* 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 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
* add a new pointcut for changing message before submitting it to message broker
* failing test
* fix test by invoking hook when hook is registered
* spotless
* update docs
* changelog
* review changes
* spotless
* 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>
* fixing a regression that prevented rebuilding golden resources with survivorship in a partitioned system
* spotless
* update var usage
---------
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
* 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>
* 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
---------
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
Ken Stevens
James Agnew
VK-SMILECDR
jmarchionatto
dotasek
Tadgh
Brenin Rhodes
Aditya Dave
jdar8
Long Ma
TipzCM
Justin McKelvy
Ken Stevens
longma1