* SearchBuilder should not allow $everything operation to follow links to Group or List resources - tests
* SearchBuilder should not allow $everything operation to follow links to Group or List resources - implementation
* SearchBuilder should not allow $everything operation to follow links to Group or List resources - spotless check fix and changelog added
* Add a new permission: FHIR_OP_PATIENT_EVERYTHING_ACCESS_ALL for $everything operation - fixes
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* MongoIncludeSvc should not allow $everything operation to follow links to Group or List resources - fixes
* MongoIncludeSvc should not allow $everything operation to follow links to Group or List resources - fixes
---------
Co-authored-by: James Agnew <jamesagnew@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
* 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>
* Convert PartitionLookupSvcImpl to use MemoryCacheService
* Convert PartitionLookupSvcImpl to use MemoryCacheService
* add test
* add test
* add test
* fix tests
* version bump
* Bump to core release 6.0.22 (#5028)
* Bump to core release 6.0.16
* Bump to core version 6.0.20
* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper
* Bump to core 6.0.22
* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)
* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID
* added changelog
* changed to valid version number
* changed to valid version number, need to be ordered by version number...
* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)
5123 - Use DEFAULT partition for server-based requests if none specified
* consent remove all suppresses next link in bundle (#5119)
* added FIXME with source of issue
* added FIXME with root cause
* added FIXME with root cause
* Providing solution to the issue and removing fixmes.
* Providing changelog
* auto-formatting.
* Adding new test.
* Adding a new test for standard paging
* let's try this and see if it works...?
* fix tests
* cleanup to trigger a new run
* fixing tests
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118)
* fix, test, changelog
* fix, test, changelog
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* Rename file to force IT mode
* _source search parameter needs to support modifiers (#5095)
_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers
* Fix HFQL docs (#5151)
* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)
* Initial failing test.
* Solution with changelog.
* fixing format.
* Addressing comment from code review.
* fixing failing test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* documentation update (#5154)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Fix hsql jdbc driver deps (#5168)
Avoid non-included classes in jdbc driver dependencies.
* $delete-expunge over 10k resources will now delete all resources (#5144)
* First commit with very rough fix and unit test.
* Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest.
* Spotless
* Fix checkstyle errors.
* Fix test failures.
* Minor refactoring. New unit test. Finalize changelist.
* Spotless fix.
* Delete now useless code from unit test.
* Delete more useless code.
* Test pre-commit hook
* More spotless fixes.
* Address most code review feedback.
* Remove use of pageSize parameter and see if this breaks the pipeline.
* Remove use of pageSize parameter and see if this breaks the pipeline.
* Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases.
* Deprecate the old method and have it call the new one by default.
* updating documentation (#5170)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* _source search parameter modifiers for Subscription matching (#5159)
* _source search parameter modifiers for Subscription matching - test, implementation and changelog
* Removal of meta tags during updates do not trigger subscription (#5181)
* Initial failing test.
* adding solution;
fixing documentation;
* spotless apply
* adding changelog
* modifying current test
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Issue 5173 get gateway everything doesnt return all patients (#5174)
* Failing test
* Also set offset and count in base DAO override
* Changelog
* Fix for specific case where count has been set in parameters
* spotless
* Improve checks
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175)
* First commit with failing unit test and small tweaks.
* Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing.
* Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl.
* Revert PackageResourceParsingSvc to release branch baseline.
* Accept code reviewer suggestion to change changelog description.
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Fix link
* Remove target slf4j version
* dont use new API for a bit (#5191)
* Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193)
DropIdGeneratorTask.
* Dqm performance bug update and provider loader fix (#5180)
* update tests, move properties, update operation loader
* update wip
* remove test
* fixing tests, adding config
* update config and provider loader
* fix bundles
* fix cache settings on tests
* version bump and change log
* version bump
* fix formatting
* CVE-2022-45868
* wip cve change
* cve h2 add back in
---------
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
* bulkExportReuse with POST and GET (#5161)
* string manipulation
* Code to ensure bulkExportReuse works with POST and GET requests
* Added formatting changes
* Fixed tests that were not working
* Formatting
* Code clean up
* fixing test failures
* fixing test failures
* Removed arrOfParams to now utilize ObjectMapper
* Removing stack trace and adding an exception
* Fixed test issue
* formatting
* formatting
* Resolving code review comments
* Reduce size of subscription max results (#5194)
* Reduce MAX_SUBSCRIPTION_RESULTS to 10000
* Add changelog
* 5037 goldenresource remains when target resource deleted (#5038)
* draft test and fix
* remove unused fields
* remove unused fields
* remove unused fields
* draft test + solution for possible match case
* combine sql statement + more error checking
* add test case for possible duplicate
* add config for autodeleting grs
* refactoring, adding support for mongo, docs
* refactoring + fixing mongo queries
* add changelogs
* fix both way link removal
* clean up test comments
* rename method
* remove unnecessary bean
* merge master/resolve conflicts
* mvn spotless
* address comment
* changes to avoid version bumping
* spotless
* change error code
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* dont use new API for a bit (#5190)
* licenses
* wip
* Fix API usage
* wip
* Version bump
---------
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
* added validateExpungeEnabled() call to type-level expunge, moved two overloading method so that they are next to each other
* added test for expunge
enabled expunge for testExpungeAllVersionsWithTagsDeletesRow in FhirResourceDaoR4QueryCountTest
* added changelog
* optimized tests and changelogs
* version bump
* Bump to core release 6.0.22 (#5028)
* Bump to core release 6.0.16
* Bump to core version 6.0.20
* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper
* Bump to core 6.0.22
* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)
* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID
* added changelog
* changed to valid version number
* changed to valid version number, need to be ordered by version number...
* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)
5123 - Use DEFAULT partition for server-based requests if none specified
* consent remove all suppresses next link in bundle (#5119)
* added FIXME with source of issue
* added FIXME with root cause
* added FIXME with root cause
* Providing solution to the issue and removing fixmes.
* Providing changelog
* auto-formatting.
* Adding new test.
* Adding a new test for standard paging
* let's try this and see if it works...?
* fix tests
* cleanup to trigger a new run
* fixing tests
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118)
* fix, test, changelog
* fix, test, changelog
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
* Rename file to force IT mode
---------
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
* FQL tests
* Working so far
* Tests working
* Tests passing
* Work on parser
* Tests passing
* Cleanup
* Working
* Work on parser
* Work
* Working
* Work on tests
* Work on driver
* Work
* Ongoing work
* Rename SEARCH to WHERE
* Work on fhirpath
* Test fixes
* Work on statements
* Build fixes
* Spotless application
* Fix CI
* Build fixes
* Clean up changelogs
* Remove redundant gitignore
* Add docs
* Add docs
* Code cleanup
* Build cleanup
* Fix compile error
* Test fixes
* Test fix
* Test fix
* Work on integration
* Work on design
* Work on UI
* Update hapi-fhir-jpaserver-hfql/src/main/java/ca/uhn/fhir/jpa/fql/jdbc/JdbcDriver.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Address review comments
* Review comments
* HFQL work
* Cleanup
* CLeanup
* License headers
* Test fixes
* HAPI version bump
* License header update
* Changelog cleanup
* Fixes
* Test fix
* Fix spotless issues
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* returned user-friendlier message, implemented unit tests, added changelog
* reformatted file
* added Msg.code to the exception thrown
* added Msg.code in test
* Changed to catch DataIntegrityViolationException only.
* 5103 - Adjust our handling of space escape characters in URLs
* 5103 - Fix formatting
* 5103 - Adjust URL escaping and update test expectations
* 5103 - additional test for values with literal plus signs
* 5103 add changelog for this issue
* 5103 - documentation change to describe proper URL escaping
* 5103 - Minor documentation addition
* Fix bug by maintaining a separate list of resource types including the custom resources that will be used to validate the Bundle resources.
* Add custom resource types to resource types list and add conditional logic in ValidationDataInitializerSvcImpl to ensure there is no Exception when parsing a custom resource type.
* Add changelog.
* Remove unnecessary change.
* Address code review feedback.
* Address code review feedback.
* Add one more unit test.
* Bump to 6.7.14-SNAPSHOT.
* relegate surefire config to parent pom pluginManagement
* back out build fix to see if stack trace now shows up in logs
* back out the backed out fix.
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Partial implementation after this has been paused: Move trimming of value and system from BaseSearchParamExtractor to ResourceIndexedSearchParamToken. Do not throw Exceptions in TokenPredicateBuilder. Ensure that the hash computing in the search param token takes the 200+ token value into account. Other search param tokens are not yet implemented.
* in ResourceIndexedSearchParamToken,changed hardcoded length to constant MAX_LENGTH;
in BaseSearchParamExtractor, added check in createTokenIndexIfNotBlank so that the return value is null if system or value is blank.
* added test for TokenPredicateBuilder to verify that long values exceeds the max length does not cause exception.
added test in FhirSystemDaoR4SearchTest to verify searchParamToken with longer system and value than max length can be created successfully. And hash value will be calculated before truncation
* fixed a logical error in previous commits
* changed existing tests to accommodate for the changes
* modified existing tests
* added changelog
* changed truncation method name and added comments
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* modified changelog
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* combined redundant tests
---------
Co-authored-by: tyner <tyner.guo@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - test added
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix test
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - send BatchJobWorkNotification after commit
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - changelog fix
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* GenericClient POST paging support - implementation and test
* GenericClient POST paging support - fixes
* GenericClient POST paging support - fixes
* GenericClient POST paging support - failed tests fix
* GenericClient POST paging support - HAPI version bump
* Added unit test and bug fix to ensure no two partitions with the same ID can be created.
* Added changelogs, and changed the equals operator.
* Made required changes to ensure updating of partition is not affected
* Changed unit test and its location to ensure functionality.
* changing for loop to findById to avoid iteration over all partitions.
* Only allows findById when list is not empty, deals with that edge case.
* Replaced null with isPresent in if statement to fix issues regarding the creation of links on different partitions
* Removed the findAll command within the function. To avoid searching twice.
* Edited the changelogs to properly describe the issue that we have at hand
* Edited the changelogs to properly describe the issue that we have at hand pt 2, wording changes.
* Implemented fixes, created test for JPA side
* Added test and getter for test for register listener
* refactored test names to make them more descriptive
* Modified tests
* resolved comments
* created changlog
* changed test to use MAX_MANAGED_PARAM_COUNT, and created the corresponding getter
* start building tests
* add test
* Basic test and fix bug
* remove tests, fix existing test
* fix up tests
* fix up tests
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* validate-code on remote-terminology service returns NullPointerException - tests
* validate-code on remote-terminology service returns NullPointerException - fixed
* validate-code on remote-terminology service returns NullPointerException - added changelog
* validate-code on remote-terminology service returns NullPointerException - tests readability improvement and fixes
* validate-code on remote-terminology service returns NullPointerException - fixes
* added failing test
* added support for warning messages to batch2
* added change log
* fixed errors from merge, made warning work with new batch2
* fixed message parse, changed interface method to default, formatting changes
* added changelog
* code review changes
* code review change
* added new implementation for warning message processing, fixed migration
* changed column to lob, as text is not well supported
* code review changes
---------
Co-authored-by: Steven Li <steven@smilecdr.com>
* Unit tests for validation after install and uninstall IG
* Fix validation result cached after install and uninstall IG
* Fix validation result cached after install and uninstall IG - updated changelog
* Fix validation result cached after uninstalling IG - updated changelog
* Fix validation result cached after uninstalling IG - fixed unit tests
* Fix validation result cached after uninstalling IG - fixed changelog
* Fix validation result cached after uninstalling IG - test fixes
* Bump core, fix compilation errors
* Match pattern in kindling for use of version
Match the pattern used by Grahame in this update of kindling: f765642470
* Bump core, fix compilation errors
* Match pattern in kindling for use of version
Match the pattern used by Grahame in this update of kindling: f765642470
* Bump core to 6.0.5, fix compilation errors
* Bump to core version 6.0.8
* Individual message code for exception
* Bump core to 6.0.10
* Fix test message
* initial test
* Adding changelog
* Updated to remove the discarding of search params starting with an underscore
* test commit
* Updated handling of search parameters with underscores
* Revert work in progress
* Updated storage settings with new property for inline tag storage mode
* Updated storage settings to tell when inline tag storage mode is set
* simplified test failure
* Added tests for _tag and _system
* Add PreviousVersion service with tests (#4902)
* started writing PreviousVersionReader
* started writing PreviousVersionReader
* moar tests
* add partitioning to the test
* switch subscription to use previous version reader
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Updated logic to be less confusing
* Bumping version to 6.7.4
* Reverted hapi bump, added improve logic for handling missing search params
* updates
* Updated failing tests
* remove redundant tests
* more updates
* Adding Jira number.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: David Raeside <davidraeside@smilecdr.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
Co-authored-by: David Raeside <david.raeside@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* WIP
* add canonicalizer for R4 topic subscriptions
* test R4 topic subscription registration
* Add support for R4 Subscription Topic Backport
* FIXME
* add filter matching support
* add simpler signature
* add resource type matching to filter
* review feedback
* fixed
* changelog
* test both ways
* add bundle test
* change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state
* added logs
* changelog
* fix v2 issues
* Clean up WIP comments
* Switch to in-memory event numbers (instead of always 1)
* Final WIP cleanup
* Msg.code
* review feedback
* review feedback
* review feedback
* review feedback
* back out import changes
* back out import changes
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Delete expunge with cascade
* Work
* Workgin
* Version bump hibernate
* Start working on delete cascade
* Work on delete expunge
* Test fixes
* Test fixes
* Add changelog
* Work on cascade
* Fixes
* Test work
* Test fixes
* Force Verify tests
* fix ITs (#4809)
* fix RestHookTestR5IT
* fix intermittent
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix migrator error on Oracle (#4814)
* Fix Oracle SQL error
* Add changelog
* Update clinical reasoning version (#4816)
* Update clinical reasoning version
* Update version
* Update version
* Clean-up and more wireup of evaluationSettings
* Add changelog
---------
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
* Opening the care-gaps endpoint for GET. (#4823)
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
* added version to mdm golden resource tag (#4820)
Co-authored-by: Long Ma <long@smilecdr.com>
* Update the changelog for 4697 to be more descriptive (#4827)
* Update the changelog for 4697 to be more descriptive
* Futher tweaks of the changelog
* Fixes a bug with tags. (#4813)
* Test, fix
* Drop constraint, add migration
* Add changelog
* Fix userSelected null vs false
* Fix merge
* Fix up checkstyle whining
* One more failure
* Fix test
* wip
* changelog clarity
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* change index
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* fix migration issue (#4830)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Create correct version enum
* Remove superfluous migration
* fixing test (#4835)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* email subscription, throw NullPointerException (#4790)
* fix bug
* Favoring constructor initialization to autowiring.
* enhancing test.
* Making class LoggingEmailSender available outside of the hapi-fhir-japserver-uhnfhirtest module.
* Passing all tests.
* adding changelog.
* Bumping version to 6.5.20-SNAPSHOT
* addressing code review comment.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Add docs for CR operations (#4855)
* Add docs for CR operations
* Correct changelog and javadoc for $package
* Add documentation for $apply parameters
* Add additional documentation for $package
* Cleanup
* Cleanup
* Cleanup
* Address review comments
* Add documentation for $care-gaps operation. (#4862)
* Add documentation for -gaps.
* addressing the comments.
---------
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
* 4853 validation does not error when display is not the same as the display defined in the codesystem 2 (#4854)
* added failing test
* implemented the solution
* changed test name
* added change log
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4853-validation-does-not-error-when-display-is-not-the-same-as-the-display-defined-in-the-codesystem-2.yaml
Co-authored-by: James Agnew <jamesagnew@gmail.com>
---------
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* fixing patient everything operator (#4845)
* fixing patient everything operator
* review fix
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* fix link
* Move image file
* Bundle resources containing over 100 references to the same Organization will fail with HAPI-2207 (#4871)
* Add failing unit test.
* Fix JpaId Long equality comparison to use ! equals() instead of !=, which fails for different instances of the same Long value.
* Add changelog.
* added warn message and test (#4848)
* added warn message and test
* code review fixes
---------
Co-authored-by: Long Ma <long@smilecdr.com>
* Issue 4804 full table scan on mpi link during mdm clear (#4805)
* version bump for next release (#4793)
* version bump
* Bump to correctnumber
* Version Enum and folder
* Remove interim from list
* wip
* Fix operation on nested type-choices in FhirPatch implementation (#4783)
* Fix operation on nested type-choices in FhirPatch implementation
* Add credit for #4783
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* #4468 fix previous link offset no cache pagination (#4489)
* #4468 Add test reproducing the issue
* #4468 Fix previous link for no cache offset pagination
* #4468 Use unchecked URI parsing
* Credit for #4489
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Changelog and data generating test
* Add MdmLink index
* Avoid double link deletion
* Use ThreadLocal safely
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Fix erroneous batch 2 $export 75% complete count when the job is COMPLETE (#4859)
* Add failing unit test.
* Add conditional logic to the InstanceProgress progress percentage to disregard the incomplete count if this is called from the reduction step. This is to get around a race condition in which a work chunk is QUEUED and not yet complete when the reduction step calculates the progress.
* Add final.
* Add changelog.
* disable wars (#4877)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4868 fix paging hapi (#4870)
* fixing some offset and adding a test
* fixing the offset paging
* Removing duplicate
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
* 4875-binary-access-write-doest-trigger-STORAGE-BINARY-ASSIGN-BLOB-ID-PREFIX-pointcut (#4876)
* Add failing test
* Add failing test
* Fix and changelog
* Pass content type parameter
* Back to auto wiring the context
* Invoke interceptor only when getting blobId, not also when storing it
* Avoid breaking implementers
* Address review comment
* Add new exception Msg code
* Fix broken test
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Fix batch job (bulk export) processed record count (#4879)
* Remove racy stats recalc.
* Throw 404 when requesting $export of non-existent Group or Patient (#4890)
* Remove default implementation intended only for interim backwards compatibility (#4894)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Rule apply patient export (#4893)
* Test, fix, and changelog
* Better partition resolution
* Add checks based on rule applier
* Fix ordering failure due to hash set
* Allow empty auth interceptor
* Fix up operation type on invocation
* Add more tests, make hack implementation for patient instance level operation
* Tighten test name
* Changelog
* Default method
* remove dead method
* Remove dead autowire
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* cve pom changes (#4898)
Co-authored-by: Long Ma <long@smilecdr.com>
* backport subscription topic bean cleanup (#4904)
* 4891 bulk export do not recurse unasked for resources (#4895)
* updating tests
* fixing bulk export to not fetch resources not requested
* cleanup
* cleanup
* more warning suppressing
* adding error code
* blah
* fix test
* review fixes
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* lowers log level to remove bootup noise (#4908)
* CVE rel 6 6 (#4907)
* cve pom changes
* bump javax.el to jakarta.el
---------
Co-authored-by: Long Ma <long@smilecdr.com>
* Issue 4905 post binary failure invoking interceptor for pointcuts storage preshow resources (#4906)
* Initial failing test
* Avoid applying binary blob id prefix multiple times
* Remove recently introduced method not needed anymore
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Enhance LogbackCaptureTestExtension (#4869)
* repro bug with test, fix bug
* ken informed me he resolved this bug on master, so i'm switching to use his solution
* disable wars
* review feedback
* review feedback
* review feedback again
---------
Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Resolve 4863 from release branch searchparametercanonicalizer does not account for search parameters for custom resources types when converting dstu23 into runtimesearchparam (#4887)
* Modified canonicalizeSearchParameterDstu2 and 3, now correctly detect search parameters for custom resources
* Canonicalizers now correctly handle search parameters for custom resources
* created changelog
* Modification based on comments:
- remove Resource from target field when there are custom resource types
- fixed changelog typo
- removed unnecessary variable providesMembershipInCompartments
* Added tests for the SearchParameterCanonicalizer to test if base and target of RuntimeSearchParam is set as expected for DSTU2, DSTU3, R4, R4B, and R5 resources
* Fixed typo and removed commented code
* re-ordered init methods
* Update changelog
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* modifications following first code review.
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* License
* Remove _lastUpdated filtering of _revincludes. (#4899)
Remove _lastUpdated filtering of _revincludes.
* 4910-dm-migration-error-for-oracle-19c (#4916)
* Remove all_constraints references which break in oracle 19c
* Add changelog
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* 4873 empty fhirid causes missing resource (#4874)
* add check for empty fhirid string and add test
* add test for populateid
* changelog
* version bump
* version bump
* reverse version bump
* Back to 6.5.21-SNAPSHOT.
---------
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
* Fix include canonical url performance (#4919)
Use hash_identity for canonical join
* License
* Version bump
* Fix failure in test
* Licenses
* Review comments for pipeline
* Dead entry
* other typo
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Sam Gunter <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Josie <80289977+pepsiofficial@users.noreply.github.com>
Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
* Add method to get all jobs of a certain status
* add queries
* add tests
* Refactor so extra parameter is not added
* Version bump
* Fix broken test
* Revert accidental change to pom unrelated to version
---------
Co-authored-by: David Chen <david.chen@smilecdr.com>
* enforce no exceptions on the invoking thread in PointCutLatch
* comment
* Msg.code
* Catch exceptions outside of await block
* fix migration issue
* Refactor PointcutLatch and add tests
* fix tests
* fix tests
* fix tests
* fix test
* fix test
* fix test
* fix test
* fix test
* fix test
* fix test
* fix test
* fix test
* fix test
* fix test!
* fix test!
* fix test
* fix test
* clean up latch error formatting
* fix test
* fix test
* fix test
* fix test
* fix test
* fix tests
* fix test
* fix test
* Remove hapi-fhir-jpaserver-uhnfhirtest from build as it is crashing CI
* fix test
* fix intermittent
* A SNAPSHOT dependency on an upstream module was added to HAPI FHIR, which changed and caused some downstream tests to break.
* fix intermittent
* Add Maven enforcer plugin for CR dependencies
* Make maven enforcer conditional on CI builds
* Remove hapi-fhir-jpaserver-uhnfhirtest from build as it is crashing CI
* improve test logging
* pre-review cleanup
* review feedback
* remove hapi-fhir-base-test-jaxrsserver-kotlin from the build
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
* Begin work on BALP interceptor
* Work on BALP
* Basic profile
* Work on BALP
* Add BALP
* Work on balp
* Add update and delete
* Work on BALP
* Add logging
* Tests
* Modify test server
* Work on docs
* Add documentation
* Add changelog
* Fix#4728 - Typos in docs
* Test fixes
* Move changelog
* Update hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/interceptor/balp/BalpAuditCaptureInterceptor.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Resolve PR comments
* Test fixes
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Start porting changes to master that were lost from the release branch.
* Add remainder of tag changes from release branch.
* Changelog changes.
* Fix schema migration.
* Remove duplicate lines.
* Update core to 6.0.1.
* Fixes for new core.
* Bump to snapshot 19 to mirror James' changes.
* Fix migration tasks.
* Fix some of the tests due to the core upgrade.
* Fix rest of tests.
Post review batch2 cleanup.
Review fixes and cleanup from #4647
Deleted methods in IJobPersistence unused in prod paths, and replaced their usage in tests.
Lots of docs.
Replace copy-on-write pattern in JobDefinitionRegistry with simple ConcurrentHashMap
Fixed bad mappings from job ERRORED state to external APIs. People think ERRORED is a failed state. ¯\_(ツ)_/¯
Added some spec tests for chunk purging
Deprecated ERRORED. For deleting in 6.8
Lots of plans for 6.8. Too risky for 6.6
* 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>
* Use java event names for work chunk transitions.
* Cherry-pick d5ebd1f667 from rel_6_4
Avoid fetching work-chunk data (#4622)
* add end time to reduction step (#4640)
* add end time to reduction step
* add changelog
---------
Co-authored-by: Long Ma <long@smilecdr.com>
(cherry picked from commit 37f5e59ffc)
* Cancel processing
Provide error message in cancelled jobs, and avoid transitions in final states.
* Apply tx boundary to starting job and first chunk.
* cleanup
* Apply tx boundary to work chunk processing
* Delete BatchWorkChunk
* Introduce events for job create, and chunk dequeue
* Apply tx boundary to chunk handler
* Move instance cancellation to database
* tx boundary around stats collection and completion
* tx boundary around stats collection and completion
* Extend tx boundary to error, fail, and cancel
* Move failure into status calc
* ERROR is not an "ended" state.
* Revert generics cleanup to avoid noise
* Avoid sending gated chunks twice.
* Make no-data path safer. Cleanup
* Fix mock test for step advance.
* Delete unsafe updateInstace() call
* Cleanup
* Changelog and notes
* Fix cancel boundary. Cleanups
* Cleanup
* Sort mongo chunks for stable paging.
Other cleanup
* Document error handling
* Cleanup
* Update hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/Batch2JobHelper.java
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
---------
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
* Basic test for reading from provider
* Basic test for reading from provider
* Failing test
* Add changelog
* Update hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/BinaryStorageInterceptorR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* a solution for trying to avoid multi-thread issues for transaction bundle processing
* cleanup
* using retries
* mnor tweaks
* checking in
* changes
* updating changelog
* some minor tweaks
* cleanup
* flip if
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* try removing fork count from test-r4
* try removing fork count from the rest of the projects
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* First commit: New tests, logs, and comments.
* Add hacky fix to run pipelines on. Add another unit test.
* Disable baseUrl checking if hasIdentifier() is true.
* Add changelog. Tweak unit tests.
* Remove junk.
* Add more assertions to unit tests. Make new production fix code clearer.
* Add more clarity to unit tests.
* Another unit test fix.
* add tests for r4b subscriptions
* begin with failing test
* prepare for SubscriptionTopicLoader
* backwards compatibility
* subscription topic registry done
* topic matching is working
* all but delivery is working now
* yay test passes with FIXMEs
* FIXME -> WIP
* switch notification to bundle
* message codes
* fixme
* disable services for fhir versions below R4B
* fix regression
* fix intermittent
* this change will likely break some other tests
* try a safer option
* fix tests
* fix intermittent (I hope)
* unit test
* improve logic around topic subscription categorization
* moar test
* moar test
* changed to support both r4b and r5
* moar test
* cleanup for test
* moar test
* moar test
* moar test
* changelog
* comment
* Msg.code
* fix mock
* add update test
* fix test cleanup
* tracking link for version converter issue
* review
* fix test
* fix test
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 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>
* Initial commit adding support for partition awareness to Bulk Export.
* Additional cleanup and remove references in tests to "all partitions".
* Additional cleanup and remove references in tests to "all partitions".
* More cleanup, test fixes and additional checking to validate partition accesses.
* Additional changes to ensure checking of partition during polling operations.
* Add change log.
* More cleanup.
* Change recommended in code review.
---------
Co-authored-by: ianmarshall <ian@simpatico.ai>
* fix test
* fixed
* changelog
* add another test
* improve docs
* fix change log
* fix test
* fix test
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Start work optimizing transaction
* Tons of test cleanup
* Cleanup
* More optimization
* Optimize
* Many tests fixed
* Work on test fixes
* Optimization done, now doing cleanup
* Cleanup
* Add docs
* Test fixes
* Test fix
* License headers
* Test fix
* Test cleanup
* Test fix
volodymyr-korzh
James Agnew
StevenXLi
Emre Dincturk
Tadgh
Ken Stevens
Etienne Poirier
TipzCM
TynerGjs
Steve Corbett
Luke deGruchy
Brenin Rhodes
LalithE
michaelabuckley
dotasek
David
Kevin Dougan SmileCDR
JasonRoberts-smile
Zach Smith
longma1
Justin McKelvy
IanMMarshall
Jens Kristian Villadsen