* Suspend tx when refreshing version cache
* Undo refactor to reduce merge size
* changelog
* Bump to 7.1.3
* Fix version test
* Unwrap transaction proxy
* 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>
* Add setting to make broker not use JacksonMessageConverter
* Add changelog
* Implement suggestions
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.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.
* Improve readability
* Fix warnings
* Add interceptor, test doc and changelog. Also, extract common used function to utility class and add tests.
* spotless
* Fix changelog link
* Fix changelog fragment warnings
* Fix changelog link
* Fix documentation link
* Implement review comments
* Implement review comments
* Keep old exception code for tests
* Revert refactoring which lost difference between NonCompartmentMemberTypeResponse and NonCompartmentMemberInstanceResponse
* spotless
* Remove version restriction
* Differentiate exceptions thrown by different code
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@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>
* 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
* 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
* 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>
* 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>
* _source search parameter needs to support modifiers (#5095)
_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers
* Fix HFQL docs (#5151)
* repository measure refactor
* undo bundle edit, add config
* embedded library true
* undo post of bundle
* clear library cache on test
* fix sumbit-data test
* missing packages from cql
* fix test data and test cases for repository api
* 3.0.0 clinical reasoning uplift
* r4 cql execution provider and tests
* fix submitdata provider config
* wip cql tests
* debugging cql op wip
* wip debugging cql
* update tests for $cql, fix class names
* prep for Pre6 uplift
* spotless checks and test fixes
* bump to 3.0.0-PRE6
* cleanup
* fix version
* cleanup
* fix exlusions in pom
* add in cache invalidation config
* search converter bug and test for repository
* update searchconverter
* version bump, add changelog
* remove term config, move IDaoRegistryUser class
* Break out dstu3 providers and move config to version folders
* CVE-2023-26119
* remove * imports
* code review updates
---------
Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
* Test fixes
* Build cleanup
* Initial test passing
* Test fixes
* Tests all seem to be working
* Make display validation level configurable
* Should be all working
* Add changelog
* Add to changelog
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* WIP Fix compile errors
* Fix compile errors 2
* Fix test fails due to new Validation messages
* Ignore validation issues
Ignore two validation issues:
Two 'side is inherently a collection' warnings are now thrown for the following expressions:
NamingSystem nsd-1 uniqueId.type = 'uuid'
Observation obs-7 code != component.code
There is also a general error ignored because the StructureDefinition for StructureDefinition is actually for FHIR 3.0.1, and contains an invalid expression in constraint sdf-9. This is remedied in the expression used in 3.0.2, but a full update of all profile structure definitions is out of scope for this PR.
* Fix property name
* Add changelog
* Test skeleton, TODO IMPLEMENTER added all over the place
* Add test and TODO IMPLEMENTER
* Add jpa storage property to allow preventing conditional updates to invalidate match criteria
* spotless
* Implement review suggestions
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@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
* 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>
* 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>
* 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.
* extracted ResponseBundleBuilder and started writing unit tests. Currently at 71% coverage.
* asert bundle entries
* assert first entry id
* unknown size
* coverage up to 78%
* test filter nulls
* test null id check
* up to 91% test coverage
* 96% test coverage
* 98% test coverage. this is final state
* fix cyclic dep
* switch to record
* split up large method
* split up large method
* consolidate params
* consolidate params
* IntelliJ Warnings
* cleanup
* cleanup
* extract methods
* extract methods
* param names
* variable name
* formatting
* extract method
* cleanup
* javadoc
* upstream consolidation
* parameter names
* TODO
* TODO
* review feedback
---------
Co-authored-by: Ken Stevens <ken@smilecdr.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
* 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>
* 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>
* 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.
* 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>
* comments from conversation with Gino
* rewrite R5 subscription canonicalization. Expect the r5 subscription tests to fail now
* SubscriptionTopicR5Test passes now
* R4B tests pass now
* first two tests in RestHookTestR5Test now pass. just need to convert the rest
* third test passes
* fourth test passes
* tests pass up to line 294
* wow what a marathon. Turns out when we stripped the version we didn't remove it from the meta version.
* passes up to 427
* RestHookTestR5Test tests pass up to line 582
* RestHookTestR5Test tests pass up to line 591
Added SubscriptionTopicRegisteringSubscriber
* RestHookTestR5Test tests pass up to line 591
Added SubscriptionTopicRegisteringSubscriber
* RestHookTestR5Test tests pass up to line 636
Added SubscriptionTopicValidatingInterceptor
* RestHookTestR5Test tests pass up to line 689
* RestHookTestR5Test tests pass up to line 758
* 4 failures left
* woohoo all tests pass
* all tests pass and no PointCutLatch errors
* Msg.code
* changelog
* checkstyle
* fix some tests
* compile issue
* fix test
* fix regression
* fix test
* R5 currently runs tests in multiple threads, so change the sensitive one to an IT
* licenses
* review feedback
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Michael Buckley
Luke deGruchy
longma1
jmarchionatto
Tadgh
James Agnew
volodymyr-korzh
TipzCM
Justin McKelvy
Emre Dincturk
TynerGjs
Martha Mitran
Taha
Etienne Poirier
dotasek
StevenXLi
Ken Stevens
Brenin Rhodes
David
JasonRoberts-smile
Zach Smith