* Partial implementation after this has been paused: Move trimming of value and system from BaseSearchParamExtractor to ResourceIndexedSearchParamToken. Do not throw Exceptions in TokenPredicateBuilder. Ensure that the hash computing in the search param token takes the 200+ token value into account. Other search param tokens are not yet implemented.
* in ResourceIndexedSearchParamToken,changed hardcoded length to constant MAX_LENGTH;
in BaseSearchParamExtractor, added check in createTokenIndexIfNotBlank so that the return value is null if system or value is blank.
* added test for TokenPredicateBuilder to verify that long values exceeds the max length does not cause exception.
added test in FhirSystemDaoR4SearchTest to verify searchParamToken with longer system and value than max length can be created successfully. And hash value will be calculated before truncation
* fixed a logical error in previous commits
* changed existing tests to accommodate for the changes
* modified existing tests
* added changelog
* changed truncation method name and added comments
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* modified changelog
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* combined redundant tests
---------
Co-authored-by: tyner <tyner.guo@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* 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>
* 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.
* enabled test
* added explanations to disabled tests
* added explanations to disabled tests
* yay enabled another one
* yay enabled another one
* testEverythingWithLargeSet2 failing intermittently
* fix intermittent regression introduced by splitting test class
* test passes
* need to document
* updated documentation
* prereview cleanup
* change log
* cleanup
* cleanup
* added breaking changes
* update changelog and breaking changes upgrade document to reverse the change to always return 200 per the spec.
* back out documentation change
* update documentation
* fix tests
* dstu2
* dstu3
* fix r4 validation warning test
* changelog
* hapi-fhir version bump to 6.5.10-SNAPSHOT
* fix cdr test
* fix tests
* remove accidental commit
---------
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Start work optimizing transaction
* Tons of test cleanup
* Cleanup
* More optimization
* Optimize
* Many tests fixed
* Work on test fixes
* Optimization done, now doing cleanup
* Cleanup
* Add docs
* Test fixes
* Test fix
* License headers
* Test fix
* Test cleanup
* Test fix
* First commit: prototyping code.
* Push down hard-coding of MdmLink revision results into MdmLinkQuerySvcImplSvc.
* More fixes and push hard-coded MdmLink revisions to DAO. Add unit test for converter. Add largely disabled new Spring config to load the AuditReader. Add new interface method to Dao interface.
* Add config key for enabling envers. Add generated javadoc to EnversAuditConfig. Add properties for both the new config and the new mdm history REST API.
* First commit post-merge with new logic to retrieve audited MdmLinks and convert them to JSON.
* Change revision timestamp long to a Date.
* Add a separate inheritance hierarchy for BasePartitionable classes that use Hibernate Envers. Ensure MdmLink is part of this new hierarchy. Fix HapiFhirJpaMigrationTasks to properly migrate the modification of HFJ_REVINFO from long to timestamp and to add partition_id and partition_date to the MdmLink audit table.
* Deprecate IMdmLinkDao.findHistory() and mark for removal as well as related methods.
* Add changelog. Handle empty query results. Remove hard-coded disabling of envers. Clean up JPA code. Clean up unit tests and make them pass.
* Add new hapi-fhir system property to disable envers but leave it enabled by default. Fix nasty validation bug in IdHelperService. Tweak MDM dao to throw another Exception and code if envers is disabled.
* Fix error code messages. More cleanup.
* Another error code fix.
* Add documentation for new feature.
* Fix unit test. Fix migration tasks to drop and add column instead of modifying it because of a postgres error.
* Cleanup TODOs, delete dead code, tweak unit tests, move/rename classes.
* Default implementation of new history DAO method to avoid need for bump.
* Non-dupe Msg code.
* Since 6.5.7.
* Remove misleading comment.
* Set disabled to TRUE, not FALSE.
* First round of code review fixes.
* Apply documentation suggestions from code review
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Code review fix: Split out $mdm-link-history into a separate provider that's enabled by configuration.
* Change configuration strategy from system properties to JpaStorageSettings and JpaStorageSettingsConfigurer. Hook into these new settings from HibernatePropertiesProvider. Update more documentation.
* Fix unit test failure in SearchQueryBuilder.
* Apply suggested Javadoc and documentation changes from code review
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Change semantics for this feature from disabled to enabled.
* Fix failing unit test.
* Fix conditional logic for reversal of envers disabled/enabled.
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
---------
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
* Start work on refchains
* Semi working
* Add tests for transactions
* Add docs and lots of tests
* Add changelog
* Add tests
* Work on cleanup
* Add document operations
* Test fix
* Test fix
* Fixes
* Fix typo
* Test fix
* Test update
* Test updates
* Test fix
* Test fixes
* Test additions
* Test fix
* Add some javadocs
* Test fixes
* Intermittent test fix
* Doc tweak
* Test fixes
* Merge master in
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/search.md
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Review comments
* Version bump
* Add license
---------
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Creating test to reproduce the issue.
* rebasing development branch from release to master.
* adding migration task.
* providing solution to duplicate resource creation and passing initial test.
* making initial test more readable.
* Implementing test for scheduled deletion of stale searchUrl entries.
* Implementing test for scheduled deletion of stale searchUrl entries.
* Removing interface declaration since it was not needed.
* Reverting changes.
* Adding changelog.
* Adding comments for clarity.
* Adding purgeDatabase operation in IT to delete all ResourceSearchUrlEntity [before|after}Each tests.
* Adding pom.xml exclusion to get all tests passing.
* Adjusting query counts and adding pointcut name to log in interceptor.
* Fixing typos.
* WIP
* implementing edge case tests and solutions.
* wip: passing all tests.
* wip: passing more tests .
* wip: passing tests.
* wip: passing tests.
* enhancing the test.
* changes following code review.
* modifications to tests.
* minor modifications following second code review.
* passing all tests.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Start work on sharded DB
* Work on migrating
* Work
* Ongoing work
* Ongoing work
* Work
* Work
* Ongoing work
* Work
* Work
* Test fix
* Test fix
* Work
* Compile fix
* Test cleanup
* Test fix
* Resolve fixmes
* Resolve fixme
* Resolve compile errors
* Compile fix
* Fixes
* Work
* Add note for later
* Test fix
* Test fixes
* Build fix
* Test fixes
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Fixes
* Fixes
* Remove dead code in pom
* More test cleanup
* Docs fix
* Changes
* Fix
* Fixes
* Resolve merge conflicts
* Build update
* Merge build fixes
* Version bump
* Address review comments
* Review comments
* Review comments
* Test fixes
* Test fix
* Cleanup
* init rev
* id to jpa and mongo id
* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods
* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods
* fixed conflicts, pulled from master
* fixed code for passing tests successfully
* changed PersistentId to Jpa in MdmSearchInterceptor
* added the todo comments with questions
* added one more question
* renamed TODO questions
* first pass at converting to generic ResourcePersistentId
* fix test
* fix test
* fix test
* make ResourcePersistentId abstract
* Generic type MdmLink
* Final TODOs
* Final TODOs
* cleanup
* fix test
* fix id to string
* fix cyclic package dep
* add <?> to Base so we can extract interface
* Revert "add <?> to Base so we can extract interface"
This reverts commit a806f3d2bc.
* switch to interface
* javadoc
* replace base with interface
* fix test
* add generic template to mdmdao
* remove unneccessary JpaPid casts
* remove unneccessary JpaPid casts
* remove unneccessary JpaPid casts
* remove unneccessary MongoPid casts
* fix test
* fix regression
* fix compile issues arising from merging master
* fix beans
* bump version to 6.3.3-SNAPSHOT
* change logs
* review feedback
* review feedback
* fixme
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Initial test.
* Solution implementation with test adjustment.
* Adding changelog.
* Modifications following first code review.
* Moving changelog to 6.4.0
* Further reductions in query counts
* Fix for broken test
* Test fix
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Improve JPA response messages
* FIxes
* Test fixes
* Test fixes
* Ongoing testing
* Work on messages
* Work on messages
* Add valueset
* Add response code enum
* Version bump
* Undo bump
* Improve changelog
* Test fixes
* Add javadocs
* Version bump HAPI
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Account for review changes
* Test fix
* Docs fix
* Work on API
* Improve SqlQuery api
* jm wrong bundle entry url (#4213)
* Bug test
* here you go
* Generate relative URIs for bundle entry.request.url, as specified
* Point jira issue in changelog
* Adjust tests to fixes
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* improved logging (#4217)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Rel 6 1 3 mergeback (#4215)
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Revert offset mode change
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
* Updating version to: 6.1.1 post release.
* fix compile error
* Deploy to sonatype (#3934)
* adding sonatype profile to checkstyle module
* adding sonatype profile to tinder module
* adding sonatype profile to base pom
* adding final deployToSonatype profile
* wip
* Revert version enum
* Updating version to: 6.1.1 post release.
* Add test, changelog, and implementation
* Add backport info
* Create failing test
* Implemented the fix, fixed existing unit tests
* added changelog
* added test case for no filter, exclude 1 patient
* wip
* Add backport info
* Add info of new version
* Updating version to: 6.1.2 post release.
* bump info and backport for 6.1.2
* Bump for hapi
* Implement bug fixes, add new tests (#4022)
* Implement bug fixes, add new tests
* tidy
* Tidy
* refactor for cleaning
* More tidying
* Lower logging
* Split into nested tests, rename, add todos
* Typo
* Code review
* add backport info
* Updating version to: 6.1.3 post release.
* Updating version to: 6.1.3 post release.
* removed duplicate mention of ver 6.1.3 in versionEnum
* backport pr 4101
* mdm message key (#4111)
* begin with failing test
* fixed 2 tests
* fix tests
* fix tests
* change log
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* backport 6.1.3 docs changes
* fixed typo on doc backport message
* fix test breaking
* Updating version to: 6.1.4 post release.
* wip
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@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: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* pin okio-jvm for kotlin vuln (#4216)
* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)
* First commit: Failing unit test and a TODO with a vague idea of where the bug happens.
* Don't escape "+" in a URL GET parameter if it starts with "application".
* Remove unnecessary TODO.
* Add changelog.
* Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens.
* Ks 20221031 migration lock (#4224)
* started design
* complete with tests
* changelog
* cleanup
* tyop
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)
* Added test
* Added solution
* Changelog
* Changes made based on comments
* Fix bug with MDM submit
* fix
* Version bump
* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)
* Add constant for interceptor
* add test, changelog
* Allow Batch2 transition from ERRORED to COMPLETE (#4242)
* Allow Batch2 transition from ERRORED to COMPLETE
* Add changelog
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)
* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.
* Update test case.
* Cleaned up changelog.
* Added test case for multiple resource types.
* Added failing test case for not returning Binary resource.
* Refactor solution.
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* Add next version
* bulk export permanently reusing cached results (#4249)
* Add test, fix bug, add changelog
* minor refactor
* Fix broken test
* Smile 4892 DocumentReference Attachment url (#4237)
* failing test
* fix
* increase test Attachment url size to new max
* decrease limit to 500
* ci fix
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Overlapping SearchParameter with the same code and base are not allowed (#4253)
* Overlapping SearchParameter with the same code and base are not allowed
* Fix existing tests according to changes
* Cleanup dead code and remove related tests
* Version Bump
* ignore misfires in quartz
* Allowing Failures On Index Drops (#4272)
* Allowing failure on index drops.
* Adding changeLog
* Modification to changelog following code review.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Revert "ignore misfires in quartz"
This reverts commit 15c74a46bc.
* Ignore misfires in quartz (#4273)
* Reindex Behaviour Issues (#4261)
* fixmes for ND
* address FIXME comments
* fix tests
* increase max retries
* fix resource id chunking logic
* fix test
* add modular patient
* change log
* version bump
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Set official Version
* license
* Fix up numbers
* Fix up numbers
* Update numbers
* wip
* fix numbers
* Fix test:
* Fix more tests
* TEMP FIX FOR BUILD
* wip
* Updating version to: 6.2.1 post release.
* Add a whack of logging
* wip
* add implementation
* wip and test
* wip
* last-second-fetch
* expose useful method
* remove 10000 limit
* Strip some logging
* Fix up logging
* Unpublicize method
* Fix version
* Make minor changes
* once again on 6.2.1
* re-add version enum
* add folder
* fix test
* DIsable busted test
* Disable more broken tests
* Only submit queued chunks
* Quiet log
* Fix up checkstyle
* log to console
* Remove double import
* Version bump
* licenses
* Fix up version
* fix build
* wip
* wip
* Fix up search expansion to use new behaviour of idhelper service
* Fix up MDM Search Expansion
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@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: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Add failing test
* Add failing test for hsearch reference without type
* Modify cache to store forcedid type
* Disable failing test until finding out if it is a bug and strategy for fix in that case
* Remove fixmes and commented lines
* Update test. Add changelog.
* Added test that passes on this branch.
* Added Encounters to test case.
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
* POST release deferred cleanup
* Fixes
* One more test fix
* Test fixes
* Test fixes
* Test cleanup
* Test fixes
* Fixes
* ValueSet cleanup
* Test fix
* Test fixes
* Fixes
* Test fixes
* Fixed
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixc
* Build fix
* Fix merge artifact
* Build fix
* Work on tests
* Test fixes
* Work
* Fixes
* Changelog fix
* Add changelog
* Test fix
* Test fixes
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Tests
* Bumps
* Fixes
* Add errorprone
* Drop bz2 bins
* POM fix
* Build fix
* Update
* Test fix
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Tadgh
Luke deGruchy
TipzCM
michaelabuckley
James Agnew
Nathan Doef
Kevin Dougan SmileCDR
Ken Stevens
Isaac Wen
samguntersmilecdr
Etienne Poirier
kateryna-mironova
jmarchionatto
samuelwlee2