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https://github.com/hapifhir/hapi-fhir.git
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2902 Commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
acoteathn
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554bb08d01
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Add configuration setting for TTL of HTTP connections to IRestfulClientFactory (#6204)
* Add configuration setting for TTL of HTTP connections to IRestfulClientFactory * Update changelog and pom.xml * Modify changelog --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> |
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Michael Buckley
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709756d68d
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Move partition-compatibility logic into tx service. (#6220) | ||
Tadgh
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947291e7f5
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Final Mergeback of 7.4.0 (#6223)
* 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 * Add path value to _id search parameter and other missing search param… (#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 <juan.marchionatto@smilecdr.com> * update to online (#6157) * SEARCH_UUID should be non-null (#6165) Avoid using constants in migrations because it creates false history. * Handle 400 and 404 codes returned by remote terminology operation. (#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. * fix concepts with no display element for $apply-codesystem-delta-add and $apply-codesystem-delta-remove (#6164) * allow transaction with update conditional urls (#6155) * Revert "Add path value to _id search parameter and other missing search param…" (#6171) This reverts commit 2275eba1a0f379b6ccb2d1b467fa22bd9febcf54. * 7 2 2 mb (#6160) * 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> * Patient validate operation with remote terminology service enabled returns 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 * - Changing method accessibility from default to public to allow method overwriting. (#6172) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying Taha Attari's fix on branch merging to rel_7_4 (#6177) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Automated Migration Testing (HAPI-FHIR) V7_4_0 (#6170) * 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 * To provide the target resource partitionId and partitionDate in the resourceLinlk (#6149) * initial POC. * addressing comments from first code review * Adding tests * adding changelog and spotless * fixing tests * spotless --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying patch (#6190) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cve for 08 release (#6197) Co-authored-by: Long Ma <long@smilecdr.com> * Search param path missing for _id param (#6175) * 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 <juan.marchionatto@smilecdr.com> * Reverting to core fhir-test-cases 1.1.14; (#6194) re-enabling FhirPatchCoreTest Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Fix $reindex job with custom partition interceptor based on resource 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 * 6188 subscription not marked as a cross partition subscription matches 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 <etienne.poirier@smilecdr.com> * Resolve 6173 - Log unhandled Exceptions in RestfulServer (#6176) (#6205) * 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 <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Partition aware transactions (#6167) * Partition aware transactions * Address review comments * Test fixes * Remove dead issue field * Test fixes --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Add license header * rel_7_4 mergeback * Attempt fix for npe (#6213) * wip * wip * wip * remove whitespace * Add test * changelog * Version bump --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.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> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: Martha Mitran <marthamitran@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com> Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com> |
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Etienne Poirier
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3e2d84d0f7
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Query with FullText searching (_text) does not return expected result (#6217)
* sketch of scroll solution * implementation of a scrolled search to handle Lucene large resultset. * legacy code clean up * adding changelog * addressing comments from first code review * adding more test * correcting implementation after failing test * no-op change to trigger pipeline * no-op change to trigger pipeline again --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> |
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volodymyr-korzh
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568c6d20db
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rel_7_4 Merge-back (#6212)
* 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 * Add path value to _id search parameter and other missing search param… (#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 <juan.marchionatto@smilecdr.com> * update to online (#6157) * SEARCH_UUID should be non-null (#6165) Avoid using constants in migrations because it creates false history. * Handle 400 and 404 codes returned by remote terminology operation. (#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. * fix concepts with no display element for $apply-codesystem-delta-add and $apply-codesystem-delta-remove (#6164) * allow transaction with update conditional urls (#6155) * Revert "Add path value to _id search parameter and other missing search param…" (#6171) This reverts commit 2275eba1a0f379b6ccb2d1b467fa22bd9febcf54. * 7 2 2 mb (#6160) * 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> * Patient validate operation with remote terminology service enabled returns 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 * - Changing method accessibility from default to public to allow method overwriting. (#6172) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying Taha Attari's fix on branch merging to rel_7_4 (#6177) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Automated Migration Testing (HAPI-FHIR) V7_4_0 (#6170) * 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 * To provide the target resource partitionId and partitionDate in the resourceLinlk (#6149) * initial POC. * addressing comments from first code review * Adding tests * adding changelog and spotless * fixing tests * spotless --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * applying patch (#6190) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cve for 08 release (#6197) Co-authored-by: Long Ma <long@smilecdr.com> * Search param path missing for _id param (#6175) * 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 <juan.marchionatto@smilecdr.com> * Reverting to core fhir-test-cases 1.1.14; (#6194) re-enabling FhirPatchCoreTest Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Fix $reindex job with custom partition interceptor based on resource 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 * 6188 subscription not marked as a cross partition subscription matches 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 <etienne.poirier@smilecdr.com> * Resolve 6173 - Log unhandled Exceptions in RestfulServer (#6176) (#6205) * 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 <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * Partition aware transactions (#6167) * Partition aware transactions * Address review comments * Test fixes * Remove dead issue field * Test fixes --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Add license header * rel_7_4 mergeback --------- Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.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> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: Martha Mitran <marthamitran@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.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: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com> Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> |
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Aditya Dave
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4368e33fda
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6182 introduce a new pointcut to allow customization before sending message to the broker on mdm submit (#6183)
* 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 |
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jdar8
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fd5cff3d23
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5138 enhance existing historical link with mactchResultMap field (#5213) | ||
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Michael Buckley
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cd43523afe
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Mergeback 7_4 (#6158)
* 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> |
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Long Ma
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406db339ce | bump to 7.5.0-snapshot | ||
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Long Ma
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0e8f474b51 | revert 6e208f16ecdf60859ca581d089c1ff448787bdb2 | ||
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Long Ma
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6e208f16ec | bump to 7.5.0-snapshot | ||
TipzCM
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7e7aae6060
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batching subscription msgs (#6084) | ||
Justin McKelvy
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d2c12a7ac3
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6083 clinical reasoning version bump v38 (#6089)
* version bump clinical reasoning * specifying required patch type * bumping to 7.3.11-SNAPSHOT * fix file name * remove default fhirPatch until bug fixed |
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VK-SMILECDR
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e3f64c23a2
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logback test extention assert (#6087)
* initial check-in * HAPI logback test extension cleanup * bump version * revert mistake change * changes based on review |
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Aditya Dave
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ce0160e7f9
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cds hooks allow arbitrary strings for extensions (#6026)
* changes to context booter and basecdsservicejson * cleanup CdsHooksContextBooter * javadocs * change JsonNode to CdsHooksExtension * failing test for service extensions... * fix extension serialization * fix extension serialization * failing test for request extensions not getting parsed... * try adding a custom deserializer for extension * try adding a custom deserializer for extension * try adding a custom deserializer for extension * wire up CdsServiceRegistryImpl * fix wiring object mapper * merge master * get hook in deserializer * create CdsServiceRequestJsonDeserializer.. * spotless * fix for cds service feedback for CdsHooksControllerTest.java * spotless * cleanup... * spotless... * docs * enable tests for CdsHooksContextBooterTest * more cleanup... * refactor CdsServiceRequestJsonDeserializer * apply suggestion * spotless.... * fix checkstyle... * spotless * split custom extension classes into its own package for tests * add changelog * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6023-fix-allowing-arbitrary-json-for-cds-hooks-extensions.yaml Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6023-fix-allowing-arbitrary-json-for-cds-hooks-extensions.yaml Co-authored-by: Ken Stevens <khstevens@gmail.com> * Update hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/api/json/CdsHooksExtension.java Co-authored-by: Ken Stevens <khstevens@gmail.com> * fix comments * rename * fix the comment * spotless * version bump to 7.3.9-SNAPSHOT --------- Co-authored-by: Ken Stevens <khstevens@gmail.com> |
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Martha Mitran
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ecef72729f
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Add support for running the reindex job across resources in multiple partitions and all partitions (#6009)
* 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 |
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James Agnew
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5e519810ff
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Combo Parameter Permutations (#6073)
* Combo permutations * Work on combo * Add tests * Add changelog * Spotless * Test fix * Drop label * Add tests * Spotles * Account for review comments |
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dotasek
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8a41da4a18
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Add warning in javadoc (#6081) | ||
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TipzCM
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2fc873d3b6
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added PATCH (#6059) | ||
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James Agnew
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7224245217
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Combo SearchParameter improvements (#5885)
* Start supporting combo refs * Work on error codes * Add tests * Work on tests * Fixes * CLeanup * Add changelog * Test fixes * Test fix * Clean up tests * Test cleanup * Work on tests * Revert change * Optimize storage * Add tests * Work on tests * Update docs * Spotless * Test fixes * Revert breaking change * Merge * Bump guava * Address review comments * Test fixes * Test fix * FIx tests * Address review comments * Spotless * Test fix * Revert change |
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Tadgh
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bd83bc17cd
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6046 text does not work with r5 (#6051)
* Initial commit of failing test * wip * Hack a side-route to not use analyzed versions of the field * spotless * Add concept of contains for special * Changelog, docs * spotless * another test * wip * refactor * spotless |
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jdar8
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11d61a5f72
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Jd 20240614 6010 bundle entry search score missing (#6011)
* 6010 test * 6010 add bundle entry search score * 6010 support other fhir versions for search score * 6010 changelog * 6116 mvn spotless * 6010 address code review comments --------- Co-authored-by: jdar <justin.dar@smiledigitalhealth.com> |
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Jens Kristian Villadsen
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f767058239
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Subscription fhirpath criteria (#5975)
* Added fhirpath-criteria evaluation * Added test for valid fhirpath that does not evaluate to boolean * Added resolving the variables %current and %previous * Added test using only FP criteria * Added test cases for valid FhirPath expressions that return non-booleans * Added use of central cache * Added more elaborate tests for non-sunshine scenarios * Added changelog * CheckStyle'd errorcode added. * Added spotless formatting and converted FhirPathR5 expression to be Android compatible * Applied more spotless |
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TipzCM
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60f456c655
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mdm multidelete golden resource final resource pair throws (#6001)
* fixed a bug with mdm and multidelete |
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Martha Mitran
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472984ac65
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Document pointcut to use to modify request parameters (#6019)
* Document pointcut to use to modify request parameters. Add a test to exemplify. * Add another alternate pointcut to use |
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James Agnew
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47d6e357b6
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Fix JPA nullable primitive columns (#5926)
* Fix JPA nullable primitive columns * Add changelog * Spotless * License headers * Migration fix * Spotless * Cleanup * Cleanup * Add task skipping * Update docs * CLeanup * Spotless * Address review comments * Test fix * HAPI FHIR version bump |
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James Agnew
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8947706af3
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Handle Versioned Canonical Refs (#6003)
* 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 |
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Tadgh
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73a6a8ef82
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Add tests to checkstyle (#6006)
* Add tests to checkstyle * Add includede test dirs in execution * wip * wip * bump checkstyle deps * bump checkstyle deps * wip50 * wip * Handle upgrade * triple-wip * wip * Wip replacement of prints * All checkstyle now passing * wip * Reset checkstyle * spotless * reset checkstyle * Add checkstyle to pipeline * Tidy * Tidy * wip * Cut over to not empty for correct behaviour * imports |
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Ken Stevens
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c1c6d4fc49
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Added a couple more methods to the logback assert test helper (#6004)
* add negative method * add throwable matcher for logback * logback asserts * merge master * update StaticLogbackTestExtension usage |
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Ken Stevens
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57d1815b46
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Extract Subscription Settings from Storage Settings (#5887)
* first cut * first cut * cleanup * that took way too long * fix test * licenses * merge master * merge master * changelog * review feedback * bump version |
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dotasek
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0abbb1a4f4
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Core library bump 6.3.11 (#5772)
* 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> |
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Justin McKelvy
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590fe26a76
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5914 clinical reasoning v3.6.0 bump (#5964)
* version bump clinical reasoning wip * cr release 3.6.0 bump * versio bum hapi to 7.3.4-snapshot * cve dependency removed * fix merge back issues on pom * jackson update missed |
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Emre Dincturk
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48c387ecb0
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added batch job related attributes to OpenTelemetry span (#5972) | ||
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Martha Mitran
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00a6591586
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Merge pull request #5978
* Fix authorization handling for Bundle resources in the output. When t… * Merge remote-tracking branch 'origin/master' into mm-20240529-test-se… * Add test case for the described scenario * Merge remote-tracking branch 'origin/master' * Add Bundle search test with custom search parameters. * Update test to simpler one to illustrate the problem * SearchParameter for Bundle document referencing resource through comp… * Merge remote-tracking branch 'origin/master' into mm-20240605-search-… * Merge another test into the new class * Remove unused json file. Small formatting fix in a test. * Add more use cases and adjust an existing one |
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Ken Stevens
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cdf5b602c1
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Replace hamcrest with assertj (#5911)
* optimize imports * optimize imports * Hamcrest replacement * Hamcrest replacement * Test failures * migrate hapi-fhir-base * docs * Few more cutovers * Full rewrite of all assert cases * Full rewrite of all assert cases * Partial cutover * assert library conversion * wip * fix imports * remove equalto * once-over again * minor cutover * wip * wip * wip * wip * wip * Remove hamcrest asserts replace with assertj * wip * Partial hamcrest rip-out * More hamcrest stripping * wip * Partial completion * spotless * it compiles now * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fixing compile issues * fix compile issues * fix compile issues * hapi-fhir now compiles * fix test * fix test * fix test * fix tests * fix tests * fix tests * fix test * fix test * fix tests * fix tests * fix tests * yay all tests pass now! * revert assertEquals change * revert assertEquals change * organize imports * organize imports * organize imports * post merge cleanup * organize imports * more cleanup * more cleanup * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * removing hamcrest stragglers * organize imports * organize imports * remove final hamcrest stuff * remove final hamcrest usages * remove final hamcrest usages * Revert "remove final hamcrest usages" This reverts commit eaf5107396af7c0fedbb8f1dce8b75133cc790eb. * fix compile issues from a hacky search/replace * compiles with fixmes * fix tests * fix test * fix test * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge compile issues * fix post merge test issues * fix test * fix test * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * replace hamcrest with assertj * all but mdm tests * final hamcrest removed from hapi-fhir yay! * revert mdm changes. it's too hard for now * revert cdr breaking change * revert cdr breaking changes * revert cdr breaking changes * revert cdr breaking changes * revert cdr breaking changes * revert changes that break cdr * merge master with compile errors * review feedback * review feedback * review feedback: revert bad regexp change * fix test * fix test * convert new hamcrest entries * convert new hamcrest entries --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> |
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James Agnew
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ab0b62706a
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Configurable summary mode (#5944)
* Fix #5871 - Configurable summary mode * Add docs * Spotless * Add javadoc |
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Ken Stevens
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ac3a5e2ad2
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improve validation for R4 backport subscriptions in SubscriptionValidatingInterceptor (#5973)
* still need to genericise the rest of the SubscriptionValidatingInterceptorTest tests also there are Msg.code FIXMEs * cleanup still need to genericise the rest of the SubscriptionValidatingInterceptorTest tests * cleanup still need to genericise the rest of the SubscriptionValidatingInterceptorTest tests * done * done * javadoc * changelog * fix test * fix test * fix test * fix test * fix test |
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Stefan Lindström
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4ac65da2ee
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5738: Skip alternate handling if already handled by previous step (#5971)
* 5738: Skip alternate handling if already handled by previous step * Credit for #5738 --------- Co-authored-by: Stefan Lindström <stefan.lindstrom@ehalsomyndigheten.se> Co-authored-by: James Agnew <jamesagnew@gmail.com> |
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TipzCM
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f199a3ee4e
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added workchunk to step execution details (#5932)
* added workchunk to step execution details * versino bump * added deprecated constructor * spotless * review fixes * spotless --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> |
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James Agnew
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97cfb6de37
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Add utility method to convert Bundle into transaction (#5945)
* Add utility method to convert Bundle into transaction * Add utility method * Spotless * Build fix |
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Martha Mitran
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bff59b6c50
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Add support for returning subproperties for RemoteTerminologyService lookup (#5936)
* Add support for returning subproperties in the RemoteTerminologyService * Add clarifying comments to code. Simplify logic to filter properties. * Update sub-property iteration logic in the conversion code to make it more readable * Fix spotless errors * Add a few more test cases to test property filtering for the lookup |
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James Agnew
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14c364dffd
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Include profile URL in generated IPS (#5938)
* Include profile URL in generated IPS * Add changelog * Documentation tweak |
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Luke deGruchy
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9b5673e240
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Bulk export: SearchParameters evaluation for patient compartment. If non-R4 evaluation would have failed, extract using R4 FHIR path (#5931)
* Proposed change to make DSTU3 find the same patient path as R4. * Update logic based on conversation. * Update logic based on conversation with R4 gating. * Update logic again. * Tweak logic again with an even narrower code path and add a new unit test. * Add changelog. Tweak javadoc. * Code review feedback. |
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longma1
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078e87a4aa
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7 2 mergeback may 10 v2 (#5928)
* 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> |
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Tadgh
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3572d593c1
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Revert "7_2 branch mergeback (#5922)" (#5927)
This reverts commit 125513a10009041289b0d0570c30aa4fd637ab0a. |
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longma1
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125513a100
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7_2 branch mergeback (#5922)
* 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> |
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TipzCM
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ae67e7b55e
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Batch2 workchunk states hapi (#5851)
* 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 32a00f4b8169a11849611798adfd48138908e49c. * - 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 aa149b669181f25f9262cb871627d7ec59369e5f. * Revert "Revert "completed instance will not be sent to the reduction step service"" This reverts commit e18f5796a165029d693bc5b6e0d882e429072d4e. * 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> |
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Tadgh
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6653a1e1b2 | Versions added | ||
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Tadgh
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8a37223106 | Version bump | ||
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Emre Dincturk
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4125d8c9ad
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added otel span for interceptors (#5853) |