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9 Commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
TipzCM
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f97eadadc6
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rebuild golden resource from survivorship on link edit (#5250)
* adding rebuilding option for survivorship * rebuild survivorship resources * cleanup * configuring beans * fixing tests * cleanup * spotless * import fixing * cleaning up * fixing tests * fixing tests * version bump * undo change --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> |
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James Agnew
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5a88b505d0
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Upgrade Thymeleaf (#5239)
* Upgrade Thymeleaf * Apply spotless * Version bump * Test fix |
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Etienne Poirier
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fb3e141c4d
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Messages submitted to the subscription pipeline are lost when submission fails. (#4733)
* One more fix for #4467 * Enabling massIngestionMode causes incomplete resource deletion (#4476) * Adding initial test. * Adding fix and subsequent test. * Adding changelog. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Provide the capability to request that the name of the subscription matching channel be unqualified (#4464) * Adding initial test. * Adding initial solution implementation. * Adding change log and code clean up. * addressing comments from 1st code review. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Change visibility of migration method (#4471) * change migration visibility * add empty migration method for 640 --------- Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> * Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484) * First commit: Make SubscriptionValidatingInterceptor aware of which Pointcut is being called. In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED. Fix resulting compile errors in various unit tests. * Fix/enhance unit tests. Mark methods as deprecated instead of deleting them. Add proper error code. Complete changelog. * Remove erroneous TODOs and tweak the validation logic. * Enhance unit tests and fix changelog. * Reindex batch job fails when processing deleted resources. (#4482) * adding changelog. * Providing solution and adding changelog. * Adding new test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * cleaning up checkstyle files (#4470) * cleaning up checkstyle files * One more fix for #4467 (#4469) * added exlusions for files at base project level so checkstyle doesn't error out * duplicate error code from merge * changing lifecycle goal for all module checkstyle check * moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code * wip * trying to figure out why pipeline cannot copy files * removing modules that don't actually need to be built. * I messed up the version --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * Bump core to 5.6.881 (#4496) * Bump core to 5.6.881-SNAPSHOT * Work on fixing tests * Work on fixing tests 2 * Bump to core release --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> * Issue 4486 mdm inconsistent possible match score values (#4487) * Extract method for readability * Save always normalized score values in POSSIBLE_MATCH links. * Avoid setting properties to null values. Adjust test. * Simplify fix * Fix test. Add RangeTestHelper. --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Revert "cleaning up checkstyle files (#4470)" This reverts commit efae3b5d5f397ab8fd92d7aaa82b484cfdfb3c33. * core version fix * Loosen rules for id helper * initial test implementation/changes and solution wiring. * adding support for jpa/mongo abstraction. * refact completed. need to start implementing scheduling of subscription re-submission with the scheduler service. * post release, merging in master. * wip: commit before merging in branch master. * wip: resuming work on the issue. * wip: before merging in master. * wip: partial implementation of mongo support. * wip: more work to support partial implementation on mongo. * Test implementation * providing method getMessageKeyOrDefault(); * providing changelog * preping codereview. * wip: passing tests * wip: finally solving the Meta issue. * wip: adjusting interfaces * Adding IT and * IT test; fixing rollback issue. * removing non required logging * fixing merge conflict * Preparing for code review. * Preparing for code review. * Compiling code after merging in master. * Fixing checkstyle failure. * Modifications towards getting all tests to pass. * addressing comments from code review. * compiling code after switching target merge branch to rel_pub_2023_05 * compiling code after switching target merge branch to rel_6_6 * Addressing comments made in design meeting. wip. * Addressing comments made in design meeting. finally completed. and last 2 comments addressed. * removing non required override * reverting changes as they are not required. * Modified test and implementation. * implementation of a SynchronousSubscriptionMatcherInterceptor to submit modifiedResources to the subscription pipeline for testing only. * fix tests by modifying the matchingInterceptor to call pointcut when processing * fixing more tests. * WIP to pass all tests in jpaserer-4504-a-resource-submitted-to-the-subscription-pipeline-is-lost-when-the-pipeline-encounters-an-issue * fixing circular dependency * Adding import dependency to class TestSubscriptionSubmitterConfig to allow submission of messages with the SynchronousSubscriptionMatcherInterceptor. * bumping version 6.7.7-SNAPSHOT * bumping HAPI version to 6.7.7-SNAPSHOT * fixing tests failure caused by asynch deliver of resourceModifiedMsg to the processing pipeline. * passing all tests. * unbumping to 6.7.7 * compiling after merging in master. * creating a custom hapi version * providing an synchronous subscription matcher interceptor for testing. * updating pom version to generate artifacts. * fixing tests, WIP/0 * fixing tests, WIP/1 * fixing tests, WIP/2 * Matching entity annotation with migration task declarations. * Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage. * Moving AsynchResourceModified Scheduler and Submitter to hapi-fhir-storage. * Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc]. * Reverting move of AsyncResourceModified[ProcessingSchedulerSvc|SubmitterSvc] again. * Removing creation of new transaction to inflate PersistedRresourceModifiedMessages since it is already executing in a transaction. * bumping to version 6.7.14-ASYNC-SNAPSHOT for pipeline. * bumping hapi version to 6.7.14-ASYNC-SNAPSHOT for pipeline. * Formatter changes. * add generic * add generic * Addressing code review comments. * Adding file asynch_subscription_610.md to docs/upgrades * changing poms to 6.9.2-SNAPSHOT before merging in master. * compiling after merging in master. * Lowering logging level to debug. * Bumping to 6.9.3-SNAPSHOT * Bumping hapi version to 6.9.4-SNAPSHOT * Adding update documentation. * Modifying update file following review. --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Mark Iantorno <markiantorno@gmail.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> |
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James Agnew
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1e45506526
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Improve ID filtering (#5215)
* Improve ID filtering * Formatting * Add license header * Address review comments |
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Tadgh
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a10856e091
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GM1 Mergeback (#5203)
* version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * Rename file to force IT mode * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * wip * Fix API usage * wip * Version bump --------- Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> |
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TipzCM
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a48c602f71
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adding pointcuts for mdm operations (#5116)
* adding pointcuts for mdm operations * adding changelog * cleanup * cleaning up * formatting * review fixes * formatting * more cleanup * cleanup * moving changelog * fixing a bug * cleanup * formatting * version bump * fixing broken merge * fixing the version --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> |
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James Agnew
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2b91f0a232
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Version bump HAPI FHIR and a couple of deps (#5121)
* Version bumps * Version bump HAPI * Add enum for next release * Changelog update * HAPI version bump |
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Tadgh
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53ceb7cac4
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Bump to nov (#5120)
* bump version, make new folders * Fix typo in versionenum |
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James Agnew
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6d745b4f2d
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Initial HFQL SQL Implementation (#5083)
* FQL tests * Working so far * Tests working * Tests passing * Work on parser * Tests passing * Cleanup * Working * Work on parser * Work * Working * Work on tests * Work on driver * Work * Ongoing work * Rename SEARCH to WHERE * Work on fhirpath * Test fixes * Work on statements * Build fixes * Spotless application * Fix CI * Build fixes * Clean up changelogs * Remove redundant gitignore * Add docs * Add docs * Code cleanup * Build cleanup * Fix compile error * Test fixes * Test fix * Test fix * Work on integration * Work on design * Work on UI * Update hapi-fhir-jpaserver-hfql/src/main/java/ca/uhn/fhir/jpa/fql/jdbc/JdbcDriver.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Address review comments * Review comments * HFQL work * Cleanup * CLeanup * License headers * Test fixes * HAPI version bump * License header update * Changelog cleanup * Fixes * Test fix * Fix spotless issues --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> |