* 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>
* 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>
* 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 37f5e59ffc41e20a3ea7e7f6d3bb05ca6840f642)
* 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>
* Basic test for reading from provider
* Basic test for reading from provider
* Failing test
* Add changelog
* Update hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/BinaryStorageInterceptorR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* created failing test for issue
* remove unused code from IT
* Fixed an issue where marking a golden resource as no match would fail.
---------
Co-authored-by: Steven Li <steven@smilecdr.com>
* 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>
* The Lenient error handler will throw exceptions when encode invalid extension containing value and nested extensions
* Addressing suggestions
* Minor changes
* Minor fix
* First commit: New tests, logs, and comments.
* Add hacky fix to run pipelines on. Add another unit test.
* Disable baseUrl checking if hasIdentifier() is true.
* Add changelog. Tweak unit tests.
* Remove junk.
* Add more assertions to unit tests. Make new production fix code clearer.
* Add more clarity to unit tests.
* Another unit test fix.
* 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>
* care gaps integration
* fix review comments.
* Clean up for HAPI Conventions
* More cleanup to share constants
* More cleanup of tests
* More cleanup
* Update CQL versions
* Added changelog
* fix failing test cases for care gaps.
* WIP care-gaps tests
* implementation of end to end care gaps test case.
* addressing the code review comments.
* addressing comments to bring to hapi-fhir standards.
* added the docs required.
* Adding hapi-fhir-storage-cr module for test coverage inclusion.
* Addressing the comments.
* addressing comments and updated with master.
* Addressing comments for minor changes requested.
---------
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
* Try removing the IFhirResourceDaoValueSet Bean.
* Add more TODOs.
* Push changes before testing with master.
* Prevent the following error from happening with mongo, dqm, and no validation support module configured:
org.springframework.context.annotation.AnnotationConfigApplicationContext@4a5b9e6b has not been refreshed yet
* Cleanup unnecessary changes.
* Add changelog.
* Add test to check template returned is not empty
* Check operation is diff so web template does not error
* Refactor for clarity
* add changelog
---------
Co-authored-by: David Chen <david.chen@smilecdr.com>
* Initial stub out of the CR repo API
* Pagination first pass
* cleanup
* add transaction tests
* add search param conversion working logic
* add result parameter conversion
* add test for keymap
* add type checking logic and tests
* remove and / or logic from test and cleanup
* Initial stub out of the CR repo API
* Pagination first pass
* cleanup
* add transaction tests
* add search param conversion working logic
* add result parameter conversion
* add test for keymap
* add type checking logic and tests
* Fix repository tests to use parameters
* Cleanup after latest merge
* Cleanup
* Cleanup
* Fix Msg codes
* Fix Msg codes
* Rename variable for clinical reasoning module
* Update clinical-reasoning version
* Fix version
* review comments
---------
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Rosie Elphick <rosalie.elphick@smilecdr.com>
* 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>
* Ensure querying $mdm-link-history on only golden resource or resource ID does not result in an error.
* Change MdmHistorySearchParameters semantics back to set**** so we don't need to a hapi-fhir to cdr bump.
* Remove envers disabling from HibernatePropertiesProvider.getDialect as by then it's too late.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4680-mdm-link-history-only-one-of-each-param-no-error.yaml
Co-authored-by: Ken Stevens <khstevens@gmail.com>
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 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>
* handle empty values for QueryParameterUtils.toEqualToOrInPredicate and QueryParameterUtils.toNotEqualToOrInPredicate
* fix tests that were improperly mocked
* Revert "handle empty values for QueryParameterUtils.toEqualToOrInPredicate and QueryParameterUtils.toNotEqualToOrInPredicate"
This reverts commit 4382cd31
* throw InvalidRequestException if non-existent reference field is provided for a _has query
* fix test
* fixed
* changelog
* add another test
* improve docs
* fix change log
* fix test
* fix test
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 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
* 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>
