* 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>
* 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>
* 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
* 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>
* One more fix for #4467
* Enabling massIngestionMode causes incomplete resource deletion (#4476)
* Adding initial test.
* Adding fix and subsequent test.
* Adding changelog.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Provide the capability to request that the name of the subscription matching channel be unqualified (#4464)
* Adding initial test.
* Adding initial solution implementation.
* Adding change log and code clean up.
* addressing comments from 1st code review.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Change visibility of migration method (#4471)
* change migration visibility
* add empty migration method for 640
---------
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484)
* First commit: Make SubscriptionValidatingInterceptor aware of which Pointcut is being called. In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED. Fix resulting compile errors in various unit tests.
* Fix/enhance unit tests. Mark methods as deprecated instead of deleting them. Add proper error code. Complete changelog.
* Remove erroneous TODOs and tweak the validation logic.
* Enhance unit tests and fix changelog.
* Reindex batch job fails when processing deleted resources. (#4482)
* adding changelog.
* Providing solution and adding changelog.
* Adding new test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* cleaning up checkstyle files (#4470)
* cleaning up checkstyle files
* One more fix for #4467 (#4469)
* added exlusions for files at base project level so checkstyle doesn't error out
* duplicate error code from merge
* changing lifecycle goal for all module checkstyle check
* moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code
* wip
* trying to figure out why pipeline cannot copy files
* removing modules that don't actually need to be built.
* I messed up the version
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Bump core to 5.6.881 (#4496)
* Bump core to 5.6.881-SNAPSHOT
* Work on fixing tests
* Work on fixing tests 2
* Bump to core release
---------
Co-authored-by: dotasek <david.otasek@smilecdr.com>
* Issue 4486 mdm inconsistent possible match score values (#4487)
* Extract method for readability
* Save always normalized score values in POSSIBLE_MATCH links.
* Avoid setting properties to null values. Adjust test.
* Simplify fix
* Fix test. Add RangeTestHelper.
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Revert "cleaning up checkstyle files (#4470)"
This reverts commit efae3b5d5f.
* core version fix
* Loosen rules for id helper
* License
* fix batch2 reduction step (#4499)
* fix bug where FINALIZE jobs are not cancellable
* moved reduction step to message hander
* moving reduction step to queue
* addingchangelog
* cleaning up
* review fixes
* review fix'
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* Scheduled batch 2 bulk export job and binary delete (#4492)
* First commit: Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.
* Refine solution and add a concrete unit test but still work to do.
* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.
* Unit tests complete. New Msg code for new IJobPersistence.fetchInstances() method. Cleanup TODOs and add others.
* Finish final touches on implementation.
* Add changelog.
* Various cleanup.
* Code review feedback.
* Small tweak to changelog.
* Last code review tweak.
* Address more code review comments.
* Reverse changes to consider work chunks. Add a constant for write-to-binary.
* Change bulk import test for valueUri type (#4503)
* change tests
* suggested test change
* CVE resolutions (#4513)
* Bump Postgres for CVE
* Bump jetty
* Verison bump
* Remove comments
* Revrt bump
* Add check in scanner (#4518)
* 4516 create hapi fhir cli command to clear stale lock entries (#4517)
* Initial implementation
* better tests
* Add changelog and docs
* Forgotten files
* Code review comments
* Fix checkstyle
* Unable to Expunge CodeSystem (#4507)
* changes for GL-3943
* changes for GL-3943
---------
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
* New line::
* Update to documentation regarding narrative generation; (#4521)
Providing changelog;
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* changed what score is set for mdmlinks that created new golden resource (#4514)
* changed what score is set for mdmlinks that created new golden resource
* fix test
---------
Co-authored-by: Long Ma <long@smilecdr.com>
* REVERT: change to operationoutcome.html
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527)
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp
* added change log
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* fix build (#4530)
* Making narrative_generation.md reference an html snippet (#4531)
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)
* fix + test
* minor fix
* Addressing suggestion
* Minor changes
* 4441 rel 6 4 bad references creation bug (#4519)
* adding a test
* fail in the case of ref enforce on type and on write and autocreate are all true
* update to code
* removing a line
* cleanup
* removing check on urn
* changing just to trigger a build
* adding a comment to the pom
* updating test for better information
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* fixed channel import null pointer exception from null header (#4534)
* retryCount 0 on null header + test + changelog
* suggested changes
* Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535)
This reverts commit 53252b8d15.
* Better error handling for when channel type is not supported (#4538)
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Avoid logging message payloads that contain sensitive data (#4537)
Don't log payloads - they may contain sensitive data.
* Bulk Export Bug With Many Resources and Low Max File Size (#4506)
* failing test
* fix + changelog
* tweak
* add method to IJobPersistence to use a Stream
* tweak
* tweak
* decrease test time
* clean up
* code review comments
* version bump
* Increase timeout limit to match BulkExportUseCaseTest
* shorten test
* maintenance pass
* add logging
* Revert "add logging"
This reverts commit b0453fd953.
* Revert "maintenance pass"
This reverts commit bbc7418d51.
* test
* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp
* shorten tests
* logging
* move test location
* fixes a regression caused my change in hapi-fhir
* timeout
* Revert "fixes a regression caused my change in hapi-fhir"
This reverts commit 4b58013149.
* testing
* Revert "testing"
This reverts commit aafc95c2f3.
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* bump ver
* License updates'
* Remove checkstyle
* Verison bump
* Move migrations
* semicolon
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: dotasek <dotasek.dev@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com>
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* jm wrong bundle entry url (#4213)
* Bug test
* here you go
* Generate relative URIs for bundle entry.request.url, as specified
* Point jira issue in changelog
* Adjust tests to fixes
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* improved logging (#4217)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Rel 6 1 3 mergeback (#4215)
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Revert offset mode change
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
* Updating version to: 6.1.1 post release.
* fix compile error
* Deploy to sonatype (#3934)
* adding sonatype profile to checkstyle module
* adding sonatype profile to tinder module
* adding sonatype profile to base pom
* adding final deployToSonatype profile
* wip
* Revert version enum
* Updating version to: 6.1.1 post release.
* Add test, changelog, and implementation
* Add backport info
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
* wip
* Add backport info
* Add info of new version
* Updating version to: 6.1.2 post release.
* bump info and backport for 6.1.2
* Bump for hapi
* Implement bug fixes, add new tests (#4022)
* Implement bug fixes, add new tests
* tidy
* Tidy
* refactor for cleaning
* More tidying
* Lower logging
* Split into nested tests, rename, add todos
* Typo
* Code review
* add backport info
* Updating version to: 6.1.3 post release.
* Updating version to: 6.1.3 post release.
* removed duplicate mention of ver 6.1.3 in versionEnum
* backport pr 4101
* mdm message key (#4111)
* begin with failing test
* fixed 2 tests
* fix tests
* fix tests
* change log
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* backport 6.1.3 docs changes
* fixed typo on doc backport message
* fix test breaking
* Updating version to: 6.1.4 post release.
* wip
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* pin okio-jvm for kotlin vuln (#4216)
* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)
* First commit: Failing unit test and a TODO with a vague idea of where the bug happens.
* Don't escape "+" in a URL GET parameter if it starts with "application".
* Remove unnecessary TODO.
* Add changelog.
* Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens.
* Ks 20221031 migration lock (#4224)
* started design
* complete with tests
* changelog
* cleanup
* tyop
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)
* Added test
* Added solution
* Changelog
* Changes made based on comments
* Fix bug with MDM submit
* fix
* Version bump
* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)
* Add constant for interceptor
* add test, changelog
* Allow Batch2 transition from ERRORED to COMPLETE (#4242)
* Allow Batch2 transition from ERRORED to COMPLETE
* Add changelog
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)
* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.
* Update test case.
* Cleaned up changelog.
* Added test case for multiple resource types.
* Added failing test case for not returning Binary resource.
* Refactor solution.
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add next version
* bulk export permanently reusing cached results (#4249)
* Add test, fix bug, add changelog
* minor refactor
* Fix broken test
* Smile 4892 DocumentReference Attachment url (#4237)
* failing test
* fix
* increase test Attachment url size to new max
* decrease limit to 500
* ci fix
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Overlapping SearchParameter with the same code and base are not allowed (#4253)
* Overlapping SearchParameter with the same code and base are not allowed
* Fix existing tests according to changes
* Cleanup dead code and remove related tests
* Version Bump
* ignore misfires in quartz
* Allowing Failures On Index Drops (#4272)
* Allowing failure on index drops.
* Adding changeLog
* Modification to changelog following code review.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Revert "ignore misfires in quartz"
This reverts commit 15c74a46bc.
* Ignore misfires in quartz (#4273)
* Reindex Behaviour Issues (#4261)
* fixmes for ND
* address FIXME comments
* fix tests
* increase max retries
* fix resource id chunking logic
* fix test
* add modular patient
* change log
* version bump
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Set official Version
* license
* Fix up numbers
* Fix up numbers
* Update numbers
* wip
* fix numbers
* Fix test:
* Fix more tests
* TEMP FIX FOR BUILD
* wip
* Updating version to: 6.2.1 post release.
* Add a whack of logging
* wip
* add implementation
* wip and test
* wip
* last-second-fetch
* expose useful method
* remove 10000 limit
* Strip some logging
* Fix up logging
* Unpublicize method
* Fix version
* Make minor changes
* once again on 6.2.1
* re-add version enum
* add folder
* fix test
* DIsable busted test
* Disable more broken tests
* Only submit queued chunks
* Quiet log
* Fix wrong pinned version
* Updating version to: 6.2.2 post release.
* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https… (#4291)
* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https://github.com/hapifhir/hapi-fhir/issues/4276
* Credit for #4291
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* backport and changelog for 6.2.2
* Updating version to: 6.2.3 post release.
* fix https://simpaticois.atlassian.net/browse/SMILE-5781
* Version bump to 6.2.3-SNAPSHOT
* Auto retry on MDM Clear conflicts (#4398)
* Auto-retry mdm-clear on conflict
* Add changelog
* Build fix
* Disable failing test
* Update to 6.2.3 again
* Update license dates
* Dont fail on batch2 double delivery (#4400)
* Don't fail on Batch2 double delivery
* Add changelog
* Update docker for release ppipeline
* Updating version to: 6.2.4 post release.
* Add test and implementation to fix potential NPE in pre-show resources (#4388)
* Add test and implementation to fix potential NPE in pre-show resources
* add test
* WIP getting identical test scenario
* More robust solution
* Finalize Code
* Add changelog, move a bunch of changelogs
* Remove not needed test
* Minor refactor and reporting
* Fix up megeback
* update backport info
* update backport info
* Updating version to: 6.2.5 post release.
* Prevent chunk from returning to in-progress unless it is errorred, in-progress, or queued
* changelog
* Update logger
* Indicate backport
* Add version and upgrade info. add backport
* hapi-fhir side done
* cdr side
* add assert
* add test
* Fix import
* prevent multiple reduction step runs in maintenance run (#4423)
* setting job to inprog to prevent multiple maintenance passes from running reduction steps
* added a new status
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* Add backport info
* Fix up tests
* Fix discrepancies
* Fix test
* Version bump
* bump ips
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* breaking up package installer and package config
* breaking out parsing of resources
* wrong nullable
* added an integration test
* adding a changelog
* added a few minor tests
* review fixes
* unit test fixes
* fixing code checkstyle
* moving fetching local package data to package loader svc
* updating the method name
* splitting the fhirversion parsing
* updating table creation task for pretty printing and use in RTE
* adding foreign keys
* Adding mroe info
* minor prettiness changes
* fixing fk generation
* minor changes
* update version
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Add new Clinical Reasoning module
* Add config to get test up and running
* Removed FhirClient from tests
* First passing test
* Remove unused utilities
* Build updates
* exclude xxp3 and substitute with unbundled version
* Refactor to use provider factory and loader pattern
* First passing dstu3 test
* CR r4 test config and immunization tests
* Add base test classes
* Exclude transitive dependency xmlpull
* More dependency cleanup
* Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr
* Fixes for duplicate xpp3 classes
* Remove more references to jpa
* Add mock FHIR server for terminology endpoint tests
* fix cql file for making providerr4 tests pass
* fix pom
* fix generic
* Adding r4 test cases for measure operations.
* Fix endpoint tests
* javadoc comment, temporarily comment out test results for practitioner sync
* javadoc typo fix
* adding java docs for cr module WIP
* Updates to clinical reasoning documentation
* More documentation updates
* docs now compile
* fix test
* DqmR4IT now successfully starts up, but the test does not pass
* Fix additionalData test
* Make measure service bean overridable
* adding clinical reasoning javadoc information
* Rename interfaces to start with I
* More styleguide updates
* Reformat all code in the storage-cr module
* More coding convention updates
* Remove bunches of unused code, reogranize so that fhir version in package name is consistent
* Clean up some static array initializations
* add practitioner patient list
* refactor product-line constant
* test dependency update
* add change log for cr module
* Add hapi-validation to the pom
* Exclude dependencies that are causing duplicates
* More dependencies and exclusions
* Make some base MeasureService components protected
* Update to latest cql compiler release
* fix measure service for null subject & practitioner and open up practitioner test
* Rev to release versions
* Add remaining Dstu3 tests
* update hedis bundle from policyHolder to beneficiary
* update snapshot
* Delete old CQL module
* Post-master-merge recovery
* Fix Java 17 feature usage issue
* update changelog with more information about new functionality
* Remove support chain wrapper usage
* Add javadocs to IResourceLoader
* added the property versioning for antlr jar.
* addressing code review comments.
* addressing code review comments.
* Fix typos in changelog
* Remove azure pipeline for cql module, add it for cr module
* Address exception comments, add Msg.code calls to exceptions
* Fix self-assignment bug
* Add storage-cr module to bom
* addressing coding comments.
* Addressed the variable naming convention to camelCase.
* Snapshot version bump
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Added Solution + test
* Removed old methods
* fixed issues
* Added refactoring
* Deprecated methods on the interfaces
* Remove todo
* Documentation
* Changelog
* Changelog
* Changelog
* Changes made based on comments
* Changes made based on comments
* Clean up
* hapi bumping to version 6.3.6-SNAPSHOT
* hapi bumping to version 6.3.6-SNAPSHOT
* Start work on sharded DB
* Work on migrating
* Work
* Ongoing work
* Ongoing work
* Work
* Work
* Ongoing work
* Work
* Work
* Test fix
* Test fix
* Work
* Compile fix
* Test cleanup
* Test fix
* Resolve fixmes
* Resolve fixme
* Resolve compile errors
* Compile fix
* Fixes
* Work
* Add note for later
* Test fix
* Test fixes
* Build fix
* Test fixes
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Fixes
* Fixes
* Remove dead code in pom
* More test cleanup
* Docs fix
* Changes
* Fix
* Fixes
* Resolve merge conflicts
* Build update
* Merge build fixes
* Version bump
* Address review comments
* Review comments
* Review comments
* Test fixes
* Test fix
* Cleanup
* init rev
* id to jpa and mongo id
* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods
* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods
* fixed conflicts, pulled from master
* fixed code for passing tests successfully
* changed PersistentId to Jpa in MdmSearchInterceptor
* added the todo comments with questions
* added one more question
* renamed TODO questions
* first pass at converting to generic ResourcePersistentId
* fix test
* fix test
* fix test
* make ResourcePersistentId abstract
* Generic type MdmLink
* Final TODOs
* Final TODOs
* cleanup
* fix test
* fix id to string
* fix cyclic package dep
* add <?> to Base so we can extract interface
* Revert "add <?> to Base so we can extract interface"
This reverts commit a806f3d2bc.
* switch to interface
* javadoc
* replace base with interface
* fix test
* add generic template to mdmdao
* remove unneccessary JpaPid casts
* remove unneccessary JpaPid casts
* remove unneccessary JpaPid casts
* remove unneccessary MongoPid casts
* fix test
* fix regression
* fix compile issues arising from merging master
* fix beans
* bump version to 6.3.3-SNAPSHOT
* change logs
* review feedback
* review feedback
* fixme
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Improve JPA response messages
* FIxes
* Test fixes
* Test fixes
* Ongoing testing
* Work on messages
* Work on messages
* Add valueset
* Add response code enum
* Version bump
* Undo bump
* Improve changelog
* Test fixes
* Add javadocs
* Version bump HAPI
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Account for review changes
* Test fix
* Docs fix
* Work on API
* Improve SqlQuery api
* jm wrong bundle entry url (#4213)
* Bug test
* here you go
* Generate relative URIs for bundle entry.request.url, as specified
* Point jira issue in changelog
* Adjust tests to fixes
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* improved logging (#4217)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Rel 6 1 3 mergeback (#4215)
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Revert offset mode change
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
* Updating version to: 6.1.1 post release.
* fix compile error
* Deploy to sonatype (#3934)
* adding sonatype profile to checkstyle module
* adding sonatype profile to tinder module
* adding sonatype profile to base pom
* adding final deployToSonatype profile
* wip
* Revert version enum
* Updating version to: 6.1.1 post release.
* Add test, changelog, and implementation
* Add backport info
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
* wip
* Add backport info
* Add info of new version
* Updating version to: 6.1.2 post release.
* bump info and backport for 6.1.2
* Bump for hapi
* Implement bug fixes, add new tests (#4022)
* Implement bug fixes, add new tests
* tidy
* Tidy
* refactor for cleaning
* More tidying
* Lower logging
* Split into nested tests, rename, add todos
* Typo
* Code review
* add backport info
* Updating version to: 6.1.3 post release.
* Updating version to: 6.1.3 post release.
* removed duplicate mention of ver 6.1.3 in versionEnum
* backport pr 4101
* mdm message key (#4111)
* begin with failing test
* fixed 2 tests
* fix tests
* fix tests
* change log
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* backport 6.1.3 docs changes
* fixed typo on doc backport message
* fix test breaking
* Updating version to: 6.1.4 post release.
* wip
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* pin okio-jvm for kotlin vuln (#4216)
* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)
* First commit: Failing unit test and a TODO with a vague idea of where the bug happens.
* Don't escape "+" in a URL GET parameter if it starts with "application".
* Remove unnecessary TODO.
* Add changelog.
* Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens.
* Ks 20221031 migration lock (#4224)
* started design
* complete with tests
* changelog
* cleanup
* tyop
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)
* Added test
* Added solution
* Changelog
* Changes made based on comments
* Fix bug with MDM submit
* fix
* Version bump
* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)
* Add constant for interceptor
* add test, changelog
* Allow Batch2 transition from ERRORED to COMPLETE (#4242)
* Allow Batch2 transition from ERRORED to COMPLETE
* Add changelog
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)
* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.
* Update test case.
* Cleaned up changelog.
* Added test case for multiple resource types.
* Added failing test case for not returning Binary resource.
* Refactor solution.
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add next version
* bulk export permanently reusing cached results (#4249)
* Add test, fix bug, add changelog
* minor refactor
* Fix broken test
* Smile 4892 DocumentReference Attachment url (#4237)
* failing test
* fix
* increase test Attachment url size to new max
* decrease limit to 500
* ci fix
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Overlapping SearchParameter with the same code and base are not allowed (#4253)
* Overlapping SearchParameter with the same code and base are not allowed
* Fix existing tests according to changes
* Cleanup dead code and remove related tests
* Version Bump
* ignore misfires in quartz
* Allowing Failures On Index Drops (#4272)
* Allowing failure on index drops.
* Adding changeLog
* Modification to changelog following code review.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Revert "ignore misfires in quartz"
This reverts commit 15c74a46bc.
* Ignore misfires in quartz (#4273)
* Reindex Behaviour Issues (#4261)
* fixmes for ND
* address FIXME comments
* fix tests
* increase max retries
* fix resource id chunking logic
* fix test
* add modular patient
* change log
* version bump
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Set official Version
* license
* Fix up numbers
* Fix up numbers
* Update numbers
* wip
* fix numbers
* Fix test:
* Fix more tests
* TEMP FIX FOR BUILD
* wip
* Updating version to: 6.2.1 post release.
* Add a whack of logging
* wip
* add implementation
* wip and test
* wip
* last-second-fetch
* expose useful method
* remove 10000 limit
* Strip some logging
* Fix up logging
* Unpublicize method
* Fix version
* Make minor changes
* once again on 6.2.1
* re-add version enum
* add folder
* fix test
* DIsable busted test
* Disable more broken tests
* Only submit queued chunks
* Quiet log
* Fix up checkstyle
* log to console
* Remove double import
* Version bump
* licenses
* Fix up version
* fix build
* wip
* wip
* Fix up search expansion to use new behaviour of idhelper service
* Fix up MDM Search Expansion
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Extracting a Cache interface and building service loaders for Caffeine and Guava
* Fix estimated size interface
* Use LoadingCache when needed.
* Removing Caffeine from dependency lists.
* Adding hapi-fhir-cache-caffeine as a test dependency
* Putting caching solutions in a single module.
* Fixing the spacing
* Standardizing the use of TimeUnits
* Making a new module to simplify the switch of the cache library in tests.
* Making sure the Guava design matches the behavior of Caffeine.
* Making sure the Cache structure also does not throw InvalidCacheLoading exception to match the LoadingCache.
* Renaming module names for the caching group.
* Better error handing that informs devs what to do.
* Improving documentation
* Typo
* Matching error message design with Caffeine.
* Matching the behavior of Caffeine with Guava
* Final adjustments for the test dependencies on the cache modules.
* Fixing relative pom path.
* Adding caffeine as a testing requirement for the new modules.
* Add changelog and set JPA server to use caffeine cache
* POM fixes
* Build fix
* Buid fix
* Fixes
* Address review comment
* One more cache
* Move changelog to next release
* Update pom versions
* Build fix
* Build fixes
* Build fix
* Try to get build working
* Experiment with failing build
* Rever change
* Fix POM version
* Build fix
* Build fix
* Add Msg.code to new exceptions
Co-authored-by: Vitor Pamplona <vitor@vitorpamplona.com>
* POST release deferred cleanup
* Fixes
* One more test fix
* Test fixes
* Test fixes
* Test cleanup
* Test fixes
* Fixes
* ValueSet cleanup
* Test fix
* Test fixes
* Fixes
* Test fixes
* Fixed
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixc
* Build fix
* Fix merge artifact
* Build fix
* Work on tests
* Test fixes
* Work
* Fixes
* Changelog fix
* Add changelog
* Test fix
* Test fixes
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Tests
* Bumps
* Fixes
* Add errorprone
* Drop bz2 bins
* POM fix
* Build fix
* Update
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* jm wrong bundle entry url (#4213)
* Bug test
* here you go
* Generate relative URIs for bundle entry.request.url, as specified
* Point jira issue in changelog
* Adjust tests to fixes
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* improved logging (#4217)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Rel 6 1 3 mergeback (#4215)
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Revert offset mode change
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
* Updating version to: 6.1.1 post release.
* fix compile error
* Deploy to sonatype (#3934)
* adding sonatype profile to checkstyle module
* adding sonatype profile to tinder module
* adding sonatype profile to base pom
* adding final deployToSonatype profile
* wip
* Revert version enum
* Updating version to: 6.1.1 post release.
* Add test, changelog, and implementation
* Add backport info
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
* wip
* Add backport info
* Add info of new version
* Updating version to: 6.1.2 post release.
* bump info and backport for 6.1.2
* Bump for hapi
* Implement bug fixes, add new tests (#4022)
* Implement bug fixes, add new tests
* tidy
* Tidy
* refactor for cleaning
* More tidying
* Lower logging
* Split into nested tests, rename, add todos
* Typo
* Code review
* add backport info
* Updating version to: 6.1.3 post release.
* Updating version to: 6.1.3 post release.
* removed duplicate mention of ver 6.1.3 in versionEnum
* backport pr 4101
* mdm message key (#4111)
* begin with failing test
* fixed 2 tests
* fix tests
* fix tests
* change log
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* backport 6.1.3 docs changes
* fixed typo on doc backport message
* fix test breaking
* Updating version to: 6.1.4 post release.
* wip
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* pin okio-jvm for kotlin vuln (#4216)
* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)
* First commit: Failing unit test and a TODO with a vague idea of where the bug happens.
* Don't escape "+" in a URL GET parameter if it starts with "application".
* Remove unnecessary TODO.
* Add changelog.
* Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens.
* Ks 20221031 migration lock (#4224)
* started design
* complete with tests
* changelog
* cleanup
* tyop
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)
* Added test
* Added solution
* Changelog
* Changes made based on comments
* Fix bug with MDM submit
* fix
* Version bump
* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)
* Add constant for interceptor
* add test, changelog
* Allow Batch2 transition from ERRORED to COMPLETE (#4242)
* Allow Batch2 transition from ERRORED to COMPLETE
* Add changelog
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)
* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.
* Update test case.
* Cleaned up changelog.
* Added test case for multiple resource types.
* Added failing test case for not returning Binary resource.
* Refactor solution.
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add next version
* bulk export permanently reusing cached results (#4249)
* Add test, fix bug, add changelog
* minor refactor
* Fix
* Bump HAPI version
* Remove jetbrains
* Fix broken test
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add r4b stuff
* Work on R4B
* Core version bump
* Revert some changes
* Add R4B
* Docs
* Test fixes
* Work on R4B
* Tests passgin
* Add config
* Work on merging
* Work
* Work
* Work
* Test fix
* Fixes
* Test fixes
* Test fix
* Work
* Work
* Fixes
* Test fixes
* Fixes
* Test fix
* Test fix
* Test fix
* Version bump
* Test fix
* Test fix
* ompile fixes
* Fix
* Resolve build warnings
* Updates
* Test fixes
* Fix docs
* 3052 Changed IBinaryStorageSvc MaximumBinarySize from int to long.
* 3052 Added changelog
* 3052 Bumped version
* 3052 Remove mysterious +1 on maximum binary size causing overflow.
* Bumping version to 6.2.0-PRE16-SNAPSHOT
* Adding + 1L as original implementation.
* Getting all tests to pass dealing with + 1L.
* Getting all tests to pass dealing with + 1L.
* Adding migration definition and removing unnecessary comment.
* Preventing register overflow when setting maxBinaryStorage.
* Mering relevant test.
* Fixing typo in migration script
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Standardize on one Transactional annotation
* Add changelog
* Disable checkstyle rule
* Fix up transactions
* Test fixes
* Test cleanup
* License headers
* One more dep bump
* Resolve commit issue
* Test fixes
* Test fix
* Dep bump
* Fix
* Fix test
* Version bump
* Test fixes
* Add unit tests and supporting classes from gitlab issue.
* Commit with changes thus far to be reviewed. Namely, add savepoint capabilities to HapiTransactionService, inject HapiTransactionService into CascadingDeleteInterceptor, add savepoint capabilities to the TransactionDetails, and catch an Exception in BaseHapiFhirResourceDao.delete() then rollback to the checkpoint.
* Fix compile error.
* hapi transaction service test
* hapi transaction service test
* hapi transaction service test
* First draft of RetryTemplate and flush() logic. Try unit testing with PointcutLatch.
* hapi transaction service test
* Latest changes including moving RetryTemplate, cleaning up unit tests.
* First attempt at correct design. Fix compile errors.
* Add failed rollback savepoint test.
* fix propogation
* interesting test failure in SafeDeleterTest
* Latest code
* move delete
* test passing
* all tests pass
* yay we're done just cleanup
* First round of cleanup: Get rid of all exploratory logging, remove unneeded dependencies, move creation of RetryTemplate to SafeDeleter.
* More cleanup. Add changelog.
* Bump to 6.2.0-PRE13-SNAPSHOT.
* Code review feedback: Refactor SafeDeleter to a service and bean. Add comments.
* Code review feedback: Comments on unit test assertions.
* Code review feedback: Rename SafeDeleterSvc to ThreadSafeResourceDeleterSvc. Add javadoc. Add logger to DelayListener. Remove useless commented out code.
* Fix unit test failure in CascadingDeleteInterceptorTest.
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* removed flyway, started coding persistence
* started wiring up new dao service
* replace jpa with sqlbuilder
* down to 16 failed tests
* remove outOfOrder test. We no longer support validating order.
* Removed noFlyway mode. It is no longer a thing.
* merge migrator
* down to 1 failing test
* cleanup
* removed unused noflyway cli arguments
* cleanup
* cleanup
* cleanup
* cleanup
* create MigrationTaskList to replace the List<BaseTask> that gets passed around a lot. This allows us to add a bunch of behaviour to that as a first-order thing
* fix test
* fix test
* improve migration table detection to use the catalogue
* Msg.code()
* cleanup
* save version in same format as flyway
* cleanup
* add migration result to migration result class
* failed migrations stay in the table and don't really affect anything.
* change log
* docs
* ugh Flyway requires lower-case column names
* integration test fixes
* log
* fix oracle issue
* lowercase tablenames for postgres. fussy fussy!
* Revert "lowercase tablenames for postgres. fussy fussy!"
This reverts commit 92c9cb263b.
* revert to capital table names. surround table name by quotes for Postgres.
* added log message before executing find all query
* changed log message from info to debug
* javadoc
* pom cleanup
* review feedback
* Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/MigrationTaskList.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* review feedback
* review feedback. Use prepared statement.
* Change installedOn insert from timestamp to date
* Change installedOn column type from timestamp to date
* bump hapi version
* fix poms
* fix poms and cdr compile
* add exclusions to clean up build
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Tadgh
David
James Agnew
longma1
Etienne Poirier
Ken Stevens
Justin McKelvy
Luke deGruchy
michaelabuckley
Qingyixia
TipzCM
karneet1212
Nathan Doef
kateryna-mironova
samuelwlee2
KGJ-software