* Added failing test, and the methods that are necessary to not break the build
* Implemented solution to cancel jobs via delete request for poll status
* change log added
* change log name change to pass test
* Changed implementation to work with existing infrastructure
* code review changes
Co-authored-by: Steven Li <steven@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>
* Add license headers
* Move partition interceptor
* More cleanup
* One more tweak
* Headers
* Add changelog
* Test logging enhancement
* Test fix
* Test fixes
* Add test method
* 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>
* Fixing response message when deleting non-existing or deleted resource.
* Changed names of properties.
* The full ID shown in message, not just IdPart
* Fallback direct resource HSearch to JPA when resources are not found in index
* Use specific exception instead of identifying it by the message
* Add Message code to exception
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add simple local implementation of UCUM temperature canonicalization for Celsius and Fahrenheit
* Adjust conversion to not increase precision, as it matter when finding ranges
* Simplify test variables
Co-authored-by: juan.marchionatto <juan.marchionatto@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
* added support for OO.issue.details from Java RI Validator
* remove duplicated Msg.code
* 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
* removed duplicated dependency with wrong version
* fixed test file(added a Base64 string)
* fixed tests
* fixed test:
history?_since is an instant
* removing time from date-strings in examples
* fixed more instant strings
* changed filtering of messages to messageId
* fixed messageId filter on missing profiles
* changed messageID system string to Grahames preferred String
* updated MsgIds of unsupported methods
* removed fixed commons-codec version as fhir.core uses commons-codec:1.15
This will introduce issues with the android built.
* fixed GraphQL Test
* fixing test issue caused by different message string, switch to details code assertion
* fixing test issue caused by different message string, switch to details code assertion
* updated Msg.codes
* updated Msg.codes
* fixed duplicated Msg.codes
* setErrorOnInvalidValue set to false in test
* reverted date precision test changes
* updated r5 resources to latest build version
* updated to latest snapshot, https://github.com/hapifhir/org.hl7.fhir.core/issues/884 causes test failures.
* Try to fix message codes
* Test fixes
* Checkstyle fix
* Test fix
* Try to avoid CME
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.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: James Agnew <jamesagnew@gmail.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
* Fix test
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>
* Add logback definition to project to stop debugging all output
* Fix limit definition to include _offset=0 case
* Move test required resources from previous test module
* Add changelog
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* step one
* blah
* no working test
* updated existing tests
* delete code system version and code system jobs
* trying to get terminology fixed
* updating tests
* need to have some movement
* added completion handler
* added clearing code for failsafe
* review points
* fixing tests
* fixing tests
* more test fixes
* fixing more tests
* review fixes
* todo
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 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>
* broke some tests
* invoke batch 2 reindex
* changelog
* fix compile error after merge
* fix failing test
* hook up partition support
* fix some failing tests
* deprecate the old reindex service
* fix more failing tests
* fix broken test
* move elastic tests out into their own project in the hopes it solves ci memory issues
* move elastic tests out into their own project in the hopes it solves ci memory issues
* disable elastic tests temporarily
Co-authored-by: Ken Stevens <ken@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>
* Start direct HSearch path
* Support no HSearch
* Spike out the direct resource query
* Implement hsearch fast load
* Fix last master merge in issues
* Implement revision requests
* Test direct resources (no IDs query) sorting
* Use mock to count freetext searches to avoid implementing interface in test
* Remove fixme
* Make listener optional as it is used only for tests
* Provide new dependency
* Widen fast path test scope and fix previously untested configurations
* Make method transactional as it can be called from outside a TX (at least testObservationLastNAllParamsPopulated does)
* Update test validation
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Implement token :not and fix :not-in in InMemoryMatcher
Both `:not` and `:not-in` require that NONE of the values in an OR-list match, so we need some machinery to do a none-match instead of any-match.
* 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
* Version bump
* Add implementation, testing, and changelog
* Add backport info, make aware of 6_0_0
* add jira ref
* Fix test
* Add versionenum
* Bump dep for spring, add changelog, add versionenum, add changelog folder
* Actually do the version bump
* 3654 postgres lobs (#3656)
* Implementation, test, changelog
* Modify changelog
* Fix changelog
* Add upgrade.md file
* Modify to yaml changes
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_3/3654-lob-problems.yaml
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* tidy
* more work
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Fix bad yaml indent
* Version bump
* Back out the reindex changes introduced in 5.7.3
* update changelog
* version bump
* added fix for subscription in default partition when default partition's id is null
* added changelog
* Add version info and changelog folder
* adding release pipeline yml file fo azure
* Fix parameter count limitation on MSSQL/Oracle large transactions (#3075)
* Fix parameter count limitation on MSSQL/Oracle large transactions
* Changelog fix
* Move changelog
* Force a change to trigger CI
* Test refactoring
* Backport oracle fix
* Fix backport
* upping version to 5.7.5 for release
* add versionenum
* Updating version to: 5.7.6 post release.
* Add query-chunk-aware code
* Add new folder
* Fix up versionenum
* Remove imports
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>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.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>
* Start direct HSearch path
* Support no HSearch
* Spike out the direct resource query
* Implement hsearch fast load
* Fix last master merge in issues
* Implement revision requests
* Test direct resources (no IDs query) sorting
* Use mock to count freetext searches to avoid implementing interface in test
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* add system SPs to resource
* populate include list
* wip
* wip
* Tighten test
* Chaneglog
* Use old-style collectors
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Extend rules with filters.
New rule extension, and consent service for post-query filtering.
Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.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>
* 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
* Replicate new normalizer configuration from HapiElasticsearchAnalysisConfigurer to HapiLuceneAnalysisConfigurer.
Replace deprecated word filter factory
Co-authored-by: juan.marchionatto <juan.marchionatto@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>
* Updating With History Rewrite implementation
* Missed new files
* Updated changelog and documentation
* Fixed test failures and doc
* minor fix
* lgtm code refactor
* Fixed test to clear DaoConfig
* Removed unused class
* Code review changes
* Simplified updateHistoryRewrite's fluent, combining with normal update's, also changed logic on custom header error checking, updated tests
* refactored method to extracted common code
* removed `updateHistoryRewrite()` and replaced with `update()`, updated tests accordingly
Co-authored-by: Steven Li <steven@smilecdr.com>
* Refactor test to cause failure
* Handle patch for entry response building
* add changelog
* Update hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 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>
* Initial test exerting the issue.
* Providing fix and changelog
* Providing fix and changelog
* Providing a searchUrl or matchUrl based on the requestUrl.
* Providing fix and changelog
* Modification on test
* Modification on test
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: qingyixia <cherry.xia@smilecdr.com>
* Adding test reproducing the issue.
* Providing implementation fixing the issue and strengthening integrated test.
* Cleaning up commended code.
* Preparing code for review.
* Adding test class SynchronousSearchSvcImplTest.
* Addressing first code review comments.
* Addressing first code review comments.
* Forcing one extra processing step to ensure exit condition is met.
* Adding tests
* Clean up in preparation of second code review.
* Addition of setting page size if required.
* Grouping synch test in nested test class.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* SRP refactor maintenance
* SRP refactor maintenance
* cache jobDefinition in jobInstance when processing (rather than looking it up in a bunch of different places)
* begin with failing test
* test passes
* tests pass. still need to add a few more tests
* add comment to trigger new ci
* added positive and negative tests for new behaviour
* fix IJ warnings
* change log
* change log
* fix test race condition
* resolved feedback
* review feedback
* 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
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>
Add support for _total, _count, and _offset to Lucene backend.
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Implementation, parameterize test, changelog
* Bump spring framework for a vuln while i'm in here
* Fix number of changelog
* Add IS NOT NULL to query
* Preliminary test work to generate forward-reference data
* Complete implementation
* Permit Practitioner/Organization as forward references in bulk export group params
* Wip
* Fix test
* Add error number
* Address review comments
* Update assert
* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation
* GraphQLQueryBodyParameter to recognize application/graphql
* fix 500 error on method without @GraphQLQueryBody
* refactor to processGraphQlGetRequest and processGraphQlPostRequest
* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest
* fix imports
* implement GraphQL Connection
* add tests
* add cacheControlDirective and requestDetails to registerSearch
* fix tests and fix bugs
* set error code
* Refactor to restore LGTM functionality
* Compile fix
* Work on cleanup
* Attempt to restore LGTM
* Work on tests
* Fixes
* Build fixes
* Build fix
* Test fix
* Test fixes
* Work on build
* License header updates
* Test fixes
* Test fixes
* License header
* Test fix
* Test fix
* Test fixes
* Restore LGTM
* Fix azure
* Disable test
* Test fixes
* Test cleanup
* Build fix
* Build fix
* Test fix
* Test fix
* Test fixes
StevenXLi
Tadgh
James Agnew
Etienne Poirier
MykolaMedynskyiSCDR
michaelabuckley
jmarchionatto
Patrick Werner
TipzCM
jdar8
David
longma1
Ken Stevens
JasonRoberts-smile
Qingyixia
Gjergj Sheldija
Nathan Doef
Jaison Baskaran
seanmikalson-smilecdr
samuelwlee2
Ibrohim Kholilul Islam
Olivia You