* 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
* 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.
* Add indexes to foreign keys
* Add new version enum
* Add TermCodeSystem and TermCodeSystemVersion deletion job artifacts
* Add Propagation.NOT_SUPPORTED to allow starting jobs from transactional code
* New jobs artifacts
* Improve comments
* Restructure job configurations to avoid bean name collisions
* Restructure job configurations to avoid bean name collisions
* Use new offline deletion by job
* Test using multiple versions
* Retrieve only Pids
* Revert to master
* Maintain deferred functions synchronization as similar as possible to the way it was
* Bypass validations to allow calling an index same as a foreign key to make SchemaMigrationTest happy as H2 adds FK indexes automatically
* Adjust tests
* Add copyrights
* Add test
* Revert to delete CodeSystemVersions using deferred ITermDeferredStorageSvc
* Allow to wait for jobs tentatively
* Organize imports
* Fix tests
* Increase timeout to cover for possible additional heavy DB activity
* Add indexes to two remaining non-indexed foreign key fields to avoid much longer transactions which produce locks on heavy DB load
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3108-terminology-large-code-system-deletion-performance.yaml
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Remove opening stars from logging messages
* Relax index name checking logic to allow for indexes on FK columns to be called same as the FKs, to make SchemaMigrationTest happy even when H2 adds indexes to FKs automatically.
* Use static array to enumerate platforms which doesn't add indexes to foreign keys automatically.
* Cleanup also job executions when performing test artifact cleanup
* Adjust to property name change
* Add ABANDONED status to the list of waited job statuses to avoid test failures due to wait timeouts
* Add also UNKNOWN status to the list of waited job statuses to avoid test failures due to wait timeouts
* Filter job executions to be stopped
* Set trace to debug test problem
* Add STOPPED status to the list of waited job statuses to avoid test failures due to wait timeouts
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Add check before mapping storage ID to resource ID in TransactionDetails.
* Add change log.
* Changed to instead prevent creation of ResourcePersistentId with null ID value.
* Changed to instead prevent ResourcePersistentId being created with null resource ID.
Co-authored-by: ianmarshall <ian@simpatico.ai>
* 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>
* small change to support change to string length of spring batch execution parameters
* added comment to indicate function is empty on purpose
* added javadoc for this method to note it's for overriding purpose
Co-authored-by: Steven Li <steven@smilecdr.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 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
* added eq and gt test cases
* added missing gt search param tests
* 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
* Fixed incomplete date issue
* Set to the last millisecond 23:59:59.999
* Disabled 4 failed JVM/TZ related test cases
* Added changelog
Co-authored-by: Long Ma <longma@Longs-MacBook-Pro.local>
Co-authored-by: Frank Tao <frankjtao@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
* code review
* fix broken tests
* added AbstractResourceToFileWriter
* Added AbstractBaseBulkItemReader
* added bulkExportStatusEnum fromBatchStatus test
* Code review name change
Co-authored-by: Long Ma <longma@Longs-MBP.hitronhub.home>
Co-authored-by: Steven Li <steven@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
* 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
VK-SMILECDR
Ken Stevens
jamesagnew
Mark Iantorno
katiesmilecdr
Tadgh
Patrick
jmarchionatto
Kevin Dougan SmileCDR
IanMMarshall
TipzCM
michaelabuckley
StevenXLi
longma1
JasonRoberts-smile
Jing Tang