* 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
* 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>
* version bump clinical reasoning
* specifying required patch type
* bumping to 7.3.11-SNAPSHOT
* fix file name
* remove default fhirPatch until bug fixed
* 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>
* 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>
* Enhance RuleBuilder code to support multiple instances (#5852)
* Overhaul bulk export permissions.
* Overhaul bulk export permissions.
* Small tweak to rule builder.
* Cleanup validation.
* Cleanup validation.
* Code review feedback.
* Postgres terminology service hard coded column names migration (#5866)
* updating parent pids column name
* updating name of the fullTestField Search
* updating name of the fullTestField Search
* fixing typo.
* failing test.
* - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity;
- reverting the name of the FullTextField entity to its previous name of 'myParentPids';
- reverting the name of the lucene index to search on in the terminology service.
- updating the changelog;
* making spotless happy
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881)
* initial failing test.
* solution
* adding changelog
* spotless
* moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811)
* Expose BaseRequestPartitionHelperSvc validate and normalize methods
* Compilation errors
* change mock test to jpa test
* change mock test to jpa test
* validateAndNormalizePartitionIds
* validateAndNormalizePartitionNames
* validateAndNormalizePartitionIds validation + bug fix
* validateAndNormalizePartitionNames validation
* fix test
* version bump
* Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883)
* Add failing test as well as commented out potential solution.
* Fix for NumberFormatException.
* Add conditional test for survivorship rules.
* Spotless.
* Add changelog.
* Code review feedback.
* updating documentation (#5889)
* Ensure temp file ends with "." and then suffix. (#5894)
* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
* Enhance mdm interceptor (#5899)
* Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened.
* Added javadoc
* Cahngelog
* spotless
---------
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
* Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896)
* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.
* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.
* Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug.
* Add changelog.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml
Commit code reviewer suggestion.
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Fix query chained on sort bug where we over-filter results (#5903)
* Failing test.
* Ensure test cleanup doesn't fail by deleting Patients before Practitioners.
* Implement fix.
* Spotless.
* Clean up unit test and add changelog. Fix unit test.
* Fix changelog file.
* Apply suggestions from code review
Apply code review suggestions.
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* Spotless
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* cve fix (#5906)
Co-authored-by: Long Ma <long@smilecdr.com>
* Fixing issues with postgres LOB migration. (#5895)
* Fixing issues with postgres LOB migration.
* addressing code review comments for audit/transaction logs.
* test and implementation for BinaryStorageEntity migration post code review.
* test and implementation for BinaryStorageEntity migration post code review.
* test and implementation for TermConcept
migration post code review.
* applying spotless
* test and implementation for TermConceptProperty
migration post code review.
* test and implementation for TermValueSetConcept
migration post code review.
* fixing migration version
* fixing migration task
* changelog
* fixing changelog
* Minor renames
* addressing comments and suggestions from second code review.
* passing tests
* fixing more tests
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* 6051 bulk export security errors (#5915)
* Enhance RuleBuilder code to support multiple instances (#5852)
* Overhaul bulk export permissions.
* Overhaul bulk export permissions.
* Small tweak to rule builder.
* Cleanup validation.
* Cleanup validation.
* Code review feedback.
* Postgres terminology service hard coded column names migration (#5866)
* updating parent pids column name
* updating name of the fullTestField Search
* updating name of the fullTestField Search
* fixing typo.
* failing test.
* - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity;
- reverting the name of the FullTextField entity to its previous name of 'myParentPids';
- reverting the name of the lucene index to search on in the terminology service.
- updating the changelog;
* making spotless happy
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881)
* initial failing test.
* solution
* adding changelog
* spotless
* moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811)
* Expose BaseRequestPartitionHelperSvc validate and normalize methods
* Compilation errors
* change mock test to jpa test
* change mock test to jpa test
* validateAndNormalizePartitionIds
* validateAndNormalizePartitionNames
* validateAndNormalizePartitionIds validation + bug fix
* validateAndNormalizePartitionNames validation
* fix test
* version bump
* Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883)
* Add failing test as well as commented out potential solution.
* Fix for NumberFormatException.
* Add conditional test for survivorship rules.
* Spotless.
* Add changelog.
* Code review feedback.
* updating documentation (#5889)
* Ensure temp file ends with "." and then suffix. (#5894)
* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
* Enhance mdm interceptor (#5899)
* Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened.
* Added javadoc
* Cahngelog
* spotless
---------
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
* Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896)
* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.
* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.
* Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug.
* Add changelog.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml
Commit code reviewer suggestion.
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Fix query chained on sort bug where we over-filter results (#5903)
* Failing test.
* Ensure test cleanup doesn't fail by deleting Patients before Practitioners.
* Implement fix.
* Spotless.
* Clean up unit test and add changelog. Fix unit test.
* Fix changelog file.
* Apply suggestions from code review
Apply code review suggestions.
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* Spotless
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* cve fix (#5906)
Co-authored-by: Long Ma <long@smilecdr.com>
* Fixing issues with postgres LOB migration. (#5895)
* Fixing issues with postgres LOB migration.
* addressing code review comments for audit/transaction logs.
* test and implementation for BinaryStorageEntity migration post code review.
* test and implementation for BinaryStorageEntity migration post code review.
* test and implementation for TermConcept
migration post code review.
* applying spotless
* test and implementation for TermConceptProperty
migration post code review.
* test and implementation for TermValueSetConcept
migration post code review.
* fixing migration version
* fixing migration task
* changelog
* fixing changelog
* Minor renames
* addressing comments and suggestions from second code review.
* passing tests
* fixing more tests
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* refactor bulk export rule, add concept of appliestoallpatients, fix tests
* spotless
* Cahgnelog, tests
* more tests
* refactor style checks
---------
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
* Convert a few nulls to aggressive denies
* Change chain sort syntax for MS SQL (#5917)
* Change sort type on chains
* Change sort type on chains
* Test for MS SQL
* Comments
* Version bump
* version bump to 7.3.1-SNAPSHOT
---------
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
* step 1
* updated batch 2 framework with READY state
* spotless
* remove entity manager
* spotless
* fixing up more tests for batch2
* updating documentation
* cleanup
* removing checkstyle violation
* code review points
* review points continued
* review poitns finished
* updating tests
* updates
* spotless
* updated
* step 1
* updated
* sketch out test cases
* basic state transition shell work
* typos
* spotless
* adding spy override
* fixing tests
* spotless
* changing comment to complete build
* fixing some tests and adding a view
* adding different paging mechanism
* spotless
* waiting step 1
* commit changes
* remove text
* review fixes
* spotless
* some tweaks
* updating documentation and adding change log
* spotless
* added documentation
* review comments 1
* more review fixes
* spotless
* fixing bug
* fixing path
* spotless
* update state diagram
* review points round 1
* revert
* updating diag
* review fixes round 2
* spotless
* - Implemented GATE_WAITING state for the batch2 state machine.
- This will be the initial status for all workchunks of a gated job.
- made compatible with the equivalent "fake QUEUED" state in the Old batch2 implementation.
- Updated corresponding docs.
- added corresponding tests and changelog
* Revert "- Implemented GATE_WAITING state for the batch2 state machine."
This reverts commit 32a00f4b81.
* - Implemented GATE_WAITING state for the batch2 state machine.
- This will be the initial status for all workchunks of a gated job.
- made compatible with the equivalent "fake QUEUED" state in the Old batch2 implementation.
- Updated corresponding docs.
- added corresponding tests and changelog
* fixing a bug
* spotless
* fixing
* - fix merges conflicts
- set first chunk to be always created in READY
* - have only one path through the equeueReady method
- fixed tests
* - hid the over-powered transition function behind a proper state action
* spotless
* resolved review comments
* fixing tests
* resolved review comments
* resolved review comments
* resolved review comments
* resolved review comments
* resolved review comments
* updating migration script number
* fixed bugs
* spotless
* fix test high concurrency
* fixing a test
* code fix
* fixing tests in bulkexportit
* fixing tests
* fixing tests
* cleanup
* completed instance will not be sent to the reduction step service
* Revert "completed instance will not be sent to the reduction step service"
This reverts commit aa149b6691.
* Revert "Revert "completed instance will not be sent to the reduction step service""
This reverts commit e18f5796a1.
* removing dead code
* changed db query for step advance to take statuses as parameter instead
* test fixes
* spotless
* test fix
* spotless
* fixing tests
* migration fix
* fixing test
* testing pipeline with `testGroupBulkExportNotInGroup_DoesNotShowUp` disabled
* fixing some tests
* Add new race test for simultaneous queue/dequeue
* re-enabling `testGroupBulkExportNotInGroup_DoesNotShowUp`
* cascade tag deletes
* test fixes
* some logging
* a test case
* adding job id
* more test code
* marking purge checks
* test fix
* testing
* pausing schedulers on cleanup
* adding a wait
* max thread count guarantee
* fixing the tests again
* removing dead code
* spotless
* checking
* msg codes:
* Fixing a test
* review points
* spotless
* required pom values
* step 1 of reduction ready
* update
* reductoin ready
* annother test
* spotless
* cleanup
* cleanup
* simplifying check in reduction step
* review fixes
* updating version
* using 7.3.1
* adding check
* test finessing
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: tyner <tyner.guo@smilecdr.com>
* collect-data and data-requirements operations and tests
* remove unused imports
* additional test coverage
* move assertions out of method to pass static code analysis
* camelCase test names
* remove underscore on test methods
* requested edits to changelog
* version bump to 7.1.10-SNAPSHOT
* condense unit tests to prevent pipeline timeout
* method camel case naming
* added new customizer filter factory. have not yet deleted old code it replaces.
* added new customizer filter factory. have not yet deleted old code it replaces.
* replaced websocket filter. works. still some cleanup to do
* replaced websocket filter. works. still some cleanup to do
* cosmetic change
* add coverage and fix bugs it found
* spotless
* move capability statement classes
* add changelog and rename new classes
* review feedback
* Add support for latest version of CR and new $questionnaire operation
* Fix formatting in javadoc causing warning
* Update to 3.0.0 CR release
* Add support for expected parameter names from updated IG's
* Update Clinical Reasoning documentation
* Update pom.xml
* Create 5750-update-cr-operations.yaml
* fix doc
* Update to latest CR version
* Update pom.xml
* In version
* Update changelog
* Remove commented code
* pom bump to 7.0.0 (#5615)
* pom bump to 7.0.0
* add version enum
* fixed feb release name
---------
Co-authored-by: Long Ma <long@smilecdr.com>
* Check index existence on raw SQL creation (#5624)
* Add conditional check on index existence before we try again
* Add conditional check on index existence before we try again
* Changelog
* remit
* remit
* debug statements
* 5621 deadlock on caffeine cache when creating a resource with conditional create (#5622)
* Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback.
* Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations.
* adding changelog and spotless.
* Fixing typo.
* Addressing comments from code review.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)
* Failing test
* fix
* changelog
* Avoiding Exception being thrown on @EventListener invocation (#5628)
* replaced EventListener annotation with @PreDestroy
* adding changelog
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* simple fix (#5630)
Co-authored-by: Long Ma <long@smilecdr.com>
* Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625)
* Incorrect version from versioned_references.auto_at_paths for conditional update - implementation
* Oracle: Ensure migrated database still takes large resource text updates (#5629)
* First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration.
* First stab at agreed upon solution.
* Fix error with 4001 by removing unnecessary annotation.
* Spotless and TODO.
* Remove annotation for good and set length to LONG32.
* Fix copyright year.
* Finalize changelog.
* Remove migration changes. Fix unit test.
* Fix compile error.
* Log output.
* Refactor resource history code into new ResourceHistoryCalculator.
* Spotless.
* Convert record to POJO.
* Restore pre-17 switch statement.
* Finalize new resource history calculator code and tests.
* Spotless.
* Remove logging.
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml
Apply code reviewer suggestion
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* Code review feedback.
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638)
* When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases.
* Minor change to fix test
* Rename changelog file
* Remove TODOs as they're replaced by reported issue
* Revert accidental change added with TODO removal
* $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)
* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation
* Fix Measure group id null pointer exception (#5620)
* Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id
* add changelog
---------
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
* Rule evaluation: Allow Bundles with PATCH Parameters (#5641)
* Remove parameters clause.
* Finalize changelog. Add tests. Finalize implementation.
* Undo changes to this test.
* Revert all changes to FhirQueryRuleImplTest. Add new RuleImplOpTest. Ensure that proper nested Bundle is created for test and other fixes.
* Tweak test.
* Use real rule applier in test and remove all mocks.
* Prevent batch2 job execution to stop for empty chunk when last job st… (#5635)
* Prevent batch2 job execution to stop for empty chunk when last job step is a reduction.
Add output to bulk export result even when empty.
* Fix test
* Unimportant change to force fresh build
* Implement review suggestions
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Index review fixes (#5649)
* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.
* Fix conditional creates without leading '?' (#5646)
* First commit with failing test.
* More tests and logs.
* More logs
* Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl().
* Simplify solution. Add more tests.
* Changelog.
* javadoc
* Searching for Bundles with read all Bundles permission returns 403 (#5644)
* failing test
* another failing test case
* fix
* changelog
* fix bug
* spotless
* cr
* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660)
* Bump json-path
* Pin parrson
* Bump elastic
* Bump spring version
* Exclude JDBC
* Serializing changes for sensitive data (#5655)
* Add new senstiive data serializer
* Add new senstiive data serializer
* Add new senstiive data serializer
* Remove dead comments
* Change up the test
* review comments
* wip
* Tighten tests and push annotation down
* Tighten tests and push annotation down
* Changelog
* Add test
* 7.0.1-SNAPSHOT bump
* Error code
* Add method used by CDR
* add version enum
* Fix test
* Revert change to other safe version to stop problem with deprecated field
* Rel 7 0 CVE (#5663)
* Bump json-path
* Pin parrson
* Bump elastic
* Bump spring version
* Exclude JDBC
* Descendent fix (#5669)
* Fix "is-a" ValueSet expansion, add "descendent-of" support
* Fixed tests in DSTU3 and R5
* Trigger new build
* Revert "Trigger new build"
This reverts commit 46c672b338.
* fix default partition setting on resource (#5617)
* fix default partition setting on resource
* changelog
* Handle DEFAULT partition in rule checker.
* Fix spotless
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* pom bump, doc add, version enum add (#5616)
Co-authored-by: Long Ma <long@smilecdr.com>
* fix default partition setting on resource (#5618)
* fix default partition setting on resource
* Handle DEFAULT partition in rule checker.
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Add setting to make broker not use JacksonMessageConverter (#5611)
* Add setting to make broker not use JacksonMessageConverter
* Add changelog
* Implement suggestions
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* Fix version
* add changelog, add attribution, remove accidental bring-overs
* add changelog, add attribution, remove accidental bring-overs
* Finish jira section
---------
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* $poll-export-status operation with PatientIdPartitionInterceptor fails with NullPointerException (#5681)
* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor.
* Fix NPE on -export-status operation with PatientIdPartitionInterceptor
* 5654 measurescorer bug for denominator exception (#5677)
* update measure bundles and tests for enforced populationId specification on Measure group resources
* bump CR version to PRE17
* fix bug in versionEnumTest
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5654-measurescorer-bug.yaml
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
---------
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
* Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type. (#5698)
* Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type.
* Spotless fix
* Address code review comments
* version bump to 7.0.0
* pipeline fix
* Update java home
* Updating version to: 7.0.1 post release.
* post mergeback cleanup
* bump clinical-reasoning.version to pre17
* test fix
* version bump to 7.1.5-snapshot
---------
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
* Fix#5110 - Failure in tx processing
* Test fix
* Work on narrowins
* Add changelog
* Docs cleanup
* Fix compile error
* Rollback incompatible change
* Test fix
* Test fix
* Force update
* Test fixes
* Build fixes
* Bump HTMLUnit
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5712-apply-searchnarrowing-to-conditional-urls.yaml
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Version bump to 7.1.4-SNAPSHOT
* Spotless
* Roll back version
---------
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Suspend tx when refreshing version cache
* Undo refactor to reduce merge size
* changelog
* Bump to 7.1.3
* Fix version test
* Unwrap transaction proxy
Tadgh
James Agnew
Michele Adduci
TipzCM
Ken Stevens
VK-SMILECDR
jmarchionatto
dotasek
SIJIE MEI
Brenin Rhodes
Aditya Dave
JasonRoberts-smile
Michael Buckley
Long Ma
Justin McKelvy
jdar8
longma1
TynerGjs