https://github.com/jamesagnew/hapi-fhir

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Revision Author Date Message Commit Date
82f046f Bad import setups 14 November 2023, 03:57:24 UTC
8498ba9 Remove dead import 14 November 2023, 03:49:09 UTC
80ec220 wip 14 November 2023, 03:48:48 UTC
9dace15 5426 enhance bundleutil (#5451) * failing test * fix and more tests * cleanup * spotless * remove class paths * add changelog --------- Co-authored-by: aditya_dave <aditya@smilecdr.com> 13 November 2023, 19:50:11 UTC
777859a Rel 6 10 mb (#5441) * Allow cached search with consent active when safe (#5387) Allow the search cache when using consent if safe * Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376) * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Change package installation behavior such that it updates the existing SearchParameter base with remaining resources * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable. * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation * Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177) * 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> * _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 * first fix * tests and preliminary fixes * wip, commit before switching to release branch. * adding capability to handle _lastUpdated in reverse search (_has) * adding changelog * applying spotless. * addressing code review comments. --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.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> * Br 20231019 add cr settings for cds hooks (#5394) * Add settings used in CR CDS Services. Remove config dependency on Spring Boot. * Add changelog * Use String.format rather than concat strings * spotless apply * Add javadoc * Upgrade notes for the forced-id change (#5400) Add upgrade notes for forced-id * Clean stale search results more aggressively. (#5396) Use bulk DMA statements when cleaning the search cache. The cleaner job now works as long as possible until a deadline based on the scheduling frequency. * bump version of clinical reasoning (#5406) * Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408) * Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added * removed unused alias from SQL query of mdm-clear (#5416) * Issue 5418 support Boolean class return type in BaseInterceptorService (#5421) * Enable child classes to use Boolean class return type * spotless --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420) * If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix * Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423) This reverts commit 4e295a59fb143a2ba54bc44305474096e2acd578. Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> * Use new FHIR_ID column for sorting (#5405) * Sort `_id` using new FHIR_ID column. * Fix old tests that put client-assigned ids first. * Better indexing for sort * Bump core to 6.1.2.2 (#5425) * Bump core to 6.1.2.1 Patch release that uses https for primary org.hl7.fhir.core package server * Bump core to 6.1.2.2 * Make sure to return always a value for Boolean class return type. (#5424) Implement change in a non-disruptive way for overriders Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428) Add a non-standard __pid SP. * Review changes for new _pid SP. (#5430) Change name to _pid to match our standard and add warning. * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432) * Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition. * Fix spotless issue * CVEs for 6.10.0 (#5433) * Bump jetty * Bump okio-jvm * 8.2.0 mysql connector * Jena and elastic bumps * Fix test * 5412 post bundle on partition incorrect response.link shown (#5413) * Initial fix and unit test provided * spottless check * Made relevant changes to make solution version agnostic * relevant logic changes made * spotless changes made * New logic added to fix failing test cases * formatting * New logic to make the function more robust * spotless checks * Left a trailing slash in the tests * Made relevant test changes and changed logic * spotless changes * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml changing changelog Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Formatting requirements --------- Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> * Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414) * first fix * - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber - refactored code to reduce repeated code - cleaned unnecessary comments and reformatted files * Changed myResourceModifiedMessagePersistenceSvc to be autowired * removed unused import * added error handling when inflating the message to email and message subscriber * reformatted code * Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc * Changes by gary * Reformatted file * fixed failed tests * implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File. * - implemented IT - fixed logical error - added changelog * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor * resolve code review comments * reformatted files * fixed tests * Fix for failing IT test in jpaserver-starter (#5435) Co-authored-by: dotasek <dotasek.dev@gmail.com> * wip --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Martha Mitran <martha.mitran@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: dotasek <david.otasek@smilecdr.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: 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: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> Co-authored-by: dotasek <dotasek.dev@gmail.com> 10 November 2023, 22:00:08 UTC
3bba9fb add terminology troubleshooting log (#5439) * init rev * init rev * changelog and additional logging * changelog and additional logging * changelog and additional logging * spotless * review feedback 10 November 2023, 19:54:51 UTC
8a39da4 - Added logs when MDM candidate search parameters are not defined and candidate search limit is exceeded. (#5446) - fixed extra indentation for example survivorship rule in quickstart.md 10 November 2023, 18:51:26 UTC
fd523a3 Cleanup 02 November 2023, 19:51:54 UTC
fb7d769 Test cleanup 02 November 2023, 18:42:21 UTC
81ffcd0 Remove legacy lastn implementation 02 November 2023, 12:32:02 UTC
113edef Reslve fixmes 02 November 2023, 12:16:55 UTC
5b280ed Test fix 01 November 2023, 21:35:55 UTC
c916d1e Cleanup attempt 01 November 2023, 21:01:33 UTC
92ece74 Cleanup 01 November 2023, 20:58:35 UTC
880b5a8 Test fix 01 November 2023, 16:12:59 UTC
9199f85 Merge branch 'ja_20230610_servlet_migration' of github.com:hapifhir/hapi-fhir into ja_20230610_servlet_migration 01 November 2023, 13:54:19 UTC
4f3ca50 Test fix 01 November 2023, 13:54:09 UTC
941fdb7 Merge branch 'ja_20230610_servlet_migration' of github.com:jamesagnew/hapi-fhir into ja_20230610_servlet_migration 01 November 2023, 13:46:24 UTC
c8fa49b Add license 01 November 2023, 13:46:18 UTC
b1028c4 Compile fix 01 November 2023, 13:45:57 UTC
1c7fbcb Merge branch 'master' into ja_20230610_servlet_migration 01 November 2023, 13:23:28 UTC
e11a025 Migration 01 November 2023, 13:21:35 UTC
f51fd73 Work 01 November 2023, 11:26:49 UTC
c89fc46 Add ITermConceptClientMappingSvc interface to represent terminology t… (#5410) * Add ITermConceptClientMappingSvc interface to represent terminology translate functions * Add javadoc --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 31 October 2023, 17:21:35 UTC
2411854 Add tinyint to migrator 31 October 2023, 11:56:23 UTC
81f670f Transaction service fix 29 October 2023, 21:42:52 UTC
4e0dca4 Adjust migratyions 29 October 2023, 15:20:17 UTC
46ffb67 Merge branch 'ja_20230610_servlet_migration' of github.com:hapifhir/hapi-fhir into ja_20230610_servlet_migration 28 October 2023, 14:29:23 UTC
8de3689 Disable onetoone ban 28 October 2023, 14:29:07 UTC
c02dd6d Spotless 28 October 2023, 13:40:54 UTC
1c5fb83 Fixes 28 October 2023, 13:03:22 UTC
4915b55 Work on migration 27 October 2023, 18:48:41 UTC
7f3519f CDR fix 26 October 2023, 12:50:18 UTC
a7a4469 5401 add terserutil clear by fhirpath (#5402) * begin with failing test * test passes * test passes * changelog * moar testor 26 October 2023, 03:35:20 UTC
84e3bec 6 8 5 mb (#5399) * 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> * _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 * Fixing terminology upload with large file. (#5204) * create initial test * adding fix; adding changelog; * fixing format. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * up version to 6.8.0 from snapshot * fix up some duplicate deps for skipping * Force deployment of other projects * make dummy java class to pass sonatype checks * make dummy java class to pass sonatype checks * Cheeky test removal * Another test removal * Updating version to: 6.8.1 post release. * adding back in tests for release pipelines * Fix bad version insert * Bump to core library version 6.0.22.2 (#5261) * Bump to core library version 6.0.22.2 * Bump HAPI to 6.8.1-SNAPSHOT, core library version to 6.0.22.2 * up version to 6.8.1 * Prevent remote deployment * Updating version to: 6.8.2 post release. * Re-add deploy plugin skip * re-add version * Bump core library version to 6.0.22.2 * Bump HAPI to 6.8.2-SNAPSHOT * Fix up version enum * Version bump * Updating version to: 6.8.3 post release. * Make display name validation configurable (#5321) * Test fixes * Build cleanup * Initial test passing * Test fixes * Tests all seem to be working * Make display validation level configurable * Should be all working * Add changelog * Add to changelog --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> * wip * wip * Fix conflicts * add backport info * Fix versioning * test fixes * disabled 1 test * backported 5271 to fix validation message tests * wip * Changelog * Fix tests * Fix backport * Add upgrade.md * Fix test * Fix key * Updating version to: 6.8.4 post release. * 5353 iterate on revincludes and includes does not return correct resources when used with non iterate revincludes (#5354) * added failing test * implemented solution * added doc generation * added changelog * fixed the order of includes and revincludes, based on what was implemented before * fixed formatting * fixed wording --------- Co-authored-by: Steven Li <steven@smilecdr.com> * added changelog * Updating version to: 6.8.5 post release. * merge back 5377 * changelog * undo unintended changes from mergeback --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: 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> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: StevenXLi <stevenli_8118@hotmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> 25 October 2023, 17:40:17 UTC
e9570d1 Work on fixes 25 October 2023, 15:21:35 UTC
2236c4f Merge branch 'master' into ja_20230610_servlet_migration 24 October 2023, 20:59:10 UTC
7cc2b07 Fixes 24 October 2023, 20:54:35 UTC
4b66578 Merge branch 'master' into ja_20230610_servlet_migration 24 October 2023, 13:14:19 UTC
029672f Work on test fixes 24 October 2023, 13:09:54 UTC
1776a8a Bump version (#5386) 21 October 2023, 16:35:21 UTC
953f735 Review changes for #4803 (#5381) review changes 20 October 2023, 17:26:24 UTC
ee36926 Move forced-id to HFJ_RESOURCE - step 2 (#4803) * First cut at forced-id step 2 Start using new fhir_id column in hfj_resource instead. * demote fixme for build * Start changelog * Merge cleanups * forced-id migration various fixme cleanups * checkstyle * fix bad conversions to computeIfAbsent * Ugh. Lame checkstyle. * Revert optimistic null assert * missed import. * Fixup broken tests * Fix invalid test * Add missing index annotation 20 October 2023, 16:14:31 UTC
fa45796 All tests have passed! 20 October 2023, 14:54:38 UTC
af1d46f adding additional logging to resource modified submitter svc (#5370) * adding additional logging to resource modified submitter svc * s[otlestt * review fixes * spotless * fixing test --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> 20 October 2023, 13:56:32 UTC
20c8109 Speed up subscription triggering (#5377) * Improve subscription trigger speed * Speed up subscription triggering * Add changelogf * Spotless * Move changelog 20 October 2023, 10:51:35 UTC
e2ca967 Force _summary=false when fetching CodeSystems and ValueSets with remote terminology (#5372) Force _summary=false when fetching CodeSystems and ValueSets with remote terminology 19 October 2023, 13:18:01 UTC
bd74ad1 Work on migration 18 October 2023, 15:28:48 UTC
1e6bb84 Version bump 18 October 2023, 10:42:26 UTC
5df670f Test fixe 18 October 2023, 02:18:08 UTC
1a9bb84 Work on websockets 17 October 2023, 21:22:14 UTC
25ce7d0 fix broken version 16 October 2023, 19:16:58 UTC
90bfe05 Fix version enum (#5352) * Fix version enum * Add license 16 October 2023, 12:19:16 UTC
71bff1f API additions 14 October 2023, 16:12:23 UTC
c832cf0 Hapi cr codecache (#5360) * WIP code cache config * WIP test * Passing unit test * cachelistener IT * hardening cache listener tests * cache listener fixes & tests, measureService migration, add reporter parameter to r4 * fix ELMCache listener to match on version, update test, remove reporter parameter * edit inline notes * changelog, version bump, spotless apply --------- Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> 11 October 2023, 18:47:52 UTC
12fdff2 Test fixes 11 October 2023, 09:43:07 UTC
88e9780 Add additional resource docs to generated OpenAPI documentation (#5359) * Add additional resource docs to generated OpenAPI documentation * Test fix 11 October 2023, 00:36:33 UTC
424f26b Removed helperSvc bean override from JpaConfig (#5350) * Removed helperSvc bean override from JpaConfig * Added change log entry 10 October 2023, 15:13:21 UTC
a0a2050 Some test fixes 10 October 2023, 14:40:19 UTC
a836a55 Refactor ID strategy 09 October 2023, 23:52:48 UTC
6742d34 Schema generator 09 October 2023, 17:59:47 UTC
925e5c3 Work on migration 09 October 2023, 15:01:13 UTC
02f25a9 typo fix (#5358) 06 October 2023, 20:30:44 UTC
12519bd 5353 iterate on revincludes and includes does not return correct resources when used with non iterate revincludes (#5354) * added failing test * implemented solution * added doc generation * added changelog * fixed the order of includes and revincludes, based on what was implemented before * fixed formatting * fixed wording --------- Co-authored-by: Steven Li <steven@smilecdr.com> 06 October 2023, 15:54:26 UTC
e5f700f 5344 $expunge operation fails when the operation is executed on a specific partition (#5347) * initial failing test. * solution with changelog * fixing pom dependency version * fixing pom circular dependency issue and making the new wrapper class generic. * Fixing tests assertion. * Moving test to solve dependency issues. * addressing code review comments. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> 05 October 2023, 16:40:16 UTC
f4aa389 All tests passing 04 October 2023, 16:40:34 UTC
c2810d2 Test fix 03 October 2023, 22:57:11 UTC
dc6638c Merge branch 'master' into ja_20230610_servlet_migration 03 October 2023, 20:33:10 UTC
719b4a7 Work on tests 03 October 2023, 20:30:38 UTC
743e2c1 Add Registries for CDS CR Services (#5342) * Add registries for CdsCrServices and CrDiscoveryServices to allow registration of custom services * Add changelog * Fix broken find method * Fix crDiscoveryServiceFactory 03 October 2023, 11:15:32 UTC
4e9bd15 5339 bulk export errors when patient compartment searchparameter of the resource is not present (#5340) * added failing test * implemented solution, and fixed test * added changelog * fixed formatting * fixed test not passing * fixed test and formatting * added warning for failing the active search param check * code review change --------- Co-authored-by: Steven Li <steven@smilecdr.com> 02 October 2023, 15:32:58 UTC
5411622 add exclusions to terser reference method (#5343) 02 October 2023, 13:23:42 UTC
7e0fa98 adding metrics (#5301) * hapi metrics * step 1 * metrics service * adding metrics service * adding documentation * refactor * refactoring * cleanup * changing * adding changelog * some refactoring * format * review fixes part 1 * review points * review fixes * updates for code review * updates for code review * bumping versions --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 29 September 2023, 13:23:11 UTC
a07598a Imports fix 28 September 2023, 21:14:15 UTC
89d81d5 Work on fixes 28 September 2023, 10:42:42 UTC
c3ff3da Resolve 5336 Mdm Link History Would Fail If Provided with Unknown Ids On Postgres (#5337) * - Added checks in MdmLinkDaoJpaImpl to make sure no empty IN clauses are sent to database. - Implemented tests for the above change. * modified changelog 27 September 2023, 19:01:45 UTC
9b75a95 Work on migration 27 September 2023, 17:41:51 UTC
a220465 Implement CDS on FHIR in CDS Hooks (#5240) * WIP * WIP refactor * Initial commit * measureRefactor WIP * 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 * adding tests WIP * Rework MeasureServiceFActory * measure refactor WIP * 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... * generic provider loader * provider loader update * tests wip * 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> * measureRefactor tests WIP * update tests wip * remove baseCrR4Test * update imports * add paging provider config to tests * dstu3 tests * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * latest work * cleanup * Refactor operation providers to support use in multiple modules * Fix HFQL docs (#5151) * repository measure refactor * undo bundle edit, add config * embedded library true * undo post of bundle * clear library cache on test * fix sumbit-data test * Fix tests * cleanup * Update MeasureService.java * latest * 3.0.0 engine update * merge cleanup * cr updates * cleanup * Only create services for PlanDefs that have a trigger with a named event * Fix parameters being sent through invoke * Handle system actions * cleanup * missing packages from cql * fix test data and test cases for repository api * latest * fix pom * fix test config * cleanup * 3.0.0 clinical reasoning uplift * r4 cql execution provider and tests * fix submitdata provider config * wip cql tests * debugging cql op wip * wip debugging cql * update tests for $cql, fix class names * prep for Pre6 uplift * spotless checks and test fixes * bump to 3.0.0-PRE6 * cleanup * fix version * cleanup * cleanup * fix exlusions in pom * add in cache invalidation config * fix resource resolution * cleanup * search converter bug and test for repository * update pom * update searchconverter * version bump, add changelog * remove term config, move IDaoRegistryUser class * Break out dstu3 providers and move config to version folders * merge cleanup * merge cleanup * Add changelog * spotless * fix error codes * cleanup * cleanup * Handle missing beans in Operation configs * spotless * Use CondtionalOnBean for CR Operation and Repository configs * Fix test config * Add RepositoryFactory and RestfulServer to CdsConfigService * Move createRequestDetails into CdsConfigService * spotless * review comments --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.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: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> 27 September 2023, 17:34:57 UTC
6ee6031 CapabilityStatement doe not declare conformance to IG when a bulk data export provider is registered. (#5329) * adding initial test * adding initial test * solution implementation * spotless apply * bumping to 6.9.8-SNAPSHOT * addressing comments from review and fixing typo * spotless --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> 26 September 2023, 17:56:13 UTC
3226cfc Work on servlet migration 26 September 2023, 09:46:18 UTC
bc0ee99 Resolve MDM query links operation score field imprecise value (#5332) * - Fixed precision error and rounded to 4 decimal places - Removed the vector field from the return value of mdmlink toJSON - modified tests for the above changes. * changed to use BigDecimal instead of Precision to round score * reformatted file 25 September 2023, 14:44:36 UTC
7930735 Work 23 September 2023, 21:17:37 UTC
10d9d96 Binary storage prefix during update (#5334) * wip * Changelog * Fix tests 23 September 2023, 00:55:23 UTC
6a0b279 5089 cr measure refactor (#5324) * 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> * _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) * repository measure refactor * undo bundle edit, add config * embedded library true * undo post of bundle * clear library cache on test * fix sumbit-data test * missing packages from cql * fix test data and test cases for repository api * 3.0.0 clinical reasoning uplift * r4 cql execution provider and tests * fix submitdata provider config * wip cql tests * debugging cql op wip * wip debugging cql * update tests for $cql, fix class names * prep for Pre6 uplift * spotless checks and test fixes * bump to 3.0.0-PRE6 * cleanup * fix version * cleanup * fix exlusions in pom * add in cache invalidation config * search converter bug and test for repository * update searchconverter * version bump, add changelog * remove term config, move IDaoRegistryUser class * Break out dstu3 providers and move config to version folders * CVE-2023-26119 * remove * imports * code review updates --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> 22 September 2023, 23:51:36 UTC
0049319 updating partition interceptor to allow multiple patient ids (#5326) * updating partition interceptor to allow multiple patient ids * spotless --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 22 September 2023, 17:23:43 UTC
cfa5e2e 5327 improve error code 1227 message (#5328) * Improve error code 1227 message * spotless 21 September 2023, 19:51:37 UTC
4541c15 Test fixes 20 September 2023, 14:00:40 UTC
2b7ebbc Make display name validation configurable (#5321) * Test fixes * Build cleanup * Initial test passing * Test fixes * Tests all seem to be working * Make display validation level configurable * Should be all working * Add changelog * Add to changelog --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> 19 September 2023, 22:25:33 UTC
50d2eac Update codeql-analysis.yml (#4973) * Update codeql-analysis.yml * Update checkout version in codeql-analysis.yml 19 September 2023, 18:58:25 UTC
9f9aeb9 Bump core version to 6.1.2 (#5317) * WIP Fix compile errors * Fix compile errors 2 * Fix test fails due to new Validation messages * Ignore validation issues Ignore two validation issues: Two 'side is inherently a collection' warnings are now thrown for the following expressions: NamingSystem nsd-1 uniqueId.type = 'uuid' Observation obs-7 code != component.code There is also a general error ignored because the StructureDefinition for StructureDefinition is actually for FHIR 3.0.1, and contains an invalid expression in constraint sdf-9. This is remedied in the expression used in 3.0.2, but a full update of all profile structure definitions is out of scope for this PR. * Fix property name * Add changelog 19 September 2023, 18:26:20 UTC
8d4f07c Resolve 5262 adding new parameter strictmatch to the mdm history link operation 1 (#5282) * implemented the strictMatch parameter, added corresponding test * implemented the strictMatch parameter, added corresponding test * updated mdm link history documentation created changelog * reverted previous changes. Made the default behaviour of history link as AND instead of OR * optimized imports * modified changelog * modified tests 19 September 2023, 16:15:47 UTC
7eb3150 Update DSTU 3 Validation resources (#5320) * Update resources with FHIR 3.0.1 * Minimize profiles * Minimize valuesets * Restore minimizer * Changelog * Remove FIXME, improve specificity of comments 19 September 2023, 15:56:01 UTC
49a28ef 5290 - Feature Request - Implement toggle to prevent conditional updates from invalidating match criteria. (#5291) * Test skeleton, TODO IMPLEMENTER added all over the place * Add test and TODO IMPLEMENTER * Add jpa storage property to allow preventing conditional updates to invalidate match criteria * spotless * Implement review suggestions --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 19 September 2023, 14:01:33 UTC
964b2c4 Test fixes 18 September 2023, 14:30:30 UTC
67e4216 Reindex operation fails when operation is executed on a specific partition (#5311) * adding initial test. * adding solution * adding changeLog. * satisfying spotless check. * fixing changelog * addressing code review comments. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> 18 September 2023, 13:08:45 UTC
04ca5a7 Test fixes 18 September 2023, 10:25:30 UTC
7e00db3 Start working on JPA migration 18 September 2023, 05:52:44 UTC
e05cf5f Merge branch 'master' into ja_20230610_servlet_migration 18 September 2023, 00:03:23 UTC
1988aa1 Work on migration 17 September 2023, 10:09:05 UTC
9be3b6e Apply spotless 17 September 2023, 04:22:16 UTC
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