* 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.
* First draft of disabling JsonParser "fhir_comment" code. Unit test assertion that JSON is not generated with "fhir_comment" in the resulting resource String.
* Surround fhir_comments logic with conditional logic. Set this to false while awaiting final word from stakeholders. Add unit tests for STU3 and STU2 proving that fhir_comments do not get generated.
* Add conditional logic for JsonParser and fhir_comments and adjust unit tests accordingly. Also, move the HapiFhirStorageResponseCode.json file to the same module as DefaultProfileValidationSupport, namely, the code that actually reads it.
* Add changelog.
* Add missing change to JsonParser that I thought I had pushed. Fix changelog. Fix unit tests assertions to be clearer.
* JsonParser: Cache value of isSupportsFhirComment.
* Support version DSTU2_1 as well and add a new unit test.
* Fix pipeline unit test failures.
* 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
* Start working on FHIRPatch
* More work on fhirpatch
* Work on FHIR Patch
* Add patch
* Test fixes
* Test fixes
* Get tests fixed
* Chnage to trigger a build
* Compile fix
* Dependency version fixes
* Test fix
* COmpile fix
* Try to fix build
* Test fix attempt
* Another build attempt
* Another build tweak
* Cleanup
* [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
* Work on upgrading core
* Work on R5 updates
* Work on core updates
* Test fix
* Update model version properties file for R5
* Bump core version
* Test fixes
* Add 4.2.0-SNAPSHOT version to versions page in docs
* Don't succeed validation on unknown codesystem
* Test fixes
* Work on error messages
* Work on code validation API
* work on tests
* Work on validation
* Test fix
* Update DSTU3 validation reources
* Upgrade structures
* Test fixes
* Start refactoring terminology delta operations
* Work on delta operations
* Work on concept saving
* Split term services into smaller services
* Work on term delta operations
* Work on term svcs
* Work on term operations
* More work on delta uploader
* Add a test
* Wrk on term service
* Fix compile error
* Some refactoring
* Test fix
* Test fix
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Work on delta
* Work on tests#
* Test fixes
* Improve resequencing logic
* Build test
* More testing
* More build testing
* More work on tests
* CHange test logging
* Fix term service PID issue
* Update src/changes/changes.xml
Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>
* Address review comment
* Some cleanup
* Test fix
* Fix some tests
* Work on upload command
* Test fixes
* Work on validation fixes
* Work on validation against pre-expansion
* Work on direct validation
* A bit of cleanup
* Add some javadoc
* Force another build
* Test fixes
* Fix tests
* Fix tests
* Resolve XXE issue in validator
* Ensure that we're blocking XXE events into validator XML parser
* A bit of cleanup
* Add an LGTM config
* Add one more fix
Added missing @Override annotations so that if/when methods in superclasses change
there will be a compile-time error if subclasses haven't been changed accordingly.
This was done using IntelliJ IDEA's "Missing @Override annotation" inspection.
* Start working on subscription processor
* Work on new scheduler
* Test fixes
* Scheduler refactoring
* Fix test failure
* One more test fix
* Updates to scheduler
* More scheduler work
* Tests now all passing
* Ongoing work on export
* Ongoing scheduler work
* Ongoing testing
* Work on export task
* Sync master
* Ongoing work
* Bump xml patch version
* Work on provider
* Work on bulk
* Work on export scheduler
* More test fies
* More test fixes
* Compile fix
* Reduce logging
* Improve logging
* Reuse bulk export jobs
* Export provider
* Improve logging in bulk export
* Work on bulk export service
* One more bugfix
* Ongoing work on Bulk Data
* Add changelog
* Start work on delta operations
* Add changelog
* Some build fixes
* Move upload terminology command to CodeSystem resource
* Updates
* Some test fixes
* Add changelog
* Some test fixes
* More test fixes
* Test fix
* Add additional tests
* Transaction boundary 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
* Start working on this
* Ongoing fixes to H2 branch
* Work on fixing tests
* Updated fixes
* Some test fixes
* More work on H2 migration
* Fixes to try and get the H2 migration building
* Test seem to be passing!
* Tweaks to locale randomization
* Add changelog
* 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
Ken Stevens
William Denton
Tadgh
Max Bureck
Isaac Wen
michaelabuckley
James Agnew
Luke deGruchy
Patrick Werner
Johnson Lu
Tadgh
Clayton Bodendein
Stig Rohde Døssing