Commit Graph

254 Commits

Author SHA1 Message Date
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 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
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
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
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
James Agnew a3c33d2a53
Add BasicAuditEventLogging (BALP) Interceptor (#4787)
* Begin work on BALP interceptor

* Work on BALP

* Basic profile

* Work on BALP

* Add BALP

* Work on balp

* Add update and delete

* Work on BALP

* Add logging

* Tests

* Modify test server

* Work on docs

* Add documentation

* Add changelog

* Fix #4728 - Typos in docs

* Test fixes

* Move changelog

* Update hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/interceptor/balp/BalpAuditCaptureInterceptor.java

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

* Resolve PR comments

* Test fixes

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-05-03 15:46:22 +00:00
Zach Smith 9c1d235f90
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>
2023-05-01 09:52:34 +00:00
Tadgh 9a095cc2d7
version bump for next release (#4793)
* version bump

* Bump to correctnumber

* Version Enum and folder

* Remove interim from list

* wip
2023-04-30 15:01:28 -04:00
Luke deGruchy 79c96dc1bb
Port changes to master from release branch 6_4 (#4785)
* Start porting changes to master that were lost from the release branch.

* Add remainder of tag changes from release branch.

* Changelog changes.

* Fix schema migration.

* Remove duplicate lines.

* Update core to 6.0.1.

* Fixes for new core.

* Bump to snapshot 19 to mirror James' changes.

* Fix migration tasks.

* Fix some of the tests due to the core upgrade.

* Fix rest of tests.
2023-04-28 19:56:02 +00:00
James Agnew e2e5ff6bb8
Version bump HAPI FHIR (#4788) 2023-04-28 19:30:51 +00:00
James Agnew 69a79e39a1
Subscription retriggering enhancements (#4758)
* Work on forward porting reindex optimize storage

* Subscription retriggering performance enhancements

* Adjust readmes

* Add a test

* Add test

* Cleanup

* Test cleanup

* Add comment

* Add changelogs

* Test fixes

* Test fixes

* Bump size

* Fixes

* Test logging

* Restore forkcount

* Test fix

* Test fix

* Version bump

* Clean up changelogs

* Address review comment
2023-04-28 12:06:38 -04:00
James Agnew e2717bd63a
Bump corelib to FHIR R5 Final (#4727)
* Core bump

* Build build issues

* Bump core

* Cleanup

* Cleanup

* Resolve intermittent

* Work on core

* Add failing test for a check

* Test fixes

* Fixes

* DOn't mangle subscriptions

* Fix

* License headers

* Build fixes

* Version bump

* Compile fixes

* Fix compile issues
2023-04-28 06:28:22 -04:00
longma1 2171ad04a2
3924 mdm match resources across partitions and storing golden resources on a specific partition (#4770)
* added mdm search all partition for golden resource functionality

* added mdm partition setting

* build header fix

* test fixes and added missing side effect of allowing cross partition links on opeartions

* added changelog, also test fixes

* fixed changelog to an actual yaml file

* review fixes,  also simplified tests

* reverted one test because the original test schenario was correct

* added setting clearing in afterEach method so test dont fail while run in maven

* bump to pre-15

---------

Co-authored-by: Long Ma <long@smilecdr.com>
2023-04-28 02:15:35 -06:00
David 457b39bac1
Fix $mdm clear doesn't expunge golden record resources (#4767)
* Failing test

* Add method to expunge collection of deleted resources

* Failing test passes

* Add changelog

* Version bump

* Forgot to commit change

* Update test

* Check type validity

* Fix broken tests

---------

Co-authored-by: David Chen <david.chen@smilecdr.com>
2023-04-27 21:35:27 -06:00
JasonRoberts-smile ae1e7400dd
delete operation removes element from list (#4782)
* delete operation removes element from list

* changelog
2023-04-28 00:01:28 +00:00
Tadgh 78b3b148ba
Support `_exportId` for bulk exports. (#4781)
* Full implementation, test, changelogs

* Add changelogs

* Add default method

* Update hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/export/WriteBinaryStep.java

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

* Code Review Comments

* Compilation failures

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-04-27 21:46:09 +00:00
James Agnew f9de5c918e
Apply fixes to review comments for #4772 (#4780)
* Add post-fetch filtering to bulk export

* Add changelog

* Add validator

* Test fixes

* Test fix

* Review comments for #4772

* Commit fix
2023-04-27 14:23:01 +00:00
James Agnew 855e10a62d
Add post-fetch filtering to bulk export (#4772)
* Add post-fetch filtering to bulk export

* Add changelog

* Add validator

* Test fixes

* Test fix
2023-04-26 17:05:03 -04:00
Ken Stevens 6b9af3291e
R5 Subscriptions (#4748)
* comments from conversation with Gino

* rewrite R5 subscription canonicalization.  Expect the r5 subscription tests to fail now

* SubscriptionTopicR5Test passes now

* R4B tests pass now

* first two tests in RestHookTestR5Test now pass.  just need to convert the rest

* third test passes

* fourth test passes

* tests pass up to line 294

* wow what a marathon.  Turns out when we stripped the version we didn't remove it from the meta version.

* passes up to 427

* RestHookTestR5Test tests pass up to line 582

* RestHookTestR5Test tests pass up to line 591
Added SubscriptionTopicRegisteringSubscriber

* RestHookTestR5Test tests pass up to line 591
Added SubscriptionTopicRegisteringSubscriber

* RestHookTestR5Test tests pass up to line 636
Added SubscriptionTopicValidatingInterceptor

* RestHookTestR5Test tests pass up to line 689

* RestHookTestR5Test tests pass up to line 758

* 4 failures left

* woohoo all tests pass

* all tests pass and no PointCutLatch errors

* Msg.code

* changelog

* checkstyle

* fix some tests

* compile issue

* fix test

* fix regression

* fix test

* R5 currently runs tests in multiple threads, so change the sensitive one to an IT

* licenses

* review feedback

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-26 17:01:00 +00:00
michaelabuckley 8813d9beda
Batch stabilization (#4647)
* Use java event names for work chunk transitions.

* Cherry-pick d5ebd1f667 from rel_6_4

Avoid fetching work-chunk data (#4622)

* add end time to reduction step (#4640)

* add end time to reduction step

* add changelog

---------

Co-authored-by: Long Ma <long@smilecdr.com>
(cherry picked from commit 37f5e59ffc)

* Cancel processing

Provide error message in cancelled jobs, and avoid transitions in final states.

* Apply tx boundary to starting job and first chunk.

* cleanup

* Apply tx boundary to work chunk processing

* Delete BatchWorkChunk

* Introduce events for job create, and chunk dequeue

* Apply tx boundary to chunk handler

* Move instance cancellation to database

* tx boundary around stats collection and completion

* tx boundary around stats collection and completion

* Extend tx boundary to error, fail, and cancel

* Move failure into status calc

* ERROR is not an "ended" state.

* Revert generics cleanup to avoid noise

* Avoid sending gated chunks twice.

* Make no-data path safer.  Cleanup

* Fix mock test for step advance.

* Delete unsafe updateInstace() call

* Cleanup

* Changelog and notes

* Fix cancel boundary.  Cleanups

* Cleanup

* Sort mongo chunks for stable paging.

Other cleanup

* Document error handling

* Cleanup

* Update hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/Batch2JobHelper.java

Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>

---------

Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
2023-04-25 15:47:23 -07:00
TipzCM 1c0addafeb
transaction bundle multi-threading issues (#4739)
* a solution for trying to avoid multi-thread issues for transaction bundle processing

* cleanup

* using retries

* mnor tweaks

* checking in

* changes

* updating changelog

* some minor tweaks

* cleanup

* flip if

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-20 18:43:37 +00:00
Ken Stevens 9e741cb145
remove enabled flag and instead only create the subscription topic beans in the fhir versions that use them (#4737)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-18 10:20:43 -04:00
Etienne Poirier 88459d0d00
4657 method name is inconsistent with the method behavior (#4659)
* Test implementation

* providing method getMessageKeyOrDefault();

* providing changelog

* preping codereview.

* Deprecating method getMessageKeyOrNull in favor of getMessagekey()

* updating comments following code review.

* Bumping version to 6.5.13-SNAPSHOT

* passing all tests.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-04-17 10:41:08 -04:00
James Agnew 7bdbda9ef0
Improve Subscription Retriggering Efficiency (#4742)
* Improve subscription efficiency

* Reduce number of queries

* Add changelog

* Fix ITs

* Review comments

* Test fix
2023-04-17 08:18:57 -04:00
James Agnew 869b6c306a
Allow transaction with conditional create and patch in same bundle (#4735)
* Allow transaction with conditional create and patch in same bundle

* Add changelog

* Cleanup
2023-04-13 15:51:46 -04:00
Ken Stevens cc9d1b992d
fix subscription module restart bug (#4734)
* fix subscription module restart bug

* changelog

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-13 17:06:04 +00:00
Ken Stevens b88ccbc7b0
R4B SubscriptionTopic support (#4724)
* add tests for r4b subscriptions

* begin with failing test

* prepare for SubscriptionTopicLoader

* backwards compatibility

* subscription topic registry done

* topic matching is working

* all but delivery is working now

* yay test passes with FIXMEs

* FIXME -> WIP

* switch notification to bundle

* message codes

* fixme

* disable services for fhir versions below R4B

* fix regression

* fix intermittent

* this change will likely break some other tests

* try a safer option

* fix tests

* fix intermittent (I hope)

* unit test

* improve logic around topic subscription categorization

* moar test

* moar test

* changed to support both r4b and r5

* moar test

* cleanup for test

* moar test

* moar test

* moar test

* changelog

* comment

* Msg.code

* fix mock

* add update test

* fix test cleanup

* tracking link for version converter issue

* review

* fix test

* fix test

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-12 00:44:08 +00:00
James Agnew e500b23fe6
Instance level reindex operations (#4699)
* Reindex improvements

* Work

* Work on reindex

* Test fixes

* Generator now working

* Add instance reindex

* Work

* Build fixes

* Build fix

* Fixes

* Add changelog

* Test fixes

* Resolve checkstyle fix

* Version bump

* Address review comments

* Resolve imports

* Address review comments

* Test fix
2023-04-06 17:00:41 -04:00
James Agnew a2bc9a7212
Partition aware search cleanup (#4706)
* Partition aware search cleanup

* Compile fixes

* Build fixes

* HAPI FHIR version bump

* License

* License header

* Tests
2023-04-02 11:50:20 -04:00
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
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
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
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
Luke deGruchy 7e25008d9f
Implement $mdm-link-history on JPA (#4648)
* First commit:  prototyping code.

* Push down hard-coding of MdmLink revision results into MdmLinkQuerySvcImplSvc.

* More fixes and push hard-coded MdmLink revisions to DAO.  Add unit test for converter.  Add largely disabled new Spring config to load the AuditReader.  Add new interface method to Dao interface.

* Add config key for enabling envers.  Add generated javadoc to EnversAuditConfig.  Add properties for both the new config and the new mdm history REST API.

* First commit post-merge with new logic to retrieve audited MdmLinks and convert them to JSON.

* Change revision timestamp long to a Date.

* Add a separate inheritance hierarchy for BasePartitionable classes that use Hibernate Envers.  Ensure MdmLink is part of this new hierarchy.  Fix HapiFhirJpaMigrationTasks to properly migrate the modification of HFJ_REVINFO from long to timestamp and to add partition_id and partition_date to the MdmLink audit table.

* Deprecate IMdmLinkDao.findHistory() and mark for removal as well as related methods.

* Add changelog.   Handle empty query results.  Remove hard-coded disabling of envers.  Clean up JPA code.  Clean up unit tests and make them pass.

* Add new hapi-fhir system property to disable envers but leave it enabled by default.  Fix nasty validation bug in IdHelperService.  Tweak MDM dao to throw another Exception and code if envers is disabled.

* Fix error code messages.  More cleanup.

* Another error code fix.

* Add documentation for new feature.

* Fix unit test.  Fix migration tasks to drop and add column instead of modifying it because of a postgres error.

* Cleanup TODOs, delete dead code, tweak unit tests, move/rename classes.

* Default implementation of new history DAO method to avoid need for bump.

* Non-dupe Msg code.

* Since 6.5.7.

* Remove misleading comment.

* Set disabled to TRUE, not FALSE.

* First round of code review fixes.

* Apply documentation suggestions from code review

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

* Code review fix:  Split out $mdm-link-history into a separate provider that's enabled by configuration.

* Change configuration strategy from system properties to JpaStorageSettings and JpaStorageSettingsConfigurer.   Hook into these new settings from HibernatePropertiesProvider.  Update more documentation.

* Fix unit test failure in SearchQueryBuilder.

* Apply suggested Javadoc and documentation changes from code review

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

* Change semantics for this feature from disabled to enabled.

* Fix failing unit test.

* Fix conditional logic for reversal of envers disabled/enabled.

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-03-22 12:15:37 -04:00
Isaac Wen 14be0553d0
Moving all license comments to the first line (#4656)
* changes for GL-4023

* changes for GL-4023

* changes for GL-4023

* changes for GL-4023

* changes for GL-4023

* changes for GL-4023

---------

Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
2023-03-20 10:04:26 -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
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
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
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