1
0
mirror of https://github.com/hapifhir/hapi-fhir.git synced 2025-02-27 16:56:07 +00:00

9534 Commits

Author SHA1 Message Date
JasonRoberts-smile
0475cb682f
Jr 20230502 fhir patch test coverage ()
* add tests for fhir patch

* extract constants

* extract some methods

* isolate add operation

* isolate delete operation

* isolate replace operation

* isolate move operation

* clean up integer handling

* enumeration creation

* improve variable naming

* code review feedback
2023-05-11 16:40:57 -04:00
Tadgh
9d34e6b248
Credit for ()
* Add credit

* Typo
2023-05-11 18:34:22 +00:00
Nicolai Gjøderum
679b809bf3
Fix: Replace basic field with empty value in TerserUtil ()
* add test proving bug

* fix: handle empty fromValue in TerserUtil.replaceField

* add comment to TerserUtilTest.testReplaceFieldByEmptyValue
2023-05-10 20:09:43 -07:00
JP
c052663561
Change to a release version of the Clinical Reasoning dependency. ()
* A SNAPSHOT dependency on an upstream module was added to HAPI FHIR, which changed and caused some downstream tests to break.

* Add Maven enforcer plugin for CR dependencies

* Make maven enforcer conditional on CI builds
2023-05-10 20:25:42 +00:00
Ken Stevens
224b7f6206
SubscriptionTopic part3 ()
* Force Verify tests

* wip

* merge troubleshooting rel_6_6 troubleshooting changes

* fix ITs ()

* fix RestHookTestR5IT

* fix intermittent

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* post-merge cleanup

* fix test

* fix mock test

* fix wiring

* fix mock test

* fix test

* use IBaseResource.isDeleted()

* fixmes

* cleanup

* change log

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-09 16:29:21 -04:00
Tadgh
e3545446eb
Mergeback of release into master branch ()
* Force Verify tests

* fix ITs ()

* fix RestHookTestR5IT

* fix intermittent

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Fix migrator error on Oracle ()

* Fix Oracle SQL error

* Add changelog

* Update clinical reasoning version ()

* Update clinical reasoning version

* Update version

* Update version

* Clean-up and more wireup of evaluationSettings

* Add changelog

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>

* Opening the care-gaps endpoint for GET. ()

Co-authored-by: Chalma Maadaadi <chalma@alphora.com>

* added version to mdm golden resource tag ()

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

* Update the changelog for 4697 to be more descriptive ()

* Update the changelog for 4697 to be more descriptive

* Futher tweaks of the changelog

* Fixes a bug with tags.  ()

* Test, fix

* Drop constraint, add migration

* Add changelog

* Fix userSelected null vs false

* Fix merge

* Fix up checkstyle whining

* One more failure

* Fix test

* wip

* changelog clarity

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

* change index

---------

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

* fix migration issue ()

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Create correct version enum

* Remove superfluous migration

* fixing test ()

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-05-09 11:23:02 -07:00
Max Bureck
648d14c52c
Parser: Reporting unexpected repeating element for choice () ()
* Parser: Reporting unexpected repeating element for choice ()

IParserErrorHandler.unexpectedRepeatingElement is now also called for
unexpected repeating elements of type choice, where concrete names
may be different based on the choice's data type.

* setting test-utilities java version to the test version

* added changelog

* added Max to the developer liss

* removed unneeded dependency

---------

Co-authored-by: patrick-werner <pa.f.werner@gmail.com>
2023-05-08 20:42:25 +00:00
Dominique Villard
9ae71aba95
4379: allow interceptor annotation on methods ()
* 4379: allow interceptor annotation on methods

* 4379: document order parameter when annotation set on method

* Credit for 

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-07 12:25:29 +00:00
James Agnew
d5184a8a57
Don't generate empty JSON element for comment ()
* Don't generate empty JSON element for comment

* Fixed
2023-05-06 16:05:48 -04:00
Tadgh
93f93d5e41
Add Migration Reviewer Workflow ()
* Add new workflow

* Add some whitespace

* Empty spaces in non-migration file

* wip

* Tidy up workflow
2023-05-06 10:33:17 -07:00
Ken Stevens
17423e4831
fix migration issue ()
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-06 09:13:50 -07:00
Tadgh
f0726a32d5
Fixes a bug with tags. ()
* Test, fix

* Drop constraint, add migration

* Add changelog

* Fix userSelected null vs false

* Fix merge

* Fix up checkstyle whining

* One more failure

* Fix test

* wip

* changelog clarity

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

* change index

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-05 19:06:03 +00:00
Kevin Dougan SmileCDR
c637cec622
4801 - Added new Index on HFJ_RESOURCE table ()
* 4801 - Added new Index on HFJ_RESOURCE table.

* 4801 - Added new migration task for new Index on HFJ_RESOURCE table.

* Update hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

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

* Applied review changes.

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-05-05 17:37:25 +00:00
Brenin Rhodes
87e8a810cd
Merge 4821 back to master ()
* Merge 4821 into master

* Update to PRE3 snapshot
2023-05-05 08:50:53 -07:00
Ken Stevens
350d1a422c
merge release branch to master ()
* Force Verify tests

* fix ITs ()

* fix RestHookTestR5IT

* fix intermittent

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-03 19:51:43 +00:00
James Agnew
a3c33d2a53
Add BasicAuditEventLogging (BALP) Interceptor ()
* Begin work on BALP interceptor

* Work on BALP

* Basic profile

* Work on BALP

* Add BALP

* Work on balp

* Add update and delete

* Work on BALP

* Add logging

* Tests

* Modify test server

* Work on docs

* Add documentation

* Add changelog

* Fix  - Typos in docs

* Test fixes

* Move changelog

* Update hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/interceptor/balp/BalpAuditCaptureInterceptor.java

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

* Resolve PR comments

* Test fixes

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-05-03 15:46:22 +00:00
Aleksej Parovysnik
f4c0f6e9fc
fix previous link offset no cache pagination ()
*  Add test reproducing the issue

*  Fix previous link for no cache offset pagination

*  Use unchecked URI parsing

* Credit for 

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-02 12:49:36 +00:00
Zach Smith
9c1d235f90
Fix operation on nested type-choices in FhirPatch implementation ()
* Fix operation on nested type-choices in FhirPatch implementation

* Add credit for 

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-01 09:52:34 +00:00
Tadgh
9a095cc2d7
version bump for next release ()
* version bump

* Bump to correctnumber

* Version Enum and folder

* Remove interim from list

* wip
2023-04-30 15:01:28 -04:00
Luke deGruchy
79c96dc1bb
Port changes to master from release branch 6_4 ()
* Start porting changes to master that were lost from the release branch.

* Add remainder of tag changes from release branch.

* Changelog changes.

* Fix schema migration.

* Remove duplicate lines.

* Update core to 6.0.1.

* Fixes for new core.

* Bump to snapshot 19 to mirror James' changes.

* Fix migration tasks.

* Fix some of the tests due to the core upgrade.

* Fix rest of tests.
2023-04-28 19:56:02 +00:00
michaelabuckley
81854baa02
Batch2 cleanup ()
Post review batch2 cleanup.

Review fixes and cleanup from 

Deleted methods in IJobPersistence unused in prod paths, and replaced their usage in tests.
Lots of docs.
Replace copy-on-write pattern in JobDefinitionRegistry with simple ConcurrentHashMap
Fixed bad mappings from job ERRORED state to external APIs. People think ERRORED is a failed state. ¯\_(ツ)_/¯
Added some spec tests for chunk purging
Deprecated ERRORED. For deleting in 6.8
Lots of plans for 6.8. Too risky for 6.6
2023-04-28 15:44:30 -04:00
James Agnew
e2e5ff6bb8
Version bump HAPI FHIR () 2023-04-28 19:30:51 +00:00
James Agnew
69a79e39a1
Subscription retriggering enhancements ()
* Work on forward porting reindex optimize storage

* Subscription retriggering performance enhancements

* Adjust readmes

* Add a test

* Add test

* Cleanup

* Test cleanup

* Add comment

* Add changelogs

* Test fixes

* Test fixes

* Bump size

* Fixes

* Test logging

* Restore forkcount

* Test fix

* Test fix

* Version bump

* Clean up changelogs

* Address review comment
2023-04-28 12:06:38 -04:00
James Agnew
78ff58277a
Make inline resource storage use a better column type ()
* Use text column on postgres

* Add changelog

* Test fix

* Merge
2023-04-28 12:06:27 -04:00
James Agnew
e2717bd63a
Bump corelib to FHIR R5 Final ()
* Core bump

* Build build issues

* Bump core

* Cleanup

* Cleanup

* Resolve intermittent

* Work on core

* Add failing test for a check

* Test fixes

* Fixes

* DOn't mangle subscriptions

* Fix

* License headers

* Build fixes

* Version bump

* Compile fixes

* Fix compile issues
2023-04-28 06:28:22 -04:00
longma1
2171ad04a2
3924 mdm match resources across partitions and storing golden resources on a specific partition ()
* added mdm search all partition for golden resource functionality

* added mdm partition setting

* build header fix

* test fixes and added missing side effect of allowing cross partition links on opeartions

* added changelog, also test fixes

* fixed changelog to an actual yaml file

* review fixes,  also simplified tests

* reverted one test because the original test schenario was correct

* added setting clearing in afterEach method so test dont fail while run in maven

* bump to pre-15

---------

Co-authored-by: Long Ma <long@smilecdr.com>
2023-04-28 02:15:35 -06:00
David
457b39bac1
Fix $mdm clear doesn't expunge golden record resources ()
* Failing test

* Add method to expunge collection of deleted resources

* Failing test passes

* Add changelog

* Version bump

* Forgot to commit change

* Update test

* Check type validity

* Fix broken tests

---------

Co-authored-by: David Chen <david.chen@smilecdr.com>
2023-04-27 21:35:27 -06:00
JasonRoberts-smile
ae1e7400dd
delete operation removes element from list ()
* delete operation removes element from list

* changelog
2023-04-28 00:01:28 +00:00
Tadgh
78b3b148ba
Support _exportId for bulk exports. ()
* Full implementation, test, changelogs

* Add changelogs

* Add default method

* Update hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/export/WriteBinaryStep.java

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

* Code Review Comments

* Compilation failures

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-04-27 21:46:09 +00:00
James Agnew
f9de5c918e
Apply fixes to review comments for ()
* Add post-fetch filtering to bulk export

* Add changelog

* Add validator

* Test fixes

* Test fix

* Review comments for 

* Commit fix
2023-04-27 14:23:01 +00:00
markiantorno
f6094eed47 removing backport tag from 4772 2023-04-27 08:22:13 -04:00
James Agnew
855e10a62d
Add post-fetch filtering to bulk export ()
* Add post-fetch filtering to bulk export

* Add changelog

* Add validator

* Test fixes

* Test fix
2023-04-26 17:05:03 -04:00
Ken Stevens
6b9af3291e
R5 Subscriptions ()
* comments from conversation with Gino

* rewrite R5 subscription canonicalization.  Expect the r5 subscription tests to fail now

* SubscriptionTopicR5Test passes now

* R4B tests pass now

* first two tests in RestHookTestR5Test now pass.  just need to convert the rest

* third test passes

* fourth test passes

* tests pass up to line 294

* wow what a marathon.  Turns out when we stripped the version we didn't remove it from the meta version.

* passes up to 427

* RestHookTestR5Test tests pass up to line 582

* RestHookTestR5Test tests pass up to line 591
Added SubscriptionTopicRegisteringSubscriber

* RestHookTestR5Test tests pass up to line 591
Added SubscriptionTopicRegisteringSubscriber

* RestHookTestR5Test tests pass up to line 636
Added SubscriptionTopicValidatingInterceptor

* RestHookTestR5Test tests pass up to line 689

* RestHookTestR5Test tests pass up to line 758

* 4 failures left

* woohoo all tests pass

* all tests pass and no PointCutLatch errors

* Msg.code

* changelog

* checkstyle

* fix some tests

* compile issue

* fix test

* fix regression

* fix test

* R5 currently runs tests in multiple threads, so change the sensitive one to an IT

* licenses

* review feedback

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-26 17:01:00 +00:00
michaelabuckley
8813d9beda
Batch stabilization ()
* Use java event names for work chunk transitions.

* Cherry-pick d5ebd1f667 from rel_6_4

Avoid fetching work-chunk data ()

* add end time to reduction step ()

* add end time to reduction step

* add changelog

---------

Co-authored-by: Long Ma <long@smilecdr.com>
(cherry picked from commit 37f5e59ffc41e20a3ea7e7f6d3bb05ca6840f642)

* Cancel processing

Provide error message in cancelled jobs, and avoid transitions in final states.

* Apply tx boundary to starting job and first chunk.

* cleanup

* Apply tx boundary to work chunk processing

* Delete BatchWorkChunk

* Introduce events for job create, and chunk dequeue

* Apply tx boundary to chunk handler

* Move instance cancellation to database

* tx boundary around stats collection and completion

* tx boundary around stats collection and completion

* Extend tx boundary to error, fail, and cancel

* Move failure into status calc

* ERROR is not an "ended" state.

* Revert generics cleanup to avoid noise

* Avoid sending gated chunks twice.

* Make no-data path safer.  Cleanup

* Fix mock test for step advance.

* Delete unsafe updateInstace() call

* Cleanup

* Changelog and notes

* Fix cancel boundary.  Cleanups

* Cleanup

* Sort mongo chunks for stable paging.

Other cleanup

* Document error handling

* Cleanup

* Update hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/Batch2JobHelper.java

Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>

---------

Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
2023-04-25 15:47:23 -07:00
Tadgh
d6d2ff531f
4757 externalized binary npe ()
* Basic test for reading from provider

* Basic test for reading from provider

* Failing test

* Add changelog

* Update hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/BinaryStorageInterceptorR4Test.java

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

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2023-04-25 18:34:27 +00:00
michaelabuckley
20c7a32203
Add covering data to res_link index for all tgt->src queries. ()
Add covering data to res_link index for all tgt->src queries.
2023-04-24 23:24:11 +00:00
Tadgh
08c997c169
Compile CDR Master against specific HAPI Branch ()
* Create new workflow

* Remove dead calls
2023-04-24 23:18:40 +00:00
Whiteiguana
b7bc630500
4745 one source record should create no match link with no errors when two golden records are possible matches ()
* created failing test for issue

* remove unused code from IT

* Fixed an issue where marking a golden resource as no match would fail.

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-04-24 14:38:40 -04:00
Brenin Rhodes
9670150f20
4697 - Add Clinical Reasoning Operations ()
* Initial stub out of the CR repo API

* Pagination first pass

* Add HapiFhirRepository and Questionnaire operations

* Add services and providers for ActivityDefinition, PlanDefinition and QuestionnaireResponse

* Simplify the repo usage

* Simplified constructors

* Fix pom

* Setup service config

* Add test

* Add tests

* Add canonical and resource parameters to cr operations

* Add $questionnaire-package operation

* Remove services and cleanup beans

* Cleanup

* Add changelog

* Fix pom

* Add id parameter to extract

* Break out config by IG

* cleanup

* cleanup

* cleanup

* cleanup

* Add type level operations

* Move loadProvider call out of constructors with an EventListener annotation

* Cleanup package operation

* Update BaseCrR4Test.java

* cleanup

* cleanup

* Fix tests

* Fix test

* Fix $package arguments

* Remove $questionnaire-package

* Add r5 apply operation name

* Remove config

* cleanup

* cleanup

* cleanup

* cleanup

* Comment out failing tests.  Fix coming in another branch.

* Fix config for 1.3 cql measure tests

* Fix checkstyle

* Change measure service config to resolve intermittent test issues

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-04-24 14:37:55 -04:00
TipzCM
1c0addafeb
transaction bundle multi-threading issues ()
* a solution for trying to avoid multi-thread issues for transaction bundle processing

* cleanup

* using retries

* mnor tweaks

* checking in

* changes

* updating changelog

* some minor tweaks

* cleanup

* flip if

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-20 18:43:37 +00:00
Ken Stevens
58850fed82
try removing fork count from surefire ()
* try removing fork count from test-r4

* try removing fork count from the rest of the projects

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-20 13:58:35 -04:00
Qingyixia
55613a9bf2
Fixed the Null Pointer Exception on mdm-submit operation ()
* Fixed the Null Pointer Exception on mdm-submit operation

* Addressing suggestion
2023-04-19 12:24:39 -07:00
Qingyixia
6eafd3fe5d
The Lenient error handler will now throw exceptions when encode invalid extension containing value and nested extensions ()
* The Lenient error handler will throw exceptions when encode invalid extension containing value and nested extensions

* Addressing suggestions

* Minor changes

* Minor fix
2023-04-18 13:59:23 -04:00
Ken Stevens
9e741cb145
remove enabled flag and instead only create the subscription topic beans in the fhir versions that use them ()
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-18 10:20:43 -04:00
samguntersmilecdr
396007af40
test + change + changelog () 2023-04-18 09:25:15 -04:00
Etienne Poirier
88459d0d00
4657 method name is inconsistent with the method behavior ()
* Test implementation

* providing method getMessageKeyOrDefault();

* providing changelog

* preping codereview.

* Deprecating method getMessageKeyOrNull in favor of getMessagekey()

* updating comments following code review.

* Bumping version to 6.5.13-SNAPSHOT

* passing all tests.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-04-17 10:41:08 -04:00
James Agnew
7bdbda9ef0
Improve Subscription Retriggering Efficiency ()
* Improve subscription efficiency

* Reduce number of queries

* Add changelog

* Fix ITs

* Review comments

* Test fix
2023-04-17 08:18:57 -04:00
michaelabuckley
83f216bcee
Add old-intellij profile to support the old way. ()
Activate the `old-intellij` profile to get the old behaviour
where everything is Java 17.
2023-04-14 21:38:38 +00:00
Luke deGruchy
35bd1c400a
Fix bundle auto-create by checking for IBaseReference.hasIdentifier() before validating URL-based references ()
* First commit:  New tests, logs, and comments.

* Add hacky fix to run pipelines on.   Add another unit test.

* Disable baseUrl checking if hasIdentifier() is true.

* Add changelog.  Tweak unit tests.

* Remove junk.

* Add more assertions to unit tests.  Make new production fix code clearer.

* Add more clarity to unit tests.

* Another unit test fix.
2023-04-14 17:55:31 +00:00
James Agnew
869b6c306a
Allow transaction with conditional create and patch in same bundle ()
* Allow transaction with conditional create and patch in same bundle

* Add changelog

* Cleanup
2023-04-13 15:51:46 -04:00