Commit Graph

9580 Commits

Author SHA1 Message Date
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 d4717a08d6
Improve docs for NO-OP update pointcuts (#5294) 2023-09-12 16:40:48 -04:00
volodymyr-korzh fe8c6c066e
SearchBuilder should not allow $everything operation to follow links to Group or List resources (#5283)
* SearchBuilder should not allow $everything operation to follow links to Group or List resources - tests

* SearchBuilder should not allow $everything operation to follow links to Group or List resources - implementation

* SearchBuilder should not allow $everything operation to follow links to Group or List resources - spotless check fix and changelog added

* Add a new permission: FHIR_OP_PATIENT_EVERYTHING_ACCESS_ALL for $everything operation - fixes

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

* MongoIncludeSvc should not allow $everything operation to follow links to Group or List resources - fixes

* MongoIncludeSvc should not allow $everything operation to follow links to Group or List resources - fixes

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-09-12 10:39:53 -07:00
James Agnew 03ebabad5b
Several IPS fixes (#5297)
* Several IPS fixes

* One more fix

* Fix

* Fixes

* med fixes

* Null safety
2023-09-12 11:41:33 -04:00
VK-SMILECDR da58e9f250
Add dao registry to cds config service (#5292)
* add daoRegistry to CdsConfigService

* add daoRegistry to CdsConfigService
2023-09-11 16:05:50 +00:00
James Agnew 5a88b505d0
Upgrade Thymeleaf (#5239)
* Upgrade Thymeleaf

* Apply spotless

* Version bump

* Test fix
2023-09-09 09:42:29 -04:00
Kevin Dougan SmileCDR b8fcba0d45
Added changelog for 2023. (#5281) 2023-09-08 14:25:35 +00:00
Tadgh 57f6a705a5
Fix NPE in MDM post-mdm-clear on UPDATE operations. (#3851)
* Fix bug, imlpementation, changelog

* wip

* wip

* wip

* Add test

* wip

* wip
2023-09-07 22:51:12 +00:00
James Agnew a676506fc5
Improve terminology validation error messages (#5271)
* Improve terminology validation error messages

* Changelog

* Validation issues

* Test fixes

* Cleanup

* Review comments

* Fix
2023-09-07 08:52:38 -04:00
StevenXLi 3e46f71542
5276 the graphql request results in an http 400 error (#5278)
* fixed issue, added test

* added change logs

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-09-06 20:34:37 +00:00
Kevin Dougan SmileCDR 650fbe541c
Fixed HFQL Section name. (#5279) 2023-09-06 20:34:20 +00:00
jdar8 d563b97ad8
5242 mdm clear doesn't expunge redirected golden resource (#5245)
* fix + test

* changelog

* spotless

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-09-06 11:43:14 -04:00
Emre Dincturk 862c0487f6
5259 sorted tags, security labels and profiles (#5260)
* 5259 sorted tags, security labels and profiles

* fixed typos and augmented a test case for sorter
2023-09-01 11:12:26 -07:00
TynerGjs 33be707238
Added RequestDetails as part of the parameters to cleaning up possible matches to enable interceptors to MdmStorageInterceptor.cleanUpPossibleMatches (#5257)
access it
2023-09-01 10:22:43 -07:00
Tadgh 5f5b3db4a1
Fix, test changelog (#5266) 2023-08-31 14:58:28 -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
jdar8 f38df4b91a
doc change (#5248)
Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-08-30 16:10:54 -07:00
StevenXLi cd0f6d16cd
5246 bulk export merge steps (#5247)
* added failing test

* added the new step, replace existing steps

* added changelog

* fixed check style

* changed the error code

* added back the bean definition for ExpandResourcesStep, to keep test from erroring

* code review fix

* fixed placement

* mirrored the implementation in the test

* added null check

* code review change

* style fix

* missed reverts

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-08-30 12:58:47 -07:00
LalithE 293f02ad7c
Fix to Bulk Export Enabled Disrupts Custom Resource Addition (#5255)
* Required change to fix bug editing test case currently

* Solution and unit test

* Adding changelogs

* adding coverage for registerCustomTypes

* Fixing test cases, using same context for two tests messed it up
2023-08-29 17:16:01 -06:00
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
jdar8 6a7340a879
5231 MDM Link History gives 404 after MDM clear and submit (#5232)
* fix + tests

* remove comments

* docs + changelog

* spotless

* edit changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-08-25 15:59:44 -04:00
TynerGjs db6d8092f2
modified MdmLinkDaoJpaImpl.convertToLongIds so that it returns all pi… (#5244)
* modified MdmLinkDaoJpaImpl.convertToLongIds so that it returns all pid that is related to a forced id.
added tests for above changes

* joined helper methods

* joined helper methods
2023-08-25 14:49:06 -04:00
Tadgh 9ded67fb4d
Modify editorconfig to match spotless rules (#5241)
* Modify editorconfig to match spotless rules

* Fix prop

* remove redundant charsets
2023-08-24 19:12:53 +00:00
TipzCM 318b68ee0c
5192 include in search empty page results (#5211)
Fixing paging with _include query parameter
2023-08-24 16:36:31 +00:00
Emre Dincturk 8d39e3466c
cast errorcount to string for batchjob failure message (#5230) (#5233)
Co-authored-by: Emre Dincturk <emre.dincturk@smilecdr.com>
2023-08-24 10:41:01 -04:00
SouradeepSahaSmile ed616f7a6d
Automated migration test data (#5218)
* 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>

* wip run 5.2.0 migrations and then add test data

* Fix h2

* Fix postgres

* Complete until v5.4

* add sql migration scripts:

* Temp

* Add v6_0_0

* Add v6_8_0

* Final changes

* clean up

* _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

* Complete Oracle

* Remove V6_8_0

* apply mvn: spotless

* 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>

* Update CDR insert tables

* Update CDR insert tables

---------

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: nathaniel.doef <nathaniel.doef@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>
2023-08-23 10:27:02 -04:00
Justin McKelvy bbcc6148ae
5222 storage cr hapifhirretrieveprovider terminology paging bug (#5224)
* update query iterable to page results, update config for batching

* add test for large valueset issue

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
2023-08-22 16:05:05 -06:00
Ken Stevens 943a052a0b
combosp intermittent (#5225)
* fix intermittent

* spotless
2023-08-22 09:59:11 -04:00
Ken Stevens deeffe2253
fix some race conditions (#5220)
* fix memory leak

* race condition fixes and change log

* race condition fixes and change log
2023-08-21 17:27:44 +00:00
Ken Stevens b9155721a7
fix batch2 npe when no results returned (#5219)
* fix npe error

* spotless

* spotless
2023-08-20 00:37:16 +00:00
Ken Stevens ab2a86b0d5
partition cache (#5217)
* Convert PartitionLookupSvcImpl to use MemoryCacheService

* Convert PartitionLookupSvcImpl to use MemoryCacheService

* add test

* add test

* add test

* fix tests
2023-08-18 22:08:54 +00:00
James Agnew 1e45506526
Improve ID filtering (#5215)
* Improve ID filtering

* Formatting

* Add license header

* Address review comments
2023-08-18 16:30:00 +00:00
VK-SMILECDR 3512f82a6d
fix the issue (#5214) 2023-08-17 18:01:50 +00:00
TipzCM fdfda37f73
5198 fixing searching everything op (#5201)
* fixing searches

* fixing paging in master

* cleanup

* Fixing the tests

* fixing tests

* fixing test

* cleanup

* fixing

* removing unneeded class

* adding a changelog and cleaning some final details

* code styles

* cleaning up imports

* review notes

* formatting

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-08-17 15:42:06 +00:00
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
TynerGjs f2087d2ccc
added validateExpungeEnabled() call to type-level expunge, moved two … (#5197)
* added validateExpungeEnabled() call to type-level expunge, moved two overloading method so that they are next to each other

* added test for expunge
enabled expunge for testExpungeAllVersionsWithTagsDeletesRow in FhirResourceDaoR4QueryCountTest

* added changelog

* optimized tests and changelogs
2023-08-14 10:04:07 -04:00
jdar8 de9a747666
MDM operation to return total number of Possible Duplicates (#5130)
* addition, test, changelog

* update changelog

* address review comment + add test for coverage

* remove unnecessary space + changes

* mvn spotless

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-08-04 16:24:01 -04:00
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
TipzCM fd5c2c2862
all updated resources to link to existing resources (#5152)
updating mdm resources will update all links to them as well as any links that it would match after update
2023-08-02 16:29:17 +00:00
Tadgh 5eda18f500
Mergeback of rel_6_8 (#5146)
* 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

---------

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>
2023-07-30 22:28:26 +00:00
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
Ken Stevens b376778b99
change mdm interceptor loader to fail when message subscription types… (#5128)
* change mdm interceptor loader to fail when message subscription types aren't enabled.

* cleanup

* cleanup

* fix tests

* cleanup

* spotless

* fix test

* fix test

* changelog

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-07-27 10:39:32 -04:00
Tadgh dcf3240191
Proper version bump (#5135)
* Fix version

* Fix version enum
2023-07-26 18:53:15 +00:00
Ken Stevens dc3a4114ce
added test to confirm this works properly (#5134)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-07-26 14:37:23 -04:00
dependabot[bot] 85f41d5fc8
Bump h2 from 2.1.214 to 2.2.220 (#5067)
Bumps [h2](https://github.com/h2database/h2database) from 2.1.214 to 2.2.220.
- [Release notes](https://github.com/h2database/h2database/releases)
- [Commits](https://github.com/h2database/h2database/compare/version-2.1.214...version-2.2.220)

---
updated-dependencies:
- dependency-name: com.h2database:h2
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-07-26 08:52:48 -04:00
James Agnew e14bbec83b
IPS Connectathon Fixes (#4834)
* IPS Connectathon Fixes

* Fix changelog

* Cleanup
2023-07-24 19:32:42 +00:00
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
TynerGjs f68f3fbb0f
Resolve 5112 unable to expunge deleted codesystem until several minutes later (#5113)
* returned user-friendlier message, implemented unit tests, added changelog

* reformatted file

* added Msg.code to the exception thrown

* added Msg.code in test

* Changed to catch DataIntegrityViolationException only.
2023-07-21 17:08:58 +00:00