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6_4 mergeback #4547

Merged
merged 42 commits into from
Feb 13, 2023
Merged

6_4 mergeback #4547

merged 42 commits into from
Feb 13, 2023

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fil512
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@fil512 fil512 commented Feb 12, 2023

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jamesagnew and others added 30 commits January 27, 2023 08:30
* Adding initial test.

* Adding fix and subsequent test.

* Adding changelog.

---------

Co-authored-by: peartree <[email protected]>
…atching 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 <[email protected]>
* change migration visibility

* add empty migration method for 640

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Co-authored-by: nathaniel.doef <[email protected]>
… 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.
* adding changelog.

* Providing solution and adding changelog.

* Adding new test.

---------

Co-authored-by: peartree <[email protected]>
* 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

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Co-authored-by: James Agnew <[email protected]>
* Bump core to 5.6.881-SNAPSHOT

* Work on fixing tests

* Work on fixing tests 2

* Bump to core release

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Co-authored-by: dotasek <[email protected]>
* 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 <[email protected]>
* fix bug where FINALIZE jobs are not cancellable

* moved reduction step to message hander

* moving reduction step to queue

* addingchangelog

* cleaning up

* review fixes

* review fix'

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Co-authored-by: leif stawnyczy <[email protected]>
* First commit:  Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.

* Refine solution and add a concrete unit test but still work to do.

* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.

* Unit tests complete.  New Msg code for new IJobPersistence.fetchInstances() method.  Cleanup TODOs and add others.

* Finish final touches on implementation.

* Add changelog.

* Various cleanup.

* Code review feedback.

* Small tweak to changelog.

* Last code review tweak.

* Address more code review comments.

* Reverse changes to consider work chunks.  Add a constant for write-to-binary.
* change tests

* suggested test change
* Bump Postgres for CVE

* Bump jetty

* Verison bump

* Remove comments

* Revrt bump
* Initial implementation

* better tests

* Add changelog and docs

* Forgotten files

* Code review comments

* Fix checkstyle
* changes for GL-3943

* changes for GL-3943

---------

Co-authored-by: isaacwen <[email protected]>
…ce (#4514)

* changed what score is set for mdmlinks that created new golden resource

* fix test

---------

Co-authored-by: Long Ma <[email protected]>
#4527)

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* added change log

---------

Co-authored-by: leif stawnyczy <[email protected]>
…cription messages for different requests (#4524)

* fix + test

* minor fix

* Addressing suggestion

* Minor changes
* adding a test

* fail in the case of ref enforce on type and on write and autocreate are all true

* update to code

* removing a line

* cleanup

* removing check on urn

* changing just to trigger a build

* adding a comment to the pom

* updating test for better information

---------

Co-authored-by: leif stawnyczy <[email protected]>
samguntersmilecdr and others added 8 commits February 9, 2023 11:49
* retryCount 0 on null header + test + changelog

* suggested changes
… in subscription messages for different requests (#4524)" (#4535)

This reverts commit 53252b8.
Don't log payloads - they may contain sensitive data.
* failing test

* fix + changelog

* tweak

* add method to IJobPersistence to use a Stream

* tweak

* tweak

* decrease test time

* clean up

* code review comments

* version bump

* Increase timeout limit to match BulkExportUseCaseTest

* shorten test

* maintenance pass

* add logging

* Revert "add logging"

This reverts commit b0453fd.

* Revert "maintenance pass"

This reverts commit bbc7418.

* test

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* shorten tests

* logging

* move test location

* fixes a regression caused my change in hapi-fhir

* timeout

* Revert "fixes a regression caused my change in hapi-fhir"

This reverts commit 4b58013.

* testing

* Revert "testing"

This reverts commit aafc95c.

---------

Co-authored-by: leif stawnyczy <[email protected]>
@fil512 fil512 linked an issue Feb 12, 2023 that may be closed by this pull request
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codecov bot commented Feb 13, 2023

Codecov Report

Base: 81.32% // Head: 81.38% // Increases project coverage by +0.06% 🎉

Coverage data is based on head (814a145) compared to base (2f5ffe7).
Patch has no changes to coverable lines.

Additional details and impacted files
@@             Coverage Diff              @@
##             master    #4547      +/-   ##
============================================
+ Coverage     81.32%   81.38%   +0.06%     
- Complexity    23650    23854     +204     
============================================
  Files          1425     1432       +7     
  Lines         86399    87412    +1013     
  Branches      11677    11793     +116     
============================================
+ Hits          70265    71143     +878     
- Misses        10947    11029      +82     
- Partials       5187     5240      +53     
Impacted Files Coverage Δ
ca/uhn/fhir/mdm/api/MdmQuerySearchParameters.java 49.31% <0.00%> (-35.94%) ⬇️
org/hl7/fhir/r5/hapi/fhirpath/FhirPathR5.java 40.74% <0.00%> (-28.01%) ⬇️
...a/uhn/fhir/jpa/mdm/svc/MdmLinkQuerySvcImplSvc.java 41.66% <0.00%> (-25.00%) ⬇️
org/hl7/fhir/r4/hapi/fluentpath/FhirPathR4.java 62.96% <0.00%> (-24.54%) ⬇️
.../hl7/fhir/dstu3/hapi/fluentpath/FhirPathDstu3.java 76.00% <0.00%> (-17.75%) ⬇️
...ir/rest/server/messaging/json/BaseJsonMessage.java 76.92% <0.00%> (-13.99%) ⬇️
ca/uhn/fhir/jpa/mdm/svc/MdmControllerSvcImpl.java 63.44% <0.00%> (-9.40%) ⬇️
ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java 85.62% <0.00%> (-5.66%) ⬇️
...r/narrative/CustomThymeleafNarrativeGenerator.java 94.73% <0.00%> (-5.27%) ⬇️
ca/uhn/fhir/system/HapiSystemProperties.java 76.47% <0.00%> (-4.78%) ⬇️
... and 114 more

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@tadgh tadgh merged commit 794e451 into master Feb 13, 2023
@tadgh tadgh deleted the 4546-6_4_mergeback branch February 13, 2023 21:23
@tadgh tadgh restored the 4546-6_4_mergeback branch February 17, 2023 06:54
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