Commit Graph

530 Commits

Author SHA1 Message Date
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
James Agnew 564beb7211
Allow absolute links for refs with an identifier (#5295)
* Allow absolute links for refs with an identifier

* Add changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5295-fix-absolute-refs-with-identifier.yaml

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>

* Remove redundant class

* Review comments

---------

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
2023-09-13 09:55:02 +00:00
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 2da8aafad0
Add support for _lanugage SP (#5300)
* Add support for _lanugage SP

* Add changelog

* Formatting fix

* Add to JPA

* Add validator

* Validate language SP

* Assign new code

* Fixes
2023-09-13 00:35:17 +00:00
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
Ken Stevens 943a052a0b
combosp intermittent (#5225)
* fix intermittent

* spotless
2023-08-22 09:59:11 -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
Tadgh 52f3ef5992
New formatting rules and pre-commit hooks (#5027)
* pre-apply spotless

* New pre-format checkpoint

* Once-over the repository

* Add pre-commit hook

* New github action

* excludes

* Revert "Once-over the repository"

This reverts commit 89334ba8d1.

* Once-over the repo

* do not inherit

* Revert "Once-over the repo"

This reverts commit 31ed8731ad.

* Add baisc license support to spotless

* Move license

* Fix inclusions

* Fix inclusions

* Fix licensing

* license fixes

* Remove dead file that is only a license

* Remove dead class

* remove dead file

* Tighten licensing

* Tighten licensing

* Tighten licensing

* Tighten licensing

* Remove specific package

* Make the precommit hook executable

* Fix ordering

* rollback license

* wip

* Add to deployable pom

* remove file

* Fix location

* Remove dead comment

* wipP

* Fix ratchet

* Fix up error

* Add pre-commit

* precommit fixes

* wip

* wip

* Autoformat

* remove dead pom parts

* replace internal hook with pre-commit

* Fix fetch-depth for checker action

* Remove ratchet and filter

* fix up

* rename

* Add comment check

* rework message

* First once-over of the repo

* wip

* format
2023-07-11 17:36:44 -07:00
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
Ken Stevens 216c6ed4f1
fix surefire config (#5049)
* relegate surefire config to parent pom pluginManagement

* back out build fix to see if stack trace now shows up in logs

* back out the backed out fix.

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-07-04 14:08:44 -04:00
Luke deGruchy ad71755c2b
Resolve 5029 Token params with system and value longer than maximum length should be created and searched differently (#4998)
* Partial implementation after this has been paused:  Move trimming of value and system from BaseSearchParamExtractor to ResourceIndexedSearchParamToken.  Do not throw Exceptions in TokenPredicateBuilder.  Ensure that the hash computing in the search param token takes the 200+ token value into account.  Other search param tokens are not yet implemented.

* in ResourceIndexedSearchParamToken,changed hardcoded length to constant MAX_LENGTH;
in BaseSearchParamExtractor, added check in createTokenIndexIfNotBlank so that the return value is null if system or value is blank.

* added test for TokenPredicateBuilder to verify that long values exceeds the max length does not cause exception.

added test in FhirSystemDaoR4SearchTest to verify searchParamToken with longer system and value than max length can be created successfully. And hash value will be calculated before truncation

* fixed a logical error in previous commits

* changed existing tests to accommodate for the changes

* modified existing tests

* added changelog

* changed truncation method name and added comments

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

* modified changelog

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

* combined redundant tests

---------

Co-authored-by: tyner <tyner.guo@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-06-30 10:48:33 -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
TynerGjs ac9eaf9d89
4959 loadsynchronousupto will affect searchforids when set to small value (#4966)
* Implemented fixes, created test for JPA side

* Added test and getter for test for register listener

* refactored test names to make them more descriptive

* Modified tests

* resolved comments

* created changlog

* changed test to use MAX_MANAGED_PARAM_COUNT, and created the corresponding getter
2023-06-19 09:54:39 -04:00
Luke deGruchy e5699bcbfc
Add auto-generated headers to Java files. (#4999) 2023-06-16 13:53:20 -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
volodymyr-korzh e28398fc4c
4888 Add validation for composite SearchParameter components types (#4909)
* Added unit tests for composite SearchParameter validator

* Added validation for composite SearchParameter components

* validation for composite SearchParameter components - fixes

* Modified tests

* fixed string in setDefinition

* validation for composite SearchParameter components - fixed validation and Unit tests

* validation for composite SearchParameter components - added method getActiveSearchParameterByComponentDefinition and unit tests

* validation for composite SearchParameter components - minor fixes

* validation for composite SearchParameter components - remove getActiveSearchParameterByComponentDefinition method

* validation for composite SearchParameter components - optimise import

* validation for composite SearchParameter components - fix changelog

* validation for composite SearchParameter components - improved validation logic

* validation for composite SearchParameter components - improved validation logic (remove unused lines)

* validation for composite SearchParameter components - improved validation logic

* validation for composite SearchParameter components - improved validation logic

* validation for composite SearchParameter components - fixed validation logic

* validation for composite SearchParameter components - added test for uri and number combo search

* validation for composite SearchParameter components - added test for uri and number combo search

* validation for composite SearchParameter components - validation logic fix

* validation for composite SearchParameter components - fixes

* validation for composite SearchParameter components - fixes

* validation for composite SearchParameter components - test fixes

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-06-08 11:00:27 -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
Tadgh 6c03a512f5
Revert "refactoring nickname matching (#4918)" (#4954)
This reverts commit 7a18f17a01.
2023-06-02 19:40:50 +00:00
TipzCM 7a18f17a01
refactoring nickname matching (#4918)
* 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

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-02 14:04:30 -04:00
Etienne Poirier e068a2f32b
4799 searching on paramname profile with and missing modifier does not match resources (#4840)
* initial test

* Adding changelog

* Updated to remove the discarding of search params starting with an underscore

* test commit

* Updated handling of search parameters with underscores

* Revert work in progress

* Updated storage settings with new property for inline tag storage mode

* Updated storage settings to tell when inline tag storage mode is set

* simplified test failure

* Added tests for _tag and _system

* Add PreviousVersion service with tests (#4902)

* started writing PreviousVersionReader

* started writing PreviousVersionReader

* moar tests

* add partitioning to the test

* switch subscription to use previous version reader

---------

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

* Updated logic to be less confusing

* Bumping version to 6.7.4

* Reverted hapi bump, added improve logic for handling missing search params

* updates

* Updated failing tests

* remove redundant tests

* more updates

* Adding Jira number.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: David Raeside <davidraeside@smilecdr.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
Co-authored-by: David Raeside <david.raeside@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-30 07:12:53 -04:00
Ken Stevens b84e8c0bcc
Canonicalize R4 topic subscriptions (#4913)
* WIP

* add canonicalizer for R4 topic subscriptions

* test R4 topic subscription registration

* Add support for R4 Subscription Topic Backport

* FIXME

* add filter matching support

* add simpler signature

* add resource type matching to filter

* review feedback

* fixed

* changelog

* test both ways

* add bundle test

* change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state

* added logs

* changelog

* fix v2 issues

* Clean up WIP comments

* Switch to in-memory event numbers (instead of always 1)

* Final WIP cleanup

* Msg.code

* review feedback

* review feedback

* review feedback

* review feedback

* back out import changes

* back out import changes

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-29 05:32:22 +00:00
James Agnew 46857711c9
Delete expunge with cascade (#4931)
* Delete expunge with cascade

* Work

* Workgin

* Version bump hibernate

* Start working on delete cascade

* Work on delete expunge

* Test fixes

* Test fixes

* Add changelog

* Work on cascade

* Fixes

* Test work

* Test fixes
2023-05-27 11:07:59 -04:00
James Agnew a04a49cb68
Schema migrator returns status (#4937)
* Migrator should return status

* Cleanup

* Add changelog

* Delete unused

* Test fix
2023-05-24 19:31:39 -04:00
Tadgh 805e80e61f
6.6.0 Mergeback (#4924)
* Force Verify tests

* fix ITs (#4809)

* fix RestHookTestR5IT

* fix intermittent

---------

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

* Fix migrator error on Oracle (#4814)

* Fix Oracle SQL error

* Add changelog

* Update clinical reasoning version (#4816)

* Update clinical reasoning version

* Update version

* Update version

* Clean-up and more wireup of evaluationSettings

* Add changelog

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>

* Opening the care-gaps endpoint for GET. (#4823)

Co-authored-by: Chalma Maadaadi <chalma@alphora.com>

* added version to mdm golden resource tag (#4820)

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

* Update the changelog for 4697 to be more descriptive (#4827)

* Update the changelog for 4697 to be more descriptive

* Futher tweaks of the changelog

* Fixes a bug with tags.  (#4813)

* Test, fix

* Drop constraint, add migration

* Add changelog

* Fix userSelected null vs false

* Fix merge

* Fix up checkstyle whining

* One more failure

* Fix test

* wip

* changelog clarity

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

* change index

---------

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

* fix migration issue (#4830)

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

* Create correct version enum

* Remove superfluous migration

* fixing test (#4835)

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

* email subscription, throw NullPointerException (#4790)

* fix bug

* Favoring constructor initialization to autowiring.

* enhancing test.

* Making class LoggingEmailSender available outside of the hapi-fhir-japserver-uhnfhirtest module.

* Passing all tests.

* adding changelog.

* Bumping version to 6.5.20-SNAPSHOT

* addressing code review comment.

---------

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

* Add docs for CR operations (#4855)

* Add docs for CR operations

* Correct changelog and javadoc for $package

* Add documentation for $apply parameters

* Add additional documentation for $package

* Cleanup

* Cleanup

* Cleanup

* Address review comments

* Add documentation for $care-gaps operation. (#4862)

* Add documentation for -gaps.

* addressing the comments.

---------

Co-authored-by: Chalma Maadaadi <chalma@alphora.com>

* 4853 validation does not error when display is not the same as the display defined in the codesystem 2 (#4854)

* added failing test

* implemented the solution

* changed test name

* added change log

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4853-validation-does-not-error-when-display-is-not-the-same-as-the-display-defined-in-the-codesystem-2.yaml

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

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>

* fixing patient everything operator (#4845)

* fixing patient everything operator

* review fix

---------

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

* fix link

* Move image file

* Bundle resources containing over 100 references to the same Organization will fail with HAPI-2207 (#4871)

* Add failing unit test.

* Fix JpaId Long equality comparison to use ! equals() instead of !=, which fails for different instances of the same Long value.

* Add changelog.

* added warn message and test (#4848)

* added warn message and test

* code review fixes

---------

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

* Issue 4804 full table scan on mpi link during mdm clear (#4805)

* version bump for next release  (#4793)

* version bump

* Bump to correctnumber

* Version Enum and folder

* Remove interim from list

* wip

* Fix operation on nested type-choices in FhirPatch implementation (#4783)

* Fix operation on nested type-choices in FhirPatch implementation

* Add credit for #4783

---------

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

* #4468 fix previous link offset no cache pagination (#4489)

* #4468 Add test reproducing the issue

* #4468 Fix previous link for no cache offset pagination

* #4468 Use unchecked URI parsing

* Credit for #4489

---------

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

* Changelog and data generating test

* Add MdmLink index

* Avoid double link deletion

* Use ThreadLocal safely

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Fix erroneous batch 2 $export 75% complete count when the job is COMPLETE (#4859)

* Add failing unit test.

* Add conditional logic to the InstanceProgress progress percentage to disregard the incomplete count if this is called from the reduction step.  This is to get around a race condition in which a work chunk is QUEUED and not yet complete when the reduction step calculates the progress.

* Add final.

* Add changelog.

* disable wars (#4877)

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

* 4868 fix paging hapi (#4870)

* fixing some offset and adding a test

* fixing the offset paging

* Removing duplicate

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>

* 4875-binary-access-write-doest-trigger-STORAGE-BINARY-ASSIGN-BLOB-ID-PREFIX-pointcut (#4876)

* Add failing test

* Add failing test

* Fix and changelog

* Pass content type parameter

* Back to auto wiring the context

* Invoke interceptor only when getting blobId, not also when storing it

* Avoid breaking implementers

* Address review comment

* Add new exception Msg code

* Fix broken test

---------

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

* Fix batch job (bulk export) processed record count (#4879)

* Remove racy stats recalc.

* Throw 404 when requesting $export of non-existent Group or Patient (#4890)

* Remove default implementation intended only for interim backwards compatibility (#4894)

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

* Rule apply patient export (#4893)

* Test, fix, and changelog

* Better partition resolution

* Add checks based on rule applier

* Fix ordering failure due to hash set

* Allow empty auth interceptor

* Fix up operation type on invocation

* Add more tests, make hack implementation for patient instance level operation

* Tighten test name

* Changelog

* Default method

* remove dead method

* Remove dead autowire

---------

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

* cve pom changes (#4898)

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

* backport subscription topic bean cleanup (#4904)

* 4891 bulk export do not recurse unasked for resources (#4895)

* updating tests

* fixing bulk export to not fetch resources not requested

* cleanup

* cleanup

* more warning suppressing

* adding error code

* blah

* fix test

* review fixes

---------

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

* lowers log level to remove bootup noise (#4908)

* CVE rel 6 6 (#4907)

* cve pom changes

* bump javax.el to jakarta.el

---------

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

* Issue 4905 post binary failure invoking interceptor for pointcuts storage preshow resources (#4906)

* Initial failing test

* Avoid applying binary blob id prefix multiple times

* Remove recently introduced method not needed anymore

---------

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

* Enhance LogbackCaptureTestExtension (#4869)

* repro bug with test, fix bug

* ken informed me he resolved this bug on master, so i'm switching to use his solution

* disable wars

* review feedback

* review feedback

* review feedback again

---------

Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Resolve 4863 from release branch searchparametercanonicalizer does not account for search parameters for custom resources types when converting dstu23 into runtimesearchparam (#4887)

* Modified canonicalizeSearchParameterDstu2 and 3, now correctly detect search parameters for custom resources

* Canonicalizers now correctly handle search parameters for custom resources

* created changelog

* Modification based on comments:
- remove Resource from target field when there are custom resource types
- fixed changelog typo
- removed unnecessary variable providesMembershipInCompartments

* Added tests for the SearchParameterCanonicalizer to test if base and target of RuntimeSearchParam is set as expected for DSTU2, DSTU3, R4, R4B, and R5 resources

* Fixed typo and removed commented code

* re-ordered init methods

* Update changelog

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

* modifications following first code review.

---------

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

* License

* Remove _lastUpdated filtering of _revincludes. (#4899)

Remove _lastUpdated filtering of _revincludes.

* 4910-dm-migration-error-for-oracle-19c (#4916)

* Remove all_constraints references which break in oracle 19c

* Add changelog

---------

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

* 4873 empty fhirid causes missing resource (#4874)

* add check for empty fhirid string and add test

* add test for populateid

* changelog

* version bump

* version bump

* reverse version bump

* Back to 6.5.21-SNAPSHOT.

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>

* Fix include canonical url performance (#4919)

Use hash_identity for canonical join

* License

* Version bump

* Fix failure in test

* Licenses

* Review comments for pipeline

* Dead entry

* other typo

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Sam Gunter <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com>
Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Josie <80289977+pepsiofficial@users.noreply.github.com>
Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-05-20 20:38:35 -07:00
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
James Agnew 8cf14c8c0e
Dont crash indexing contained references on Bundle (#4881)
* Dont crash indexing contained references on Bundle

* Add changelog
2023-05-14 21:33:32 -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
David 457b39bac1
Fix $mdm clear doesn't expunge golden record resources (#4767)
* Failing test

* Add method to expunge collection of deleted resources

* Failing test passes

* Add changelog

* Version bump

* Forgot to commit change

* Update test

* Check type validity

* Fix broken tests

---------

Co-authored-by: David Chen <david.chen@smilecdr.com>
2023-04-27 21:35:27 -06:00
TipzCM 1c0addafeb
transaction bundle multi-threading issues (#4739)
* a solution for trying to avoid multi-thread issues for transaction bundle processing

* cleanup

* using retries

* mnor tweaks

* checking in

* changes

* updating changelog

* some minor tweaks

* cleanup

* flip if

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-20 18:43:37 +00:00
Etienne Poirier 88459d0d00
4657 method name is inconsistent with the method behavior (#4659)
* Test implementation

* providing method getMessageKeyOrDefault();

* providing changelog

* preping codereview.

* Deprecating method getMessageKeyOrNull in favor of getMessagekey()

* updating comments following code review.

* Bumping version to 6.5.13-SNAPSHOT

* passing all tests.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-04-17 10:41:08 -04:00
James Agnew 7bdbda9ef0
Improve Subscription Retriggering Efficiency (#4742)
* Improve subscription efficiency

* Reduce number of queries

* Add changelog

* Fix ITs

* Review comments

* Test fix
2023-04-17 08:18:57 -04:00
Luke deGruchy 35bd1c400a
Fix bundle auto-create by checking for IBaseReference.hasIdentifier() before validating URL-based references (#4731)
* First commit:  New tests, logs, and comments.

* Add hacky fix to run pipelines on.   Add another unit test.

* Disable baseUrl checking if hasIdentifier() is true.

* Add changelog.  Tweak unit tests.

* Remove junk.

* Add more assertions to unit tests.  Make new production fix code clearer.

* Add more clarity to unit tests.

* Another unit test fix.
2023-04-14 17:55:31 +00:00
Ken Stevens b88ccbc7b0
R4B SubscriptionTopic support (#4724)
* add tests for r4b subscriptions

* begin with failing test

* prepare for SubscriptionTopicLoader

* backwards compatibility

* subscription topic registry done

* topic matching is working

* all but delivery is working now

* yay test passes with FIXMEs

* FIXME -> WIP

* switch notification to bundle

* message codes

* fixme

* disable services for fhir versions below R4B

* fix regression

* fix intermittent

* this change will likely break some other tests

* try a safer option

* fix tests

* fix intermittent (I hope)

* unit test

* improve logic around topic subscription categorization

* moar test

* moar test

* changed to support both r4b and r5

* moar test

* cleanup for test

* moar test

* moar test

* moar test

* changelog

* comment

* Msg.code

* fix mock

* add update test

* fix test cleanup

* tracking link for version converter issue

* review

* fix test

* fix test

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-12 00:44:08 +00:00
James Agnew e500b23fe6
Instance level reindex operations (#4699)
* Reindex improvements

* Work

* Work on reindex

* Test fixes

* Generator now working

* Add instance reindex

* Work

* Build fixes

* Build fix

* Fixes

* Add changelog

* Test fixes

* Resolve checkstyle fix

* Version bump

* Address review comments

* Resolve imports

* Address review comments

* Test fix
2023-04-06 17:00:41 -04:00
James Agnew a2bc9a7212
Partition aware search cleanup (#4706)
* Partition aware search cleanup

* Compile fixes

* Build fixes

* HAPI FHIR version bump

* License

* License header

* Tests
2023-04-02 11:50:20 -04:00
Ken Stevens 4fbeeccda4
enable some disabled tests (#4662)
* enabled test

* added explanations to disabled tests

* added explanations to disabled tests

* yay enabled another one

* yay enabled another one

* testEverythingWithLargeSet2 failing intermittently

* fix intermittent regression introduced by splitting test class

* test passes

* need to document

* updated documentation

* prereview cleanup

* change log

* cleanup

* cleanup

* added breaking changes

* update changelog and breaking changes upgrade document to reverse the change to always return 200 per the spec.

* back out documentation change

* update documentation

* fix tests

* dstu2

* dstu3

* fix r4 validation warning test

* changelog

* hapi-fhir version bump to 6.5.10-SNAPSHOT

* fix cdr test

* fix tests

* remove accidental commit

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-02 08:47:16 -04:00