Commit Graph

746 Commits

Author SHA1 Message Date
holly-smile 72ff192df8
Fix error message for HAPI-0302 showing misleading names for known resource types (#5875)
* A solution, but perhaps not the best one

* Make behavior more robust and extendable. Fixes #5874

* Apply spotless

* Add changelog

* 😅

* Add unit test

* Get name from context instead of hard-coding remapping
2024-04-25 16:39:10 -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
JasonRoberts-smile e3cc83a694
fix bug (#5843) 2024-04-12 00:19:56 +00:00
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
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
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
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
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
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
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
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
volodymyr-korzh 8e69170c89
Xml encoded fhir resource created with decimal element that has leading plus sign value couldn't be retrieved or modified (#5670)
* XML encoded FHIR resource created with decimal element that has leading plus sign value couldn't be retrieved or modified - implementation
2024-02-06 18:04:03 -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
James Agnew 01c748163d
Don't contain resources in Bundle with only fullUrl (#5589)
* Don't contain resources in Bundle with only fullUrl

* Add changelog

* Spotless

* Fix RDF issue
2024-01-10 12:32:44 -05:00
Martha Mitran effbc98b30
Fix fhirpath expression evaluation with _fhirpath parameter when resolve() references resources within a Bundle (#5565)
* Fix fhirpath expression evaluation with _fhirpath parameter when resolve() references resources within a Bundle

* Update parameters for getBundleReference method

* Addressing some code review comments

* Spotless fix and update test logic to address code review comment
2024-01-09 13:15:01 -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
Ken Stevens 32f5da37e0
mdm duplicate identifier (#5563)
* test and fix bug

* cleanup

* cleanup
2023-12-19 21:55:52 +00:00
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
Luke deGruchy 78a50f92bc
Replace all nullable/nonnull imports of javax.annotation with jakarta.annotation (#5540)
* Replace all nullable/nonnull imports of javax.annotation with jakarta.annotation.

* Fix checkstyle.  Update checkstyle version.
2023-12-07 09:16:48 -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
Ken Stevens d5a1b0cdf3
fix terserutil clear (#5473)
* fix test

* review
2023-11-21 16:39:18 +00:00
TynerGjs 41d9abf6ac
Resolve 5452-mdm-query-link-returns-scientific-notation-in-linkcreated-and-linkupdated (#5453)
* set the scale to 0 when transforming double to BigDecimal

* - set negative scale to 0 when transforming double to BigDecimal
- added test
2023-11-14 13:53:49 -08:00
Aditya Dave 9dace159b4
5426 enhance bundleutil (#5451)
* failing test

* fix and more tests

* cleanup

* spotless

* remove class paths

* add changelog

---------

Co-authored-by: aditya_dave <aditya@smilecdr.com>
2023-11-13 19:50:11 +00:00
Tadgh 777859ad00
Rel 6 10 mb (#5441)
* Allow cached search with consent active when safe (#5387)

Allow the search cache when using consent if safe

* Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376)

* Change package installation behavior such that it updates the existing SearchParameter base with remaining resources

* Change package installation behavior such that it updates the existing SearchParameter base with remaining resources

* Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable.

* Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable.

* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389)

* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation

* Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177)

* 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)

* 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

* first fix

* tests and preliminary fixes

* wip, commit before switching to release branch.

* adding capability to handle _lastUpdated in reverse search (_has)

* adding changelog

* applying spotless.

* addressing code review comments.

---------

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

* Br 20231019 add cr settings for cds hooks (#5394)

* Add settings used in CR CDS Services.  Remove config dependency on Spring Boot.

* Add changelog

* Use String.format rather than concat strings

* spotless apply

* Add javadoc

* Upgrade notes for the forced-id change (#5400)

Add upgrade notes for forced-id

* Clean stale search results more aggressively. (#5396)

Use bulk DMA statements when cleaning the search cache.
The cleaner job now works as long as possible until a deadline based on the scheduling frequency.

* bump version of clinical reasoning (#5406)

* Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408)

* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added

* removed unused alias from SQL query of mdm-clear (#5416)

* Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)

* Enable child classes to use Boolean class return type

* spotless

---------

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

* If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420)

* If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix

* Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423)

This reverts commit 4e295a59fb.

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

* Use new FHIR_ID column for sorting (#5405)

* Sort `_id` using new FHIR_ID column.
* Fix old tests that put client-assigned ids first.

* Better indexing for sort

* Bump core to 6.1.2.2 (#5425)

* Bump core to 6.1.2.1

Patch release that uses https for primary org.hl7.fhir.core package server

* Bump core to 6.1.2.2

* Make sure to return always a value for Boolean class return type. (#5424)

Implement change in a non-disruptive way for overriders

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

* Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428)

Add a non-standard __pid SP.

* Review changes for new _pid SP. (#5430)

Change name to _pid to match our standard and add warning.

* Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432)

* Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition.

* Fix spotless issue

* CVEs for 6.10.0 (#5433)

* Bump jetty

* Bump okio-jvm

* 8.2.0 mysql connector

* Jena and elastic bumps

* Fix test

* 5412 post bundle on partition incorrect response.link shown (#5413)

* Initial fix and unit test provided

* spottless check

* Made relevant changes to make solution version agnostic

* relevant logic changes made

* spotless changes made

* New logic added to fix failing test cases

* formatting

* New logic to make the function more robust

* spotless checks

* Left a trailing slash in the tests

* Made relevant test changes and changed logic

* spotless changes

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml

changing changelog

Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>

* Formatting requirements

---------

Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>

* Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414)

* first fix

* - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber
- refactored code to reduce repeated code
- cleaned unnecessary comments and reformatted files

* Changed myResourceModifiedMessagePersistenceSvc to be autowired

* removed unused import

* added error handling when inflating the message to email and message subscriber

* reformatted code

* Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc

* Changes by gary

* Reformatted file

* fixed failed tests

* implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File.

* - implemented IT
- fixed logical error
- added changelog

* fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor

* fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor

* resolve code review comments

* reformatted files

* fixed tests

* Fix for failing IT test in jpaserver-starter (#5435)

Co-authored-by: dotasek <dotasek.dev@gmail.com>

* wip

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: dotasek <david.otasek@smilecdr.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: 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: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.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: Nathan Doef <nathaniel.doef@smilecdr.com>
Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com>
Co-authored-by: dotasek <dotasek.dev@gmail.com>
2023-11-10 14:00:08 -08:00
Ken Stevens a7a446903f
5401 add terserutil clear by fhirpath (#5402)
* begin with failing test

* test passes

* test passes

* changelog

* moar testor
2023-10-26 03:35:20 +00:00
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
JasonRoberts-smile 5411622dee
add exclusions to terser reference method (#5343) 2023-10-02 09:23:42 -04:00
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
dotasek 9f9aeb980c
Bump core version to 6.1.2 (#5317)
* WIP Fix compile errors

* Fix compile errors 2

* Fix test fails due to new Validation messages

* Ignore validation issues

Ignore two validation issues:

Two 'side is inherently a collection' warnings are now thrown for the following expressions:

NamingSystem nsd-1 uniqueId.type = 'uuid'
Observation obs-7 code != component.code

There is also a general error ignored because the StructureDefinition for StructureDefinition is actually for FHIR 3.0.1, and contains an invalid expression in constraint sdf-9. This is remedied in the expression used in 3.0.2, but a full update of all profile structure definitions is out of scope for this PR.

* Fix property name

* Add changelog
2023-09-19 11:26:20 -07:00
longma1 0c42229985
Rel 6 8 2 mb (#5299)
* 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)

* 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

* Fixing terminology upload with large file. (#5204)

* create initial test

* adding fix;
adding changelog;

* fixing format.

---------

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

* up version to 6.8.0 from snapshot

* fix up some duplicate deps for skipping

* Force deployment of other projects

* make dummy java class to pass sonatype checks

* make dummy java class to pass sonatype checks

* Cheeky test removal

* Another test removal

* Updating version to: 6.8.1 post release.

* adding back in tests for release pipelines

* Fix bad version insert

* Bump to core library version 6.0.22.2 (#5261)

* Bump to core library version 6.0.22.2

* Bump HAPI to 6.8.1-SNAPSHOT, core library version to 6.0.22.2

* up version to 6.8.1

* Prevent remote deployment

* Updating version to: 6.8.2 post release.

* Re-add deploy plugin skip

* re-add version

* Bump core library version to 6.0.22.2

* Bump HAPI to 6.8.2-SNAPSHOT

* Fix up version enum

* Version bump

* Updating version to: 6.8.3 post release.

* mvn spotless:apply

---------

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: 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>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
2023-09-13 14:21:38 -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
Nathan Doef cc283b7732
Respect response status code set in MethodOutcome of a Resource provider (#5267)
* failing test

* fix

* extract response code modifying resource provider for testing

* comment

* remove TestResponseCodeModifyingPatientProvider
2023-08-31 14:08:45 -04:00
Ken Stevens 590e6ba88f
use ClasspathUtil (#5263) 2023-08-31 13:23:00 -04:00