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

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Revision Author Date Message Commit Date
e92bf2b Fix key 22 September 2023, 23:54:34 UTC
e05e94c Fix test 22 September 2023, 23:49:45 UTC
2ad816e Add upgrade.md 22 September 2023, 20:33:15 UTC
1e10004 Fix backport 22 September 2023, 19:41:19 UTC
d4405bf Fix tests 22 September 2023, 19:30:32 UTC
380978b Changelog 22 September 2023, 19:30:28 UTC
51b2b89 wip 22 September 2023, 19:30:22 UTC
bdad38f backported 5271 to fix validation message tests 22 September 2023, 18:58:52 UTC
bea1371 disabled 1 test 22 September 2023, 18:15:06 UTC
90f6123 test fixes 22 September 2023, 16:05:19 UTC
606756f Fix versioning 21 September 2023, 03:21:10 UTC
f444168 add backport info 21 September 2023, 02:49:31 UTC
1b78937 Fix conflicts 21 September 2023, 02:46:57 UTC
6888770 wip 21 September 2023, 02:41:28 UTC
a15a3dc wip 21 September 2023, 02:38:01 UTC
f4dfefa 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> 21 September 2023, 02:23:25 UTC
d94bec7 Updating version to: 6.8.3 post release. 06 September 2023, 00:53:50 UTC
c411789 Version bump 05 September 2023, 16:44:07 UTC
528a7be Fix up version enum 05 September 2023, 16:23:22 UTC
20366ce Bump HAPI to 6.8.2-SNAPSHOT 05 September 2023, 14:43:24 UTC
ccc0895 Bump core library version to 6.0.22.2 05 September 2023, 14:10:18 UTC
71c3848 re-add version 04 September 2023, 02:57:43 UTC
098c8bf Merge branch 'rel_6_8' of github.com:hapifhir/hapi-fhir into rel_6_8 04 September 2023, 02:57:11 UTC
7e56d78 Re-add deploy plugin skip 04 September 2023, 02:57:00 UTC
51012ba Updating version to: 6.8.2 post release. 04 September 2023, 00:33:55 UTC
6008215 Prevent remote deployment 03 September 2023, 20:51:41 UTC
0e54b7c merge rel6_8 31 August 2023, 20:48:48 UTC
d24817f up version to 6.8.1 31 August 2023, 20:46:47 UTC
79177a6 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 31 August 2023, 14:39:55 UTC
8e5f844 Fix bad version insert 30 August 2023, 23:25:38 UTC
5845216 adding back in tests for release pipelines 17 August 2023, 13:49:31 UTC
3eff70b Updating version to: 6.8.1 post release. 17 August 2023, 12:27:58 UTC
f336270 Another test removal 17 August 2023, 11:14:24 UTC
5398387 Cheeky test removal 17 August 2023, 11:01:46 UTC
8b62689 make dummy java class to pass sonatype checks 17 August 2023, 10:48:42 UTC
5ae3a48 make dummy java class to pass sonatype checks 17 August 2023, 10:48:19 UTC
e8d92d3 Force deployment of other projects 17 August 2023, 05:15:53 UTC
27f7b5d fix up some duplicate deps for skipping 16 August 2023, 22:36:16 UTC
47a28b7 up version to 6.8.0 from snapshot 16 August 2023, 19:24:47 UTC
204eb37 Fixing terminology upload with large file. (#5204) * create initial test * adding fix; adding changelog; * fixing format. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> 11 August 2023, 22:08:05 UTC
7e849a8 Merge branch 'rel_6_8' of github.com:hapifhir/hapi-fhir into rel_6_8 11 August 2023, 17:26:32 UTC
be1a9d4 licenses 11 August 2023, 17:26:13 UTC
0d4c983 dont use new API for a bit (#5190) 11 August 2023, 15:37:19 UTC
f538997 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> 10 August 2023, 21:19:58 UTC
9fa41d3 Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog 10 August 2023, 19:49:01 UTC
c3b8844 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 10 August 2023, 18:00:12 UTC
d306760 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> 10 August 2023, 17:57:47 UTC
ebdecef Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. 09 August 2023, 20:21:44 UTC
cfe6622 dont use new API for a bit (#5191) 09 August 2023, 19:09:04 UTC
f358a0b Remove target slf4j version 09 August 2023, 18:43:16 UTC
9792122 Fix link 09 August 2023, 18:25:55 UTC
5e30780 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> 08 August 2023, 20:29:47 UTC
7a13fcc 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> 08 August 2023, 13:54:31 UTC
a6d64bf 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> 08 August 2023, 13:52:40 UTC
4cd93fd _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog 03 August 2023, 18:40:47 UTC
f6f855b updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 03 August 2023, 13:46:57 UTC
4fc99e7 $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. 03 August 2023, 02:13:10 UTC
f82da96 Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. 02 August 2023, 21:30:24 UTC
d970ca5 documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 02 August 2023, 19:53:11 UTC
b816844 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> 02 August 2023, 18:02:18 UTC
ca2c7bd Fix HFQL docs (#5151) 01 August 2023, 14:44:16 UTC
4ec17c9 _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers 31 July 2023, 21:21:51 UTC
e077393 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> 27 July 2023, 20:27:23 UTC
4820759 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> 27 July 2023, 16:53:50 UTC
ff507cd 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified 27 July 2023, 15:37:55 UTC
1697783 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... 26 July 2023, 15:01:59 UTC
9a996ce 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 24 July 2023, 15:13:14 UTC
902df2d version bump 21 July 2023, 23:33:59 UTC
6d745b4 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> 21 July 2023, 22:51:23 UTC
f68f3fb Resolve 5112 unable to expunge deleted codesystem until several minutes later (#5113) * returned user-friendlier message, implemented unit tests, added changelog * reformatted file * added Msg.code to the exception thrown * added Msg.code in test * Changed to catch DataIntegrityViolationException only. 21 July 2023, 17:08:58 UTC
d31da21 Fix openapi for R5 (#5115) * Fix openapi for R5 * Add changelog 21 July 2023, 15:17:13 UTC
66f428d 5103 - Adjust our handling of space escape characters in URLs (#5104) * 5103 - Adjust our handling of space escape characters in URLs * 5103 - Fix formatting * 5103 - Adjust URL escaping and update test expectations * 5103 - additional test for values with literal plus signs * 5103 add changelog for this issue * 5103 - documentation change to describe proper URL escaping * 5103 - Minor documentation addition 20 July 2023, 20:14:28 UTC
a0c8593 fix split-package conflicts with org.hl7.fhir.*.model packages in FHIR (#5109) Core projects 20 July 2023, 18:54:43 UTC
e02468b 5080 new similarity algorithm to handle numeric normalization (#5082) * solution * test * docs + changelog * fix formatting --------- Co-authored-by: justindar <justin.dar@smilecdr.com> 20 July 2023, 17:20:51 UTC
2fbd3fa Lowering the logging severity level from info to debug for specific services (#4948) * Changed the two files to reduce info level to debug level for select services. * Adding change log --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> 20 July 2023, 14:52:11 UTC
41a1d0a add extra logging to troubleshoot partition creation (#5108) Co-authored-by: Ken Stevens <ken@smilecdr.com> 20 July 2023, 00:31:47 UTC
c75dd41 6 8 cves (#5107) * bump * Update deps * reduce thymeleaf * Remove dead import 19 July 2023, 21:58:31 UTC
675699a 5092 results ordering for mdm link history is incorrect (#5093) * update docs to be more specific * fix ordering when client assigned id doesn't match pid * remove fix ordering when client assigned id doesn't match pid --------- Co-authored-by: justindar <justin.dar@smilecdr.com> 19 July 2023, 20:57:21 UTC
cd3c4d2 Issue 5102 mdm link history ordering is incorrect when client assigned id and pid are different (#5105) * Failing test * Add some self-assigned Patient IDs * Sort after client-selected ID is interpolated into the result * spotless * changelog * Keep DAO level ordering enforced by tests * Filter out non-client-provider ids from test as they are unpredictable in build pipeline --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 19 July 2023, 19:35:51 UTC
cf8c709 fixing bug in findcandidatebyexamplesvc (#5101) * fixing build * cleanup * review fix * review changes --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 19 July 2023, 12:26:05 UTC
d6fae7c fix bug on hapifhirdal searchbyurl to account for version (#5087) * fix bug on hapifhirdal searchbyurl to account for version * update return type to bundleIterable, update test to validate * add clinical-reasoning 3.0.0-PRE5 * added test comments, updated search, explicit variables * add example comment to search cases * fix typo * spotless apply edits --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> 14 July 2023, 18:17:13 UTC
633a2d1 5097 - Fixed a couple of links in the javadocs for the IValidationSupport class. (#5098) 14 July 2023, 17:34:32 UTC
6178075 wip (#5091) 13 July 2023, 22:56:23 UTC
2401b23 fixing a bug with duplicte golden resources being returned (#5085) * fixing a bug with duplicte golden resources being returned * review points * fixing tests * blah --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 13 July 2023, 19:58:27 UTC
906355d adding block list for mdm (#5059) * using any/exact enum * bluck rule evaluation svc * adding blocklist * adding documentation * cleanup * adding mdm blocking service and code cleanup * review points * another review point * review points --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> 13 July 2023, 13:59:02 UTC
c886622 implement cds hooks (#5076) * move json and interfaces to hapi * move serialization over * moar test move * move prefetch service * move service registry * moved everything we can. now just need to add a controller and controller test * controller done * IJ Warnings * Move test * licenses * mvn spotless:apply * checkstyle * spotless --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> 12 July 2023, 20:47:37 UTC
43694f3 Ensure FhirContext loads custom resources in the list of resource names (#5073) * Fix bug by maintaining a separate list of resource types including the custom resources that will be used to validate the Bundle resources. * Add custom resource types to resource types list and add conditional logic in ValidationDataInitializerSvcImpl to ensure there is no Exception when parsing a custom resource type. * Add changelog. * Remove unnecessary change. * Address code review feedback. * Address code review feedback. * Add one more unit test. * Bump to 6.7.14-SNAPSHOT. 12 July 2023, 14:32:09 UTC
52f3ef5 New formatting rules and pre-commit hooks (#5027) * pre-apply spotless * New pre-format checkpoint * Once-over the repository * Add pre-commit hook * New github action * excludes * Revert "Once-over the repository" This reverts commit 89334ba8d107ce92c101ad11b0de2586d434e7c5. * Once-over the repo * do not inherit * Revert "Once-over the repo" This reverts commit 31ed8731ad7430d31388e2d942730c150f9edd91. * Add baisc license support to spotless * Move license * Fix inclusions * Fix inclusions * Fix licensing * license fixes * Remove dead file that is only a license * Remove dead class * remove dead file * Tighten licensing * Tighten licensing * Tighten licensing * Tighten licensing * Remove specific package * Make the precommit hook executable * Fix ordering * rollback license * wip * Add to deployable pom * remove file * Fix location * Remove dead comment * wipP * Fix ratchet * Fix up error * Add pre-commit * precommit fixes * wip * wip * Autoformat * remove dead pom parts * replace internal hook with pre-commit * Fix fetch-depth for checker action * Remove ratchet and filter * fix up * rename * Add comment check * rework message * First once-over of the repo * wip * format 12 July 2023, 00:36:44 UTC
1ce2043 Add JPA_PERFTRACE_INFO invocation to Fulltext Searches (#5072) * Changelog * basic test * Api change for fulltext, add test * Add javadocs * Refactor to use a simpler method * Review comments 11 July 2023, 20:32:02 UTC
eb06b47 Update version of the Clinical Reasoning module (#5045) * Update version of the Clinical Reasoning module * cleanup * Add changelog * Update snapshot * Inc version 07 July 2023, 14:05:10 UTC
10af143 Delete expunge fails with identical update timestamps (#5047) * 4759 - WIP unit test for this issue * WIP updating unit test for ResourceIdListStep * WIP candidate fix for ResourceIdListStep batch size problem * Enhance unit test with ArgumentCaptor. * WIP Parameterized the ResourceIdListStepTest and added assertions * Adding changelog for this issue * Updating changelog message for 5055 * Code formatting and import cleanup --------- Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> 06 July 2023, 15:59:56 UTC
a87321a add instantiateBackboneElement method to TerserUtil (#5060) * add instantiateBackboneElement method to TerserUtil * changelog 05 July 2023, 21:57:19 UTC
a93d06c Restrict bulk export download to specific user (#5052) * Work * Bulk export partitioning fixes * Changelog fixes * cleanup * Work on security * Compile fixes * Work * Test fix * Work * Add changelog * License header changes * Test fix * Test fix * Fixes * Version bump * Test fix * Fix accidental change 05 July 2023, 16:48:15 UTC
9a6288c fix hapi paging regression (#5057) * fix regression * change log --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> 04 July 2023, 18:43:43 UTC
216c6ed fix surefire config (#5049) * relegate surefire config to parent pom pluginManagement * back out build fix to see if stack trace now shows up in logs * back out the backed out fix. --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> 04 July 2023, 18:08:44 UTC
754bd49 #5023 Unexpected usage of awssdk StringUtils in hapi 6.6 jpa migration (#5024) task Replace usage of awssdk 03 July 2023, 21:42:07 UTC
39ee86d fix: typo in 'opposed' (#5051) 02 July 2023, 19:48:20 UTC
a73b748 5014 only positive ints (#5050) * limit ints, add test and changelog * changelog 01 July 2023, 17:02:52 UTC
2c6cd60 bundle paging cleanup (#5044) * extracted ResponseBundleBuilder and started writing unit tests. Currently at 71% coverage. * asert bundle entries * assert first entry id * unknown size * coverage up to 78% * test filter nulls * test null id check * up to 91% test coverage * 96% test coverage * 98% test coverage. this is final state * fix cyclic dep * switch to record * split up large method * split up large method * consolidate params * consolidate params * IntelliJ Warnings * cleanup * cleanup * extract methods * extract methods * param names * variable name * formatting * extract method * cleanup * javadoc * upstream consolidation * parameter names * TODO * TODO * review feedback --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> 01 July 2023, 04:23:32 UTC
ad71755 Resolve 5029 Token params with system and value longer than maximum length should be created and searched differently (#4998) * Partial implementation after this has been paused: Move trimming of value and system from BaseSearchParamExtractor to ResourceIndexedSearchParamToken. Do not throw Exceptions in TokenPredicateBuilder. Ensure that the hash computing in the search param token takes the 200+ token value into account. Other search param tokens are not yet implemented. * in ResourceIndexedSearchParamToken,changed hardcoded length to constant MAX_LENGTH; in BaseSearchParamExtractor, added check in createTokenIndexIfNotBlank so that the return value is null if system or value is blank. * added test for TokenPredicateBuilder to verify that long values exceeds the max length does not cause exception. added test in FhirSystemDaoR4SearchTest to verify searchParamToken with longer system and value than max length can be created successfully. And hash value will be calculated before truncation * fixed a logical error in previous commits * changed existing tests to accommodate for the changes * modified existing tests * added changelog * changed truncation method name and added comments Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * modified changelog Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * combined redundant tests --------- Co-authored-by: tyner <tyner.guo@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> 30 June 2023, 14:48:33 UTC
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