* 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
* initial roughout of mdm clear batch job
* still roughing out classes
* finished first draft of reader
* most tests passing now
* all tests pass. now FIXMEs
* FIXMEs done. Time for regression.
* fix test
* changelog and docs
* fix test
* pre-review cleanup
* version bump
* move spring autowire deps for cdr
* move spring autowire deps for cdr
* finally got beans working phew
* rearrange method calls so persistence module can perform clear operation on its own
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* review feedback
* review feedback
* Remove inheritance
* fix beans
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Impl displayLanguage for $lookup - first cut
* Added original lookupCode method
* Added original lookupCode method to IFhirResourceDaoCodeSystem
* Added more test cases and changelog
* 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
* 2572 - Add master Branch changes related to backport of fix for #2171 for new 5.3.3 release.
* 2572 - Added some missing changelog folders for the v5.3.1 and v5.3.2 releases.
* 2572 - Added a missing backport changelog entry for the v5.3.1 release.
* 2572 - Added a missing VersionEnum entry for the V5_3_1 release.
* Start work on OpenAPI
* Fixes
* Work on OpenAPI
* Cleanup
* Cleanup
* More swagger work
* Build fix
* More work
* More work
* Add documentation
* Docs fixes
* Add changelog
* License updates
* Add API
* Cleanup
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
* Work on scripts
* Add docs
* Compile fix
* Work on fixes
* Fix tests
* Test fix
* Test fix
* Build fix
* Tests
* Build fix
* Work on pipeline
* Version bump
* Test fix
* Version bump
* Test fix attempts
* Test fix
* Test fix
* Remove accidentally committed files
* Fixes
* Tets fixes
* Test fix
* Test fix
* Test fix
* Test fixes
* Test fixes
* Test fixes
* License header updates
* test fix
* Test fixes
* Test fix
* Test fixes
* Test fix
* Checkstyle bump
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
* Start work on bul;k import
* Work on bulk import
* Have batch working
* Working
* Working
* More work
* More work on bulk export
* Address fixmes
* License header updates
* Test fixes
* License header updates
* Test fix
* Test fix
* Version bumps
* Work on config
* Test cleanup
* One more version bump
* Version bump
* CLeanup
* A few additions
* Test fixes
* Test fix
* Test fix
* Migration fix
* Test fix
* Test fix
* 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
* 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
* improved DateQuery and removed 'OR' in the SQL
* improved DateQuery and removed 'OR' in the SQL
* Date handling cleanup (#2316)
* Date handling cleanup
* Fix codecov
* One more fix
* Fix tests
Co-authored-by: James Agnew <jamesagnew@gmail.com>
+ relative URL resolution in RDFParser
+ test non-DomainResources in RDFParserTest
~ factor/organize RDFParserTest
~ avoid EXTERNAL shapes (for now) in shex-java
- disable the bundle-response.json example as it is apparently malformed
+ added urn:-guard to PreResourceStateHl7Org.wereBack ID update
* Beginning work on converting to hibernate search 6
* replace all out of date properties
* replace all POM references to old versions
* remove the shaded ES jars as HS6 supports 7.9
* Convert "Bridges" to RoutingBinder and RoutingBridge
* Modernize all indexing annotations
* Begin refactoring of search queries (wip)
* Fix spatial API changes, work on BaseTermReadSvcImpl
* Most of the way through the various filter property conversions
* Finished i think with BaseTermReadSvcImpl
* Compiling, but definitely broken
* Start test compilation failures
* All tests compiling (i think)
* remove suggest keywords operation
* Fix bootstrap errors, still have to deal with transient fields
* Rollback CR
* More refactoring, got IDs baked back into docs
* Fix coord util, fix a few more fields which require projection
* merge fixes
* begin refactor of valuesetexpansion tests
* fix another test
* Update tests
* remove todos, add TestContainers
* Fix descendant in
* Add testcontainers, fix another test
* fix more tests, replace embedded es
* Rip out embedded elastic, replace with TestContainer
* merge conflicts for new analyzers
* Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs
* Remove dead deps, update testcontainer
* Remove java-hamcrest
* Pull asserts up, refactor tests to pass in RP tests
* Update V2 check
* Remove suggest keyword tests
* Split line for testing
* Fix perhaps one of the dumbest programming mistakes in my career so far
* Refactor tests which no longer rely on a strict known order
* Fix up test config, disable log test temporarily
* Remove log4j from being transitively pulled in. re-enable test
* Update log4j exclusions with new bridge. Update test to check for core class
* Move dependency to root pom in dep management section
* Update changelog, add changelog for HS6 with ES requirements. Remove dead comment
* update testst, remove todos
* Add hibernate props provider method, add elastic regexp query
* Add todo for high level client builder
* Modify ElasticsearchRestClientFactory to support HTTPS hosts
* Remove protocol extraction from rest url
* do we even need to index this...?
* remove purge of non-indexed resources
* Add longer timeout to testcontainers
* Add task to add docker CLI to azure pipeline via task, for testcontainers
* WIP remove this
* Dont update version
* Add test for duplicate termconcepts
* Use real hibernate ORM methods
* merge issues
* Add partitionsettigns bean to match master
* Trying to debug testcontainers on azure...
* Trying to debug testcontainers on azure...
* Run even on previous failure
* Fix testcontainer port binds
* Add full text logs attaching, and test reporting
* I love yaml
* Remove comment
* Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue
* Modify TX beheaviour
* wip
* Rework to use config and mocked beans for partition-aware lastN
* rework to not use beans and just inject vars i need for test, keps test envs cleaner
* update azure pipeline to only copy test results
* Remove erroneous publish
* Always get test logs
* Make it so indexing works,
* Add todos
* revert deleteByPid
* Work on test fixes
* Test fixes
* Test fixes
* Another test fix
* Test fix
* Work on tests
* Test fixes
* All tests passing locally
* Fix test failure
* FIx build error
* Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider
* Update ngram of token filters
* Tidying
* subvert the purpose of hibernate elastic props builder to inject template
* dead space
* Rename changed class
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
* Start work on validation rules interceptor
* Work on interceptor
* Add tests
* Work on validation interceptor
* Work on interceptor
* Test fix
* Documentation tweaks
* Partitioning rework
* Work on partition improvements
* Partition updates
* Work on partitiong
* Test fixes
* Add docs
* Add changelog
* Resolve FIXME
* Test fixes
* Test fixes
* Test fixes
* Compile fix
* Fix compile error
* Test fix
* Test fixes
* init rev
* fix build
* Tweaked the POM config settings and also added some dependency exclusions (commented out for now).
* More re-factoring of the CQL Unit Tests.
* Removed a LogMessages.html file and a minor Unit Test change.
* Unit Tests.
* added debug logging to troubleshoot the dao that has no name
* added debug logging to troubleshoot the dao that has no name
* workaround to get past null dao resourceName issue
* fix jsons to get test to pass. Test still fails with library id problem
* gitignore
* gitignore
* test passes! Woohoo!
* undo troubleshooting logging
* added timer and logging.
* added asserts and time multiple evaluations and measure the average
* readme
* adding explanations
* added more explanatory notes
* measure 2 patients
* move pom to use cqf snapshot
* roughed out cache
* roughed out cache
* Added code to VersionChangeCache class.
* added tests
* added polling test
* wrote init version
* wrote init version
* optimized versioncache
* worked on getting tests to pass
* redesigned interfaces
* all tests pass
* fixmes
* fixmes
* rename param
* Added Unit Tests.
* javadoc
* Fixed the 2-Patient Unit Test.
* More Unit Test work.
* make ResourceVersionMap immutable
* Fixed a Unit Test that was failing intermittently by adding a new way to refresh the cache.
* Use a new method called doRefreshAllCaches(0) to force a refresh and have all Listeners called immediately.
* Cleaned up IVersionChangeListenerRegistry interface to make methods more clear and resolved all Unit Tests.
* disabled tests
* disabled tests
* removed unused test method
* fixed refresh logic and added asserts
* moved cache so it can be used by searchparamregistry
* Updated the Cql Unit Tests to be properly configured for Dstu3 or R4.
* started rewriting SearchParamRegistryImpl to use new cache
added init method to listener interface
* added fixmes
* adding tests
* tests pass
* added tests
* Fixed the way CqlProviderFactory Autowires Beans so it can work with both Dstu3 and R4 contexts.
* moar tests
* fix test
* work tests
* reverting unneccessary refactors
* undo unneccessary import changes to reduce MR size
* undo unneccessary import changes to reduce MR size
* Unit Test fixes...more to come...
* add unregister
* fix tests
* Changed ResourceVersionCache to use a Map of Maps.
* searchparam test
* test passes
* resolved fixme
* fixmies
* strengthen test asserts
* More Unit Test changes and added some FIMXME items.
* changed from long to changeresult
* renamed VersionChange -> ResourceChange
* fixed delete bug
* organize imports
* fix test
* add update test
* add test reset function
* fix stack overflow
* fix startup race condition (might still be intermittent)
* found the problem. delete doesn't work because we can't look up the deleted resource to find out what its name is
* fixed regression
* abandoned idea of incrementally updating searchparam registry. Rebuilding every time--it doesn't change that often.
* fix test
* begin with failing test
* test passes
* fixmes and javadoc
* fix test
* fixme
* fix test
* whack-a-mole. Either subs pass or cql passes. Something's fishy with the FhirContext
* fix subscription test initialization
* fix method name
* Re-factored the CqlProvider Unit Tests.
* changed ResourceChange API
* add interface
* add interface
* fix test
* add schedule test
* add doc
* init rev
* FIXME
* modify FhirContext change
* change fhirContext.getResourceTypes to lazy load
* converted subscriptions
* converted subscriptions
* begin with failing test
* test passes
* fix test
* test coverage
* test coverage
* test coverage
* test coverage
* good coverage now
* pre-review cleanup. I think I found a bug.
* moved cache into listener entry
tests pass with fixmes
* fix test
* fix test
* fix test
* fixme
* FIXMEs
* merge cache and registry
* method reorg
* javadoc
* javadoc done. all FIXMEs resolved.
* change log
* changes needed by cdr
* spring config cleanup
* james feedback
* james feedback
* might not work. Try moving resourcechangeconfig into searchparam config
* merge ResourceChangeListenerRegistryConfig.java into SearchParamConfig
* fix test
* fix SubscriptionLoader
* fix SubscriptionLoader
* create ResourceVersionMap from resources
* added cache handle interface
* fix test
* javadoc
* fix test
* fix test
* James feedback: clone searchparametermap
* fix startup
* fix test
* fix test
* fix intermittent
* pre-review cleanup
* FIXME
* final FIXME yay!
* Address a couple of my own reviw comments
Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
* switched to adding annotations. Just did a test with Token, but the sql looks clean.
* switched to adding annotations. Just did a test with Token, but the sql looks clean.
* added the other six index links
* trying different annotations
* Start testing
* Update resources on package install
* Add changelog
* Join rework
* CLean up SQL builder
* Add docs
* SP rework
* Join work
* Work on params
* Work on refactor
* Work on chains
* Work on joins
* Rework queries
* Work on queries
* Many more tests passing
* Refs test
* Work on sorting
* Work on tests
* More joins work
* Work on tests
* Work on queries
* Tests passing
* More test fixes
* Test fixes
* Work on SQL
* Tests passing
* Add some tests
* Add some tests
* License headers
* Use entity manager to get datasourcd
* One more fix
* Model cleanup
* Ongoing work
* Fixes
* Fixes
* Work on joins
* Ongoing fixes
* Merge conflict
* Cleanup
* clean up unused fields
* Work on join
* COmpile fix
* Rework querying
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Resolve fixmes
* Test fix
* Test fixes
* Test fix
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Improve synchronous searching by providing offset & limit support
Add support for offset querying which leverages paging at the query level
Add configuration for search default page size and search maximum page size
If using offset, always use synchronous searching to avoid extra database insert/update etc.
When using offset, only calculate count if it's wanted
Validate params closer to provider and handle size if search returned "all" (or last)
* Review and test fixes
Comment _offset as nonstandard parameter
Make synchronous search always count the total value (for now)
Fix issue with FulltextSearchSvcImpl mutating param map
Dirty fix for BaseJpaTest (not sure how to fix the including resources issue)
* Remove temporary count querying fix for synchronous loads
* Fix offsetting of everything operations, do not drop zero offset
* Fix jpa test default and maximum page size, add some fixmes to tests before resolved
* Ignore one failing test, fix others
* Fix Dereferenced variable may be null
* Fix everything paging in R4 by adding DISTINCT if synchronous load is used
Also fix assertion of size when hitting fetchSizeDefaultMaximum
* Add documentation about offset annotation and paging
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* RDF Support in HAPI FHIR
* Ability to read/write FHIR resources as RDF (turtle serialization)
* Test suite to test roundtrip-ability of RDF parser
* Add null checks to appease LGTM
* Correct null check logic
* [(release_3_7_SSE)] cache timezone since timezone.gettimezone is static synchronized and performs poorly
* [(fixgettimezoneperformanceissue)] fiximport
* Add test
* Fix
* Add changelog
* Test fixes
* Test fix
* Test fixes
* Resolve fixme
* Test fixes
* Remove debug logs
* Try to get CI tests passing again
Ken Stevens
Jaison B
Tadgh
James Agnew
Tadgh
Nick Goupinets
leif stawnyczy
Frank Tao
juan.marchionatto
jmarchionatto
Nick Goupinets
Kevin Dougan SmileCDR
Eric Prud'hommeaux
Diederik Muylwyk
long
Kevin Hartmann
Michael Buckley
Michael Buckley
Marcelo Avancini
dependabot[bot]
Bill Denton
Tuomo Ala-Vannesluoma
Josh Collins
Oliver Egger
abrsystematic
ianmarshall
IanMMarshall
Frank Tao
christian ohr