* Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - failing test
* Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - implementation
* 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
* Updating version to: 7.2.1 post release.
* Fix queries with chained sort with Lucene by checking supported SortSpecs (#5958)
* First commit with very rough solution.
* Solidify solutions for both requirements. Add new tests. Enhance others.
* Spotless.
* Add new chained sort spec algorithm. Add new Msg.codes. Finalize tests. Update docs. Add changelog.
* pom remove the snapshot
* Updating version to: 7.2.2 post release.
* cherry-picked pr 6051
* changelog fix
* cherry-picked 6027
* docs and changelog
* merge fix for issue with infinite cache refresh loop
* Use lockless mode when adding index on Azure Sql server (#6100) (#6129)
* 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
* added fix for 6133
* failing Test
* Add fix
* spotless
* Remove useless file
* Fix claeaner
* cleanup
* Remove dead class
* Changelog
* test description
* Add test. Fix broken logic.
* fix quantity search parameter test to pass
* reverted test testDirectPathWholeResourceNotIndexedWorks in FhirResourceDaoR4SearchWithElasticSearchIT
* spotless
* cleanup mistake during merge
* added missing imports
* fix more mergeback oopsies
* bump to 7.3.13-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>
Co-authored-by: markiantorno <markiantorno@gmail.com>
* Handle 400 and 404 codes returned by remote terminology operation.
* Some simplification
* Adjust changelog
* Add a comment to explain alternate solution which can be reused.
* Add path value to _id search parameter and other missing search parameters to IAnyResource.
* Adjust tests and remove now unnecessary addition of meta parameters which are now provided by IAnyResource
* Revert unneeded change
* _security param is not token but uri
* Add tests for new defined resource-level standard parameters
* Adjust test
---------
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* 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>
* 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
* Move IncomingRequestAddressStrategy::determineServletContextPath into IServerAddressStrategy to permit overriding (#6038)
* add changelog
* add contributor as developer
---------
Co-authored-by: Alex Kopp <akopp@athenahealth.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
* - reverting commented out changes
- removing personal todo
* removing changelog since the related change was reverted.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* version bump clinical reasoning
* specifying required patch type
* bumping to 7.3.11-SNAPSHOT
* fix file name
* remove default fhirPatch until bug fixed
* Use server name as narrative text in CapabilityStatement
* Credit for #6060
* Fix spotless
---------
Co-authored-by: James Agnew <jamesagnew@gmail.com>
* wip test writing
* add test to ES suite as well
* wip
* Changelog
* spotless
* Address review comments
* Test corrections
* Fixes for tests
* Fix changelog
* wrapping metaAdd/Delete operation in transactionService.execute to have the tenant acknowledged by Spring.
* spotless happiness.
* fixing broken test.
---------
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
* Cleanup and fix compile warnings
* Cleanup and enhance batch2 jobs to support running them across multiple partitions.
* Add some documentation and fix build in the pipeline.
* Fix tests
* Add support for RequestPartitionId.allPartitions as input to the IJobPartitionProvider. Add tests and fix one test. Add missing changelog.
* Separate basic partition provider logic so it can be reused by Mongo. Update documentation.
* Revert change to apply certain validation only for creates.
* Remove added logs
* spotless fix
* Address code review comments
* Remove code to SQL query from BaseTask. Move code to DropPrimaryKeyTask and gate it for NOT dry-run.
* Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropPrimaryKeyTask.java
Commit code review suggestion
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
* Code review feedback.
* Code review feedback.
* Remove isTransactional().
---------
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Etienne Poirier
volodymyr-korzh
longma1
TipzCM
Emre Dincturk
Martha Mitran
Michael Buckley
jmarchionatto
JP
Luke deGruchy
jdar8
Luke deGruchy
Long Ma
Tadgh
Justin McKelvy
Renaud Subiger
Ken Stevens
Aditya Dave
VK-SMILECDR
James Agnew
dotasek