* Begin work on PK schema selector
* Work on generator
* Filter working
* Add tests
* Work on tests
* Work on contributor
* Work
* Tests passing
* Drop unneeded annotation
* Partition cleanup
* About to merge JpaPid
* Work on IDs
* Tests passing
* Working on query count tests
* Ongoing work
* Ongoing work
* Working on tests - Running but about to try removing
ResourceHistoryProvenanceEntity link
* More tests passing
* Fix some more tests
* Test fixes
* About to add partition ID to selector
* Most query count tests passing
* Work on tests
* Working on includes
* All conditional tests passing again
* About to modify joins in SQL builder
* Search generator refactored, and tests passing
* Tag tests done
* Work on tests
* Everything operation fixed
* Clean up PIDs for batch job
* Clean up search paging
* Work on expunge service
* Work on tests
* Test fixes
* Work on same transaction updates
* Work on JPA R4 tests
* Work on tests
* Fixes
* Work
* Test fix
* Work on tests
* Cleanup
* Test fixes
* Test fix
* Spotless
* License headers
* Test fix
* License headers
* Compile fix
* Test fix
* Test fix
* Test fixes
* Test fixes
* Cleanup
* Test fixes
* Test fixes
* Starting to address fixmes
* Spotless
* More test cleanup
* Test cleanup
* Test fixes
* Test fixes
* Spotless
* Test cleanup
* Test fix
* Deal with test failures
* Spotless
* Test fixes
* About to modify RESOURCE_LOOKUP cache
* Test cleanup
* Intermittent test fix
* Try to resolve intermittent
* More test work
* Test fixing
* Add tests
* Spotless
* Add troubleshooting logs
* Add test logging
* More test logging
* Test fix
* Test fixes
* Test fix
* Test fixes
* Test cleanup
* Test cleanup
* Test fix
* Test fix
* Fixes
* Add tests
* Test cleanup
* Remove stale test
* Test fix
* Imports cleaniup
* Work on migrations
* Work on migrations
* Work on PKs
* Work on tests
* Cleanup
* Test fix
* Test fix
* Spotless
* Test fixes
* Test fix
* Test fixes
* Test fix
* t fix
* Test fixes
* Test fix
* Test fixes
* Add test method
* Test cleanup
* Test fixes
* Cleanup
* Test fixes
* Cleanup
* Test cleanup
* Test fix
* Add migrator support
* More test work
* Spotless
* Add header
* License header
* Test fix
* MDM test fixes
* Test fix
* Add tests
* Cleanup
* Compile fix
* Spotless
* Work on docs
* Cleanup
* Add partitioned test
* Work on tests
* Rename JpaPidValueTuples
* Test cleanup
* Test fixes
* Cleanup
* Cleanup
* Spotless
* Spotless
* Test fixes
* Test fixes
* Build fix
* test fix
* Test fixes
* Build fix
* Cleanup
* Merge master
* Cleanup
* Work on tests
* Test fixes
* i
* Cleanup
* Cleanup
* Cleanup
* Work on docs
* Work on cleanup
* Compile fix
* Test fix
* Spotless
* Compile fix
* Refactor for CDR work
* Disable test
* Add constants
* Vdersion bump
* Rename class and add error codes
* Compile fix
* DDL plugin tweak
* Test fix
* Add javadocs
* Cleanup
* Address review comments
* Plugin version bump
* Address review comments
* Test fixes
* Test cleanup
* Partitionable indexes
* Address fixmes
* Test fix
* Bump to force CI job
* Docs fix
* Fix typo
* Test fixes
* Docs fix
* Test cleanup
* Remove unused field
* Work on migration
* License headeer updates
* 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.
* 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
* 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>
* 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
* 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
* fail test
* potential fix
* spotless
* alternative fix
* spotless
* remove the new method and replace usage for the old one
* spotless
* fix issue with context failing deserialization
* add validation for context, hook and hook instance
* spotless
* add message codes
* spotless
* changelog
* cleanup
* spotless
* bump version to 7.5.1-SNAPSHOT
* 6173 - Log unhandled Exceptions in RestfulServer.
* Use placeholder for failed streams.
* Starting test for server handling.
* Got test working.
* Fixed use of synchronized keyword.
* Applied mvn spotless.
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* use SearchParamater validator in package installer (#6112)
* Ensure ' ' is treated as '+' in timezones with offsets. (#6115)
* Use lockless mode when adding index on Azure Sql server (#6100)
* Use lockless mode when adding index on Azure Sql server
Use try-catch for Online add-index on Sql Server.
This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support.
Warnings in docs, and cleanups
* make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT (#6127)
* fix hfj search migration task (#6143)
* fix migration task
* changelog
* changelog
* code review
* spotless
---------
Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
* Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive (#6135)
* MSSQL: Migrate HFJ_RESOURCE.FHIR_ID to new collation: SQL_Latin1_General_CP1_CS_AS
* Spotless.
* Enhance test. Fix case in ResourceSearchView to defend against future migration to case insensitive collation.
* Remove TODOs. Add comment to ResourceSearchView explaining why all columns are uppercase. Changelog.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml
Code reviewer suggestion
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone.
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* Common API for FHIR Data Access (#6141)
* Add initial interface for common FHIR API
* Fix formatting
* Update javadocs
* Address code review comments
---------
Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
* Move IncomingRequestAddressStrategy::determineServletContextPath into IServerAddressStrategy to permit overriding (#6038)
* add changelog
* add contributor as developer
---------
Co-authored-by: Alex Kopp <akopp@athenahealth.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* version bump clinical reasoning
* specifying required patch type
* bumping to 7.3.11-SNAPSHOT
* fix file name
* remove default fhirPatch until bug fixed
* Use server name as narrative text in CapabilityStatement
* Credit for #6060
* Fix spotless
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Cleanup and fix compile warnings
* Cleanup and enhance batch2 jobs to support running them across multiple partitions.
* Add some documentation and fix build in the pipeline.
* Fix tests
* Add support for RequestPartitionId.allPartitions as input to the IJobPartitionProvider. Add tests and fix one test. Add missing changelog.
* Separate basic partition provider logic so it can be reused by Mongo. Update documentation.
* Revert change to apply certain validation only for creates.
* Remove added logs
* spotless fix
* Address code review comments
James Agnew
Emre Dincturk
Luke deGruchy
Martha Mitran
Aditya Dave
Michele Adduci
TipzCM
jmarchionatto
Ken Stevens
Michael Buckley
Tadgh
VK-SMILECDR
dotasek
Jens Kristian Villadsen
Brenin Rhodes
Thomas Papke
Kevin Dougan
Long Ma
Justin McKelvy
Renaud Subiger
Martha Mitran
volodymyr-korzh