Rel 7 4 mb 20241018 #6385
Open
Rel 7 4 mb 20241018 #6385
+12
−3
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* 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
…resource is AUTHORIZED or REJECT (#6127)
* fix migration task * changelog * changelog * code review * spotless --------- Co-authored-by: jdar <[email protected]>
…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 <[email protected]> * Code review fixes: Make changes conditional on the collation including _CI_, otherwise, leave it alone. --------- Co-authored-by: Michael Buckley <[email protected]>
* Add initial interface for common FHIR API * Fix formatting * Update javadocs * Address code review comments
#6128) * 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 <[email protected]>
Avoid using constants in migrations because it creates false history.
…6151) * 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.
…and $apply-codesystem-delta-remove (#6164)
* 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 <[email protected]> * 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 <[email protected]> * 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 hapifhir/hapi-fhir-jpaserver-starter#675 (#5892) Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: Tadgh <[email protected]> * 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 <[email protected]> * Spotless --------- Co-authored-by: Michael Buckley <[email protected]> * cve fix (#5906) Co-authored-by: Long Ma <[email protected]> * 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 <[email protected]> Co-authored-by: Tadgh <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 hapifhir/hapi-fhir-jpaserver-starter#675 (#5892) Co-authored-by: Jens Kristian Villadsen <[email protected]> * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: Tadgh <[email protected]> * 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 <[email protected]> * Spotless --------- Co-authored-by: Michael Buckley <[email protected]> * cve fix (#5906) Co-authored-by: Long Ma <[email protected]> * 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 <[email protected]> Co-authored-by: Tadgh <[email protected]> * refactor bulk export rule, add concept of appliestoallpatients, fix tests * spotless * Cahgnelog, tests * more tests * refactor style checks --------- Co-authored-by: Luke deGruchy <[email protected]> Co-authored-by: Etienne Poirier <[email protected]> Co-authored-by: peartree <[email protected]> Co-authored-by: Nathan Doef <[email protected]> Co-authored-by: TipzCM <[email protected]> Co-authored-by: dotasek <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> Co-authored-by: Michael Buckley <[email protected]> Co-authored-by: longma1 <[email protected]> Co-authored-by: Long Ma <[email protected]> * 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 <[email protected]> Co-authored-by: Etienne Poirier <[email protected]> Co-authored-by: peartree <[email protected]> Co-authored-by: Nathan Doef <[email protected]> Co-authored-by: TipzCM <[email protected]> Co-authored-by: dotasek <[email protected]> Co-authored-by: Jens Kristian Villadsen <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: Michael Buckley <[email protected]> Co-authored-by: Long Ma <[email protected]> Co-authored-by: markiantorno <[email protected]>
…turns 400 bad request (#6124) * 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
…d overwriting. (#6172) Co-authored-by: peartree <[email protected]>
Co-authored-by: peartree <[email protected]>
* Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_2_0
…esourceLinlk (#6149) * initial POC. * addressing comments from first code review * Adding tests * adding changelog and spotless * fixing tests * spotless --------- Co-authored-by: peartree <[email protected]>
Co-authored-by: peartree <[email protected]>
Co-authored-by: Long Ma <[email protected]>
* Add path tp _id search param and definitions for _lastUpdated _tag, _profile and _security * Add tests and changelog * Increase snapshot version * Irrelevant change to force new build --------- Co-authored-by: juan.marchionatto <[email protected]>
re-enabling FhirPatchCoreTest Co-authored-by: peartree <[email protected]>
…type. Update reindex job to always run with urls. (#6185) * Refactor logic to bring together partition related logic in batch2 jobs using IJobPartitionProvider. Update logic such that reindex job without urls will attempt to create urls for all supported resource types. * Small changes and fix of pipeline error. * Small change to enable mdm-submit to use PartitionedUrl in the job parameters * Revert logback change. Fix dependency version generating errors in the pipeline. * Spotless fix. Add test dependency back without version. * Upgrade test dependency to another version * Add javadoc for PartitionedUrl. Other small fixes and refactoring in tests. * Spotless fix. * Change to JobParameters to fix some of the tests. * Small changes for code review in test * Address code review comments. * Revert change from bad merge. * Address remaining code review comments
…s operation on resources in other partitions (#6191) * initial failing test * WIP * fixing/adding tests * added changelog * spotless * fixing tests * Cleaning up tests * addressing commetns from first code review. * no-op to get pipelines going --------- Co-authored-by: peartree <[email protected]>
* 6173 - Log unhandled Exceptions in RestfulServer. * Use placeholder for failed streams. * Starting test for server handling. * Got test working. * Fixed use of synchronized keyword. * Applied mvn spotless. --------- Co-authored-by: Kevin Dougan <[email protected]> Co-authored-by: Michael Buckley <[email protected]>
* Partition aware transactions * Address review comments * Test fixes * Remove dead issue field * Test fixes --------- Co-authored-by: Tadgh <[email protected]>
* wip * wip * wip * remove whitespace * Add test * changelog
* version bumps and change log * cherry pick 6420 * various updates to changelogs * build formatting changes --------- Co-authored-by: jdar <[email protected]> Co-authored-by: Etienne Poirier <[email protected]>
* Composite unique search parameter with dateTime component does not reject resource duplication (#6318) * Composite Unique Search Parameter with dateTime component does not reject resource duplication - failing tests * Composite Unique Search Parameter with dateTime component does not reject resource duplication - implementation * Composite Unique Search Parameter with dateTime component does not reject resource duplication - changelog and test fixes * 2024.08.R03 backport - version bump
* bumping fhir core version * default methods * adding changelog * fixes * remove commented out code * version bump and some minor test fixes * version bump * changelog * review fixes --------- Co-authored-by: leif stawnyczy <[email protected]>
…on (#6360) * Add support for response parameter issues for validate-code operation. Implement workaround for missing error for invalid codes by adding an issue when it is absent. * address minor code review comments * revert functionality of adding original code from remote validate-code call to the CodeValidationResult * revert change to FhirInstanceValidatorR4Test * Revert some of the code review addressal after responding. * Remove populating message in success scenarios. * Fix compilation failure in test after reverting method rename. * Revert change to populate the code from the response again as it implies more refactoring. --------- Co-authored-by: nathaniel.doef <[email protected]>
|
Formatting check succeeded! |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #6385 +/- ##
============================================
- Coverage 83.54% 83.54% -0.01%
- Complexity 27432 27770 +338
============================================
Files 1707 1738 +31
Lines 106185 107447 +1262
Branches 13397 13489 +92
============================================
+ Hits 88710 89762 +1052
- Misses 11750 11900 +150
- Partials 5725 5785 +60 ☔ View full report in Codecov by Sentry. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.