* move json and interfaces to hapi
* move serialization over
* moar test move
* move prefetch service
* move service registry
* moved everything we can. now just need to add a controller and controller test
* controller done
* IJ Warnings
* Move test
* licenses
* mvn spotless:apply
* checkstyle
* spotless
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 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.
* relegate surefire config to parent pom pluginManagement
* back out build fix to see if stack trace now shows up in logs
* back out the backed out fix.
---------
Co-authored-by: Ken Stevens <ken@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
* Bump core, fix compilation errors
* Match pattern in kindling for use of version
Match the pattern used by Grahame in this update of kindling: f765642470
* Bump core, fix compilation errors
* Match pattern in kindling for use of version
Match the pattern used by Grahame in this update of kindling: f765642470
* Bump core to 6.0.5, fix compilation errors
* Bump to core version 6.0.8
* Individual message code for exception
* Bump core to 6.0.10
* Fix test message
* 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>
* 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>
* 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>
* A SNAPSHOT dependency on an upstream module was added to HAPI FHIR, which changed and caused some downstream tests to break.
* Add Maven enforcer plugin for CR dependencies
* Make maven enforcer conditional on CI builds
* 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>
* #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.
* 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>
* 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>
* try removing fork count from test-r4
* try removing fork count from the rest of the projects
---------
Co-authored-by: Ken Stevens <ken@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>
* 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>
* 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.
- 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
Ken Stevens
Luke deGruchy
Tadgh
Brenin Rhodes
James Agnew
volodymyr-korzh
TipzCM
dotasek
David
JP
Max Bureck
Dominique Villard
Aleksej Parovysnik
Zach Smith
longma1
Etienne Poirier
michaelabuckley
Primož Delopst
Justin McKelvy