* version bump
* Bump to core release 6.0.22 (#5028)
* Bump to core release 6.0.16
* Bump to core version 6.0.20
* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper
* Bump to core 6.0.22
* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)
* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID
* added changelog
* changed to valid version number
* changed to valid version number, need to be ordered by version number...
* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)
5123 - Use DEFAULT partition for server-based requests if none specified
* consent remove all suppresses next link in bundle (#5119)
* added FIXME with source of issue
* added FIXME with root cause
* added FIXME with root cause
* Providing solution to the issue and removing fixmes.
* Providing changelog
* auto-formatting.
* Adding new test.
* Adding a new test for standard paging
* let's try this and see if it works...?
* fix tests
* cleanup to trigger a new run
* fixing tests
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118)
* fix, test, changelog
* fix, test, changelog
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* Rename file to force IT mode
* _source search parameter needs to support modifiers (#5095)
_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers
* Fix HFQL docs (#5151)
* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)
* Initial failing test.
* Solution with changelog.
* fixing format.
* Addressing comment from code review.
* fixing failing test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* documentation update (#5154)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Fix hsql jdbc driver deps (#5168)
Avoid non-included classes in jdbc driver dependencies.
* $delete-expunge over 10k resources will now delete all resources (#5144)
* First commit with very rough fix and unit test.
* Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest.
* Spotless
* Fix checkstyle errors.
* Fix test failures.
* Minor refactoring. New unit test. Finalize changelist.
* Spotless fix.
* Delete now useless code from unit test.
* Delete more useless code.
* Test pre-commit hook
* More spotless fixes.
* Address most code review feedback.
* Remove use of pageSize parameter and see if this breaks the pipeline.
* Remove use of pageSize parameter and see if this breaks the pipeline.
* Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases.
* Deprecate the old method and have it call the new one by default.
* updating documentation (#5170)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* _source search parameter modifiers for Subscription matching (#5159)
* _source search parameter modifiers for Subscription matching - test, implementation and changelog
* Removal of meta tags during updates do not trigger subscription (#5181)
* Initial failing test.
* adding solution;
fixing documentation;
* spotless apply
* adding changelog
* modifying current test
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Issue 5173 get gateway everything doesnt return all patients (#5174)
* Failing test
* Also set offset and count in base DAO override
* Changelog
* Fix for specific case where count has been set in parameters
* spotless
* Improve checks
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175)
* First commit with failing unit test and small tweaks.
* Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing.
* Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl.
* Revert PackageResourceParsingSvc to release branch baseline.
* Accept code reviewer suggestion to change changelog description.
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Fix link
* Remove target slf4j version
* dont use new API for a bit (#5191)
* Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193)
DropIdGeneratorTask.
* Dqm performance bug update and provider loader fix (#5180)
* update tests, move properties, update operation loader
* update wip
* remove test
* fixing tests, adding config
* update config and provider loader
* fix bundles
* fix cache settings on tests
* version bump and change log
* version bump
* fix formatting
* CVE-2022-45868
* wip cve change
* cve h2 add back in
---------
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
* bulkExportReuse with POST and GET (#5161)
* string manipulation
* Code to ensure bulkExportReuse works with POST and GET requests
* Added formatting changes
* Fixed tests that were not working
* Formatting
* Code clean up
* fixing test failures
* fixing test failures
* Removed arrOfParams to now utilize ObjectMapper
* Removing stack trace and adding an exception
* Fixed test issue
* formatting
* formatting
* Resolving code review comments
* Reduce size of subscription max results (#5194)
* Reduce MAX_SUBSCRIPTION_RESULTS to 10000
* Add changelog
* 5037 goldenresource remains when target resource deleted (#5038)
* draft test and fix
* remove unused fields
* remove unused fields
* remove unused fields
* draft test + solution for possible match case
* combine sql statement + more error checking
* add test case for possible duplicate
* add config for autodeleting grs
* refactoring, adding support for mongo, docs
* refactoring + fixing mongo queries
* add changelogs
* fix both way link removal
* clean up test comments
* rename method
* remove unnecessary bean
* merge master/resolve conflicts
* mvn spotless
* address comment
* changes to avoid version bumping
* spotless
* change error code
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* dont use new API for a bit (#5190)
* licenses
* wip
* Fix API usage
* wip
* Version bump
---------
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@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: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.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: LalithE <132382565+LalithE@users.noreply.github.com>
* added validateExpungeEnabled() call to type-level expunge, moved two overloading method so that they are next to each other
* added test for expunge
enabled expunge for testExpungeAllVersionsWithTagsDeletesRow in FhirResourceDaoR4QueryCountTest
* added changelog
* optimized tests and changelogs
* version bump
* Bump to core release 6.0.22 (#5028)
* Bump to core release 6.0.16
* Bump to core version 6.0.20
* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper
* Bump to core 6.0.22
* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)
* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID
* added changelog
* changed to valid version number
* changed to valid version number, need to be ordered by version number...
* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)
5123 - Use DEFAULT partition for server-based requests if none specified
* consent remove all suppresses next link in bundle (#5119)
* added FIXME with source of issue
* added FIXME with root cause
* added FIXME with root cause
* Providing solution to the issue and removing fixmes.
* Providing changelog
* auto-formatting.
* Adding new test.
* Adding a new test for standard paging
* let's try this and see if it works...?
* fix tests
* cleanup to trigger a new run
* fixing tests
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118)
* fix, test, changelog
* fix, test, changelog
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* Rename file to force IT mode
---------
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
* FQL tests
* Working so far
* Tests working
* Tests passing
* Work on parser
* Tests passing
* Cleanup
* Working
* Work on parser
* Work
* Working
* Work on tests
* Work on driver
* Work
* Ongoing work
* Rename SEARCH to WHERE
* Work on fhirpath
* Test fixes
* Work on statements
* Build fixes
* Spotless application
* Fix CI
* Build fixes
* Clean up changelogs
* Remove redundant gitignore
* Add docs
* Add docs
* Code cleanup
* Build cleanup
* Fix compile error
* Test fixes
* Test fix
* Test fix
* Work on integration
* Work on design
* Work on UI
* Update hapi-fhir-jpaserver-hfql/src/main/java/ca/uhn/fhir/jpa/fql/jdbc/JdbcDriver.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Address review comments
* Review comments
* HFQL work
* Cleanup
* CLeanup
* License headers
* Test fixes
* HAPI version bump
* License header update
* Changelog cleanup
* Fixes
* Test fix
* Fix spotless issues
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* returned user-friendlier message, implemented unit tests, added changelog
* reformatted file
* added Msg.code to the exception thrown
* added Msg.code in test
* Changed to catch DataIntegrityViolationException only.
* 5103 - Adjust our handling of space escape characters in URLs
* 5103 - Fix formatting
* 5103 - Adjust URL escaping and update test expectations
* 5103 - additional test for values with literal plus signs
* 5103 add changelog for this issue
* 5103 - documentation change to describe proper URL escaping
* 5103 - Minor documentation addition
* Changed the two files to reduce info level to debug level for select services.
* Adding change log
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* update docs to be more specific
* fix ordering when client assigned id doesn't match pid
* remove fix ordering when client assigned id doesn't match pid
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* Failing test
* Add some self-assigned Patient IDs
* Sort after client-selected ID is interpolated into the result
* spotless
* changelog
* Keep DAO level ordering enforced by tests
* Filter out non-client-provider ids from test as they are unpredictable in build pipeline
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* fixing a bug with duplicte golden resources being returned
* review points
* fixing tests
* blah
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Fix bug by maintaining a separate list of resource types including the custom resources that will be used to validate the Bundle resources.
* Add custom resource types to resource types list and add conditional logic in ValidationDataInitializerSvcImpl to ensure there is no Exception when parsing a custom resource type.
* Add changelog.
* Remove unnecessary change.
* Address code review feedback.
* Address code review feedback.
* Add one more unit test.
* Bump to 6.7.14-SNAPSHOT.
* 4759 - WIP unit test for this issue
* WIP updating unit test for ResourceIdListStep
* WIP candidate fix for ResourceIdListStep batch size problem
* Enhance unit test with ArgumentCaptor.
* WIP Parameterized the ResourceIdListStepTest and added assertions
* Adding changelog for this issue
* Updating changelog message for 5055
* Code formatting and import cleanup
---------
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
* Partial implementation after this has been paused: Move trimming of value and system from BaseSearchParamExtractor to ResourceIndexedSearchParamToken. Do not throw Exceptions in TokenPredicateBuilder. Ensure that the hash computing in the search param token takes the 200+ token value into account. Other search param tokens are not yet implemented.
* in ResourceIndexedSearchParamToken,changed hardcoded length to constant MAX_LENGTH;
in BaseSearchParamExtractor, added check in createTokenIndexIfNotBlank so that the return value is null if system or value is blank.
* added test for TokenPredicateBuilder to verify that long values exceeds the max length does not cause exception.
added test in FhirSystemDaoR4SearchTest to verify searchParamToken with longer system and value than max length can be created successfully. And hash value will be calculated before truncation
* fixed a logical error in previous commits
* changed existing tests to accommodate for the changes
* modified existing tests
* added changelog
* changed truncation method name and added comments
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* modified changelog
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* combined redundant tests
---------
Co-authored-by: tyner <tyner.guo@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - test added
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix test
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - send BatchJobWorkNotification after commit
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - changelog fix
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Allow PageMethodBinding to bind also for POST
* Add changelog
* Adjust test
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* GenericClient POST paging support - implementation and test
* GenericClient POST paging support - fixes
* GenericClient POST paging support - fixes
* GenericClient POST paging support - failed tests fix
* GenericClient POST paging support - HAPI version bump
* Added unit test and bug fix to ensure no two partitions with the same ID can be created.
* Added changelogs, and changed the equals operator.
* Made required changes to ensure updating of partition is not affected
* Changed unit test and its location to ensure functionality.
* changing for loop to findById to avoid iteration over all partitions.
* Only allows findById when list is not empty, deals with that edge case.
* Replaced null with isPresent in if statement to fix issues regarding the creation of links on different partitions
* Removed the findAll command within the function. To avoid searching twice.
* Edited the changelogs to properly describe the issue that we have at hand
* Edited the changelogs to properly describe the issue that we have at hand pt 2, wording changes.
* log specific error message + test
* changelog
* remove draft tests
* remove another comment i left behind
* update issue number in changelog
* update error location
* update error location
* update test
* change to exception
* address review comments: add test with submit and also update change log
* format test nicer
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* Implemented fixes, created test for JPA side
* Added test and getter for test for register listener
* refactored test names to make them more descriptive
* Modified tests
* resolved comments
* created changlog
* changed test to use MAX_MANAGED_PARAM_COUNT, and created the corresponding getter
* start building tests
* add test
* Basic test and fix bug
* remove tests, fix existing test
* fix up tests
* fix up tests
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* First commit: Patch bad implementation of RuleBulkExportImpl to fix this use case.
* Fix changelog. Fix comments on unit tests.
* Fix TODO with correct issue number.
* Default search mode to MATCH when creating SearchBundleEntryParts
* Add changelog
* Use enum name instead of explicit constant
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* validate-code on remote-terminology service returns NullPointerException - tests
* validate-code on remote-terminology service returns NullPointerException - fixed
* validate-code on remote-terminology service returns NullPointerException - added changelog
* validate-code on remote-terminology service returns NullPointerException - tests readability improvement and fixes
* validate-code on remote-terminology service returns NullPointerException - fixes
* Ensure StepExecutor only logs a stack trace and error if the retries have been exhausted. Otherwise, just log a debug.
* Accept code reviewer suggestion to amend log message
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* added failing test
* added support for warning messages to batch2
* added change log
* fixed errors from merge, made warning work with new batch2
* fixed message parse, changed interface method to default, formatting changes
* added changelog
* code review changes
* code review change
* added new implementation for warning message processing, fixed migration
* changed column to lob, as text is not well supported
* code review changes
---------
Co-authored-by: Steven Li <steven@smilecdr.com>
* Unit tests for validation after install and uninstall IG
* Fix validation result cached after install and uninstall IG
* Fix validation result cached after install and uninstall IG - updated changelog
* Fix validation result cached after uninstalling IG - updated changelog
* Fix validation result cached after uninstalling IG - fixed unit tests
* Fix validation result cached after uninstalling IG - fixed changelog
* Fix validation result cached after uninstalling IG - test fixes
* initial test
* Adding changelog
* Updated to remove the discarding of search params starting with an underscore
* test commit
* Updated handling of search parameters with underscores
* Revert work in progress
* Updated storage settings with new property for inline tag storage mode
* Updated storage settings to tell when inline tag storage mode is set
* simplified test failure
* Added tests for _tag and _system
* Add PreviousVersion service with tests (#4902)
* started writing PreviousVersionReader
* started writing PreviousVersionReader
* moar tests
* add partitioning to the test
* switch subscription to use previous version reader
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Updated logic to be less confusing
* Bumping version to 6.7.4
* Reverted hapi bump, added improve logic for handling missing search params
* updates
* Updated failing tests
* remove redundant tests
* more updates
* Adding Jira number.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: David Raeside <davidraeside@smilecdr.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
Co-authored-by: David Raeside <david.raeside@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* WIP
* add canonicalizer for R4 topic subscriptions
* test R4 topic subscription registration
* Add support for R4 Subscription Topic Backport
* FIXME
* add filter matching support
* add simpler signature
* add resource type matching to filter
* review feedback
* fixed
* changelog
* test both ways
* add bundle test
* change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state
* added logs
* changelog
* fix v2 issues
* Clean up WIP comments
* Switch to in-memory event numbers (instead of always 1)
* Final WIP cleanup
* Msg.code
* review feedback
* review feedback
* review feedback
* review feedback
* back out import changes
* back out import changes
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Delete expunge with cascade
* Work
* Workgin
* Version bump hibernate
* Start working on delete cascade
* Work on delete expunge
* Test fixes
* Test fixes
* Add changelog
* Work on cascade
* Fixes
* Test work
* Test fixes
* Force Verify tests
* fix ITs (#4809)
* fix RestHookTestR5IT
* fix intermittent
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix migrator error on Oracle (#4814)
* Fix Oracle SQL error
* Add changelog
* Update clinical reasoning version (#4816)
* Update clinical reasoning version
* Update version
* Update version
* Clean-up and more wireup of evaluationSettings
* Add changelog
---------
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
* Opening the care-gaps endpoint for GET. (#4823)
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
* added version to mdm golden resource tag (#4820)
Co-authored-by: Long Ma <long@smilecdr.com>
* Update the changelog for 4697 to be more descriptive (#4827)
* Update the changelog for 4697 to be more descriptive
* Futher tweaks of the changelog
* Fixes a bug with tags. (#4813)
* Test, fix
* Drop constraint, add migration
* Add changelog
* Fix userSelected null vs false
* Fix merge
* Fix up checkstyle whining
* One more failure
* Fix test
* wip
* changelog clarity
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* change index
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* fix migration issue (#4830)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Create correct version enum
* Remove superfluous migration
* fixing test (#4835)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* email subscription, throw NullPointerException (#4790)
* fix bug
* Favoring constructor initialization to autowiring.
* enhancing test.
* Making class LoggingEmailSender available outside of the hapi-fhir-japserver-uhnfhirtest module.
* Passing all tests.
* adding changelog.
* Bumping version to 6.5.20-SNAPSHOT
* addressing code review comment.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Add docs for CR operations (#4855)
* Add docs for CR operations
* Correct changelog and javadoc for $package
* Add documentation for $apply parameters
* Add additional documentation for $package
* Cleanup
* Cleanup
* Cleanup
* Address review comments
* Add documentation for $care-gaps operation. (#4862)
* Add documentation for -gaps.
* addressing the comments.
---------
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
* 4853 validation does not error when display is not the same as the display defined in the codesystem 2 (#4854)
* added failing test
* implemented the solution
* changed test name
* added change log
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4853-validation-does-not-error-when-display-is-not-the-same-as-the-display-defined-in-the-codesystem-2.yaml
Co-authored-by: James Agnew <jamesagnew@gmail.com>
---------
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* fixing patient everything operator (#4845)
* fixing patient everything operator
* review fix
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* fix link
* Move image file
* Bundle resources containing over 100 references to the same Organization will fail with HAPI-2207 (#4871)
* Add failing unit test.
* Fix JpaId Long equality comparison to use ! equals() instead of !=, which fails for different instances of the same Long value.
* Add changelog.
* added warn message and test (#4848)
* added warn message and test
* code review fixes
---------
Co-authored-by: Long Ma <long@smilecdr.com>
* Issue 4804 full table scan on mpi link during mdm clear (#4805)
* version bump for next release (#4793)
* version bump
* Bump to correctnumber
* Version Enum and folder
* Remove interim from list
* wip
* Fix operation on nested type-choices in FhirPatch implementation (#4783)
* Fix operation on nested type-choices in FhirPatch implementation
* Add credit for #4783
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* #4468 fix previous link offset no cache pagination (#4489)
* #4468 Add test reproducing the issue
* #4468 Fix previous link for no cache offset pagination
* #4468 Use unchecked URI parsing
* Credit for #4489
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Changelog and data generating test
* Add MdmLink index
* Avoid double link deletion
* Use ThreadLocal safely
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Fix erroneous batch 2 $export 75% complete count when the job is COMPLETE (#4859)
* Add failing unit test.
* Add conditional logic to the InstanceProgress progress percentage to disregard the incomplete count if this is called from the reduction step. This is to get around a race condition in which a work chunk is QUEUED and not yet complete when the reduction step calculates the progress.
* Add final.
* Add changelog.
* disable wars (#4877)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4868 fix paging hapi (#4870)
* fixing some offset and adding a test
* fixing the offset paging
* Removing duplicate
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
* 4875-binary-access-write-doest-trigger-STORAGE-BINARY-ASSIGN-BLOB-ID-PREFIX-pointcut (#4876)
* Add failing test
* Add failing test
* Fix and changelog
* Pass content type parameter
* Back to auto wiring the context
* Invoke interceptor only when getting blobId, not also when storing it
* Avoid breaking implementers
* Address review comment
* Add new exception Msg code
* Fix broken test
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Fix batch job (bulk export) processed record count (#4879)
* Remove racy stats recalc.
* Throw 404 when requesting $export of non-existent Group or Patient (#4890)
* Remove default implementation intended only for interim backwards compatibility (#4894)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Rule apply patient export (#4893)
* Test, fix, and changelog
* Better partition resolution
* Add checks based on rule applier
* Fix ordering failure due to hash set
* Allow empty auth interceptor
* Fix up operation type on invocation
* Add more tests, make hack implementation for patient instance level operation
* Tighten test name
* Changelog
* Default method
* remove dead method
* Remove dead autowire
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* cve pom changes (#4898)
Co-authored-by: Long Ma <long@smilecdr.com>
* backport subscription topic bean cleanup (#4904)
* 4891 bulk export do not recurse unasked for resources (#4895)
* updating tests
* fixing bulk export to not fetch resources not requested
* cleanup
* cleanup
* more warning suppressing
* adding error code
* blah
* fix test
* review fixes
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* lowers log level to remove bootup noise (#4908)
* CVE rel 6 6 (#4907)
* cve pom changes
* bump javax.el to jakarta.el
---------
Co-authored-by: Long Ma <long@smilecdr.com>
* Issue 4905 post binary failure invoking interceptor for pointcuts storage preshow resources (#4906)
* Initial failing test
* Avoid applying binary blob id prefix multiple times
* Remove recently introduced method not needed anymore
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Enhance LogbackCaptureTestExtension (#4869)
* repro bug with test, fix bug
* ken informed me he resolved this bug on master, so i'm switching to use his solution
* disable wars
* review feedback
* review feedback
* review feedback again
---------
Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Resolve 4863 from release branch searchparametercanonicalizer does not account for search parameters for custom resources types when converting dstu23 into runtimesearchparam (#4887)
* Modified canonicalizeSearchParameterDstu2 and 3, now correctly detect search parameters for custom resources
* Canonicalizers now correctly handle search parameters for custom resources
* created changelog
* Modification based on comments:
- remove Resource from target field when there are custom resource types
- fixed changelog typo
- removed unnecessary variable providesMembershipInCompartments
* Added tests for the SearchParameterCanonicalizer to test if base and target of RuntimeSearchParam is set as expected for DSTU2, DSTU3, R4, R4B, and R5 resources
* Fixed typo and removed commented code
* re-ordered init methods
* Update changelog
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* modifications following first code review.
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* License
* Remove _lastUpdated filtering of _revincludes. (#4899)
Remove _lastUpdated filtering of _revincludes.
* 4910-dm-migration-error-for-oracle-19c (#4916)
* Remove all_constraints references which break in oracle 19c
* Add changelog
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* 4873 empty fhirid causes missing resource (#4874)
* add check for empty fhirid string and add test
* add test for populateid
* changelog
* version bump
* version bump
* reverse version bump
* Back to 6.5.21-SNAPSHOT.
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
* Fix include canonical url performance (#4919)
Use hash_identity for canonical join
* License
* Version bump
* Fix failure in test
* Licenses
* Review comments for pipeline
* Dead entry
* other typo
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Sam Gunter <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Josie <80289977+pepsiofficial@users.noreply.github.com>
Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
* review feedback
* fixed
* changelog
* test both ways
* add bundle test
* change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state
* fix v2 issues
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Extract SubscriptionTopicBundleDispatcher into a separate service for use by custom interceptors that need to dispatch their own notifications
* rename
* changelog
* rename
* review feedback
* Msg.code
* review feedback
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Add method to get all jobs of a certain status
* add queries
* add tests
* Refactor so extra parameter is not added
* Version bump
* Fix broken test
* Revert accidental change to pom unrelated to version
---------
Co-authored-by: David Chen <david.chen@smilecdr.com>
* Force Verify tests
* fix ITs (#4809)
* fix RestHookTestR5IT
* fix intermittent
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix migrator error on Oracle (#4814)
* Fix Oracle SQL error
* Add changelog
* Update clinical reasoning version (#4816)
* Update clinical reasoning version
* Update version
* Update version
* Clean-up and more wireup of evaluationSettings
* Add changelog
---------
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
* Opening the care-gaps endpoint for GET. (#4823)
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
* added version to mdm golden resource tag (#4820)
Co-authored-by: Long Ma <long@smilecdr.com>
* Update the changelog for 4697 to be more descriptive (#4827)
* Update the changelog for 4697 to be more descriptive
* Futher tweaks of the changelog
* Fixes a bug with tags. (#4813)
* Test, fix
* Drop constraint, add migration
* Add changelog
* Fix userSelected null vs false
* Fix merge
* Fix up checkstyle whining
* One more failure
* Fix test
* wip
* changelog clarity
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* change index
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* fix migration issue (#4830)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Create correct version enum
* Remove superfluous migration
* fixing test (#4835)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Parser: Reporting unexpected repeating element for choice (#4574)
IParserErrorHandler.unexpectedRepeatingElement is now also called for
unexpected repeating elements of type choice, where concrete names
may be different based on the choice's data type.
* setting test-utilities java version to the test version
* added changelog
* added Max to the developer liss
* removed unneeded dependency
---------
Co-authored-by: patrick-werner <pa.f.werner@gmail.com>
* 4379: allow interceptor annotation on methods
* 4379: document order parameter when annotation set on method
* Credit for #4380
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* 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>
* #4468 Add test reproducing the issue
* #4468 Fix previous link for no cache offset pagination
* #4468 Use unchecked URI parsing
* Credit for #4489
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* 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.
jdar8
TipzCM
Emre Dincturk
Ken Stevens
James Agnew
VK-SMILECDR
Tadgh
TynerGjs
Steve Corbett
LalithE
jmarchionatto
Luke deGruchy
Brenin Rhodes
JasonRoberts-smile
Yusuf Daniju
volodymyr-korzh
StevenXLi
Etienne Poirier
yueshi9988
Nathan Doef
David
Max Bureck
Dominique Villard
Aleksej Parovysnik
Zach Smith