* Add r4b stuff
* Work on R4B
* Core version bump
* Revert some changes
* Add R4B
* Docs
* Test fixes
* Work on R4B
* Tests passgin
* Add config
* Work on merging
* Work
* Work
* Work
* Test fix
* Fixes
* Test fixes
* Test fix
* Work
* Work
* Fixes
* Test fixes
* Fixes
* Test fix
* Test fix
* Test fix
* Version bump
* Test fix
* Test fix
* ompile fixes
* Fix
* Resolve build warnings
* Updates
* Test fixes
* Fix docs
* 3052 Changed IBinaryStorageSvc MaximumBinarySize from int to long.
* 3052 Added changelog
* 3052 Bumped version
* 3052 Remove mysterious +1 on maximum binary size causing overflow.
* Bumping version to 6.2.0-PRE16-SNAPSHOT
* Adding + 1L as original implementation.
* Getting all tests to pass dealing with + 1L.
* Getting all tests to pass dealing with + 1L.
* Adding migration definition and removing unnecessary comment.
* Preventing register overflow when setting maxBinaryStorage.
* Mering relevant test.
* Fixing typo in migration script
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Standardize on one Transactional annotation
* Add changelog
* Disable checkstyle rule
* Fix up transactions
* Test fixes
* Test cleanup
* License headers
* One more dep bump
* Resolve commit issue
* Test fixes
* Test fix
* Dep bump
* Fix
* Fix test
* Version bump
* Test fixes
* Add unit tests and supporting classes from gitlab issue.
* Commit with changes thus far to be reviewed. Namely, add savepoint capabilities to HapiTransactionService, inject HapiTransactionService into CascadingDeleteInterceptor, add savepoint capabilities to the TransactionDetails, and catch an Exception in BaseHapiFhirResourceDao.delete() then rollback to the checkpoint.
* Fix compile error.
* hapi transaction service test
* hapi transaction service test
* hapi transaction service test
* First draft of RetryTemplate and flush() logic. Try unit testing with PointcutLatch.
* hapi transaction service test
* Latest changes including moving RetryTemplate, cleaning up unit tests.
* First attempt at correct design. Fix compile errors.
* Add failed rollback savepoint test.
* fix propogation
* interesting test failure in SafeDeleterTest
* Latest code
* move delete
* test passing
* all tests pass
* yay we're done just cleanup
* First round of cleanup: Get rid of all exploratory logging, remove unneeded dependencies, move creation of RetryTemplate to SafeDeleter.
* More cleanup. Add changelog.
* Bump to 6.2.0-PRE13-SNAPSHOT.
* Code review feedback: Refactor SafeDeleter to a service and bean. Add comments.
* Code review feedback: Comments on unit test assertions.
* Code review feedback: Rename SafeDeleterSvc to ThreadSafeResourceDeleterSvc. Add javadoc. Add logger to DelayListener. Remove useless commented out code.
* Fix unit test failure in CascadingDeleteInterceptorTest.
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* removed flyway, started coding persistence
* started wiring up new dao service
* replace jpa with sqlbuilder
* down to 16 failed tests
* remove outOfOrder test. We no longer support validating order.
* Removed noFlyway mode. It is no longer a thing.
* merge migrator
* down to 1 failing test
* cleanup
* removed unused noflyway cli arguments
* cleanup
* cleanup
* cleanup
* cleanup
* create MigrationTaskList to replace the List<BaseTask> that gets passed around a lot. This allows us to add a bunch of behaviour to that as a first-order thing
* fix test
* fix test
* improve migration table detection to use the catalogue
* Msg.code()
* cleanup
* save version in same format as flyway
* cleanup
* add migration result to migration result class
* failed migrations stay in the table and don't really affect anything.
* change log
* docs
* ugh Flyway requires lower-case column names
* integration test fixes
* log
* fix oracle issue
* lowercase tablenames for postgres. fussy fussy!
* Revert "lowercase tablenames for postgres. fussy fussy!"
This reverts commit 92c9cb263b.
* revert to capital table names. surround table name by quotes for Postgres.
* added log message before executing find all query
* changed log message from info to debug
* javadoc
* pom cleanup
* review feedback
* Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/MigrationTaskList.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* review feedback
* review feedback. Use prepared statement.
* Change installedOn insert from timestamp to date
* Change installedOn column type from timestamp to date
* bump hapi version
* fix poms
* fix poms and cdr compile
* add exclusions to clean up build
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* add failing test
* Fix history search bug and add tests for two more scenarios
* Fix history search bug and add tests for two more scenarios
* - added failing test condition
* Fix history search bug and add tests for two more scenarios
* Fix build test failures
* Fix build test failures
* Add extra verifications for scenarios of _since
* Refactor dao.history interface to add overload method and shall come back to remove old method once cdr is refactored.
* Update with new hapi interface
* Add depreciate comment
* Add depreciate comment
* Version bump to mvn 6.2.0-PRE11-SNAPSHOT
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* remove spring batch
it compiles
expect test failures
* fix test transaction manager bean name (wow that was quite the hunt the wumpus!)
* fix test and fix build
* fix test and fix build
* fix test
* remove spring batch schema initialization
* bump hapi version
* fix schema migrator
* bump to PRE-10
* merge master
* change logs
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* check for valid resource type
* add test and refactor test class
* refactor auto get method name
* introduce parameter object to patient everything methods
* introduce parameter object to patient everything methods
* change record to class
* add hapi error code
* refactor
* refactor
* change code num
* refactor getmethodname to util method
* add docs and rename fields to conform to fhir standard
* typo
* version bump
* resolving merge conflicts.
* Bumping version
* Bumping version to 6.2.0-PRE5-SNAPSHOT
* Encapsulating parameters in a PatientEverythingParameters object.
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* consolidated Batch2Helper
check status in assert before running maintenance
ignore illegal job instance state transition
* Fix mock tests
* rename intermittent to IT
* extra logging
* into to debug
* review feedback
* added more logging
* removed fasttracking. replaced with support for triggering a maintenance run
* fixed tests
* fixed tests
* add asserts
* licenses
* snakeyaml cve version bump
* data migration
* merge origin/master
* merge origin/master
* fix test (support triggering jobs when scheduling is disabled)
* add counter to abort potential infinite loop after 100000 calls
* compile error
* move multipartition mdm tests out to a separate IT
update mongo job instance creation with new logic
* fix race condition
* back out infinite loop circuit breaker. it breaks terminology tests that depend on this loop running > 100000 times.
* fix test (triggered job key was missing group)
* revert saveAllDeferred
* Almost finished getting JpaPersistenceR4IT to pass
* testBulkExportDeleteForOnGoingJob still not passing
* testBulkExportDeleteForOnGoingJob still not passing
* Removed method `fetchInstanceAndMarkInProgress`. It was clobbering other state transitions like CANCELLED.
* undo rename of cancelled to cancelRequested. Thymeleaf depends on the old name
* ExpandResourcesStep requires a synchronous search
* Tests are passing but man testBulkExportDeleteForOnGoingJob is a flakey test
* fix test
* fix test
* change log
* allow ERRORED -> FAILED state transition
* add a timeout to saveAllDeferred()
* improve error message on timeout message
* fix tests
* added more logging
* added more logging
* fix semaphore issue
* Msg.code
* fix test
* javadoc
* switch all batch loggers to batch troubleshooting log
* add unit test, improve logging
* move TimeoutManager to its own class. Add tests.
* fix tests
* comment cleanup
* test race condition
* review feedback
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* adding version.yaml, updating version in pom.xml
* It is possible to write to a resource in a partition the user is not authorized to. (#3397)
* fixed
* remove sout
* add msg.code
* fix failed tests
* fix equal sign
* update msg code
* extract method
* Fix up code numbers
* Clean changelog
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Revert final artifact version
* add graphql test (#3585)
* added graphql birthdate test
* fix variable name
* typo
* 3506 mdm log enhancement (#3543)
* Providing Fixme's to be reworked at a later time.
* Adding // FIXME Anna to assist our Austrian friend.
* Adding logging test as a first step in addressing issue #2822.
* hapifhir#3506 part 2: enhance logging for (un)successful MDM matching
hapifhir#3506 part 2: enhance logging for (un)successful MDM matching
* Update MdmMatchLinkSvc.java
#3506 move "narrowed down" log to different place
* #3506 added scores and tests
#3506 added scores and tests
* #3506 formatting
#3506 formatting
* #3506 create changelog file
#3506 create changelog file
* #3506 fix typo
#3506 fix typo
* #3506 fix part 3, minor formatting
#3506 fix part 3, minor formatting
* #3506 fix tests
#3506 fix tests
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
* mdm matching (#3579)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328
* Update HapiFhirJpaMigrationTasks.java
Corrected ordering
* Update HapiFhirJpaMigrationTasks.java
Moving index status to be last operation
* Revert "Update HapiFhirJpaMigrationTasks.java"
This reverts commit 37bfd3e66e.
* Moved to bottom
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
* begin with failing test
* fixed
* changelog
* add jira tag
* Update to 6 1 (#3582)
* added changelog folder, upped version
* version enum
* add a few more unit tests to assert proper NO_MATCH exclusion
* revert merge master doh! bad reflexes
* revert merge origin master
* unrevert revert. ugh what a pain
* merge recovery. fix poms.
* merge recovery. more reverting
* merge recovery. more reverting
* merge recovery. more reverting
* Revert "merge recovery. fix poms."
This reverts commit ae6e0ddb06.
* more revert revert reversions
* more revert revert reversions
* pre-review cleanup
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
* Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586)
* When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller.
* License
* Ks 20220508 log colour (#3592)
* don't use colours when output is redirected to a file
* change log
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328
* Update HapiFhirJpaMigrationTasks.java
Corrected ordering
* Update HapiFhirJpaMigrationTasks.java
Moving index status to be last operation
* Revert "Update HapiFhirJpaMigrationTasks.java"
This reverts commit 37bfd3e66e.
* Moved to bottom
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
* 3584 case sensitive string elasticsearch (#3596)
* Fix for case-sensitive search with newer elasticsearch
* Test and fix ascii normalization too
* more test cases
* comments
* Docs update empi usecase (#3598)
* Update diagram for use case 5
* Add new page for database support
* Licnese
* Mb norm fix (#3604)
* Normalize query since wildcard searches aren't normalized in elastic
* Handle batch2 job cancellation (#3603)
* Handle batch2 job cancellation
* Add CANCELLED status
* Remove unuseful test
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add batch2 interfaces to obtain recent instances (#3601)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* changelog folder
* Documentation change, added warning log and change log for ticket (#3609)
Co-authored-by: Steven Li <steven@smilecdr.com>
* fix ne for lastUpdated search param (#3589)
* init/wip
* add implementation, add tests
* add checks and some refactoring
* refactor and simplify tests
* refactor
* get rid of some of the warnings
* add changelog
* remove my todos
* redo ne logic to account for less precise dates
* add tests
* refactoring
* rename to follow convention
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
* Version bump
* Add skip of checkstyle to upload
* Typo
* upping version enum, upping version number, 6.0.1
* Group Bulk Export rules exiting too early. (#3643)
* Implementation, test, changelog
* Add jira link
* adding backport in yaml for 3642
* adding folder for 6.0.1 release
* pom changes to publish checkstyle to sonatype
* bad version in pom file
* Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider
* AUtomcplete error code
* updating comment indicating final erorr code
* Bump error code
* fixing version enum so release docs generate correctly, adding additional changelog for 3650
* 3684 subscription for delivering delete events formatted wrong (#3685)
* Fixed issue with delivering delete events Subscriptions
* Extracted deliverer class name to a constant, now shared across tests and interceptor class
* Added change log and doc changes
* moved the constant to a more appropriate place
Co-authored-by: Steven Li <steven@smilecdr.com>
* Version bump
* Add version enum
* Version enum and folder
* adding release pipeline yml file fo azure
* Adding autoclose for sonatype publishing (#3797)
* Add impl test and changelog (#3713)
* fix up changelog, new version
* Version bump
* Updating version to: 6.0.4 post release.
* reverting 6.0.4 commit
* Updating version to: 6.0.4 post release.
* removing double entry from preious release
* Add support for DSTU3 delete subscrion events, add test
* Add changelogP
* Add version enum
* Remove notnull
* Add test for DSTU2
* Updating version to: 6.0.5 post release.
* Fix up
* wip
* Adding solution and changeLog file.
* Adding failing test.
* fix up
* Version bump
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
* 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
* Bump Version for non-breaking purposes
* Fix broken test
* bump error code
* revert internal logic
* Revert offset mode change
* wip
* 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
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>
* wip functional
TODO
- add tests
- look at adding TLS to other RestfulClientFactory classes (FhirwebRestfulClientFactory, JaxRsRestfulClientFactory, OkHttpRestfulClientFactory)
* move BaseRestServerHelper to Hapi-Fhir
* - add TLS support for JaxRsClient and OkHttpClient
- add tests
* - to use resources and files
* - ci fixes
* - ci fixes
* - ci fixes
* - ci fixes
* - refactor and tests
* - ci fixes
* - tests
* - tests
* - tests / refactor
* - clean up
* - changelog
* - remove OkHttpClient HTTPS support
* - ci
* - Ken's code review changes
* - Ken's code review: method renaming
* - Ken's code review: javadoc
* - Code coverage
* - Create HapiFhirCliRestfulClientFactory to encapsulate new HTTPS functionality. Remove modifications to the FhirContext API.
* - version bump
* - fix unable to bind port errors by using Jetty functionality to assign random ports
* Revert "- version bump"
This reverts commit cfce82576a.
* - version bump
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
* added a paging api to ijobcoordinator
* adding changelog
* moved location
* added a comment
* Added Sort parameter to JobInstanceFetchRequest
* Bump HAPI-FHIR version
* Updated JPA api to include sort
* Add changelog
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: David Chen <david.chen@smilecdr.com>
* small refactor
* refactored MDM module to use iterface IMDMLink, refactored MDMLink to use ResourcePersistenceId wrapper rather than pid as long
* removing IJpaIdHelperService and refactor IIdHelperService
* fixed bugs for GoldenResourceMergerSvcImpl and FindCandidateByExampleSvc
* changes to IIdHelperService
* move MdmSearchParamSvc and MdmSubmitSvcImpl out of jpaserver-mdm
* moved JpaResourceLoader to hapi-fhir-storage, renamed to ResourceLoaderImpl
* added error Msg code, removed Fixme
* fixed error code, update last used code in Msg.java to 2083
* fixed accidentally throwing unprocessableentityException
* added MdmLinkExpandSvc interface
* build adding license to files
* MdmLinkdao refactor
* fix build
* mdm config refactoring
* MdmStorageInterceptor and IExpungeEverythingService changes
* fix bug where a pid is converted to ResourcePersistenceId twice
* minor refactor to IMdmLink, change id from long to ResourcePersistenceId
* changed PageImpl to Page interface
* refactor MdmSearchExpandingInterceptor to use interface
* fixed missed refactor where the resourcePersistenceId is still assumed to be long
* resolve test failures resulting from merging master
* changed conflicting exception code
* fixed issue with bulk export wrapping resourcePid inside resourcePersistenceId
* added IMdmLinkImpl to MdmSettings
* fixed missing import in IdHelperService from merging master
* fixed MdmLinkDaoSvcTest importing wrong MdmLinkTuple
* restored JpaIdHelperService and added changelog
* modified msg.code to non-duplicate
* code review changes
* refactored some bulk export batch 2 files to accomodate change in beans being exported
* fixed jpa bulk export failing tests
* removed duplicate bean declaration of MdmLinkImplFactory in BaseMdmR4Test
* merged master and bump version to pre25
* extracted expungeEverythingByType to IExpungeEverythingService
* fixed wiring issue
* messed up merging pom with master
* fixed broken changelog
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Samuel Lee <samuel.lee@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* added a paging api to ijobcoordinator
* adding changelog
* moved location
* added a comment
* blah
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Revert "test passes with a lot of copy/paste"
This reverts commit f2f28e22ef.
* make translateOutcomeToResults public
* double RAM
* final consolidation. move shared code out to static utility methods
* revert azure memory
disable jacoco on jpaserver test prokect
* bump hapi version
* rebump hapi to PRE-21
* licenses
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Creating an exception to be raised when searching for _tag/_provide/_security where the associated tokenParam is not properly formatted.
* Adding changelogs.
* Adding integration test.
* Rewording ChangeLog.
* Rewording exception message.
* Addressing code review comments.
* Addressing code review comments.
* Bumping hapi-fhir version to 6.1.0-PRE20-SNAPSHOT
* Modifications to pass checkstyle.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Not the final version
* Support PATCH operation
* minor modifications
* minor modifications
* Final version
* Final version
* Version Bump
* bump version again
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* base batch2 bulk export steps - unimplemented
* added the basic steps
* adding tests
* we have added the tests
* added tests for bulk export stages
* implementing jpa
* 3531 adding the jpabukexportprocessorimplementation
* 3531 first step for mongo bulk export
* jpa stuff updated
* 3531 hapi fhir stuff
* trying to fix up tests
* fixing test
* fixed most tests in batch export
* deprecate
* need some more guidance here
* fixing some tests
* some steps taken
* blah
* stashing
* test
* fixing tests round 1
* many a changes
* updating version
* small updates
* merging in mster again
* fixing up serialization
* added the permission checkers
* cleanup and sonarkube crap
* some more tests
* updating adding tests
* crimes
* blah
* updatingmsg number again
* removal of commented code
* cleanup
* merge confflicts
* fixing msg
* review fixes round 1
* more review fixes
* merging in master
* fixing poms
* review points
* test fix
* test fix
* fix test race condition
* truncate error
* add stack trace to error
* rename to IT
* fix race condition in test
* finally fixed race condition in test. this time I'm optimistic hapi ci will finally pass
* fix mock test. not a fan of mock tests like this.
* any job definition with a reducer step must be gated.
* fixed common batch bean wiring
* fix test
* lazy init ResponseTerminologyTranslationSvc
* change the way we lazy init ResponseTerminologyTranslationSvc
* change the way we lazy init ResponseTerminologyTranslationSvc (for the third time. this is super tricky!)
* disabling testGoldenResourceWithCircularReferenceCanBeCleared for now
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 3770 fixing error handling
* some updates to error handling
* changelog
* blah
* bumping version
* fix test failures
* code review points
* review points
* add retry test
* assert counts in the test
* test fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* added failing test for Map Response Terminology for bulk export
* moved logic for terminology translation out of the interceptor to svc, added translation logic to bulk export file writer, added more tests
* added changelog
* Wip refactor dependency fix
* wip terminology translation code refactor
* terminology translation code refactor
* refactor clean up
* Remove circular dependency
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3719-enable-map-response-terminology-for-bulk-export.yaml
* bump version of hapi to 6.1.0-PRE7-SNAPSHOT
* doc update
* fix issue when search param registry doesn't contain search param for the resource type
* fix beans
* hapi version bump from PRE7 to PRE10
* doc update
* add ResponseTerminologyTranslationSvc as a constructor variable to the interceptor
* fixed ResponseTerminologyInterceptorLoaderTest, added IT for cdr side
* version bump to PRE13
* removed unused import
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* begin with failing test
* begin with failing test
* remove unused Spring Batch classes.
convert service classes
* move provider
* just one test left to fix
* fix test
* msg.code
* change log
* bumping hapi to PRE12
* fix test
* review feedback
* license update
* fix intermittent and status update atomicity
* restore url-level partition selection
* fix tests
Co-authored-by: Ken Stevens <ken@smilecdr.com>
- Added functionality to optionally filter out deleted resources when resolving forced ids to persistent ids
- Bumps version
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* rename field that drives everything includes
* discovered design flaw in completion
* fix intermittent
* ensure batch2 completion handler can't be called twice
* changelog
* changelog
* javadoc
* bump hapi version
* licences
* Batch2 job definitions can now optionally provide an error handler callback that will be called when a job
instance fails, errors or is cancelled.
* Changed error handler and completion handler to take a "read-only" copy of an instance instead of just certain fields.
* comment
* javadoc
* fix test
* change step execution context from taking instance id to instance
* review feedback
* fix test
* replace 20 or so jetbrains annotations
* fixed a few incorrect @NotNull annotations
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* first test passes. onto the next one
* two down two to go
* three down one to go
* licenses
* basic admin-json plumbing confirmed with IT
* FIXME
* FIXME
* FIXME
* FIXME
* changelog
* bump hapi version to 6.1.0-PRE6-SNAPSHOT
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Initial implementation
* Implement job cancellation
* Works for date and token. Cleanup required.
* Works for string and quantity.Cleanup pending.
* Works for reference and perform cleanup.
* Cleanup configuration and add missing tests
* Eliminate sort property registry (no go for a cluster) for a static property map.
* Missed in previous commit
* Implement HSearch number parameter
* Implement HSearch number sorting
* Unify different hibernate search names (HibernateSearch, Freetext and Lucene) to HSearch
* Move analysis configures for lucene and elastic to same file to enforce the need to keep them in synch
* Use new defined constant
* Rename package too
* Rename additional elastic references
* bump version to 6.1.0-PRE5-SNAPSHOT
* Restore Hap prefix to hapi configurers
* fixing hapi version of new maven module
* fix pom
* fix pom
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* begin with failing test
* continue building out
* continue building out
* reworking chunk api
* replace ChunkId zippers with proper iterator
* progressing test
* yay test passes!
* switch to idchunk interface
* fixmes
* compiles
* fixme
* fixme
* rename classes
* rename json classes with json suffix
* work towards homogeneous chunks
* fixme
* fixme
* unit test
* fixme
* fixme
* pull out builder
* moar tests
* moar tests
* preserve order
* moar test
* moar test
* fixme
* fixme -> wip to start ci
* msg code
* msg code fix test
* fixme
* change provider implementation
* final WIPs
* IT failing
* IT passes
* java 11
* fix test
* fix test
* fix test
* changelog
* use batch size if provided
* last WIP
* fix test
* fix test
* fix test
* whitespace change to trigger new build
* fix test
* bumping hapi version
* bumping hapi version
* fix test
* review feedback
Co-authored-by: Ken Stevens <ken@Kens-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* adding a bunch of stuff
* most of the steps are working now
* writing more tests
* adding more tests
* updated the batch2 coordinators
* updating version
* some minor test tweaks
* added a new test
* adding more tests
* blah
* blah
* review fixes 1
* fixing tests and refactoring
* review points
* updated for code review
* review fixes
* updated
* step 1 on review step 5
* final touches
* blah
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* fix config settings for system-level expunge
* clean up expunge everything interface
* extract common system provider
* changelog
* version bump
* touch changelog to force a fresh pipeline
* re-enable publishing of checkstyle
* back out Gary's Sonatype change entirely
* adding version.yaml, updating version in pom.xml
* It is possible to write to a resource in a partition the user is not authorized to. (#3397)
* fixed
* remove sout
* add msg.code
* fix failed tests
* fix equal sign
* update msg code
* extract method
* Fix up code numbers
* Clean changelog
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Revert final artifact version
* add graphql test (#3585)
* added graphql birthdate test
* fix variable name
* typo
* 3506 mdm log enhancement (#3543)
* Providing Fixme's to be reworked at a later time.
* Adding // FIXME Anna to assist our Austrian friend.
* Adding logging test as a first step in addressing issue #2822.
* hapifhir#3506 part 2: enhance logging for (un)successful MDM matching
hapifhir#3506 part 2: enhance logging for (un)successful MDM matching
* Update MdmMatchLinkSvc.java
#3506 move "narrowed down" log to different place
* #3506 added scores and tests
#3506 added scores and tests
* #3506 formatting
#3506 formatting
* #3506 create changelog file
#3506 create changelog file
* #3506 fix typo
#3506 fix typo
* #3506 fix part 3, minor formatting
#3506 fix part 3, minor formatting
* #3506 fix tests
#3506 fix tests
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
* mdm matching (#3579)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328
* Update HapiFhirJpaMigrationTasks.java
Corrected ordering
* Update HapiFhirJpaMigrationTasks.java
Moving index status to be last operation
* Revert "Update HapiFhirJpaMigrationTasks.java"
This reverts commit 37bfd3e66e.
* Moved to bottom
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
* begin with failing test
* fixed
* changelog
* add jira tag
* Update to 6 1 (#3582)
* added changelog folder, upped version
* version enum
* add a few more unit tests to assert proper NO_MATCH exclusion
* revert merge master doh! bad reflexes
* revert merge origin master
* unrevert revert. ugh what a pain
* merge recovery. fix poms.
* merge recovery. more reverting
* merge recovery. more reverting
* merge recovery. more reverting
* Revert "merge recovery. fix poms."
This reverts commit ae6e0ddb06.
* more revert revert reversions
* more revert revert reversions
* pre-review cleanup
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
* Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586)
* When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller.
* License
* Ks 20220508 log colour (#3592)
* don't use colours when output is redirected to a file
* change log
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328
* Update HapiFhirJpaMigrationTasks.java
Corrected ordering
* Update HapiFhirJpaMigrationTasks.java
Moving index status to be last operation
* Revert "Update HapiFhirJpaMigrationTasks.java"
This reverts commit 37bfd3e66e.
* Moved to bottom
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
* 3584 case sensitive string elasticsearch (#3596)
* Fix for case-sensitive search with newer elasticsearch
* Test and fix ascii normalization too
* more test cases
* comments
* Docs update empi usecase (#3598)
* Update diagram for use case 5
* Add new page for database support
* Licnese
* Mb norm fix (#3604)
* Normalize query since wildcard searches aren't normalized in elastic
* Handle batch2 job cancellation (#3603)
* Handle batch2 job cancellation
* Add CANCELLED status
* Remove unuseful test
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add batch2 interfaces to obtain recent instances (#3601)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* changelog folder
* Documentation change, added warning log and change log for ticket (#3609)
Co-authored-by: Steven Li <steven@smilecdr.com>
* fix ne for lastUpdated search param (#3589)
* init/wip
* add implementation, add tests
* add checks and some refactoring
* refactor and simplify tests
* refactor
* get rid of some of the warnings
* add changelog
* remove my todos
* redo ne logic to account for less precise dates
* add tests
* refactoring
* rename to follow convention
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
* Version bump
* Add skip of checkstyle to upload
* Typo
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
* committed changes discussed at tasking
* Changed the subscription message to store the request partition
* modified mdm subscription loader to create a cross partition subscription in the default partition if multitenancy is enabled
* Fix errors when running Multitenant IT for mdm
* Added partition id to mdm golden resource search and creating/updating golden resource
* added partition id column to the mdm link table
* Added partition id of the source resource to partition id column of the mdm link table
* broken build
* working -links, missing hapi tests
* Fixed the mdm link db table due to feedback
* added IT for create link mdm operation, also added changes to pass the IT
* Fixed test for create mdm links, added test for update mdm link on partitioned server
* changed mdmLink search from searchbyExample to criteriaBuilder, added partitionHelperSvc to determine partition
* added test for merge golden resource and search golden resource on partitioned server
* added unit test for not duplicate on partitioned and non-partitioned server
* added criteriabuilder search and tests
* code cleanup
* added partition support to -merge-golden-resources operation
* test cleanup
* fixed operations with multitenancy
* added test for mdm clear operation
* added waiting for batch job to finish in mdm clear operation test
* added query to dao to support partitioned server for mdm clear operation
* resolve mistake from merge conflict
* added mdm-submit operations, also fixed paging for -query
* added partitionIds constant
* fixed build issue where there was no Code.msg in mdm partition exceptions
* code review fixes
* fix broken test, also fix a bug where query link could not query by linkSource properly
* fix test stubbing
* bump hapi version to 6.0.0-PRE10-SNAPSHOT
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Long Ma <long@smilecdr.com>
* moved classes
* Bump version
* licensing
* Repackage, fix messages
* reject empty streams
* Remove dead import
* Version bump
* Fix up test to actually return a data stream
* Move null binary svc to storage
* Start working on reindex job
* Updates
* Ongoing work
* Ongoing work
* Work on reindex
* Reindex work
* Add logging
* Fix typo
* Test fix
* Test fix
* Address fixme
* Liocense header
* Resolve fixme
* Add logging
* Update logs
* Address review comments
* License header
* Test fixes
* Test fix
* Test fixes
* Test fix
* Version bump
* Version bump
* Enable search narrowing on large ValueSets
* ValueSet improvements
* Work on narrowing
* Work on narrowing
* Work on narrowing
* Work on narrowing
* Add test
* Work on narrowing interceptor
* Work on narrowing
* License headers
* Refactor code narrowing
* Add docs
* Version bump
* Test fix
* Test fixes
* Build fix
* Fixes
* Version bump
* Test fix
* License header updates
* Build fix
* Test fixes
* Test fix
* Test fix
* Docs fix
* Test fix
* Test fix
* Resolve fixme
* Bump
* Force a CI build
* Make CI happen again
* Work on new batch framework
* Work on new batch framework
* Work on new batch framework
* Work on batch
* Compile working
* Work on bulk import
* Adjust import
* Work
* Work on batch
* Bump version
* WOrk on new batch processes
* Work on bath
* Bump to PRE4
* Build fixes
* CLeanup
* Small tweak
* Add exception code
* Test fixes
* Test fixes
* Test fix
* Additional synchronization
* Add license headers
* Test fixes
* Test fixes
* Add changelogs
* Address PG
* Test fix
* Test fix
* Test fixes
* Review notes
* Work on tests
* Test fixes
* Test fix
* Work on tests
* Tets fix
* Test fixes
* Test fixes
* Add missing exception codes
* Test fix
* Test fixes
* More test fixing
* License headers
* Test fix
* Add new test logging
* Work on tests
* Test fixes
* Test fix
* Resolve fixme
* Try to avoid test failure
* Add import command
* Work on storage
* Fix error codes
* Fixes
* License header
* Build fix
* Build fixes
* Fix dep
* fix handling of common search parameters
* Revert "fix handling of common search parameters"
This reverts commit 89c45eebdc.
* Fix implementation, add test (#3378)
* Fix implementation, add test
* Tighten test
* Rip out dead modules
* Add changelog
* Jr 20220210 handle common search params in contained searches (#3377)
* fix handling of common search parameters
* add support for reference search parameters with multiple paths
* Issue 3357
* Version bump
* Fixed null pointer exception for re-loading subscription on cdr restart and when there's no partition id in the request, and added tests
* added changelogs for this fix
* Fix broken changelog file
* Can't specify specific resource type permissions for bulk export (#3376)
* deny user from exporting without perms
* add unit tests
* add changelog
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
* Make migration donothing as it was added in error
* Remove ehcache
* Add version.yaml:
* Add to sources/javadocs for dist
* Fix typo
* fix up pom
* wip test removing checkstyle plugin from deployable pom
* remove test pom changes, instead just dont deploy to sonatype
* typo
* Remove ehcache
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com>
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
* Initial design of adding exception codes to exceptions
* Initial design of adding exception codes to exceptions
* change int module name to string
* add comment
* shorten message
* shorten message
* added checkstyle
* developing checker
* completed checkstyle plugin and unit test for it
* fix NPE
* fix checker so it ignores throws on exceptions that aren't new
* change parameter order in InvalidResponseException
* accept Msg.code() in any parameter since some exceptions like MessageException have the message string as the second parameter
* exclude generated files
* BIG COMMIT added error codes to all exception throws
* example test fix
* Modified tests such that the assert statements would better match the message responses.
* Modified additional tests such that the assert statements would better match the message responses.
* fix test
* merge master
* merge master
* Fourth commit of modified tests such that the assert statements would better match the message response
* Changes made to modify assert statements such that they match the new errors which now use error codes. Also changed ResourceNotFoundException to include error codes in its messages.
* Modified assert messages to better match new error codes
* Time Zone changes DRAFT. Certain tests pass in intellij and fail during mvn install
* Modified assert messages to better match new error codes
* Added comments for time zone fixes. Previous commit comment on time zone fixes was incorrect. By invaliding caches, all tests on both intellij and mvn install passed.
* Reverted changes on azure-pipelines.yml
* updated hapi-fhir version for checkstyle module
* changes to azure-pipelines.yml
* changes to azure-pipelines.yml
* change to pom.xml to include hapi-fhir-checkstyle in ALLMODULES
* changes to azure-piplines (these changes are to be reverted after testing)
* reverted changes to azure-piplines
* reverted change where hapi-fhir-checkstyle was added to pom.xml (hapi-fhir)
* Attempted fix on checkstyle build error
* modified azure-piplines.yml to change maven repository for checkstyle build
* Attempted fix on checkstyle build error
* checkstyle config location change for hapi-depoloyable-pom. (will be reverted if it does not work)
* attempted dependency add for hapi-depoloyable-pom. (will be reverted if it does not work)
* reverted changes for hapi-deployable-pom
* add javadoc
* update last code
* Attempted fix on checkstyle build error
* Finished adding in missing error codes to pass Checkstyle checks
* Test pipelining
* Fixing errors and bumping version (as suggested by Gary)
* Merge
* Fixing Checkstyle error
* Attempted fix for date error
* Add error code onto assert statement
* Add in a couple more error codes
* Fixing assert statements
* Bump to static version for dependency
* Adding error code to message
* Adding error codes to exceptions
* Adding error codes to exceptions
* Change to work with cdr branch
* Update to faulty error message
* Merge changes
* allow checkstyle pom to deploy
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com>
Co-authored-by: Predap <simon.zuccherato@gmail.com>
Co-authored-by: Predap <46201929+Predap@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
James Agnew
KGJ-software
Luke deGruchy
Ken Stevens
weiping202209
Tadgh
jdar8
Nathan Doef
David
longma1
TipzCM
Etienne Poirier
Qingyixia
Mark Iantorno
StevenXLi
jmarchionatto
JasonRoberts-smile
Tadgh
Johnson Lu