Commit Graph

10002 Commits

Author SHA1 Message Date
James Agnew 91f2c8f526 Cleanup 2024-11-14 08:42:57 -05:00
James Agnew c79a705124 Test cleanup 2024-11-14 07:38:46 -05:00
James Agnew bd0502e368 Remove fixme 2024-11-13 15:59:30 -05:00
James Agnew 0e1be114ee MDM virtualization 2024-11-13 15:41:27 -05:00
James Agnew 7c98bfdd9f Merge branch 'master' into ja_20241106_mdm_virtualization 2024-11-13 14:10:46 -05:00
James Agnew 76865940d1 Fixes 2024-11-13 14:10:33 -05:00
James Agnew 034d9a9b48 Cleanup 2024-11-13 12:54:47 -05:00
James Agnew 1c13ccd2d5 Merge branch 'master' into ja_20241106_mdm_virtualization 2024-11-13 11:24:55 -05:00
jmarchionatto cdb0a9c480
Add tinder plugin to pluginManagement to allow to run generate-ddl from parent (#6192)
* Add tinder to parent project's pluginManagement

* Use specific version to avoid inheriting projects to replace by theirs

* Move dialects down to executing project because appendFile included in postgres dialect precludes to define it at the parent level

* Improve logging

* Use temporary project version

* Revert "Use temporary project version"

This reverts commit 24f5e648ed.

* Increment version

* Increment missed version

* Added headers

* Document new command

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-11-10 09:21:24 -05:00
dotasek ef78b46621
Bump org.hl7.fhir.core to 6.4.0 (#6410)
* Add missing implementations + update changed classnames

* Fix breaking test due to new validation rules

* Add changes.yaml

* Bump to HAPI version 7.7.1-SNAPSHOT

* Copyright autogen

***NO_CI***

* Bump to HAPI 7.7.2-SNAPSHOT
2024-11-07 13:10:58 -08:00
James Agnew 96e1c2a5db
Add extension for disabling search params (#6107)
* Combo permutations

* Work on combo

* Add tests

* Add changelog

* Spotless

* Test fix

* Drop label

* Add tests

* Spotles

* Work on disable code

* Cleanup

* CLeanup

* Cleanup

* Add changelog

* Test cleanup

* Review comments

* Spotless

* Compile fix

* Version bump

* Test fix

* Test fixes
2024-11-07 09:11:19 -05:00
James Agnew 20a2c2e1c3 Fixes 2024-11-06 18:01:08 -05:00
James Agnew 4a1880fa89 Work on virtualization 2024-11-06 13:32:00 -05:00
Tadgh 9365ad9509
Revert "Fixes for the translation of parameter issues as part of the output f…" (#6441)
This reverts commit fca3ea4445.
2024-11-05 09:14:18 -08:00
Martha Mitran fca3ea4445
Fixes for the translation of parameter issues as part of the output for $validate-code operation. (#6423)
* Move the validation providers to the test utilities package such that they can be reused.

* Update IValidationSupport.CodeValidationIssue structure such that it meets the FHIR specification. Update RemoteTerminologyServiceValidationSupport and VersionSpecificWorkerContextWrapper translation for issues.

* New tests for issue translation. Move test class to a different package so that we can add another test class.

* Some simplification in the issue API to simplify building of issues.

* Fix compilation errors.

* Update providers to allow multiple responses and add  support for the fetchCodeSystem call through method find.

* Setup the first test for resource validation with remote terminology providers.

* Fix NullPointerException

* avoid calling validateCode for CodeSystem where system is null

* Keep old public API methods (and class name) in IValidationSupport and mark them as deprecated to avoid breaking dependencies.

* Revert local change to debug for duplicate errors.

* Add more test cases for resource validation. Throw exception to signal missing test setup to make it obvious.

* Simplify test setup.

* Add some more javadoc

* Add javadoc for the new test class

* Add more tests

* Address code review comments in IValidationSupport.

* Add changelog
2024-11-05 09:13:44 -08:00
Vadim Peretokin a52578e798
Fix wording of _include (#6432) 2024-11-04 10:23:56 -05:00
James Agnew f17e5fbb4e
Second attempt at improving auth handling (#6382)
* Revert "Revert "Improve auth interceptor operation handling (#6278)" (#6381)"

This reverts commit 422d4f0741.

* Move changelog
2024-11-01 07:41:08 -04:00
James Agnew c5476532b7
Credit for #6224 (#6418) 2024-10-30 10:09:12 -04:00
Ibrahim e43c140a24
Refactor BaseHapiFhirDao.getOrCreateTag method to run in a separate thread for XA transaction compatibility (#6224)
* Fix typo in docs.

* Refactor the use of ConcurrentTaskScheduler to use the non-deprecated constructor.

* Refactor getOrCreateTag method to prevent transaction suspension for XA transaction compatibility

    The getOrCreateTag method previously used a propagation behavior that caused issues with
    XA transactions when using the PostgreSQL JDBC driver. The PGXAConnection does not support
    transaction suspend/resume, which made it incompatible with the existing propagation strategy
    'PROPAGATION_REQUIRES_NEW'.

    This refactor changes the getOrCreateTag logic to perform a lookup/write in a new transaction
    as before, but running in a separate thread, such that the main transaction is not suspended.
    The result is retrieved through a future.

    This change aims to improve compatibility and prevent transaction-related issues when using HAPI-FHIR with
    XA transactions and PostgreSQL.

    Closes #3412

* Refactor tag creation logic and handle concurrent access:

- Simplified tag creation by removing unnecessary transaction complexity, since we allow duplicate tags in hfj_tag_def from #4813
- Removed redundant retry logic based on updated DB constraints
2024-10-30 10:06:45 -04:00
Michal Sevcik ba05db1097
Configurable submit ResourceModifiedMessage immediately if of type Subscription, store in DB on failure (#6395)
* Attempt to submit ResourceModifiedMessage immediately, store in DB on failure

* Configurable immediate submission of Subscription

* Formating

* Change setting from JPA to Subscription Settings

* Formating

* Add configurable interval of subscription submission

* Add unit test covering the new logic for immediate subscription submission

* Credit for #6395

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-10-29 13:17:59 -04:00
Jens Kristian Villadsen b6c27cd933
Missing split of auditevents (#5373)
* Simple test showing missing auditevent

* Added one more test and fix to the bug

* Removed unused variable

* Added changelog

* Corrected based on feedback
2024-10-28 14:54:12 -07:00
Jens Kristian Villadsen 0235c517f8
Update version.yaml (#5763) 2024-10-28 10:45:14 -07:00
Jens Kristian Villadsen 0f545586e9
Update version.yaml (#5762) 2024-10-28 10:45:03 -07:00
volodymyr-korzh ebe140ef5b
Release V7_4_5 mergeback (#6393)
* mergeback for 7.4.5

* backport - fixing bug with fulltext and jpa search filters (#6374)

* 2024.08.R05 backport - version bump

---------

Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>

* Updating version to 7.4.5

---------

Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
2024-10-25 18:12:13 -06:00
James Agnew 71cb097aa6
Add author searchin to NPM package search (#6398)
* Add author searchin to NPM package search

* Add changelog

* License header

* Address review comments
2024-10-25 17:01:02 +00:00
SIJIE MEI 6784ac528a
Fix tests about elementsSubset (#6399)
* fix: elementSubset order issue

* change import asserthat
2024-10-24 12:23:44 -04:00
Tadgh 443b59a78b
Bump For February Release (#6392)
* Bump Version

* new versions, new folder
2024-10-21 21:03:07 -07:00
Tadgh 60ed1fd225
Rel 7 4 mb 20241018 (#6385)
* 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 2275eba1a0.

* 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

* Attempt fix for npe (#6213)

* wip

* wip

* wip

* remove whitespace

* Add test

* changelog

* Version bump

* Updating version to: 7.4.1 post release.

* Backport for 7.4.2 (#6303)

* version bumps and change log

* cherry pick 6420

* various updates to changelogs

* build formatting changes

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>

* Updating version to: 7.4.3 post release.

* Backport for 7.4.3 (#6322)

* Composite unique search parameter with dateTime component does not reject resource duplication (#6318)

* Composite Unique Search Parameter with dateTime component does not reject resource duplication - failing tests

* Composite Unique Search Parameter with dateTime component does not reject resource duplication - implementation

* Composite Unique Search Parameter with dateTime component does not reject resource duplication - changelog and test fixes

* 2024.08.R03 backport - version bump

* merge conflicts

* conflicts

* Updating version to: 7.4.4 post release.

* bumping fhir core version (#6364)

* bumping fhir core version

* default methods

* adding changelog

* fixes

* remove commented out code

* version bump and some minor test fixes

* version bump

* changelog

* review fixes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* Fix up folders, rewrite changelog

* Add support for response parameter issues for `validate-code` operation (#6360)

* Add support for response parameter issues for validate-code operation. Implement workaround for missing error for invalid codes by adding an issue when it is absent.

* address minor code review comments

* revert functionality of adding original code from remote validate-code call to the CodeValidationResult

* revert change to FhirInstanceValidatorR4Test

* Revert some of the code review addressal after responding.

* Remove populating message in success scenarios.

* Fix compilation failure in test after reverting method rename.

* Revert change to populate the code from the response again as it implies more refactoring.

---------

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Backport info

* resolution

* bad merge

* wip

* spotless

* duplicate changelog

* bad merges

* Fix NPE

* Test failure

* wip

---------

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: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2024-10-21 09:07:28 -07:00
James Agnew a59f009b95
Revert "Added support for HTTP HEAD against metadata endpoint (#6152)" (#6387)
This reverts commit 3e715665a1.
2024-10-18 19:14:03 -04:00
dotasek 0170145d95
Fix core version in 7.6.0 changes.yaml (#6384)
Changelog is missing last update to org.hl7.fhir.core
2024-10-18 10:17:54 -07:00
James Agnew 422d4f0741
Revert "Improve auth interceptor operation handling (#6278)" (#6381)
This reverts commit 2b3858572d.
2024-10-18 09:01:04 -04:00
James Agnew 2b3858572d
Improve auth interceptor operation handling (#6278)
* Fix #6258 - Improve auth interceptor operation handling

* Cleanup
2024-10-18 07:21:24 -04:00
Jens Kristian Villadsen 3e715665a1
Added support for HTTP HEAD against metadata endpoint (#6152)
* Added support for HTTP HEAD

* Renamed file to issue number and added issue number

* Moved to 7.6
2024-10-18 05:45:04 -04:00
TipzCM 5b23e1bbec
fixing bug with fulltext and jpa search filters (#6374) 2024-10-17 14:46:21 +00:00
Brenin Rhodes 161a077f2a
Update Clinical Reasoning to 3.13.0 (#6358)
* Update Clinical Reasoning to 3.12.0

* Update to 3.13.0

* add stub for new not document parameter

* Add new client Timezone header and enhance JsonUtil to handle ZonedDateTime.

* Add StringTimePeriodHandler and test.  Add new code to DateUtils and new test class.  Inject StringTimePeriodHandler into MeasureOperationsProvider and CareGapsOperationProvider.   Change CareGapsOperationProvider to take String params instead of IPrimitiveType<Date>.

* Remove old LibraryEvaluationOperationProvider

* Fix test

* Fix tests

* Add $data-requirement parameters to docs

* Update docs for new measures timezone header.

* Add prefetchData parameter to $apply doc

* Add changelog

* Fix test

* Update snapshot version

* Add new $extract parameters to docs

* Remove old test

* fix test and properties for care-gaps

* Fix dstu3 config

* remove property for fhirserverurl

* update upgrade.md doc

* fix formatting of upgrade doc

* comment on measureidentifier param

* nonDocument parameter inclusion

* java doc on care-gaps

* No longer dead code.

* Spotless.

* Change CareGapsOperationProvider to R4 BooleanType.

* Update to release

* change log update

* change log edit

* cleanup

* Use existing bean

* spotless

* Ensure CollectDataOperationProvider uses StringTimePeriodHandler to convert periods.

* Spotless.

* Add tests for id

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* cleanup and comments

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md

Implement code reviewer suggestion on timezone docs

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md

Implement code reviewer suggestion on timezone docs

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md

Implement code reviewer suggestion on timezone docs

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md

Implement code reviewer suggestion on timezone docs

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Code review feedback:  Add logging for StringTimePeriodHandler.

* Spotless.

* cleanup

* Code review feedback:  measures.md style changes.  Change code 2560 to 2561.

* Change error code.

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
2024-10-17 08:38:42 -04:00
Nathan Doef 8f52f1c769
Fix Regression (#6376)
* failing test

* fix
2024-10-17 07:12:21 -04:00
James Agnew 4ab958a58f
Add hash identity token mode (#6375)
* Add hash identity token mode

* Spotless

* Test fix
2024-10-16 22:08:43 +00:00
Michael Buckley d4227baf2a
Add partition_id to search joins (#6325)
* Failing test

* cleanup

* revert partition in group by clause

* test update for new joins

* Give up on nullable join

:not joins require sub-selects
and the nullability can't
support an in(select ) clause.

Bring in flag, and set based on partition settings

* spotless

* changelog

* cleanup

* cleanup

* fixmes

* partitioned sql test

* get sort tested

* revert tests expecting nullable partition joins

* Fix result set parsing when coord-sort is present.

* Cleanup sql test

* Change to default select partition_id

Add sort test cases.

* Fix everything sql

* Fix everything sql

* Fix group-by on offset path

* More sql test fixups

* More sql test fixups

* Test case for cache key

* review feedback

* Revert to HFJ_RES_VER_PROV until we get the migration

* fix for everything from james

* fixme

* Revert column name

* Cleanup

* Test fix

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-10-16 15:19:20 -04:00
David Raeside 3acc95d45b
7.5.0 snapshot midcycle branch mergeback (#6371)
* 6323 resource creation deadlock (#6324)

* make map reads concurrent

* change log

* CUstom version number for guaranteed build determinism

* licenses

* Expand translation cache (#6341)

* Expand translation cache

* Add changelog

* Correction to #6341 (#6342)

---------

Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-10-16 12:37:56 -04:00
Martha Mitran 7581920a15
Add support for response parameter issues for `validate-code` operation (#6360)
* Add support for response parameter issues for validate-code operation. Implement workaround for missing error for invalid codes by adding an issue when it is absent.

* address minor code review comments

* revert functionality of adding original code from remote validate-code call to the CodeValidationResult

* revert change to FhirInstanceValidatorR4Test

* Revert some of the code review addressal after responding.

* Remove populating message in success scenarios.

* Fix compilation failure in test after reverting method rename.

* Revert change to populate the code from the response again as it implies more refactoring.

---------

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2024-10-16 10:16:41 -04:00
craig mcclendon 5462471579
fix for 6199 - search include on sqlserver fails (#6365)
* fix for 6199 - search include on sqlserver fails

* fix sql server tests to reflect new orderby col

* noop - force PR rebuild

* spotless formatting fix

* Add a test and rework to use in other SQL

* Fix offset

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-10-16 07:13:59 -04:00
James Agnew d2d6b5959b
Add license headers (#6373) 2024-10-15 21:23:22 -04:00
TipzCM eadd8c6f0d
improved performance of date searching (#6353) 2024-10-15 16:56:35 -04:00
jdar8 96cc20dc0d
add delete partition pointcut (#6314)
Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
2024-10-15 13:53:58 -06:00
JasonRoberts-smile b08c59528d
Jr 20241008 merge data absent reason (#6370)
* handle single cardinality case

* multiple cardinality case

* change log
2024-10-15 11:47:32 -04:00
Michael Buckley 239bf8d441
Add ChainedDelegateConsentService with pluggable vote strategy
Introduce some plumbing utils to combine consent votes.
2024-10-14 20:13:14 +00:00
jdar8 6a365f8722
add batch and chunk ids to logging context (#6268)
* add batch and chunk id to logging mdc context, test

* changelogs

* spotless

* address code review comments

* Update changelog from code review comment

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2024-10-11 10:47:15 -06:00
Mathieu Stempell 0daa1a0fde
fix(BundleFetcher): correct API URL (#6356) 2024-10-08 10:49:33 -04:00
Max Bureck 9a73079c33
Improving performance, using caching when testing for primitives (#6252) (#6253)
* Improving performance, using caching when testing for primitives (#6252)

Caching primitive type names for faster lookup if a type is primitive.

* Credit for #6253

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-10-08 09:29:42 -04:00
Ken Stevens 6f94e228b0
batch2 new svc methods (#6310)
* started work on adding new methods

* started work on adding new methods

* review feedback. move dto from api to model

* checkstyle
2024-10-08 08:57:00 -04:00