* 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>
* 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
* 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>
* wip
* The updated changes to the validator that were pulled in from the core dependencies are not backwards compat. Need to bump HAPI version.
* pointing to stable core version
* review feedback
* Add changelog
Co-authored-by: markiantorno <miantorno@pop-os.localdomain>
* 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
* publish test-jar from hapi-fhir-storage
* Extract BaseDateSearchDaoTests up to hapi-fhir-storage.
Share a date search tests between JPA and Mongo.
* Use ITestDataBuilder for setup
* Move Mongo date cases into common set
* cleanup
* More cleanup
* naming
* fix equal case
* Use -DskipTests instead of the more agressive -Dmaven.test.skip
* publish test-jar from hapi-fhir-storage
* Extract BaseDateSearchDaoTests up to hapi-fhir-storage.
Share a date search tests between JPA and Mongo.
* Use ITestDataBuilder for setup
* Move Mongo date cases into common set
* cleanup
* More cleanup
* naming
* issue-1134 initial work on adding retry handler
* issue-1134 subdscription creation fixes
* issue-1134 update the test
* issue-1134 retry policy off canonicalsubscription
* issue 1134 base subscription changes
* add failing test
* issue 1134 retry configs on base parameters
* issue 1134 passing forward params
* issue-1134 added more tests for making sure subscriptions create their channels correctly
* issue-1134 updates to get the retry to channels
* issue-1134 updating channel factory
* issue-1134 remove the dlq since it's not defineable
* issue-3120 changelog added
* issue-3120 cleaning up
* issue-3120 test fix
* issue-3120 review fixes
* issue-3120 fixed bad master merge
* issue-3120 updates for new release
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* issue-1134 initial work on adding retry handler
* issue-1134 subdscription creation fixes
* issue-1134 update the test
* issue-1134 retry policy off canonicalsubscription
* issue 1134 base subscription changes
* add failing test
* issue 1134 retry configs on base parameters
* issue 1134 passing forward params
* issue-1134 added more tests for making sure subscriptions create their channels correctly
* issue-1134 updates to get the retry to channels
* issue-1134 updating channel factory
* issue-1134 remove the dlq since it's not defineable
* issue-3120 changelog added
* issue-3120 cleaning up
* issue-3120 test fix
* issue-3120 review fixes
* issue-3120 fixed bad master merge
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Add tests. Add implementation in R4. Add changelog
* Wip partial fixup of other STU versions
* Updated usages of new patient type everything api
* Partial commit of incomplete documentation
* Remove docs
* Cut to token instead of string
* Bump hapi version due to breaking api changes
* Remove the unused dependency on net.sf.saxon:Saxon-HE
* Remove Saxon-HE dependency in hapi-fhir-jpaserver-base
* Remove unused comment in hapi-fhir-structures-dstu2.1/pom.xml
* Migration finished
* Work on LOBS
* Add to ClobMigrated annotation
* Deal with lobs
* Work on new approach
* HAPI FHIR version bump
* Add changelog
* Add license header
* Fix intermittent
* CLeanup
* Cleanup
* first pass moving core storage classes to storage-api
* move term service apis
* nearly done
* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor
* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor
* create new SearchConstants class to store platform independent search constants
* move a couple of subscription services
* move transaction processor adapter to storage
* version bump
* move searchparam
* fix test
* fix compile includes
* fix text
* fix docs
* 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>
* 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
Bumps `fhir_core_version` from 5.3.10 to 5.3.11.
Updates `org.hl7.fhir.utilities` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.convertors` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.validation` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.dstu2` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.dstu2016may` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.dstu3` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.r4` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.r4` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.r5` from 5.3.10 to 5.3.11
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* 2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.9.
* 2540 - Updated the Unit Test messages due to the upgraded dependencies.
* 2540 - Fixed some additional Unit Test message checks.
* 2540 - Updated the POM to refer to fhir_core_version 5.3.10-SNAPSHOT so a FULL Pipeline Build can run to verify that everything is fixed now.
* 2540 - Added some DEBUG Sysout logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...
* 2540 - Added some more logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...
* 2540 - Updated a Unit Test to account for a newly returned search param.
* 2540 - Updated a Unit Test to account for a newly returned search param and removed some debug output.
* WIP for elm caching
* Bug fixes and a working DSTU3 unit test
* More tests, Address review feedback, add initial docs
* Update to cql-evaluator 1.2.0
* Fixes for documentation
* 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
* 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
* Bump jaxb-runtime from 2.3.1 to 3.0.0
Bumps jaxb-runtime from 2.3.1 to 3.0.0.
Signed-off-by: dependabot[bot] <support@github.com>
* Bump jaxb-runtime from 2.3.1 to 3.0.0
Bumps jaxb-runtime from 2.3.1 to 3.0.0.
Signed-off-by: dependabot[bot] <support@github.com>
* Add jakarta bindings
* Dependency cleanup
* More depndency cleanup
* Work on deps
* Replace transaction annotation
* Cleanup
* Another fix
* Build fix
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
Bumps `jersey_version` from 2.25.1 to 3.0.0.
Updates `jersey-server` from 2.25.1 to 3.0.0
Updates `jersey-container-servlet-core` from 2.25.1 to 3.0.0
Updates `jersey-container-jetty-http` from 2.25.1 to 3.0.0
Updates `jersey-media-moxy` from 2.25.1 to 3.0.0
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* 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>
* 2229 - Remove support for the upload-igpack CLI command.
* 2229 - Revert changes made to the ValidateCommand class since it only takes an igpack as a parameter and therefore, should NOT have been removed.
* 2229 - Remove the igpack option from the Validate command.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_0/2229-remove-upload-igpack-command.yaml
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Kevin Dougan <kevindougan@kevins-mbp.lan>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Tadgh
longma1
Patrick Werner
VK-SMILECDR
Ken Stevens
jamesagnew
Mark Iantorno
jmarchionatto
michaelabuckley
TipzCM
dependabot[bot]
Jing Tang
Tadgh
Michael Buckley
Kevin Dougan SmileCDR
JP
Nick Goupinets
Diederik Muylwyk
JP