* pom bump to 7.0.0 (#5615)
* pom bump to 7.0.0
* add version enum
* fixed feb release name
---------
Co-authored-by: Long Ma <long@smilecdr.com>
* Check index existence on raw SQL creation (#5624)
* Add conditional check on index existence before we try again
* Add conditional check on index existence before we try again
* Changelog
* remit
* remit
* debug statements
* 5621 deadlock on caffeine cache when creating a resource with conditional create (#5622)
* Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback.
* Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations.
* adding changelog and spotless.
* Fixing typo.
* Addressing comments from code review.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)
* Failing test
* fix
* changelog
* Avoiding Exception being thrown on @EventListener invocation (#5628)
* replaced EventListener annotation with @PreDestroy
* adding changelog
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* simple fix (#5630)
Co-authored-by: Long Ma <long@smilecdr.com>
* Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625)
* Incorrect version from versioned_references.auto_at_paths for conditional update - implementation
* Oracle: Ensure migrated database still takes large resource text updates (#5629)
* First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration.
* First stab at agreed upon solution.
* Fix error with 4001 by removing unnecessary annotation.
* Spotless and TODO.
* Remove annotation for good and set length to LONG32.
* Fix copyright year.
* Finalize changelog.
* Remove migration changes. Fix unit test.
* Fix compile error.
* Log output.
* Refactor resource history code into new ResourceHistoryCalculator.
* Spotless.
* Convert record to POJO.
* Restore pre-17 switch statement.
* Finalize new resource history calculator code and tests.
* Spotless.
* Remove logging.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml
Apply code reviewer suggestion
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* Code review feedback.
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638)
* When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases.
* Minor change to fix test
* Rename changelog file
* Remove TODOs as they're replaced by reported issue
* Revert accidental change added with TODO removal
* $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)
* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation
* Fix Measure group id null pointer exception (#5620)
* Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id
* add changelog
---------
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
* Rule evaluation: Allow Bundles with PATCH Parameters (#5641)
* Remove parameters clause.
* Finalize changelog. Add tests. Finalize implementation.
* Undo changes to this test.
* Revert all changes to FhirQueryRuleImplTest. Add new RuleImplOpTest. Ensure that proper nested Bundle is created for test and other fixes.
* Tweak test.
* Use real rule applier in test and remove all mocks.
* Prevent batch2 job execution to stop for empty chunk when last job st… (#5635)
* Prevent batch2 job execution to stop for empty chunk when last job step is a reduction.
Add output to bulk export result even when empty.
* Fix test
* Unimportant change to force fresh build
* Implement review suggestions
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Index review fixes (#5649)
* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.
* Fix conditional creates without leading '?' (#5646)
* First commit with failing test.
* More tests and logs.
* More logs
* Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl().
* Simplify solution. Add more tests.
* Changelog.
* javadoc
* Searching for Bundles with read all Bundles permission returns 403 (#5644)
* failing test
* another failing test case
* fix
* changelog
* fix bug
* spotless
* cr
* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660)
* Serializing changes for sensitive data (#5655)
* Add new senstiive data serializer
* Add new senstiive data serializer
* Add new senstiive data serializer
* Remove dead comments
* Change up the test
* review comments
* wip
* Tighten tests and push annotation down
* Tighten tests and push annotation down
* Changelog
* Add test
* 7.0.1-SNAPSHOT bump
* Error code
* Add method used by CDR
* add version enum
* Fix test
* Rel 7 0 CVE (#5663)
* Bump json-path
* Pin parrson
* Bump elastic
* Bump spring version
* Exclude JDBC
* Descendent fix (#5669)
* Fix "is-a" ValueSet expansion, add "descendent-of" support
* Fixed tests in DSTU3 and R5
* Trigger new build
* Revert "Trigger new build"
This reverts commit 46c672b338.
* fix default partition setting on resource (#5617)
* fix default partition setting on resource
* changelog
* Handle DEFAULT partition in rule checker.
* Fix spotless
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* pom bump, doc add, version enum add (#5616)
Co-authored-by: Long Ma <long@smilecdr.com>
* fix default partition setting on resource (#5618)
* fix default partition setting on resource
* Handle DEFAULT partition in rule checker.
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Add setting to make broker not use JacksonMessageConverter (#5611)
* Add setting to make broker not use JacksonMessageConverter
* Add changelog
* Implement suggestions
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Fix version
* add changelog, add attribution, remove accidental bring-overs
* add changelog, add attribution, remove accidental bring-overs
* Finish jira section
---------
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* fix conflict mistake
* removed test assert that is no longer true:
* version bumpb to 7.1.1
* fix version Enum test
---------
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@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: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Allow cached search with consent active when safe (#5387)
Allow the search cache when using consent if safe
* Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376)
* Change package installation behavior such that it updates the existing SearchParameter base with remaining resources
* Change package installation behavior such that it updates the existing SearchParameter base with remaining resources
* Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable.
* Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable.
* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389)
* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation
* Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177)
* 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)
* 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
* first fix
* tests and preliminary fixes
* wip, commit before switching to release branch.
* adding capability to handle _lastUpdated in reverse search (_has)
* adding changelog
* applying spotless.
* addressing code review comments.
---------
Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.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>
* Br 20231019 add cr settings for cds hooks (#5394)
* Add settings used in CR CDS Services. Remove config dependency on Spring Boot.
* Add changelog
* Use String.format rather than concat strings
* spotless apply
* Add javadoc
* Upgrade notes for the forced-id change (#5400)
Add upgrade notes for forced-id
* Clean stale search results more aggressively. (#5396)
Use bulk DMA statements when cleaning the search cache.
The cleaner job now works as long as possible until a deadline based on the scheduling frequency.
* bump version of clinical reasoning (#5406)
* Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408)
* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added
* removed unused alias from SQL query of mdm-clear (#5416)
* Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)
* Enable child classes to use Boolean class return type
* spotless
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420)
* If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix
* Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423)
This reverts commit 4e295a59fb.
Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com>
* Use new FHIR_ID column for sorting (#5405)
* Sort `_id` using new FHIR_ID column.
* Fix old tests that put client-assigned ids first.
* Better indexing for sort
* Bump core to 6.1.2.2 (#5425)
* Bump core to 6.1.2.1
Patch release that uses https for primary org.hl7.fhir.core package server
* Bump core to 6.1.2.2
* Make sure to return always a value for Boolean class return type. (#5424)
Implement change in a non-disruptive way for overriders
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428)
Add a non-standard __pid SP.
* Review changes for new _pid SP. (#5430)
Change name to _pid to match our standard and add warning.
* Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432)
* Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition.
* Fix spotless issue
* CVEs for 6.10.0 (#5433)
* Bump jetty
* Bump okio-jvm
* 8.2.0 mysql connector
* Jena and elastic bumps
* Fix test
* 5412 post bundle on partition incorrect response.link shown (#5413)
* Initial fix and unit test provided
* spottless check
* Made relevant changes to make solution version agnostic
* relevant logic changes made
* spotless changes made
* New logic added to fix failing test cases
* formatting
* New logic to make the function more robust
* spotless checks
* Left a trailing slash in the tests
* Made relevant test changes and changed logic
* spotless changes
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml
changing changelog
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
* Formatting requirements
---------
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
* Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414)
* first fix
* - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber
- refactored code to reduce repeated code
- cleaned unnecessary comments and reformatted files
* Changed myResourceModifiedMessagePersistenceSvc to be autowired
* removed unused import
* added error handling when inflating the message to email and message subscriber
* reformatted code
* Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc
* Changes by gary
* Reformatted file
* fixed failed tests
* implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File.
* - implemented IT
- fixed logical error
- added changelog
* fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor
* fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor
* resolve code review comments
* reformatted files
* fixed tests
* Fix for failing IT test in jpaserver-starter (#5435)
Co-authored-by: dotasek <dotasek.dev@gmail.com>
* wip
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: dotasek <david.otasek@smilecdr.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: 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: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
Co-authored-by: dotasek <dotasek.dev@gmail.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>
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
---------
Co-authored-by: isaacwen <isaac.wen@smilecdr.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>
* 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
* Refactor to restore LGTM functionality
* Compile fix
* Work on cleanup
* Attempt to restore LGTM
* Work on tests
* Fixes
* Build fixes
* Build fix
* Test fix
* Test fixes
* Work on build
* License header updates
* Test fixes
* Test fixes
* License header
* Test fix
* Test fix
* Test fixes
* Restore LGTM
* Fix azure
* Disable test
* Test fixes
* Test cleanup
* Build fix
* Build fix
* Test fix
* Test fix
* Test fixes
longma1
Luke deGruchy
Tadgh
michaelabuckley
Emre Dincturk
Etienne Poirier
Isaac Wen
Kevin Dougan SmileCDR
Ken Stevens
James Agnew
michaelabuckley