Commit Graph

419 Commits

Author SHA1 Message Date
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
Etienne Poirier bd31bcb290
emergency fix - reverting changes introduced in 6092 to get pipeline running. (#6101)
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-07-11 21:26:39 +00:00
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
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
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
Etienne Poirier aafa445d19
Wrapping $meta-add and $meta-delete operation in transactionService execution to support partitioning (#6082)
* wrapping metaAdd/Delete operation in transactionService.execute to have the tenant acknowledged by Spring.

* spotless happiness.

* fixing broken test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-07-08 07:33:02 -04:00
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 90251b31ab
fixing issue with infinite cache refresh loop (#6045)
* fixing step 1

* spotless

* cleanup

* cleanup

* cleanup

* review fixes

* review fix

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-06-27 09:27:33 -04:00
James Agnew 7224245217
Combo SearchParameter improvements (#5885)
* Start supporting combo refs

* Work on error codes

* Add tests

* Work on tests

* Fixes

* CLeanup

* Add changelog

* Test fixes

* Test fix

* Clean up tests

* Test cleanup

* Work on tests

* Revert change

* Optimize storage

* Add tests

* Work on tests

* Update docs

* Spotless

* Test fixes

* Revert breaking change

* Merge

* Bump guava

* Address review comments

* Test fixes

* Test fix

* FIx tests

* Address review comments

* Spotless

* Test fix

* Revert change
2024-06-27 08:42:04 -04:00
TipzCM 7b68c4d91d
fixed validation issue (#6041)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-06-25 15:10:26 -04:00
Luke deGruchy d4e3698f37
Handle conditional creates across partitions with duplicate search URLs by updating ResourceSearchUrlEntity (#5983)
* First commit.

* SQLs in test class work for Postgres.

* Refine DropPrimaryKeyTask.  Add migration code to do all operations except drop and add primary key.   Comment out stub test code to do all non drop and add primary key operations.  Add verification code to test to verify schema and record counts.

* Oracle drop primary key working.

* Oracle drop primary key working in test code.  Proper drop primary and add primary key tasks working in H2.

* Migration tests work on all 4 databases.

* Spotless.

* Fix compile error.

* Add hapi error codes for new Exceptions.

* Add another hapi error code.

* Cleanup TODOs.  Fix error codes.  Spotless.

* Add new partition conditional create test.  Fix bug from merging tasks class.  Add new unit Add changelog without hapi-fhir issue.

* Add test for conditional create with partitions.

* Fix TODOs.  Reverse unneeded changes.  Rename changelog.  Refinements.  Javadoc.

* Tweak changelog.

* Rename config key internally.  Spotless.

* Fix a newly introduced bug.  Cleanup.  Tweak changelog.

* Small fix.  Spotless.

* Fix compile error.

* Spotless.

* Address code review comments.

* Address more code review comments.

* Fix test.

* Fix test.
2024-06-25 12:11:47 -04:00
volodymyr-korzh 0397b9ddc8
Reduce storage required for indexing - stop writing sp_name, res_type, and sp_updated to hfj_spidx_* tables (#5941)
* Reduce storage required for indexing - implementation
2024-06-20 14:10:40 -06:00
TipzCM 5799c6b42b
hibernate search cannot be used for count query if non-active parameters are present (#6027)
fixing count query with fulltextsearch bug
2024-06-19 22:21:20 +00:00
Martha Mitran 472984ac65
Document pointcut to use to modify request parameters (#6019)
* Document pointcut to use to modify request parameters. Add a test to exemplify.

* Add another alternate pointcut to use
2024-06-18 21:57:04 +00:00
Tadgh 61b5103535
Final hamcrest conversions (#6015)
* wip

* wip

* revert'

* Delete existing things

* docs

* removing last of hamcrest

* removing last of hamcrest

* manual fix

* remove matchers used in awaitility

* remove matchers used in awaitility

* Final checkstyle removals

* Disable suppression rule for mdm checkstyle

* Fix some awaitility, remove dead matchers

* manual fixes

* manual fixes

* filter all hamcrest mentions

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-06-18 20:46:09 +00:00
James Agnew 47d6e357b6
Fix JPA nullable primitive columns (#5926)
* Fix JPA nullable primitive columns

* Add changelog

* Spotless

* License headers

* Migration fix

* Spotless

* Cleanup

* Cleanup

* Add task skipping

* Update docs

* CLeanup

* Spotless

* Address review comments

* Test fix

* HAPI FHIR version bump
2024-06-18 13:05:29 -04:00
James Agnew ec0021cd40
Add error checker for duplicate codesystem codes (#6014)
* Add error checker

* Add changelog

* Address review comment
2024-06-18 14:25:07 +00:00
James Agnew 8947706af3
Handle Versioned Canonical Refs (#6003)
* Work on versioned canonidal refs

* Merge

* Tests working

* Working without version support

* CLean refactor

* Targets

* Remove redundant parameter

* Fix up tests

* Remove fixme

* Add changelog

* Improve changelog

* Update version

* Test fixes
2024-06-17 08:14:24 -04:00
Tadgh 73a6a8ef82
Add tests to checkstyle (#6006)
* Add tests to checkstyle

* Add includede test dirs in execution

* wip

* wip

* bump checkstyle deps

* bump checkstyle deps

* wip50

* wip

* Handle upgrade

* triple-wip

* wip

* Wip replacement of prints

* All checkstyle now passing

* wip

* Reset checkstyle

* spotless

* reset checkstyle

* Add checkstyle to pipeline

* Tidy

* Tidy

* wip

* Cut over to not empty for correct behaviour

* imports
2024-06-15 17:15:46 -07:00
Ken Stevens 57d1815b46
Extract Subscription Settings from Storage Settings (#5887)
* first cut

* first cut

* cleanup

* that took way too long

* fix test

* licenses

* merge master

* merge master

* changelog

* review feedback

* bump version
2024-06-15 00:31:55 +00:00
dotasek 0abbb1a4f4
Core library bump 6.3.11 (#5772)
* Bump to core 6.2.6 + fix compilation errors

* Fix signature error

* Error ordering

* WIP 1 Fixing failing tests

* Fix FhirInstanceValidatorR4Test

* Fix FhirInstanceValidatorR5Test

* Fix FhirInstanceValidatorR4BTest

* Fix FhirInstanceValidatorDstu3Test.testValidateBuiltInProfiles()

* WIP Fix FhirInstanceValidatorDstu3Test

* Fix isPrimitiveType

* Add placeholder narratives to ServerCapabilityStatement

* Fix QuestionnaireResponseValidatorR4Test

* Newline cleanup

* Fix QuestionnaireResponseValidatorDstu3Test

* Fix QuestionnaireResponseValidatorR5Test

* Increase expected error messages by two because VALIDATION_HL7_WG_NEEDED

New validation requirement as of 2023-09-16

* Add placeholder fix for Balp narrative

* Fix expected validation messages

* Fix more expected validation messages

* Don't generate a master IPS narrative

* Fix IPS generation tests expecting old composition narrative

* Update fhir core and clinical-reasoning

* Remove commented code

* Bump to core 6.2.16-SNAPSHOT

* Add missing methods

* Add missing methods 2

* Fix error codes

* Fix error code

* Fix failing tests for Unsupported method 2488

* Fix error text

* Fix another expected error message

* Apply spotless

* Fix error strings

* Add minimal implementation to fix failing test

* Fix error message

* Fix some validation tests (r4)

* Fix more R5 tests

* Update for changing API

* Fix some R4B test failures

* Fix android incompatibility

* Fix more tests

* Switch back to LF

* Fix more tests 2

* Fix R4 IPS generation use of relative references, switch to random UUID

* Fix missing codes and patient ID in IPS test

* Fix missing codes in IPS R4 Test 2

* Fix display value

* Fix display value

* Reorg wrapper issue collection; fixes errors with Balp and others

* Update for API changes

* Fix code set typo causing test failure

* Fix DiffProviderR4Test

* Fix RepositoryValidatingInterceptorHttpR4Test fails

due to stricter code validation

* More code fixes

* Don't expect an extra error.

* Use more specific logic for details tx code

* Catch expected error

* Clean up

* Account for HAPI isEnabledValidationForCodingsLogicalAnd cases

* Apply spotless

* Change outputs for en_US single code test

* Add missing system from code to pass validation

* Account for DSTU3 and R4 including different code systems for race

* Add expected loinc codes to test dao

* Add some codesystem support for test

* Bump core version

* WIP pass on a list of CodeValidationIssue from CodeValidationResults

* Re-use v2 and v3 data from r4 in r4b

* CodeSystems can be supported, but not have a resource

* Remove hack around unitsofmeasure + return false LookupCodeResult

* Clean up chatter.

* Update test cases, remove FIXME

* Stop returning before adding all issues to ValidationResults

* Update for changes in core API

* Add severity to code issues + return to unknown system support

* Use new CollectionUtils

* Fix more issue messages and orders + null in TermReadSvcImpl

* After checking valueSet, also check codeSystem

* On second thought, always check the codesystem

* Improve validation message

* Refactor

* Add error consistent with core validator results

* Decrement query counts for validation

* Improve code validation messages + don't miss invalid display on cs

* Fix expected messages (added code details)

* More expected message fixes

* Remove redundant text from diagnostics + match core exception handling

* Explicitly send tx passthrough messages no longer managed in core

* Apply spotless

* Add issue to code validation in TermReadSvcImpl

* Adjust indexes of expected errors now that TermReadSvc is reporting

* Bump to released core version

* Code cleanup: commented code

* More commented code cleanup

* Fix parameter names

* Use Set.of and List.of + fix duplicate values in set

* Revert animal sniffed breakage, make field private

* Add comments to describe disabled test

* Remove System.out chatter

* Fix javadoc generation for r5 structures module

* More comments and move disabled annotation

It was working when it left the shop.

* Move older changelog into 7.4.0 and create core update changelog

* Switch changelog type to change

* Bump HAPI version

* Add validation utils for FATAL issue severity

* Handle FATAL codeValidationIssue severity

* Fix test (validation throws more warnings)

* Bump to version 7.3.4-SNAPSHOT

* Bump to SNAPSHOT version of core + add necessary method implementations

* Add comments to explain R4 terminology resources in R4B

* Add test for Observation vital signs profile validation

* Try using default validatorPolicyAdvisor

* Return an empty set for fetchCanonicalResourceVersions

* Profile now gives more explicit error instead of valueSet

* Revert commit

* Add CodeValidationIssues and additional error info

* Do not return first successful match from codings. Check all.

+ adjust for extra errors.

* apply spotless

* Fix failing test, add comments re: invocations

* Fix test to expect more informative error

* Fix stray compilation errors from merge.

* Fix merge overwrite of validation messages and indices

* Fix merge overwrite of new validation results

* Use core release 6.3.11

* Update HAPI version to 7.3.5-SNAPSHOT

* Fix changelog

* Remove commented code

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
2024-06-12 11:24:26 -06:00
Tadgh 432167011d
Fix a regression in Valueset Expansion (#5993)
* Add forgotten ISA

* revert non-standard property behaviour on is-a match type

* Changelog
2024-06-07 22:57:10 -06:00
Justin McKelvy 590fe26a76
5914 clinical reasoning v3.6.0 bump (#5964)
* version bump clinical reasoning wip

* cr release 3.6.0 bump

* versio bum hapi to 7.3.4-snapshot

* cve dependency removed

* fix merge back issues on pom

* jackson update missed
2024-06-07 09:43:19 -07:00
TipzCM 5b75639718
fixing value expansion filtered by url (#5969)
* test

* adding support for expansion based on filters and properties

* added changelog

* adding test cases

* spotless

* fixed some warnings

* spotless

* merge conflict resolution

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-06-06 11:41:38 -07:00
Martha Mitran 00a6591586
Merge pull request #5978
* Fix authorization handling for Bundle resources in the output. When t…

* Merge remote-tracking branch 'origin/master' into mm-20240529-test-se…

* Add test case for the described scenario

* Merge remote-tracking branch 'origin/master'

* Add Bundle search test with custom search parameters.

* Update test to simpler one to illustrate the problem

* SearchParameter for Bundle document referencing resource through comp…

* Merge remote-tracking branch 'origin/master' into mm-20240605-search-…

* Merge another test into the new class

* Remove unused json file. Small formatting fix in a test.

* Add more use cases and adjust an existing one
2024-06-06 10:09:30 -07:00
Ken Stevens cdf5b602c1
Replace hamcrest with assertj (#5911)
* optimize imports

* optimize imports

* Hamcrest replacement

* Hamcrest replacement

* Test failures

* migrate hapi-fhir-base

* docs

* Few more cutovers

* Full rewrite of all assert cases

* Full rewrite of all assert cases

* Partial cutover

* assert library conversion

* wip

* fix imports

* remove equalto

* once-over again

* minor cutover

* wip

* wip

* wip

* wip

* wip

* Remove hamcrest asserts replace with assertj

* wip

* Partial hamcrest rip-out

* More hamcrest stripping

* wip

* Partial completion

* spotless

* it compiles now

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fixing compile issues

* fix compile issues

* fix compile issues

* hapi-fhir now compiles

* fix test

* fix test

* fix test

* fix tests

* fix tests

* fix tests

* fix test

* fix test

* fix tests

* fix tests

* fix tests

* yay all tests pass now!

* revert assertEquals change

* revert assertEquals change

* organize imports

* organize imports

* organize imports

* post merge cleanup

* organize imports

* more cleanup

* more cleanup

* removing hamcrest stragglers

* removing hamcrest stragglers

* removing hamcrest stragglers

* removing hamcrest stragglers

* removing hamcrest stragglers

* removing hamcrest stragglers

* removing hamcrest stragglers

* removing hamcrest stragglers

* removing hamcrest stragglers

* removing hamcrest stragglers

* removing hamcrest stragglers

* organize imports

* organize imports

* remove final hamcrest stuff

* remove final hamcrest usages

* remove final hamcrest usages

* Revert "remove final hamcrest usages"

This reverts commit eaf5107396.

* fix compile issues from a hacky search/replace

* compiles with fixmes

* fix tests

* fix test

* fix test

* fix post merge compile issues

* fix post merge compile issues

* fix post merge compile issues

* fix post merge compile issues

* fix post merge compile issues

* fix post merge test issues

* fix test

* fix test

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* replace hamcrest with assertj

* all but mdm tests

* final hamcrest removed from hapi-fhir yay!

* revert mdm changes. it's too hard for now

* revert cdr breaking change

* revert cdr breaking changes

* revert cdr breaking changes

* revert cdr breaking changes

* revert cdr breaking changes

* revert changes that break cdr

* merge master with compile errors

* review feedback

* review feedback

* review feedback: revert bad regexp change

* fix test

* fix test

* convert new hamcrest entries

* convert new hamcrest entries

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2024-06-05 16:02:46 -04:00
Martha Mitran a9815c8857
Fix authorization handling for Bundle resources in the output (#5953)
* Fix authorization handling for Bundle resources in the output. When the Bundle is standalone, authorization should not be checked for resources included in the Bundle.

* Add some more tests to cover more use cases.

* Add more tests. Exclude collection type as it can be returned by a custom operation and it is not a standalone type.

* Address code review comment. Remove unused method.
2024-05-28 09:00:06 -04:00
TipzCM f199a3ee4e
added workchunk to step execution details (#5932)
* added workchunk to step execution details

* versino bump

* added deprecated constructor

* spotless

* review fixes

* spotless

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-05-26 21:59:17 -04:00
Luke deGruchy 7f91f1fbf3
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.
2024-05-24 14:30:07 -04:00
Luke deGruchy 0fe3380c4a
Ensure Delete Expunge removes corresponding HFJ_RES_SEARCH_URL records for affected resources (#5940)
* Delete HFJ_RES_SEARCH_URL record when delete expunging a resource.  Add a new foreign key on RES_ID to HFJ_RESOURCE to HFJ_RES_SEARCH_URL.  Add a migration task to set up the new FK.

* Cleanup logging.

* Fix unit test failures and ensure ResourceSearchUrlEntity is created with a ResourceTable.

* Remove TODO.

* Fix more unit tests.

* Add more unit test assertions.

* Add changelog.

* Code review feedback.

* Fix unit test failures due to lazy loading lack of session.

* Reverse original code review feedback changes.
2024-05-22 18:54:40 +00:00
Martha Mitran bff59b6c50
Add support for returning subproperties for RemoteTerminologyService lookup (#5936)
* Add support for returning subproperties in the RemoteTerminologyService

* Add clarifying comments to code. Simplify logic to filter properties.

* Update sub-property iteration logic in the conversion code to make it more readable

* Fix spotless errors

* Add a few more test cases to test property filtering for the lookup
2024-05-16 14:02:53 -07:00
longma1 078e87a4aa
7 2 mergeback may 10 v2 (#5928)
* Enhance RuleBuilder code to support multiple instances (#5852)

* Overhaul bulk export permissions.

* Overhaul bulk export permissions.

* Small tweak to rule builder.

* Cleanup validation.

* Cleanup validation.

* Code review feedback.

* Postgres terminology service hard coded column names migration (#5866)

* updating parent pids column name

* updating name of the fullTestField Search

* updating name of the fullTestField Search

* fixing typo.

* failing test.

* - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity;

- reverting the name of the FullTextField entity to its previous name of 'myParentPids';

- reverting the name of the lucene index to search on in the terminology service.

- updating the changelog;

* making spotless happy

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881)

* initial failing test.

* solution

* adding changelog

* spotless

* moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811)

* Expose BaseRequestPartitionHelperSvc validate and normalize methods

* Compilation errors

* change mock test to jpa test

* change mock test to jpa test

* validateAndNormalizePartitionIds

* validateAndNormalizePartitionNames

* validateAndNormalizePartitionIds validation + bug fix

* validateAndNormalizePartitionNames validation

* fix test

* version bump

* Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883)

* Add failing test as well as commented out potential solution.

* Fix for NumberFormatException.

* Add conditional test for survivorship rules.

* Spotless.

* Add changelog.

* Code review feedback.

* updating documentation (#5889)

* Ensure temp file ends with "." and then suffix. (#5894)

* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Enhance mdm interceptor (#5899)

* Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened.

* Added javadoc

* Cahngelog

* spotless

---------

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896)

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug.

* Add changelog.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml

Commit code reviewer suggestion.

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

---------

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

* Fix query chained on sort bug where we over-filter results (#5903)

* Failing test.

* Ensure test cleanup doesn't fail by deleting Patients before Practitioners.

* Implement fix.

* Spotless.

* Clean up unit test and add changelog.  Fix unit test.

* Fix changelog file.

* Apply suggestions from code review

Apply code review suggestions.

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

* Spotless

---------

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

* cve fix (#5906)

Co-authored-by: Long Ma <long@smilecdr.com>

* Fixing issues with postgres LOB migration. (#5895)

* Fixing issues with postgres LOB migration.

* addressing code review comments for audit/transaction logs.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for TermConcept
 migration post code review.

* applying spotless

* test and implementation for TermConceptProperty
 migration post code review.

* test and implementation for TermValueSetConcept
 migration post code review.

* fixing migration version

* fixing migration task

* changelog

* fixing changelog

* Minor renames

* addressing comments and suggestions from second code review.

* passing tests

* fixing more tests

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* 6051 bulk export security errors (#5915)

* Enhance RuleBuilder code to support multiple instances (#5852)

* Overhaul bulk export permissions.

* Overhaul bulk export permissions.

* Small tweak to rule builder.

* Cleanup validation.

* Cleanup validation.

* Code review feedback.

* Postgres terminology service hard coded column names migration (#5866)

* updating parent pids column name

* updating name of the fullTestField Search

* updating name of the fullTestField Search

* fixing typo.

* failing test.

* - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity;

- reverting the name of the FullTextField entity to its previous name of 'myParentPids';

- reverting the name of the lucene index to search on in the terminology service.

- updating the changelog;

* making spotless happy

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881)

* initial failing test.

* solution

* adding changelog

* spotless

* moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811)

* Expose BaseRequestPartitionHelperSvc validate and normalize methods

* Compilation errors

* change mock test to jpa test

* change mock test to jpa test

* validateAndNormalizePartitionIds

* validateAndNormalizePartitionNames

* validateAndNormalizePartitionIds validation + bug fix

* validateAndNormalizePartitionNames validation

* fix test

* version bump

* Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883)

* Add failing test as well as commented out potential solution.

* Fix for NumberFormatException.

* Add conditional test for survivorship rules.

* Spotless.

* Add changelog.

* Code review feedback.

* updating documentation (#5889)

* Ensure temp file ends with "." and then suffix. (#5894)

* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Enhance mdm interceptor (#5899)

* Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened.

* Added javadoc

* Cahngelog

* spotless

---------

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896)

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug.

* Add changelog.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml

Commit code reviewer suggestion.

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

---------

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

* Fix query chained on sort bug where we over-filter results (#5903)

* Failing test.

* Ensure test cleanup doesn't fail by deleting Patients before Practitioners.

* Implement fix.

* Spotless.

* Clean up unit test and add changelog.  Fix unit test.

* Fix changelog file.

* Apply suggestions from code review

Apply code review suggestions.

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

* Spotless

---------

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

* cve fix (#5906)

Co-authored-by: Long Ma <long@smilecdr.com>

* Fixing issues with postgres LOB migration. (#5895)

* Fixing issues with postgres LOB migration.

* addressing code review comments for audit/transaction logs.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for TermConcept
 migration post code review.

* applying spotless

* test and implementation for TermConceptProperty
 migration post code review.

* test and implementation for TermValueSetConcept
 migration post code review.

* fixing migration version

* fixing migration task

* changelog

* fixing changelog

* Minor renames

* addressing comments and suggestions from second code review.

* passing tests

* fixing more tests

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* refactor bulk export rule, add concept of appliestoallpatients, fix tests

* spotless

* Cahgnelog, tests

* more tests

* refactor style checks

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>

* Convert a few nulls to aggressive denies

* Change chain sort syntax for MS SQL (#5917)

* Change sort type on chains

* Change sort type on chains

* Test for MS SQL

* Comments

* Version bump

* version bump to 7.3.1-SNAPSHOT

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
2024-05-13 15:51:03 -07:00
Tadgh 3572d593c1
Revert "7_2 branch mergeback (#5922)" (#5927)
This reverts commit 125513a100.
2024-05-12 16:04:43 -07:00
longma1 125513a100
7_2 branch mergeback (#5922)
* Enhance RuleBuilder code to support multiple instances (#5852)

* Overhaul bulk export permissions.

* Overhaul bulk export permissions.

* Small tweak to rule builder.

* Cleanup validation.

* Cleanup validation.

* Code review feedback.

* Postgres terminology service hard coded column names migration (#5866)

* updating parent pids column name

* updating name of the fullTestField Search

* updating name of the fullTestField Search

* fixing typo.

* failing test.

* - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity;

- reverting the name of the FullTextField entity to its previous name of 'myParentPids';

- reverting the name of the lucene index to search on in the terminology service.

- updating the changelog;

* making spotless happy

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881)

* initial failing test.

* solution

* adding changelog

* spotless

* moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811)

* Expose BaseRequestPartitionHelperSvc validate and normalize methods

* Compilation errors

* change mock test to jpa test

* change mock test to jpa test

* validateAndNormalizePartitionIds

* validateAndNormalizePartitionNames

* validateAndNormalizePartitionIds validation + bug fix

* validateAndNormalizePartitionNames validation

* fix test

* version bump

* Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883)

* Add failing test as well as commented out potential solution.

* Fix for NumberFormatException.

* Add conditional test for survivorship rules.

* Spotless.

* Add changelog.

* Code review feedback.

* updating documentation (#5889)

* Ensure temp file ends with "." and then suffix. (#5894)

* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Enhance mdm interceptor (#5899)

* Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened.

* Added javadoc

* Cahngelog

* spotless

---------

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896)

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug.

* Add changelog.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml

Commit code reviewer suggestion.

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

---------

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

* Fix query chained on sort bug where we over-filter results (#5903)

* Failing test.

* Ensure test cleanup doesn't fail by deleting Patients before Practitioners.

* Implement fix.

* Spotless.

* Clean up unit test and add changelog.  Fix unit test.

* Fix changelog file.

* Apply suggestions from code review

Apply code review suggestions.

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

* Spotless

---------

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

* cve fix (#5906)

Co-authored-by: Long Ma <long@smilecdr.com>

* Fixing issues with postgres LOB migration. (#5895)

* Fixing issues with postgres LOB migration.

* addressing code review comments for audit/transaction logs.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for TermConcept
 migration post code review.

* applying spotless

* test and implementation for TermConceptProperty
 migration post code review.

* test and implementation for TermValueSetConcept
 migration post code review.

* fixing migration version

* fixing migration task

* changelog

* fixing changelog

* Minor renames

* addressing comments and suggestions from second code review.

* passing tests

* fixing more tests

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* 6051 bulk export security errors (#5915)

* Enhance RuleBuilder code to support multiple instances (#5852)

* Overhaul bulk export permissions.

* Overhaul bulk export permissions.

* Small tweak to rule builder.

* Cleanup validation.

* Cleanup validation.

* Code review feedback.

* Postgres terminology service hard coded column names migration (#5866)

* updating parent pids column name

* updating name of the fullTestField Search

* updating name of the fullTestField Search

* fixing typo.

* failing test.

* - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity;

- reverting the name of the FullTextField entity to its previous name of 'myParentPids';

- reverting the name of the lucene index to search on in the terminology service.

- updating the changelog;

* making spotless happy

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881)

* initial failing test.

* solution

* adding changelog

* spotless

* moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811)

* Expose BaseRequestPartitionHelperSvc validate and normalize methods

* Compilation errors

* change mock test to jpa test

* change mock test to jpa test

* validateAndNormalizePartitionIds

* validateAndNormalizePartitionNames

* validateAndNormalizePartitionIds validation + bug fix

* validateAndNormalizePartitionNames validation

* fix test

* version bump

* Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883)

* Add failing test as well as commented out potential solution.

* Fix for NumberFormatException.

* Add conditional test for survivorship rules.

* Spotless.

* Add changelog.

* Code review feedback.

* updating documentation (#5889)

* Ensure temp file ends with "." and then suffix. (#5894)

* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Enhance mdm interceptor (#5899)

* Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened.

* Added javadoc

* Cahngelog

* spotless

---------

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896)

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug.

* Add changelog.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml

Commit code reviewer suggestion.

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

---------

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

* Fix query chained on sort bug where we over-filter results (#5903)

* Failing test.

* Ensure test cleanup doesn't fail by deleting Patients before Practitioners.

* Implement fix.

* Spotless.

* Clean up unit test and add changelog.  Fix unit test.

* Fix changelog file.

* Apply suggestions from code review

Apply code review suggestions.

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

* Spotless

---------

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

* cve fix (#5906)

Co-authored-by: Long Ma <long@smilecdr.com>

* Fixing issues with postgres LOB migration. (#5895)

* Fixing issues with postgres LOB migration.

* addressing code review comments for audit/transaction logs.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for TermConcept
 migration post code review.

* applying spotless

* test and implementation for TermConceptProperty
 migration post code review.

* test and implementation for TermValueSetConcept
 migration post code review.

* fixing migration version

* fixing migration task

* changelog

* fixing changelog

* Minor renames

* addressing comments and suggestions from second code review.

* passing tests

* fixing more tests

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* refactor bulk export rule, add concept of appliestoallpatients, fix tests

* spotless

* Cahgnelog, tests

* more tests

* refactor style checks

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>

* Convert a few nulls to aggressive denies

* Change chain sort syntax for MS SQL (#5917)

* Change sort type on chains

* Change sort type on chains

* Test for MS SQL

* Comments

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
2024-05-10 14:52:43 -07:00
Luke deGruchy c87b5b1d2a
Ensure "Device" is not considered as a resource type for R5 (#5909)
* Preliminary fix.

* Refine fix.  Refine existing tests.  Rename existing test to R4.  Disable tests that don't work due to newly discovered bug with R5 POST poll.  Reverse logging changes and TODOs.

* Reverse more logging changes.

* Check for whitelist of FHIR versions that support device in patient compartment.

* Refine solution.  Add a new test.

* Add changelog.

* Code review fix.
2024-05-08 12:45:56 -07:00
TipzCM ae67e7b55e
Batch2 workchunk states hapi (#5851)
* step 1

* updated batch 2 framework with READY state

* spotless

* remove entity manager

* spotless

* fixing up more tests for batch2

* updating documentation

* cleanup

* removing checkstyle violation

* code review points

* review points continued

* review poitns finished

* updating tests

* updates

* spotless

* updated

* step 1

* updated

* sketch out test cases

* basic state transition shell work

* typos

* spotless

* adding spy override

* fixing tests

* spotless

* changing comment to complete build

* fixing some tests and adding a view

* adding different paging mechanism

* spotless

* waiting step 1

* commit changes

* remove text

* review fixes

* spotless

* some tweaks

* updating documentation and adding change log

* spotless

* added documentation

* review comments 1

* more review fixes

* spotless

* fixing bug

* fixing path

* spotless

* update state diagram

* review points round 1

* revert

* updating diag

* review fixes round 2

* spotless

* - Implemented GATE_WAITING state for the batch2 state machine.
- This will be the initial status for all workchunks of a gated job.
- made compatible with the equivalent "fake QUEUED" state in the Old batch2 implementation.
- Updated corresponding docs.
- added corresponding tests and changelog

* Revert "- Implemented GATE_WAITING state for the batch2 state machine."

This reverts commit 32a00f4b81.

* - Implemented GATE_WAITING state for the batch2 state machine.
- This will be the initial status for all workchunks of a gated job.
- made compatible with the equivalent "fake QUEUED" state in the Old batch2 implementation.
- Updated corresponding docs.
- added corresponding tests and changelog

* fixing a bug

* spotless

* fixing

* - fix merges conflicts
- set first chunk to be always created in READY

* - have only one path through the equeueReady method
- fixed tests

* - hid the over-powered transition function behind a proper state action

* spotless

* resolved review comments

* fixing tests

* resolved review comments

* resolved review comments

* resolved review comments

* resolved review comments

* resolved review comments

* updating migration script number

* fixed bugs

* spotless

* fix test high concurrency

* fixing a test

* code fix

* fixing tests in bulkexportit

* fixing tests

* fixing tests

* cleanup

* completed instance will not be sent to the reduction step service

* Revert "completed instance will not be sent to the reduction step service"

This reverts commit aa149b6691.

* Revert "Revert "completed instance will not be sent to the reduction step service""

This reverts commit e18f5796a1.

* removing dead code

* changed db query for step advance to take statuses as parameter instead

* test fixes

* spotless

* test fix

* spotless

* fixing tests

* migration fix

* fixing test

* testing pipeline with `testGroupBulkExportNotInGroup_DoesNotShowUp` disabled

* fixing some tests

* Add new race test for simultaneous queue/dequeue

* re-enabling `testGroupBulkExportNotInGroup_DoesNotShowUp`

* cascade tag deletes

* test fixes

* some logging

* a test case

* adding job id

* more test code

* marking purge checks

* test fix

* testing

* pausing schedulers on cleanup

* adding a wait

* max thread count guarantee

* fixing the tests again

* removing dead code

* spotless

* checking

* msg codes:

* Fixing a test

* review points

* spotless

* required pom values

* step 1 of reduction ready

* update

* reductoin ready

* annother test

* spotless

* cleanup

* cleanup

* simplifying check in reduction step

* review fixes

* updating version

* using 7.3.1

* adding check

* test finessing

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: tyner <tyner.guo@smilecdr.com>
2024-05-07 18:23:03 -04:00
Etienne Poirier 660de6cc60
5877 attempting to update a tokenparam with a value greater than 200 characters raises a sqlexception (#5878)
* initial failing test.

* solution

* adding changelog

* spotless

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-04-26 15:03:59 +00:00
Tadgh 8a37223106 Version bump 2024-04-21 13:20:55 -07:00
volodymyr-korzh d05009e526
Delete-expunge does not honor delete resourcesOfType permissions (#5857)
* Delete-expunge does not honor delete resourcesOfType permissions - fix
2024-04-19 18:33:10 -06:00
Etienne Poirier aeb4299864
Postgres migrate from lob datatypes (#5837)
* wip - before moving JpaEmbeddedDatabase to test-utilities

* failing test

* BinaryStorageEntity migration with associated test.

* BinaryStorageEntity migration with associated test - fix finger fumble.

* TermConceptProperty Entity migration with associated test.

* TermValueSetConcept Entity migration with associated test.

* TermConcept Entity migration

* fixing merge issue

* spotless

* adding error code 2513 for exception

* adding tests.

* spotless

* adding unique message code for exceptions.

* fixing test failure - 1

* fixing test failure - 2

* fixing test failure - 3

* fixing test failure - 4

* fixing test failure - 5

* troubleshooting test failure

* migration for audit/transaction logs.

* spotless

* preparation for initial code review.

* adding changelog.

* files headers

* addressing comments from first code review.

* modifying RenameTableTask to drop table with newTableName if configured to do so.

* modifications to pass tests.

* passing all tests

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-04-18 22:21:29 -07:00
Justin McKelvy e400db5fb8
collect-data and data-requirements operations and tests (#5854)
* collect-data and data-requirements operations and tests

* remove unused imports

* additional test coverage

* move assertions out of method to pass static code analysis

* camelCase test names

* remove underscore on test methods

* requested edits to changelog

* version bump to 7.1.10-SNAPSHOT

* condense unit tests to prevent pipeline timeout

* method camel case naming
2024-04-18 15:34:26 -07:00
TipzCM 80d382d8cd
5845 add new bulk export hook for parameter massaging (#5846)
* added an additional pointcut

* spotless

* version bump

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-04-15 19:36:27 -04:00
Luke deGruchy 4d8427ad60
Ensure CanonicalizedSubscription reflects StorageSettings.isCrossPartitionSubscriptionEnabled if it's true. Make that setting is true by default (#5810)
* First commit with TODOs and logging.

* Try to add cross partition config at startup to subscription module.

* Barely working solution with JpaStorageSettings injected into the Subscription module with the correct config for cross partition enabled.

* Implement agreed upon solution where StorageSettings used in the subscription module uses the JpaStorageSettings cross partition enabled setting.  Fix all compile errors.  TODOs for tests to add and known test failures.

* Fix test errors caused by bad log code.   Ensure all modules use StorageSettings for canonicalizer.

* Cleanup.

* Reintroduce old SubscriptionCanonicalizer constructor, but add a StorageSettings and deprecate it.  Cleanup logs and TODOs.

* Deprecate FHIR_PATCH.  More cleanup.

* Deprecate FHIR_PATCH correctly.

* Small fix.

* Set myCrossPartitionSubscriptionEnabled to true by default.

* Fix test failures.

* Fix another test.

* Code review feedback.

* Resolve static analysis warnings.
2024-04-09 14:27:15 +00:00
TipzCM 107de2cfba
reduction step failing fails jobs (#5831)
* adding a catch for failing reduction step

* spotless

* added changelog

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-04-08 13:51:41 -04:00
TipzCM 5d55594a73
Batch2 test refactor only (#5823)
* refactoring

* test refactor only

* spotless

* bumping version

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-04-05 21:39:03 -04:00
Michael Buckley bdea4b6900
Merge history table prefetch with resource table. (#5825) 2024-04-04 23:53:35 +00:00
Michael Buckley fcf0a85584
Stop writing to hfj_forced_id (#5817)
Stop writing to hfj_forced_id
Stop reading ForcedId
Cleanup client-id assignment
Fix query counts in tests
Drop the unused indexes and fk
2024-04-03 18:25:23 +00:00
JasonRoberts-smile 1736dadfcf
Jr 20240325 concept map unmatched codes (#5809)
* update model

* convert results

* migration

* extend test coverage in cli

* fix broken test

* change log

* code review feedback

* spotless
2024-04-02 16:46:03 -04:00
Lila Mikalson e39ee7f47d
Add _language param to providers (#5801)
* Add _language param to providers and tests

* add pr number to docs

* fix test

* remove unnecessary code

---------

Co-authored-by: Lila Mikalson <lila.mikalson@smilecdr.com>
2024-04-02 20:26:33 +00:00
Emre Dincturk 70843cdf45
fixed resource fullUrl in _history bundles (#5815) 2024-04-01 15:21:18 -04:00
James Agnew 6ce3b17460
Enforce maximum chunk size in bulk export (#5800)
* Limit bulk export chunk size

* Cleanup

* Work on tests

* Working

* Add some docs

* Address revuew comments

* Spotless

* Test fix
2024-04-01 09:28:46 -04:00
Brenin Rhodes 9ddd8bf4d9
Update CR Operation Providers to latest version of CR release (#5751)
* Add support for latest version of CR and new $questionnaire operation

* Fix formatting in javadoc causing warning

* Update to 3.0.0 CR release

* Add support for expected parameter names from updated IG's

* Update Clinical Reasoning documentation

* Update pom.xml

* Create 5750-update-cr-operations.yaml

* fix doc

* Update to latest CR version

* Update pom.xml

* In version

* Update changelog

* Remove commented code
2024-03-28 11:44:29 -07:00
Nathan Doef 7742aa76c5
Retain X-Request-ID header key casing in responses (#5787)
* failing test

* fix

* changelog

* spotless

* fix tests
2024-03-20 16:08:05 +00:00
Michael Buckley d6bc8f2e1b
Sort by Bundle chained composition SPs (#5785)
Add support for sorting by special Bundle chained composition SPs
2024-03-15 18:50:50 +00:00
Etienne Poirier fc4c31a779
5771 patch operation failing for complex extension (#5776)
* initial failing test

* tightening initial test.

* fix with changelog

* addressing comment from code review.

* clean up from code analysis recommendations

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-03-12 13:59:36 -04:00
TynerGjs df047a9dea
Resolve 5758-completion-handler-for-reduction-steps-are-not-called-with-the-up-to-date-job-instance-status (#5759)
* updated instance status after run is called.

* added changelog

* version bump
2024-03-06 11:01:42 -05:00
Luke deGruchy 4570c28cb6
Fix _has then chain then _has searches (#5735)
* Add SQL logging:  Attempt to add test.

* Small fix.

* moar tests

* Tweak unit tests to be parameterized.

* Enhance tests and more logging.

* Better tests.  More logging.  More TODOs.

* Better tests.  More logging.  More TODOs.

* Changes

* Changes

* Updates to tests.  More logging and experimental code.

* Introduce fix along with more logging and TODOs and tweaks to tests.

* Cleanup solution.  Get rid of logs and todos.  Rename test class, test methods and clean up unnecessary code.

* Add changelog.

* Implement simpler chain algorithm without conditional logic and leave a long comment explaining why.

* Implement simpler chain algorithm without conditional logic and leave a long comment explaining why.

* Fix comment.

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-03-04 15:52:04 +00:00
Nathan Doef 9ec8882457
Unable to POST a transaction Bundle with nested collection Bundle entries (#5693)
* failing test

* fix

* fix

* improve / fix old tests

* changelog

* cleanup

* comment
2024-03-04 10:50:05 -05:00
TipzCM 370d2c16b1
5746 fixing reducer step (#5753)
* fixing reduction step to fire job completion handler

* unwinding

* fixing changelog

* spotless

* review fixes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-03-04 09:12:31 -05:00
Tadgh 3a1a0418a0
Readd migration (#5747)
* Re-add removed migration

* spotless
2024-02-29 21:07:24 +00:00
longma1 28a1a4d4df
Rel 7 0 mb 2 (#5714)
* pom bump to 7.0.0 (#5615)

* pom bump to 7.0.0

* add version enum

* fixed feb release name

---------

Co-authored-by: Long Ma <long@smilecdr.com>

* Check index existence on raw SQL creation (#5624)

* Add conditional check on index existence before we try again

* Add conditional check on index existence before we try again

* Changelog

* remit

* remit

* debug statements

* 5621 deadlock on caffeine cache when creating a resource with conditional create (#5622)

* Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback.

* Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations.

* adding changelog and spotless.

* Fixing typo.

* Addressing comments from code review.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)

* Failing test

* fix

* changelog

* Avoiding Exception being thrown on @EventListener invocation (#5628)

* replaced EventListener annotation with @PreDestroy

* adding changelog

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* simple fix (#5630)

Co-authored-by: Long Ma <long@smilecdr.com>

* Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625)

* Incorrect version from versioned_references.auto_at_paths for conditional update - implementation

* Oracle:  Ensure migrated database still takes large resource text updates (#5629)

* First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration.

* First stab at agreed upon solution.

* Fix error with 4001 by removing unnecessary annotation.

* Spotless and TODO.

* Remove annotation for good and set length to LONG32.

* Fix copyright year.

* Finalize changelog.

* Remove migration changes.  Fix unit test.

* Fix compile error.

* Log output.

* Refactor resource history code into new ResourceHistoryCalculator.

* Spotless.

* Convert record to POJO.

* Restore pre-17 switch statement.

* Finalize new resource history calculator code and tests.

* Spotless.

* Remove logging.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml

Apply code reviewer suggestion

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

* Code review feedback.

---------

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

* Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638)

* When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases.

* Minor change to fix test

* Rename changelog file

* Remove TODOs as they're replaced by reported issue

* Revert accidental change added with TODO removal

* $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)

* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation

* Fix Measure group id null pointer exception (#5620)

* Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id

* add changelog

---------

Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>

* Rule evaluation:  Allow Bundles with PATCH Parameters (#5641)

* Remove parameters clause.

* Finalize changelog.  Add tests.  Finalize implementation.

* Undo changes to this test.

* Revert all changes to FhirQueryRuleImplTest.  Add new RuleImplOpTest.  Ensure that proper nested Bundle is created for test and other fixes.

* Tweak test.

* Use real rule applier in test and remove all mocks.

* Prevent batch2 job execution to stop for empty chunk when last job st… (#5635)

* Prevent batch2 job execution to stop for empty chunk when last job step is a reduction.
Add output to bulk export result even when empty.

* Fix test

* Unimportant change to force fresh build

* Implement review suggestions

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Index review fixes (#5649)

* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.

* Fix conditional creates without leading '?' (#5646)

* First commit with failing test.

* More tests and logs.

* More logs

* Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl().

* Simplify solution.  Add more tests.

* Changelog.

* javadoc

* Searching for Bundles with read all Bundles permission returns 403 (#5644)

* failing test

* another failing test case

* fix

* changelog

* fix bug

* spotless

* cr

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* Serializing changes for sensitive data (#5655)

* Add new senstiive data serializer

* Add new senstiive data serializer

* Add new senstiive data serializer

* Remove dead comments

* Change up the test

* review comments

* wip

* Tighten tests and push annotation down

* Tighten tests and push annotation down

* Changelog

* Add test

* 7.0.1-SNAPSHOT bump

* Error code

* Add method used by CDR

* add version enum

* Fix test

* Revert change to other safe version to stop problem with deprecated field

* Rel 7 0 CVE (#5663)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* Descendent fix (#5669)

* Fix "is-a" ValueSet expansion, add "descendent-of" support

* Fixed tests in DSTU3 and R5

* Trigger new build

* Revert "Trigger new build"

This reverts commit 46c672b338.

* fix default partition setting on resource (#5617)

* fix default partition setting on resource

* changelog

* Handle DEFAULT partition in rule checker.

* Fix spotless

---------

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

* pom bump, doc add, version enum add (#5616)

Co-authored-by: Long Ma <long@smilecdr.com>

* fix default partition setting on resource (#5618)

* fix default partition setting on resource
* Handle DEFAULT partition in rule checker.

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Add setting to make broker not use JacksonMessageConverter (#5611)

* Add setting to make broker not use JacksonMessageConverter

* Add changelog

* Implement suggestions

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Fix version

* add changelog, add attribution, remove accidental bring-overs

* add changelog, add attribution, remove accidental bring-overs

* Finish jira section

---------

Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* $poll-export-status operation with PatientIdPartitionInterceptor fails with NullPointerException (#5681)

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor.

* Fix NPE on -export-status operation with PatientIdPartitionInterceptor

* 5654 measurescorer bug for denominator exception (#5677)

* update measure bundles and tests for enforced populationId specification on Measure group resources

* bump CR version to PRE17

* fix bug in versionEnumTest

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5654-measurescorer-bug.yaml

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

---------

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

* Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type. (#5698)

* Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type.

* Spotless fix

* Address code review comments

* version bump to 7.0.0

* pipeline fix

* Update java home

* Updating version to: 7.0.1 post release.

* post mergeback cleanup

* bump clinical-reasoning.version to pre17

* test fix

* version bump to 7.1.5-snapshot

---------

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.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: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
2024-02-23 11:03:26 -07:00
James Agnew ec525f4457
Apply SearchNarrowingInterceptor to conditional URLs (#5712)
* Fix #5110 - Failure in tx processing

* Test fix

* Work on narrowins

* Add changelog

* Docs cleanup

* Fix compile error

* Rollback incompatible change

* Test fix

* Test fix

* Force update

* Test fixes

* Build fixes

* Bump HTMLUnit

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5712-apply-searchnarrowing-to-conditional-urls.yaml

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Version bump to 7.1.4-SNAPSHOT

* Spotless

* Roll back version

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-02-23 08:42:26 -05:00
Martha Mitran e5d410d10b
Refactor and fix functionality dealing with ReadPartitionIdRequestDetails (#5691)
* Throw exception when resourceType of parameter value is invalid when performing FHIR search with non-chained reference

* Fix changelog issue id and spotless warning

* Cleanup unnecessary test

* Validate resourceType only when using relative reference

* Fix test for search using _type parameter

* Refactor and fix functionality dealing with ReadPartitionIdRequestDetails

* Spotless fixes

* Revert some of the refactoring changes to BaseRequestPartitionHelperSvc and fix tests

* Small cleanup

* Missing change

* Small changes

* Fix tests and add a few more

* Spotless fix

* Address code review comments

* Some polishing on the interface annotations and documentation

* Spotless fix

* Fix test

* Fix tests and test method rename

* Ensure SearchParameterMap is not null

---------

Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
2024-02-17 16:16:14 -05:00
Luke deGruchy c8d6e9fb73
Fix validation caching issue with initially unpopulated StructureDefinitions (#5705)
* Solution to caching issue with new tests.

* Fix animal sniffer issue.  Clean up unit tests.  Finalize changelog.  Add TODO referencing change in validation cache behaviour.

* Spotless.

* Fix unit test.

* Code review feedback.
2024-02-15 21:54:24 +00:00
Luke deGruchy bdaedb605b
Return HAPI-2498 if a REST request contains an :identifier modifier (#5696)
* Failing tests and logging.

* Spotless.

* Fix error message for bad modifiers.  Add more tests.

* Spotless.

* Fix conditional logic for detecting modifiers to check for colon (:).

* Finalize tests.  Fix animal sniffer error.  Remove logging code.  Finalize changelog.

* Try again to fix animal sniffer error.

* Null handling on request.
2024-02-14 00:51:37 +00:00
Jens Kristian Villadsen 1deca0756c
Feature/chained location.near search (#5668)
* Added support for chained location search

* Added unit tests

* Assigned new error code

* Reworked according to review
2024-02-12 10:47:50 -08:00
Michael Buckley d71736bf9d
Suspend tx when refreshing version cache (#5671)
* Suspend tx when refreshing version cache
* Undo refactor to reduce merge size
* changelog
* Bump to 7.1.3
* Fix version test
* Unwrap transaction proxy
2024-02-08 14:01:39 -05:00
Luke deGruchy a7eceda5d7
Enforce limit on the number of resources resolved by a deleteByUrl call. (#5689)
* Enforce limit on the number of resources resolved by a deleteByUrl call.

* Add changelog and TODO comment.

* Code review suggestion.
2024-02-08 11:13:21 -05:00
Martha Mitran 43f1e4b2dd
Handle invalid resourceType when performing FHIR search with non-chained reference (#5674)
* Throw exception when resourceType of parameter value is invalid when performing FHIR search with non-chained reference

* Fix changelog issue id and spotless warning

* Cleanup unnecessary test

* Validate resourceType only when using relative reference

* Fix test for search using _type parameter
2024-02-08 11:08:13 -05:00
longma1 993cfcce99
7 0 0 mb (#5678)
* pom bump to 7.0.0 (#5615)

* pom bump to 7.0.0

* add version enum

* fixed feb release name

---------

Co-authored-by: Long Ma <long@smilecdr.com>

* Check index existence on raw SQL creation (#5624)

* Add conditional check on index existence before we try again

* Add conditional check on index existence before we try again

* Changelog

* remit

* remit

* debug statements

* 5621 deadlock on caffeine cache when creating a resource with conditional create (#5622)

* Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback.

* Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations.

* adding changelog and spotless.

* Fixing typo.

* Addressing comments from code review.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)

* Failing test

* fix

* changelog

* Avoiding Exception being thrown on @EventListener invocation (#5628)

* replaced EventListener annotation with @PreDestroy

* adding changelog

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* simple fix (#5630)

Co-authored-by: Long Ma <long@smilecdr.com>

* Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625)

* Incorrect version from versioned_references.auto_at_paths for conditional update - implementation

* Oracle:  Ensure migrated database still takes large resource text updates (#5629)

* First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration.

* First stab at agreed upon solution.

* Fix error with 4001 by removing unnecessary annotation.

* Spotless and TODO.

* Remove annotation for good and set length to LONG32.

* Fix copyright year.

* Finalize changelog.

* Remove migration changes.  Fix unit test.

* Fix compile error.

* Log output.

* Refactor resource history code into new ResourceHistoryCalculator.

* Spotless.

* Convert record to POJO.

* Restore pre-17 switch statement.

* Finalize new resource history calculator code and tests.

* Spotless.

* Remove logging.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml

Apply code reviewer suggestion

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

* Code review feedback.

---------

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

* Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638)

* When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases.

* Minor change to fix test

* Rename changelog file

* Remove TODOs as they're replaced by reported issue

* Revert accidental change added with TODO removal

* $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)

* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation

* Fix Measure group id null pointer exception (#5620)

* Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id

* add changelog

---------

Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>

* Rule evaluation:  Allow Bundles with PATCH Parameters (#5641)

* Remove parameters clause.

* Finalize changelog.  Add tests.  Finalize implementation.

* Undo changes to this test.

* Revert all changes to FhirQueryRuleImplTest.  Add new RuleImplOpTest.  Ensure that proper nested Bundle is created for test and other fixes.

* Tweak test.

* Use real rule applier in test and remove all mocks.

* Prevent batch2 job execution to stop for empty chunk when last job st… (#5635)

* Prevent batch2 job execution to stop for empty chunk when last job step is a reduction.
Add output to bulk export result even when empty.

* Fix test

* Unimportant change to force fresh build

* Implement review suggestions

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Index review fixes (#5649)

* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.

* Fix conditional creates without leading '?' (#5646)

* First commit with failing test.

* More tests and logs.

* More logs

* Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl().

* Simplify solution.  Add more tests.

* Changelog.

* javadoc

* Searching for Bundles with read all Bundles permission returns 403 (#5644)

* failing test

* another failing test case

* fix

* changelog

* fix bug

* spotless

* cr

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660)

* Serializing changes for sensitive data (#5655)

* Add new senstiive data serializer

* Add new senstiive data serializer

* Add new senstiive data serializer

* Remove dead comments

* Change up the test

* review comments

* wip

* Tighten tests and push annotation down

* Tighten tests and push annotation down

* Changelog

* Add test

* 7.0.1-SNAPSHOT bump

* Error code

* Add method used by CDR

* add version enum

* Fix test

* Rel 7 0 CVE (#5663)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* Descendent fix (#5669)

* Fix "is-a" ValueSet expansion, add "descendent-of" support

* Fixed tests in DSTU3 and R5

* Trigger new build

* Revert "Trigger new build"

This reverts commit 46c672b338.

* fix default partition setting on resource (#5617)

* fix default partition setting on resource

* changelog

* Handle DEFAULT partition in rule checker.

* Fix spotless

---------

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

* pom bump, doc add, version enum add (#5616)

Co-authored-by: Long Ma <long@smilecdr.com>

* fix default partition setting on resource (#5618)

* fix default partition setting on resource
* Handle DEFAULT partition in rule checker.

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Add setting to make broker not use JacksonMessageConverter (#5611)

* Add setting to make broker not use JacksonMessageConverter

* Add changelog

* Implement suggestions

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Fix version

* add changelog, add attribution, remove accidental bring-overs

* add changelog, add attribution, remove accidental bring-overs

* Finish jira section

---------

Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* fix conflict mistake

* removed test assert that is no longer true:

* version bumpb to 7.1.1

* fix version Enum test

---------

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.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: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-02-07 22:16:34 -07:00
Jens Kristian Villadsen bc955b8539
introduced _list fix (#5664)
* introduced fix

* Add value

* Added backing tests

* Ignore _list as _has is done
2024-02-05 17:26:20 -08:00
Martha Mitran cbd733c340
Refactor `CommonCodeSystemTerminologyService` method `validateCode` (#5631)
* Refactored CommonCodeSystemTerminologyService validateCode method and added more tests
2024-02-02 15:20:43 -07:00
longma1 29fec706de
pom bump, doc add, version enum add (#5616)
Co-authored-by: Long Ma <long@smilecdr.com>
2024-01-22 22:42:54 +00:00
TynerGjs 6e1a56d520
Resolve 5602 bulk export would fail if type parameter is not provided (#5605)
* default _type to all resource types in the patient compartment for patient type&instance level bulk export

* parametrized test so that it calls both type and instance level

* added change log and spotless check

* resolved code review comments
2024-01-19 15:05:32 -05:00
Michael Buckley 6a370c60cb
Cleanup and some tests (#5609)
Cleanup warnings, and add some missing tests.
2024-01-19 17:42:50 +00:00
Tadgh 84f0bb4f34
5606 trigger subscription failure (#5607)
* Fix, test, changelog

* Fix, test, changelog

* Add backwards compat

* Add backwards compat

* set all partitions if enabled

* Test fixes
2024-01-18 19:18:10 -08:00
James Agnew 878e27b06d
HAPI FHIR Dependency Bumps (#5576)
* HAPI FHIR Dependency Bumps

* Hibernate search 6

* Dep bumps

* Bump mockito

* Fix memory leak

* Test cleanup

* Test fix

* Test fixes

* Test fix

* Test fix

* Test fix

* Test fix

* Prepare to try and rework max clauses

* Refactor large VS expansion

* Spotless

* Test fix

* Version bump

* Test fixes

* Bump maven container

* Build fix

* Add license headers

* Version bump

* License headers
2024-01-14 14:15:08 -05:00
volodymyr-korzh 5286829585
New extension for auto versioning references of the resource (#5591)
New extension for auto-versioning references of the resource
2024-01-12 17:00:58 -07:00
TipzCM d6128dece0
adding additional data to (bulk data export) parameters (#5541)
* adding additional data to parameters

* checkstyle

* updated consent service

* updating documentation

* working

* updating and cleaning

* some review points

* spotless

* review fixes

* bumping version

* consent interceotpr fixes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2024-01-12 09:49:45 -05:00
Justin McKelvy b5c028f80a
Add Evaluate Library operation and bump CR (#5570)
* add evaluateLibrary operation

* add tests and constants for operations

* move off snapshot

* code review comments

* version bump to 6.11.8-SNAPSHOT

* spotless edit
2024-01-03 12:16:08 -05:00
Luke deGruchy 644c68872f
Update copyright headers for 2024. (#5575)
* Update copyright headers for 2024.

* Fix more copyright headers.

* Add <name> to hapi-fhir-jpa pom.
2024-01-03 14:47:05 +00:00
James Agnew 15509bc321
Remove duplicate indexes on update (#5567)
* Remove duplicate indexes on update

* Add changelog

* Remove fixmes

* Update changelog
2023-12-22 01:30:57 +00:00
jmarchionatto 836b755ad3
5558 disallow resource updates crossing patient compartment (#5562)
* Improve readability

* Fix warnings

* Add interceptor, test doc and changelog. Also, extract common used function to utility class and add tests.

* spotless

* Fix changelog link

* Fix changelog fragment warnings

* Fix changelog link

* Fix documentation link

* Implement review comments

* Implement review comments

* Keep old exception code for tests

* Revert refactoring which lost difference between NonCompartmentMemberTypeResponse and NonCompartmentMemberInstanceResponse

* spotless

* Remove version restriction

* Differentiate exceptions thrown by different code

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-12-21 12:57:58 -05:00
James Agnew 7863f03c68
Fix postgres / Remove use of LOB content column (#5555)
* Work on fixing postgres

* Test fix

* wip

* wip

* wip

* wip

* wip

* adding support for h2 embedded and renaming postgressIT

* Work on postgres

* Remove use of gzip content on postgres

* Cleanup

* Test fixes

* Spotless

* Restore fake db for DDL generator

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-12-15 08:07:26 -05:00
Martha Mitran 564ae46008
Fixes for validation lookupCode method and improve remote terminology tests (#5535)
* Fixes for validation lookupCode method:

(1) NullPointerException when processing designation in the remote terminology implementation
(2) Inconsistency between input and output type  vs.  for property parameter across the board
(3) Fix most of the warnings in the updated classes.
(4) Code review changes

* Fix unit test failure by reverting assertion to FOO_COLUMN.

* Revert commit.

* Update tests

* Update tests - move utility class back

* Update fix and tests

* spotless fix

* Missing branches for exception cases and add tests for the same

* Spotless fix

* fix tests

* fix test

* Address code review comments. Write the remote terminology tests in a way to make them more readable.

* Revert moving utility test class

* Small changes in tests

* Small changes

* fix checkstyle

* Minor changes in exception handling and add a missing test

* Address code review comments. Decouple other tests from lookupCode tests.

* Update declaration of constants

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
2023-12-12 10:05:21 -05:00
James Agnew b28fe3b882
Jakarta Bump Part 2 (#5533)
* Make expunge service extensible

* Work

* Licence headers

* Version bump some dependencies

* Version bumps

* Adapt to new html unit version

* Reintroduce errorprone

* Test fix

* Header

* Work on jakarta

* Test fixes

* Restore errorprone

* More pom tweaks

* Apply spotless

* Errorprone tweak

* errorprone tweak

* Version bump

* License headers

* Version bump

* Postgres bump
2023-12-11 18:24:40 -05:00
TynerGjs d8298e38d4
Resovle 5505-remove-broken-member-match-from-hapi (#5517)
* - Removed IConsentExtensionProvider, MemberMatchR4ResourceProvider and MemberMatcherR4Helper, as well as corresponding usages and tests

* - Removed IMemberMatchConsentHook.java

* spotless reformat

* added changelog

* removed constants for $member-match parameters

* removed error message for $member-match

* completely removed MemberMatchR4ResourceProvider.java

* removed operation constant for $member-match

* version bump
2023-12-07 13:16:31 -05:00
volodymyr-korzh 4d0670b0ad
Empty, id-only content Payload types are not supported for Topic based Subscriptions (#5499)
* added support of Empty, id-only content Payload types for Topic based Subscriptions
2023-12-07 09:05:51 -07:00
Luke deGruchy 78a50f92bc
Replace all nullable/nonnull imports of javax.annotation with jakarta.annotation (#5540)
* Replace all nullable/nonnull imports of javax.annotation with jakarta.annotation.

* Fix checkstyle.  Update checkstyle version.
2023-12-07 09:16:48 -05:00
Tadgh 293cd3ef3c
Fix case sensitivity on package name lookup (#5524)
* 90% working test

* wip

* Modify test, changelog, add implementation

* Revert "90% working test"

This reverts commit 64a8f1d806.

* fix typo

* spotless
2023-12-05 17:43:00 +00:00
Etienne Poirier fdeaf8384f
Request for exposing client id and username in batch job status api (#5526)
* initial tests and implementation of the feature persistence layer.

* initial tests and implementation pointcut to modify JobInstance before persistence.

* spotless happy.

* Addressing comments from first code review.

* happy spotless

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-12-04 11:44:48 -05:00
James Agnew 6d58df0f44
Jakarta/Javax Servlet Migration (#5429)
* Servlet migrsation changes

* Apply spotless

* Work on migration

* Start working on JPA migration

* Test fixes

* Test fixes

* Test fixes

* Work

* Work on servlet migration

* Work on migration

* Work on fixes

* Imports fix

* Work on tests

* Test fix

* All tests passing

* Work on migration

* Schema generator

* Refactor ID strategy

* Some test fixes

* Test fixes

* API additions

* Work on websockets

* Test fixe

* Version bump

* Work on migration

* All tests have passed!

* Work on test fixes

* Fixes

* Work on fixes

* CDR fix

* Work on migration

* Fixes

* Spotless

* Disable onetoone ban

* Adjust migratyions

* Transaction service fix

* Add tinyint to migrator

* Work

* Migration

* Compile fix

* Add license

* Test fix

* Test fix

* Cleanup

* Cleanup attempt

* Test fix

* Reslve fixmes

* Remove legacy lastn implementation

* Test cleanup

* Cleanup

* Remove dead import

* Bad import setups

* Review comments

* Review fixes

* Build fix

* Test fix

* Spotless

* Account for CR changes

* Compile fixes

* Rollback one change

* Test tweak

* License header

* Test fix

* Test fix part 2:

* Clean up tx isolation

* Spotless

* Spotless apply

* Drop min SQL Server level

* Attempted test fix

* Test fix

* Test fix

* Test fix

* Bump hibernate

* Test fix

* Test fixes

* Test fixes

* Test fixes

* Test cleanup

* One more test fix

* Test fix

* Try to fix test

* Clean up expunge

* Test fix

* Remove unneeded task

* Spotless

* Bump compiler plugin

* Spotless

* Compile fix

* Add license headers

* License header

* Test fixes

* Bump animal sniffer

* Spotless

* Bump Jetty version

* Test fix and version bump

* Cleanup

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
James Agnew d597cf2763
Allow chained searches in Bundles where the fullUrl is fully qualified (#5529)
* Allow chained searches in Bundles where the fullUrl is fully qualified

* Add changelog

* Spotless
2023-12-01 20:19:51 +00:00
Michael Buckley fab00ca3a0
Expose the desired Propagation in a tx template (#5516) 2023-11-30 21:43:10 +00:00
Luke deGruchy 8fbbaef079
Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient. (#5488)
* Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient.

* Add FhirContext to ClientResponseContext.

* Introduce a ModifiedStringApacheHttpResponse.  Run spotless.

* Remove TDOOs, add and update javadoc.

* Spotless and copyright header.

* Add changelog.

* Unique error message code.

* Only trigger the interceptor if the expected return type is a Bundle.

* Fix spotless.

* Code review feedback.

* Spotless.

* Bump to 6.11.3-SNAPSHOT
2023-11-30 14:56:46 -05:00