Commit Graph

1807 Commits

Author SHA1 Message Date
Tadgh 377e44b6ca
attribution and pom change (#6309) 2024-09-25 20:38:22 +00:00
Martha Mitran 20d3e6bb25
Fix missing qualifier search for reference search parameters (#6306)
* Fix missing qualifier search for reference search parameter. Reuse tests and run them for both indexing enabled and disabled.

* Fix edge case where the search parameter has multiple paths. Add a test. Fix some of the compile warnings in a test class.

* Fix test setup.
2024-09-24 23:46:38 +00:00
Aditya Dave 1fad912193
6262 cds hooks returns 400 when extension passed in the cdsservicerequestjson (#6274)
* fail test

* potential fix

* spotless

* alternative fix

* spotless

* remove the new method and replace usage for the old one

* spotless

* fix issue with context failing deserialization

* add validation for context, hook and hook instance

* spotless

* add message codes

* spotless

* changelog

* cleanup

* spotless

* bump version to 7.5.1-SNAPSHOT
2024-09-18 10:01:17 -04:00
TipzCM 02d38bce14
removing unneeded fields from HRJ_RESOURCE table (#6284) 2024-09-13 16:33:40 +00:00
dotasek d9f3ac1c3b
Bump org.hl7.fhir.core to 6.3.23 (#6266)
* Bump org.hl7.fhir.core to 6.3.23

* Fix breaking test (check for no value and null)

* Fix typo
2024-09-06 14:51:05 -04:00
jdar8 12765ac397
Disabling enforce referential integrity on write still checks references (#6219)
* fix

* tests, changelog, spotless

* document tests better

* address review comments

* reset settings so other tests don't fail

* unused import

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
2024-09-06 13:16:49 -04:00
JasonRoberts-smile 0f2eb08a77
Jr 20240830 merge references (#6263)
* enhance clone operation

* change log
2024-09-05 12:20:28 -04:00
jdar8 46d4e28d59
7.2.3 mergeback (#6247)
* 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

* version bumps

* Patient everything operation with offset query parameter throws exception (#6085)

* Patient $everything operation with _offset query parameter throws exception - tests and implementation
* Patient $everything operation with _offset query parameter throws exception - added changelog

* 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>

* 6420 change test to use hamcrest

* change test back to use assertj

* add backports to changelogs

* remove unused imports, add copyright header from build

* fix falsely identified changes

* bring missed version enum changes in

* spotless

---------

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: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
2024-08-28 14:51:29 -06:00
volodymyr-korzh 18293eba89
Release V7_0_3 mergeback (#6249)
* added docs for 7.0.3

* mergeback rel_7_0_3

* spotless fix

* changelog update for 6099 - Use lockless mode when adding index on Azure Sql server
2024-08-28 08:58:21 -06:00
Jonas Beyer 049c28d3e6
close ResultSets in JdbcUtils (#6206)
* close ResultSets in JdbcUtils

* Credit for #6206

* Apply spotless

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-08-28 08:11:22 -04:00
Etienne Poirier 5e48e38b1d
6203 subscriptionvalidatinginterceptor allows invalid url for rest hook endpoint (#6225)
* 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>

* initial failing test

* providing capability to tailor resthook endpoint url validation through supplied regex

* adding necessary import.

* conformance with spotless

* adding tests

* adding test for payload

* spotless

* adding changelogs

* passing all tests

* passing all tests

* no-op commit to kickstart the pipeline.

* - slight modification to the solution;
- spotless;

* pre-code review submission.

* moving validator instantiation to the submitter configuration so it is create along side the subscriptionValidatorInterceptor

* last min tweeking before submission for review.

* fixing spotless post merging in master

---------

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: 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: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
2024-08-28 07:20:49 -04:00
Ken Stevens 48d8fac6ea
fix patientId interceptor partition selection (#6236)
* fixed

* fixed

* detect uuid references earlier in the PatientIdPartitionInterceptor

* TODO
2024-08-27 16:06:42 -07:00
acoteathn 554bb08d01
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>
2024-08-27 10:36:41 -04:00
dotasek 19af077c2a
Bump dependencies (#6235)
* Bump elasticsearch version

* Bump htmlunit version

* Bump bower/moment version

* Changes

***NO_CI***
2024-08-27 07:38:18 -04:00
Tadgh 947291e7f5
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 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

* 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>
2024-08-20 09:03:09 -07:00
Etienne Poirier 3e2d84d0f7
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>
2024-08-19 14:53:50 -04:00
volodymyr-korzh 568c6d20db
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 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

* 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>
2024-08-14 15:03:35 -06:00
Aditya Dave 4368e33fda
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
2024-08-09 18:52:05 +00:00
jdar8 fd5cff3d23
5138 enhance existing historical link with mactchResultMap field (#5213) 2024-08-01 09:49:19 -04:00
Michael Buckley cd43523afe
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>
2024-07-26 08:59:24 -04:00
Tadgh 497eb6002f
Correct a typo (#6136) 2024-07-20 14:09:40 -07:00
Alberto Acebes 17158c071a
Adding Eviden BSD R&D Spain to the Atlas (#6132)
Adding Eviden BSD R&D Spain to the Atlas by adding an entry to points.json
2024-07-19 08:06:57 -04:00
Long Ma 406db339ce bump to 7.5.0-snapshot 2024-07-16 12:25:25 -06:00
Long Ma 39cbec8aa4 Merge branch 'rel_7_4' of https://github.com/hapifhir/hapi-fhir into rel_7_4 2024-07-16 12:24:29 -06:00
Long Ma 0e8f474b51 revert 6e208f16ec 2024-07-16 12:24:19 -06:00
Tadgh 88f8a66596
Add attribution (#6103) 2024-07-16 11:08:59 -07:00
Long Ma 6e208f16ec bump to 7.5.0-snapshot 2024-07-16 10:43:14 -06:00
TipzCM 7e7aae6060
batching subscription msgs (#6084) 2024-07-16 09:22:35 -04:00
jmarchionatto 5f9b40e3f5
Allow overriding RestfulServer's contextPath (#6113)
* Move IncomingRequestAddressStrategy::determineServletContextPath into IServerAddressStrategy to permit overriding (#6038)

* add changelog

* add contributor as developer

---------

Co-authored-by: Alex Kopp <akopp@athenahealth.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-07-15 16:24:17 -07:00
Etienne Poirier e07684474f
Cleanup work following merge of 6101 (#6110)
* - reverting commented out changes
- removing personal todo

* removing changelog since the related change was reverted.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-07-15 13:47:08 -04:00
TipzCM 875b224ac6
fixing canonical search (#6105) 2024-07-15 13:29:00 -04:00
Justin McKelvy d2c12a7ac3
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
2024-07-12 18:24:26 -07:00
Renaud Subiger b6bcb292b6
Use server name as narrative text in CapabilityStatement (#6060)
* Use server name as narrative text in CapabilityStatement

* Credit for #6060

* Fix spotless

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-07-12 16:56:28 -04:00
jdar8 ec7538c78f
Jd 20240704 fix mdm phonetic matching on humanname exception (#6078)
* failing test

* fix and changelog

* edit changelog issue number

* mvn spotless

* address code review comment

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
2024-07-12 09:54:45 -07:00
volodymyr-korzh 6c446277e3
Patient everything operation with offset query parameter throws exception (#6085)
* Patient $everything operation with _offset query parameter throws exception - tests and implementation
* Patient $everything operation with _offset query parameter throws exception - added changelog
2024-07-11 15:24:54 -06:00
Aditya Dave 16b002d1dd
fix changelog (#6093) 2024-07-10 18:04:31 +00:00
Etienne Poirier c235488580
6090 requestpartitionhelpersvc throws an unexpected exception when resolving partition for non partitionable resource (#6092)
* initial failing test.

* fix and test modification

* adding changelog

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-07-10 10:59:17 -04:00
VK-SMILECDR e3f64c23a2
logback test extention assert (#6087)
* initial check-in

* HAPI logback test extension cleanup

* bump version

* revert mistake change

* changes based on review
2024-07-09 20:06:06 +00:00
Aditya Dave ce0160e7f9
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>
2024-07-09 09:45:21 -04:00
Tadgh 3ffb695b6b
increase string value storage length to accomodate larger contains searches (#6037)
* wip test writing

* add test to ES suite as well

* wip

* Changelog

* spotless

* Address review comments

* Test corrections

* Fixes for tests

* Fix changelog
2024-07-09 06:54:24 +00:00
Tadgh fee1b75242
6056 drop derby jars (#6057)
* Remove most of derby, add changelog

* Upgrade information

* Upgrade notes, bump to jdk17 version

* Fix issue#
2024-07-08 22:50:17 +00:00
Luke deGruchy ef0aa11e00
Introduce TRM_CONCEPT_DESIG.VAL_VC column to replace VAL (#6080)
* Extend TRM_CONCEPT_DESIG.VAL column from 2,000 to 4,000 characters.

* Increase to 8,000 chars.  Add jira to changelog.

* Implement new design.   Still needs new/updated tests.

* Fix setter.

* Make both columns nullable.  Fix changelog.  Add better error message for HapiMigrator.

* Enhance test.

* Small code review suggestion.

* Cosmetic change to re-trigger build.
2024-07-08 18:19:33 +00:00
Martha Mitran ecef72729f
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
2024-07-05 22:23:07 -07:00
James Agnew 5e519810ff
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
2024-07-05 12:05:58 -04:00
TipzCM 371aad2b08
fixing deprecated thymeleaf syntax (#6064) 2024-07-04 15:08:26 +00:00
dotasek 724339c886
Bump jetty_version from 12.0.3 to 12.0.9 (#6022)
* jetty_version from 12.0.3 to 12.0.9

* Changelog

* Try to resolve test issue

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-07-02 08:22:18 -07:00
Luke deGruchy 34da5c1b34
Ensure DropPrimaryKeyTask respects dry-run (#6062)
* Remove code to SQL query from BaseTask.  Move code to DropPrimaryKeyTask and gate it for NOT dry-run.

* Update hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropPrimaryKeyTask.java

Commit code review suggestion

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>

* Code review feedback.

* Code review feedback.

* Remove isTransactional().

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
2024-07-02 09:22:55 -04:00
TipzCM 2fc873d3b6
added PATCH (#6059) 2024-06-28 11:53:22 -04:00
TipzCM 315a05eeb8
schema migrator validation skips skippable tasks (#6050) 2024-06-27 13:16:47 -04:00
TipzCM 39396b136f
update release date (#6055) 2024-06-27 15:44:53 +00:00