* Fix#5110 - Failure in tx processing
* Test fix
* Work on narrowins
* Add changelog
* Docs cleanup
* Fix compile error
* Rollback incompatible change
* Test fix
* Test fix
* Force update
* Test fixes
* Build fixes
* Bump HTMLUnit
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5712-apply-searchnarrowing-to-conditional-urls.yaml
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Version bump to 7.1.4-SNAPSHOT
* Spotless
* Roll back version
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Throw exception when resourceType of parameter value is invalid when performing FHIR search with non-chained reference
* Fix changelog issue id and spotless warning
* Cleanup unnecessary test
* Validate resourceType only when using relative reference
* Fix test for search using _type parameter
* Refactor and fix functionality dealing with ReadPartitionIdRequestDetails
* Spotless fixes
* Revert some of the refactoring changes to BaseRequestPartitionHelperSvc and fix tests
* Small cleanup
* Missing change
* Small changes
* Fix tests and add a few more
* Spotless fix
* Address code review comments
* Some polishing on the interface annotations and documentation
* Spotless fix
* Fix test
* Fix tests and test method rename
* Ensure SearchParameterMap is not null
---------
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
* Solution to caching issue with new tests.
* Fix animal sniffer issue. Clean up unit tests. Finalize changelog. Add TODO referencing change in validation cache behaviour.
* Spotless.
* Fix unit test.
* Code review feedback.
* Suspend tx when refreshing version cache
* Undo refactor to reduce merge size
* changelog
* Bump to 7.1.3
* Fix version test
* Unwrap transaction proxy
* Throw exception when resourceType of parameter value is invalid when performing FHIR search with non-chained reference
* Fix changelog issue id and spotless warning
* Cleanup unnecessary test
* Validate resourceType only when using relative reference
* Fix test for search using _type parameter
* 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>
* HAPI FHIR Dependency Bumps
* Hibernate search 6
* Dep bumps
* Bump mockito
* Fix memory leak
* Test cleanup
* Test fix
* Test fixes
* Test fix
* Test fix
* Test fix
* Test fix
* Prepare to try and rework max clauses
* Refactor large VS expansion
* Spotless
* Test fix
* Version bump
* Test fixes
* Bump maven container
* Build fix
* Add license headers
* Version bump
* License headers
* Reverse changes from 5493. Add a stub changelist.
* Add various changes including stub changelist, beginnings of integration test, pass request details to interceptor, obtain partition ID, and stub code for each partition-aware query.
* Spotless. Implement methods and SQLs for both golden and source IDs. Not yet tested. Add default interface methods.
* Fix HQLs that were referring to incorrect columns. Rename parameter. Formatting.
* Fix logic to use single queries by source and golden resource. Filter by partition IDs in Java instead of in SQL. Write a new unit test for MdmLinkExpandSvc.
* Spotless.
* Ensure $everything with mdm expansion works on POST as well as GET. Some cleanup.
* More cleanup.
* Null safety for mdmExpand.
* Spotless.
* Small changes.
* Enhance changelog.
* Delete commented out code.
* First round of code review changes.
* More code review changes.
* 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
* Bump jackson databind
* Pin Version
* Ignored duplicate classes
* Updating version to: 6.10.1 post release.
* Fix pom
* Skip remorte nexus
* make release faster
* Updating version to: 6.10.1 post release.
* remove skiptests
* Oracle create index migration recovery (#5511)
* CLI tool command migrate-database executing in dry-run mode insert entries into table FLY_HFJ_MIGRATION (#5487)
* initial test
* Solution with changelog.
* making spotless hapi
* addressing comments from code reviews
* making the test better.
* addressing code review comment and adding test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* added changelog, fix 6.10.0's version.yaml
* Fix bad resource id migration (#5548)
* 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
* Merge the fhir_id copy migration with the fhir_id fix to avoid traversing hfj_resource twice. (#5552)
Turn off the original migration ForceIdMigrationCopyTask.
Fix it anyway so nobody copies bad code.
Also add another migration ForceIdMigrationFixTask
that fixes the bad data, as well as fills in the fhir_id column for new migrations.
* Fix spacing
* move to non snapshot version
* Fix fixed migration (#5571)
* Fix bad migration, prep for 6.10.2
* spotless
* Version bump
* Updating version to: 6.10.3 post release.
* reorder migrations
* tidy
---------
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>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.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
* Bump jackson databind
* Pin Version
* Ignored duplicate classes
* Updating version to: 6.10.1 post release.
* Fix pom
* Skip remorte nexus
* make release faster
* Updating version to: 6.10.1 post release.
* remove skiptests
* Oracle create index migration recovery (#5511)
* CLI tool command migrate-database executing in dry-run mode insert entries into table FLY_HFJ_MIGRATION (#5487)
* initial test
* Solution with changelog.
* making spotless hapi
* addressing comments from code reviews
* making the test better.
* addressing code review comment and adding test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* added changelog, fix 6.10.0's version.yaml
* Fix bad resource id migration (#5548)
* 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
* Merge the fhir_id copy migration with the fhir_id fix to avoid traversing hfj_resource twice. (#5552)
Turn off the original migration ForceIdMigrationCopyTask.
Fix it anyway so nobody copies bad code.
Also add another migration ForceIdMigrationFixTask
that fixes the bad data, as well as fills in the fhir_id column for new migrations.
---------
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>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
* Work on fixing postgres
* Test fix
* wip
* wip
* wip
* wip
* wip
* adding support for h2 embedded and renaming postgressIT
* Work on postgres
* Remove use of gzip content on postgres
* Cleanup
* Test fixes
* Spotless
* Restore fake db for DDL generator
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* First commit for conditional logic in execute migration tasks along with logic to create new indexes on hfj_spidx_string and hfj_spidx_uri if sp_normalized_value or sp_uri, respectively, have a collation other than "C".
* More fixes. Still TODOs to resolve.
* Add changelog. Clean up TODOs. New message code for precondition SQL checking. javadoc. Unit test enhancements.
* Spotless. Small tweaks. Fix conditional logic for more than one checking.
* Add details to upgrade document.
* Code review feedback.
* Spotless
* Make expunge service extensible
* Work
* Licence headers
* Version bump some dependencies
* Version bumps
* Adapt to new html unit version
* Reintroduce errorprone
* Test fix
* Header
* Work on jakarta
* Test fixes
* Restore errorprone
* More pom tweaks
* Apply spotless
* Errorprone tweak
* errorprone tweak
* Version bump
* License headers
* Version bump
* Postgres bump
* Fixed search for resources for $everything operation with partitions and client id mode = ANY
* fixed formatting
* changelog file renamed for tests
* code review fixes: moved generics mocks to class fields, changed size > 0 to empty check
* removed unused fields
* moved fields back to methods, changed generic anys
* changed imports from javax to jakarta
* code review fixes
* initial tests and implementation of the feature persistence layer.
* initial tests and implementation pointcut to modify JobInstance before persistence.
* spotless happy.
* Addressing comments from first code review.
* happy spotless
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Servlet migrsation changes
* Apply spotless
* Work on migration
* Start working on JPA migration
* Test fixes
* Test fixes
* Test fixes
* Work
* Work on servlet migration
* Work on migration
* Work on fixes
* Imports fix
* Work on tests
* Test fix
* All tests passing
* Work on migration
* Schema generator
* Refactor ID strategy
* Some test fixes
* Test fixes
* API additions
* Work on websockets
* Test fixe
* Version bump
* Work on migration
* All tests have passed!
* Work on test fixes
* Fixes
* Work on fixes
* CDR fix
* Work on migration
* Fixes
* Spotless
* Disable onetoone ban
* Adjust migratyions
* Transaction service fix
* Add tinyint to migrator
* Work
* Migration
* Compile fix
* Add license
* Test fix
* Test fix
* Cleanup
* Cleanup attempt
* Test fix
* Reslve fixmes
* Remove legacy lastn implementation
* Test cleanup
* Cleanup
* Remove dead import
* Bad import setups
* Review comments
* Review fixes
* Build fix
* Test fix
* Spotless
* Account for CR changes
* Compile fixes
* Rollback one change
* Test tweak
* License header
* Test fix
* Test fix part 2:
* Clean up tx isolation
* Spotless
* Spotless apply
* Drop min SQL Server level
* Attempted test fix
* Test fix
* Test fix
* Test fix
* Bump hibernate
* Test fix
* Test fixes
* Test fixes
* Test fixes
* Test cleanup
* One more test fix
* Test fix
* Try to fix test
* Clean up expunge
* Test fix
* Remove unneeded task
* Spotless
* Bump compiler plugin
* Spotless
* Compile fix
* Add license headers
* License header
* Test fixes
* Bump animal sniffer
* Spotless
* Bump Jetty version
* Test fix and version bump
* Cleanup
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient.
* Add FhirContext to ClientResponseContext.
* Introduce a ModifiedStringApacheHttpResponse. Run spotless.
* Remove TDOOs, add and update javadoc.
* Spotless and copyright header.
* Add changelog.
* Unique error message code.
* Only trigger the interceptor if the expected return type is a Bundle.
* Fix spotless.
* Code review feedback.
* Spotless.
* Bump to 6.11.3-SNAPSHOT
* Pass properties through to Remote Terminology Service on CodeSystem operation
* Propagate list of property names throughout. Introduce a parameter object for the lookupCode method. Mark other lookupCode methods as deprecated. Add unit tests.
* Update remote terminology service tests
* Address code review comments
* Fix unit tests
* Address latest code review comments to update default methods
* Address latest code review comments to update default methods - update fallback condition
* Address latest code review comments to update default methods - update fallback condition
* - Changed member-match function param names, and return value
- modified existing tests to accomodate for the change
* removed tests unsuitable for new return value
* resolve code review comments
* version bump
* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted
* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted
* Small changes after code review. Doing some variable/method renaming and correcting changelog Jira issue number.
* There is a programmatic filter enabled which skips installation for certain resources based on their status
in PackageInstallerSvcImpl. The filter can now be controlled via StorageSettings.
* Fix typo in variable name from recent pull request 5461.
* Update to a version of Clinical Reasoning/CQL that no longer includes javax dependencies
* Rev to CR 3.0.0-PRE10
* version bump, pom changes for jakarta conflicts
* undo exclusions from other modules
* Rework exclusions
* Fix type in dependency
* new cr version, exclude conflicts in cr and cds-hooks
* remove exclusions
* pom update
* Redo the exclusions
* add retrieveSettings config
* new CR retrieve settings and config
* update config to new enums and parameters
* update unit tests and config for new cql and terminology properties
* bump CR to 3.0.0-PRE12
* spotless edits, update class path for CR config
* missing dependencies
* swap for jakarta
* moving conflicting dependencies
* Fix a couple code review items
---------
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted
* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted
* Small changes after code review. Doing some variable/method renaming and correcting changelog Jira issue number.
James Agnew
pano-smals
Martha Mitran
Luke deGruchy
Tadgh
Jens Kristian Villadsen
Michael Buckley
Martha Mitran
longma1
Ken Stevens
TipzCM
Justin McKelvy
TynerGjs
kateryna-mironova
Etienne Poirier