* Fix bad migration of fhir id.
Fix the original migration ForceIdMigrationCopyTask.
Also add another migration ForceIdMigrationFixTask to trim
the fhir id to correct the data.
* Bump to 6.10.1-SNAPSHOT
* version bump
* Bump to core release 6.0.22 (#5028)
* Bump to core release 6.0.16
* Bump to core version 6.0.20
* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper
* Bump to core 6.0.22
* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)
* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID
* added changelog
* changed to valid version number
* changed to valid version number, need to be ordered by version number...
* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)
5123 - Use DEFAULT partition for server-based requests if none specified
* consent remove all suppresses next link in bundle (#5119)
* added FIXME with source of issue
* added FIXME with root cause
* added FIXME with root cause
* Providing solution to the issue and removing fixmes.
* Providing changelog
* auto-formatting.
* Adding new test.
* Adding a new test for standard paging
* let's try this and see if it works...?
* fix tests
* cleanup to trigger a new run
* fixing tests
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118)
* fix, test, changelog
* fix, test, changelog
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* _source search parameter needs to support modifiers (#5095)
_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers
* Fix HFQL docs (#5151)
* repository measure refactor
* undo bundle edit, add config
* embedded library true
* undo post of bundle
* clear library cache on test
* fix sumbit-data test
* missing packages from cql
* fix test data and test cases for repository api
* 3.0.0 clinical reasoning uplift
* r4 cql execution provider and tests
* fix submitdata provider config
* wip cql tests
* debugging cql op wip
* wip debugging cql
* update tests for $cql, fix class names
* prep for Pre6 uplift
* spotless checks and test fixes
* bump to 3.0.0-PRE6
* cleanup
* fix version
* cleanup
* fix exlusions in pom
* add in cache invalidation config
* search converter bug and test for repository
* update searchconverter
* version bump, add changelog
* remove term config, move IDaoRegistryUser class
* Break out dstu3 providers and move config to version folders
* CVE-2023-26119
* remove * imports
* code review updates
---------
Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.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
* initial test implementation/changes and solution wiring.
* adding support for jpa/mongo abstraction.
* refact completed. need to start implementing scheduling of subscription re-submission with the scheduler service.
* post release, merging in master.
* wip: commit before merging in branch master.
* wip: resuming work on the issue.
* wip: before merging in master.
* wip: partial implementation of mongo support.
* wip: more work to support partial implementation on mongo.
* Test implementation
* providing method getMessageKeyOrDefault();
* providing changelog
* preping codereview.
* wip: passing tests
* wip: finally solving the Meta issue.
* wip: adjusting interfaces
* Adding IT and
* IT test;
fixing rollback issue.
* removing non required logging
* fixing merge conflict
* Preparing for code review.
* Preparing for code review.
* Compiling code after merging in master.
* Fixing checkstyle failure.
* Modifications towards getting all tests to pass.
* addressing comments from code review.
* compiling code after switching target merge branch to rel_pub_2023_05
* compiling code after switching target merge branch to rel_6_6
* Addressing comments made in design meeting. wip.
* Addressing comments made in design meeting. finally completed.
and last 2 comments addressed.
* removing non required override
* reverting changes as they are not required.
* Modified test and implementation.
* implementation of a SynchronousSubscriptionMatcherInterceptor to submit modifiedResources to the subscription pipeline for testing only.
* fix tests by modifying the matchingInterceptor to call pointcut when processing
* fixing more tests.
* WIP to pass all tests in jpaserer-4504-a-resource-submitted-to-the-subscription-pipeline-is-lost-when-the-pipeline-encounters-an-issue
* fixing circular dependency
* Adding import dependency to class TestSubscriptionSubmitterConfig to allow submission of messages with the SynchronousSubscriptionMatcherInterceptor.
* bumping version 6.7.7-SNAPSHOT
* bumping HAPI version to 6.7.7-SNAPSHOT
* fixing tests failure caused by asynch deliver of resourceModifiedMsg to the processing pipeline.
* passing all tests.
* unbumping to 6.7.7
* compiling after merging in master.
* creating a custom hapi version
* providing an synchronous subscription matcher interceptor for testing.
* updating pom version to generate artifacts.
* fixing tests, WIP/0
* fixing tests, WIP/1
* fixing tests, WIP/2
* Matching entity annotation with migration task declarations.
* Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage.
* Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage.
* Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc].
* Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc] again.
* Removing creation of new transaction to inflate PersistedRresourceModifiedMessages since it is already executing in a transaction.
* bumping to version 6.7.14-ASYNC-SNAPSHOT for pipeline.
* bumping hapi version to 6.7.14-ASYNC-SNAPSHOT for pipeline.
* Formatter changes.
* add generic
* add generic
* Addressing code review comments.
* Adding file asynch_subscription_610.md to docs/upgrades
* changing poms to 6.9.2-SNAPSHOT before merging in master.
* compiling after merging in master.
* Lowering logging level to debug.
* Bumping to 6.9.3-SNAPSHOT
* Bumping hapi version to 6.9.4-SNAPSHOT
* Adding update documentation.
* Modifying update file following review.
---------
Co-authored-by: James Agnew <jamesagnew@gmail.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: Ken Stevens <ken@smilecdr.com>
* version bump
* Bump to core release 6.0.22 (#5028)
* Bump to core release 6.0.16
* Bump to core version 6.0.20
* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper
* Bump to core 6.0.22
* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)
* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID
* added changelog
* changed to valid version number
* changed to valid version number, need to be ordered by version number...
* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)
5123 - Use DEFAULT partition for server-based requests if none specified
* consent remove all suppresses next link in bundle (#5119)
* added FIXME with source of issue
* added FIXME with root cause
* added FIXME with root cause
* Providing solution to the issue and removing fixmes.
* Providing changelog
* auto-formatting.
* Adding new test.
* Adding a new test for standard paging
* let's try this and see if it works...?
* fix tests
* cleanup to trigger a new run
* fixing tests
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118)
* fix, test, changelog
* fix, test, changelog
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* Rename file to force IT mode
* _source search parameter needs to support modifiers (#5095)
_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers
* Fix HFQL docs (#5151)
* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)
* Initial failing test.
* Solution with changelog.
* fixing format.
* Addressing comment from code review.
* fixing failing test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* documentation update (#5154)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Fix hsql jdbc driver deps (#5168)
Avoid non-included classes in jdbc driver dependencies.
* $delete-expunge over 10k resources will now delete all resources (#5144)
* First commit with very rough fix and unit test.
* Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest.
* Spotless
* Fix checkstyle errors.
* Fix test failures.
* Minor refactoring. New unit test. Finalize changelist.
* Spotless fix.
* Delete now useless code from unit test.
* Delete more useless code.
* Test pre-commit hook
* More spotless fixes.
* Address most code review feedback.
* Remove use of pageSize parameter and see if this breaks the pipeline.
* Remove use of pageSize parameter and see if this breaks the pipeline.
* Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases.
* Deprecate the old method and have it call the new one by default.
* updating documentation (#5170)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* _source search parameter modifiers for Subscription matching (#5159)
* _source search parameter modifiers for Subscription matching - test, implementation and changelog
* Removal of meta tags during updates do not trigger subscription (#5181)
* Initial failing test.
* adding solution;
fixing documentation;
* spotless apply
* adding changelog
* modifying current test
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Issue 5173 get gateway everything doesnt return all patients (#5174)
* Failing test
* Also set offset and count in base DAO override
* Changelog
* Fix for specific case where count has been set in parameters
* spotless
* Improve checks
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175)
* First commit with failing unit test and small tweaks.
* Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing.
* Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl.
* Revert PackageResourceParsingSvc to release branch baseline.
* Accept code reviewer suggestion to change changelog description.
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Fix link
* Remove target slf4j version
* dont use new API for a bit (#5191)
* Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193)
DropIdGeneratorTask.
* Dqm performance bug update and provider loader fix (#5180)
* update tests, move properties, update operation loader
* update wip
* remove test
* fixing tests, adding config
* update config and provider loader
* fix bundles
* fix cache settings on tests
* version bump and change log
* version bump
* fix formatting
* CVE-2022-45868
* wip cve change
* cve h2 add back in
---------
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
* bulkExportReuse with POST and GET (#5161)
* string manipulation
* Code to ensure bulkExportReuse works with POST and GET requests
* Added formatting changes
* Fixed tests that were not working
* Formatting
* Code clean up
* fixing test failures
* fixing test failures
* Removed arrOfParams to now utilize ObjectMapper
* Removing stack trace and adding an exception
* Fixed test issue
* formatting
* formatting
* Resolving code review comments
* Reduce size of subscription max results (#5194)
* Reduce MAX_SUBSCRIPTION_RESULTS to 10000
* Add changelog
* 5037 goldenresource remains when target resource deleted (#5038)
* draft test and fix
* remove unused fields
* remove unused fields
* remove unused fields
* draft test + solution for possible match case
* combine sql statement + more error checking
* add test case for possible duplicate
* add config for autodeleting grs
* refactoring, adding support for mongo, docs
* refactoring + fixing mongo queries
* add changelogs
* fix both way link removal
* clean up test comments
* rename method
* remove unnecessary bean
* merge master/resolve conflicts
* mvn spotless
* address comment
* changes to avoid version bumping
* spotless
* change error code
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* dont use new API for a bit (#5190)
* licenses
* wip
* Fix API usage
* wip
* Version bump
---------
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
* FQL tests
* Working so far
* Tests working
* Tests passing
* Work on parser
* Tests passing
* Cleanup
* Working
* Work on parser
* Work
* Working
* Work on tests
* Work on driver
* Work
* Ongoing work
* Rename SEARCH to WHERE
* Work on fhirpath
* Test fixes
* Work on statements
* Build fixes
* Spotless application
* Fix CI
* Build fixes
* Clean up changelogs
* Remove redundant gitignore
* Add docs
* Add docs
* Code cleanup
* Build cleanup
* Fix compile error
* Test fixes
* Test fix
* Test fix
* Work on integration
* Work on design
* Work on UI
* Update hapi-fhir-jpaserver-hfql/src/main/java/ca/uhn/fhir/jpa/fql/jdbc/JdbcDriver.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Address review comments
* Review comments
* HFQL work
* Cleanup
* CLeanup
* License headers
* Test fixes
* HAPI version bump
* License header update
* Changelog cleanup
* Fixes
* Test fix
* Fix spotless issues
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* 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.
* 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
* 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>
* First commit: prototyping code.
* Push down hard-coding of MdmLink revision results into MdmLinkQuerySvcImplSvc.
* More fixes and push hard-coded MdmLink revisions to DAO. Add unit test for converter. Add largely disabled new Spring config to load the AuditReader. Add new interface method to Dao interface.
* Add config key for enabling envers. Add generated javadoc to EnversAuditConfig. Add properties for both the new config and the new mdm history REST API.
* First commit post-merge with new logic to retrieve audited MdmLinks and convert them to JSON.
* Change revision timestamp long to a Date.
* Add a separate inheritance hierarchy for BasePartitionable classes that use Hibernate Envers. Ensure MdmLink is part of this new hierarchy. Fix HapiFhirJpaMigrationTasks to properly migrate the modification of HFJ_REVINFO from long to timestamp and to add partition_id and partition_date to the MdmLink audit table.
* Deprecate IMdmLinkDao.findHistory() and mark for removal as well as related methods.
* Add changelog. Handle empty query results. Remove hard-coded disabling of envers. Clean up JPA code. Clean up unit tests and make them pass.
* Add new hapi-fhir system property to disable envers but leave it enabled by default. Fix nasty validation bug in IdHelperService. Tweak MDM dao to throw another Exception and code if envers is disabled.
* Fix error code messages. More cleanup.
* Another error code fix.
* Add documentation for new feature.
* Fix unit test. Fix migration tasks to drop and add column instead of modifying it because of a postgres error.
* Cleanup TODOs, delete dead code, tweak unit tests, move/rename classes.
* Default implementation of new history DAO method to avoid need for bump.
* Non-dupe Msg code.
* Since 6.5.7.
* Remove misleading comment.
* Set disabled to TRUE, not FALSE.
* First round of code review fixes.
* Apply documentation suggestions from code review
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Code review fix: Split out $mdm-link-history into a separate provider that's enabled by configuration.
* Change configuration strategy from system properties to JpaStorageSettings and JpaStorageSettingsConfigurer. Hook into these new settings from HibernatePropertiesProvider. Update more documentation.
* Fix unit test failure in SearchQueryBuilder.
* Apply suggested Javadoc and documentation changes from code review
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Change semantics for this feature from disabled to enabled.
* Fix failing unit test.
* Fix conditional logic for reversal of envers disabled/enabled.
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Michael Buckley
markiantorno
longma1
Tadgh
Justin McKelvy
TipzCM
Etienne Poirier
James Agnew
Luke deGruchy
Brenin Rhodes
volodymyr-korzh
David
longma1
Ken Stevens