mirror of
https://github.com/hapifhir/hapi-fhir.git
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24 Commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
michaelabuckley
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d1f9c94038
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Make WorkChunk handling transactional at state transitions. (#4621)
- use a separate enum for the states - chunks have different transitions than instances. - use transactional update events for work-chunk state transitions - introduce spec-test to define behaviour of batch2 storage - replace synchronized facade with simpler ProxyUtil handler. - change job cancellation to db update query |
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James Agnew
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ae1d249d99
|
Bulk export reducer step fix mergeback (#4606)
* 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 efae3b5d5f397ab8fd92d7aaa82b484cfdfb3c33. * core version fix * Loosen rules for id helper * License * fix batch2 reduction step (#4499) * 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' --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * Scheduled batch 2 bulk export job and binary delete (#4492) * 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 bulk import test for valueUri type (#4503) * change tests * suggested test change * CVE resolutions (#4513) * Bump Postgres for CVE * Bump jetty * Verison bump * Remove comments * Revrt bump * Add check in scanner (#4518) * 4516 create hapi fhir cli command to clear stale lock entries (#4517) * Initial implementation * better tests * Add changelog and docs * Forgotten files * Code review comments * Fix checkstyle * Unable to Expunge CodeSystem (#4507) * changes for GL-3943 * changes for GL-3943 --------- Co-authored-by: isaacwen <isaac.wen@smilecdr.com> * New line:: * Update to documentation regarding narrative generation; (#4521) Providing changelog; Co-authored-by: peartree <etienne.poirier@smilecdr.com> * changed what score is set for mdmlinks that created new golden resource (#4514) * changed what score is set for mdmlinks that created new golden resource * fix test --------- Co-authored-by: Long Ma <long@smilecdr.com> * REVERT: change to operationoutcome.html * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527) * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp * added change log --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * fix build (#4530) * Making narrative_generation.md reference an html snippet (#4531) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524) * fix + test * minor fix * Addressing suggestion * Minor changes * 4441 rel 6 4 bad references creation bug (#4519) * 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 <leifstawnyczy@leifs-mbp.home> * fixed channel import null pointer exception from null header (#4534) * retryCount 0 on null header + test + changelog * suggested changes * Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535) This reverts commit 53252b8d153f97f4a66a7d20751913911a71f098. * Better error handling for when channel type is not supported (#4538) Co-authored-by: kylejule <kyle.jule@smilecdr.com> * Avoid logging message payloads that contain sensitive data (#4537) Don't log payloads - they may contain sensitive data. * Bulk Export Bug With Many Resources and Low Max File Size (#4506) * 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 b0453fd9538d6858e6bd212f402d4b04c6306136. * Revert "maintenance pass" This reverts commit bbc7418d519260c4b9827546a0bf822db1c78b1b. * 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 4b58013149836eededc568d295c5baf8fb3df989. * testing * Revert "testing" This reverts commit aafc95c2f36bf89ae935c6c342017ec300fe4289. --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * bump ver * License updates' * Downgrade dep' * Updating version to: 6.4.1 post release. * Add javadocs and sources to our serviceloaders * Reset version * Change parent * Remove bumped version * License fixes, new parent * Updating version to: 6.4.1 post release. * Fix bad creation of versionenum * Improve performance on bulk export * Add changelog * Start working on cleaned up reducer * Clean up batch calls * Work on issues * Build fixes * typedbundleprovider getallresources override (#4552) * typedbundleprovider getallresources override * added test to immunization tests that validates pagination does not result in null pointer if over default queryCount * moved HapiFhirDal test to its own test class * removed unused imports * Update to use JpaStorageSettings * adding changelog for issue 4551 * fix changelog spacing * changelog type to fix --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> * Add backport info * Upgrade core to 5.6.97, make adjustments in hapi-fhir, and ensure that all tests pass (#4579) * First commit: Create new branch from the release branch with changes from James' branch. This probably won't compile as the work is incomplete. * Second round of changes from integrating James' branch. * Mark most test failures with TODOs. * Add whitespace * Add changes to FhirPathR4 to set FHIRPathEngine to non-strict FP evaluation. * Fix CreatePackageCommandTest to assert null instead of empty string. Comments on tests that fail due to the double-quote encoding problem. * Downgrade to core 5.6.97. * Fix another test and remove TODOs. * Fix changelog. * Clean up some erroneous changes and TODOs. --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix up dal test * Address leftover code review feedback from the upgrade to core 5.6.97. (#4585) * Exclude pinned core deps * Force pin structs * Add model changes to IBaseCoding and related changes (#4587) * Add IbaseCoding changes, and tinder changes * Fix up tag definition * converter addition * Fix unit test and add changelog. * Add jira to changelog. --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Fix changelog * Tidy metadata * Test fixing * Test fixes * Work on progress * Add changelog * Build tweak * Fixes * Disable intermittently failing tests. (#4593) * rename tests to IT * Disable more intermittently failing tests (#4595) * Disable more intermittently failing tests. * Disable another intermittently failing tests. * ITify * Disable yet another intermittently failing tests. (#4596) * disable * disables * Fixes * disables * Fix compile * Test fixes * Updating version to: 6.4.2 post release. * Bump to 6.4.2-SNAPSHOT * Fix compile * fix version * Address review comments * Review comments * Version bump * Compile fix * Test fixes * Compile fixes * One more compile fix * Test fixes * Version bump * Resolve fixme --------- Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: 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: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com> Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com> Co-authored-by: isaacwen <isaac.wen@smilecdr.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com> Co-authored-by: kylejule <kyle.jule@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.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: Jonathan Percival <jonathan.i.percival@gmail.com> |
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James Agnew
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bf495e2d92
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Don't merge yet: MegaScale API Changes 2 (#4544)
* Megascale changes 2 * Cleanup * CLeanup * Sync master * Cleanup * Ongoing work * Move service * Fixes * Ongoing megascaler work * Work * Work * Fixes * Work * Test fixes * Work on remote services * Interceptor rework * Work on config refactor * Fixes * Docs tweaks * Address review comments * Test tweak * Test fixes * Try to fix tests * Test tweaks * Fix changelogs * Work on merging * Changes * Megascale fixes * Remove accidental commit * Address fixmes * Cleanup * Test fixes * Compile fix * Test fixes * Account for review comments * Bump HAPI FHIR version |
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Tadgh
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428acff31b
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6.4.0 Mergeback (#4563)
* 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 efae3b5d5f397ab8fd92d7aaa82b484cfdfb3c33. * core version fix * Loosen rules for id helper * License * fix batch2 reduction step (#4499) * 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' --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * Scheduled batch 2 bulk export job and binary delete (#4492) * 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 bulk import test for valueUri type (#4503) * change tests * suggested test change * CVE resolutions (#4513) * Bump Postgres for CVE * Bump jetty * Verison bump * Remove comments * Revrt bump * Add check in scanner (#4518) * 4516 create hapi fhir cli command to clear stale lock entries (#4517) * Initial implementation * better tests * Add changelog and docs * Forgotten files * Code review comments * Fix checkstyle * Unable to Expunge CodeSystem (#4507) * changes for GL-3943 * changes for GL-3943 --------- Co-authored-by: isaacwen <isaac.wen@smilecdr.com> * New line:: * Update to documentation regarding narrative generation; (#4521) Providing changelog; Co-authored-by: peartree <etienne.poirier@smilecdr.com> * changed what score is set for mdmlinks that created new golden resource (#4514) * changed what score is set for mdmlinks that created new golden resource * fix test --------- Co-authored-by: Long Ma <long@smilecdr.com> * REVERT: change to operationoutcome.html * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527) * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp * added change log --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * fix build (#4530) * Making narrative_generation.md reference an html snippet (#4531) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524) * fix + test * minor fix * Addressing suggestion * Minor changes * 4441 rel 6 4 bad references creation bug (#4519) * 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 <leifstawnyczy@leifs-mbp.home> * fixed channel import null pointer exception from null header (#4534) * retryCount 0 on null header + test + changelog * suggested changes * Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535) This reverts commit 53252b8d153f97f4a66a7d20751913911a71f098. * Better error handling for when channel type is not supported (#4538) Co-authored-by: kylejule <kyle.jule@smilecdr.com> * Avoid logging message payloads that contain sensitive data (#4537) Don't log payloads - they may contain sensitive data. * Bulk Export Bug With Many Resources and Low Max File Size (#4506) * 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 b0453fd9538d6858e6bd212f402d4b04c6306136. * Revert "maintenance pass" This reverts commit bbc7418d519260c4b9827546a0bf822db1c78b1b. * 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 4b58013149836eededc568d295c5baf8fb3df989. * testing * Revert "testing" This reverts commit aafc95c2f36bf89ae935c6c342017ec300fe4289. --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * bump ver * License updates' * Remove checkstyle * Verison bump * Move migrations * semicolon * Downgrade dep' * Updating version to: 6.4.1 post release. * Add javadocs and sources to our serviceloaders * Reset version * Change parent * Remove bumped version * License fixes, new parent * Updating version to: 6.4.1 post release. * Fix bad creation of versionenum * re-add checkstyle * respect move-up into storage settings from jpastoragesettings * remove duplicate test --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: 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: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com> Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com> Co-authored-by: isaacwen <isaac.wen@smilecdr.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com> Co-authored-by: kylejule <kyle.jule@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> |
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James Agnew
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eea6193df9
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JPA config refactoring (#4545)
* Interceptor rework * Work on config refactor * Fixes * Docs tweaks * Address review comments * Test tweak * Test fixes * Try to fix tests * Test tweaks |
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Ken Stevens
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794e4510c6
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6_4 mergeback (#4547)
* 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 efae3b5d5f397ab8fd92d7aaa82b484cfdfb3c33. * core version fix * Loosen rules for id helper * License * fix batch2 reduction step (#4499) * 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' --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * Scheduled batch 2 bulk export job and binary delete (#4492) * 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 bulk import test for valueUri type (#4503) * change tests * suggested test change * CVE resolutions (#4513) * Bump Postgres for CVE * Bump jetty * Verison bump * Remove comments * Revrt bump * Add check in scanner (#4518) * 4516 create hapi fhir cli command to clear stale lock entries (#4517) * Initial implementation * better tests * Add changelog and docs * Forgotten files * Code review comments * Fix checkstyle * Unable to Expunge CodeSystem (#4507) * changes for GL-3943 * changes for GL-3943 --------- Co-authored-by: isaacwen <isaac.wen@smilecdr.com> * New line:: * Update to documentation regarding narrative generation; (#4521) Providing changelog; Co-authored-by: peartree <etienne.poirier@smilecdr.com> * changed what score is set for mdmlinks that created new golden resource (#4514) * changed what score is set for mdmlinks that created new golden resource * fix test --------- Co-authored-by: Long Ma <long@smilecdr.com> * REVERT: change to operationoutcome.html * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527) * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp * added change log --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * fix build (#4530) * Making narrative_generation.md reference an html snippet (#4531) Co-authored-by: peartree <etienne.poirier@smilecdr.com> * fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524) * fix + test * minor fix * Addressing suggestion * Minor changes * 4441 rel 6 4 bad references creation bug (#4519) * 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 <leifstawnyczy@leifs-mbp.home> * fixed channel import null pointer exception from null header (#4534) * retryCount 0 on null header + test + changelog * suggested changes * Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535) This reverts commit 53252b8d153f97f4a66a7d20751913911a71f098. * Better error handling for when channel type is not supported (#4538) Co-authored-by: kylejule <kyle.jule@smilecdr.com> * Avoid logging message payloads that contain sensitive data (#4537) Don't log payloads - they may contain sensitive data. * Bulk Export Bug With Many Resources and Low Max File Size (#4506) * 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 b0453fd9538d6858e6bd212f402d4b04c6306136. * Revert "maintenance pass" This reverts commit bbc7418d519260c4b9827546a0bf822db1c78b1b. * 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 4b58013149836eededc568d295c5baf8fb3df989. * testing * Revert "testing" This reverts commit aafc95c2f36bf89ae935c6c342017ec300fe4289. --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * bump ver * License updates' * Remove checkstyle * Verison bump * Move migrations * semicolon --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: 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: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com> Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com> Co-authored-by: isaacwen <isaac.wen@smilecdr.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com> Co-authored-by: kylejule <kyle.jule@smilecdr.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> |
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Tadgh
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54c9b9422a
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Bump to 6.5 post-release-branch (#4472)
* Create version enum and bump * Version bump * fix typo |
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Tadgh
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456cc81b32
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Rel 6 2 5 mergeback (#4459)
* jm wrong bundle entry url (#4213) * Bug test * here you go * Generate relative URIs for bundle entry.request.url, as specified * Point jira issue in changelog * Adjust tests to fixes Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * improved logging (#4217) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Rel 6 1 3 mergeback (#4215) * Bump for CVE (#3856) * Bump for CVE * Bump spring-data version * Fix compile * Cut over to spring bom * Bump to RC1 * remove RC * do not contrain reindex for common SP updates (#3876) * only fast-track jobs with exactly one chunk (#3879) * Fix illegalstateexception when an exception is thrown during stream response (#3882) * Finish up changelog, minor refactor * reset buffer only * Hack for some replacements * Failure handling * wip * Fixed the issue (#3845) * Fixed the issue * Changelog modification * Changelog modification * Implemented seventh character extended code and the corresponding dis… (#3709) * Implemented seventh character extended code and the corresponding display * Modifications * Changes on previous test according to modifications made in ICD10-CM XML file * Subscription sending delete events being skipped (#3888) * fixed bug and added test * refactor * Update for CVE (#3895) * updated pointcuts to work as intended (#3903) * updated pointcuts to work as intended * added changelog * review fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905) * Add test and implementation * Add changelog * 3899 code in limits (#3901) * Add implementation, changelog, test * Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> * 3884 overlapping searchparameter undetected rel 6 1 (#3909) * Applying all changes from previous dev branch to current one pointing to rel_6_1 * Fixing merge conflict related to Msg.code value. * Fixing Msg.code value. * Making checkstyle happy. * Making sure that all tests are passing. * Passing all tests after fixing Msg.code * Passing all tests. Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746) * 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete * created unit test for skip of delete operation while processing duplicating create entries * moved unit test to FhirSystemDaoR4Test * 3379 mdm fixes (#3906) * added MdmLinkCreateSvcimplTest * fixed creating mdm-link not setting the resource type correctly * fixed a bug where ResourcePersistenceId was being duplicated instead of passed on * Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java Change order of tests such that assertEquals takes expected value then actual value Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * added changelog, also changed a setup function in test to beforeeach Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * Fix to the issue (#3855) * Fix to the issue * Progress * fixed the issue * Addressing suggestions * add response status code to MethodOutcome * Addressing suggestions Co-authored-by: Ken Stevens <ken@smilecdr.com> * Fix for caching appearing broken in batch2 for bulkexport jobs (#3912) * Respect caching in bullk export, fix bug with completed date on empty jobs * add changelog * Add impl * Add breaking test * Complete failing test * more broken tests * Fix more tests' * Fix paging bug * Fix another brittle test * 3915 do not collapse rules with filters (#3916) * do not attempt to merge compartment permissions with filters * changelog * Rename to IT for concurrency problems Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Version bump * fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Gl3407 bundle offset size (#3918) * begin with failing test * fixed * change log * rollback default count change and corresponding comments Co-authored-by: Ken Stevens <ken@smilecdr.com> * Offset interceptor now only works for external calls * Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup. * do not reindex searchparam jobs on startup * Fix oracle non-enterprise attempting online index add (#3925) * 3922 delete expunge large dataset (#3923) * lower batchsize of delete requests so that we do not get sql exceptions * blah * fix test * updated tests to not fail Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * add index * Fix up colun grab * Revert offset mode change * Revert fix for null/system request details checks for reindex purposes * Fix bug and add test for SP Validating Interceptor (#3930) * wip * Fix uptests * Fix index online test * Fix SP validating interceptor logic * Updating version to: 6.1.1 post release. * fix compile error * Deploy to sonatype (#3934) * adding sonatype profile to checkstyle module * adding sonatype profile to tinder module * adding sonatype profile to base pom * adding final deployToSonatype profile * wip * Revert version enum * Updating version to: 6.1.1 post release. * Add test, changelog, and implementation * Add backport info * Create failing test * Implemented the fix, fixed existing unit tests * added changelog * added test case for no filter, exclude 1 patient * wip * Add backport info * Add info of new version * Updating version to: 6.1.2 post release. * bump info and backport for 6.1.2 * Bump for hapi * Implement bug fixes, add new tests (#4022) * Implement bug fixes, add new tests * tidy * Tidy * refactor for cleaning * More tidying * Lower logging * Split into nested tests, rename, add todos * Typo * Code review * add backport info * Updating version to: 6.1.3 post release. * Updating version to: 6.1.3 post release. * removed duplicate mention of ver 6.1.3 in versionEnum * backport pr 4101 * mdm message key (#4111) * begin with failing test * fixed 2 tests * fix tests * fix tests * change log Co-authored-by: Ken Stevens <ken@smilecdr.com> * backport 6.1.3 docs changes * fixed typo on doc backport message * fix test breaking * Updating version to: 6.1.4 post release. * wip Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@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: Ken Stevens <khstevens@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> * pin okio-jvm for kotlin vuln (#4216) * Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220) * First commit: Failing unit test and a TODO with a vague idea of where the bug happens. * Don't escape "+" in a URL GET parameter if it starts with "application". * Remove unnecessary TODO. * Add changelog. * Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens. * Ks 20221031 migration lock (#4224) * started design * complete with tests * changelog * cleanup * tyop Co-authored-by: Ken Stevens <ken@smilecdr.com> * 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209) * Added test * Added solution * Changelog * Changes made based on comments * Fix bug with MDM submit * fix * Version bump * 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236) * Add constant for interceptor * add test, changelog * Allow Batch2 transition from ERRORED to COMPLETE (#4242) * Allow Batch2 transition from ERRORED to COMPLETE * Add changelog * Test fix Co-authored-by: James Agnew <james@jamess-mbp.lan> * 3685 When bulk exporting, if no resource type param is provided, defa… (#4233) * 3685 When bulk exporting, if no resource type param is provided, default to all registered types. * Update test case. * Cleaned up changelog. * Added test case for multiple resource types. * Added failing test case for not returning Binary resource. * Refactor solution. Co-authored-by: kylejule <kyle.jule@smilecdr.com> * Add next version * bulk export permanently reusing cached results (#4249) * Add test, fix bug, add changelog * minor refactor * Fix broken test * Smile 4892 DocumentReference Attachment url (#4237) * failing test * fix * increase test Attachment url size to new max * decrease limit to 500 * ci fix Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> * Overlapping SearchParameter with the same code and base are not allowed (#4253) * Overlapping SearchParameter with the same code and base are not allowed * Fix existing tests according to changes * Cleanup dead code and remove related tests * Version Bump * ignore misfires in quartz * Allowing Failures On Index Drops (#4272) * Allowing failure on index drops. * Adding changeLog * Modification to changelog following code review. Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Revert "ignore misfires in quartz" This reverts commit 15c74a46bc1fd9797b42ad6ddbe6ba34605975cb. * Ignore misfires in quartz (#4273) * Reindex Behaviour Issues (#4261) * fixmes for ND * address FIXME comments * fix tests * increase max retries * fix resource id chunking logic * fix test * add modular patient * change log * version bump Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> * Set official Version * license * Fix up numbers * Fix up numbers * Update numbers * wip * fix numbers * Fix test: * Fix more tests * TEMP FIX FOR BUILD * wip * Updating version to: 6.2.1 post release. * Add a whack of logging * wip * add implementation * wip and test * wip * last-second-fetch * expose useful method * remove 10000 limit * Strip some logging * Fix up logging * Unpublicize method * Fix version * Make minor changes * once again on 6.2.1 * re-add version enum * add folder * fix test * DIsable busted test * Disable more broken tests * Only submit queued chunks * Quiet log * Fix wrong pinned version * Updating version to: 6.2.2 post release. * fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https… (#4291) * fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https://github.com/hapifhir/hapi-fhir/issues/4276 * Credit for #4291 Co-authored-by: James Agnew <jamesagnew@gmail.com> * backport and changelog for 6.2.2 * Updating version to: 6.2.3 post release. * fix https://simpaticois.atlassian.net/browse/SMILE-5781 * Version bump to 6.2.3-SNAPSHOT * Auto retry on MDM Clear conflicts (#4398) * Auto-retry mdm-clear on conflict * Add changelog * Build fix * Disable failing test * Update to 6.2.3 again * Update license dates * Dont fail on batch2 double delivery (#4400) * Don't fail on Batch2 double delivery * Add changelog * Update docker for release ppipeline * Updating version to: 6.2.4 post release. * Add test and implementation to fix potential NPE in pre-show resources (#4388) * Add test and implementation to fix potential NPE in pre-show resources * add test * WIP getting identical test scenario * More robust solution * Finalize Code * Add changelog, move a bunch of changelogs * Remove not needed test * Minor refactor and reporting * Fix up megeback * update backport info * update backport info * Updating version to: 6.2.5 post release. * Prevent chunk from returning to in-progress unless it is errorred, in-progress, or queued * changelog * Update logger * Indicate backport * Add version and upgrade info. add backport * hapi-fhir side done * cdr side * add assert * add test * Fix import * prevent multiple reduction step runs in maintenance run (#4423) * setting job to inprog to prevent multiple maintenance passes from running reduction steps * added a new status Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> * Add backport info * Fix up tests * Fix discrepancies * Fix test * Version bump * bump ips Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@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: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: James Agnew <james@jamess-mbp.lan> Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com> Co-authored-by: kylejule <kyle.jule@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> |
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James Agnew
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d584e14048
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Add IPS Generator (#4438)
* Begin IPS refactor * Commit work so far * Fix test bug * Fix typo * Fix typo * Narrative generator cleanup * Narrative generator working * Add test for bad reference in narrative * Tests passing * Start docs * Tests passing * Cleanup * Update cyangelog * Doc tweaks * Version bump * Address review comments * Address review comments * Build fix * Cleanup * Compile fix * Test fix * Test fix * Version bump * Build update * Test fix * Test fix * Add one utility method * Add doc |
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Ken Stevens
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5dda16d467
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Reduce postconstruct use (#4445) | ||
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Ken Stevens
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bf53a08b83
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Batch2 fastracking configurable (#4453)
* licenses * hapi-fhir side done * cdr side * add assert * add test * bump hapi version Co-authored-by: Ken Stevens <ken@smilecdr.com> |
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Qingyixia
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663834ddfe
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Added resourceType as a parameter to $mdm-duplicate-golden-resources operation (#4434)
* Solution + changelog * Addressing suggestions * Minor changes * Version Bump |
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TipzCM
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23b593aa17
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breaking up package installer and package config (#4319)
* breaking up package installer and package config * breaking out parsing of resources * wrong nullable * added an integration test * adding a changelog * added a few minor tests * review fixes * unit test fixes * fixing code checkstyle * moving fetching local package data to package loader svc * updating the method name * splitting the fhirversion parsing * updating table creation task for pretty printing and use in RTE * adding foreign keys * Adding mroe info * minor prettiness changes * fixing fk generation * minor changes * update version Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> |
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Ken Stevens
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04c28b6c08
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Schedule jobs via IJobScheduler instead of in @PostConstruct (#4415)
* parameterizing BinaryStorageInterceptor * parameterizing BinaryStorageInterceptor * changed jobs scheduling from @PostConstruct to coordinated by HapiLifecycleService events * fix test * remove events for now * fix test * simplify design * FIXME * changelog * fix compile issue * review feedback. partially implemented * review feedback * review feedback * bump hapi version to 6.3.8-SNAPSHOT * fix test * mirror contextclosedevent handlers with contextrefreshedevent * version bump * licenses Co-authored-by: Ken Stevens <ken@smilecdr.com> |
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Justin McKelvy
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8c48a6fb91
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Clinical reasoning module (#4347)
* Add new Clinical Reasoning module * Add config to get test up and running * Removed FhirClient from tests * First passing test * Remove unused utilities * Build updates * exclude xxp3 and substitute with unbundled version * Refactor to use provider factory and loader pattern * First passing dstu3 test * CR r4 test config and immunization tests * Add base test classes * Exclude transitive dependency xmlpull * More dependency cleanup * Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr * Fixes for duplicate xpp3 classes * Remove more references to jpa * Add mock FHIR server for terminology endpoint tests * fix cql file for making providerr4 tests pass * fix pom * fix generic * Adding r4 test cases for measure operations. * Fix endpoint tests * javadoc comment, temporarily comment out test results for practitioner sync * javadoc typo fix * adding java docs for cr module WIP * Updates to clinical reasoning documentation * More documentation updates * docs now compile * fix test * DqmR4IT now successfully starts up, but the test does not pass * Fix additionalData test * Make measure service bean overridable * adding clinical reasoning javadoc information * Rename interfaces to start with I * More styleguide updates * Reformat all code in the storage-cr module * More coding convention updates * Remove bunches of unused code, reogranize so that fhir version in package name is consistent * Clean up some static array initializations * add practitioner patient list * refactor product-line constant * test dependency update * add change log for cr module * Add hapi-validation to the pom * Exclude dependencies that are causing duplicates * More dependencies and exclusions * Make some base MeasureService components protected * Update to latest cql compiler release * fix measure service for null subject & practitioner and open up practitioner test * Rev to release versions * Add remaining Dstu3 tests * update hedis bundle from policyHolder to beneficiary * update snapshot * Delete old CQL module * Post-master-merge recovery * Fix Java 17 feature usage issue * update changelog with more information about new functionality * Remove support chain wrapper usage * Add javadocs to IResourceLoader * added the property versioning for antlr jar. * addressing code review comments. * addressing code review comments. * Fix typos in changelog * Remove azure pipeline for cql module, add it for cr module * Address exception comments, add Msg.code calls to exceptions * Fix self-assignment bug * Add storage-cr module to bom * addressing coding comments. * Addressed the variable naming convention to camelCase. * Snapshot version bump Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> |
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karneet1212
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cfa6c13262
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Add resource type as a parameter for $mdm-query-links (#4372)
* Added Solution + test * Removed old methods * fixed issues * Added refactoring * Deprecated methods on the interfaces * Remove todo * Documentation * Changelog * Changelog * Changelog * Changes made based on comments * Changes made based on comments * Clean up * hapi bumping to version 6.3.6-SNAPSHOT * hapi bumping to version 6.3.6-SNAPSHOT |
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James Agnew
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0d5f8da93f
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API improvements for MegaScale (#4112)
* Start work on sharded DB * Work on migrating * Work * Ongoing work * Ongoing work * Work * Work * Ongoing work * Work * Work * Test fix * Test fix * Work * Compile fix * Test cleanup * Test fix * Resolve fixmes * Resolve fixme * Resolve compile errors * Compile fix * Fixes * Work * Add note for later * Test fix * Test fixes * Build fix * Test fixes * Fixes * Test fixes * Test fixes * Test fixes * Test fix * Fixes * Fixes * Remove dead code in pom * More test cleanup * Docs fix * Changes * Fix * Fixes * Resolve merge conflicts * Build update * Merge build fixes * Version bump * Address review comments * Review comments * Review comments * Test fixes * Test fix * Cleanup |
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Nathan Doef
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7b86eda8a9
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Refactor Common SearchParameter Functionality (#4321)
* refactor checkpoint * clean up * add method to find runtime search param by id * new search param cache tests * extract SearchParameter validation functionality * create common interface for combo searchparameters * Remove ResourceTable from extractor interface * clean up * move SearchParameterDaoValidator * resolve code review comments * remove reflection * change log * bump version to 6.3.4-SNAPSHOT Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> |
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kateryna-mironova
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017cc4e29c
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4244 - Deprecate usages of ResourcePersitentId in jpa (#4245)
* init rev * id to jpa and mongo id * 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods * 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods * fixed conflicts, pulled from master * fixed code for passing tests successfully * changed PersistentId to Jpa in MdmSearchInterceptor * added the todo comments with questions * added one more question * renamed TODO questions * first pass at converting to generic ResourcePersistentId * fix test * fix test * fix test * make ResourcePersistentId abstract * Generic type MdmLink * Final TODOs * Final TODOs * cleanup * fix test * fix id to string * fix cyclic package dep * add <?> to Base so we can extract interface * Revert "add <?> to Base so we can extract interface" This reverts commit a806f3d2bcef81842917734b04c90cd8df6b7938. * switch to interface * javadoc * replace base with interface * fix test * add generic template to mdmdao * remove unneccessary JpaPid casts * remove unneccessary JpaPid casts * remove unneccessary JpaPid casts * remove unneccessary MongoPid casts * fix test * fix regression * fix compile issues arising from merging master * fix beans * bump version to 6.3.3-SNAPSHOT * change logs * review feedback * review feedback * fixme Co-authored-by: Ken Stevens <ken@smilecdr.com> |
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James Agnew
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50ca94eded
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Improve JPA response messages (#4293)
* Improve JPA response messages * FIxes * Test fixes * Test fixes * Ongoing testing * Work on messages * Work on messages * Add valueset * Add response code enum * Version bump * Undo bump * Improve changelog * Test fixes * Add javadocs * Version bump HAPI * Test fixes * Test fix * Test fixes * Test fixes * Account for review changes * Test fix * Docs fix * Work on API * Improve SqlQuery api |
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James Agnew
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c3697a5f87
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JPA Cleanup (#4278)
* JPA cleanup * Test fixes * Cleanup * Resolve fixme * Fix bad changelog entry * A bit of documentation reworking * Version bump * POM bump * Avoid timeout * Build fix * HTMLUnit bump |
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James Agnew
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9eeb1545a1
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Avoid race condition in ServiceLoader (#4295)
* Avoid race condition in ServiceLoader * Changelog |
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Tadgh
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b1e3468dcd
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Rel 6 2 1 mergeback (#4288)
* jm wrong bundle entry url (#4213) * Bug test * here you go * Generate relative URIs for bundle entry.request.url, as specified * Point jira issue in changelog * Adjust tests to fixes Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> * improved logging (#4217) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Rel 6 1 3 mergeback (#4215) * Bump for CVE (#3856) * Bump for CVE * Bump spring-data version * Fix compile * Cut over to spring bom * Bump to RC1 * remove RC * do not contrain reindex for common SP updates (#3876) * only fast-track jobs with exactly one chunk (#3879) * Fix illegalstateexception when an exception is thrown during stream response (#3882) * Finish up changelog, minor refactor * reset buffer only * Hack for some replacements * Failure handling * wip * Fixed the issue (#3845) * Fixed the issue * Changelog modification * Changelog modification * Implemented seventh character extended code and the corresponding dis… (#3709) * Implemented seventh character extended code and the corresponding display * Modifications * Changes on previous test according to modifications made in ICD10-CM XML file * Subscription sending delete events being skipped (#3888) * fixed bug and added test * refactor * Update for CVE (#3895) * updated pointcuts to work as intended (#3903) * updated pointcuts to work as intended * added changelog * review fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905) * Add test and implementation * Add changelog * 3899 code in limits (#3901) * Add implementation, changelog, test * Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> * 3884 overlapping searchparameter undetected rel 6 1 (#3909) * Applying all changes from previous dev branch to current one pointing to rel_6_1 * Fixing merge conflict related to Msg.code value. * Fixing Msg.code value. * Making checkstyle happy. * Making sure that all tests are passing. * Passing all tests after fixing Msg.code * Passing all tests. Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746) * 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete * created unit test for skip of delete operation while processing duplicating create entries * moved unit test to FhirSystemDaoR4Test * 3379 mdm fixes (#3906) * added MdmLinkCreateSvcimplTest * fixed creating mdm-link not setting the resource type correctly * fixed a bug where ResourcePersistenceId was being duplicated instead of passed on * Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java Change order of tests such that assertEquals takes expected value then actual value Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * added changelog, also changed a setup function in test to beforeeach Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * Fix to the issue (#3855) * Fix to the issue * Progress * fixed the issue * Addressing suggestions * add response status code to MethodOutcome * Addressing suggestions Co-authored-by: Ken Stevens <ken@smilecdr.com> * Fix for caching appearing broken in batch2 for bulkexport jobs (#3912) * Respect caching in bullk export, fix bug with completed date on empty jobs * add changelog * Add impl * Add breaking test * Complete failing test * more broken tests * Fix more tests' * Fix paging bug * Fix another brittle test * 3915 do not collapse rules with filters (#3916) * do not attempt to merge compartment permissions with filters * changelog * Rename to IT for concurrency problems Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Version bump * fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Gl3407 bundle offset size (#3918) * begin with failing test * fixed * change log * rollback default count change and corresponding comments Co-authored-by: Ken Stevens <ken@smilecdr.com> * Offset interceptor now only works for external calls * Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup. * do not reindex searchparam jobs on startup * Fix oracle non-enterprise attempting online index add (#3925) * 3922 delete expunge large dataset (#3923) * lower batchsize of delete requests so that we do not get sql exceptions * blah * fix test * updated tests to not fail Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * add index * Fix up colun grab * Revert offset mode change * Revert fix for null/system request details checks for reindex purposes * Fix bug and add test for SP Validating Interceptor (#3930) * wip * Fix uptests * Fix index online test * Fix SP validating interceptor logic * Updating version to: 6.1.1 post release. * fix compile error * Deploy to sonatype (#3934) * adding sonatype profile to checkstyle module * adding sonatype profile to tinder module * adding sonatype profile to base pom * adding final deployToSonatype profile * wip * Revert version enum * Updating version to: 6.1.1 post release. * Add test, changelog, and implementation * Add backport info * Create failing test * Implemented the fix, fixed existing unit tests * added changelog * added test case for no filter, exclude 1 patient * wip * Add backport info * Add info of new version * Updating version to: 6.1.2 post release. * bump info and backport for 6.1.2 * Bump for hapi * Implement bug fixes, add new tests (#4022) * Implement bug fixes, add new tests * tidy * Tidy * refactor for cleaning * More tidying * Lower logging * Split into nested tests, rename, add todos * Typo * Code review * add backport info * Updating version to: 6.1.3 post release. * Updating version to: 6.1.3 post release. * removed duplicate mention of ver 6.1.3 in versionEnum * backport pr 4101 * mdm message key (#4111) * begin with failing test * fixed 2 tests * fix tests * fix tests * change log Co-authored-by: Ken Stevens <ken@smilecdr.com> * backport 6.1.3 docs changes * fixed typo on doc backport message * fix test breaking * Updating version to: 6.1.4 post release. * wip Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@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: Ken Stevens <khstevens@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> * pin okio-jvm for kotlin vuln (#4216) * Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220) * First commit: Failing unit test and a TODO with a vague idea of where the bug happens. * Don't escape "+" in a URL GET parameter if it starts with "application". * Remove unnecessary TODO. * Add changelog. * Code review feedback on naming. Also, make logic more robust by putting plus and should escape boolean && in parens. * Ks 20221031 migration lock (#4224) * started design * complete with tests * changelog * cleanup * tyop Co-authored-by: Ken Stevens <ken@smilecdr.com> * 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209) * Added test * Added solution * Changelog * Changes made based on comments * Fix bug with MDM submit * fix * Version bump * 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236) * Add constant for interceptor * add test, changelog * Allow Batch2 transition from ERRORED to COMPLETE (#4242) * Allow Batch2 transition from ERRORED to COMPLETE * Add changelog * Test fix Co-authored-by: James Agnew <james@jamess-mbp.lan> * 3685 When bulk exporting, if no resource type param is provided, defa… (#4233) * 3685 When bulk exporting, if no resource type param is provided, default to all registered types. * Update test case. * Cleaned up changelog. * Added test case for multiple resource types. * Added failing test case for not returning Binary resource. * Refactor solution. Co-authored-by: kylejule <kyle.jule@smilecdr.com> * Add next version * bulk export permanently reusing cached results (#4249) * Add test, fix bug, add changelog * minor refactor * Fix broken test * Smile 4892 DocumentReference Attachment url (#4237) * failing test * fix * increase test Attachment url size to new max * decrease limit to 500 * ci fix Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> * Overlapping SearchParameter with the same code and base are not allowed (#4253) * Overlapping SearchParameter with the same code and base are not allowed * Fix existing tests according to changes * Cleanup dead code and remove related tests * Version Bump * ignore misfires in quartz * Allowing Failures On Index Drops (#4272) * Allowing failure on index drops. * Adding changeLog * Modification to changelog following code review. Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Revert "ignore misfires in quartz" This reverts commit 15c74a46bc1fd9797b42ad6ddbe6ba34605975cb. * Ignore misfires in quartz (#4273) * Reindex Behaviour Issues (#4261) * fixmes for ND * address FIXME comments * fix tests * increase max retries * fix resource id chunking logic * fix test * add modular patient * change log * version bump Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> * Set official Version * license * Fix up numbers * Fix up numbers * Update numbers * wip * fix numbers * Fix test: * Fix more tests * TEMP FIX FOR BUILD * wip * Updating version to: 6.2.1 post release. * Add a whack of logging * wip * add implementation * wip and test * wip * last-second-fetch * expose useful method * remove 10000 limit * Strip some logging * Fix up logging * Unpublicize method * Fix version * Make minor changes * once again on 6.2.1 * re-add version enum * add folder * fix test * DIsable busted test * Disable more broken tests * Only submit queued chunks * Quiet log * Fix up checkstyle * log to console * Remove double import * Version bump * licenses * Fix up version * fix build * wip * wip * Fix up search expansion to use new behaviour of idhelper service * Fix up MDM Search Expansion Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@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: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: James Agnew <james@jamess-mbp.lan> Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com> Co-authored-by: kylejule <kyle.jule@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> |
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James Agnew
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9a45576793
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Cache service loaders (#4196)
* Extracting a Cache interface and building service loaders for Caffeine and Guava * Fix estimated size interface * Use LoadingCache when needed. * Removing Caffeine from dependency lists. * Adding hapi-fhir-cache-caffeine as a test dependency * Putting caching solutions in a single module. * Fixing the spacing * Standardizing the use of TimeUnits * Making a new module to simplify the switch of the cache library in tests. * Making sure the Guava design matches the behavior of Caffeine. * Making sure the Cache structure also does not throw InvalidCacheLoading exception to match the LoadingCache. * Renaming module names for the caching group. * Better error handing that informs devs what to do. * Improving documentation * Typo * Matching error message design with Caffeine. * Matching the behavior of Caffeine with Guava * Final adjustments for the test dependencies on the cache modules. * Fixing relative pom path. * Adding caffeine as a testing requirement for the new modules. * Add changelog and set JPA server to use caffeine cache * POM fixes * Build fix * Buid fix * Fixes * Address review comment * One more cache * Move changelog to next release * Update pom versions * Build fix * Build fixes * Build fix * Try to get build working * Experiment with failing build * Rever change * Fix POM version * Build fix * Build fix * Add Msg.code to new exceptions Co-authored-by: Vitor Pamplona <vitor@vitorpamplona.com> |