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* 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 * Temp disable * Make this dependency provided * Updating version to: 6.6.1 post release. * Bump snakeyaml * Bump jackson to be compatible with new snakeyaml * Bump deps (#4926) * resolve CVEs, add new notes * Updating version to: 6.6.2 post release. * #5023 Unexpected usage of awssdk StringUtils in hapi 6.6 jpa migration (#5024) task Replace usage of awssdk * added docs * mssql test fixes * Updating version to: 6.6.3 post release. * fix up random errors when merging back * undisable test * remove mention of 6.6.3 which does not exist --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> 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: 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> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Thomas Papke <web@thopap.de>
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