Commit Graph

1712 Commits

Author SHA1 Message Date
leif stawnyczy 441fd67bc7 Merge branch '5745-ready-state-batch2' into 5767-add-poll-waiting-step 2024-04-12 09:55:42 -04:00
leif stawnyczy e72016482f Merge branch 'master' into 5745-ready-state-batch2 2024-04-12 09:54:10 -04:00
JasonRoberts-smile e3cc83a694
fix bug (#5843) 2024-04-12 00:19:56 +00:00
leif stawnyczy e483736f73 Merge branch '5745-ready-state-batch2' into 5767-add-poll-waiting-step 2024-04-08 16:03:10 -04:00
leif stawnyczy 8d84ed0b94 merging in masters 2024-04-08 15:46:33 -04:00
TipzCM 107de2cfba
reduction step failing fails jobs (#5831)
* adding a catch for failing reduction step

* spotless

* added changelog

---------

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

* test refactor only

* spotless

* bumping version

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-04-05 21:39:03 -04:00
TipzCM 620b46dd0a
unify bulk export patient type and bulk export patient instance (#5822)
* step one of unifying the bulk exports

* adding changelog

* review points

* spotless

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-04-05 19:03:16 +00:00
Ken Stevens 3a5ff47c58
Add CapabilityStatementFilterFactory to register filters that can modify the capability statement (#5814)
* added new customizer filter factory.  have not yet deleted old code it replaces.

* added new customizer filter factory.  have not yet deleted old code it replaces.

* replaced websocket filter.  works.  still some cleanup to do

* replaced websocket filter.  works.  still some cleanup to do

* cosmetic change

* add coverage and fix bugs it found

* spotless

* move capability statement classes

* add changelog and rename new classes

* review feedback
2024-04-05 01:24:05 +00:00
Michael Buckley bdea4b6900
Merge history table prefetch with resource table. (#5825) 2024-04-04 23:53:35 +00:00
Michael Buckley fcf0a85584
Stop writing to hfj_forced_id (#5817)
Stop writing to hfj_forced_id
Stop reading ForcedId
Cleanup client-id assignment
Fix query counts in tests
Drop the unused indexes and fk
2024-04-03 18:25:23 +00:00
leif stawnyczy 571b4cb210 merging up 2024-04-03 14:08:05 -04:00
tyner 6c5e1a118f Revert "- Implemented GATE_WAITING state for the batch2 state machine."
This reverts commit 32a00f4b81.
2024-04-03 10:47:18 -04:00
tyner 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
2024-04-03 10:44:08 -04:00
JasonRoberts-smile 1736dadfcf
Jr 20240325 concept map unmatched codes (#5809)
* update model

* convert results

* migration

* extend test coverage in cli

* fix broken test

* change log

* code review feedback

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

* add pr number to docs

* fix test

* remove unnecessary code

---------

Co-authored-by: Lila Mikalson <lila.mikalson@smilecdr.com>
2024-04-02 20:26:33 +00:00
leif stawnyczy 74319a7b6d Merge branch 'master' into 5745-ready-state-batch2 2024-04-02 14:55:07 -04:00
leif stawnyczy 7f6d1aa9c7 review fixes round 2 2024-04-02 10:57:14 -04:00
Emre Dincturk 70843cdf45
fixed resource fullUrl in _history bundles (#5815) 2024-04-01 15:21:18 -04:00
leif stawnyczy ba67d6fa82 Merge branch '5745-ready-state-batch2' into 5767-add-poll-waiting-step 2024-04-01 11:16:33 -04:00
leif stawnyczy 439d24376d updating diag 2024-04-01 11:16:16 -04:00
leif stawnyczy eb852e06d6 revert 2024-04-01 11:16:03 -04:00
leif stawnyczy da86cd1dd8 Merge branch '5745-ready-state-batch2' into 5767-add-poll-waiting-step 2024-04-01 11:14:21 -04:00
leif stawnyczy c8b33881f0 update state diagram 2024-04-01 11:13:34 -04:00
James Agnew 6ce3b17460
Enforce maximum chunk size in bulk export (#5800)
* Limit bulk export chunk size

* Cleanup

* Work on tests

* Working

* Add some docs

* Address revuew comments

* Spotless

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

* Fix formatting in javadoc causing warning

* Update to 3.0.0 CR release

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

* Update Clinical Reasoning documentation

* Update pom.xml

* Create 5750-update-cr-operations.yaml

* fix doc

* Update to latest CR version

* Update pom.xml

* In version

* Update changelog

* Remove commented code
2024-03-28 11:44:29 -07:00
James Agnew 6175807f58
Reduce use of LOB columns (#5799)
* Reducer LOB usage in Batch2 and Search (#5748)

* Reducer LOB usage in Batch2 and Search

* Add changelog

* Rework a number of LOB columns

* Test fix

* Test fix

* Column fixes

* Test fix

* Formatting

* Fixes

* patching bad oracle test

* Apply spotless

---------

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

* Clean up

* Revert change

* One more revert

* Resolve compile issue

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2024-03-27 18:19:07 +00:00
Etienne Poirier 2f9693a1e4
MDM expansion doesn't work when using the :mdm qualifier in query string (#5803)
* 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
leif stawnyczy bde9947283 updating documentation and adding change log 2024-03-25 15:30:27 -04:00
Nathan Doef 7742aa76c5
Retain X-Request-ID header key casing in responses (#5787)
* failing test

* fix

* changelog

* spotless

* fix tests
2024-03-20 16:08:05 +00:00
Michael Buckley 7067cf4491 sketch out test cases 2024-03-18 13:29:41 -04:00
Michael Buckley d6bc8f2e1b
Sort by Bundle chained composition SPs (#5785)
Add support for sorting by special Bundle chained composition SPs
2024-03-15 18:50:50 +00:00
Tadgh 7344f01217
Improve search bundle parts (#5781)
* Respect other non-match/include entries

* Changelog

* minor license files

* Another test
2024-03-15 09:29:53 -07:00
Brenin Rhodes 7005e83b03
Change CDS on FHIR Prefetch (#5778)
* Change CR services to use auto prefetch and not pass fhirServer as dataEndpoint

* Add documentation for CDS Hooks
2024-03-15 10:01:58 -04:00
Etienne Poirier fc4c31a779
5771 patch operation failing for complex extension (#5776)
* initial failing test

* tightening initial test.

* fix with changelog

* addressing comment from code review.

* clean up from code analysis recommendations

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2024-03-12 13:59:36 -04:00
dotasek 2f53a32f9d
Fix for #5773 (#5774)
* Breaking test and null check

* Changelog
2024-03-11 16:15:44 +00:00
leif stawnyczy 5f5ea1c49e Merge branch '5745-ready-state-batch2' of github.com:hapifhir/hapi-fhir into 5745-ready-state-batch2 2024-03-08 15:10:42 -05:00
leif stawnyczy 3f190009b3 code review points 2024-03-08 15:09:29 -05:00
leif stawnyczy 65d9d0d34b Merge branch 'master' into 5745-ready-state-batch2 2024-03-08 11:40:29 -05:00
leif stawnyczy d7633a80a4 updated batch 2 framework with READY state 2024-03-06 15:25:25 -05:00
TynerGjs df047a9dea
Resolve 5758-completion-handler-for-reduction-steps-are-not-called-with-the-up-to-date-job-instance-status (#5759)
* updated instance status after run is called.

* added changelog

* version bump
2024-03-06 11:01:42 -05:00
leif stawnyczy 56f5697149 step 1 2024-03-05 14:36:28 -05:00
Luke deGruchy 4570c28cb6
Fix _has then chain then _has searches (#5735)
* Add SQL logging:  Attempt to add test.

* Small fix.

* moar tests

* Tweak unit tests to be parameterized.

* Enhance tests and more logging.

* Better tests.  More logging.  More TODOs.

* Better tests.  More logging.  More TODOs.

* Changes

* Changes

* Updates to tests.  More logging and experimental code.

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

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

* Add changelog.

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

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

* Fix comment.

---------

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

* fix

* fix

* improve / fix old tests

* changelog

* cleanup

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

* unwinding

* fixing changelog

* spotless

* review fixes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-03-04 09:12:31 -05:00
longma1 f5cc015ff3
Added correction to generated resource providers (#5743)
* Added correction to generated resource providers

* add changelog and fix issue that was adding languange SP to version that does not have language as a SP

* actually fix the test

* fix changelog wrong issue number

---------

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
2024-02-27 22:12:23 +00:00
Tadgh 28b8662637
Rel 6 4 mb update (#5741)
* Add backport and folder

* Add missing changelog

* Cherry p icking

* Update upgrade.md

* added new version version.yaml

* Provide default update time to batch2 entities (#4630)

* Data migration - default value for batch2 UPDATE_TIME

* fixed changelog, added 6.4.3 changelog folder

* Spotless

---------

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: longma1 <long@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2024-02-27 17:50:01 +00:00
Luke deGruchy 497b9f2e53
Fix FhirTerser to handle Enumeration correctly (#5726)
* Add test for CDA with binary database blog storage and some logging for the Terser.

* More logging and a new FhirTerser test.

* Add more comments and prove Enumeration is a valid subtype of Type.

* More logging and comments.

* James solution:  Comment out some code.  Spotless.

* Get rid of logging and TODOs.  Use AtomicBoolean for test.

* Try just commenting out the continue; line.

* Integrate changes from ja_20240222_choice_specialization_fix.

* Spotless.

* Changelog and fix for bad import.

* Code review feedback.
2024-02-26 15:10:12 +00:00
Artiom Darie d8f6c10df2
Added content message delivery for SubscriptionWebsocketHandler (#5692)
* Added content message delivery for SubscriptionWebsocketHandler

* 5687: Code clean up and small bug fix on empty payload

* 5687: Provided unit tests for the SubscriptionWebsocketHandler with subscription topic content: id-only, empty and full-resource

* 5687: Apply mvn spotless:apply

* 5687: Code formatting

* Credit for #5692

---------

Co-authored-by: artiom.darie <artiom.darie@adswizz.com>
Co-authored-by: Artiom Darie <5781864-artiom.darie@users.noreply.gitlab.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-02-26 08:54:04 -05:00
jmarchionatto 2c2afd4a83
Hibernate SQL log filtering feature (#5594)
* Hibernate SQL log filtering feature

* changelog

* Add exception msg codes

* Improve test which failed in pipeline

* Join tests to avoid threading issues

* Fix comment

* Add review suggestions

* Add extra documentation including example.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/appendix/logging.md

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

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-02-25 09:09:56 -05:00