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14 November 2023, 18:36:22 UTC
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672a4ad Long Ma 20 July 2023, 20:27:05 UTC upgrade.md message uninteded 20 July 2023, 20:27:05 UTC
90910b2 Long Ma 20 July 2023, 20:25:18 UTC also disabled a test 20 July 2023, 20:25:18 UTC
aa9334b Long Ma 20 July 2023, 20:24:45 UTC backport had pipeline changes, this is unintended 20 July 2023, 20:24:45 UTC
1dd1014 Long Ma 20 July 2023, 20:22:41 UTC merge master, change changelog message to thank community contributor 20 July 2023, 20:22:41 UTC
66f428d Steve Corbett 20 July 2023, 20:14:28 UTC 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 William Denton 20 July 2023, 18:54:43 UTC fix split-package conflicts with org.hl7.fhir.*.model packages in FHIR (#5109) Core projects 20 July 2023, 18:54:43 UTC
e02468b jdar8 20 July 2023, 17:20:51 UTC 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 LalithE 20 July 2023, 14:52:11 UTC 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 Ken Stevens 20 July 2023, 00:31:47 UTC add extra logging to troubleshoot partition creation (#5108) Co-authored-by: Ken Stevens <ken@smilecdr.com> 20 July 2023, 00:31:47 UTC
c75dd41 Tadgh 19 July 2023, 21:58:31 UTC 6 8 cves (#5107) * bump * Update deps * reduce thymeleaf * Remove dead import 19 July 2023, 21:58:31 UTC
675699a jdar8 19 July 2023, 20:57:21 UTC 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 jmarchionatto 19 July 2023, 19:35:51 UTC 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 TipzCM 19 July 2023, 12:26:05 UTC 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 Justin McKelvy 14 July 2023, 18:17:13 UTC 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 Kevin Dougan SmileCDR 14 July 2023, 17:34:32 UTC 5097 - Fixed a couple of links in the javadocs for the IValidationSupport class. (#5098) 14 July 2023, 17:34:32 UTC
6178075 Tadgh 13 July 2023, 22:56:23 UTC wip (#5091) 13 July 2023, 22:56:23 UTC
2401b23 TipzCM 13 July 2023, 19:58:27 UTC 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 TipzCM 13 July 2023, 13:59:02 UTC 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 Ken Stevens 12 July 2023, 20:47:37 UTC 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 Luke deGruchy 12 July 2023, 14:32:09 UTC 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 Tadgh 12 July 2023, 00:36:44 UTC 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 Tadgh 11 July 2023, 20:32:02 UTC 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 Brenin Rhodes 07 July 2023, 14:05:10 UTC 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 Steve Corbett 06 July 2023, 15:59:56 UTC 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
8d55781 Long Ma 06 July 2023, 15:48:55 UTC mssql test fixes 06 July 2023, 15:48:55 UTC
a87321a JasonRoberts-smile 05 July 2023, 21:57:19 UTC add instantiateBackboneElement method to TerserUtil (#5060) * add instantiateBackboneElement method to TerserUtil * changelog 05 July 2023, 21:57:19 UTC
a93d06c James Agnew 05 July 2023, 16:48:15 UTC 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
806a628 Long Ma 05 July 2023, 01:04:16 UTC added docs 05 July 2023, 01:04:16 UTC
4ea0ba2 Thomas Papke 03 July 2023, 21:42:07 UTC #5023 Unexpected usage of awssdk StringUtils in hapi 6.6 jpa migration (#5024) task Replace usage of awssdk 05 July 2023, 00:56:53 UTC
9a6288c Ken Stevens 04 July 2023, 18:43:43 UTC 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 Ken Stevens 04 July 2023, 18:08:44 UTC 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 Thomas Papke 03 July 2023, 21:42:07 UTC #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 Yusuf Daniju 02 July 2023, 19:48:20 UTC fix: typo in 'opposed' (#5051) 02 July 2023, 19:48:20 UTC
a73b748 Tadgh 01 July 2023, 17:02:52 UTC 5014 only positive ints (#5050) * limit ints, add test and changelog * changelog 01 July 2023, 17:02:52 UTC
2c6cd60 Ken Stevens 01 July 2023, 04:23:32 UTC 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 Luke deGruchy 30 June 2023, 14:48:33 UTC 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
93a4155 volodymyr-korzh 29 June 2023, 18:29:37 UTC Reindex Batch Jobs stuck in QUEUED status after SearchParameter update (#5043) * Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - test added * Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix * Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix test * Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - send BatchJobWorkNotification after commit * Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - changelog fix Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> 29 June 2023, 18:29:37 UTC
6e0651e James Agnew 29 June 2023, 12:34:32 UTC Bulk export partitioning fixes (#5039) * Work * Bulk export partitioning fixes * Changelog fixes * cleanup * Compile fixes * Test fix * Add JIRA note * Version bump * Drop unneeded tag 29 June 2023, 12:34:32 UTC
ed04dd2 jmarchionatto 28 June 2023, 19:46:54 UTC Issue 5004 make bundleutil also accept name prev for previous links (#5042) * Add test * Fix * Changelog * Small details to reset build pipe * Reformat * Make definition animal-sniffer (check-android-26-compliance) compliant --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 28 June 2023, 19:46:54 UTC
ce04e89 TipzCM 28 June 2023, 19:37:45 UTC 5033 fk indexing round2 (#5040) * updated query to find more results and be simpler * updating query in fhir --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> 28 June 2023, 19:37:45 UTC
17eeb07 jmarchionatto 28 June 2023, 16:58:51 UTC Issue 5032 gateway pagination throws NPE when targets use usehttppostforallsearches true (#5036) * Allow PageMethodBinding to bind also for POST * Add changelog * Adjust test --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 28 June 2023, 16:58:51 UTC
9fb7188 Tadgh 28 June 2023, 14:14:22 UTC Complete change, changelog, test (#5035) * Complete change, changelog, test * whitespace * Update hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/StorageSettings.java Co-authored-by: James Agnew <jamesagnew@gmail.com> --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> 28 June 2023, 14:14:22 UTC
73d6997 StevenXLi 23 June 2023, 13:06:38 UTC fixed batch jobs on Postgres (#5022) * fixed issue * fixed pipeline issue * review changes --------- Co-authored-by: Steven Li <steven@smilecdr.com> 23 June 2023, 13:06:38 UTC
1f44ac1 volodymyr-korzh 22 June 2023, 19:28:47 UTC GenericClient POST paging support (#5013) * GenericClient POST paging support - implementation and test * GenericClient POST paging support - fixes * GenericClient POST paging support - fixes * GenericClient POST paging support - failed tests fix * GenericClient POST paging support - HAPI version bump 22 June 2023, 19:28:47 UTC
a59eb1a LalithE 22 June 2023, 15:23:39 UTC Partitioning: creating two partitions with the same ID overwrites the first (#5012) * Added unit test and bug fix to ensure no two partitions with the same ID can be created. * Added changelogs, and changed the equals operator. * Made required changes to ensure updating of partition is not affected * Changed unit test and its location to ensure functionality. * changing for loop to findById to avoid iteration over all partitions. * Only allows findById when list is not empty, deals with that edge case. * Replaced null with isPresent in if statement to fix issues regarding the creation of links on different partitions * Removed the findAll command within the function. To avoid searching twice. * Edited the changelogs to properly describe the issue that we have at hand * Edited the changelogs to properly describe the issue that we have at hand pt 2, wording changes. 22 June 2023, 15:23:39 UTC
d7bdabb TipzCM 22 June 2023, 12:26:47 UTC nickname svc refatoring (#5006) * nickname svc refatoring * moving things around * cleanup * gitignore * removing factory * added changelog * version bump * fixing test * fix test --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> 22 June 2023, 12:26:47 UTC
20a9ad0 Tadgh 22 June 2023, 01:19:12 UTC Make Partition ID non-mandatory during partition creation. (#5016) * closes #5014, fix, changelog, docs * documentationf fixes * checkstyle fix 22 June 2023, 01:19:12 UTC
ddf3b72 James Agnew 21 June 2023, 17:02:40 UTC Encode non-resource types (#5003) * Encode non-resource types * Add changelog * Compile fix 21 June 2023, 17:02:40 UTC
ee3c59a jdar8 20 June 2023, 18:41:22 UTC 4968 mdm throws nonsensical error when updating resources after mdm clear (#4975) * log specific error message + test * changelog * remove draft tests * remove another comment i left behind * update issue number in changelog * update error location * update error location * update test * change to exception * address review comments: add test with submit and also update change log * format test nicer --------- Co-authored-by: justindar <justin.dar@smilecdr.com> 20 June 2023, 18:41:22 UTC
8eec285 Ken Stevens 20 June 2023, 11:54:20 UTC revinclude order (#5009) * start building tests * add test * merge master * fix bug * fix regression * changelog * documentation --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> 20 June 2023, 11:54:20 UTC
ac9eaf9 TynerGjs 19 June 2023, 13:54:39 UTC 4959 loadsynchronousupto will affect searchforids when set to small value (#4966) * Implemented fixes, created test for JPA side * Added test and getter for test for register listener * refactored test names to make them more descriptive * Modified tests * resolved comments * created changlog * changed test to use MAX_MANAGED_PARAM_COUNT, and created the corresponding getter 19 June 2023, 13:54:39 UTC
6296884 volodymyr-korzh 19 June 2023, 13:31:05 UTC Error when expanding task code ValueSet resource (#4974) * Error when expanding task-code ValueSet resource - tests * Error when expanding task-code ValueSet resource - fix valuesets.xml for R4 and R4B * Error when expanding task-code ValueSet resource - throw exception in case of Not found CodeSystem * Error when expanding task-code ValueSet resource - added changelog * Error when expanding task-code ValueSet resource - fixed changelog * Error when expanding task-code ValueSet resource - fixes * Error when expanding task-code ValueSet resource - fixes * Error when expanding task-code ValueSet resource - fixes and tests * Error when expanding task-code ValueSet resource - added tests for TermCodeSystemVersionDao methods * Error when expanding task-code ValueSet resource - added comments to valuesets.xml * Error when expanding task-code ValueSet resource - test fixes 19 June 2023, 13:31:05 UTC
a544a54 Tadgh 17 June 2023, 09:52:10 UTC Raw sql revincludes (#5001) * start building tests * add test * Basic test and fix bug * remove tests, fix existing test * fix up tests * fix up tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> 17 June 2023, 09:52:10 UTC
e5699bc Luke deGruchy 16 June 2023, 17:53:20 UTC Add auto-generated headers to Java files. (#4999) 16 June 2023, 17:53:20 UTC
65ae178 TipzCM 16 June 2023, 00:32:21 UTC mdm-clear will now use batch-size parameter (#4985) * using delete expunge service * test fixing * update version * review points --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> 16 June 2023, 00:32:21 UTC
f79ac19 Luke deGruchy 15 June 2023, 15:34:00 UTC First commit: Patch bad implementation of RuleBulkExportImpl to fix … (#4986) * First commit: Patch bad implementation of RuleBulkExportImpl to fix this use case. * Fix changelog. Fix comments on unit tests. * Fix TODO with correct issue number. 15 June 2023, 15:34:00 UTC
048c1f9 jmarchionatto 15 June 2023, 14:03:45 UTC issue-4987-searchbundle-parts-are-labeled-by-default-as-include-instead-of-match (#4988) * Default search mode to MATCH when creating SearchBundleEntryParts * Add changelog * Use enum name instead of explicit constant --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 15 June 2023, 14:03:45 UTC
c87ff96 TipzCM 14 June 2023, 13:20:53 UTC 4976 adding indexes to foreign keys (#4980) * adding test and initial migrations * indexing and verifying foreign keys * connection with resources * fixing migration for oracle * adding change log * updates and cleanup * cleanup * fixing broken tests * remove unique constraints * debug code * cleanup --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> 14 June 2023, 13:20:53 UTC
49c3a18 dotasek 09 June 2023, 15:25:24 UTC Bump core to 6.0.15 (#4972) * Bump core to 6.0.14 * Bump core to 6.0.15 09 June 2023, 15:25:24 UTC
737238b volodymyr-korzh 08 June 2023, 16:47:39 UTC validate code on remote terminology service returns nullpointerexception (#4958) * validate-code on remote-terminology service returns NullPointerException - tests * validate-code on remote-terminology service returns NullPointerException - fixed * validate-code on remote-terminology service returns NullPointerException - added changelog * validate-code on remote-terminology service returns NullPointerException - tests readability improvement and fixes * validate-code on remote-terminology service returns NullPointerException - fixes 08 June 2023, 16:47:39 UTC
fddea8d TynerGjs 08 June 2023, 16:38:24 UTC Resolve 4952 PUT requests for resources that don't exist get created in sequential format rather than abiding by the ResourceServerIdStrategy (#4953) * Test implemented, issue resolved * fixed a logical bug in the previous change * modified comment * added tests for Dstu2&3 resources * Adding afterEach constructions to reset spring context beans. * resolved comments --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> 08 June 2023, 16:38:24 UTC
e28398f volodymyr-korzh 08 June 2023, 15:00:27 UTC 4888 Add validation for composite SearchParameter components types (#4909) * Added unit tests for composite SearchParameter validator * Added validation for composite SearchParameter components * validation for composite SearchParameter components - fixes * Modified tests * fixed string in setDefinition * validation for composite SearchParameter components - fixed validation and Unit tests * validation for composite SearchParameter components - added method getActiveSearchParameterByComponentDefinition and unit tests * validation for composite SearchParameter components - minor fixes * validation for composite SearchParameter components - remove getActiveSearchParameterByComponentDefinition method * validation for composite SearchParameter components - optimise import * validation for composite SearchParameter components - fix changelog * validation for composite SearchParameter components - improved validation logic * validation for composite SearchParameter components - improved validation logic (remove unused lines) * validation for composite SearchParameter components - improved validation logic * validation for composite SearchParameter components - improved validation logic * validation for composite SearchParameter components - fixed validation logic * validation for composite SearchParameter components - added test for uri and number combo search * validation for composite SearchParameter components - added test for uri and number combo search * validation for composite SearchParameter components - validation logic fix * validation for composite SearchParameter components - fixes * validation for composite SearchParameter components - fixes * validation for composite SearchParameter components - test fixes --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> 08 June 2023, 15:00:27 UTC
e37edfc Luke deGruchy 07 June 2023, 13:05:08 UTC Ensure StepExecutor only logs a stack trace and error if the retries have been exhausted. Otherwise, just log a debug. (#4961) * Ensure StepExecutor only logs a stack trace and error if the retries have been exhausted. Otherwise, just log a debug. * Accept code reviewer suggestion to amend log message Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> 07 June 2023, 13:05:08 UTC
8c6cba3 markiantorno 07 June 2023, 01:12:08 UTC Updating version to: 6.6.2 post release. 07 June 2023, 01:12:08 UTC
0a7f97a TipzCM 06 June 2023, 13:00:14 UTC 4917 refactor nicknaming hapi with version bump (#4955) * refactoring 1 * refactoring step 2 * refactoring matches * cleanup * fixing some tests * fixing more tests * remove dbugcode * adding the nickname factory * code review fixes * review fixes * put default to prevent breaking * refactor review fixes * more review points * more review points * review points * review points * more review changes * review points * review points * adding bean * updating version --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> 06 June 2023, 13:00:14 UTC
6c03a51 Tadgh 02 June 2023, 19:40:50 UTC Revert "refactoring nickname matching (#4918)" (#4954) This reverts commit 7a18f17a01d6d2db163eec97e909db881fa5fe37. 02 June 2023, 19:40:50 UTC
7a18f17 TipzCM 02 June 2023, 18:04:30 UTC refactoring nickname matching (#4918) * refactoring 1 * refactoring step 2 * refactoring matches * cleanup * fixing some tests * fixing more tests * remove dbugcode * adding the nickname factory * code review fixes * review fixes * put default to prevent breaking * refactor review fixes * more review points * more review points * review points * review points * more review changes * review points * review points * adding bean --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home> 02 June 2023, 18:04:30 UTC
9838f8a michaelabuckley 02 June 2023, 00:27:14 UTC Delete dead code now that Hapi has merged. (#4946) 02 June 2023, 00:27:14 UTC
83411e5 StevenXLi 01 June 2023, 17:16:44 UTC 4570 add support for warning messages to the batch framework (#4571) * added failing test * added support for warning messages to batch2 * added change log * fixed errors from merge, made warning work with new batch2 * fixed message parse, changed interface method to default, formatting changes * added changelog * code review changes * code review change * added new implementation for warning message processing, fixed migration * changed column to lob, as text is not well supported * code review changes --------- Co-authored-by: Steven Li <steven@smilecdr.com> 01 June 2023, 17:16:44 UTC
6c314ed Tadgh 31 May 2023, 21:34:14 UTC add Adi (#4939) * add Adi * Name typo 31 May 2023, 21:34:14 UTC
08a0844 Tadgh 30 May 2023, 22:54:08 UTC Touch codeowners 30 May 2023, 22:54:08 UTC
8288eba dependabot[bot] 30 May 2023, 22:52:58 UTC Bump snakeyaml from 1.33 to 2.0 in /hapi-fhir-docs (#4928) Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.33 to 2.0. - [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-2.0..snakeyaml-1.33) --- updated-dependencies: - dependency-name: org.yaml:snakeyaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 30 May 2023, 22:52:58 UTC
4d90719 Luke deGruchy 30 May 2023, 19:21:20 UTC Delete methods deleted in previous release. (#4944) 30 May 2023, 19:21:20 UTC
31ae8d8 volodymyr-korzh 30 May 2023, 18:02:14 UTC 4934 validation doesn't consider loaded ig immediately (#4935) * Unit tests for validation after install and uninstall IG * Fix validation result cached after install and uninstall IG * Fix validation result cached after install and uninstall IG - updated changelog * Fix validation result cached after uninstalling IG - updated changelog * Fix validation result cached after uninstalling IG - fixed unit tests * Fix validation result cached after uninstalling IG - fixed changelog * Fix validation result cached after uninstalling IG - test fixes 30 May 2023, 18:02:14 UTC
34f4c90 dotasek 30 May 2023, 13:36:40 UTC Bump org.hl7.fhir.core dependency to 6.0.8 (#4942) * Bump core, fix compilation errors * Match pattern in kindling for use of version Match the pattern used by Grahame in this update of kindling: https://github.com/HL7/kindling/commit/f765642470fe5d3b8bb3c859a85cecf295d6911a * Bump core, fix compilation errors * Match pattern in kindling for use of version Match the pattern used by Grahame in this update of kindling: https://github.com/HL7/kindling/commit/f765642470fe5d3b8bb3c859a85cecf295d6911a * Bump core to 6.0.5, fix compilation errors * Bump to core version 6.0.8 * Individual message code for exception * Bump core to 6.0.10 * Fix test message 30 May 2023, 13:36:40 UTC
e068a2f Etienne Poirier 30 May 2023, 11:12:53 UTC 4799 searching on paramname profile with and missing modifier does not match resources (#4840) * initial test * Adding changelog * Updated to remove the discarding of search params starting with an underscore * test commit * Updated handling of search parameters with underscores * Revert work in progress * Updated storage settings with new property for inline tag storage mode * Updated storage settings to tell when inline tag storage mode is set * simplified test failure * Added tests for _tag and _system * Add PreviousVersion service with tests (#4902) * started writing PreviousVersionReader * started writing PreviousVersionReader * moar tests * add partitioning to the test * switch subscription to use previous version reader --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> * Updated logic to be less confusing * Bumping version to 6.7.4 * Reverted hapi bump, added improve logic for handling missing search params * updates * Updated failing tests * remove redundant tests * more updates * Adding Jira number. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: David Raeside <davidraeside@smilecdr.com> Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com> Co-authored-by: David Raeside <david.raeside@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> 30 May 2023, 11:12:53 UTC
e6367f0 yueshi9988 29 May 2023, 16:18:24 UTC change $mdm-link-history param to resourceId (#4945) 29 May 2023, 16:18:24 UTC
b84e8c0 Ken Stevens 29 May 2023, 05:32:22 UTC Canonicalize R4 topic subscriptions (#4913) * WIP * add canonicalizer for R4 topic subscriptions * test R4 topic subscription registration * Add support for R4 Subscription Topic Backport * FIXME * add filter matching support * add simpler signature * add resource type matching to filter * review feedback * fixed * changelog * test both ways * add bundle test * change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state * added logs * changelog * fix v2 issues * Clean up WIP comments * Switch to in-memory event numbers (instead of always 1) * Final WIP cleanup * Msg.code * review feedback * review feedback * review feedback * review feedback * back out import changes * back out import changes --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> 29 May 2023, 05:32:22 UTC
ead537c Tadgh 28 May 2023, 16:44:51 UTC resolve CVEs, add new notes 28 May 2023, 16:44:51 UTC
8d56c57 Tadgh 23 May 2023, 16:53:52 UTC Bump deps (#4926) 28 May 2023, 01:21:59 UTC
f1aa6b7 Tadgh 22 May 2023, 04:22:55 UTC Bump jackson to be compatible with new snakeyaml 28 May 2023, 01:20:37 UTC
0d7a4de Tadgh 22 May 2023, 02:17:14 UTC Bump snakeyaml 28 May 2023, 01:20:29 UTC
4685771 James Agnew 27 May 2023, 15:07:59 UTC Delete expunge with cascade (#4931) * Delete expunge with cascade * Work * Workgin * Version bump hibernate * Start working on delete cascade * Work on delete expunge * Test fixes * Test fixes * Add changelog * Work on cascade * Fixes * Test work * Test fixes 27 May 2023, 15:07:59 UTC
2fc08b5 markiantorno 27 May 2023, 02:18:39 UTC Updating version to: 6.6.1 post release. 27 May 2023, 02:18:39 UTC
f8548c5 William Denton 26 May 2023, 23:05:16 UTC let schematron use hapi-fhir-base classloader (#4366) 26 May 2023, 23:05:16 UTC
3191cea Tadgh 26 May 2023, 18:32:16 UTC Make this dependency provided 26 May 2023, 18:32:16 UTC
1d2b2f7 Tadgh 26 May 2023, 06:27:50 UTC Temp disable 26 May 2023, 06:27:50 UTC
a04a49c James Agnew 24 May 2023, 23:31:39 UTC Schema migrator returns status (#4937) * Migrator should return status * Cleanup * Add changelog * Delete unused * Test fix 24 May 2023, 23:31:39 UTC
c98c4a4 Tadgh 24 May 2023, 21:48:55 UTC Implement codeowners (#4938) * Initial run through codeowners * Remove dead action * Add consent intercept and auth interceptor 24 May 2023, 21:48:55 UTC
d9530a9 Tadgh 24 May 2023, 04:39:38 UTC Bump snake yaml (#4929) * Bump snakeyaml * Bump jackson to be compatible with new snakeyaml 24 May 2023, 04:39:38 UTC
3b9a9c6 Nathan Doef 23 May 2023, 22:59:41 UTC Oracle Testcontainers and Test Data (#4897) * OracleEmbeddedDatabase + test data 23 May 2023, 22:59:41 UTC
970befa Nathan Doef 23 May 2023, 21:06:27 UTC Fixes broken Oracle migration (#4933) 23 May 2023, 21:06:27 UTC
93a4a7b Tadgh 23 May 2023, 16:53:52 UTC Bump deps (#4926) 23 May 2023, 16:53:52 UTC
32a4ee0 Tadgh 23 May 2023, 16:32:55 UTC Bump snake yaml (#4929) * Bump snakeyaml * Bump jackson to be compatible with new snakeyaml 23 May 2023, 16:32:55 UTC
cfc8b02 dependabot[bot] 21 May 2023, 22:17:59 UTC Bump spring-security-core from 5.7.5 to 5.7.8 in /hapi-fhir-storage-cr (#4927) Bumps [spring-security-core](https://github.com/spring-projects/spring-security) from 5.7.5 to 5.7.8. - [Release notes](https://github.com/spring-projects/spring-security/releases) - [Changelog](https://github.com/spring-projects/spring-security/blob/main/RELEASE.adoc) - [Commits](https://github.com/spring-projects/spring-security/compare/5.7.5...5.7.8) --- updated-dependencies: - dependency-name: org.springframework.security:spring-security-core dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 21 May 2023, 22:17:59 UTC
82ab61f James Agnew 21 May 2023, 17:56:31 UTC Expunge performance tweak (#4920) * Expunge performance tweak * Add changelog * Address review comment 21 May 2023, 17:56:31 UTC
805e80e Tadgh 21 May 2023, 03:38:35 UTC 6.6.0 Mergeback (#4924) * Force Verify tests * fix ITs (#4809) * fix RestHookTestR5IT * fix intermittent --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> * Fix migrator error on Oracle (#4814) * Fix Oracle SQL error * Add changelog * Update clinical reasoning version (#4816) * Update clinical reasoning version * Update version * Update version * Clean-up and more wireup of evaluationSettings * Add changelog --------- Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> * Opening the care-gaps endpoint for GET. (#4823) Co-authored-by: Chalma Maadaadi <chalma@alphora.com> * added version to mdm golden resource tag (#4820) Co-authored-by: Long Ma <long@smilecdr.com> * Update the changelog for 4697 to be more descriptive (#4827) * Update the changelog for 4697 to be more descriptive * Futher tweaks of the changelog * Fixes a bug with tags. (#4813) * Test, fix * Drop constraint, add migration * Add changelog * Fix userSelected null vs false * Fix merge * Fix up checkstyle whining * One more failure * Fix test * wip * changelog clarity Co-authored-by: James Agnew <jamesagnew@gmail.com> * change index --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> * fix migration issue (#4830) Co-authored-by: Ken Stevens <ken@smilecdr.com> * Create correct version enum * Remove superfluous migration * fixing test (#4835) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * email subscription, throw NullPointerException (#4790) * fix bug * Favoring constructor initialization to autowiring. * enhancing test. * Making class LoggingEmailSender available outside of the hapi-fhir-japserver-uhnfhirtest module. * Passing all tests. * adding changelog. * Bumping version to 6.5.20-SNAPSHOT * addressing code review comment. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Add docs for CR operations (#4855) * Add docs for CR operations * Correct changelog and javadoc for $package * Add documentation for $apply parameters * Add additional documentation for $package * Cleanup * Cleanup * Cleanup * Address review comments * Add documentation for $care-gaps operation. (#4862) * Add documentation for -gaps. * addressing the comments. --------- Co-authored-by: Chalma Maadaadi <chalma@alphora.com> * 4853 validation does not error when display is not the same as the display defined in the codesystem 2 (#4854) * added failing test * implemented the solution * changed test name * added change log * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4853-validation-does-not-error-when-display-is-not-the-same-as-the-display-defined-in-the-codesystem-2.yaml Co-authored-by: James Agnew <jamesagnew@gmail.com> --------- Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> * fixing patient everything operator (#4845) * fixing patient everything operator * review fix --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * fix link * Move image file * Bundle resources containing over 100 references to the same Organization will fail with HAPI-2207 (#4871) * Add failing unit test. * Fix JpaId Long equality comparison to use ! equals() instead of !=, which fails for different instances of the same Long value. * Add changelog. * added warn message and test (#4848) * added warn message and test * code review fixes --------- Co-authored-by: Long Ma <long@smilecdr.com> * Issue 4804 full table scan on mpi link during mdm clear (#4805) * version bump for next release (#4793) * version bump * Bump to correctnumber * Version Enum and folder * Remove interim from list * wip * Fix operation on nested type-choices in FhirPatch implementation (#4783) * Fix operation on nested type-choices in FhirPatch implementation * Add credit for #4783 --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * #4468 fix previous link offset no cache pagination (#4489) * #4468 Add test reproducing the issue * #4468 Fix previous link for no cache offset pagination * #4468 Use unchecked URI parsing * Credit for #4489 --------- Co-authored-by: James Agnew <jamesagnew@gmail.com> * Changelog and data generating test * Add MdmLink index * Avoid double link deletion * Use ThreadLocal safely --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Fix erroneous batch 2 $export 75% complete count when the job is COMPLETE (#4859) * Add failing unit test. * Add conditional logic to the InstanceProgress progress percentage to disregard the incomplete count if this is called from the reduction step. This is to get around a race condition in which a work chunk is QUEUED and not yet complete when the reduction step calculates the progress. * Add final. * Add changelog. * disable wars (#4877) Co-authored-by: Ken Stevens <ken@smilecdr.com> * 4868 fix paging hapi (#4870) * fixing some offset and adding a test * fixing the offset paging * Removing duplicate --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com> * 4875-binary-access-write-doest-trigger-STORAGE-BINARY-ASSIGN-BLOB-ID-PREFIX-pointcut (#4876) * Add failing test * Add failing test * Fix and changelog * Pass content type parameter * Back to auto wiring the context * Invoke interceptor only when getting blobId, not also when storing it * Avoid breaking implementers * Address review comment * Add new exception Msg code * Fix broken test --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Fix batch job (bulk export) processed record count (#4879) * Remove racy stats recalc. * Throw 404 when requesting $export of non-existent Group or Patient (#4890) * Remove default implementation intended only for interim backwards compatibility (#4894) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Rule apply patient export (#4893) * Test, fix, and changelog * Better partition resolution * Add checks based on rule applier * Fix ordering failure due to hash set * Allow empty auth interceptor * Fix up operation type on invocation * Add more tests, make hack implementation for patient instance level operation * Tighten test name * Changelog * Default method * remove dead method * Remove dead autowire --------- Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> * cve pom changes (#4898) Co-authored-by: Long Ma <long@smilecdr.com> * backport subscription topic bean cleanup (#4904) * 4891 bulk export do not recurse unasked for resources (#4895) * updating tests * fixing bulk export to not fetch resources not requested * cleanup * cleanup * more warning suppressing * adding error code * blah * fix test * review fixes --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * lowers log level to remove bootup noise (#4908) * CVE rel 6 6 (#4907) * cve pom changes * bump javax.el to jakarta.el --------- Co-authored-by: Long Ma <long@smilecdr.com> * Issue 4905 post binary failure invoking interceptor for pointcuts storage preshow resources (#4906) * Initial failing test * Avoid applying binary blob id prefix multiple times * Remove recently introduced method not needed anymore --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Enhance LogbackCaptureTestExtension (#4869) * repro bug with test, fix bug * ken informed me he resolved this bug on master, so i'm switching to use his solution * disable wars * review feedback * review feedback * review feedback again --------- Co-authored-by: josie <josie.vandewetering@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> * Resolve 4863 from release branch searchparametercanonicalizer does not account for search parameters for custom resources types when converting dstu23 into runtimesearchparam (#4887) * Modified canonicalizeSearchParameterDstu2 and 3, now correctly detect search parameters for custom resources * Canonicalizers now correctly handle search parameters for custom resources * created changelog * Modification based on comments: - remove Resource from target field when there are custom resource types - fixed changelog typo - removed unnecessary variable providesMembershipInCompartments * Added tests for the SearchParameterCanonicalizer to test if base and target of RuntimeSearchParam is set as expected for DSTU2, DSTU3, R4, R4B, and R5 resources * Fixed typo and removed commented code * re-ordered init methods * Update changelog Co-authored-by: Tadgh <garygrantgraham@gmail.com> * modifications following first code review. --------- Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * License * Remove _lastUpdated filtering of _revincludes. (#4899) Remove _lastUpdated filtering of _revincludes. * 4910-dm-migration-error-for-oracle-19c (#4916) * Remove all_constraints references which break in oracle 19c * Add changelog --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * 4873 empty fhirid causes missing resource (#4874) * add check for empty fhirid string and add test * add test for populateid * changelog * version bump * version bump * reverse version bump * Back to 6.5.21-SNAPSHOT. --------- Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> * Fix include canonical url performance (#4919) Use hash_identity for canonical join * License * Version bump * Fix failure in test * Licenses * Review comments for pipeline * Dead entry * other typo --------- Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: Brenin Rhodes <brenin@alphora.com> Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com> Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com> Co-authored-by: Chalma Maadaadi <chalma@alphora.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Michael Buckley <michaelabuckley@gmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Sam Gunter <123124187+samguntersmilecdr@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: StevenXLi <stevenli_8118@hotmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Zach Smith <85943952+zachdoctolib@users.noreply.github.com> Co-authored-by: Aleksej Parovysnik <100864000+alparodev@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Josie <80289977+pepsiofficial@users.noreply.github.com> Co-authored-by: josie <josie.vandewetering@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> 21 May 2023, 03:38:35 UTC
307e52f James Agnew 20 May 2023, 21:29:56 UTC Index name fix (#4921) * Index name fix * Build fix * Test restore * Revert change 20 May 2023, 21:29:56 UTC
d932730 Ken Stevens 20 May 2023, 00:32:25 UTC Fixed R5 Subscription deserialization (#4922) * review feedback * fixed * changelog * test both ways * add bundle test * change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state * fix v2 issues --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> 20 May 2023, 00:32:25 UTC
124b0dc Tadgh 19 May 2023, 05:17:08 UTC Version bump 19 May 2023, 05:17:08 UTC
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