10131 Commits

Author SHA1 Message Date
Michael Buckley
ecd0507315
Add lighter description to pointcut invoker (#6774)
* Hapi pointcuts in file
* Bump
2025-03-06 10:36:44 -08:00
TipzCM
7f3ff6fde4
6716 fixing error msg update code (#6764) 2025-03-06 08:51:00 -05:00
Joanne Mendoza
1321fa312c
6713 support for patient parameter in group export (#6753)
* Parse patientIds from reference list

* spotless

* changes to search parameter map for group export

* spotless

* minor change

* fix test and code

* test for group export on id with patient parameter and minor cleanup to JpaBulkExportProcessor

* spotless

* cleanup

* Use ReferenceParam for ID

---------

Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>
Co-authored-by: Vadim Karantayer <vadim.karantayer@smilecdr.com>
Co-authored-by: ad1306 <adave.dev@gmail.com>
2025-03-04 08:58:01 -05:00
Ken Stevens
2712bdefe6 fix warnings 2025-03-02 22:19:29 -04:00
Ken Stevens
f4d1315494 clean up kafka receiver 2025-03-02 21:16:59 -04:00
markiantorno
8676cf2045 removing azure pipelines pull request files 2025-02-27 16:53:57 -05:00
Luke deGruchy
f3c09d6cc1
hapi-fhir-storage-cr: Disable conformance validation to speed up storage-cr tests. (#6760)
* Disable conformance validation to speed up storage-cr tests.

* Code review suggestions.
2025-02-26 13:12:56 -08:00
TipzCM
41c2e49669
Validation with unknown profile (#6608)
* failing test for invalid profile during validation

* to address validation to fail for unknown profile

* updates to address bringing back the class name that was mistakenly dropped out

* updated the logic and some dependent test cases

* spotless:apply changes

* fixed the existing test cases that were failling due to invalid profile validation logic being added

* remove unnecessary comments

* added changelog

* added jira: SMILE-9129 to changelog

* addressing PR comments

* spotless:apply updates

* addressing code review suggestions

* code review updates

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: Buland Malik <bulandaltaf@gmail.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2025-02-24 08:22:35 -08:00
tadgh
250dae3c73
Final 8.0.0 Mergeback (#6756)
* 6711 everything operation with partitioning enabled returns duplicates since the dbpm merge (#6712)

* Add test stub

* Changelog

* Wording

* Trying to get test working

* Initial commit of tests and potential hash fix

* Remove json file

* Remove dead code

* Remove dead test, spotless, fix changelog

* Limitation

* Version bump to 8.0

* With partitioning selection mode set to request tenant, creating a cross partition subscription will fail if the default partition id is not null (#6748)

* initial failing test

* fix with changelog and modification to previous changelog

---------

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

* Updating version to: 8.0.1 post release.

* Spotless

---------

Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: tadgh <garygraham@smiledigitalhealth.com>
2025-02-24 08:18:39 -08:00
Xun Ma
9ae60f1203
Ignore contained resources in IPA generation reference check so they are not removed (#6754)
* Ignore contained resources in IPA generation reference check so they are not removed

* Fix coding display to exactly match LOINC, otherwise validator complains

* Add test case to verify contained resource reference being retained

* Credit for #6754

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2025-02-24 08:40:54 -05:00
Michael Buckley
20a1c56985
Add troubleshooting log for partition routing. (#6719)
* Create new log and docs.

* Implement start of logging.

* add to logback

* spotless

* Fix refactor error

* spotless

* Add details to SRD logs

* Add details to SRD logs

* Commit to trigger fresh build
2025-02-23 22:34:20 -08:00
Nathan Doef
5153ac70de
Fix Malformed Headings in caregaps.md (#6752)
* fix malformed headings

* more fixes
2025-02-20 11:58:30 -05:00
TipzCM
52d2c9599d
intermittent fix (#6751) 2025-02-20 07:55:14 -05:00
TipzCM
d812a08408
truncate error messages for storage on workchunks (#6717) 2025-02-19 20:05:09 +00:00
James Agnew
4d66c6c042
Remove vagrant (#6746)
* Remove vagrant

* Add changelog
2025-02-18 16:15:40 -05:00
James Agnew
df6abd1674
Remove HTTPClient dependency in hapi-fhir-base (#6707)
* Remove HTTPClient dependency in hapi-fhir-base

* Spotless

* Compile fix
2025-02-18 11:23:51 -05:00
Etienne Poirier
57ee0240d4
Fix to unnecessary resource version bump on update (#6715)
* initial failing test.

* solution with changelog

* spotless

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2025-02-14 10:50:03 -05:00
Tadgh
066c242619 Merge branch 'rel_8_0_mb' 2025-02-12 14:06:41 -08:00
Tadgh
78537ba9b0 Spotless 2025-02-12 13:42:29 -08:00
Dylan Krause
c9889a9048
Upgrade uses of Jena to 5.3.0 (#6704)
* Upgrade uses of Jena to 5.3.0
-fixes CVE-2024-7254 in dependencies prior to 5.2.0
-hapi-fhir-base: include httpclient dependency which was removed from jena-arq
-hapi-fhir-base RDFParser: init JenaSystem on initialization
-hapi-fhir-base RDFParser: specify signature for null values on methods that are overloaded
-hapi-fhir-base RDFUtil: Jena Riot RDFDataMgr no longer accepts reading and writing
into generic reader and writer. Handle reading for StringReader and InputStreamReader.
Handle writing by building an output stream from the writer.
-hapi-fhir-structures-r4: Remove shexjava dependency - unmaintained
-hapi-fhir-structures-r4: Use jena-shex for shex validation
-hapi-fhir-structures-r4 RDFParserTest: use jena libraries - compatibile with jena-shex
-hapi-fhir-structures-r4 RDFParserTest: simplify FixedShapeMapEntry by attaching nodes vs recreating them (handles blank nodes)
-hapi-fhir-structures-r4 RDFParserR4Test: jena 5.0.0 defaults to using PREFIX, not @prefix. Read testing strings and
use isomorphic comparison to check for equality. Added extra assertion to test isomorphism check.

* Credit for #6704

* Add missing error codes to exceptions

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2025-02-12 16:41:34 -05:00
Tadgh
750c7ee1ef Merge branch 'master' into rel_8_0_mb 2025-02-12 13:30:17 -08:00
Tadgh
7bf0379371 Merge branch 'rel_8_0' into rel_8_0_mb 2025-02-12 13:22:13 -08:00
Tadgh
6f49934c04 Interim folder holder 2025-02-12 13:21:57 -08:00
Tadgh
a9be258278 Merge rel 8 in 2025-02-12 13:21:07 -08:00
elavy-harris
a8a6600c86
Typo fix from 5368 (#6705) 2025-02-12 15:31:32 -05:00
Tadgh
e720011321 licenses 2025-02-12 11:07:25 -08:00
Tadgh
7bc81b10cd Move to 8.0.0 2025-02-12 10:58:13 -08:00
elavy-harris
51da282870
5227-Documentation-for-STORAGE_TRANSACTION_PROCESS (#6676)
* 5227-Documentation-for-STORAGE_TRANSACTION_PROCESS

* Update Pointcut.java
2025-02-12 13:56:54 -05:00
elavy-harris
71aefee8c5
5368-Lenient-error-handler-doesn't-always-include-location-information (#6678)
* 5368---Lenient-error-handler-doesn't-always-include-location-information

* Credit for #6678

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2025-02-12 13:56:40 -05:00
tadgh
0a79f4e153
6700 alternate api (#6702)
* Make the Canonicalizer non-null-default-partition-id aware

* Rename test

* Changelog

* Rework

* Remove dead IT

* remove fixme
2025-02-12 18:48:03 +00:00
Mark Iantorno
1385edc59b
Update pull-request.yml
Triggering on MR again.
2025-02-11 16:44:18 -05:00
James Agnew
d503a24cfd
Add flag to disable schema check (#6699)
* Add flag to disable schema check

* Spotless
2025-02-11 14:48:13 -05:00
markiantorno
d5ff993f6b Update to github pr pipeline to cache HAPI inter-module deps separately from all other maven deps. 2025-02-11 14:08:41 -05:00
James Agnew
6b4acc3811
Account for case differences in DBPM contributor (#6698)
* Account for case differences in DBPM contributor

* Test fix

* Cleanup
2025-02-11 10:28:33 -05:00
Etienne Poirier
a579d8ff28
Fixing Failure when creating a cross-partition subscription if the default partition id is not null (#6687)
* initial test, solution and changelog

* addressing comments from code review.

* addressing code review comments and fixing tests.

* addressing code analysis issues.

* addressing code analysis issues.

* fixing failing tests

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2025-02-11 00:57:33 +00:00
Abayomi Adebowale
ce0c41c2ef
Fixed an issue with the _lastUpdated search param not being recognised as a valid sort spec with Elastic Search enabled. (#6670)
* added test for '-delt-add' in hapi

* fixed an issue with the _lastUpdated search param not being recognized as a valid sort spec with Hsearch enabled in CDR

* added null check

* added tests

* added comments

* addressed comments

* updated static class property name

* modified test

* added changelog and addressed more comments

* ran mvn spotless

* addressed comments

* ran mvn spotless

* addressed comments

---------

Co-authored-by: Abayomi Adebowale <abayomi.adebowale@smiledigitalhealth.com>
2025-02-10 17:00:11 -05:00
TipzCM
65e4b13c80
6673 fixing search builder with fulltext search (#6674) 2025-02-10 17:14:37 +00:00
Nathan Doef
d9f86a92ac
Fix _security label filtering with :not operator in the in-memory matcher (#6691)
* failing test

* narrow failing test

* fix

* changelog

* clean up

* spotless
2025-02-10 10:27:32 -05:00
Michael Buckley
ebb016f9a7
Provide access to the wrapped ConsentService delegates for testing (#6694)
Add getters to delegating ConsentService classes
2025-02-08 11:43:39 -05:00
Emre Dincturk
637a79f2ba
made $hapi.fhir.replace-references not replace versioned references (#6684)
* made replace-references not replace versioned references
2025-02-07 08:29:19 -05:00
Emre Dincturk
489bfc837d
fix high cardinality field patching in replace-references (#6671) 2025-02-04 22:35:54 +00:00
VK-SMILECDR
bbff855f70
revert (#6682) 2025-02-04 20:24:40 +00:00
Tadgh
c096c31dea License 2025-02-04 10:52:33 -05:00
Tadgh
becbf1de78 Merge branch 'rel_8_0' into rel_8_0_mb 2025-02-04 10:39:25 -05:00
Buland Malik
a708949d38
SearchParameter validation was not being skipped on updates, even if … (#6667)
* SearchParameter validation was not being skipped on updates, even if requested. This has been fixed

* spotless fixes

* removed unecessary code

* reverting the code back

* added external JIRA ref
2025-02-03 17:15:34 -08:00
jdar8
a4fa6540bb
Fix NPE in Storage with Mass Ingestion and Compartment Interceptor (#6598)
* add tests and fix mass ingestion and patient compartment interceptor compatibility in mass ingestion mode

* changelogs

* address review - add parameter class for method with 10 params

* spotless

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>
Co-authored-by: Kevin Dougan <72025369+KevinDougan@users.noreply.github.com>
2025-02-03 19:45:34 +00:00
volodymyr-korzh
024515e0c1
Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_8_0 (#6668) 2025-02-01 02:18:38 +00:00
Emre Dincturk
d636df3d8f
fix fhir patch replace in a list (#6657) 2025-01-31 22:28:01 +00:00
Mark Iantorno
7e8ac9007d
Update pull-request.yml 2025-01-31 13:15:10 -05:00
jmarchionatto
8d60820554
6662 remote terminology boolean properties as string (#6663)
* Add test for failing use case and fix by adding Boolean property for remote validation

* changelog

* Revert not yet supported change
2025-01-29 16:24:23 -05:00