Commit Graph

256 Commits

Author SHA1 Message Date
longma1 078e87a4aa
7 2 mergeback may 10 v2 (#5928)
* Enhance RuleBuilder code to support multiple instances (#5852)

* 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 (#5866)

* 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 (#5881)

* 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 (#5811)

* 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 (#5883)

* 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 (#5889)

* Ensure temp file ends with "." and then suffix. (#5894)

* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)

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

* Enhance mdm interceptor (#5899)

* 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 (#5896)

* 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 (#5903)

* 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 (#5906)

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

* Fixing issues with postgres LOB migration. (#5895)

* 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 (#5915)

* Enhance RuleBuilder code to support multiple instances (#5852)

* 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 (#5866)

* 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 (#5881)

* 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 (#5811)

* 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 (#5883)

* 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 (#5889)

* Ensure temp file ends with "." and then suffix. (#5894)

* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)

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

* Enhance mdm interceptor (#5899)

* 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 (#5896)

* 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 (#5903)

* 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 (#5906)

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

* Fixing issues with postgres LOB migration. (#5895)

* 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 (#5917)

* 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 (#5851)
* 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
Tadgh 8a37223106 Version bump 2024-04-21 13:20:55 -07:00
Justin McKelvy e400db5fb8
collect-data and data-requirements operations and tests (#5854)
* 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 (#5846)
* added an additional pointcut

* spotless

* version bump

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2024-04-15 19:36:27 -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
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
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
longma1 28a1a4d4df
Rel 7 0 mb 2 (#5714)
* pom bump to 7.0.0 (#5615)

* pom bump to 7.0.0

* add version enum

* fixed feb release name

---------

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

* Check index existence on raw SQL creation (#5624)

* Add conditional check on index existence before we try again

* Add conditional check on index existence before we try again

* Changelog

* remit

* remit

* debug statements

* 5621 deadlock on caffeine cache when creating a resource with conditional create (#5622)

* Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback.

* Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations.

* adding changelog and spotless.

* Fixing typo.

* Addressing comments from code review.

---------

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

* Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)

* Failing test

* fix

* changelog

* Avoiding Exception being thrown on @EventListener invocation (#5628)

* replaced EventListener annotation with @PreDestroy

* adding changelog

---------

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

* simple fix (#5630)

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

* Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625)

* Incorrect version from versioned_references.auto_at_paths for conditional update - implementation

* Oracle:  Ensure migrated database still takes large resource text updates (#5629)

* First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration.

* First stab at agreed upon solution.

* Fix error with 4001 by removing unnecessary annotation.

* Spotless and TODO.

* Remove annotation for good and set length to LONG32.

* Fix copyright year.

* Finalize changelog.

* Remove migration changes.  Fix unit test.

* Fix compile error.

* Log output.

* Refactor resource history code into new ResourceHistoryCalculator.

* Spotless.

* Convert record to POJO.

* Restore pre-17 switch statement.

* Finalize new resource history calculator code and tests.

* Spotless.

* Remove logging.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml

Apply code reviewer suggestion

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

* Code review feedback.

---------

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

* Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638)

* When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases.

* Minor change to fix test

* Rename changelog file

* Remove TODOs as they're replaced by reported issue

* Revert accidental change added with TODO removal

* $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)

* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation

* Fix Measure group id null pointer exception (#5620)

* Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id

* add changelog

---------

Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>

* Rule evaluation:  Allow Bundles with PATCH Parameters (#5641)

* Remove parameters clause.

* Finalize changelog.  Add tests.  Finalize implementation.

* Undo changes to this test.

* Revert all changes to FhirQueryRuleImplTest.  Add new RuleImplOpTest.  Ensure that proper nested Bundle is created for test and other fixes.

* Tweak test.

* Use real rule applier in test and remove all mocks.

* Prevent batch2 job execution to stop for empty chunk when last job st… (#5635)

* Prevent batch2 job execution to stop for empty chunk when last job step is a reduction.
Add output to bulk export result even when empty.

* Fix test

* Unimportant change to force fresh build

* Implement review suggestions

---------

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

* Index review fixes (#5649)

* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.

* Fix conditional creates without leading '?' (#5646)

* First commit with failing test.

* More tests and logs.

* More logs

* Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl().

* Simplify solution.  Add more tests.

* Changelog.

* javadoc

* Searching for Bundles with read all Bundles permission returns 403 (#5644)

* failing test

* another failing test case

* fix

* changelog

* fix bug

* spotless

* cr

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* Serializing changes for sensitive data (#5655)

* Add new senstiive data serializer

* Add new senstiive data serializer

* Add new senstiive data serializer

* Remove dead comments

* Change up the test

* review comments

* wip

* Tighten tests and push annotation down

* Tighten tests and push annotation down

* Changelog

* Add test

* 7.0.1-SNAPSHOT bump

* Error code

* Add method used by CDR

* add version enum

* Fix test

* Revert change to other safe version to stop problem with deprecated field

* Rel 7 0 CVE (#5663)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* Descendent fix (#5669)

* Fix "is-a" ValueSet expansion, add "descendent-of" support

* Fixed tests in DSTU3 and R5

* Trigger new build

* Revert "Trigger new build"

This reverts commit 46c672b338.

* fix default partition setting on resource (#5617)

* fix default partition setting on resource

* changelog

* Handle DEFAULT partition in rule checker.

* Fix spotless

---------

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

* pom bump, doc add, version enum add (#5616)

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

* fix default partition setting on resource (#5618)

* fix default partition setting on resource
* Handle DEFAULT partition in rule checker.

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

* Add setting to make broker not use JacksonMessageConverter (#5611)

* Add setting to make broker not use JacksonMessageConverter

* Add changelog

* Implement suggestions

---------

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

* Fix version

* add changelog, add attribution, remove accidental bring-overs

* add changelog, add attribution, remove accidental bring-overs

* Finish jira section

---------

Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* $poll-export-status operation with PatientIdPartitionInterceptor fails with NullPointerException (#5681)

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor.

* Fix NPE on -export-status operation with PatientIdPartitionInterceptor

* 5654 measurescorer bug for denominator exception (#5677)

* update measure bundles and tests for enforced populationId specification on Measure group resources

* bump CR version to PRE17

* fix bug in versionEnumTest

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5654-measurescorer-bug.yaml

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

---------

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

* Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type. (#5698)

* Revert Remote Terminology lookup operation to support all types of CodeSystem property and convert to them to string type.

* Spotless fix

* Address code review comments

* version bump to 7.0.0

* pipeline fix

* Update java home

* Updating version to: 7.0.1 post release.

* post mergeback cleanup

* bump clinical-reasoning.version to pre17

* test fix

* version bump to 7.1.5-snapshot

---------

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.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: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
2024-02-23 11:03:26 -07:00
James Agnew ec525f4457
Apply SearchNarrowingInterceptor to conditional URLs (#5712)
* Fix #5110 - Failure in tx processing

* Test fix

* Work on narrowins

* Add changelog

* Docs cleanup

* Fix compile error

* Rollback incompatible change

* Test fix

* Test fix

* Force update

* Test fixes

* Build fixes

* Bump HTMLUnit

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5712-apply-searchnarrowing-to-conditional-urls.yaml

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

* Address review comments

* Version bump to 7.1.4-SNAPSHOT

* Spotless

* Roll back version

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2024-02-23 08:42:26 -05:00
Michael Buckley d71736bf9d
Suspend tx when refreshing version cache (#5671)
* Suspend tx when refreshing version cache
* Undo refactor to reduce merge size
* changelog
* Bump to 7.1.3
* Fix version test
* Unwrap transaction proxy
2024-02-08 14:01:39 -05:00
longma1 993cfcce99
7 0 0 mb (#5678)
* pom bump to 7.0.0 (#5615)

* pom bump to 7.0.0

* add version enum

* fixed feb release name

---------

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

* Check index existence on raw SQL creation (#5624)

* Add conditional check on index existence before we try again

* Add conditional check on index existence before we try again

* Changelog

* remit

* remit

* debug statements

* 5621 deadlock on caffeine cache when creating a resource with conditional create (#5622)

* Modifying the CacheProvider to avoid doing db I/O within the cache miss value supplier callback.

* Setting the initial capacity of instantiated caches to the cache max size to avoid resizing during operations.

* adding changelog and spotless.

* Fixing typo.

* Addressing comments from code review.

---------

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

* Searching with more than one chained Bundle SearchParameter returns incorrect results (#5614)

* Failing test

* fix

* changelog

* Avoiding Exception being thrown on @EventListener invocation (#5628)

* replaced EventListener annotation with @PreDestroy

* adding changelog

---------

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

* simple fix (#5630)

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

* Incorrect version of auto versioned reference for conditional update with urn id placeholder (#5625)

* Incorrect version from versioned_references.auto_at_paths for conditional update - implementation

* Oracle:  Ensure migrated database still takes large resource text updates (#5629)

* First pass at fix to Oracle HFJ_RES_VER.RES_TEXT_VC migration.

* First stab at agreed upon solution.

* Fix error with 4001 by removing unnecessary annotation.

* Spotless and TODO.

* Remove annotation for good and set length to LONG32.

* Fix copyright year.

* Finalize changelog.

* Remove migration changes.  Fix unit test.

* Fix compile error.

* Log output.

* Refactor resource history code into new ResourceHistoryCalculator.

* Spotless.

* Convert record to POJO.

* Restore pre-17 switch statement.

* Finalize new resource history calculator code and tests.

* Spotless.

* Remove logging.

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5633-oracle-hfj-res-ver-clob-migration.yaml

Apply code reviewer suggestion

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

* Code review feedback.

---------

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

* Fix expansion for `ValueSet` with no concepts based on CodeSystem `urn:ietf:bcp:13` (#5638)

* When fetching the mimetype code system, return empty CodeSystem with NOTSUPPORTED content. Update expansion logic to handle this case. Add some test cases.

* Minor change to fix test

* Rename changelog file

* Remove TODOs as they're replaced by reported issue

* Revert accidental change added with TODO removal

* $expunge operation ignoring ExpungeThreadCount setting in certain cases (#5637)

* $expunge operation ignoring ExpungeThreadCount setting in certain cases - implementation

* Fix Measure group id null pointer exception (#5620)

* Update to new version of clinical reasoning, includes a fix for null pointers on Measure group id

* add changelog

---------

Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>

* Rule evaluation:  Allow Bundles with PATCH Parameters (#5641)

* Remove parameters clause.

* Finalize changelog.  Add tests.  Finalize implementation.

* Undo changes to this test.

* Revert all changes to FhirQueryRuleImplTest.  Add new RuleImplOpTest.  Ensure that proper nested Bundle is created for test and other fixes.

* Tweak test.

* Use real rule applier in test and remove all mocks.

* Prevent batch2 job execution to stop for empty chunk when last job st… (#5635)

* Prevent batch2 job execution to stop for empty chunk when last job step is a reduction.
Add output to bulk export result even when empty.

* Fix test

* Unimportant change to force fresh build

* Implement review suggestions

---------

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

* Index review fixes (#5649)

* Don't hold locks while adding indices during upgrade.
* concurrent indexing is non-transactional in PG.

* Fix conditional creates without leading '?' (#5646)

* First commit with failing test.

* More tests and logs.

* More logs

* Try new solution for BaseTransactionProcessor.performIdSubstitutionsInMatchUrl().

* Simplify solution.  Add more tests.

* Changelog.

* javadoc

* Searching for Bundles with read all Bundles permission returns 403 (#5644)

* failing test

* another failing test case

* fix

* changelog

* fix bug

* spotless

* cr

* Fix NullPointerException when performing a system bulk export in the presence of PatientIdPartitionInterceptor. (#5660)

* Serializing changes for sensitive data (#5655)

* Add new senstiive data serializer

* Add new senstiive data serializer

* Add new senstiive data serializer

* Remove dead comments

* Change up the test

* review comments

* wip

* Tighten tests and push annotation down

* Tighten tests and push annotation down

* Changelog

* Add test

* 7.0.1-SNAPSHOT bump

* Error code

* Add method used by CDR

* add version enum

* Fix test

* Rel 7 0 CVE (#5663)

* Bump json-path

* Pin parrson

* Bump elastic

* Bump spring version

* Exclude JDBC

* Descendent fix (#5669)

* Fix "is-a" ValueSet expansion, add "descendent-of" support

* Fixed tests in DSTU3 and R5

* Trigger new build

* Revert "Trigger new build"

This reverts commit 46c672b338.

* fix default partition setting on resource (#5617)

* fix default partition setting on resource

* changelog

* Handle DEFAULT partition in rule checker.

* Fix spotless

---------

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

* pom bump, doc add, version enum add (#5616)

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

* fix default partition setting on resource (#5618)

* fix default partition setting on resource
* Handle DEFAULT partition in rule checker.

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

* Add setting to make broker not use JacksonMessageConverter (#5611)

* Add setting to make broker not use JacksonMessageConverter

* Add changelog

* Implement suggestions

---------

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

* Fix version

* add changelog, add attribution, remove accidental bring-overs

* add changelog, add attribution, remove accidental bring-overs

* Finish jira section

---------

Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* fix conflict mistake

* removed test assert that is no longer true:

* version bumpb to 7.1.1

* fix version Enum test

---------

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.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: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: JP <jonathan.i.percival@gmail.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ole Hedegaard <ohe@trifork.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2024-02-07 22:16:34 -07:00
longma1 29fec706de
pom bump, doc add, version enum add (#5616)
Co-authored-by: Long Ma <long@smilecdr.com>
2024-01-22 22:42:54 +00:00
James Agnew 878e27b06d
HAPI FHIR Dependency Bumps (#5576)
* HAPI FHIR Dependency Bumps

* Hibernate search 6

* Dep bumps

* Bump mockito

* Fix memory leak

* Test cleanup

* Test fix

* Test fixes

* Test fix

* Test fix

* Test fix

* Test fix

* Prepare to try and rework max clauses

* Refactor large VS expansion

* Spotless

* Test fix

* Version bump

* Test fixes

* Bump maven container

* Build fix

* Add license headers

* Version bump

* License headers
2024-01-14 14:15:08 -05:00
TipzCM d6128dece0
adding additional data to (bulk data export) parameters (#5541)
* adding additional data to parameters

* checkstyle

* updated consent service

* updating documentation

* working

* updating and cleaning

* some review points

* spotless

* review fixes

* bumping version

* consent interceotpr fixes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2024-01-12 09:49:45 -05:00
Justin McKelvy b5c028f80a
Add Evaluate Library operation and bump CR (#5570)
* add evaluateLibrary operation

* add tests and constants for operations

* move off snapshot

* code review comments

* version bump to 6.11.8-SNAPSHOT

* spotless edit
2024-01-03 12:16:08 -05:00
James Agnew b28fe3b882
Jakarta Bump Part 2 (#5533)
* Make expunge service extensible

* Work

* Licence headers

* Version bump some dependencies

* Version bumps

* Adapt to new html unit version

* Reintroduce errorprone

* Test fix

* Header

* Work on jakarta

* Test fixes

* Restore errorprone

* More pom tweaks

* Apply spotless

* Errorprone tweak

* errorprone tweak

* Version bump

* License headers

* Version bump

* Postgres bump
2023-12-11 18:24:40 -05:00
TynerGjs d8298e38d4
Resovle 5505-remove-broken-member-match-from-hapi (#5517)
* - Removed IConsentExtensionProvider, MemberMatchR4ResourceProvider and MemberMatcherR4Helper, as well as corresponding usages and tests

* - Removed IMemberMatchConsentHook.java

* spotless reformat

* added changelog

* removed constants for $member-match parameters

* removed error message for $member-match

* completely removed MemberMatchR4ResourceProvider.java

* removed operation constant for $member-match

* version bump
2023-12-07 13:16:31 -05:00
James Agnew 6d58df0f44
Jakarta/Javax Servlet Migration (#5429)
* Servlet migrsation changes

* Apply spotless

* Work on migration

* Start working on JPA migration

* Test fixes

* Test fixes

* Test fixes

* Work

* Work on servlet migration

* Work on migration

* Work on fixes

* Imports fix

* Work on tests

* Test fix

* All tests passing

* Work on migration

* Schema generator

* Refactor ID strategy

* Some test fixes

* Test fixes

* API additions

* Work on websockets

* Test fixe

* Version bump

* Work on migration

* All tests have passed!

* Work on test fixes

* Fixes

* Work on fixes

* CDR fix

* Work on migration

* Fixes

* Spotless

* Disable onetoone ban

* Adjust migratyions

* Transaction service fix

* Add tinyint to migrator

* Work

* Migration

* Compile fix

* Add license

* Test fix

* Test fix

* Cleanup

* Cleanup attempt

* Test fix

* Reslve fixmes

* Remove legacy lastn implementation

* Test cleanup

* Cleanup

* Remove dead import

* Bad import setups

* Review comments

* Review fixes

* Build fix

* Test fix

* Spotless

* Account for CR changes

* Compile fixes

* Rollback one change

* Test tweak

* License header

* Test fix

* Test fix part 2:

* Clean up tx isolation

* Spotless

* Spotless apply

* Drop min SQL Server level

* Attempted test fix

* Test fix

* Test fix

* Test fix

* Bump hibernate

* Test fix

* Test fixes

* Test fixes

* Test fixes

* Test cleanup

* One more test fix

* Test fix

* Try to fix test

* Clean up expunge

* Test fix

* Remove unneeded task

* Spotless

* Bump compiler plugin

* Spotless

* Compile fix

* Add license headers

* License header

* Test fixes

* Bump animal sniffer

* Spotless

* Bump Jetty version

* Test fix and version bump

* Cleanup

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-12-03 11:15:37 -05:00
Michael Buckley fab00ca3a0
Expose the desired Propagation in a tx template (#5516) 2023-11-30 21:43:10 +00:00
Luke deGruchy 8fbbaef079
Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient. (#5488)
* Add a new field to the CLIENT_RESPONSE pointcut in order to allow clients to mutate an HTTP response from the BaseClient.

* Add FhirContext to ClientResponseContext.

* Introduce a ModifiedStringApacheHttpResponse.  Run spotless.

* Remove TDOOs, add and update javadoc.

* Spotless and copyright header.

* Add changelog.

* Unique error message code.

* Only trigger the interceptor if the expected return type is a Bundle.

* Fix spotless.

* Code review feedback.

* Spotless.

* Bump to 6.11.3-SNAPSHOT
2023-11-30 14:56:46 -05:00
TynerGjs 9f827a75c7
Resolve 5480 Update member-match signature to match the spec (#5481)
* - Changed member-match function param names, and return value
- modified existing tests to accomodate for the change

* removed tests unsuitable for new return value

* resolve code review comments

* version bump
2023-11-24 09:49:33 -05:00
Justin McKelvy 86ea069437
feature swap to non javax clinical reasoning (#5463)
* Update to a version of Clinical Reasoning/CQL that no longer includes javax dependencies

* Rev to CR 3.0.0-PRE10

* version bump, pom changes for jakarta conflicts

* undo exclusions from other modules

* Rework exclusions

* Fix type in dependency

* new cr version, exclude conflicts in cr and cds-hooks

* remove exclusions

* pom update

* Redo the exclusions

* add retrieveSettings config

* new CR retrieve settings and config

* update config to new enums and parameters

* update unit tests and config for new cql and terminology properties

* bump CR to 3.0.0-PRE12

* spotless edits, update class path for CR config

* missing dependencies

* swap for jakarta

* moving conflicting dependencies

* Fix a couple code review items

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-11-22 10:30:51 -05:00
Tadgh 1776a8a395
Bump version (#5386) 2023-10-21 09:35:21 -07:00
Justin McKelvy c832cf0507
Hapi cr codecache (#5360)
* WIP code cache config

* WIP test

* Passing unit test

* cachelistener IT

* hardening cache listener tests

* cache listener fixes & tests, measureService migration, add reporter parameter to r4

* fix ELMCache listener to match on version, update test, remove reporter parameter

* edit inline notes

* changelog, version bump, spotless apply

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-10-11 11:47:52 -07:00
TipzCM 7e0fa9833c
adding metrics (#5301)
* hapi metrics

* step 1

* metrics service

* adding metrics service

* adding documentation

* refactor

* refactoring

* cleanup

* changing

* adding changelog

* some refactoring

* format

* review fixes part 1

* review points

* review fixes

* updates for code review

* updates for code review

* bumping versions

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-09-29 09:23:11 -04:00
Etienne Poirier 6ee6031a5f
CapabilityStatement doe not declare conformance to IG when a bulk data export provider is registered. (#5329)
* adding initial test

* adding initial test

* solution implementation

* spotless apply

* bumping to 6.9.8-SNAPSHOT

* addressing comments from review and fixing typo

* spotless

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-09-26 13:56:13 -04:00
Justin McKelvy 6a0b2794eb
5089 cr measure refactor (#5324)
* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

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

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* _source search parameter needs to support modifiers (#5095)

_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers

* Fix HFQL docs (#5151)

* repository measure refactor

* undo bundle edit, add config

* embedded library true

* undo post of bundle

* clear library cache on test

* fix sumbit-data test

* missing packages from cql

* fix test data and test cases for repository api

* 3.0.0 clinical reasoning uplift

* r4 cql execution provider and tests

* fix submitdata provider config

* wip cql tests

* debugging cql op wip

* wip debugging cql

* update tests for $cql, fix class names

* prep for Pre6 uplift

* spotless checks and test fixes

* bump to 3.0.0-PRE6

* cleanup

* fix version

* cleanup

* fix exlusions in pom

* add in cache invalidation config

* search converter bug and test for repository

* update searchconverter

* version bump, add changelog

* remove term config, move IDaoRegistryUser class

* Break out dstu3 providers and move config to version folders

* CVE-2023-26119

* remove * imports

* code review updates

---------

Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
2023-09-22 16:51:36 -07:00
TipzCM f97eadadc6
rebuild golden resource from survivorship on link edit (#5250)
* adding rebuilding option for survivorship

* rebuild survivorship resources

* cleanup

* configuring beans

* fixing tests

* cleanup

* spotless

* import fixing

* cleaning up

* fixing tests

* fixing tests

* version bump

* undo change

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-09-12 23:03:24 -04:00
James Agnew 5a88b505d0
Upgrade Thymeleaf (#5239)
* Upgrade Thymeleaf

* Apply spotless

* Version bump

* Test fix
2023-09-09 09:42:29 -04:00
Etienne Poirier fb3e141c4d
Messages submitted to the subscription pipeline are lost when submission fails. (#4733)
* One more fix for #4467

* Enabling massIngestionMode causes incomplete resource deletion (#4476)

* Adding initial test.

* Adding fix and subsequent test.

* Adding changelog.

---------

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

* Provide the capability to request that the name of the subscription matching channel be unqualified (#4464)

* Adding initial test.

* Adding initial solution implementation.

* Adding change log and code clean up.

* addressing comments from 1st code review.

---------

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

* Change visibility of migration method (#4471)

* change migration visibility

* add empty migration method for 640

---------

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484)

* First commit:  Make SubscriptionValidatingInterceptor aware of which Pointcut is being called.  In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED.   Fix resulting compile errors in various unit tests.

* Fix/enhance unit tests.  Mark methods as deprecated instead of deleting them.  Add proper error code.  Complete changelog.

* Remove erroneous TODOs and tweak the validation logic.

* Enhance unit tests and fix changelog.

* Reindex batch job fails when processing deleted resources. (#4482)

* adding changelog.

* Providing solution and adding changelog.

* Adding new test.

---------

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

* cleaning up checkstyle files (#4470)

* cleaning up checkstyle files

* One more fix for #4467 (#4469)

* added exlusions for files at base project level so checkstyle doesn't error out

* duplicate error code from merge

* changing lifecycle goal for all module checkstyle check

* moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code

* wip

* trying to figure out why pipeline cannot copy files

* removing modules that don't actually need to be built.

* I messed up the version

---------

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

* Bump core to 5.6.881 (#4496)

* Bump core to 5.6.881-SNAPSHOT

* Work on fixing tests

* Work on fixing tests 2

* Bump to core release

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>

* Issue 4486 mdm inconsistent possible match score values (#4487)

* Extract method for readability

* Save always normalized score values in POSSIBLE_MATCH links.

* Avoid setting properties to null values. Adjust test.

* Simplify fix

* Fix test. Add RangeTestHelper.

---------

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

* Revert "cleaning up checkstyle files (#4470)"

This reverts commit efae3b5d5f.

* core version fix

* Loosen rules for id helper

* initial test implementation/changes and solution wiring.

* adding support for jpa/mongo abstraction.

* refact completed.  need to start implementing scheduling of subscription re-submission with the scheduler service.

* post release, merging in master.

* wip: commit before merging in branch master.

* wip: resuming work on the issue.

* wip: before merging in master.

* wip: partial implementation of mongo support.

* wip: more work to support partial implementation on mongo.

* Test implementation

* providing method getMessageKeyOrDefault();

* providing changelog

* preping codereview.

* wip: passing tests

* wip: finally solving the Meta issue.

* wip: adjusting interfaces

* Adding IT and

* IT test;
fixing rollback issue.

* removing non required logging

* fixing merge conflict

* Preparing for code review.

* Preparing for code review.

* Compiling code after merging in master.

* Fixing checkstyle failure.

* Modifications towards getting all tests to pass.

* addressing comments from code review.

* compiling code after switching target merge branch to rel_pub_2023_05

* compiling code after switching target merge branch to rel_6_6

* Addressing comments made in design meeting.  wip.

* Addressing comments made in design meeting. finally completed.
and last 2 comments addressed.

* removing non required override

* reverting changes as they are not required.

* Modified test and implementation.

* implementation of a SynchronousSubscriptionMatcherInterceptor to submit modifiedResources to the subscription pipeline for testing only.

* fix tests by modifying the matchingInterceptor to call pointcut when processing

* fixing more tests.

* WIP to pass all tests in jpaserer-4504-a-resource-submitted-to-the-subscription-pipeline-is-lost-when-the-pipeline-encounters-an-issue

* fixing circular dependency

* Adding import dependency to class TestSubscriptionSubmitterConfig to allow submission of messages with the SynchronousSubscriptionMatcherInterceptor.

* bumping version 6.7.7-SNAPSHOT

* bumping HAPI version to 6.7.7-SNAPSHOT

* fixing tests failure caused by asynch deliver of resourceModifiedMsg to the processing pipeline.

* passing all tests.

* unbumping to 6.7.7

* compiling after merging in master.

* creating a custom hapi version

* providing an synchronous subscription matcher interceptor for testing.

* updating pom version to generate artifacts.

* fixing tests, WIP/0

* fixing tests, WIP/1

* fixing tests, WIP/2

* Matching entity annotation with migration task declarations.

* Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage.

* Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage.

* Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc].

* Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc] again.

* Removing creation of new transaction to inflate PersistedRresourceModifiedMessages since it is already executing in a transaction.

* bumping to version 6.7.14-ASYNC-SNAPSHOT for pipeline.

* bumping hapi version to 6.7.14-ASYNC-SNAPSHOT for pipeline.

* Formatter changes.

* add generic

* add generic

* Addressing code review comments.

* Adding file asynch_subscription_610.md to docs/upgrades

* changing poms to 6.9.2-SNAPSHOT before merging in master.

* compiling after merging in master.

* Lowering logging level to debug.

* Bumping to 6.9.3-SNAPSHOT

* Bumping hapi version to 6.9.4-SNAPSHOT

* Adding update documentation.

* Modifying update file following review.

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: dotasek <dotasek.dev@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-08-28 12:47:53 -04:00
Tadgh a10856e091
GM1 Mergeback (#5203)
* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

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

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* Rename file to force IT mode

* _source search parameter needs to support modifiers (#5095)

_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers

* Fix HFQL docs (#5151)

* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)

* Initial failing test.

* Solution with changelog.

* fixing format.

* Addressing comment from code review.

* fixing failing test.

---------

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

* documentation update (#5154)

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

* Fix hsql jdbc driver deps (#5168)

Avoid non-included classes in jdbc driver dependencies.

* $delete-expunge over 10k resources will now delete all resources (#5144)

* First commit with very rough fix and unit test.

* Refinements to ResourceIdListStep and Batch2DaoSvcImpl.  Make LoadIdsStepTest pass.   Enhance Batch2DaoSvcImplTest.

* Spotless

* Fix checkstyle errors.

* Fix test failures.

* Minor refactoring.  New unit test.  Finalize changelist.

* Spotless fix.

* Delete now useless code from unit test.

* Delete more useless code.

* Test pre-commit hook

* More spotless fixes.

* Address most code review feedback.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Fix the noUrl case by passing an unlimited Pegeable instead.  Effectively stop using page size for most databases.

* Deprecate the old method and have it call the new one by default.

* updating documentation (#5170)

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

* _source search parameter modifiers for Subscription matching (#5159)

* _source search parameter modifiers for Subscription matching - test, implementation and changelog

* Removal of meta tags during updates do not trigger subscription (#5181)

* Initial failing test.

* adding solution;
fixing documentation;

* spotless apply

* adding changelog

* modifying current test

---------

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

* Issue 5173 get gateway everything doesnt return all patients (#5174)

* Failing test

* Also set offset and count in base DAO override

* Changelog

* Fix for specific case where count has been set in parameters

* spotless

* Improve checks

---------

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

* Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175)

* First commit with failing unit test and small tweaks.

* Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead.  Add more detailed unit testing.

* Tweaks to logic and update the changelog.  Reverse all changes to TermReadSvcImpl.

* Revert PackageResourceParsingSvc to release branch baseline.

* Accept code reviewer suggestion to change changelog description.

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

---------

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

* Fix link

* Remove target slf4j version

* dont use new API for a bit (#5191)

* Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193)

DropIdGeneratorTask.

* Dqm performance bug update and provider loader fix (#5180)

* update tests, move properties, update operation loader

* update wip

* remove test

* fixing tests, adding config

* update config and provider loader

* fix bundles

* fix cache settings on tests

* version bump and change log

* version bump

* fix formatting

* CVE-2022-45868

* wip cve change

* cve h2 add back in

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>

* bulkExportReuse with POST and GET (#5161)

* string manipulation

* Code to ensure bulkExportReuse works with POST and GET requests

* Added formatting changes

* Fixed tests that were not working

* Formatting

* Code clean up

* fixing test failures

* fixing test failures

* Removed arrOfParams to now utilize ObjectMapper

* Removing stack trace and adding an exception

* Fixed test issue

* formatting

* formatting

* Resolving code review comments

* Reduce size of subscription max results (#5194)

* Reduce MAX_SUBSCRIPTION_RESULTS to 10000

* Add changelog

* 5037 goldenresource remains when target resource deleted (#5038)

* draft test and fix

* remove unused fields

* remove unused fields

* remove unused fields

* draft test + solution for possible match case

* combine sql statement + more error checking

* add test case for possible duplicate

* add config for autodeleting grs

* refactoring, adding support for mongo, docs

* refactoring + fixing mongo queries

* add changelogs

* fix both way link removal

* clean up test comments

* rename method

* remove unnecessary bean

* merge master/resolve conflicts

* mvn spotless

* address comment

* changes to avoid version bumping

* spotless

* change error code

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* dont use new API for a bit (#5190)

* licenses

* wip

* Fix API usage

* wip

* Version bump

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
2023-08-15 12:32:10 -07:00
TipzCM a48c602f71
adding pointcuts for mdm operations (#5116)
* adding pointcuts for mdm operations

* adding changelog

* cleanup

* cleaning up

* formatting

* review fixes

* formatting

* more cleanup

* cleanup

* moving changelog

* fixing a bug

* cleanup

* formatting

* version bump

* fixing broken merge

* fixing the version

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-08-02 16:38:33 -04:00
James Agnew 2b91f0a232
Version bump HAPI FHIR and a couple of deps (#5121)
* Version bumps

* Version bump HAPI

* Add enum for next release

* Changelog update

* HAPI version bump
2023-07-28 09:46:01 -04:00
Tadgh 53ceb7cac4
Bump to nov (#5120)
* bump version, make new folders

* Fix typo in versionenum
2023-07-24 08:49:40 -07:00
James Agnew 6d745b4f2d
Initial HFQL SQL Implementation (#5083)
* FQL tests

* Working so far

* Tests working

* Tests passing

* Work on parser

* Tests passing

* Cleanup

* Working

* Work on parser

* Work

* Working

* Work on tests

* Work on driver

* Work

* Ongoing work

* Rename SEARCH to WHERE

* Work on fhirpath

* Test fixes

* Work on statements

* Build fixes

* Spotless application

* Fix CI

* Build fixes

* Clean up changelogs

* Remove redundant gitignore

* Add docs

* Add docs

* Code cleanup

* Build cleanup

* Fix compile error

* Test fixes

* Test fix

* Test fix

* Work on integration

* Work on design

* Work on UI

* Update hapi-fhir-jpaserver-hfql/src/main/java/ca/uhn/fhir/jpa/fql/jdbc/JdbcDriver.java

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

* Address review comments

* Review comments

* HFQL work

* Cleanup

* CLeanup

* License headers

* Test fixes

* HAPI version bump

* License header update

* Changelog cleanup

* Fixes

* Test fix

* Fix spotless issues

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-07-21 22:51:23 +00:00
Luke deGruchy 43694f378c
Ensure FhirContext loads custom resources in the list of resource names (#5073)
* Fix bug by maintaining a separate list of resource types including the custom resources that will be used to validate the Bundle resources.

* Add custom resource types to resource types list and add conditional logic in ValidationDataInitializerSvcImpl to ensure there is no Exception when parsing a custom resource type.

* Add changelog.

* Remove unnecessary change.

* Address code review feedback.

* Address code review feedback.

* Add one more unit test.

* Bump to 6.7.14-SNAPSHOT.
2023-07-12 14:32:09 +00:00
Brenin Rhodes eb06b473b9
Update version of the Clinical Reasoning module (#5045)
* Update version of the Clinical Reasoning module

* cleanup

* Add changelog

* Update snapshot

* Inc version
2023-07-07 10:05:10 -04:00
James Agnew a93d06c25f
Restrict bulk export download to specific user (#5052)
* Work

* Bulk export partitioning fixes

* Changelog fixes

* cleanup

* Work on security

* Compile fixes

* Work

* Test fix

* Work

* Add changelog

* License header changes

* Test fix

* Test fix

* Fixes

* Version bump

* Test fix

* Fix accidental change
2023-07-05 12:48:15 -04:00
James Agnew 6e0651e261
Bulk export partitioning fixes (#5039)
* Work

* Bulk export partitioning fixes

* Changelog fixes

* cleanup

* Compile fixes

* Test fix

* Add JIRA note

* Version bump

* Drop unneeded tag
2023-06-29 08:34:32 -04:00
volodymyr-korzh 1f44ac1092
GenericClient POST paging support (#5013)
* GenericClient POST paging support - implementation and test

* GenericClient POST paging support - fixes

* GenericClient POST paging support - fixes

* GenericClient POST paging support - failed tests fix

* GenericClient POST paging support - HAPI version bump
2023-06-22 15:28:47 -04:00
TipzCM d7bdabb91b
nickname svc refatoring (#5006)
* nickname svc refatoring

* moving things around

* cleanup

* gitignore

* removing factory

* added changelog

* version bump

* fixing test

* fix test

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-22 08:26:47 -04:00
TipzCM 65ae1785e8
mdm-clear will now use batch-size parameter (#4985)
* using delete expunge service

* test fixing

* update version

* review points

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-15 20:32:21 -04:00
TipzCM 0a7f97adb7
4917 refactor nicknaming hapi with version bump (#4955)
* refactoring 1

* refactoring step 2

* refactoring matches

* cleanup

* fixing some tests

* fixing more tests

* remove dbugcode

* adding the nickname factory

* code review fixes

* review fixes

* put default to prevent breaking

* refactor review fixes

* more review points

* more review points

* review points

* review points

* more review changes

* review points

* review points

* adding bean

* updating version

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-06 09:00:14 -04:00
David d94627c382
4847 allow filtering batch jobs by status (#4849)
* Add method to get all jobs of a certain status

* add queries

* add tests

* Refactor so extra parameter is not added

* Version bump

* Fix broken test

* Revert accidental change to pom unrelated to version

---------

Co-authored-by: David Chen <david.chen@smilecdr.com>
2023-05-18 14:46:44 -04:00
James Agnew 483ddca3be
Transaction with delete then update should not fail (#4831)
* Fixed

* Test fixes

* Add test

* Ongoing work

* Work on xactx

* Cleanup

* Changelog cleanup

* Resolve fixme

* Rework broken APIs

* Version bump

* Add license headers

* License header update

* License

* rk on fixes

* Test fixes

* Address review comments

* Test fixes

* Add license headers

* License header
2023-05-15 07:41:40 -04:00
Tadgh 9a095cc2d7
version bump for next release (#4793)
* version bump

* Bump to correctnumber

* Version Enum and folder

* Remove interim from list

* wip
2023-04-30 15:01:28 -04:00
James Agnew e2e5ff6bb8
Version bump HAPI FHIR (#4788) 2023-04-28 19:30:51 +00:00
James Agnew e2717bd63a
Bump corelib to FHIR R5 Final (#4727)
* 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 (#4770)
* 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