* add ability to skip loading package resources that already exists, to avoid reindex when loading IGs
* Add a test for validating no updates or creates are called on anything but binaries
* Add changelog
Co-authored-by: Craig McClendon <craig.mcclendon@accenture.com>
* Bump for CVE (#3856)
* Bump for CVE
* Bump spring-data version
* Fix compile
* Cut over to spring bom
* Bump to RC1
* remove RC
* do not contrain reindex for common SP updates (#3876)
* only fast-track jobs with exactly one chunk (#3879)
* Fix illegalstateexception when an exception is thrown during stream response (#3882)
* Finish up changelog, minor refactor
* reset buffer only
* Hack for some replacements
* Failure handling
* wip
* Fixed the issue (#3845)
* Fixed the issue
* Changelog modification
* Changelog modification
* Implemented seventh character extended code and the corresponding dis… (#3709)
* Implemented seventh character extended code and the corresponding display
* Modifications
* Changes on previous test according to modifications made in ICD10-CM XML file
* Subscription sending delete events being skipped (#3888)
* fixed bug and added test
* refactor
* Update for CVE (#3895)
* updated pointcuts to work as intended (#3903)
* updated pointcuts to work as intended
* added changelog
* review fixes
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)
* Add test and implementation
* Add changelog
* 3899 code in limits (#3901)
* Add implementation, changelog, test
* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 3884 overlapping searchparameter undetected rel 6 1 (#3909)
* Applying all changes from previous dev branch to current one pointing to rel_6_1
* Fixing merge conflict related to Msg.code value.
* Fixing Msg.code value.
* Making checkstyle happy.
* Making sure that all tests are passing.
* Passing all tests after fixing Msg.code
* Passing all tests.
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)
* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete
* created unit test for skip of delete operation while processing duplicating create entries
* moved unit test to FhirSystemDaoR4Test
* 3379 mdm fixes (#3906)
* added MdmLinkCreateSvcimplTest
* fixed creating mdm-link not setting the resource type correctly
* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on
* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java
Change order of tests such that assertEquals takes expected value then actual value
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* added changelog, also changed a setup function in test to beforeeach
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
* Fix to the issue (#3855)
* Fix to the issue
* Progress
* fixed the issue
* Addressing suggestions
* add response status code to MethodOutcome
* Addressing suggestions
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)
* Respect caching in bullk export, fix bug with completed date on empty jobs
* add changelog
* Add impl
* Add breaking test
* Complete failing test
* more broken tests
* Fix more tests'
* Fix paging bug
* Fix another brittle test
* 3915 do not collapse rules with filters (#3916)
* do not attempt to merge compartment permissions with filters
* changelog
* Rename to IT for concurrency problems
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Version bump
* fix $mdm-submit output (#3917)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Gl3407 bundle offset size (#3918)
* begin with failing test
* fixed
* change log
* rollback default count change and corresponding comments
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Offset interceptor now only works for external calls
* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.
* do not reindex searchparam jobs on startup
* Fix oracle non-enterprise attempting online index add (#3925)
* 3922 delete expunge large dataset (#3923)
* lower batchsize of delete requests so that we do not get sql exceptions
* blah
* fix test
* updated tests to not fail
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* add index
* Fix up colun grab
* Bump Version for non-breaking purposes
* Fix broken test
* bump error code
* revert internal logic
* Revert offset mode change
* wip
* Revert fix for null/system request details checks for reindex purposes
* Fix bug and add test for SP Validating Interceptor (#3930)
* wip
* Fix uptests
* Fix index online test
* Fix SP validating interceptor logic
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* Make sure that direct resource load path is only executed for synchronous searches
* Remove unneeded mockito extension
* Only allow for resource loading from fulltext index when advanced search (indexed parameters) is also enabled
Co-authored-by: juan.marchionatto <juan.marchionatto@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>
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.
* 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>
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>
* 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>
* 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>
* adding version.yaml, updating version in pom.xml
* It is possible to write to a resource in a partition the user is not authorized to. (#3397)
* fixed
* remove sout
* add msg.code
* fix failed tests
* fix equal sign
* update msg code
* extract method
* Fix up code numbers
* Clean changelog
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Revert final artifact version
* add graphql test (#3585)
* added graphql birthdate test
* fix variable name
* typo
* 3506 mdm log enhancement (#3543)
* Providing Fixme's to be reworked at a later time.
* Adding // FIXME Anna to assist our Austrian friend.
* Adding logging test as a first step in addressing issue #2822.
* hapifhir#3506 part 2: enhance logging for (un)successful MDM matching
hapifhir#3506 part 2: enhance logging for (un)successful MDM matching
* Update MdmMatchLinkSvc.java
#3506 move "narrowed down" log to different place
* #3506 added scores and tests
#3506 added scores and tests
* #3506 formatting
#3506 formatting
* #3506 create changelog file
#3506 create changelog file
* #3506 fix typo
#3506 fix typo
* #3506 fix part 3, minor formatting
#3506 fix part 3, minor formatting
* #3506 fix tests
#3506 fix tests
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
* mdm matching (#3579)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328
* Update HapiFhirJpaMigrationTasks.java
Corrected ordering
* Update HapiFhirJpaMigrationTasks.java
Moving index status to be last operation
* Revert "Update HapiFhirJpaMigrationTasks.java"
This reverts commit 37bfd3e66e.
* Moved to bottom
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
* begin with failing test
* fixed
* changelog
* add jira tag
* Update to 6 1 (#3582)
* added changelog folder, upped version
* version enum
* add a few more unit tests to assert proper NO_MATCH exclusion
* revert merge master doh! bad reflexes
* revert merge origin master
* unrevert revert. ugh what a pain
* merge recovery. fix poms.
* merge recovery. more reverting
* merge recovery. more reverting
* merge recovery. more reverting
* Revert "merge recovery. fix poms."
This reverts commit ae6e0ddb06.
* more revert revert reversions
* more revert revert reversions
* pre-review cleanup
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
* Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586)
* When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller.
* License
* Ks 20220508 log colour (#3592)
* don't use colours when output is redirected to a file
* change log
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594)
* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328
* Update HapiFhirJpaMigrationTasks.java
Corrected ordering
* Update HapiFhirJpaMigrationTasks.java
Moving index status to be last operation
* Revert "Update HapiFhirJpaMigrationTasks.java"
This reverts commit 37bfd3e66e.
* Moved to bottom
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
* 3584 case sensitive string elasticsearch (#3596)
* Fix for case-sensitive search with newer elasticsearch
* Test and fix ascii normalization too
* more test cases
* comments
* Docs update empi usecase (#3598)
* Update diagram for use case 5
* Add new page for database support
* Licnese
* Mb norm fix (#3604)
* Normalize query since wildcard searches aren't normalized in elastic
* Handle batch2 job cancellation (#3603)
* Handle batch2 job cancellation
* Add CANCELLED status
* Remove unuseful test
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add batch2 interfaces to obtain recent instances (#3601)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* changelog folder
* Documentation change, added warning log and change log for ticket (#3609)
Co-authored-by: Steven Li <steven@smilecdr.com>
* fix ne for lastUpdated search param (#3589)
* init/wip
* add implementation, add tests
* add checks and some refactoring
* refactor and simplify tests
* refactor
* get rid of some of the warnings
* add changelog
* remove my todos
* redo ne logic to account for less precise dates
* add tests
* refactoring
* rename to follow convention
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
* Version bump
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
Add support for _total, _count, and _offset to Lucene backend.
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Rely on context refresh event instead of postconstruct. Load bean lazily.
* Remove parent autowire
* Break termcodesystem circular dependency with new bean
* Break cycle between BaseTermReadSvcImpl and TermCodeSystemStorageSvcImpl
* move back into helper method
* Rip out scheduling and submission to spring batch away from BulkDataExportSvcImpl
* wip
* Fix bean naming
* Revert
* re-add autowiring
* Reformat
* docs and reformat
* Back out change
* feedback from review
* merge conflicts
* 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>
* Change token and reference search params to 'keyword' field type
* remove normalizer for keyword field
* WIP - refactor lastN operation to use hibernate search generated ES index.
* Add ES native aggregation builder for lastN
* added date search param support for searching resourcetable ES index
* * Added DateSearch parameterized tests to ElasticSearch test suite
* Added more tests cases for Date searches
* WIP refactor LastN test data to central generator class and use it for both hibernate-search and elastic search implementations.
* WIP fix lastNDataGenerator to avoid assertion errors.
* Fixed tests to run test suite on both existing lastN search implementation and newer extended lucene index based search.
* Cleanup json string to avoid carriage return noise
* Fix checkstyle issues
* Fix checkstyle Msg code issues
* Fix checkstyle Msg code issues
* Add more test case for GT, SA precision modifier
* Fix date precision test cases
* Fix Msg Code conflicts
* Add more logging
* Add way more loggging
* even more logging
* fix msg code conflicts
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>
* 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
* First cut at multithreading bundle validation
* javadoc
* change test to a red-green test
* add daoconfig
* move bundle concurrency config from validationsupport to request validator
* Moved concurrent details from ValidationOptions to FhirValidator
* Remove bundleValidationThreadCount (it's set by creating an appropriate executor)
* validate threadpool prefixes
* FIXME cleanup
* reassign FIXMEs to JB
* only create the threadpool if it will be used
* Add the MdcTaskDectorator to all threadpools
* Add bundle path to concurrently validated bundle resource validation messages.
* Add test to check bundle entry path being added to validation messages
* Threaded validation of contained resources initial checkin
* FHIR validator refactored to maintain correct bundle path and async validation task
* Refactored to use validation complete invoke callback to support raw string resource or resource object
* switch from XML to JSON
* # Conflicts:
# hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java
# hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
* Updated to use new HAPI-FHIR version
* merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation
* Updated to use new HAPI-FHIR version
* Revert "Updated to use new HAPI-FHIR version"
This reverts commit 910b7f676b.
* Revert "merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation"
This reverts commit c7d60fc3e6.
* Revert "Updated to use new HAPI-FHIR version"
This reverts commit aa8a7af455.
# Conflicts:
# hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
* Fix Test dependencies after reverting changes.
* merge 'validate_contains_change' to 2564-contained-resource-validation-flag
* Disable threadpool prefix name validate check.
* merge master
* fix thread regexp
* pre-review cleanup
* change log
* fix test
* revert to XML as default validation serialization
* fix test
* fix test
Co-authored-by: Jaison B <jaisonb@gmail.com>
* Synthea perf work
* Cleanup
* Work on performance
* Ongoing perf work
* More perf work
* Perf work
* Test fixes
* Updates
* Test fix
* Test fixes
* Clean up tests
* Test cleanup
* Cleanup
* Add test
* One more perf tweak
* Fixes
* Add changelog
* Add changelog
* License header update
* License header updates
* Add failing test
* Tidy test for new tokenparam style
* Add removeByQualifier to SearchParameterMap
* Add new property binder for search terms
* Member move, add test for new parser
* whoops missed an add
* Passing test.
Introduced SearchParamTextWrapper to give a type for the binder.
Enhance FulltextSearchSvcImpl to understand TokenParams as well as StringParams.
* Add more to test, change analyzer for template
* Optimize imports
* Minor refactoring
* added eq and gt test cases
* added missing gt search param tests
* Search all CodeableConcepts
* Extract new LuceneRuntimeSearchParam to mediate indexing and searching.
* Fix up broken test with mock
* Add support for identifier type
* Bump for special maven package
* fix-me to todo
* Prevent version check
* FIx version for test
* DSTU2 does not support fluent path
* Don't accidentally strip SPs in DSTU2
* added lt tests
* Add some high-bound test cases
* More test cases and new compressed format
* More test cases
* More test cases
* Re-order columns for easier reading
* Comments
* Cleanup and comments
* Make support :text for all token SPs
* Make support :text for all token SPs
* Fixed incomplete date issue
* Set to the last millisecond 23:59:59.999
* Disabled 4 failed JVM/TZ related test cases
* add test for failing batch bug, remove bounding on queue
* remove parallelism from non-get batch operations
* Fix count for test
* New index layout
* Notes and cleanup
* Notes and cleanup
* remove the jetbrains
* Demote FIXME to WIP
* Change :text search to be lucene simple search and use standardAnalyzer.
* Change :text to require * for prefix match.
* add prefix negative test
* Bump version
* Added changelog
* Add more search parameters to lucene indexing (#3000)
* dirty the branch
* Add oversight to changelog
* Start using jpa indexing for es
* Correct negative search test
* Update templates, index tokens, write new test. TODO gotta modify SB
* Add test for code token search
* add comment
* Flesh out token search
* minor cleanup and comments
* Extract index handling from FulltextSearchSvcImpl
* D'oh. Actually use elastic to search.
* Move supported query check closer to query builder
* String search test before activating lucene
* Add string:exact to hibernate search.
* Add string:contains search
* cleanup
* demote fixmes to allow build to run.
* Add unmodified string search.
* empty stubs for quantity and reference
* Ignore magic search params in lucene index
* Support full-text on all FHIR releases
* Include reference lookups in ES
* Fix and/or logic in _text
* Test for string with space
* Cherry-pick the NoFT fix
* Disable advanced indexing in a bunch of tests of emitted sql.
* Stub changelog
* Fix :missing flag
* Move DaoConfig up to BaseJpaTest to share teardown
* Disable new indexing for partition test
* Add a different analyzer and field for default string search vs text
* checkstyle for a pre-build
* Index full prefix for string search when using Lucene
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3000-Extend-lucene-indexing.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/HibernateSearchQueryBuilder.java
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Review feedback.
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Remove double-check
* Version bump
* Fix typo
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Long Ma <longma@Longs-MacBook-Pro.local>
Co-authored-by: Frank Tao <frankjtao@gmail.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* 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
* 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 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 failling test, works on #2843
* Partial hack to get this working
* Move implementation into pre-processing
* Add changelog
* Move implementation
* Minify Test
* Remove fixmes
* Tidying
* Ensure this only operates on STU versions which support canonical
* Add test
* Test fixes
* Work on expansion errors
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Work on fix
* Test fixes
* Test fixes
* Test fix
* Cleanup
* Test fixes
* Remove accidental commit
* Test fixes
* Version bump
* Add changelog
* Fixes
* Test fix
* Fix conflicts
* Try commenting out clearAllStaticFieldsForUnitTest to see what happens
* Rename clearAllStaticFieldsForUnitTest to randomizeLocaleAndTimezone and only do that
* failed attempt to get it to work
* Use simplified FhirContext.forCached methods
* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Avoid dead SearchParameter links in CapabilityStatement
* Resolve fixmes
* Build fix
* Test fix
* Test fix
* Test fix
* Work on metadata
* Fixes
* Test fixes
* Test fix
* Test fix
* Test fixes
* Test fix
* Work on test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Fix params
* Resolve fixme
* Adjust changelogs
* Version bump to 5.6.0-PRE7
* Add license header
* Bump version to 5.6.0-PRE5-SNAPSHOT
* Start work on nonunique combo search params
* Work on SQL
* Version bump
* A fix
* Test fixes
* Fixes
* Undo version bump
* Test fixes
* Resolve fixme
* prepare to add $delete-expunge operation that will create a spring batch job
* Add operation
* Wire up jpa provider. Begin with failing test.
* Copy/paste bulk import job as a starting point.
FIXME with proposed design
* delete expunge job parameter validation with test
* implemented reader
stubbed processor, writer
* wip for master merge
* started implementing reader
* started implementing reader
* working with stubs
* happy path batch delete expunge is done
* Provider done but test not passing. Guessing batch infrastructure not running in that test.
* IT test works now
* add reader test
* Converted delete _expunge=true to use new batch job
* DeleteExpungeDaoTest passes
* Fix test
* Change batch size to integer
* rename search count to batch size
* Make delete expunge partition aware
* updated docs
* pre-review cleanup
* change log
* add partition id to SystemRequestDetails
* Make RequestPartitionId serializable
* Change delete expunge provider to use partition id instead of tenant name
* fix tests
* test pointcut gets called
* assert on pointcut calls
* Add resource type to STORAGE_PARTITION_SELECTED pointcut
* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants
* bump hapi-fhir version
* copyrights
* restore deleteexpungeservice for mdm
* restore deleteexpungeservice for mdm
* fix test
* public constants
* convert instant to date
* Moved expunge constants to ProviderConstants
* final review
* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run
* fix tests
* fix tests
* fix tests
* fix tests
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* improve logging
* bump version
* version bump
* recovering from failed merge
* unzip RequestListJson per Gary's suggestion. I didn't want to do it at first, but as usual Gary was right.
* fix serialization
* Search param service cleanup
* Work on collapsing search param
* Search param cleanup
* Work on build
* Test fix
* Test fixes
* Ongoing work
* Test fix
* Compile fix
* Test fixes
* Test fix
* Test fix
* License header updates
* Remove fixme
* Cleanup
* Cleanup
* Add support for revincludes to CapabilotyStatement generator
* Add changelog
* Fixes
* Test fix
* Test fixes
* Test fix
* Test fix
* More fixes to CS cache
* Test fix
* Test fix
* Test fix
* Start work
* Work on testing
* Version bump
* Test fix
* Compile fix
* Test Fixes
* Test fix
* Test fix
* Compile fix
* Tst fix
* Test fix
* Test fix
* Test fix
* Performance tweaks
* Work on processing speed
* Disable no longer relevant tests
* Work on performance
* Work on tests
* Work on large transaction performance
* Add changelog
* Perf tweaks
* Test fixes
* Resolve FIXME
* Fixes
* Test cleanup
* Fix broken changelog entry
* POC for indexing on contained resource - test case may failed
* Test contained url
* Add a spt to handle contained flag
* Added search option for contained resource
* Impl contained resource search
* fixed typo
* Reworked on creating index based on the review comments
* Added changelog
* Added more test cases
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
* Automatic reference versions
* Auto reference versions
* resolve fixmes
* Add changelog
* Test fixes
* Test fixes
* Resolve fixmes
* Work on versioning
* Add support for _includes
* Update headers
* Change visibility
* One more tweak
* One more API tweak
* Fixes
* Account for review comments
* Fix errorprone reported issue
* Test fix
* Test fixes
* Test fixes
Tadgh
Ken Stevens
jmarchionatto
longma1
michaelabuckley
JasonRoberts-smile
James Agnew
Jaison Baskaran
StevenXLi
Johnson Lu
TipzCM
Tadgh
jdar8
Justin Dar
Frank Tao
Diederik Muylwyk
Kevin Hartmann
Patrick Werner
Jari Maijenburg
Mike G