* begin with failing test
* wpi merge operation provider
* wip code resolve references and some refactoring
* respect status code set in providers
* more validation and code to update resources after refs are updated
* added source-delete parameter and some validation tests on result-patient
* update test
* update test
* return target patient as output parameter, do not add replacedby link to target if src is to be deleted
* output definition
* ignore identifiers in ref, more unit tests, return target in preview mode
* output definition
* return input parameters in the merge operation output
* copy identifiers from source to target (no duplicate check)
* add shared identifier
* add shared identifier
* moar asserts
* moar asserts
* fixing result patient
* fixing result patient
* fixing result patient
* add duplicate check when copying source identifiers to target
* copy result-patient before passing it to service
* add preview to test
* update preview asserts
* move IReplaceReferencesSvc to storage-package, and call replaceReference in patient merge
* moar tests
* cleanup
* add task test
* add replace references test
* kebab-case replace references
* add sync -> async switch
* test
* test
* start migrating to stream
* validate result-patient does not have link to source if delete-source is true
* add update count to msg in preview mode
* spotless
* change page size -> batch size and create new default max in storage settings
* spotless
* switched to patch transaction
* switched to patch transaction
* switched to patch transaction
* switched to patch transaction
* strip version from returned task
* spotless
* spotless
* async replace references test passes
* align tests
* test small batch size
* do src and target updates in trx, add validation src is not already replaced
* start building batch 2
improve dao
* start building batch 2
improve dao
* start building batch 2
improve dao
* move test setup out to helper
* move replace references tests out
* switch helper to use dao
* incresed unit test coverage
* build out batch
* build out batch
* update test to add link to result-patient only if the source is not to be deleted
* batch passes test
* batch passes test
* batch passes test
* made patient-merge return the Task returned from replace references
* batch passes test
* batch passes test
* consolidate async and sync supporting methods into a single storage service
* consolidate async and sync supporting methods into a single storage service
* add merge batch job
* add merge batch job
* added FIXMES for ED
* added FIXMES for ED
* update test to not validate task in preview mode
* mark identfier copied from source to target as old
* copyright headers
* runMaintenancePass before checking merge task status, and renamed test method for merge
* fix test
* fix test
* default
* invoke async merge job in merge service
* starting work on new docs
* starting work on new docs
* document $replace-references
* separate default from max
* fixme
* moar fixme
* moar fixme
* ken last fixme
* return 202 status on async merge, update MergeBatchTest to do more validations
* async success message, inject mergeservice, add async merge unit tests
* make validatePatchResultBundle static again
* added test for adding reference while merge in progress, and merge error handler
* fixed
* fixed
* added error handler to replace references job
* review
* javadoc
* organize imports
* make ValidationResult immutable
* make ValidationResult immutable
* rename ReplaceReferencesRequest
* rename ReplaceReferencesRequest
* rename MergeResourceHelper
* rename MergeResourceHelper
* javadoc
* split merge validation service out from merge service
* split merge validation service out from merge service
* split merge validation service out from merge service
* review feedback
* review feedback
* rename param constants
* rename param constants
* remove IdentifierUtil for visibility
* remove IdentifierUtil for visibility
* final review of hapi side
* review feedback
* review feedback
* fix checkstyle errors, rename MergeOperationInputParameters and add Msg.code
* fix replace reference parameter type, and some copyright headers
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* move $merge into JPA R4
* move $merge into JPA R4
* still need to return 412
* still need to return 412
* return 412
* moar tests
* moar tests
* fix async batch size
* fix async batch size
* fix async batch size
* exception code
* exception code
* fix bean wiring
* fix bean wiring
* fix test
* fix test
* fix test
* fix test
* fix test
* bump pom versions
---------
Co-authored-by: Ken Stevens <ken@smiledigitalhealth.com>
* Integrate with clinical-reasoning master.
* Have IMeasureServiceFactory return R4MeasureEvaluatorSingle.
* Revert MeasureServiceFactory back to returning R4MeasureService. Introduce R4MeasureEvaluatorSingleFactory to return a R4MeasureEvaluatorSingle.
* Update MeasureOperationsProvider to take an R4MeasureEvaluatorSingleFactory instead of an IMeasureServiceFactory.
* Delete obsolete unit test and copyright header.
* Add javadoc.
* Link to CR 3.15.0.
* Link to CR 3.15.0.
* Fix test failures.
* Add changelog and upgrade notes.
* Fix changelog with wrong issue number.
* Upgrade docs: Specify reportTypes that will be accepted.
* Code review fixes.
* Bump to 7.7.14-SNAPS.
* tests
* address review comments
* remove a test since IdHelperSvc#resolveResourceIdentity no longer depends on client id strategy
* remove commented out code
* update due to code changes
---------
Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
* Add support for disabling prefixChannelName to message broker ChannelSettings
* Add support for disabling ChannelNamePrefix to message broker ChannelSettings - method names update
* Added support for overriding message broker channel settings for MDM message processing
* Added support for overriding message broker channel settings for MDM message processing
* Start mods for round 2
* Work on changes
* Work on build
* Work on tests
* Test fixes
* Test fixes
* Test fixes
* Add dump
* potless
* Cleanup
* Cleanup
* Work on mock validation support
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Test fixes
* Remove redundant test
* Compile fixes
* Test fix
* Add javadocs
* Rename class
* Spotless
* Test fixes
* Compile fix
* Add test logging
* Add test logging
* Work on tracking down intermittent
* Intermittent test fix
* Add logging for another intermittent
* Merge master
* Cleanup
* Work on tests
* Work on tests
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Cleanup
* Merge issues
* HAPI version bump
* Test fix
* [6463] use version in canonical url of StructureDefinition to identify it
* Add credit for #6534
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* removing bootstrap 4 dep in favour of bootstrap 5
* accordions
* fixing some tabs
* radios
* some tweaks
* adding changelog
* updated version
* tweaks
* updating the webtest webclient for better es script support
* disabling tests in hapi
* unwrapping from transaction boundary
* bumping version
* config issue
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* feat: Introduce hapi-fhir-client-apache-http5 module for Apache HttpClient 5 support
- Added a new module `hapi-fhir-client-apache-http5` to provide HAPI FHIR Client functionality using Apache HttpClient 5.
- Supports gradual migration from HttpClient 4 to HttpClient 5.
- Aligns with Spring Boot 3.0's adoption of HttpClient 5, enabling consistent HTTP client configuration for users of both libraries.
Key Changes:
- Integrated Apache HttpClient 5 for modern, high-performance HTTP requests.
- Ensured compatibility with existing `hapi-fhir-client` and `hapi-fhir-client-okhttp` modules.
- Added basic tests to validate functionality and coexistence of HttpClient 4 and 5.
Impact:
- Non-breaking change; the new module can be adopted independently.
- Facilitates eventual migration of HAPI FHIR to HttpClient 5 across the codebase."
* Add new error codes to the apache-httpclient5 client module.
* First pass at segmenting out changes
* Test fixes
* Test fixes
* Test fix
* Work on tests
* Fix test
* Test fix
* Test fix
* Fixes
* Test fixes
* Test fix
* License headers
* Test fix
* Add changelog
* Address review comments
* Review comments
* Fixes
* Work on tests
* Address review comments
* Fix
* Add tests
* Cleanup
* Rename JpaPidValueTuples
* Add changelog
* Spotless
* Resolve compile issues
* Fix signature issue
* Test fix
* Add header
* Spotless
* Test cleanup
* Work on merge
* Work on tests
* Tests passing
* Cleanup
* Cleanupo
* Test fixes
* Test fix
* Cleanup
* Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Account for review comments
* Spotless
* Compile fix
* Test fixes
* Test cleanup
* Test cleanup
* Test fixes
* Resolve fixme
* Test fix
* Test fixes
* Test fixes
* Test fixes
* Fix
* Test fix
* Test fixes
* Test fixes
* HAPI version bump
* Try to address intermittent
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* 6323 resource creation deadlock (#6324)
* make map reads concurrent
* change log
* CUstom version number for guaranteed build determinism
* licenses
* Expand translation cache (#6341)
* Expand translation cache
* Add changelog
* Correction to #6341 (#6342)
* Contained bug (#6402)
* Contained bug
* more tests
* changelog, tests, implementation
* code review
* backwards logic
* Fix Questionnaire doc (#6400)
* fix reindex optimizeStorage=ALL_VERSIONS (#6421)
* fixing broken rename of last step of reindex (#6429)
* Fixes for the translation of parameter issues as part of the output for $validate-code operation. (#6438)
* Move the validation providers to the test utilities package such that they can be reused.
* Update IValidationSupport.CodeValidationIssue structure such that it meets the FHIR specification. Update RemoteTerminologyServiceValidationSupport and VersionSpecificWorkerContextWrapper translation for issues.
* New tests for issue translation. Move test class to a different package so that we can add another test class.
* Some simplification in the issue API to simplify building of issues.
* Fix compilation errors.
* Update providers to allow multiple responses and add support for the fetchCodeSystem call through method find.
* Setup the first test for resource validation with remote terminology providers.
* Fix NullPointerException
* avoid calling validateCode for CodeSystem where system is null
* Keep old public API methods (and class name) in IValidationSupport and mark them as deprecated to avoid breaking dependencies.
* Revert local change to debug for duplicate errors.
* Add more test cases for resource validation. Throw exception to signal missing test setup to make it obvious.
* Simplify test setup.
* Add some more javadoc
* Add javadoc for the new test class
* Add more tests
* Address code review comments in IValidationSupport.
* Add changelog
* Change Repository search interface from Map to Multimap (#6445)
Change Map to Multimap to support multiple and clauses.
* licenses
* fix interceptor hooks from requestDetails not getting called for STORAGE_PRECHECK_FOR_CACHED_SEARCH (#6436)
* fix interceptor hooks from requestDetails not getting called for STORAGE_PRECHECK_FOR_CACHED_SEARCH
* added unit tests and updated changelog
* added one more test case
* Add Adapter api (#6450)
Lightweight implementation of the adapter pattern.
* Bulk Import job status not changed after activation - failing test, fix, changelog (#6452)
* Update CR to 3.13.1 (#6433)
* Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 (#6439)
* Rel 7 6 CVE (#6446)
* Bump commons io
* Bump HS and Lucene, and hibernate
* Jetty bump for CVE
* Resolve CVES
* Bump with mismatch lucene
* Bump velocity template engine
* Revert bom bump
* wip
* Version bump
* move changelog, fix cve
* Bump commons-lang
* Replace imports
* wip
* fix HQL break
* remove dead code
* Fix changelog entry
* Bump org.hl7.fhir.core to 6.4.0 (#6454)
* Bump HAPI version + org.hl7.fhir.core to 6.4.0
* Apply spotless
* Correct a bug with duplicate parser IDs being assigned. (#6456)
* Fix changelog entry
* wip
* compilation problem
* Correct tests
* changelog
* Update hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
* Correct a bug with duplicate parser IDs being assigned - test fixes
* Correct a bug with duplicate parser IDs being assigned - spotless
* Correct a bug with duplicate parser IDs being assigned - added test-utilities dependency to fhir-structures poms
* Correct a bug with duplicate parser IDs being assigned - test fixes
* Contained resources without assigned IDs are now assigned GUIDs - address comments
---------
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
* licenses
* ValueSet expansion fails if Hibernate Search configured to use Lucene - fixed incompatibility between Hibernate Search and Lucene versions (#6468)
* Change the migrator to avoid table locks when adding an index. (#6489)
* version bump
* Updating version to: 7.6.1 post release.
* Bump to 7.7.7.
* deadsapce
* Profile reference param (#6501)
* updated QueryStack to not throw error with _profile as a ReferenceParam
* update QueryStack
* remove warnings
* cleanup cast
* cleanup test
* add changelog
* cleanup imports
* updates per review feedback
* updates per review feedback
---------
Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com>
* move changelog
---------
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Gary Graham <garygraham@smiledigitalhealth.com>
Co-authored-by: Taha <TahaAttari@users.noreply.github.com>
Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com>
* Optimize transaction writes
* Cleanup
* Work on tests
* Work on fixes
* Fixes
* Fixes
* Test fixes
* Cleanup
* Cleanup
* Work on tests
* Work on tests
* Test fixes
* Test fixes
* Remove redundant test
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Test fixes
* Add changelog
* Checkstyle fixes
* Test fixes
* Spotless
* Test cleanup
* Spotless
* Test fix
* Work on review comments
* Address review comments
* Test fixes
* Ongoing test cleanup work
* Work on tests
* Query count tests passing
* Test fixes
* Test fixes
* Rmove fixme
* Test cleanup
* Test fix
* Remove default method
* Service celanup
* Test fix
* version bump
* Test cleanup
* Excessive Hibernate warnings when processing conditional create and delete operations on referenced resources in a transaction bundle - failing test
* Excessive Hibernate warnings when processing conditional create and delete operations on referenced resources in a transaction bundle - fix
* Excessive Hibernate warnings when processing conditional create and delete operations on referenced resources in a transaction bundle - changelog
* Add tinder to parent project's pluginManagement
* Use specific version to avoid inheriting projects to replace by theirs
* Move dialects down to executing project because appendFile included in postgres dialect precludes to define it at the parent level
* Improve logging
* Use temporary project version
* Revert "Use temporary project version"
This reverts commit 24f5e648ed.
* Increment version
* Increment missed version
* Added headers
* Document new command
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Add missing implementations + update changed classnames
* Fix breaking test due to new validation rules
* Add changes.yaml
* Bump to HAPI version 7.7.1-SNAPSHOT
* Copyright autogen
***NO_CI***
* Bump to HAPI 7.7.2-SNAPSHOT
James Agnew
Emre Dincturk
Luke deGruchy
Martha Mitran
David Raeside
Tadgh
jdar8
volodymyr-korzh
Aditya Dave
TipzCM
Michele Adduci
Bart Embregts
Mangala Ekanayake
Ibrahim Tallouzi
Patrick Werner
jmarchionatto
Ken Stevens
Michael Buckley
JasonRoberts-smile
VK-SMILECDR
dotasek