* validation for composite SearchParameter components - fixes

* validation for composite SearchParameter components - test fixes

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-06-08 11:00:27 -04:00
Luke deGruchy e37edfcf84
Ensure StepExecutor only logs a stack trace and error if the retries have been exhausted. Otherwise, just log a debug. (#4961)
* Ensure StepExecutor only logs a stack trace and error if the retries have been exhausted.  Otherwise, just log a debug.

* Accept code reviewer suggestion to amend log message

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

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-06-07 09:05:08 -04:00
TipzCM 0a7f97adb7
4917 refactor nicknaming hapi with version bump (#4955)
* refactoring 1

* refactoring step 2

* refactoring matches

* cleanup

* fixing some tests

* fixing more tests

* remove dbugcode

* adding the nickname factory

* code review fixes

* review fixes

* put default to prevent breaking

* refactor review fixes

* more review points

* more review points

* review points

* review points

* more review changes

* review points

* review points

* adding bean

* updating version

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-06 09:00:14 -04:00
Tadgh 6c03a512f5
Revert "refactoring nickname matching (#4918)" (#4954)
This reverts commit 7a18f17a01.
2023-06-02 19:40:50 +00:00
TipzCM 7a18f17a01
refactoring nickname matching (#4918)
* refactoring 1

* refactoring step 2

* refactoring matches

* cleanup

* fixing some tests

* fixing more tests

* remove dbugcode

* adding the nickname factory

* code review fixes

* review fixes

* put default to prevent breaking

* refactor review fixes

* more review points

* more review points

* review points

* review points

* more review changes

* review points

* review points

* adding bean

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-02 14:04:30 -04:00
michaelabuckley 9838f8a19a
Delete dead code now that Hapi has merged. (#4946) 2023-06-01 17:27:14 -07:00
StevenXLi 83411e585b
4570 add support for warning messages to the batch framework (#4571)
* added failing test

* added support for warning messages to batch2

* added change log

* fixed errors from merge, made warning work with new batch2

* fixed message parse, changed interface method to default, formatting changes

* added changelog

* code review changes

* code review change

* added new implementation for warning message processing, fixed migration

* changed column to lob, as text is not well supported

* code review changes

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-06-01 13:16:44 -04:00
Tadgh 6c314edee9
add Adi (#4939)
* add Adi

* Name typo
2023-05-31 21:34:14 +00:00
Tadgh 08a0844c12 Touch codeowners 2023-05-30 15:54:08 -07:00
dependabot[bot] 8288ebabcf
Bump snakeyaml from 1.33 to 2.0 in /hapi-fhir-docs (#4928)
Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.33 to 2.0.
- [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-2.0..snakeyaml-1.33)

---
updated-dependencies:
- dependency-name: org.yaml:snakeyaml
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-05-30 15:52:58 -07:00
Luke deGruchy 4d90719552
Delete methods deleted in previous release. (#4944) 2023-05-30 15:21:20 -04:00
volodymyr-korzh 31ae8d8f27
4934 validation doesn't consider loaded ig immediately (#4935)
* Unit tests for validation after install and uninstall IG

* Fix validation result cached after install and uninstall IG

* Fix validation result cached after install and uninstall IG - updated changelog

* Fix validation result cached after uninstalling IG - updated changelog

* Fix validation result cached after uninstalling IG - fixed unit tests

* Fix validation result cached after uninstalling IG - fixed changelog

* Fix validation result cached after uninstalling IG - test fixes
2023-05-30 14:02:14 -04:00
dotasek 34f4c90eb9
Bump org.hl7.fhir.core dependency to 6.0.8 (#4942)
* Bump core, fix compilation errors

* Match pattern in kindling for use of version

Match the pattern used by Grahame in this update of kindling: f765642470

* Bump core, fix compilation errors

* Match pattern in kindling for use of version

Match the pattern used by Grahame in this update of kindling: f765642470

* Bump core to 6.0.5, fix compilation errors

* Bump to core version 6.0.8

* Individual message code for exception

* Bump core to 6.0.10

* Fix test message
2023-05-30 09:36:40 -04:00
Etienne Poirier e068a2f32b
4799 searching on paramname profile with and missing modifier does not match resources (#4840)
* initial test

* Adding changelog

* Updated to remove the discarding of search params starting with an underscore

* test commit

* Updated handling of search parameters with underscores

* Revert work in progress

* Updated storage settings with new property for inline tag storage mode

* Updated storage settings to tell when inline tag storage mode is set

* simplified test failure

* Added tests for _tag and _system

* Add PreviousVersion service with tests (#4902)

* started writing PreviousVersionReader

* started writing PreviousVersionReader

* moar tests

* add partitioning to the test

* switch subscription to use previous version reader

---------

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

* Updated logic to be less confusing

* Bumping version to 6.7.4

* Reverted hapi bump, added improve logic for handling missing search params

* updates

* Updated failing tests

* remove redundant tests

* more updates

* Adding Jira number.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: David Raeside <davidraeside@smilecdr.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
Co-authored-by: David Raeside <david.raeside@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-30 07:12:53 -04:00
yueshi9988 e6367f03fd
change $mdm-link-history param to resourceId (#4945) 2023-05-29 12:18:24 -04:00
Ken Stevens b84e8c0bcc
Canonicalize R4 topic subscriptions (#4913)
* WIP

* add canonicalizer for R4 topic subscriptions

* test R4 topic subscription registration

* Add support for R4 Subscription Topic Backport

* FIXME

* add filter matching support

* add simpler signature

* add resource type matching to filter

* review feedback

* fixed

* changelog

* test both ways

* add bundle test

* change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state

* added logs

* changelog

* fix v2 issues

* Clean up WIP comments

* Switch to in-memory event numbers (instead of always 1)

* Final WIP cleanup

* Msg.code

* review feedback

* review feedback

* review feedback

* review feedback

* back out import changes

* back out import changes

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-29 05:32:22 +00:00
James Agnew 46857711c9
Delete expunge with cascade (#4931)
* Delete expunge with cascade

* Work

* Workgin

* Version bump hibernate

* Start working on delete cascade

* Work on delete expunge

* Test fixes

* Test fixes

* Add changelog

* Work on cascade

* Fixes

* Test work

* Test fixes
2023-05-27 11:07:59 -04:00
William Denton f8548c5d7b
let schematron use hapi-fhir-base classloader (#4366) 2023-05-26 19:05:16 -04:00
James Agnew a04a49cb68
Schema migrator returns status (#4937)
* Migrator should return status

* Cleanup

* Add changelog

* Delete unused

* Test fix
2023-05-24 19:31:39 -04:00
Tadgh c98c4a4dca
Implement codeowners (#4938)
* Initial run through codeowners

* Remove dead action

* Add consent intercept and auth interceptor
2023-05-24 21:48:55 +00:00
Tadgh d9530a9aff
Bump snake yaml (#4929)
* Bump snakeyaml

* Bump jackson to be compatible with new snakeyaml
2023-05-23 21:39:38 -07:00
Nathan Doef 3b9a9c6193
Oracle Testcontainers and Test Data (#4897)
* OracleEmbeddedDatabase + test data
2023-05-23 18:59:41 -04:00
Nathan Doef 970befad90
Fixes broken Oracle migration (#4933) 2023-05-23 17:06:27 -04:00
Tadgh 93a4a7bb33
Bump deps (#4926) 2023-05-23 09:53:52 -07:00
Tadgh 32a4ee056c
Bump snake yaml (#4929)
* Bump snakeyaml

* Bump jackson to be compatible with new snakeyaml
2023-05-23 09:32:55 -07:00
dependabot[bot] cfc8b02b93
Bump spring-security-core from 5.7.5 to 5.7.8 in /hapi-fhir-storage-cr (#4927)
Bumps [spring-security-core](https://github.com/spring-projects/spring-security) from 5.7.5 to 5.7.8.
- [Release notes](https://github.com/spring-projects/spring-security/releases)
- [Changelog](https://github.com/spring-projects/spring-security/blob/main/RELEASE.adoc)
- [Commits](https://github.com/spring-projects/spring-security/compare/5.7.5...5.7.8)

---
updated-dependencies:
- dependency-name: org.springframework.security:spring-security-core
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-05-21 22:17:59 +00:00
James Agnew 82ab61f796
Expunge performance tweak (#4920)
* Expunge performance tweak

* Add changelog

* Address review comment
2023-05-21 17:56:31 +00:00
Tadgh 805e80e61f
6.6.0 Mergeback (#4924)
* 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

* Fix failure in test

* Licenses

* Review comments for pipeline

* Dead entry

* other typo

---------

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: longma1 <32119004+longma1@users.noreply.github.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>
2023-05-20 20:38:35 -07:00
James Agnew 307e52f88f
Index name fix (#4921)
* Index name fix

* Build fix

* Test restore

* Revert change
2023-05-20 21:29:56 +00:00
Ken Stevens d932730525
Fixed R5 Subscription deserialization (#4922)
* review feedback

* fixed

* changelog

* test both ways

* add bundle test

* change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state

* fix v2 issues

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-20 00:32:25 +00:00
Ken Stevens a722cc46a9
SubscriptionTopicDispatcher (#4911)
* Extract SubscriptionTopicBundleDispatcher into a separate service for use by custom interceptors that need to dispatch their own notifications

* rename

* changelog

* rename

* review feedback

* Msg.code

* review feedback

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-18 22:46:00 +00:00
David d94627c382
4847 allow filtering batch jobs by status (#4849)
* Add method to get all jobs of a certain status

* add queries

* add tests

* Refactor so extra parameter is not added

* Version bump

* Fix broken test

* Revert accidental change to pom unrelated to version

---------

Co-authored-by: David Chen <david.chen@smilecdr.com>
2023-05-18 14:46:44 -04:00
James Agnew 1c66e57465
Update resource provenance indexing strategy (#4883)
* Add migration

* Update indexes

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

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

* Address review comments

* Test fixes

* Test fixes

* Test fix

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-05-18 13:23:57 -04:00
Ken Stevens 54cec79a65
fix subscription topic beans (#4903)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-17 10:45:36 -04:00
Ken Stevens 55940bdf27
Add PreviousVersion service with tests (#4902)
* started writing PreviousVersionReader

* started writing PreviousVersionReader

* moar tests

* add partitioning to the test

* switch subscription to use previous version reader

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-16 22:59:47 -04:00
Kevin Dougan SmileCDR 2fd2d95c88
Fixed broken Unit Tester. (#4889)
* Fixed broken Unit Tester.

* Fixed issue with compilation against CDR.

* Fixed an overlay id value in the kotlin pom.xml.
2023-05-15 21:48:29 -04:00
James Agnew 05defb58c5
Server fixes from Connectathon 32 (#4838)
* NPM test cleanup

* fix imports

* Ongoing cleanup

* Rework memory queue

* Reindex cleanup

* Cleanup

* Clean up

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Test fix
2023-05-15 08:28:55 -04:00
James Agnew 483ddca3be
Transaction with delete then update should not fail (#4831)
* Fixed

* Test fixes

* Add test

* Ongoing work

* Work on xactx

* Cleanup

* Changelog cleanup

* Resolve fixme

* Rework broken APIs

* Version bump

* Add license headers

* License header update

* License

* rk on fixes

* Test fixes

* Address review comments

* Test fixes

* Add license headers

* License header
2023-05-15 07:41:40 -04:00
James Agnew 8cf14c8c0e
Dont crash indexing contained references on Bundle (#4881)
* Dont crash indexing contained references on Bundle

* Add changelog
2023-05-14 21:33:32 -04:00
Ken Stevens a308f60e16
relax (#4880)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-13 22:35:18 -04:00
Ken Stevens 4313dc9958
pointcut exceptions (#4822)
* enforce no exceptions on the invoking thread in PointCutLatch

* comment

* Msg.code

* Catch exceptions outside of await block

* fix migration issue

* Refactor PointcutLatch and add tests

* fix tests

* fix tests

* fix tests

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test!

* fix test!

* fix test

* fix test

* clean up latch error formatting

* fix test

* fix test

* fix test

* fix test

* fix test

* fix tests

* fix test

* fix test

* Remove hapi-fhir-jpaserver-uhnfhirtest from build as it is crashing CI

* fix test

* fix intermittent

* A SNAPSHOT dependency on an upstream module was added to HAPI FHIR, which changed and caused some downstream tests to break.

* fix intermittent

* Add Maven enforcer plugin for CR dependencies

* Make maven enforcer conditional on CI builds

* Remove hapi-fhir-jpaserver-uhnfhirtest from build as it is crashing CI

* improve test logging

* pre-review cleanup

* review feedback

* remove hapi-fhir-base-test-jaxrsserver-kotlin from the build

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-05-11 22:31:38 -04:00
JasonRoberts-smile 0475cb682f
Jr 20230502 fhir patch test coverage (#4841)
* add tests for fhir patch

* extract constants

* extract some methods

* isolate add operation

* isolate delete operation

* isolate replace operation

* isolate move operation

* clean up integer handling

* enumeration creation

* improve variable naming

* code review feedback
2023-05-11 16:40:57 -04:00
Tadgh 9d34e6b248
Credit for #4842 (#4865)
* Add credit

* Typo
2023-05-11 18:34:22 +00:00
Nicolai Gjøderum 679b809bf3
Fix: Replace basic field with empty value in TerserUtil (#4842)
* add test proving bug

* fix: handle empty fromValue in TerserUtil.replaceField

* add comment to TerserUtilTest.testReplaceFieldByEmptyValue
2023-05-10 20:09:43 -07:00
JP c052663561
Change to a release version of the Clinical Reasoning dependency. (#4858)
* A SNAPSHOT dependency on an upstream module was added to HAPI FHIR, which changed and caused some downstream tests to break.

* Add Maven enforcer plugin for CR dependencies

* Make maven enforcer conditional on CI builds
2023-05-10 20:25:42 +00:00
Ken Stevens 224b7f6206
SubscriptionTopic part3 (#4817)
* Force Verify tests

* wip

* merge troubleshooting rel_6_6 troubleshooting changes

* fix ITs (#4809)

* fix RestHookTestR5IT

* fix intermittent

---------

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

* post-merge cleanup

* fix test

* fix mock test

* fix wiring

* fix mock test

* fix test

* use IBaseResource.isDeleted()

* fixmes

* cleanup

* change log

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-09 16:29:21 -04:00
Tadgh e3545446eb
Mergeback of release into master branch (#4839)
* 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>

---------

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: longma1 <32119004+longma1@users.noreply.github.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>
2023-05-09 11:23:02 -07:00
Max Bureck 648d14c52c
Parser: Reporting unexpected repeating element for choice (#4574) (#4590)
* Parser: Reporting unexpected repeating element for choice (#4574)

IParserErrorHandler.unexpectedRepeatingElement is now also called for
unexpected repeating elements of type choice, where concrete names
may be different based on the choice's data type.

* setting test-utilities java version to the test version

* added changelog

* added Max to the developer liss

* removed unneeded dependency

---------

Co-authored-by: patrick-werner <pa.f.werner@gmail.com>
2023-05-08 20:42:25 +00:00