Commit Graph

9875 Commits

Author SHA1 Message Date
volodymyr de43553fb6 Patient $everything operation with _offset query parameter throws exception - draft implementation 2024-07-05 14:01:29 -06:00
volodymyr dcf164bdb8 Patient $everything operation with _offset query parameter throws exception - remove throw exception if _offset is provided 2024-07-05 10:42:01 -06:00
volodymyr ab3433aed9 Patient $everything operation with _offset query parameter throws exception - tests 2024-07-05 10:34:09 -06:00
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
dotasek 8a41da4a18
Add warning in javadoc (#6081) 2024-07-05 09:05:20 -04:00
VK-SMILECDR 2aa11b2605
add simple LogbackTestExtensionAssert (#6076) 2024-07-04 17:34:05 +00:00
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
jmarchionatto bc8d873c7f
Assertj json extension (#6039)
* Assertj json extension

* Allow chained invocations

* Rename

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-06-27 14:42:14 +00:00
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
Tadgh bd83bc17cd
6046 text does not work with r5 (#6051)
* Initial commit of failing test

* wip

* Hack a side-route to not use analyzed versions of the field

* spotless

* Add concept of contains for special

* Changelog, docs

* spotless

* another test

* wip

* refactor

* spotless
2024-06-26 23:20:15 +00:00
jmarchionatto 0c642b6113
Improve search param extraction flexibility (#6030)
* Allow extractor to extract values for Resource-level parameters also

* Rename flag

* spotless

* Allow setting test-specific resource provider

* Add tests

* Move common mockings to setup

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2024-06-26 11:36:47 -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
jdar8 11d61a5f72
Jd 20240614 6010 bundle entry search score missing (#6011)
* 6010 test

* 6010 add bundle entry search score

* 6010 support other fhir versions for search score

* 6010 changelog

* 6116 mvn spotless

* 6010 address code review comments

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
2024-06-24 08:56:00 -07:00
Tadgh bce0313458
6034 poor index generation on sql server (#6035)
* Changelog

* Remove uniqueness

* spotless

* Add migrations

* spotless

* make some space

* Handle fancier upgrade

* spotless

* Fix up where clause generation to be a bit more readable

* spotless
2024-06-22 00:36:00 +00:00
Jens Kristian Villadsen f767058239
Subscription fhirpath criteria (#5975)
* Added fhirpath-criteria evaluation

* Added test for valid fhirpath that does not evaluate to boolean

* Added resolving the variables %current and %previous

* Added test using only FP criteria

* Added test cases for valid FhirPath expressions that return non-booleans

* Added use of central cache

* Added more elaborate tests for non-sunshine scenarios

* Added changelog

* CheckStyle'd errorcode added.

* Added spotless formatting and converted FhirPathR5 expression to be Android compatible

* Applied more spotless
2024-06-21 16:46:39 -07:00
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
TipzCM 60f456c655
mdm multidelete golden resource final resource pair throws (#6001)
* fixed a bug with mdm and multidelete
2024-06-19 21:00:37 +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
James Agnew 72b50a4e6d
Feature/param matcher performance improvement (#6017)
* filter function added

* spotless

* Credit for #5999

---------

Co-authored-by: Melih Aydogdu <melih.aydogdu@formelio.nl>
2024-06-17 06:21:30 -04:00
Ahmet Melih Aydoğdu d2923da62b
Search Param Matcher Performance Improvement (#5999)
* filter function added

* spotless
2024-06-17 06:17:49 -04:00
Tadgh 87fab18123
6007 scheduler id problems with multiple instances (#6012)
* Modify cluster instance name

* spotless

* Add test for scheduler name

* Changelog

* Remove atomic int for autogenerating IDs

* Remove atomic int for autogenerating IDs

* Fix test
2024-06-16 01:15:55 +00:00
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 c1c6d4fc49
Added a couple more methods to the logback assert test helper (#6004)
* add negative method

* add throwable matcher for logback

* logback asserts

* merge master

* update StaticLogbackTestExtension usage
2024-06-15 15:27:54 -04:00
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
Adrienne Sox 024d848690
Skip MDM candidate search if parameters are missing (#5658)
* Issue #5657

Skip an MDM candidate search if any search parameter is missing (as per documentation,
and to avoid non-performant searches), rather than only when all of them are missing.

* Address the unit test failure.

* Add credit for #5658

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-06-12 13:36:02 -07:00
Luke deGruchy a8d21aa8b0
Checkin files with autogenerated Java license source headers. (#5963) 2024-06-12 10:33:11 -07:00
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
TipzCM b39e2f8909
do not throw exceptions on valueset expansion (#5997)
* fixing throwing of expcetion for unsupported filter

* updating comment

* spotless

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-06-10 20:20:16 +00:00
TipzCM 488bf6f18a
fixed bug in survivorship rebuilding service (#5995)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-06-10 08:21:02 -07:00
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 1437c356ae
fixed mdmjsonlink serialization issues (#5987)
* fixed mdmjsonlink serialization issues

* spotless

* test fixing

* spotless

* review fixes

* spotless

* fixing

* spotless

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-06-07 08:45:39 -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
Emre Dincturk 48c387ecb0
added batch job related attributes to OpenTelemetry span (#5972) 2024-06-06 11:07:03 -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
TipzCM 5302a7da52
updating field to make it nullable (#5982)
* updating field to make it nullable

* review fixes and test fixes

* review fixes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-06-06 09:35:29 -04:00
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
Tadgh 575b689d76
disable EP pattern (#5984)
* disable EP pattern

* Fix typo
2024-06-03 16:51:56 -07:00