* begin with failing test
* fixed
* spotless
* changelog
* fix intermittent in SubscriptionRestHookDstu3IT
* fix deadlocks
* hapi version bump
---------
Co-authored-by: Ken Stevens <ken@smiledigitalhealth.com>
* Add junk ine
* Add extension for placeholder ID
* Cleanup
* Header
* Cleanup
* Spotless
* Better logging
* Fix transaction conditional URL prefetch on non-token params
* Drop a check
* Adjust query counts
* Improve performance
* Single token optimized
* Test fixes
* About to try to ensure we prefetch resource bodies for conditional create
* Test fixes
* Some test fixes
* Test fixes
* Test fixes
* Test fixes
* Work on tests
* Test fix
* Spotless
* Add docs
* Add test
* Add grouping
* Spotless
* Add size option to CMD
* Adjust consumer
* Cleanup
* Work on bulk import
* Spotless
* More work
* Add logging
* More diagnostics
* add logs
* Cleanup
* Fix premature finishing of bulk import command
* Add changelogs
* Test cleanup
* Test fixes
* Fix tests
* Test fix
* Spotless
* Cleanup
* Resolve conflicts
* Clean up
* Add to transaction response parser
* TransactionUtil parsing improvements
* Work on tests
* Test fix
* Test fixes
* Spotless
* Bug fix
* Build tweak
* Test cleanup
* Add some test logging
* Bump to trigger CI
* Try to address intermittent
* Address review comments
* Version bump
* License header
* add user data to JobInstance
* add BATCH2_CHUNK_PRE_PROCESSED and BATCH2_CHUNK_PROCESSING_COMPLETED pointcuts
* add canSeeResource() processing to STORAGE_BULK_EXPORT_RESOURCE_INCLUSION
* spotless
* add BATCH2_CHUNK_PROCESSING_COMPLETED_NORMALLY and BATCH2_CHUNK_PROCESSING_COMPLETED_HANDLE_EXCEPTION hooks
* add authorizeRequest() method
* FIXMEs
* fix tests
* resolve fixme
* spotless
* remove fixme
* improve serialization logic
* clean up
* remove consent interceptor changes
* pointcuts changelog
* userdata changelog
* First cut at filter hooks
* Error checking if they dont run the runnable
* Working error checking if they dont run the runnable
* Sketch of new pointcut
* Cleanup warnings
* Convert to Supplier so we have a return value.
* Tidy
* remove old workchunk hooks and replace with BATCH2_CHUNK_PROCESS_FILTER
* spotless
* add Filter Hook Interceptor docs
* update changelogs
* cleanup
* add comment to docs
* add another changelog
* spotless
* code review comments 1
* code review comments 2
* Simplify api for filter hooks with runnable
* fix test
* clean up
* spotless
* bump version to 8.1.5-SNAPSHOT
* fix
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* begin with failing test
* test passes
* start roughing out R4 SubscriptionTopic registry
* start building topic test
* start building topic test. add r4 builder to help
* basic scenario appears to be working now
* include and revinclude failing test
* include and revinclude support added
* fix test regression
* clean up ISubscriptionTopicLoader
* sonar
* sonar
* review cleanup
* review cleanup
* spotless
* fix api
* fix api
* fix test
* consolidate code duplication
* spotless
* spotless
* need Basic searchparams for R4 SubscriptionTopic registry
* review feedback
* review feedback
* review feedback
* Update hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicPayloadBuilder.java
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* Update hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicPayloadBuilder.java
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* review feedback
* spotless
* bump version
---------
Co-authored-by: Ken Stevens <ken@smiledigitalhealth.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* version bump clinical-reasoning for testing integration
* changelog
* bump CR to release 3.17.0
* bump hapi to 7.7.18-SNAPSHOT
* removing invalid measure example
* 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>
* 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 24f5e648ed3aecf057fd90cf4398e339f4dc4a6e.
* 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
* version bump clinical reasoning
* specifying required patch type
* bumping to 7.3.11-SNAPSHOT
* fix file name
* remove default fhirPatch until bug fixed
* Work on versioned canonidal refs
* Merge
* Tests working
* Working without version support
* CLean refactor
* Targets
* Remove redundant parameter
* Fix up tests
* Remove fixme
* Add changelog
* Improve changelog
* Update version
* Test fixes
* first cut
* first cut
* cleanup
* that took way too long
* fix test
* licenses
* merge master
* merge master
* changelog
* review feedback
* bump version
* Bump to core 6.2.6 + fix compilation errors
* Fix signature error
* Error ordering
* WIP 1 Fixing failing tests
* Fix FhirInstanceValidatorR4Test
* Fix FhirInstanceValidatorR5Test
* Fix FhirInstanceValidatorR4BTest
* Fix FhirInstanceValidatorDstu3Test.testValidateBuiltInProfiles()
* WIP Fix FhirInstanceValidatorDstu3Test
* Fix isPrimitiveType
* Add placeholder narratives to ServerCapabilityStatement
* Fix QuestionnaireResponseValidatorR4Test
* Newline cleanup
* Fix QuestionnaireResponseValidatorDstu3Test
* Fix QuestionnaireResponseValidatorR5Test
* Increase expected error messages by two because VALIDATION_HL7_WG_NEEDED
New validation requirement as of 2023-09-16
* Add placeholder fix for Balp narrative
* Fix expected validation messages
* Fix more expected validation messages
* Don't generate a master IPS narrative
* Fix IPS generation tests expecting old composition narrative
* Update fhir core and clinical-reasoning
* Remove commented code
* Bump to core 6.2.16-SNAPSHOT
* Add missing methods
* Add missing methods 2
* Fix error codes
* Fix error code
* Fix failing tests for Unsupported method 2488
* Fix error text
* Fix another expected error message
* Apply spotless
* Fix error strings
* Add minimal implementation to fix failing test
* Fix error message
* Fix some validation tests (r4)
* Fix more R5 tests
* Update for changing API
* Fix some R4B test failures
* Fix android incompatibility
* Fix more tests
* Switch back to LF
* Fix more tests 2
* Fix R4 IPS generation use of relative references, switch to random UUID
* Fix missing codes and patient ID in IPS test
* Fix missing codes in IPS R4 Test 2
* Fix display value
* Fix display value
* Reorg wrapper issue collection; fixes errors with Balp and others
* Update for API changes
* Fix code set typo causing test failure
* Fix DiffProviderR4Test
* Fix RepositoryValidatingInterceptorHttpR4Test fails
due to stricter code validation
* More code fixes
* Don't expect an extra error.
* Use more specific logic for details tx code
* Catch expected error
* Clean up
* Account for HAPI isEnabledValidationForCodingsLogicalAnd cases
* Apply spotless
* Change outputs for en_US single code test
* Add missing system from code to pass validation
* Account for DSTU3 and R4 including different code systems for race
* Add expected loinc codes to test dao
* Add some codesystem support for test
* Bump core version
* WIP pass on a list of CodeValidationIssue from CodeValidationResults
* Re-use v2 and v3 data from r4 in r4b
* CodeSystems can be supported, but not have a resource
* Remove hack around unitsofmeasure + return false LookupCodeResult
* Clean up chatter.
* Update test cases, remove FIXME
* Stop returning before adding all issues to ValidationResults
* Update for changes in core API
* Add severity to code issues + return to unknown system support
* Use new CollectionUtils
* Fix more issue messages and orders + null in TermReadSvcImpl
* After checking valueSet, also check codeSystem
* On second thought, always check the codesystem
* Improve validation message
* Refactor
* Add error consistent with core validator results
* Decrement query counts for validation
* Improve code validation messages + don't miss invalid display on cs
* Fix expected messages (added code details)
* More expected message fixes
* Remove redundant text from diagnostics + match core exception handling
* Explicitly send tx passthrough messages no longer managed in core
* Apply spotless
* Add issue to code validation in TermReadSvcImpl
* Adjust indexes of expected errors now that TermReadSvc is reporting
* Bump to released core version
* Code cleanup: commented code
* More commented code cleanup
* Fix parameter names
* Use Set.of and List.of + fix duplicate values in set
* Revert animal sniffed breakage, make field private
* Add comments to describe disabled test
* Remove System.out chatter
* Fix javadoc generation for r5 structures module
* More comments and move disabled annotation
It was working when it left the shop.
* Move older changelog into 7.4.0 and create core update changelog
* Switch changelog type to change
* Bump HAPI version
* Add validation utils for FATAL issue severity
* Handle FATAL codeValidationIssue severity
* Fix test (validation throws more warnings)
* Bump to version 7.3.4-SNAPSHOT
* Bump to SNAPSHOT version of core + add necessary method implementations
* Add comments to explain R4 terminology resources in R4B
* Add test for Observation vital signs profile validation
* Try using default validatorPolicyAdvisor
* Return an empty set for fetchCanonicalResourceVersions
* Profile now gives more explicit error instead of valueSet
* Revert commit
* Add CodeValidationIssues and additional error info
* Do not return first successful match from codings. Check all.
+ adjust for extra errors.
* apply spotless
* Fix failing test, add comments re: invocations
* Fix test to expect more informative error
* Fix stray compilation errors from merge.
* Fix merge overwrite of validation messages and indices
* Fix merge overwrite of new validation results
* Use core release 6.3.11
* Update HAPI version to 7.3.5-SNAPSHOT
* Fix changelog
* Remove commented code
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
