Commit Graph

9805 Commits

Author SHA1 Message Date
Martha f7b58710ef Merge remote-tracking branch 'origin/master' into mm-20240408-introduce-container-ord-seach-parameter-and-populate 2024-04-09 11:49:33 -07:00
Martha 8b0441ae3e Fix build errors. Update containerOrd field to short instead of integer. 2024-04-09 11:13:37 -07:00
Luke deGruchy 4d8427ad60
Ensure CanonicalizedSubscription reflects StorageSettings.isCrossPartitionSubscriptionEnabled if it's true. Make that setting is true by default (#5810)
* First commit with TODOs and logging.

* Try to add cross partition config at startup to subscription module.

* Barely working solution with JpaStorageSettings injected into the Subscription module with the correct config for cross partition enabled.

* Implement agreed upon solution where StorageSettings used in the subscription module uses the JpaStorageSettings cross partition enabled setting.  Fix all compile errors.  TODOs for tests to add and known test failures.

* Fix test errors caused by bad log code.   Ensure all modules use StorageSettings for canonicalizer.

* Cleanup.

* Reintroduce old SubscriptionCanonicalizer constructor, but add a StorageSettings and deprecate it.  Cleanup logs and TODOs.

* Deprecate FHIR_PATCH.  More cleanup.

* Deprecate FHIR_PATCH correctly.

* Small fix.

* Set myCrossPartitionSubscriptionEnabled to true by default.

* Fix test failures.

* Fix another test.

* Code review feedback.

* Resolve static analysis warnings.
2024-04-09 14:27:15 +00:00
Martha 65a4fcc17f Introduce container ordinal in the search paramter index tables. Populate the value when the indexes are built. Refactor to decouple entities from settings and from hashing logic. 2024-04-08 14:37:48 -07:00
TipzCM 57fdc2d5c1 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 13:46:11 -07:00
Ken Stevens 56cc596df1 move mdm interceptor registration (#5830)
* licenses

* remove mdm placeholder interceptor

* remove mdm placeholder interceptor

* fix regression

* Remove RTE Placeholder Interceptor.
Add tests to assert proper boot sequence.

* consolidate LogbackCaptureTestExtension (removed the cdr class)

* consolidate LogbackCaptureTestExtension (removed the cdr class)
2024-04-08 13:46:11 -07:00
TipzCM f472555bd5 Batch2 test refactor only (#5823)
* refactoring

* test refactor only

* spotless

* bumping version

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-04-08 13:46:11 -07:00
TipzCM 54155d5572 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>
2024-04-08 13:46:11 -07:00
Ken Stevens 4b2db7913f 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
2024-04-08 13:46:11 -07:00
Michael Buckley b4dacb3596 Merge history table prefetch with resource table. (#5825) 2024-04-08 13:46:11 -07:00
Michael Buckley e4ba56ed3a 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
2024-04-08 13:46:11 -07:00
JasonRoberts-smile b608633dcb 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
2024-04-08 13:46:11 -07:00
Lila Mikalson c49f808d04 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>
2024-04-08 13:46:11 -07:00
Emre Dincturk 9c790f43f4 fixed resource fullUrl in _history bundles (#5815) 2024-04-08 13:46:11 -07:00
James Agnew 7428112390 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
2024-04-08 13:46:11 -07:00
Nathan Doef e6f8f9d2e3 Fix BaseOutcomeReturningMethodBinding NullPointer (#5808)
* failing test

* fix

* add @Nullable
2024-04-08 13:46:11 -07:00
Brenin Rhodes 4c519e1ec8 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
2024-04-08 13:46:11 -07:00
James Agnew 8406aac67c 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>
2024-04-08 13:46:11 -07:00
Etienne Poirier 82ba851f86 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>
2024-04-08 13:46:11 -07:00
Tadgh cf98de9b60 CVE 2024 03 26 (#5804)
* CVE-2024-1597

* CVE-2024-22243
2024-04-08 13:46:11 -07:00
TynerGjs 168a813076 Resolve 5790 Prefix a unit test log for hibernate exception in HapiFhirHibernateJpaDialect (#5791)
* prefixed the log message with "Unit test: "

* resolved review comments
2024-04-08 13:46:11 -07:00
Nathan Doef c0931bc356 Retain X-Request-ID header key casing in responses (#5787)
* failing test

* fix

* changelog

* spotless

* fix tests
2024-04-08 13:46:11 -07:00
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
Ken Stevens eafa2aba29
move mdm interceptor registration (#5830)
* licenses

* remove mdm placeholder interceptor

* remove mdm placeholder interceptor

* fix regression

* Remove RTE Placeholder Interceptor.
Add tests to assert proper boot sequence.

* consolidate LogbackCaptureTestExtension (removed the cdr class)

* consolidate LogbackCaptureTestExtension (removed the cdr class)
2024-04-08 08:59:54 -07:00
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
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
Emre Dincturk 70843cdf45
fixed resource fullUrl in _history bundles (#5815) 2024-04-01 15:21:18 -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
Nathan Doef 9e5db198bf
Fix BaseOutcomeReturningMethodBinding NullPointer (#5808)
* 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 (#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
Tadgh 4d4d8b25d4
CVE 2024 03 26 (#5804)
* CVE-2024-1597

* CVE-2024-22243
2024-03-26 14:58:16 -07:00
TynerGjs 4a726dd2d1
Resolve 5790 Prefix a unit test log for hibernate exception in HapiFhirHibernateJpaDialect (#5791)
* prefixed the log message with "Unit test: "

* resolved review comments
2024-03-20 13:36:21 -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
Martha Mitran bb7434c9cc Disable failing tests 2024-03-19 12:41:39 -07:00
Martha Mitran f730befc6f Merge remote-tracking branch 'origin/dmuylwyk-contained-search-param' into 5285-support-for-contained-true-search-parameter 2024-03-18 13:39:22 -07:00
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
Luke deGruchy ba5311d4cc
Add comment to test method making clear its dubious value. (#5782) 2024-03-14 13:46:32 +00:00
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
Tadgh 519f0cf69e
Add annotation to config class (#5769) 2024-03-08 21:51:46 +00:00
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