Commit Graph

786 Commits

Author SHA1 Message Date
Ken Stevens 0a88c31cf3
mdm match_only mode ()
* Started implementing mdm passive mode

* check subscriptions

* check kafka consumers

* switch boolean to enum

* hapi changelog

* renamed enum values per slack conversation

* checkstyle

* review feedback
move developers section out to developers.xml

* version bump

* revert moving developers out

* review feedback

* review feedback

---------

Co-authored-by: Ken Stevens <ken@smiledigitalhealth.com>
2024-12-03 12:36:54 -05:00
James Agnew ea1d179b9a
Caching cleanup ()
* Tests passing

* Cleanup

* Cleanupo

* Test fixes

* Test fix

* Cleanup

* Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java

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

* Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java

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

* Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java

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

* Account for review comments

* Spotless

* Compile fix

* Test fixes

* Test cleanup

* Test cleanup

* Test fixes

* Resolve fixme

* Test fix

* Test fixes

* Test fixes

* Test fixes

* Fix

* Test fix

* Test fixes

* Test fixes

* Cache cleanup

* Work on caches

* Add changelog

* Compile fix

* Spotless

* Test fix

* Fix

* Cache cleanup

* Trying to figure out why Lucene tests are failing

* Test fix

* More cleanuo

* Test fix

* Test fix

* Address some review comments

* HAPI FHIR version bump

* Test fixes

* Cleanup

* Add assert

* Add check

* Test fixes

* Bulk export fix

* Test fixes

* Add some test logging

* Cleanup

* Cleanup

* Test cleanup

* Add test logging

* Attemped test fix

* Add testing method

* FIx build

* Attempted test fix

* Try to fix tests

* Restore fixme

* Spotless

* Test fix

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-11-29 17:00:59 -05:00
James Agnew 362dc095ac
Streamline ValidationSupportChain ()
* Tests passing

* Cleanup

* Cleanupo

* Test fixes

* Test fix

* Cleanup

* Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java

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

* Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java

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

* Update hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java

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

* Account for review comments

* Spotless

* Compile fix

* Test fixes

* Test cleanup

* Test cleanup

* Test fixes

* Resolve fixme

* Test fix

* Test fixes

* Test fixes

* Test fixes

* Fix

* Test fix

* Test fixes

* Test fixes

* HAPI version bump

* Try to address intermittent

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-11-27 17:45:17 -05:00
Tadgh 86c2c13e0f
7.6.0 Mergeback ()
* 6323 resource creation deadlock ()

* make map reads concurrent

* change log

* CUstom version number for guaranteed build determinism

* licenses

* Expand translation cache ()

* Expand translation cache

* Add changelog

* Correction to  ()

* Contained bug ()

* Contained bug

* more tests

* changelog, tests, implementation

* code review

* backwards logic

* Fix Questionnaire doc ()

* fix reindex optimizeStorage=ALL_VERSIONS ()

* fixing broken rename of last step of reindex ()

* Fixes for the translation of parameter issues as part of the output for $validate-code operation. ()

* Move the validation providers to the test utilities package such that they can be reused.

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

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

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

* Fix compilation errors.

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

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

* Fix NullPointerException

* avoid calling validateCode for CodeSystem where system is null

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

* Revert local change to debug for duplicate errors.

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

* Simplify test setup.

* Add some more javadoc

* Add javadoc for the new test class

* Add more tests

* Address code review comments in IValidationSupport.

* Add changelog

* Change Repository search interface from Map to Multimap ()

Change Map to Multimap to support multiple and clauses.

* licenses

* fix interceptor hooks from requestDetails not getting called for STORAGE_PRECHECK_FOR_CACHED_SEARCH ()

* fix interceptor hooks from requestDetails not getting called for STORAGE_PRECHECK_FOR_CACHED_SEARCH

* added unit tests and updated changelog

* added one more test case

* Add Adapter api ()

Lightweight implementation of the adapter pattern.

* Bulk Import job status not changed after activation - failing test, fix, changelog ()

* Update CR to 3.13.1 ()

* Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 ()

* Rel 7 6 CVE ()

* Bump commons io

* Bump HS and Lucene, and hibernate

* Jetty bump for CVE

* Resolve CVES

* Bump with mismatch lucene

* Bump velocity template engine

* Revert bom bump

* wip

* Version bump

* move changelog, fix cve

* Bump commons-lang

* Replace imports

* wip

* fix HQL break

* remove dead code

* Fix changelog entry

* Bump org.hl7.fhir.core to 6.4.0 ()

* Bump HAPI version + org.hl7.fhir.core to 6.4.0

* Apply spotless

* Correct a bug with duplicate parser IDs being assigned.  ()

* Fix changelog entry

* wip

* compilation problem

* Correct tests

* changelog

* Update hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java

Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>

* Correct a bug with duplicate parser IDs being assigned - test fixes

* Correct a bug with duplicate parser IDs being assigned - spotless

* Correct a bug with duplicate parser IDs being assigned - added test-utilities dependency to fhir-structures poms

* Correct a bug with duplicate parser IDs being assigned - test fixes

* Contained resources without assigned IDs are now assigned GUIDs - address comments

---------

Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>

* licenses

* ValueSet expansion fails if Hibernate Search configured to use Lucene - fixed incompatibility between Hibernate Search and Lucene versions ()

* Change the migrator to avoid table locks when adding an index. ()

* version bump

* Updating version to: 7.6.1 post release.

* Bump to 7.7.7.

* deadsapce

* Profile reference param ()

* updated QueryStack to not throw error with _profile as a ReferenceParam

* update QueryStack

* remove warnings

* cleanup cast

* cleanup test

* add changelog

* cleanup imports

* updates per review feedback

* updates per review feedback

---------

Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com>

* move changelog

---------

Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Gary Graham <garygraham@smiledigitalhealth.com>
Co-authored-by: Taha <TahaAttari@users.noreply.github.com>
Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com>
2024-11-24 12:31:59 -08:00
James Agnew d4f1766ca5
Optimize transaction writes ()
* Optimize transaction writes

* Cleanup

* Work on tests

* Work on fixes

* Fixes

* Fixes

* Test fixes

* Cleanup

* Cleanup

* Work on tests

* Work on tests

* Test fixes

* Test fixes

* Remove redundant test

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Test fixes

* Add changelog

* Checkstyle fixes

* Test fixes

* Spotless

* Test cleanup

* Spotless

* Test fix

* Work on review comments

* Address review comments

* Test fixes

* Ongoing test cleanup work

* Work on tests

* Query count tests passing

* Test fixes

* Test fixes

* Rmove fixme

* Test cleanup

* Test fix

* Remove default method

* Service celanup

* Test fix

* version bump

* Test cleanup
2024-11-21 19:22:42 -05:00
James Agnew dea9706652
MDM Virtualization Interceptor ()
* Work on virtualization

* Fixes

* Cleanup

* Fixes

* MDM virtualization

* Remove fixme

* Test cleanup

* Cleanup

* Version bump

* Fixes

* Cleanup

* Fixes

* WIP

* Test cleanup

* Spotless

* Checkstyle

* Spotless

* Address review comments

* Test fix

* Test fix

* Address review comments

* Version bump

* Version bump

* License header
2024-11-21 11:01:54 -05:00
VK-SMILECDR cbbba75d9a
6472 move cds hooks related classes to hapi fhir server package ()
* moving CDS Hooks Json files

* spotless
2024-11-19 11:43:45 -05:00
jmarchionatto cdb0a9c480
Add tinder plugin to pluginManagement to allow to run generate-ddl from parent ()
* Add tinder to parent project's pluginManagement

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

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

* Improve logging

* Use temporary project version

* Revert "Use temporary project version"

This reverts commit 24f5e648ed.

* Increment version

* Increment missed version

* Added headers

* Document new command

---------

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

* Fix breaking test due to new validation rules

* Add changes.yaml

* Bump to HAPI version 7.7.1-SNAPSHOT

* Copyright autogen

***NO_CI***

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

* Work on combo

* Add tests

* Add changelog

* Spotless

* Test fix

* Drop label

* Add tests

* Spotles

* Work on disable code

* Cleanup

* CLeanup

* Cleanup

* Add changelog

* Test cleanup

* Review comments

* Spotless

* Compile fix

* Version bump

* Test fix

* Test fixes
2024-11-07 09:11:19 -05:00
Tadgh 443b59a78b
Bump For February Release ()
* Bump Version

* new versions, new folder
2024-10-21 21:03:07 -07:00
Brenin Rhodes 161a077f2a
Update Clinical Reasoning to 3.13.0 ()
* Update Clinical Reasoning to 3.12.0

* Update to 3.13.0

* add stub for new not document parameter

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

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

* Remove old LibraryEvaluationOperationProvider

* Fix test

* Fix tests

* Add $data-requirement parameters to docs

* Update docs for new measures timezone header.

* Add prefetchData parameter to $apply doc

* Add changelog

* Fix test

* Update snapshot version

* Add new $extract parameters to docs

* Remove old test

* fix test and properties for care-gaps

* Fix dstu3 config

* remove property for fhirserverurl

* update upgrade.md doc

* fix formatting of upgrade doc

* comment on measureidentifier param

* nonDocument parameter inclusion

* java doc on care-gaps

* No longer dead code.

* Spotless.

* Change CareGapsOperationProvider to R4 BooleanType.

* Update to release

* change log update

* change log edit

* cleanup

* Use existing bean

* spotless

* Ensure CollectDataOperationProvider uses StringTimePeriodHandler to convert periods.

* Spotless.

* Add tests for id

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

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

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

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

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

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

* cleanup and comments

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

Implement code reviewer suggestion on timezone docs

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

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

Implement code reviewer suggestion on timezone docs

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

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

Implement code reviewer suggestion on timezone docs

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

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

Implement code reviewer suggestion on timezone docs

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

* Code review feedback:  Add logging for StringTimePeriodHandler.

* Spotless.

* cleanup

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

* Change error code.

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
2024-10-17 08:38:42 -04:00
Martha Mitran 7581920a15
Add support for response parameter issues for `validate-code` operation ()
* Add support for response parameter issues for validate-code operation. Implement workaround for missing error for invalid codes by adding an issue when it is absent.

* address minor code review comments

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

* revert change to FhirInstanceValidatorR4Test

* Revert some of the code review addressal after responding.

* Remove populating message in success scenarios.

* Fix compilation failure in test after reverting method rename.

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

---------

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2024-10-16 10:16:41 -04:00
JasonRoberts-smile b08c59528d
Jr 20241008 merge data absent reason ()
* handle single cardinality case

* multiple cardinality case

* change log
2024-10-15 11:47:32 -04:00
Aditya Dave 1fad912193
6262 cds hooks returns 400 when extension passed in the cdsservicerequestjson ()
* fail test

* potential fix

* spotless

* alternative fix

* spotless

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

* spotless

* fix issue with context failing deserialization

* add validation for context, hook and hook instance

* spotless

* add message codes

* spotless

* changelog

* cleanup

* spotless

* bump version to 7.5.1-SNAPSHOT
2024-09-18 10:01:17 -04:00
JasonRoberts-smile 0f2eb08a77
Jr 20240830 merge references ()
* enhance clone operation

* change log
2024-09-05 12:20:28 -04:00
volodymyr-korzh 568c6d20db
rel_7_4 Merge-back ()
* use SearchParamater validator in package installer ()

* Ensure ' ' is treated as '+' in timezones with offsets. ()

* Use lockless mode when adding index on Azure Sql server ()

* Use lockless mode when adding index on Azure Sql server

Use try-catch for Online add-index on Sql Server.
This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support.
Warnings in docs, and cleanups

* make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT ()

* fix hfj search migration task ()

* fix migration task

* changelog

* changelog

* code review

* spotless

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>

* Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive ()

* MSSQL:  Migrate HFJ_RESOURCE.FHIR_ID to new collation:  SQL_Latin1_General_CP1_CS_AS

* Spotless.

* Enhance test.  Fix case in ResourceSearchView to defend against future migration to case insensitive collation.

* Remove TODOs.  Add comment to ResourceSearchView explaining why all columns are uppercase.  Changelog.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml

Code reviewer suggestion

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

* Code review fixes:  Make changes conditional on the collation including _CI_, otherwise, leave it alone.

---------

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

* Common API for FHIR Data Access ()

* Add initial interface for common FHIR API

* Fix formatting

* Update javadocs

* Address code review comments

* Add path value to _id search parameter and other missing search param… ()

* Add path value to _id search parameter and other missing search parameters to IAnyResource.

* Adjust tests and remove now unnecessary addition of meta parameters which are now provided by IAnyResource

* Revert unneeded change

* _security param is not token but uri

* Add tests for new defined resource-level standard parameters

* Adjust test

---------

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

* update to online ()

* SEARCH_UUID should be non-null ()

Avoid using constants in migrations because it creates false history.

* Handle 400 and 404 codes returned by remote terminology operation. ()

* Handle 400 and 404 codes returned by remote terminology  operation.

* Some simplification

* Adjust changelog

* Add a comment to explain alternate solution which can be reused.

* fix concepts with no display element for $apply-codesystem-delta-add and $apply-codesystem-delta-remove ()

* allow transaction with update conditional urls ()

* Revert "Add path value to _id search parameter and other missing search param…" ()

This reverts commit 2275eba1a0.

* 7 2 2 mb ()

* Enhance RuleBuilder code to support multiple instances ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

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

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

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

* Enhance mdm interceptor ()

* 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 ()

* 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 ()

* 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 ()

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

* Fixing issues with postgres LOB migration. ()

* 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 ()

* Enhance RuleBuilder code to support multiple instances ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

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

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

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

* Enhance mdm interceptor ()

* 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 ()

* 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 ()

* 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 ()

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

* Fixing issues with postgres LOB migration. ()

* 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 ()

* Change sort type on chains

* Change sort type on chains

* Test for MS SQL

* Comments

* Version bump

* Updating version to: 7.2.1 post release.

* Fix queries with chained sort with Lucene by checking supported SortSpecs ()

* First commit with very rough solution.

* Solidify solutions for both requirements.  Add new tests.  Enhance others.

* Spotless.

* Add new chained sort spec algorithm.  Add new Msg.codes.  Finalize tests.  Update docs.  Add changelog.

* pom remove the snapshot

* Updating version to: 7.2.2 post release.

* cherry-picked pr 6051

* changelog fix

* cherry-picked 6027

* docs and changelog

* merge fix for issue with infinite cache refresh loop

* Use lockless mode when adding index on Azure Sql server () ()

* Use lockless mode when adding index on Azure Sql server

Use try-catch for Online add-index on Sql Server.
This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support.
Warnings in docs, and cleanups

* added fix for 6133

* failing Test

* Add fix

* spotless

* Remove useless file

* Fix claeaner

* cleanup

* Remove dead class

* Changelog

* test description

* Add test. Fix broken logic.

* fix quantity search parameter test to pass

* reverted test testDirectPathWholeResourceNotIndexedWorks in FhirResourceDaoR4SearchWithElasticSearchIT

* spotless

* cleanup mistake during merge

* added missing imports

* fix more mergeback oopsies

* bump to 7.3.13-snapshot

---------

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

* Patient validate operation with remote terminology service enabled returns 400 bad request ()

* Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - failing test

* Patient $validate operation with Remote Terminology Service enabled returns 400 Bad Request - implementation

* - Changing method accessibility from default to public to allow method overwriting. ()

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

* applying Taha Attari's fix on branch merging to rel_7_4 ()

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

* Automated Migration Testing (HAPI-FHIR) V7_4_0 ()

* Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0

* Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_2_0

* To provide the target resource partitionId and partitionDate in the resourceLinlk ()

* initial POC.

* addressing comments from first code review

* Adding tests

* adding changelog and spotless

* fixing tests

* spotless

---------

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

* applying patch ()

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

* cve for 08 release ()

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

* Search param path missing for _id param ()

* Add path tp _id search param and definitions for _lastUpdated _tag, _profile and _security

* Add tests and changelog

* Increase snapshot version

* Irrelevant change to force new build

---------

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

* Reverting to core fhir-test-cases 1.1.14; ()

re-enabling FhirPatchCoreTest

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

* Fix $reindex job with custom partition interceptor based on resource type. Update reindex job to always run with urls. ()

* Refactor logic to bring together partition related logic in batch2 jobs using IJobPartitionProvider. Update logic such that reindex job without urls will attempt to create urls for all supported resource types.

* Small changes and fix of pipeline error.

* Small change to enable mdm-submit to use PartitionedUrl in the job parameters

* Revert logback change. Fix dependency version generating errors in the pipeline.

* Spotless fix. Add test dependency back without version.

* Upgrade test dependency to another version

* Add javadoc for PartitionedUrl. Other small fixes and refactoring in tests.

* Spotless fix.

* Change to JobParameters to fix some of the tests.

* Small changes for code review in test

* Address code review comments.

* Revert change from bad merge.

* Address remaining code review comments

* 6188 subscription not marked as a cross partition subscription matches operation on resources in other partitions ()

* initial failing test

* WIP

* fixing/adding tests

* added changelog

* spotless

* fixing tests

* Cleaning up tests

* addressing commetns from first code review.

* no-op to get pipelines going

---------

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

* Resolve 6173 - Log unhandled Exceptions in RestfulServer () ()

* 6173 - Log unhandled Exceptions in RestfulServer.

* Use placeholder for failed streams.

* Starting test for server handling.

* Got test working.

* Fixed use of synchronized keyword.

* Applied mvn spotless.

---------

Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>

* Partition aware transactions ()

* Partition aware transactions

* Address review comments

* Test fixes

* Remove dead issue field

* Test fixes

---------

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

* Add license header

* rel_7_4 mergeback

---------

Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: Martha Mitran <marthamitran@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smiledigitalhealth.com>
Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-08-14 15:03:35 -06:00
Kevin Dougan 44c4b87a84
Resolve 6173 - Log unhandled Exceptions in RestfulServer ()
* 6173 - Log unhandled Exceptions in RestfulServer.

* Use placeholder for failed streams.

* Starting test for server handling.

* Got test working.

* Fixed use of synchronized keyword.

* Applied mvn spotless.

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
2024-08-07 10:01:58 -04:00
Michael Buckley cd43523afe
Mergeback 7_4 ()
* use SearchParamater validator in package installer ()

* Ensure ' ' is treated as '+' in timezones with offsets. ()

* Use lockless mode when adding index on Azure Sql server ()

* Use lockless mode when adding index on Azure Sql server

Use try-catch for Online add-index on Sql Server.
This avoids having to map out the entire matrix of Sql Server product names and ONLINE index support.
Warnings in docs, and cleanups

* make consent service dont call willSeeResource on children if parent resource is AUTHORIZED or REJECT ()

* fix hfj search migration task ()

* fix migration task

* changelog

* changelog

* code review

* spotless

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>

* Enhance migration for MSSQL to change the collation for HFJ_RESOURCE.FHIR_ID to case sensitive ()

* MSSQL:  Migrate HFJ_RESOURCE.FHIR_ID to new collation:  SQL_Latin1_General_CP1_CS_AS

* Spotless.

* Enhance test.  Fix case in ResourceSearchView to defend against future migration to case insensitive collation.

* Remove TODOs.  Add comment to ResourceSearchView explaining why all columns are uppercase.  Changelog.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/6146-mssql-hfj-resource-fhir-id-colllation.yaml

Code reviewer suggestion

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

* Code review fixes:  Make changes conditional on the collation including _CI_, otherwise, leave it alone.

---------

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

* Common API for FHIR Data Access ()

* Add initial interface for common FHIR API

* Fix formatting

* Update javadocs

* Address code review comments

---------

Co-authored-by: Emre Dincturk <74370953+mrdnctrk@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smiledigitalhealth.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
2024-07-26 08:59:24 -04:00
Long Ma 406db339ce bump to 7.5.0-snapshot 2024-07-16 12:25:25 -06:00
Long Ma 0e8f474b51 revert 6e208f16ec 2024-07-16 12:24:19 -06:00
Long Ma 6e208f16ec bump to 7.5.0-snapshot 2024-07-16 10:43:14 -06:00
TipzCM 7e7aae6060
batching subscription msgs () 2024-07-16 09:22:35 -04:00
Justin McKelvy d2c12a7ac3
6083 clinical reasoning version bump v38 ()
* 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
VK-SMILECDR e3f64c23a2
logback test extention assert ()
* 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 ()
* 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
jdar8 11d61a5f72
Jd 20240614 6010 bundle entry search score missing ()
* 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 61b5103535
Final hamcrest conversions ()
* 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 ()
* 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 8947706af3
Handle Versioned Canonical Refs ()
* 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 ()
* 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 ()
* 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 ()
* 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
Justin McKelvy 590fe26a76
5914 clinical reasoning v3.6.0 bump ()
* 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
Ken Stevens cdf5b602c1
Replace hamcrest with assertj ()
* 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
Stefan Lindström 4ac65da2ee
5738: Skip alternate handling if already handled by previous step ()
* 5738: Skip alternate handling if already handled by previous step

* Credit for 

---------

Co-authored-by: Stefan Lindström <stefan.lindstrom@ehalsomyndigheten.se>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-05-28 13:15:48 -04:00
TipzCM f199a3ee4e
added workchunk to step execution details ()
* 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
James Agnew 97cfb6de37
Add utility method to convert Bundle into transaction ()
* Add utility method to convert Bundle into transaction

* Add utility method

* Spotless

* Build fix
2024-05-20 17:00:18 -04:00
longma1 078e87a4aa
7 2 mergeback may 10 v2 ()
* Enhance RuleBuilder code to support multiple instances ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

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

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

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

* Enhance mdm interceptor ()

* 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 ()

* 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 ()

* 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 ()

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

* Fixing issues with postgres LOB migration. ()

* 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 ()

* Enhance RuleBuilder code to support multiple instances ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

* 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 ()

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

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

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

* Enhance mdm interceptor ()

* 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 ()

* 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 ()

* 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 ()

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

* Fixing issues with postgres LOB migration. ()

* 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 ()

* 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
TipzCM ae67e7b55e
Batch2 workchunk states hapi ()
* 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
holly-smile 72ff192df8
Fix error message for HAPI-0302 showing misleading names for known resource types ()
* A solution, but perhaps not the best one

* Make behavior more robust and extendable. Fixes 

* Apply spotless

* Add changelog

* 😅

* Add unit test

* Get name from context instead of hard-coding remapping
2024-04-25 16:39:10 -04:00
Tadgh 8a37223106 Version bump 2024-04-21 13:20:55 -07:00
Justin McKelvy e400db5fb8
collect-data and data-requirements operations and tests ()
* 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 ()
* added an additional pointcut

* spotless

* version bump

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-04-15 19:36:27 -04:00
JasonRoberts-smile e3cc83a694
fix bug () 2024-04-12 00:19:56 +00:00
TipzCM 5d55594a73
Batch2 test refactor only ()
* refactoring

* test refactor only

* spotless

* bumping version

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-04-05 21:39:03 -04:00
Nathan Doef 9e5db198bf
Fix BaseOutcomeReturningMethodBinding NullPointer ()
* failing test

* fix

* add @Nullable
2024-03-28 16:18:27 -04:00
Brenin Rhodes 9ddd8bf4d9
Update CR Operation Providers to latest version of CR release ()
* 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
Etienne Poirier 2f9693a1e4
MDM expansion doesn't work when using the :mdm qualifier in query string ()
* wip

* cleaning up test

* adding changelog and passing spotless.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-03-27 10:12:50 -04:00
Nathan Doef 7742aa76c5
Retain X-Request-ID header key casing in responses ()
* failing test

* fix

* changelog

* spotless

* fix tests
2024-03-20 16:08:05 +00:00