Commit Graph

150 Commits

Author SHA1 Message Date
Ken Stevens 4fbeeccda4
enable some disabled tests (#4662)
* enabled test

* added explanations to disabled tests

* added explanations to disabled tests

* yay enabled another one

* yay enabled another one

* testEverythingWithLargeSet2 failing intermittently

* fix intermittent regression introduced by splitting test class

* test passes

* need to document

* updated documentation

* prereview cleanup

* change log

* cleanup

* cleanup

* added breaking changes

* update changelog and breaking changes upgrade document to reverse the change to always return 200 per the spec.

* back out documentation change

* update documentation

* fix tests

* dstu2

* dstu3

* fix r4 validation warning test

* changelog

* hapi-fhir version bump to 6.5.10-SNAPSHOT

* fix cdr test

* fix tests

* remove accidental commit

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-02 08:47:16 -04:00
Justin McKelvy 9066ad618e
Bug cql engine paging (#4664)
* WIP paging

* iterable HapifhirRetrieveProvider

* Bundle iterating action

* cr config update

* adding paging functionality for search in cr

* updating BundleIterable logic and removing paging references

* add measureeval threaded config into cr

* update properties

* adding hapi change log 4663

* version bump for hapi

* update exception with msg.code, move copyright

* exorcism of paging provider from cr

* updating IT tests for terminology evaluatemeasure

* unit test, javadocs, removed reflection code

* added comments for explanation

* fix javadoc, iterable.size instead of method

* update from master

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
2023-03-31 11:09:50 -04:00
StevenXLi 3fb9a16975
4693 enable partitioning in bulk import (#4694)
* created failing tests

* implemented feature, added more tests

* added documentation and changelog

* fixed duplicate error code

* code review changes

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-03-31 09:43:40 -04:00
James Agnew e69fe05e96
Re-enable "Flush SP cache after SP change" (#4635)
* Revert "Revert "Flush SP cache after SP change (#4566)" (#4614)"

This reverts commit 9492999ed6.

* Additions for performance

* HAPI version bump

* Test logging improvement

* Test fixes

* Test fix

* Test fix

* Compile fix

* Fix

* License headers

* Test fix
2023-03-29 19:57:57 -04:00
James Agnew 05b3bff89f
Order Location searches using near in closest distance to center of the box (#4687)
* All working

* CHangelog tweak

* Address review comments
2023-03-29 03:19:34 +00:00
Luke deGruchy 479e412786
Ensure that source resource type of Provenance is also excluded from the $everything linkage. (#4692) 2023-03-28 14:41:24 +00:00
IanMMarshall b2c0a48915
4610 enable partitioning in bulk export (#4682)
* Initial commit adding support for partition awareness to Bulk Export.

* Additional cleanup and remove references in tests to "all partitions".

* Additional cleanup and remove references in tests to "all partitions".

* More cleanup, test fixes and additional checking to validate partition accesses.

* Additional changes to ensure checking of partition during polling operations.

* Add change log.

* More cleanup.

* Change recommended in code review.

---------

Co-authored-by: ianmarshall <ian@simpatico.ai>
2023-03-27 14:22:30 -04:00
Ken Stevens 47262f5bd5
Ks 20230324 include prov (#4685)
* fix test

* fixed

* changelog

* add another test

* improve docs

* fix change log

* fix test

* fix test

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-03-25 17:50:12 -04:00
michaelabuckley 7d26a7a38d
V2 index for string (#4629)
v2 indexing for String for when sorting.
2023-03-24 19:45:14 +00:00
James Agnew bcc1ca7593
Transaction SQL Optimization (#4679)
* Start work optimizing transaction

* Tons of test cleanup

* Cleanup

* More optimization

* Optimize

* Many tests fixed

* Work on test fixes

* Optimization done, now doing cleanup

* Cleanup

* Add docs

* Test fixes

* Test fix

* License headers

* Test fix

* Test cleanup

* Test fix
2023-03-24 10:29:56 -04:00
Jens Kristian Villadsen 90895aab57
Added exposure of uninstall (#4567)
* Added exposure of uninstall

* Add changelog

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-03-23 21:08:11 +00:00
Etienne Poirier fb057d4fb1
4671 Searching with _source parameter will return matches for all resource types (#4673)
* adding solution with new test.

* adding changelog

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-03-23 14:04:01 -04:00
michaelabuckley 4b3405a456
Use java event names for work chunk transitions. (#4658)
Change work-chunk creation to be first event in state machine.
2023-03-21 13:53:16 -04:00
Ken Stevens 8b80da6441
re-enabled some disabled tests (#4644)
* re-enabled some disabled tests

* add logging

* improve logging

* removed nonsense test

* fix regression

* fix %now

* licenses

* disable searchparam reindexing on intermittent failing test

* refining fix to RetryingMessageHandlerWrapper

* licenses

* remove hapi-fhir-cli-jpaserver from azure pipelines

* undo unneeded change

* change log

* back out unneccessary changes

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-03-17 13:04:29 -04:00
samguntersmilecdr 32d224b7bc
Bring support of conditional updates into alignment with the R4 spec (#4602)
* first draft changes

* small fixes

* rename config

* allow placeholders

* fix tests

* fix concurrency test (messy fix)

* add temp comment

* test pipeline

* add placeholder check

* remove configurability

* cleanup comment

* code review suggestions

* condition changes for test

* extract conditional expression into method

* fix conditional expression
2023-03-15 18:35:25 -04:00
StevenXLi 733259a13b
4618 refactor searchparamwithinlinereferencesextractor to create a interface and a base class (#4619)
* Introduced new interface, refactored SearchParamWithInlineReferencesExtractor, added new test

* clean up, remove unused param

* added change log

* moved error message to properties file, made base class abstract

* fixed issue with test

* code review changes

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-03-15 16:27:52 +00:00
Luke deGruchy e4bb254754
Reverse disabled tests. (#4646) 2023-03-15 10:58:08 -04:00
James Agnew cf5470ae58
Search and Sort on Uplifted Refchains (#4633)
* Start work on refchains

* Semi working

* Add tests for transactions

* Add docs and lots of tests

* Add changelog

* Add tests

* Work on cleanup

* Add document operations

* Test fix

* Test fix

* Fixes

* Fix typo

* Test fix

* Test update

* Test updates

* Test fix

* Test fixes

* Test additions

* Test fix

* Add some javadocs

* Test fixes

* Intermittent test fix

* Doc tweak

* Test fixes

* Merge master in

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/search.md

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

* Review comments

* Version bump

* Add license

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-03-15 07:04:32 -04:00
Aditya Dave 8956b273f0
Concurrent Transaction Conditonal Creates (#4639)
* push broken test for testing placeholder create in transaction retry

* reproduce error for transaction retry

* cleanup test

* fix test testPlaceholderCreateTransactionRetry

* revert temp fix

* revert spacing

* Add tests

* Remove fixme

* Test fix

* test fix

* Test fix

* Remove test line

* Remove unneeded change

* Review comments

* Add docs

* Test logging

* Add test logging

* Add logging for intermittents

---------

Co-authored-by: aditya_dave <aditya@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-03-14 16:39:55 -04:00
Luke deGruchy ea8b68f5e5
Introduce hibernate envers, use it only for MdmLink, disable it for now, add to MdmLink Dao and unit test revisions. (#4615)
* First commit with new maven deps for envers and stubbed changelist.

* Add repositoryFactoryBeanClass = EnversRevisionRepositoryFactoryBean.class to BaseAppCtxPersistence.  Comment it out in JpaConfig.  Add constant for hibernate.integration.envers.enabled.  Hard-code envers to false.  App starts without error.  Basic smoke testing for MpmLink update works.

* Add mdmLink code to retrieve envers history and unit test it.

* Initial code to handle envers from HapiFhirEnversRevision along with a custom extension of the revision/REVINFO entity.

* Add changelist and tweak table/sequence/field names and clean up the HapiFhirJpaMigrationTasks method.

* Fix some unit test failures and address TODOs.

* Ensure hard-coded deactivation of envers is overridden by unit tests.

* Remove commented-out code.

* Address code review comments.

* Remove sysout traces.

* Tweaks to poms with comments explaining why I left the versions in the plugin dependencies.  Get rid of a duplicate envers dependency.

* Bump hapi-fhir version to 6.5.5-SNAPSHOT.

* Disable intermittently failing test: PartitionedSubscriptionTriggeringR4Test.testCreateSubscriptionInPartitionAndResourceInDifferentPartition

* Try disabling Batch2CoordinatorIT failing test and see if branch pipeline passes.

* Add back hapi-fhir-validation-resources-r4b to hapi-fhir-jpaserver-base pom.xml.

* Bump hapi-fhir to 6.5.6-SNAPSHOT.

* Bump rest of hapi-fhir to 6.5.6-SNAPSHOT.

* Fix compile error on Batch2CoordinatorIT.

* Change revision ID column from integer to long in both the revision entity and the migration tasks.  Fix a bug with the migration tasks having the wrong name for the timestamp column.

* Fix interface in MongoDB to return Long for the revision ID instead of Int.   Implement TINYINT for all supported database products.  Keep TARGET_TYPE column at 40 instead of 100 for now since otherwise the schema migration test will fail.  Also, don't try to rename the foreign key or the schema migration test will fail.
2023-03-14 15:32:00 -04:00
Etienne Poirier fdf7450096
4598: Possible creation of resource duplicates when ingesting large quantity of resources. (#4609)
* Creating test to reproduce the issue.

* rebasing development branch from release to master.

* adding migration task.

* providing solution to duplicate resource creation and passing initial test.

* making initial test more readable.

* Implementing test for scheduled deletion of stale searchUrl entries.

* Implementing test for scheduled deletion of stale searchUrl entries.

* Removing interface declaration since it was not needed.

* Reverting changes.

* Adding changelog.

* Adding comments for clarity.

* Adding purgeDatabase operation in IT to delete all ResourceSearchUrlEntity [before|after}Each tests.

* Adding pom.xml exclusion to get all tests passing.

* Adjusting query counts and adding pointcut name to log in interceptor.

* Fixing typos.

* WIP

* implementing edge case tests and solutions.

* wip: passing all tests.

* wip: passing more tests .

* wip: passing tests.

* wip: passing tests.

* enhancing the test.

* changes following code review.

* modifications to tests.

* minor modifications following second code review.

* passing all tests.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-03-14 08:01:06 -04:00
James Agnew 59123cf0f0
Fix intermittent in batch2 tests (#4643)
* Fix intermittent in batch2 tests

* Add changelog

* Test fix

* Resolve intermittent

* Reducer changes

* Test fix

* Test fixes

* Resolve fixme

* Fix changelog
2023-03-13 19:59:05 +00:00
michaelabuckley d1f9c94038
Make WorkChunk handling transactional at state transitions. (#4621)
- use a separate enum for the states - chunks have different transitions than instances.
- use transactional update events for work-chunk state transitions
- introduce spec-test to define behaviour of batch2 storage
- replace synchronized facade with simpler ProxyUtil handler.
- change job cancellation to db update query
2023-03-12 19:19:21 -04:00
Nathan Doef 2f3108c2b6
fix tests (#4631) 2023-03-07 14:28:31 -05:00
Tadgh bfa8ca9571
Add chaained near search test (#4611)
* Add chaained near search test

* robustify test, remove gate checking

* Add changelog

* Correct issue number

* Tidy
2023-03-03 08:30:28 -08:00
James Agnew 9492999ed6
Revert "Flush SP cache after SP change (#4566)" (#4614)
This reverts commit 2083b7ca74.
2023-03-03 02:22:42 +00:00
James Agnew ae1d249d99
Bulk export reducer step fix mergeback (#4606)
* 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

* License

* fix batch2 reduction step (#4499)

* fix bug where FINALIZE jobs are not cancellable

* moved reduction step to message hander

* moving reduction step to queue

* addingchangelog

* cleaning up

* review fixes

* review fix'

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* Scheduled batch 2 bulk export job and binary delete (#4492)

* First commit:  Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.

* Refine solution and add a concrete unit test but still work to do.

* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.

* Unit tests complete.  New Msg code for new IJobPersistence.fetchInstances() method.  Cleanup TODOs and add others.

* Finish final touches on implementation.

* Add changelog.

* Various cleanup.

* Code review feedback.

* Small tweak to changelog.

* Last code review tweak.

* Address more code review comments.

* Reverse changes to consider work chunks.  Add a constant for write-to-binary.

* Change bulk import test for valueUri type (#4503)

* change tests

* suggested test change

* CVE resolutions (#4513)

* Bump Postgres for CVE

* Bump jetty

* Verison bump

* Remove comments

* Revrt bump

* Add check in scanner (#4518)

* 4516 create hapi fhir cli command to clear stale lock entries (#4517)

* Initial implementation

* better tests

* Add changelog and docs

* Forgotten files

* Code review comments

* Fix checkstyle

* Unable to Expunge CodeSystem (#4507)

* changes for GL-3943

* changes for GL-3943

---------

Co-authored-by: isaacwen <isaac.wen@smilecdr.com>

* New line::

* Update to documentation regarding narrative generation; (#4521)

Providing changelog;

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

* changed what score is set for mdmlinks that created new golden resource (#4514)

* changed what score is set for mdmlinks that created new golden resource

* fix test

---------

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

* REVERT: change to operationoutcome.html

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527)

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* added change log

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* fix build (#4530)

* Making narrative_generation.md reference an html snippet (#4531)

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

* fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)

* fix + test

* minor fix

* Addressing suggestion

* Minor changes

* 4441 rel 6 4 bad references creation bug (#4519)

* adding a test

* fail in the case of ref enforce on type and on write and autocreate are all true

* update to code

* removing a line

* cleanup

* removing check on urn

* changing just to trigger a build

* adding a comment to the pom

* updating test for better information

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* fixed channel import null pointer exception from null header (#4534)

* retryCount 0 on null header + test + changelog

* suggested changes

* Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535)

This reverts commit 53252b8d15.

* Better error handling for when channel type is not supported (#4538)

Co-authored-by: kylejule <kyle.jule@smilecdr.com>

* Avoid logging message payloads that contain sensitive data (#4537)

Don't log payloads - they may contain sensitive data.

* Bulk Export Bug With Many Resources and Low Max File Size (#4506)

* failing test

* fix + changelog

* tweak

* add method to IJobPersistence to use a Stream

* tweak

* tweak

* decrease test time

* clean up

* code review comments

* version bump

* Increase timeout limit to match BulkExportUseCaseTest

* shorten test

* maintenance pass

* add logging

* Revert "add logging"

This reverts commit b0453fd953.

* Revert "maintenance pass"

This reverts commit bbc7418d51.

* test

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* shorten tests

* logging

* move test location

* fixes a regression caused my change in hapi-fhir

* timeout

* Revert "fixes a regression caused my change in hapi-fhir"

This reverts commit 4b58013149.

* testing

* Revert "testing"

This reverts commit aafc95c2f3.

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* bump ver

* License updates'

* Downgrade dep'

* Updating version to: 6.4.1 post release.

* Add javadocs and sources to our serviceloaders

* Reset version

* Change parent

* Remove bumped version

* License fixes, new parent

* Updating version to: 6.4.1 post release.

* Fix bad creation of versionenum

* Improve performance on bulk export

* Add changelog

* Start working on cleaned up reducer

* Clean up batch calls

* Work on issues

* Build fixes

* typedbundleprovider getallresources override (#4552)

* typedbundleprovider getallresources override

* added test to immunization tests that validates pagination does not result in null pointer if over default queryCount

* moved HapiFhirDal test to its own test class

* removed unused imports

* Update to use JpaStorageSettings

* adding changelog for issue 4551

* fix changelog spacing

* changelog type  to fix

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>

* Add backport info

* Upgrade core to 5.6.97, make adjustments in hapi-fhir, and ensure that all tests pass (#4579)

* First commit:  Create new branch from the release branch with changes from James' branch.  This probably won't compile as the work is incomplete.

* Second round of changes from integrating James' branch.

* Mark most test failures with TODOs.

* Add whitespace

* Add changes to FhirPathR4 to set FHIRPathEngine to non-strict FP evaluation.

* Fix CreatePackageCommandTest to assert null instead of empty string.  Comments on tests that fail due to the double-quote encoding problem.

* Downgrade to core 5.6.97.

* Fix another test and remove TODOs.

* Fix changelog.

* Clean up some erroneous changes and TODOs.

---------

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

* Fix up dal test

* Address leftover code review feedback from the upgrade to core 5.6.97. (#4585)

* Exclude pinned core deps

* Force pin structs

* Add model changes to IBaseCoding and related changes (#4587)

* Add IbaseCoding changes, and tinder changes

* Fix up tag definition

* converter addition

* Fix unit test and add changelog.

* Add jira to changelog.

---------

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

* Fix changelog

* Tidy metadata

* Test fixing

* Test fixes

* Work on progress

* Add changelog

* Build tweak

* Fixes

* Disable intermittently failing tests. (#4593)

* rename tests to IT

* Disable more intermittently failing tests (#4595)

* Disable more intermittently failing tests.

* Disable another intermittently failing tests.

* ITify

* Disable yet another intermittently failing tests. (#4596)

* disable

* disables

* Fixes

* disables

* Fix compile

* Test fixes

* Updating version to: 6.4.2 post release.

* Bump to 6.4.2-SNAPSHOT

* Fix compile

* fix version

* Address review comments

* Review comments

* Version bump

* Compile fix

* Test fixes

* Compile fixes

* One more compile fix

* Test fixes

* Version bump

* Resolve fixme

---------

Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: 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: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com>
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.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: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-03-01 14:52:36 -05:00
James Agnew 2083b7ca74
Flush SP cache after SP change (#4566)
* Flush SP cache after SP change

* Add changelog

* Test fix
2023-02-28 13:42:08 -05:00
michaelabuckley ec13b751fe
Support retry of $reindex version conflict (#4603)
* Support retry of $reindex conflict
* Notes and cleanup of Phaser
2023-02-28 17:53:06 +00:00
James Agnew bf495e2d92
Don't merge yet: MegaScale API Changes 2 (#4544)
* Megascale changes 2

* Cleanup

* CLeanup

* Sync master

* Cleanup

* Ongoing work

* Move service

* Fixes

* Ongoing megascaler work

* Work

* Work

* Fixes

* Work

* Test fixes

* Work on remote services

* Interceptor rework

* Work on config refactor

* Fixes

* Docs tweaks

* Address review comments

* Test tweak

* Test fixes

* Try to fix tests

* Test tweaks

* Fix changelogs

* Work on merging

* Changes

* Megascale fixes

* Remove accidental commit

* Address fixmes

* Cleanup

* Test fixes

* Compile fix

* Test fixes

* Account for review comments

* Bump HAPI FHIR version
2023-02-27 22:19:28 -05:00
michaelabuckley cedf69516b
Simultaneous $reindex and DELETE can orphan index rows (#4584)
Add optimistic write lock to $reindex operation to prevent indexing stale data.

Introduce Lockstep Phaser to make testing easier
Add 1 query to every resource reindex :-(
2023-02-26 22:12:12 -05:00
Qingyixia 3554e9cf91
Fix the issue of missing meta.tags in subscription message (#4576)
* Fix + Test

* Addressing comments

* Minor fix
2023-02-23 15:07:10 -08:00
Tadgh 607f27b686
4523 subscription sources (#4543)
* fix + test

* minor fix

* Addressing suggestion

* Minor changes

* Revert changes, add new test clas, new test consumer for queus

* Finish implementation

* fix compilation

* Remove unused method and test from the previous solution

* fix + test

* minor fix

* Addressing suggestion

* Minor changes

* Revert changes, add new test clas, new test consumer for queus

* Finish implementation

* fix compilation

* Remove unused method and test from the previous solution

* More Renaming

* fix compilation failure

* Revert compilation fix and merge master

* Fix to pipeline test failures

* Addressing suggestions

---------

Co-authored-by: qingyixia <cherry.xia@smilecdr.com>
2023-02-17 13:09:06 -05:00
James Agnew eea6193df9
JPA config refactoring (#4545)
* Interceptor rework

* Work on config refactor

* Fixes

* Docs tweaks

* Address review comments

* Test tweak

* Test fixes

* Try to fix tests

* Test tweaks
2023-02-15 08:43:01 -05:00
Ken Stevens 794e4510c6
6_4 mergeback (#4547)
* 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

* License

* fix batch2 reduction step (#4499)

* fix bug where FINALIZE jobs are not cancellable

* moved reduction step to message hander

* moving reduction step to queue

* addingchangelog

* cleaning up

* review fixes

* review fix'

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* Scheduled batch 2 bulk export job and binary delete (#4492)

* First commit:  Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.

* Refine solution and add a concrete unit test but still work to do.

* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.

* Unit tests complete.  New Msg code for new IJobPersistence.fetchInstances() method.  Cleanup TODOs and add others.

* Finish final touches on implementation.

* Add changelog.

* Various cleanup.

* Code review feedback.

* Small tweak to changelog.

* Last code review tweak.

* Address more code review comments.

* Reverse changes to consider work chunks.  Add a constant for write-to-binary.

* Change bulk import test for valueUri type (#4503)

* change tests

* suggested test change

* CVE resolutions (#4513)

* Bump Postgres for CVE

* Bump jetty

* Verison bump

* Remove comments

* Revrt bump

* Add check in scanner (#4518)

* 4516 create hapi fhir cli command to clear stale lock entries (#4517)

* Initial implementation

* better tests

* Add changelog and docs

* Forgotten files

* Code review comments

* Fix checkstyle

* Unable to Expunge CodeSystem (#4507)

* changes for GL-3943

* changes for GL-3943

---------

Co-authored-by: isaacwen <isaac.wen@smilecdr.com>

* New line::

* Update to documentation regarding narrative generation; (#4521)

Providing changelog;

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

* changed what score is set for mdmlinks that created new golden resource (#4514)

* changed what score is set for mdmlinks that created new golden resource

* fix test

---------

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

* REVERT: change to operationoutcome.html

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527)

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* added change log

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* fix build (#4530)

* Making narrative_generation.md reference an html snippet (#4531)

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

* fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)

* fix + test

* minor fix

* Addressing suggestion

* Minor changes

* 4441 rel 6 4 bad references creation bug (#4519)

* adding a test

* fail in the case of ref enforce on type and on write and autocreate are all true

* update to code

* removing a line

* cleanup

* removing check on urn

* changing just to trigger a build

* adding a comment to the pom

* updating test for better information

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* fixed channel import null pointer exception from null header (#4534)

* retryCount 0 on null header + test + changelog

* suggested changes

* Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535)

This reverts commit 53252b8d15.

* Better error handling for when channel type is not supported (#4538)

Co-authored-by: kylejule <kyle.jule@smilecdr.com>

* Avoid logging message payloads that contain sensitive data (#4537)

Don't log payloads - they may contain sensitive data.

* Bulk Export Bug With Many Resources and Low Max File Size (#4506)

* failing test

* fix + changelog

* tweak

* add method to IJobPersistence to use a Stream

* tweak

* tweak

* decrease test time

* clean up

* code review comments

* version bump

* Increase timeout limit to match BulkExportUseCaseTest

* shorten test

* maintenance pass

* add logging

* Revert "add logging"

This reverts commit b0453fd953.

* Revert "maintenance pass"

This reverts commit bbc7418d51.

* test

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* shorten tests

* logging

* move test location

* fixes a regression caused my change in hapi-fhir

* timeout

* Revert "fixes a regression caused my change in hapi-fhir"

This reverts commit 4b58013149.

* testing

* Revert "testing"

This reverts commit aafc95c2f3.

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* bump ver

* License updates'

* Remove checkstyle

* Verison bump

* Move migrations

* semicolon

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: 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: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com>
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-02-13 13:23:25 -08:00
JorisHeadease 9665476c00
The `OverridePathBasedReferentialIntegrityForDeletesInterceptor` now … (#4483)
* The `OverridePathBasedReferentialIntegrityForDeletesInterceptor` now works for a multitenant enabled server. The `RequestDetails` weren't set while requesting the conflicting resource via the `DaoRegistry`.

* Add credit

---------

Co-authored-by: Joris Scharp <joris@headease.nl>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-01-31 13:41:41 +00:00
Tadgh 54c9b9422a
Bump to 6.5 post-release-branch (#4472)
* Create version enum and bump

* Version bump

* fix typo
2023-01-28 09:28:15 -08:00
michaelabuckley 10060bef7f
Batch option processing cleanup (#4466)
* BulkDataExportOptions null safety
2023-01-26 11:50:45 -05:00
James Agnew d46f6d635e
Web Admin Console Improvements (#4456)
* Testpage improvements

* Work on tests

* Split fragment out

* Reformat command buttons

* Work on web admin console

* Work on testpage

* Fixes

* Fix

* Test fixes

* Improve examples

* Test fixes

* Address review comment
2023-01-25 09:27:12 -05:00
Tadgh 456cc81b32
Rel 6 2 5 mergeback (#4459)
* jm wrong bundle entry url (#4213)

* Bug test

* here you go

* Generate relative URIs for bundle entry.request.url, as specified

* Point jira issue in changelog

* Adjust tests to fixes

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

* improved logging (#4217)

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

* Rel 6 1 3 mergeback (#4215)

* Bump for CVE (#3856)

* Bump for CVE

* Bump spring-data version

* Fix compile

* Cut over to spring bom

* Bump to RC1

* remove RC

* do not contrain reindex for common SP updates (#3876)

* only fast-track jobs with exactly one chunk (#3879)

* Fix illegalstateexception when an exception is thrown during stream response (#3882)

* Finish up changelog, minor refactor

* reset buffer only

* Hack for some replacements

* Failure handling

* wip

* Fixed the issue (#3845)

* Fixed the issue

* Changelog modification

* Changelog modification

* Implemented seventh character extended code and the corresponding dis… (#3709)

* Implemented seventh character extended code and the corresponding display

* Modifications

* Changes on previous test according to modifications made in ICD10-CM XML file

* Subscription sending delete events being skipped (#3888)

* fixed bug and added test

* refactor

* Update for CVE (#3895)

* updated pointcuts to work as intended (#3903)

* updated pointcuts to work as intended

* added changelog

* review fixes

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

* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)

* Add test and implementation

* Add changelog

* 3899 code in limits (#3901)

* Add implementation, changelog, test

* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

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

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

* 3884 overlapping searchparameter undetected rel 6 1 (#3909)

* Applying all changes from previous dev branch to current one pointing to rel_6_1

* Fixing merge conflict related to Msg.code value.

* Fixing Msg.code value.

* Making checkstyle happy.

* Making sure that all tests are passing.

* Passing all tests after fixing Msg.code

* Passing all tests.

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

* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)

* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete

* created unit test for skip of delete operation while processing duplicating create entries

* moved unit test to FhirSystemDaoR4Test

* 3379 mdm fixes (#3906)

* added MdmLinkCreateSvcimplTest

* fixed creating mdm-link not setting the resource type correctly

* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on

* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java

Change order of tests such that assertEquals takes expected value then actual value

Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* added changelog, also changed a setup function in test to beforeeach

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* Fix to the issue (#3855)

* Fix to the issue

* Progress

* fixed the issue

* Addressing suggestions

* add response status code to MethodOutcome

* Addressing suggestions

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

* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)

* Respect caching in bullk export, fix bug with completed date on empty jobs

* add changelog

* Add impl

* Add breaking test

* Complete failing test

* more broken tests

* Fix more tests'

* Fix paging bug

* Fix another brittle test

* 3915 do not collapse rules with filters (#3916)

* do not attempt to merge compartment permissions with filters

* changelog

* Rename to IT for concurrency problems

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

* Version bump

* fix $mdm-submit output (#3917)

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

* Gl3407 bundle offset size (#3918)

* begin with failing test

* fixed

* change log

* rollback default count change and corresponding comments

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

* Offset interceptor now only works for external calls

* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.

* do not reindex searchparam jobs on startup

* Fix oracle non-enterprise attempting online index add (#3925)

* 3922 delete expunge large dataset (#3923)

* lower batchsize of delete requests so that we do not get sql exceptions

* blah

* fix test

* updated tests to not fail

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

* add index

* Fix up colun grab

* Revert offset mode change

* Revert fix for null/system request details checks for reindex purposes

* Fix bug and add test for SP Validating Interceptor (#3930)

* wip

* Fix uptests

* Fix index online test

* Fix SP validating interceptor logic

* Updating version to: 6.1.1 post release.

* fix compile error

* Deploy to sonatype (#3934)

* adding sonatype profile to checkstyle module

* adding sonatype profile to tinder module

* adding sonatype profile to base pom

* adding final deployToSonatype profile

* wip

* Revert version enum

* Updating version to: 6.1.1 post release.

* Add test, changelog, and implementation

* Add backport info

* Create failing test

* Implemented the fix, fixed existing unit tests

* added changelog

* added test case for no filter, exclude 1 patient

* wip

* Add backport info

* Add info of new version

* Updating version to: 6.1.2 post release.

* bump info and backport for 6.1.2

* Bump for hapi

* Implement bug fixes, add new tests (#4022)

* Implement bug fixes, add new tests

* tidy

* Tidy

* refactor for cleaning

* More tidying

* Lower logging

* Split into nested tests, rename, add todos

* Typo

* Code review

* add backport info

* Updating version to: 6.1.3 post release.

* Updating version to: 6.1.3 post release.

* removed duplicate mention of ver 6.1.3 in versionEnum

* backport pr 4101

* mdm message key (#4111)

* begin with failing test

* fixed 2 tests

* fix tests

* fix tests

* change log

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

* backport 6.1.3 docs changes

* fixed typo on doc backport message

* fix test breaking

* Updating version to: 6.1.4 post release.

* wip

Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@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: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>

* pin okio-jvm for kotlin vuln (#4216)

* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)

* First commit:  Failing unit test and a TODO with a vague idea of where the bug happens.

* Don't escape "+" in a URL GET parameter if it starts with "application".

* Remove unnecessary TODO.

* Add changelog.

* Code review feedback on naming.  Also, make logic more robust by putting plus and should escape boolean && in parens.

* Ks 20221031 migration lock (#4224)

* started design

* complete with tests

* changelog

* cleanup

* tyop

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

* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)

* Added test

* Added solution

* Changelog

* Changes made based on comments

* Fix bug with MDM submit

* fix

* Version bump

* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)

* Add constant for interceptor

* add test, changelog

* Allow Batch2 transition from ERRORED to COMPLETE (#4242)

* Allow Batch2 transition from ERRORED to COMPLETE

* Add changelog

* Test fix

Co-authored-by: James Agnew <james@jamess-mbp.lan>

* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)

* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.

* Update test case.

* Cleaned up changelog.

* Added test case for multiple resource types.

* Added failing test case for not returning Binary resource.

* Refactor solution.

Co-authored-by: kylejule <kyle.jule@smilecdr.com>

* Add next version

* bulk export permanently reusing cached results (#4249)

* Add test, fix bug, add changelog

* minor refactor

* Fix broken test

* Smile 4892 DocumentReference Attachment url (#4237)

* failing test

* fix

* increase test Attachment url size to new max

* decrease limit to 500

* ci fix

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

* Overlapping SearchParameter with the same code and base are not allowed (#4253)

* Overlapping SearchParameter with the same code and base are not allowed

* Fix existing tests according to changes

* Cleanup dead code and remove related tests

* Version Bump

* ignore misfires in quartz

* Allowing Failures On Index Drops (#4272)

* Allowing failure on index drops.

* Adding changeLog

* Modification to changelog following code review.

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

* Revert "ignore misfires in quartz"

This reverts commit 15c74a46bc.

* Ignore misfires in quartz (#4273)

* Reindex Behaviour Issues (#4261)

* fixmes for ND

* address FIXME comments

* fix tests

* increase max retries

* fix resource id chunking logic

* fix test

* add modular patient

* change log

* version bump

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

* Set official Version

* license

* Fix up numbers

* Fix up numbers

* Update numbers

* wip

* fix numbers

* Fix test:

* Fix more tests

* TEMP FIX FOR BUILD

* wip

* Updating version to: 6.2.1 post release.

* Add a whack of logging

* wip

* add implementation

* wip and test

* wip

* last-second-fetch

* expose useful method

* remove 10000 limit

* Strip some logging

* Fix up logging

* Unpublicize method

* Fix version

* Make minor changes

* once again on 6.2.1

* re-add version enum

* add folder

* fix test

* DIsable busted test

* Disable more broken tests

* Only submit queued chunks

* Quiet log

* Fix wrong pinned version

* Updating version to: 6.2.2 post release.

* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https… (#4291)

* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https://github.com/hapifhir/hapi-fhir/issues/4276

* Credit for #4291

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

* backport and changelog for 6.2.2

* Updating version to: 6.2.3 post release.

* fix https://simpaticois.atlassian.net/browse/SMILE-5781

* Version bump to 6.2.3-SNAPSHOT

* Auto retry on MDM Clear conflicts (#4398)

* Auto-retry mdm-clear on conflict

* Add changelog

* Build fix

* Disable failing test

* Update to 6.2.3 again

* Update license dates

* Dont fail on batch2 double delivery (#4400)

* Don't fail on Batch2 double delivery

* Add changelog

* Update docker for release ppipeline

* Updating version to: 6.2.4 post release.

* 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

* Fix up megeback

* update backport info

* update backport info

* Updating version to: 6.2.5 post release.

* Prevent chunk from returning to in-progress unless it is errorred, in-progress, or queued

* changelog

* Update logger

* Indicate backport

* Add version and upgrade info. add backport

* hapi-fhir side done

* cdr side

* add assert

* add test

* Fix import

* prevent multiple reduction step runs in maintenance run (#4423)

* setting job to inprog to prevent multiple maintenance passes from running reduction steps

* added a new status

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* Add backport info

* Fix up tests

* Fix discrepancies

* Fix test

* Version bump

* bump ips

Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@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: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-01-24 17:38:35 -08:00
KGJ-software 527a948285
Added SearchRequest.requester to Patient/everything (#4462)
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2023-01-24 13:28:19 -05:00
James Agnew d584e14048
Add IPS Generator (#4438)
* Begin IPS refactor

* Commit work so far

* Fix test bug

* Fix typo

* Fix typo

* Narrative generator cleanup

* Narrative generator working

* Add test for bad reference in narrative

* Tests passing

* Start docs

* Tests passing

* Cleanup

* Update cyangelog

* Doc tweaks

* Version bump

* Address review comments

* Address review comments

* Build fix

* Cleanup

* Compile fix

* Test fix

* Test fix

* Version bump

* Build update

* Test fix

* Test fix

* Add one utility method

* Add doc
2023-01-24 12:07:36 -05:00
Nathan Doef 320a0d895f
Fix ConceptMap processing in transaction (#4442)
* failing test

* fix

* only store ConceptMap once

* remove new myPreliminaryTransactionWrite flag and use thePerformIndexing

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2023-01-24 10:58:11 -05:00
ivagulin 758c8f12dd
fix ValueSet$expand?includeHierarchy=true with fts disabled (#4449)
* fix ValueSet$expand?includeHierarchy=true

* add test for valuset$expand with hierarchy without hibernate search

* move testExpandValueSet_PreExpandedWithHierarchyNoHibernateSearch to FhirResourceDaoR4ValueSetTest, add javadoc

* Add credit

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-01-23 10:25:24 -05:00
Ken Stevens 5dda16d467
Reduce postconstruct use (#4445) 2023-01-21 00:37:58 -05:00
Ken Stevens bf53a08b83
Batch2 fastracking configurable (#4453)
* licenses

* hapi-fhir side done

* cdr side

* add assert

* add test

* bump hapi version

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-01-20 19:03:13 -05:00
Qingyixia 663834ddfe
Added resourceType as a parameter to $mdm-duplicate-golden-resources operation (#4434)
* Solution + changelog

* Addressing suggestions

* Minor changes

* Version Bump
2023-01-19 08:43:44 -05:00
James Agnew 6eeeb7068b
Remove duplicate field in JPA bundle provider (#4435)
* Remove duplicate field in JPA bundle provider

* Add changelog

* Work on tests

* Test fixes

* Test fix

* Add logging to detect an intermittent

* Test fix

* Address review comment
2023-01-18 18:42:04 +00:00
TipzCM 23b593aa17
breaking up package installer and package config (#4319)
* breaking up package installer and package config

* breaking out parsing of resources

* wrong nullable

* added an integration test

* adding a changelog

* added a few minor tests

* review fixes

* unit test fixes

* fixing code checkstyle

* moving fetching local package data to package loader svc

* updating the method name

* splitting the fhirversion parsing

* updating table creation task for pretty printing and use in RTE

* adding foreign keys

* Adding mroe info

* minor prettiness changes

* fixing fk generation

* minor changes

* update version

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-01-17 01:58:14 +00:00
Ken Stevens 04c28b6c08
Schedule jobs via IJobScheduler instead of in @PostConstruct (#4415)
* parameterizing BinaryStorageInterceptor

* parameterizing BinaryStorageInterceptor

* changed jobs scheduling from @PostConstruct to coordinated by HapiLifecycleService events

* fix test

* remove events for now

* fix test

* simplify design

* FIXME

* changelog

* fix compile issue

* review feedback.  partially implemented

* review feedback

* review feedback

* bump hapi version to 6.3.8-SNAPSHOT

* fix test

* mirror contextclosedevent handlers with contextrefreshedevent

* version bump

* licenses

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-01-14 23:51:04 -05:00