* Enable search narrowing on large ValueSets
* ValueSet improvements
* Work on narrowing
* Work on narrowing
* Work on narrowing
* Work on narrowing
* Add test
* Work on narrowing interceptor
* Work on narrowing
* License headers
* Refactor code narrowing
* Add docs
* Version bump
* Test fix
* Test fixes
* Build fix
* Fixes
* Version bump
* Test fix
* License header updates
* Build fix
* Test fixes
* Test fix
* Test fix
* Docs fix
* Test fix
* Test fix
* Resolve fixme
* Bump
* Force a CI build
* Make CI happen again
* Work on new batch framework
* Work on new batch framework
* Work on new batch framework
* Work on batch
* Compile working
* Work on bulk import
* Adjust import
* Work
* Work on batch
* Bump version
* WOrk on new batch processes
* Work on bath
* Bump to PRE4
* Build fixes
* CLeanup
* Small tweak
* Add exception code
* Test fixes
* Test fixes
* Test fix
* Additional synchronization
* Add license headers
* Test fixes
* Test fixes
* Add changelogs
* Address PG
* Test fix
* Test fix
* Test fixes
* Review notes
* Work on tests
* Test fixes
* Test fix
* Work on tests
* Tets fix
* Test fixes
* Test fixes
* Add missing exception codes
* Test fix
* Test fixes
* More test fixing
* License headers
* Test fix
* Add new test logging
* Work on tests
* Test fixes
* Test fix
* Resolve fixme
* Try to avoid test failure
* Add import command
* Work on storage
* Fix error codes
* Fixes
* License header
* Build fix
* Build fixes
* Fix dep
* Initial design of adding exception codes to exceptions
* Initial design of adding exception codes to exceptions
* change int module name to string
* add comment
* shorten message
* shorten message
* added checkstyle
* developing checker
* completed checkstyle plugin and unit test for it
* fix NPE
* fix checker so it ignores throws on exceptions that aren't new
* change parameter order in InvalidResponseException
* accept Msg.code() in any parameter since some exceptions like MessageException have the message string as the second parameter
* exclude generated files
* BIG COMMIT added error codes to all exception throws
* example test fix
* Modified tests such that the assert statements would better match the message responses.
* Modified additional tests such that the assert statements would better match the message responses.
* fix test
* merge master
* merge master
* Fourth commit of modified tests such that the assert statements would better match the message response
* Changes made to modify assert statements such that they match the new errors which now use error codes. Also changed ResourceNotFoundException to include error codes in its messages.
* Modified assert messages to better match new error codes
* Time Zone changes DRAFT. Certain tests pass in intellij and fail during mvn install
* Modified assert messages to better match new error codes
* Added comments for time zone fixes. Previous commit comment on time zone fixes was incorrect. By invaliding caches, all tests on both intellij and mvn install passed.
* Reverted changes on azure-pipelines.yml
* updated hapi-fhir version for checkstyle module
* changes to azure-pipelines.yml
* changes to azure-pipelines.yml
* change to pom.xml to include hapi-fhir-checkstyle in ALLMODULES
* changes to azure-piplines (these changes are to be reverted after testing)
* reverted changes to azure-piplines
* reverted change where hapi-fhir-checkstyle was added to pom.xml (hapi-fhir)
* Attempted fix on checkstyle build error
* modified azure-piplines.yml to change maven repository for checkstyle build
* Attempted fix on checkstyle build error
* checkstyle config location change for hapi-depoloyable-pom. (will be reverted if it does not work)
* attempted dependency add for hapi-depoloyable-pom. (will be reverted if it does not work)
* reverted changes for hapi-deployable-pom
* add javadoc
* update last code
* Attempted fix on checkstyle build error
* Finished adding in missing error codes to pass Checkstyle checks
* Test pipelining
* Fixing errors and bumping version (as suggested by Gary)
* Merge
* Fixing Checkstyle error
* Attempted fix for date error
* Add error code onto assert statement
* Add in a couple more error codes
* Fixing assert statements
* Bump to static version for dependency
* Adding error code to message
* Adding error codes to exceptions
* Adding error codes to exceptions
* Change to work with cdr branch
* Update to faulty error message
* Merge changes
* allow checkstyle pom to deploy
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com>
Co-authored-by: Predap <simon.zuccherato@gmail.com>
Co-authored-by: Predap <46201929+Predap@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* 3156 fix race condition that results in multiple tags being created
* 3156 added changelog
* cleanup
* added smile jira ticket
* 3156 review fixes
* review fixes
* 3156 added an additional integratoin test
* cleanup
* review fix and master merge
* threadsafe stuff
* small change
* upping min threads for tests to pass
* changing test
* test check
* fix
* test testing
* one more update
* using threadpoolutil
* temporary measure
* git push
* all builds
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 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
* some fixmes to start
* Added some FIXMEs
* added RequestPartitionId to reosurceDelivryMessage and ResourceModifiedMessage
* ResourceDeliveryMessage and ResourceModifiedMessage tests
* fixed issue with test missing partitionHelperSvc mocked bean
* Added tests and implemented SubscriptionMatchingSubscriber for partition aware subscription
* modified implementation of partitionId in CanonicalSubscription
* Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)
* Revert "Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)"
This reverts commit fe40fb9733.
* Got added partitionId to subscriptions, added changes to make SubscriptionMatchingSubscriberTest work
* added SubscriptionTriggering test, also added partition support to subscriptionLoader
* Changed implementation for storing partition id of subscriptions from messages, refactored tests to new implementation
* added all subscription systemRequestDetails with all partition to subscription reader
* refactored a generic system request details with default all partition request
* Added test for dao subscriptions, fixes to get the test working
* added partition support for latest version delivery
* added doc changes and changelog for multitenancy subscription
* cleanup and added partitioned subscription manually trigger test
* fixed mocked subscriptionDao
* added package-info for subscription module
* some code review changes
* removed AllPartitionSystemRequestDetail, added new text for multitenant subscription
* renamed method for code review
* version bump to 5.7.0PRE7
Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
* try xml -> json
* Change from xml serialization to json serialization. Also fix a deadlock in how the validation cache is used.
* changelog
* back out logback
change
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3236-change-validation-from-xml-to-java.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* move mail config to mail service constructor
* update subscription email sender
* added license text
* [2669] bump HAPI version to 5.7.0-PRE6-SNAPSHOT
* add changelog
* 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>
* 3136 - Send validate-code requests to an Instance of IValidationSupport instead of directly to the DAO.
* 3136 - Added support for R4 validate-code calls to a Remote Terminology Server.
* Added more Unit Tests.
* Added NULL checks based on code analysis.
* Adding some cleanup code to the Unit Tests since some other unrelated Unit Tests were failing when running in an Azure Pipeline.
* Adding @Ignore to both of my Unit Test classes to try and see if this is the cause of other unrelated Unit Test failures in the Azure Pipeline.
* Commented out ALL CODE in my Unit Tests to see if this fixes the other Unit Tests.
* Added 1 Unit Tester called RemoteTerminologyServiceResourceProviderR4Test to see if it causes other Unit Test failures.
* Added a Unit Tester called ResourceProviderR4RemoteTerminologyTest with the code that creates a RemoteTerminologyServiceValidationSupport instance commented out for now, just to see if this allows all other Unit Tests to pass.
* Added a Unit test back in to verify how the RemoteTerminologyServiceValidationSupport works when inserted into the front of the IValidation chain. Lets see if this will mess up any other Unit Tests in the Azure Pipeline...
* Added an @AfterEach method to remove the RemoteTerminologyServiceValidationSupport instance from the ValidationSupportChain to see if it allows all the other Unit Tests to work as before.
* Added more Unit tests.
* Added more Unit Tests to increase code coverage.
* Added some NULL checks.
* Added a changelog for this feature add.
* Removed the decision logic in the REST APIs and also the isRemoteTerminologyServiceConfigured() method, and letting the ValidationSupportChain figure out how to perform the validate-code Operation.
* Removed a NULL check that was not needed.
* Reverting the previous change where I tried using the IValidationSupportChain for each and every incoming Operation request. Splitting the implementation between local and remote seems to be required at this time.
* 3170 language portion of language code is case insensitive
* 3170 adding changelog
* 3170 house keeping
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
* 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>
* Let RemoteTerminologyServiceValidationSupport.validateCodeInValueSet work when code system is present, even when theOptions.isInferSystem() is true
* Add test for specific use case added
* Consider ValueSets with multiple component includes
* Fix typo
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.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
* Let RemoteTerminologyServiceValidationSupport.validateCodeInValueSet work when code system is present, even when theOptions.isInferSystem() is true
* Add test for specific use case added
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* 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
* 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
* 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
* 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>
Ken Stevens
James Agnew
Tadgh
Tadgh
Johnson Lu
TipzCM
longma1
VK-SMILECDR
Mark Iantorno
Kevin Dougan SmileCDR
David
jmarchionatto
juan.marchionatto
Daron McIntosh
Frank Tao