* 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
* Added UcumServiceUtil
* Removed ucum-essense.xml
* Added ucum service existing test cases passed
* Added more test cases
* Merge branch 'master' into ft-ucum-support
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
* Added back extractReferenceParamsAsQueryTokens
* Added changelog and migration script
* Added length for the string type
* Moved UCUM util to hapi-fhir-jpaserver-model
* Renamed UCUM support to Normalized Quantity Search Support
* Moved setNormalizedQuantitySearchNotSupported to AfterEach
* Changed migrate task to 530
* Removed comments
* Fixed in memory search issue and added more test cases
* Fixed the version order
* License header updates
* Updated based on review comments
* Updated the migration task based on review comments
* Fixed RES_TYPE with type String and length 100
* Changed myParamsQuantityNormalizedPopulated type to Boolean class
* Start work on validation rules interceptor
* Work on interceptor
* Add tests
* Work on validation interceptor
* Work on interceptor
* Test fix
* Documentation tweaks
* 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>
* Add auto retry of transactions
* Experiment in Maven build
* Transaction autoretry
* Work on transaction retries
* Work on transaction retry
* Work on transaction retry
* Fix tests
* Avoid version conflicts
* Add changelog
* Resolve LGTM issue
* FIx transaction scope error
* Test fixes
* Test fix
* Test fixes
* Test fix
* Test fixes
* Work on junit
* Work on junit 5
* Work on junit 5
* Bump errorprone vcersion
* Work on tests
* Junit 5 tweaks
* Fixes
* Work on tests
* Work on junit5
* Work on tests
* Test fixes
* Work on junit5
* Test work
* Get junit5 working
* Test fix
* Work on tests
* WOrk on tests
* Work on tests
* fixes
* Compile fix
* One more tweak
* Compile fix
* Add changelog
* Fix compile error
* Compile fix
* Terser should create correct Enumeration on create
* Start work
* Work on subscriptions
* Work on seed bundles
* Bundle transmission
* Add changelog
* Test fix
* Fix LGTM warning
* Start working on FHIRPatch
* More work on fhirpatch
* Work on FHIR Patch
* Add patch
* Test fixes
* Test fixes
* Get tests fixed
* Chnage to trigger a build
* Compile fix
* Dependency version fixes
* Test fix
* COmpile fix
* Try to fix build
* Test fix attempt
* Another build attempt
* Another build tweak
* Cleanup
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* Add columns
* Work on multitenancy
* Work on muiltitenancy
* Work on multitenancy
* Work on uniques
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* More work on multitenancy
* Work on multitenancy
* Multitenancy work
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* Work on docs
* Work on multitenancy
* Work on docs
* DOcs work
* Tenancy docs
* Work on docs
* Finish docs
* Add changelog
* Rename config
* Add migration tasks
* Fix typo
* Migration fix
* One more migration fix
* A couple more migration fixes
* Docs cleanup
* Work on docs
* Bump boot version
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Work on review comments
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Compile fx
* Test fixes
* One more bugfix
* Update operation name
* Add one more constant
* Roll back a change that was causing test failures
* Test fixes
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Validation enhancements
* Work on validation api reworking
* Keep working on validation API
* Keep working on new term API
* Work on validation api
* Ongoing work on validation
* Work on integrating validation
* Work on validation API
* Add to validation API
* Work on validation
* Work on API
* Work on validation
* Work on validation API
* Work on validation API
* Work on validation api
* Work on validation API
* Work on validation api
* Validation API changes
* Work on API
* More work on validationo API
* Work on validation API
* FIxes
* WOrk on validation api
* Work on validation API
* Tests passing!
* More cleanup
* More validation API changes
* Fix intermittent test failure
* Package reorg
* Validation API work
* Work on doocumentation
* Work on API
* More work on new validation API
* Fix errorprone-reported error
* Test fixes
* Documentation updates
* Documentation tweaks
* Work on API
* Bean name adjustments
* Build fixes
* Some test fixes
* Start work on refactoring how PIDs work
* Some test fixes
* Test fixes
* Test fixes
* Restore accidentally deleted line
* One more tweak
* Rework resource link extraction
* Test fix
* Split out transaction processor
* Updates
* Test fix
* Test fixes
* Test fixes
* Clean up LGTM warning
* Fix compile failure
* One more test fix
* Fix LGTM issue
* Add spot for metadata
* Add test logging
* Remove testing code
* More test logging
* Add some test logging
* Attempty to fix intermittent test failure
* Improve exception tracking
* Work on simplifying search param registry
* Fix compile
* Fix compile errors
* Fix two test bugs
* Version bumps
* FIx build issues
* Address a few Semmle issues
* Work on tests
* Some test fixes
* Test fix
* Fix deletions
* Test fix
* Fix intermittent test failure
* One more dependency bump
* Add some test logging
* Remove bad import
* Add some tests
* Test updates
* Add some logging
* Add more test logging
* Work on some test logging
* Fix compile error
* Work on codecov
* Work on codecov
* Remove test debug messages
* Start working on subscription processor
* Work on new scheduler
* Test fixes
* Scheduler refactoring
* Fix test failure
* One more test fix
* Updates to scheduler
* More scheduler work
* Tests now all passing
* Ongoing work on export
* Ongoing scheduler work
* Ongoing testing
* Work on export task
* Sync master
* Ongoing work
* Bump xml patch version
* Work on provider
* Work on bulk
* Work on export scheduler
* More test fies
* More test fixes
* Compile fix
* Reduce logging
* Improve logging
* Reuse bulk export jobs
* Export provider
* Improve logging in bulk export
* Work on bulk export service
* One more bugfix
* Ongoing work on Bulk Data
* Add changelog
* Ongoing work on core structures suport
* Ongoing work on this merge
* Ongoing work to clean up structures
* Credit for #1179
* Address compile issues
* Latest changes
* Work on parallel execution
* Work on getting tests passing
* Add H2 to migrator
* Test fix
* Start working on cascading deleets
* WOrk on cascading deletes
* Work on cascading deletes
* Enable cascading deletes
* Cascade deletes almost working
* FIx test
* Test fix
* Make IBundle list interface more flexible
* Make matchResourceLinks visible
* Make matchResourceLinks visible
* Pull in-memory matching functionality out of subscription module into dedicated classes in searchparam module
* Added more accessors to version independent resource classes
* improved forcedid matching (needs to be verified by James)
filter out nulls from HashMapProvider.searchAll() (hopefully no tests depend on this)
* add AnyComposition
* cleanup of Any classes
* create searchparam config so people can use that module without using subscriptions
* create searchparam config so people can use that module without using subscriptions
* fix broken test
* added derivedFrom
* renamed daoRegistry.getResourceDaoIfExists to getResourceDaoOrNull
also added method to add a new dao to the registry and retrieve registered types
* TokenParam.equals
* add error check to searchable hashmap resource provider
* added support for R4
* add successor to measure
* delete conflict hook
start with failing test
* test passes.
hook is called.
* added delete conflict hook
all delete conflict tests pass
* added javadoc
* Performance test
* test bad interceptor case
* typo
* rename criteria matcher
* added support for multiple topics
* fix method name
* add effective period
* Temporarily excluding StressTest from build to try to get Travis under time limit
* change log
* review feedback
* review feedback
* review feedback
* move expunge out
* move to prototype
* turns parameters into fields
* cleanup control flow
* moved transactions outside of loops
* add expungeeverything
* moved daos out
* add expungeThreadCount
* add expungeBatchSize
* added partition runner to run in separate threads
* all done. just need to consolidate test code.
* Moar tests
* consolidated pointcutlatch into hapi-fhir-jpaserver-model
* final cleanup
* update javadoc
* change log
* failing test
* added delete
also @Transactional
* remove unused parameter
* fix compile
* race condition
(cherry picked from commit e1940d2fb20838859a205f2b96c833b0ce9f05eb)
# Conflicts:
# hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/PartitionRunnerTest.java
* ja feedback
* ja feedback
* fix bug in websocket subscription (It wasn't destroying the channel when there are no subscribers)
* add support for removing channel. Also synchronize removal (there was a race condition between sync and queue)
* keep deprecated method for backwards compatibility
* make websocket endpoint configurable
* make websocket context path configurable
* make websocket context path configurable
* trying mvn clean test instead of mvn clean install to see if the build goes faster
* that didn't work at all. reverting.
* change log
* subscription loader now only pulls active subscriptions
only allow websocket connections to subscriptions of type websocket
* Added a "flag for deletion" to ActiveSubscription in the SubscriptionRegistry to handle the race condition of a scheduled sync overlapping with a subscription creation. We could have used a package-scoped semaphore or a pre-remove FHIR read, but this seemed like the safest, simplest and most performant way to handle it.
* ActiveSubscriptionCacheTest
* WebsocketConnectionValidatorTest
* fix compile error in jpa example
* might keep this
* might keep this
* undoing start in interface
* fixed bug that only supported resources with ResourceType/id prefixes
* added standalone subscription support for Dstu2. untested.
* failing test
* fixed cannonicalsubscription.equals for email
* final cleanup
* fix bug in ResourceIndexSearchParamQuantity
Move transaction boundary around SubscriptionMatcherInterceptor so it can be overridden in subclass
Lots of CRLF changes from a mvn -P DIST
* FIXME
* Avoid paging links when offset is artificially set very high
* Ongoing fixes
* Adding logging and clean up transaction processing
* Add changelog
* More work on queries
* Keep working on getting tests passing
* More test fixes
* More work on tests
* More test works
* One more test attempt
* Ongoing fixes
* One more change
* FIxes to search algorithm
* Add changelog
* Clean up for review
* Fixed NPE in token matcher when system is not null and value is null
* test opposite (null system not null value)
* added null protection to all matchers
* Address review comments
* Address broken test
* Trying to resolve DB ordering issues
* Starting work on this
* Working on narrative templates
* Work on new narrative system
* Account for some failing tests due to refactoring of narrative mode
* Another test fix
* More test fixes
* One more test fix
* Work on searches
* Address review comments
Squashed commit adding subscription debug logger
* Work on subscription debug logger
* Add subscription logging interceptor
* Remove unneeded variables
* A bit of cleanup
* Tweak the output logs a bit
* Address review comments
* Fixed a bug in standalone subscription subscriber: It was adding REQUESTED subscriptions to the active subscription registry. (Only ACTIVE subscriptions should be added.)
* Start work on this
* Work on interceptors
* Attempt fix
* Avoid environment dependency
* Test fixes
* One more test fix
* One more build tweak
* Lots of cleanup
* A bit more cleanup
* Still more cleanup
* Some test fixes
* Add legacy methods temporarily
* Don't auto-scan interceptor beans
* One more test fix
* rsolve merge conflicts
* Address review comments
SearchParamRegistry and SubscriptionRegistry now both poll retrying connection to the server. This will help in particular in the scenario where the subscriptions are managed in a standalone server that depends on a FHIR Server being available to pull search parameters and subscriptions from.
jamesagnew
Ken Stevens
Nick Goupinets
Diederik Muylwyk
Frank Tao
Tadgh
Tadgh
Sean McIlvenna
Stig Rohde Døssing
Ken Stevens
Ken Stevens
Volker Schmidt