* 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>
* wip
* wip
* revert'
* Delete existing things
* docs
* removing last of hamcrest
* removing last of hamcrest
* manual fix
* remove matchers used in awaitility
* remove matchers used in awaitility
* Final checkstyle removals
* Disable suppression rule for mdm checkstyle
* Fix some awaitility, remove dead matchers
* manual fixes
* manual fixes
* filter all hamcrest mentions
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Servlet migrsation changes
* Apply spotless
* Work on migration
* Start working on JPA migration
* Test fixes
* Test fixes
* Test fixes
* Work
* Work on servlet migration
* Work on migration
* Work on fixes
* Imports fix
* Work on tests
* Test fix
* All tests passing
* Work on migration
* Schema generator
* Refactor ID strategy
* Some test fixes
* Test fixes
* API additions
* Work on websockets
* Test fixe
* Version bump
* Work on migration
* All tests have passed!
* Work on test fixes
* Fixes
* Work on fixes
* CDR fix
* Work on migration
* Fixes
* Spotless
* Disable onetoone ban
* Adjust migratyions
* Transaction service fix
* Add tinyint to migrator
* Work
* Migration
* Compile fix
* Add license
* Test fix
* Test fix
* Cleanup
* Cleanup attempt
* Test fix
* Reslve fixmes
* Remove legacy lastn implementation
* Test cleanup
* Cleanup
* Remove dead import
* Bad import setups
* Review comments
* Review fixes
* Build fix
* Test fix
* Spotless
* Account for CR changes
* Compile fixes
* Rollback one change
* Test tweak
* License header
* Test fix
* Test fix part 2:
* Clean up tx isolation
* Spotless
* Spotless apply
* Drop min SQL Server level
* Attempted test fix
* Test fix
* Test fix
* Test fix
* Bump hibernate
* Test fix
* Test fixes
* Test fixes
* Test fixes
* Test cleanup
* One more test fix
* Test fix
* Try to fix test
* Clean up expunge
* Test fix
* Remove unneeded task
* Spotless
* Bump compiler plugin
* Spotless
* Compile fix
* Add license headers
* License header
* Test fixes
* Bump animal sniffer
* Spotless
* Bump Jetty version
* Test fix and version bump
* Cleanup
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Parser: Reporting unexpected repeating element for choice (#4574)
IParserErrorHandler.unexpectedRepeatingElement is now also called for
unexpected repeating elements of type choice, where concrete names
may be different based on the choice's data type.
* setting test-utilities java version to the test version
* added changelog
* added Max to the developer liss
* removed unneeded dependency
---------
Co-authored-by: patrick-werner <pa.f.werner@gmail.com>
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
* changes for GL-4023
---------
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
Ensure resource bodies are only logged at debug or lower.
* Drop possible-phi logs to debug.
* Demote request/response log bodies to debug since they may contain PHI.
* Demote job-param logging to debug.
* Add startup hook to App for test injection.
* Change terminology cli logging to avoid logging whole resource.
* started converting System.setProperty to HapiSystem
* added a couple more. renamed class
* all the setProperty calls done
* finished System.getProperty()
* Split HapiSystemProperties into HapiSystemProperties and HapiTestSystemProperties
* Javadoc
* Javadoc
* review feedback
Co-authored-by: Ken Stevens <ken@smilecdr.com>
* 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>
* 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
* Try commenting out clearAllStaticFieldsForUnitTest to see what happens
* Rename clearAllStaticFieldsForUnitTest to randomizeLocaleAndTimezone and only do that
* 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>
* Work on junit
* Work on junit 5
* Work on junit 5
* Bump errorprone vcersion
* Work on tests
* Junit 5 tweaks
* Fixes
* Work on tests
* Work on junit5
* Work on tests
* Test fixes
* Work on junit5
* Test work
* Get junit5 working
* Test fix
* Work on tests
* WOrk on tests
* Work on tests
* fixes
* Compile fix
* One more tweak
* Compile fix
* Add changelog
* Fix compile error
* Compile fix
* [dev] Integration of a Jackson serializer and deserializer - first stage
* [fix] Fixed some serializing issues
[improve] Improved the processing, removed the loggers
* [clean] Removed the JacksonSerializer class, replaced all the Gson classes with Jackson classes
* [clean] Small cleanup
* [improve] Throw a ConfigurationException if the JsonGenerator cannot be created
* [improve] Use the ObjectMapper's `readTree` instead of `readValue`
* [dev] Latest fixes and improvements
* [dev] Use the Jackson serializer
* [clean] Removed the ObjectMapper configuration, for now
* [fix] Use the GsonStructure also for the parsing of a FHIR resource
* [clean] Removed the LinkedList usage
* Work on preparing for merge of #1673
* Resolve build errors
* Work on parser integration
* Tests passing
* Resolve fixme
* CLeanup
* Fix dependency
Co-authored-by: Bogdan Solga <bogdan.solga@gmail.com>
* Validation enhancements
* Work on validation api reworking
* Keep working on validation API
* Keep working on new term API
* Work on validation api
* Ongoing work on validation
* Work on integrating validation
* Work on validation API
* Add to validation API
* Work on validation
* Work on API
* Work on validation
* Work on validation API
* Work on validation API
* Work on validation api
* Work on validation API
* Work on validation api
* Validation API changes
* Work on API
* More work on validationo API
* Work on validation API
* FIxes
* WOrk on validation api
* Work on validation API
* Tests passing!
* More cleanup
* More validation API changes
* Fix intermittent test failure
* Package reorg
* Validation API work
* Work on doocumentation
* Work on API
* More work on new validation API
* Fix errorprone-reported error
* Test fixes
* Documentation updates
* Documentation tweaks
* Work on API
* Bean name adjustments
* Build fixes
* Some test fixes
* Start work on changing over
* Update tests
* More test fixes
* Work on generalizing binary access provider a bit
* Add expunge capability to binary storage, and also support actual binary
resources
* Work on binary provider
* Get the DB bound binary storage service working
* Test fixes
* Compile fix
* Fix compile error
* Test fix
* Test tweak
* Trying to figure out an intermittent failure
* Work on tests
* More work on tests
* Another test fix
* Ongoing work on core structures suport
* Ongoing work on this merge
* Ongoing work to clean up structures
* Credit for #1179
* Address compile issues
* Latest changes
* Work on parallel execution
* Work on getting tests passing
* Add H2 to migrator
* Test fix
* Initial consent svc
* Ongoing consent svc work
* Add docs
* Ongoing consent service work
* Work on consent service
* More work on consent svc
* License header updates
* Ongoing consent svc work
* Some test fixes
* Some test fixes
* More work on consent svc
* Tests working
* Test fix
* Propagate RequestDetails to everything in JPA server
* More interceptor tweaks
* Fix compile error
* One more tweak to captured SQL
* Ongoing interceptor tweaks
* Ongoing interceptor tweaks
* More interceptor tweaks
* Interceptor tweaks
* Tweaks to tests
* Fix tests
* Test fix
* Raise warnings when encoding extensions with missing values
* Consent service work
* More interceptor tweaks
* Consent interceptor tweaks
* Add logging to test
* Starting work on this
* Working on narrative templates
* Work on new narrative system
* Account for some failing tests due to refactoring of narrative mode
* Another test fix
* More test fixes
* One more test fix
* Work on searches
* Address review comments
Tadgh
jdar8
Ken Stevens
Luke deGruchy
James Agnew
Max Bureck
Isaac Wen
michaelabuckley
Patrick Werner
Johnson Lu
Tadgh
Stig Rohde Døssing
David Gileadi