* 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.
* 3138 externalized binary packages (#3139)
* Add test and impl
* Add changelog
* Fix test
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3138-support-externalized-binaries.yaml
* add beans to test configs
* Typo
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* 3131 - Added support for the lookup operation in the Remote Terminology code (#3134)
* Remove leading underscores from identifiers (#3146)
* Version bump
* License files
* version.yaml
* Add executeRawSql() method to Migrator (#3183)
* Add implementation, add test
* Add javadoc
* Add another helper function
* Bump version
* 3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155)
* 3153 updating the unknowncodesystemwarningvalidationsupport class
* 3153 updating version for smile
* 3153 update broken tests
* 3153 adding log
* 3153 cleanup
* 3153 cleanup
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Add backport info
* Avoid creating ResourcePersistentId for placeholder resources with null ID (#3158)
* Add check before mapping storage ID to resource ID in TransactionDetails.
* Add change log.
* Changed to instead prevent creation of ResourcePersistentId with null ID value.
* Changed to instead prevent ResourcePersistentId being created with null resource ID.
Co-authored-by: ianmarshall <ian@simpatico.ai>
* Fix bug loading packages in non-database mode (#3199)
* Add implementation
* Add changelog
* Add backports
* 3164 updating code review points (#3165)
* 3164 updating code review points
* 3164 updating code review points
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Add executeRawSqlStub (#3203)
Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>
* Add new version
* begin with failing test
* fix bug
* change log
* change log
* Add backport informationm
* begin with failing test
* fix issue
* change log
* code review
* Add backport info. Add folder
* fixed
* Add test
* Update test
* Add backport info
* Bump minor version
* 3170 language portion of language code is case insensitive (#3171)
* 3170 language portion of language code is case insensitive
* 3170 adding changelog
* 3170 house keeping
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Add backport info:
* Add version enum
* Bump hapi version to 5.6.3
* Add version enum
* Add changelog folder and version.yaml
* Patch vulnerability, add changelog
* AuthorizationInterceptor concurrency failure (#3528)
* Fix#3256 - AuthorizationInterceptor concurrency failure
* Test fixes
* Add backport info
* Fix test for lang level 8
* Bump hapi
* License updates
* Add release pipeline
* remove checkstyle from old version
* swap jdk for build
* Couple removals for arbitrary failures
* disabling tests for this next 5_6 release because we shoot from the hip here
* Updating version to: 5.6.5 post release.
* add new folder
* fix versionenum
* remove unreleased versions
* Bring back into line
Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
Co-authored-by: ianmarshall <ian@simpatico.ai>
Co-authored-by: Joanne Mendoza <joannemmendoza@gmail.com>
Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
* 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>
* #3724 added test and test resources
* #3724 adding summary report by one practitioner
* #3724 fixed some formatting and data type mistakes
* #3728 passing on practitioner parameter
* #3724 added test and test resources
* #3724 adding summary report by one practitioner
* #3724 fixed some formatting and data type mistakes
* #3724 added tests for measure by practitioner
* #3724 minor formatting and refactoring
* #3724 deleted unused cql files
* #3724 added TODO
* #3724 adding comment and changelog
Co-authored-by: Anna <anna@MacBook-Pro.local>
* 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
* duplicate import
* duplicate import
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>
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>
Ken Stevens
Tadgh
Nathan Doef
Etienne Poirier
JasonRoberts-smile
jmarchionatto
Ken Stevens
Qingyixia
TipzCM
Mark Iantorno
jdar8
michaelabuckley
jamesagnew
dependabot[bot]
Gjergj Sheldija
StevenXLi
alackerbauer
Nathan Doef