* 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>
* 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
* Allow hsearch sorted offset searches
* Add changelog
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
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>
* 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>
* 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>
* Solution baseline.
* Adding integration test.
* Parameterizing the test
* Adding to documentation.
* Modification following code review.
* Modification following code review.
* Adding documentation.
* Adding documentation specific to MDM customization with pointcut.
* Modifications following second code review.
* Code review modifications.
Co-authored-by: peartree <etienne.poirier@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>
* 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
* 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>
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>
* 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>
* 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>
* add support for in and not-in qualifiers
* fix failing test
* fix broken test
* fix broken tests
* code review comments
* Make dependency on IValidationSupport optional
* create IValidationSupport dependency only if needed
* small design improvements
* changelog
* rework validation support initialization
* Update hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/InMemoryResourceMatcher.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.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>
* 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>
* reversed order matching operation bindings are searched so custom operations override builtin ones
* change log
* add test
* reverse finding operations in interfaces and then classes so last-in-wins finds the right provider method
* 3534 - Added new multi-column Index and removed existing single-column Index.
* 3534 - Added PARTITION_ID to the new Index.
* Change migrations to have no timeout.
Co-authored-by: Michael Buckley <michael.buckley@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
* 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>
* 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
* remove doubleimport
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>
* Add versionenum, bump maven version
* failing tests
* more logs
* Add more test cases, not passing
* fixed the double chain with contained resource second case
* clean up a bit
* add tests for qualifiers
* force the resource table to be the root of the query if we might be traversing a contained reference
* tidy up
* tests for longer chains
* changelog
* code review feedback
* backport changelog
* Add version.yaml
* [2935] Escape "%" in like expression
* Add backport to changelog
* Bumping version number. Update VersionEnum to support 5.5.3
* Jr 20211013 chained references (#3079)
* Create index entries for outbound references of contained resources
* build query for chained reference
* fix case where the contained reference is an explicit id rather than a continued chain
* fix contained index to use path names not search param names
* make qualified search work
* cleanup and changelog
* code review
* fix broken tests
* add imports from bad merge
* Add forgotten import from merge
* Jr 20211018 chained references 2 (#3099)
* Create index entries for outbound references of contained resources
* build query for chained reference
* fix case where the contained reference is an explicit id rather than a continued chain
* fix contained index to use path names not search param names
* make qualified search work
* cleanup and changelog
* recurse while creating indexes on contained resources
* double link both contained
* longer contained subchains
* adding some failing test cases to illustrate the limitations of qualified searches
* clean up merge cruft
* changelog
* Jr 20211021 chained references 3 (#3107)
* Create index entries for outbound references of contained resources
* build query for chained reference
* fix case where the contained reference is an explicit id rather than a continued chain
* fix contained index to use path names not search param names
* make qualified search work
* cleanup and changelog
* recurse while creating indexes on contained resources
* double link both contained
* longer contained subchains
* adding some failing test cases to illustrate the limitations of qualified searches
* clean up merge cruft
* changelog
* create recursive resource links
* add test coverage for a more complicated case
* changelog
* remove unnecessary check for _contained flag
* fix broken tests
* Add backport information
* Bump version, add version enum
* begin with failing test
* fix bug
* change log
* change log
* Add backport information
* Improve performance of chained queries into contained resources (#3312)
* base restructuring of query
* fix unit tests
* suppress unnecessary resource type parameter
* pass the resource type used to fetch the search param as part of the chain, so later we do not need to guess what it was
* add query structure tests
* changelog
* fix test failures
* got one of the branches wrong in the 3-reference case
* Add backport info
* Bump version
* Fix errors due to merge
* Bump license year
* Add folder for release version
* Version bump
* 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
* Add backport info
* add new folder for version
* Add missing message
* New version enum, and folder
* Version bump
* Bump spring lib version
* Tidy versions
* Remove test
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
* 2991 - WIP, starting to implement test to reproduce the issue.
* Adding capability to extract url & version from the valueSet.include.url
* parsing codeSystem canonical URL to extra version if required.
* WIP
* Cleaning up the test.
* Replacing hard code value with variable.
* Removing non required test.
* Modifications following first code review.
* Further modifications following first code review.
* Refining the test for better code coverage.
* Prefixing the change log file name with the hapi-fhir issue number.
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
* added failing tests
* tests pass
* Added changelog and javadocs
* fixed package tests for resources with no active field
* adding jira ticket number
* feedback from code review'
* switching to old style switch statement'
* 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
* Improve batch2 error handling
* Build fixes
* Work on reindexing
* Test fixes
* Account for gzipped contents
* License header updates
* Register VS operations on public server
* Test fix
* Build fix
* Remove animal sniffer plugin
* Compile fix
* fix mongo date search with the NOT_EQUALS prefix
* add test & changelog
* add some unit tests
* rename unit test names to be more clear
Co-authored-by: olivia-you <olivia.you@smilecdr.com>
* Store resource data inline with lucene/es resourcetable index.
* Use fulltextsearch to load resources if resource inlined in ES/Lucene index
Co-authored-by: Jaison Baskaran <jaisonb@gmail.com>
* 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
* Add reindex-terminology batch command
* Handle number of thread throttling and concurrency with other terminology batch operations
* Add required dbcp2 dependency
* Fix test
* Improve ConnectionPoolInfoProvider setup. Handle maximum connections.
* Remove java higher version construction
* Remove unused config
* Add reindex terminology integration test.
Reset termConcept counters before pre-expanding, which otherwise accumulate if it was pre-expanded before.
* Address MR comments
* Adjust test to tested class change
* Adjust test to tested class change
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add reindex-terminology batch command
* Handle number of thread throttling and concurrency with other terminology batch operations
* Add required dbcp2 dependency
* Fix test
* Improve ConnectionPoolInfoProvider setup. Handle maximum connections.
* Remove java higher version construction
* Remove unused config
* Add reindex terminology integration test.
Reset termConcept counters before pre-expanding, which otherwise accumulate if it was pre-expanded before.
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.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
* Remove dups
* Remove unnecessary stuff
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>
* 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
* Added log to the create() and valiForUpload() methods in the PackageInstallerSvcImpl class
* Added helper methods to extract URL from SearchParameter.Tested and fixed log entries.
* Changelog entry
* Update 3384-Package-Install-added-logs-for-resources-validation.yaml
Co-authored-by: Kai Liu <kliu@Kais-MacBook-Pro.local>
* 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
* Refactor ValueSet expansion code to simplify property filtering by using new Hibernate search V6 nested classes capabilities; use generic hibernate search queries where possible (mostly everywhere but regex queries) and add R4 integration tests for both elastic and lucene.
* Refactor ValueSet expansion code to simplify property filtering by using new Hibernate search V6 nested classes capabilities; use generic hibernate search queries where possible (mostly everywhere but regex queries) and add R4 integration tests for both elastic and lucene.
* Add comment for trick
* Add codes to exception messages
* Add test specific for the fix
* Move changelog to current release. Add upgrade notice.
* Improve fail-fast method
* Update upgrade instructions
* Try luck with new exception codes
* Update hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/search/ElasticsearchNestedQueryBuilderUtilTest.java
Add missed quote
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
* Add FK index to avoid timeout when deleting large ValueSet
* Add exception to allow same name for index and FK
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Start working on graphql Schema
* Start testing
* Work on introspection
* Work on introspection
* Use integers for date ordinals
* Add changelog
* GraphQL updates
* Ongoing wrk
* Cleanup
* Bump core lib
* Add changelog
* Clean up dependencies
* CLeanup
* Add missing message
* Test fix
* Change to force CI
* export rules are applied now
* add changelog and test
* add changelog
* Delete 2797-bulk-export-getting-incorrect-group-data.yml
* update test
* add test
Co-authored-by: olivia-you <olivia.you@smilecdr.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
* 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>
* 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
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
* 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
Co-authored-by: Steven Li <steven@smilecdr.com>
* feat: added support for package.zgz uri in the "file:/" format
* added changelog entry
* add error code to thrown message
Co-authored-by: Tadgh <garygrantgraham@gmail.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>
* 3156 fix race condition that results in multiple tags being created
* 3156 added changelog
* cleanup
* added smile jira ticket
* 3156 review fixes
* review fixes
* 3156 added an additional integratoin test
* cleanup
* review fix and master merge
* threadsafe stuff
* small change
* upping min threads for tests to pass
* changing test
* test check
* fix
* test testing
* one more update
* using threadpoolutil
* temporary measure
* git push
* all builds
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* failing test
* failing test
* Fixes
* Updated note to self
* Improve pre-caching of resource IDs
* Work on tests
* Test fixes
* Add changelog
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* added settings for cross-partition to Dao and Model config
* modified subscription validator to validate cross partition subscriptions
* modify subscription matcher to allow matching on all partitions when subscription is set to cross partition
* added cross partition to canonicalSubscription
* end of day commit, changed how we are checking if default partition in subscription validator
* fixed issue with i memory matching for cross partition subscriptions
* added test for parsing legacy CanonicalSubscription
* added changelog and doc changes
* addressed comments in pr
* added assertdoesnotthrow
* test fixes, added new mocks
* added check for if resource can have extension before checking for extensions
* removed unnecessary semicolon
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Long Ma <long@smilecdr.com>
* Make RestfulClientFactory.myValidatedServerBaseUrls usage thread safe so capability validation request is sent only once per client-endpoint
* Can't use @GuardedBy for fields which are not always locked by annotation object
* Use same variable when checking and setting
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* base restructuring of query
* fix unit tests
* suppress unnecessary resource type parameter
* pass the resource type used to fetch the search param as part of the chain, so later we do not need to guess what it was
* add query structure tests
* changelog
* fix test failures
* got one of the branches wrong in the 3-reference case
* Added IT for Payload Search REST HOOK subscription, fixed issue with null pointer exception
* removed todo comment, added changelog
Co-authored-by: Steven Li <steven@smilecdr.com>
* 3283 delete will not return a 404 if resource is not found
* minor tweaks
* checking if tests fail due to asynchronicity
* 3283 added integration test
* cleanup
* review fixes
* changed id names
* cleanup
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3274 throw if url is full url
* 3274 will throw on invalid urls
* 3274 fixing the tests
* 3274 cleanup
* anonymize the data
* review fixes
* 3274 fixed for backward compatibility
* added review fixes
* fixing tests
* some more test fixes
* test fixes
* 3274 fixing the check to only look for resource at begining
* 3274 fixed test
* test fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Run intended job
* Add test ti validate right method is invoked by inner job
* Add changelog
* Make test fail with proper message instead of crash
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Fix PatientIdPartitionInterceptor for case where patient ID has hashCode equal to Integer.MIN_VALUE
* Fix PatientIdPartitionInterceptor for case where patient ID has hashCode equal to Integer.MIN_VALUE
Co-authored-by: ianmarshall <ian@simpatico.ai>
* Bump a number of versions
* Fixes
* Work on version bump
* Bump
* Test fix
* More version bumps
* Build fixes
* Test fixes
* Fixes
* Fixes
* Test fix
* Bump jacoco
* Test fix
* Test fix
* Test fix
* Build fix
* Build fix
* Remove versioned H2
* Build fix
* Avoid memory issue in validation tests
* JDK bump
* Restore compile with errorprone
* Force coloured output
* Force jansi
* Try again to force jansi
* Fix for hardcoded date that just passed
* Fixes to JPA
* Improve changelog
* Work on failing test
* Test fix
* Compile fix
* One more version bump
* Test fixes
* Add flag in DaoConfig to enable storing resources in lucene index
* Update loadResourceByPid to use ElasticSearch for loading observation resource and test added to check it
* Added parsing to elastic search to parse inlined observation resources json to resource object
* 2521 will set subscriptionst hat cant be initialized to error state to prevent infinite retries
* 2521 add changelog
* cleanup
* fix issue in merge
* fix bad merge
* bad merge
* 2521 review fixes and test fixes
* 2521 review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* Allow Subscription to be configured to send delete messages
* Add tests and implement MR suggestions
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* some fixmes to start
* Added some FIXMEs
* added RequestPartitionId to reosurceDelivryMessage and ResourceModifiedMessage
* ResourceDeliveryMessage and ResourceModifiedMessage tests
* fixed issue with test missing partitionHelperSvc mocked bean
* Added tests and implemented SubscriptionMatchingSubscriber for partition aware subscription
* modified implementation of partitionId in CanonicalSubscription
* Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)
* Revert "Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)"
This reverts commit fe40fb9733.
* Got added partitionId to subscriptions, added changes to make SubscriptionMatchingSubscriberTest work
* added SubscriptionTriggering test, also added partition support to subscriptionLoader
* Changed implementation for storing partition id of subscriptions from messages, refactored tests to new implementation
* added all subscription systemRequestDetails with all partition to subscription reader
* refactored a generic system request details with default all partition request
* Added test for dao subscriptions, fixes to get the test working
* added partition support for latest version delivery
* added doc changes and changelog for multitenancy subscription
* cleanup and added partitioned subscription manually trigger test
* fixed mocked subscriptionDao
* added package-info for subscription module
* some code review changes
* removed AllPartitionSystemRequestDetail, added new text for multitenant subscription
* renamed method for code review
* version bump to 5.7.0PRE7
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* try xml -> json
* Change from xml serialization to json serialization. Also fix a deadlock in how the validation cache is used.
* changelog
* back out logback
change
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3236-change-validation-from-xml-to-java.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* move mail config to mail service constructor
* update subscription email sender
* added license text
* [2669] bump HAPI version to 5.7.0-PRE6-SNAPSHOT
* add changelog
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