* fix handling of Windows line ends
* some tests need to wait a little longer for things to get done
* Windows path separator fix
* simpler lineend fix
* more timeouts and another path separator issue
* redo some timeout issues
* Issue in Windows: URI is not hierarchical
* another timeout issue
* Check for a null request resource in the ResponseHighlighterInterceptor when handling the response.
* Small fix to check the right resource, namely, the response resource, not the request resource.
* Check for theGraphqlResponse being null also, as otherwise this breaks a unit test.
* Add a new test to ResponseHighlighterInterceptor.
* 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 wrong pinned version
* Updating version to: 6.2.2 post release.
* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https… (#4291)
* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https://github.com/hapifhir/hapi-fhir/issues/4276
* Credit for #4291
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* backport and changelog for 6.2.2
* Updating version to: 6.2.3 post release.
* fix https://simpaticois.atlassian.net/browse/SMILE-5781
* Version bump to 6.2.3-SNAPSHOT
* Auto retry on MDM Clear conflicts (#4398)
* Auto-retry mdm-clear on conflict
* Add changelog
* Build fix
* Disable failing test
* Update to 6.2.3 again
* Update license dates
* Dont fail on batch2 double delivery (#4400)
* Don't fail on Batch2 double delivery
* Add changelog
* Update docker for release ppipeline
* Updating version to: 6.2.4 post release.
* Add test and implementation to fix potential NPE in pre-show resources (#4388)
* Add test and implementation to fix potential NPE in pre-show resources
* add test
* WIP getting identical test scenario
* More robust solution
* Finalize Code
* Add changelog, move a bunch of changelogs
* Remove not needed test
* Minor refactor and reporting
* Fix up megeback
* update backport info
* update backport info
* Updating version to: 6.2.5 post release.
* please
* fix test
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>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
* Adding plugin to investigate compatibility with Android APIs:
Run with:
- mvn animal-sniffer:check
* No need to declare woodstox here
* Moving the Android check to the Plugin Management and activating it in all projects being used on the platform: base + android + converter + structures + validation.
* Removing `List.of` and `Optional.isEmpty` for Android compatibility.
* Moving animal-sniffer to the CI profile.
* Adding Android check to structures-r4b as well
* Removing Xml-apis from Xerces to see if CI passes.
* Activating Android check in the client lib
* Moving Xerces to the base-lib, the only place needed for Animal Sniffer
* Applying Xerces as a dependency only on CI
* Removing xml-apis from shexjava
* Add test and implementation to fix potential NPE in pre-show resources
* add test
* WIP getting identical test scenario
* More robust solution
* Finalize Code
* Add changelog, move a bunch of changelogs
* Remove not needed test
* Minor refactor and reporting
* Remove duplicate dependency (MemberMatcherR4Helper) from JpaConfig that was present in both JpaConfig and JpaR4Config.
* Add back @Import for JpaConfig to JpaDstu2Config to resolve DSTU2 unit test issue in jpaserver-starter.
* Added Solution + test
* Removed old methods
* fixed issues
* Added refactoring
* Deprecated methods on the interfaces
* Remove todo
* Documentation
* Changelog
* Changelog
* Changelog
* Changes made based on comments
* Changes made based on comments
* Clean up
* hapi bumping to version 6.3.6-SNAPSHOT
* hapi bumping to version 6.3.6-SNAPSHOT
* 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
* First draft of disabling JsonParser "fhir_comment" code. Unit test assertion that JSON is not generated with "fhir_comment" in the resulting resource String.
* Surround fhir_comments logic with conditional logic. Set this to false while awaiting final word from stakeholders. Add unit tests for STU3 and STU2 proving that fhir_comments do not get generated.
* Add conditional logic for JsonParser and fhir_comments and adjust unit tests accordingly. Also, move the HapiFhirStorageResponseCode.json file to the same module as DefaultProfileValidationSupport, namely, the code that actually reads it.
* Add changelog.
* Add missing change to JsonParser that I thought I had pushed. Fix changelog. Fix unit tests assertions to be clearer.
* JsonParser: Cache value of isSupportsFhirComment.
* Support version DSTU2_1 as well and add a new unit test.
* Fix pipeline unit test failures.
* Added possible solution - needs to be refined
* Small changes
* Refactoring
* Refactoring + Test
* Changelog
* Small edits to changelog
* Small changes
* Changes made based on comments
* Clean up
* Changes made based on comments
* Changes made based on comments
Co-authored-by: qingyixia <cherry.xia@smilecdr.com>
* added failing test
* implemented solution
* added more tests
* added changelog
* changed the implementation, now extended to get all the patient based search params for a given resource instead of 2 in a fixed list of resources
* added test for patient bulk export for resources not in patient compartment, fixed implementation to pass test
Co-authored-by: Steven Li <steven@smilecdr.com>
* fix index migration error
* add exception to duplicateNameValidationExceptionList
* - change index name to match convention
- drop old index h2 automatically created
* Revert "- change index name to match convention"
This reverts commit 59f35a1891.
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* Add a failing unit test if we update a link after the MDM version had been bumped.
* Fix bug with new MdmLinkFactory method: newMdmLinkVersionless(). Call this new method from MdmLinkDaoSvc.getLinkByGoldenResourceAndSourceResource() only. Think about other use cases for versionless MDM links.
* Replace all read uses of MdmLinkFactory with newMdmLinkVersionless(). Add detailed documentation about why to do this.
* Add changelog. Reverse wildcard change.
* 4337 - Added a new Index on the HFJ_SEARCH_INCLUDE Table on SEARCH_PID Column. Also, added a migration task for the Index.
* 4337 - Renamed the new DB Index to keep it to 30 chars.
* 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>
* Add "distinct" and "sorted" to "Server knows how to handle" error message.
* Add code comments. No functional changed.
* Add credit for #4311
Co-authored-by: shollid3 <sloan.h.holliday@optum.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* added failing test
* implemented solution
* added change log
* removed special character in change log file name
* added check for member identifier of type MB
* changed msg code to latest
* fixed test for updated msg code
Co-authored-by: Steven Li <steven@smilecdr.com>
* WIP. Basic adjustment of r5 IWorkerContext to core refactor
* Replace FIXME with UnsupportedOperationException
* use fetchResource(class_, uri) instead of UnsupportedOperationException
* Fix breaking tests related to fetchResource
* Fix breaking validation test
Co-authored-by: dotasek <david.otasek@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>
* Move partition ID up from ResourceModifiedMessage to BaseResourceModifiedMessage.
* Add a changelog. Add a new constructor that contains partition ID to ResourceOperationMessage. Add partition ID to the toString() for BaseResourceModifiedMessage. Tweak constructors of all classes to make sure ResourceModifiedMessage always sets default partition IDs, but BaseResourceModifiedMessage and ResourceOperationMessage do not.
* Reverse an accidental whitespace change.
* Small code review fixes including removing comments and updating changelog description.
* Restore whitespace to what it was on master.
* Fix YAML error.
James Agnew
William Denton
Luke deGruchy
Tadgh
Kevin Dougan SmileCDR
alackerbauer
Ken Stevens
Vitor Pamplona
Dimitri04
Qingyixia
karneet1212
michaelabuckley
KGJ-software
Nathan Doef
StevenXLi
jmarchionatto
JasonRoberts-smile
JP
VK-SMILECDR
kateryna-mironova
granadaCoder
dotasek
Etienne Poirier
Mark Iantorno