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

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Revision Author Date Message Commit Date
0b02bd4 Implemented the fix the RIGHT way this time. 16 March 2023, 22:36:39 UTC
5a6282b Fixed migration step for MS SQL Server. 16 March 2023, 19:21:17 UTC
1bd8f0a added new version changelogs 15 March 2023, 18:16:50 UTC
17cb2e1 fix mistakes when cherry-picking 15 March 2023, 18:03:59 UTC
4ac490e Merge branch 'rel_6_4' of https://github.com/hapifhir/hapi-fhir into rel_6_4 15 March 2023, 17:19:34 UTC
5f7ccb3 backported pr 4609, fixed merge conflicts 15 March 2023, 17:19:28 UTC
47d7809 Updating version to: 6.4.4 post release. 15 March 2023, 16:07:25 UTC
cfc9af8 fix regression 14 March 2023, 15:53:24 UTC
37f5e59 add end time to reduction step (#4640) * add end time to reduction step * add changelog --------- Co-authored-by: Long Ma <long@smilecdr.com> 10 March 2023, 22:01:28 UTC
5eca889 4636 - Fixed Oracle syntax problem with fix provided via PR 4630. (#4637) * 4636 - Fixed Oracle syntax problem with fix provided via PR 4630. * 4636 - Added a changelog file for this fix. 10 March 2023, 13:45:48 UTC
b450729 fixed changelog, added 6.4.3 changelog folder 08 March 2023, 16:56:27 UTC
6fa1270 Merge branch 'rel_6_4' of https://github.com/hapifhir/hapi-fhir into rel_6_4 07 March 2023, 19:42:49 UTC
efe1be4 Provide default update time to batch2 entities (#4630) * Data migration - default value for batch2 UPDATE_TIME 07 March 2023, 18:35:09 UTC
c83dc29 set version back to 6.4.3 07 March 2023, 16:48:32 UTC
a288b65 adding 6.4.3 to enum so it builds 04 March 2023, 18:47:33 UTC
02169f9 Bump to 6.4.3-SNAPSHOT 04 March 2023, 17:58:21 UTC
d5ebd1f Avoid fetching work-chunk data (#4622) * Replace work-chunk maintenance query with projection to avoid fetching clob data. * Add processing logging 04 March 2023, 17:12:04 UTC
98b0dc3 temp removal 03 March 2023, 17:51:02 UTC
65f1bfe Remove cache 03 March 2023, 16:26:46 UTC
0829442 Fix hashcode 02 March 2023, 21:33:27 UTC
b6f9cc8 add message code to error 02 March 2023, 20:49:45 UTC
8e8c6b8 Fix up changelog folder 28 February 2023, 03:09:08 UTC
9d65707 Fix daoconfig name 28 February 2023, 00:35:05 UTC
c51aa39 Set back to 6.4.2 28 February 2023, 00:27:59 UTC
9d88868 Remove unnecessary changelog 28 February 2023, 00:20:53 UTC
1d3627b Fix up backport 28 February 2023, 00:20:29 UTC
49e7ade Merge branch 'rel_6_4' of github.com:hapifhir/hapi-fhir into rel_6_4 28 February 2023, 00:20:22 UTC
795baa1 Fix null Tag.userSelected error by defaulting to false if the value is null. (#4605) 28 February 2023, 00:19:09 UTC
7a4a8c9 Simultaneous $reindex and DELETE can orphan index rows (#4584) Add optimistic write lock to $reindex operation to prevent indexing stale data. Introduce Lockstep Phaser to make testing easier Add 1 query to every resource reindex :-( 28 February 2023, 00:17:34 UTC
fe288fb Temporarily set to snapshot 27 February 2023, 17:59:32 UTC
9d70dbd Add UserSelected and Version to resource tag (#4591) * First commit: Add userSelected and version to ResourceTag and ResourceHistoryTag. Add migration step to migration tasks. For some reason SchemaMigrationTest is failing. * Fix nullability, update constructors, truncate versions over 30 chars. * yay we're done just cleanup * Checkpoint for recent changes. * Last commit before pausing work. * Fix bad code to find the version, tweak unit test pid ID to versionless and add TODO about why is update part of the test not passing? * Fix bad code in extractTagsRi(): Make it leverage the IBaseCoding variable already in the for loop. Fix bad code in populateResourceMetadataRi(). Leverage the existing BaseTag and use it to populate the IBaseCoding tag instance instead. Add more and better assertions in the unit test. * Merge rel_6_4 in * Current state for pairing * Fix CodingDt.getUserSelected method return code in tinder * Complete migration task and cleanup * Remove missed fixme * Bump version temporarily to use it for building core lib * Use primitive for compatibility with tinder generated CodingDt * Copyright updates * Hack to bypass NPE generated by bogus tinder-generated code * Simplify by removing temporary deprecations as version bump is needed anyway because of TagDefinition entity changes * Adjust tests * Fix migration task * Add test to show problem with tinder generated BooleanDt * More test adjustments * Improve BooleanDt NPE avoidance * Update core dep * Reverse Juan CVE VersionEnumTest changes. * Fix unit test. --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> 27 February 2023, 17:58:27 UTC
ce46f4d Re-enable tests disabled to make the 6_4 release build pass. (#4600) 27 February 2023, 16:50:49 UTC
59cc7ad Change backport pointers 27 February 2023, 16:14:34 UTC
3a8b42d Improve bulk export performance (#4569) * Improve performance on bulk export * Add changelog * Start working on cleaned up reducer * Clean up batch calls * Work on issues * Build fixes * Test fixing * Test fixes * Work on progress * Add changelog * Build tweak * Fixes * Fixes * Fix compile * Test fixes * Bump to 6.4.2-SNAPSHOT * Fix compile --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> 27 February 2023, 12:32:39 UTC
e14b289 fix version 27 February 2023, 01:19:08 UTC
31610cd Updating version to: 6.4.2 post release. 26 February 2023, 22:29:48 UTC
69f2527 disables 26 February 2023, 18:14:59 UTC
b227005 Merge branch 'rel_6_4' of github.com:hapifhir/hapi-fhir into rel_6_4 26 February 2023, 15:35:39 UTC
49c548d disables 26 February 2023, 15:34:24 UTC
bd83f33 disable 25 February 2023, 23:08:55 UTC
6915b85 Disable yet another intermittently failing tests. (#4596) 25 February 2023, 21:29:53 UTC
97d6e30 Merge branch 'rel_6_4' of github.com:hapifhir/hapi-fhir into rel_6_4 25 February 2023, 17:02:14 UTC
0ada4e7 ITify 25 February 2023, 17:02:06 UTC
2d4b8d9 Disable more intermittently failing tests (#4595) * Disable more intermittently failing tests. * Disable another intermittently failing tests. 25 February 2023, 16:36:29 UTC
d4a5153 rename tests to IT 25 February 2023, 06:41:13 UTC
d192bce Disable intermittently failing tests. (#4593) 25 February 2023, 03:07:53 UTC
79692df Tidy metadata 24 February 2023, 18:30:19 UTC
9fe44ee Fix changelog 24 February 2023, 18:13:19 UTC
9ede6b3 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> 24 February 2023, 18:12:01 UTC
4af1a50 Force pin structs 24 February 2023, 18:08:29 UTC
eee6128 Exclude pinned core deps 24 February 2023, 17:04:39 UTC
b2ebdec Address leftover code review feedback from the upgrade to core 5.6.97. (#4585) 24 February 2023, 16:32:54 UTC
baa494c Fix up dal test 24 February 2023, 03:42:20 UTC
2c34bf0 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> 23 February 2023, 23:32:13 UTC
bbe437a Add backport info 23 February 2023, 00:03:49 UTC
8698abf 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> 23 February 2023, 00:02:53 UTC
6b6f1e2 Fix bad creation of versionenum 17 February 2023, 07:11:11 UTC
827bbba Updating version to: 6.4.1 post release. 17 February 2023, 04:29:53 UTC
71fa4f2 License fixes, new parent 17 February 2023, 01:02:14 UTC
23b7acf Remove bumped version 17 February 2023, 00:47:36 UTC
529e478 Change parent 17 February 2023, 00:45:04 UTC
96855fb Reset version 17 February 2023, 00:33:56 UTC
384bea1 Merge branch 'rel_6_4' of github.com:hapifhir/hapi-fhir into rel_6_4 17 February 2023, 00:33:24 UTC
f08823b Add javadocs and sources to our serviceloaders 17 February 2023, 00:33:19 UTC
b2644c1 Updating version to: 6.4.1 post release. 16 February 2023, 23:33:58 UTC
acfde15 Downgrade dep' 14 February 2023, 23:24:39 UTC
a0e4c29 License updates' 11 February 2023, 04:51:17 UTC
9578610 bump ver 11 February 2023, 04:42:38 UTC
9754a72 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> 10 February 2023, 18:14:29 UTC
fb0512f Avoid logging message payloads that contain sensitive data (#4537) Don't log payloads - they may contain sensitive data. 10 February 2023, 14:30:55 UTC
03ccf3e Better error handling for when channel type is not supported (#4538) Co-authored-by: kylejule <kyle.jule@smilecdr.com> 10 February 2023, 05:49:44 UTC
e99aebd Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535) This reverts commit 53252b8d153f97f4a66a7d20751913911a71f098. 09 February 2023, 22:33:53 UTC
f3847b1 fixed channel import null pointer exception from null header (#4534) * retryCount 0 on null header + test + changelog * suggested changes 09 February 2023, 19:49:54 UTC
fe078c2 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> 09 February 2023, 19:48:59 UTC
53252b8 fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524) * fix + test * minor fix * Addressing suggestion * Minor changes 09 February 2023, 15:48:55 UTC
3d9a318 Making narrative_generation.md reference an html snippet (#4531) Co-authored-by: peartree <etienne.poirier@smilecdr.com> 09 February 2023, 14:47:14 UTC
b4778f4 fix build (#4530) 09 February 2023, 00:25:05 UTC
6b3b954 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> 08 February 2023, 21:54:25 UTC
71ea1b4 REVERT: change to operationoutcome.html 08 February 2023, 20:04:23 UTC
f321573 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> 08 February 2023, 16:45:59 UTC
697bd27 Update to documentation regarding narrative generation; (#4521) Providing changelog; Co-authored-by: peartree <etienne.poirier@smilecdr.com> 08 February 2023, 13:47:13 UTC
e724040 New line:: 08 February 2023, 01:22:36 UTC
85ecbf1 Unable to Expunge CodeSystem (#4507) * changes for GL-3943 * changes for GL-3943 --------- Co-authored-by: isaacwen <isaac.wen@smilecdr.com> 07 February 2023, 20:26:10 UTC
ca21abf 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 07 February 2023, 19:37:52 UTC
d08995a Add check in scanner (#4518) 07 February 2023, 18:13:29 UTC
e160325 CVE resolutions (#4513) * Bump Postgres for CVE * Bump jetty * Verison bump * Remove comments * Revrt bump 06 February 2023, 21:44:52 UTC
33f6ed3 Change bulk import test for valueUri type (#4503) * change tests * suggested test change 06 February 2023, 17:19:21 UTC
2a963ac 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. 06 February 2023, 14:04:04 UTC
0996124 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> 03 February 2023, 19:00:29 UTC
7d554d5 License 03 February 2023, 18:25:19 UTC
df83d05 Merge branch 'rel_6_4' of github.com:hapifhir/hapi-fhir into rel_6_4 02 February 2023, 23:22:28 UTC
a855af5 Loosen rules for id helper 02 February 2023, 23:11:32 UTC
c642853 core version fix 02 February 2023, 22:40:13 UTC
740fec9 Revert "cleaning up checkstyle files (#4470)" This reverts commit efae3b5d5f397ab8fd92d7aaa82b484cfdfb3c33. 02 February 2023, 22:24:34 UTC
0a213a5 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> 02 February 2023, 19:42:38 UTC
b1770ab 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> 02 February 2023, 14:52:04 UTC
efae3b5 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> 01 February 2023, 23:00:45 UTC
dd8c8a3 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> 01 February 2023, 13:15:33 UTC
67ace43 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. 31 January 2023, 20:42:39 UTC
882f22f Change visibility of migration method (#4471) * change migration visibility * add empty migration method for 640 --------- Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> 31 January 2023, 15:19:25 UTC
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