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14 November 2023, 18:36:22 UTC
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b0020a2 Tadgh 15 February 2022, 20:13:38 UTC Add version.yaml: 15 February 2022, 20:13:38 UTC
062bd3f Tadgh 15 February 2022, 18:31:31 UTC Remove ehcache 15 February 2022, 18:31:31 UTC
39bbd2b Tadgh 14 February 2022, 23:16:08 UTC Make migration donothing as it was added in error 14 February 2022, 23:16:08 UTC
a918e12 Olivia You 14 February 2022, 21:52:57 UTC Can't specify specific resource type permissions for bulk export (#3376) * deny user from exporting without perms * add unit tests * add changelog Co-authored-by: olivia-you <olivia.you@smilecdr.com> 14 February 2022, 21:52:57 UTC
e80ebcf Tadgh 14 February 2022, 20:58:48 UTC Fix broken changelog file 14 February 2022, 20:58:48 UTC
02faf6f Steven Li 09 February 2022, 17:55:16 UTC added changelogs for this fix 14 February 2022, 20:31:45 UTC
17d172f Steven Li 09 February 2022, 17:30:38 UTC Fixed null pointer exception for re-loading subscription on cdr restart and when there's no partition id in the request, and added tests 14 February 2022, 20:31:32 UTC
c507b4b Tadgh 13 February 2022, 00:18:51 UTC Version bump 13 February 2022, 00:18:51 UTC
552ba9b Mark Iantorno 12 February 2022, 18:48:04 UTC Issue 3357 12 February 2022, 18:48:04 UTC
f1823bd JasonRoberts-smile 11 February 2022, 00:56:17 UTC Jr 20220210 handle common search params in contained searches (#3377) * fix handling of common search parameters * add support for reference search parameters with multiple paths 11 February 2022, 00:56:17 UTC
4e785e2 Tadgh 10 February 2022, 20:16:51 UTC Add changelog 10 February 2022, 20:16:51 UTC
630fb60 Tadgh 10 February 2022, 20:14:35 UTC Rip out dead modules 10 February 2022, 20:14:35 UTC
155a809 Tadgh 10 February 2022, 20:01:13 UTC Fix implementation, add test (#3378) * Fix implementation, add test * Tighten test 10 February 2022, 20:01:13 UTC
02b821e Jason Roberts 10 February 2022, 19:14:00 UTC Revert "fix handling of common search parameters" This reverts commit 89c45eebdc31c3dd9533570d9c709ecc7ed5a7a6. 10 February 2022, 19:14:00 UTC
89c45ee Jason Roberts 10 February 2022, 18:59:18 UTC fix handling of common search parameters 10 February 2022, 18:59:18 UTC
3531d9b michaelabuckley 10 February 2022, 01:27:40 UTC Fix exception when contained indexing met hibernate search. (#3372) * Fix exception when contained indexing met hibernate search. 10 February 2022, 01:27:40 UTC
a9348b6 Tadgh 07 February 2022, 12:56:25 UTC Bump dependencies for CVES (#3359) * Bump dependencies for CVES * Add to cchangesyaml * Bump java agent 07 February 2022, 12:56:25 UTC
2531e6e Patrick Werner 05 February 2022, 18:25:50 UTC feat: added support for package.tgz uri in the "file:/" format (#3347) * feat: added support for package.zgz uri in the "file:/" format * added changelog entry * add error code to thrown message Co-authored-by: Tadgh <garygrantgraham@gmail.com> 05 February 2022, 18:25:50 UTC
f6181fb TipzCM 03 February 2022, 23:30:58 UTC 3354 fixing flakey tests (#3355) * 3354 fixing flakey tests * must fix code * updating number again * fixing test Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 03 February 2022, 23:30:58 UTC
c42ecc5 Johnson Lu 31 January 2022, 21:10:15 UTC Add error codes to all exceptions (#3278) * Initial design of adding exception codes to exceptions * Initial design of adding exception codes to exceptions * change int module name to string * add comment * shorten message * shorten message * added checkstyle * developing checker * completed checkstyle plugin and unit test for it * fix NPE * fix checker so it ignores throws on exceptions that aren't new * change parameter order in InvalidResponseException * accept Msg.code() in any parameter since some exceptions like MessageException have the message string as the second parameter * exclude generated files * BIG COMMIT added error codes to all exception throws * example test fix * Modified tests such that the assert statements would better match the message responses. * Modified additional tests such that the assert statements would better match the message responses. * fix test * merge master * merge master * Fourth commit of modified tests such that the assert statements would better match the message response * Changes made to modify assert statements such that they match the new errors which now use error codes. Also changed ResourceNotFoundException to include error codes in its messages. * Modified assert messages to better match new error codes * Time Zone changes DRAFT. Certain tests pass in intellij and fail during mvn install * Modified assert messages to better match new error codes * Added comments for time zone fixes. Previous commit comment on time zone fixes was incorrect. By invaliding caches, all tests on both intellij and mvn install passed. * Reverted changes on azure-pipelines.yml * updated hapi-fhir version for checkstyle module * changes to azure-pipelines.yml * changes to azure-pipelines.yml * change to pom.xml to include hapi-fhir-checkstyle in ALLMODULES * changes to azure-piplines (these changes are to be reverted after testing) * reverted changes to azure-piplines * reverted change where hapi-fhir-checkstyle was added to pom.xml (hapi-fhir) * Attempted fix on checkstyle build error * modified azure-piplines.yml to change maven repository for checkstyle build * Attempted fix on checkstyle build error * checkstyle config location change for hapi-depoloyable-pom. (will be reverted if it does not work) * attempted dependency add for hapi-depoloyable-pom. (will be reverted if it does not work) * reverted changes for hapi-deployable-pom * add javadoc * update last code * Attempted fix on checkstyle build error * Finished adding in missing error codes to pass Checkstyle checks * Test pipelining * Fixing errors and bumping version (as suggested by Gary) * Merge * Fixing Checkstyle error * Attempted fix for date error * Add error code onto assert statement * Add in a couple more error codes * Fixing assert statements * Bump to static version for dependency * Adding error code to message * Adding error codes to exceptions * Adding error codes to exceptions * Change to work with cdr branch * Update to faulty error message * Merge changes * allow checkstyle pom to deploy Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Simon Zuccherato <simon.zuccherato@smilecdr.com> Co-authored-by: Predap <simon.zuccherato@gmail.com> Co-authored-by: Predap <46201929+Predap@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> 31 January 2022, 21:10:15 UTC
65398ca TipzCM 31 January 2022, 16:49:12 UTC 3156 multiple tag race condition (#3297) * 3156 fix race condition that results in multiple tags being created * 3156 added changelog * cleanup * added smile jira ticket * 3156 review fixes * review fixes * 3156 added an additional integratoin test * cleanup * review fix and master merge * threadsafe stuff * small change * upping min threads for tests to pass * changing test * test check * fix * test testing * one more update * using threadpoolutil * temporary measure * git push * all builds Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 31 January 2022, 16:49:12 UTC
ad3e282 Tadgh 28 January 2022, 18:46:57 UTC Fix globbing pattern for log files 28 January 2022, 18:46:57 UTC
fc84fdc Jens Kristian Villadsen 28 January 2022, 12:16:44 UTC Update instance_validator.md (#3328) 28 January 2022, 12:16:44 UTC
3d4a0d8 Tadgh 28 January 2022, 03:03:13 UTC add needed dependendencies for mysql and mssql (#3343) * add mssql and mysql flyway dependencies * add exclusions to CQL to prevent duplicate classes on the classpath * wip * ad more databases * finish test 28 January 2022, 03:03:13 UTC
0df3327 Tadgh 27 January 2022, 22:03:37 UTC Add okhttp dep 27 January 2022, 22:03:37 UTC
41193c6 TipzCM 27 January 2022, 17:29:07 UTC 3335 allow alternative character encoding length in searchparam (#3336) * added fixme * 2714 added support for specifying max code lengths for supported phonetic encoders * 3335git status * 3335 updated changelog * 3335 review fixes * review fixes * fixing test Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 27 January 2022, 17:29:07 UTC
6506527 Tadgh 27 January 2022, 11:18:44 UTC Fix mdm config for single application context environment. (#3338) * wip * remove beans * Remove javax.mail from the classpath as we use simplemail instead, which uses jakarta. 27 January 2022, 11:18:44 UTC
3f42414 James Agnew 26 January 2022, 14:16:28 UTC Validate include statements for JPA (#3331) * Validate include statements for JPA * Add changelog * Optmize test fix 26 January 2022, 14:16:28 UTC
cd29d36 Tadgh 25 January 2022, 18:39:32 UTC Add okhttp dep to r5 and indicate which deps need to be included (#3332) 25 January 2022, 18:39:32 UTC
31bb1d9 James Agnew 25 January 2022, 01:15:41 UTC Bump RestEasy to 5.0.2 (#3329) * Bump deps * Test fix * Add test logging * Add test logging * Add logging 25 January 2022, 01:15:41 UTC
a11d72b katiesmilecdr 24 January 2022, 16:53:21 UTC 3322 graph ql searches cannot be executed when number of matching results exceeds default page size (#3323) * fix NPE * check if size is null 24 January 2022, 16:53:21 UTC
37e7d6e Patrick Werner 24 January 2022, 16:12:56 UTC populate ValueSet.url in $expand Operation (#3241) 24 January 2022, 16:12:56 UTC
715a4c4 James Agnew 24 January 2022, 00:05:02 UTC Fix resource version regression caused by Hibernate 5.6 (#3325) * failing test * failing test * Fixes * Updated note to self * Improve pre-caching of resource IDs * Work on tests * Test fixes * Add changelog Co-authored-by: Ken Stevens <khstevens@gmail.com> 24 January 2022, 00:05:02 UTC
ed2ea91 Ken Stevens 23 January 2022, 20:55:31 UTC concurrent validation performance improvement (#3327) 23 January 2022, 20:55:31 UTC
42ff607 Tadgh 22 January 2022, 17:47:34 UTC Rel 5 5 5 merge back (#3326) * Add backport * Add versions * remove not real versions 22 January 2022, 17:47:34 UTC
2b4ace3 dependabot[bot] 22 January 2022, 16:18:57 UTC Bump h2 from 2.0.206 to 2.1.210 (#3324) * Bump h2 from 2.0.206 to 2.1.210 Bumps [h2](https://github.com/h2database/h2database) from 2.0.206 to 2.1.210. - [Release notes](https://github.com/h2database/h2database/releases) - [Commits](https://github.com/h2database/h2database/compare/version-2.0.206...version-2.1.210) --- updated-dependencies: - dependency-name: com.h2database:h2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Add chasngelog Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> 22 January 2022, 16:18:57 UTC
3ab59f2 James Agnew 22 January 2022, 00:24:20 UTC Avoid JsonParser load (just a test) (#3303) * Fix #3268 - Avoid JsonParser load (just a test) * Clean up tests * Bump core version * Test fix * Bump 22 January 2022, 00:24:20 UTC
ab22fd6 longma1 21 January 2022, 22:04:39 UTC 2718 cross partition support for subscription (#3298) * added settings for cross-partition to Dao and Model config * modified subscription validator to validate cross partition subscriptions * modify subscription matcher to allow matching on all partitions when subscription is set to cross partition * added cross partition to canonicalSubscription * end of day commit, changed how we are checking if default partition in subscription validator * fixed issue with i memory matching for cross partition subscriptions * added test for parsing legacy CanonicalSubscription * added changelog and doc changes * addressed comments in pr * added assertdoesnotthrow * test fixes, added new mocks * added check for if resource can have extension before checking for extensions * removed unnecessary semicolon Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Long Ma <long@smilecdr.com> 21 January 2022, 22:04:39 UTC
62966de jmarchionatto 21 January 2022, 19:29:24 UTC Issue 3299 conformance validation is happening once per client endpoint thread instead as just once per client endpoint (#3319) * Make RestfulClientFactory.myValidatedServerBaseUrls usage thread safe so capability validation request is sent only once per client-endpoint * Can't use @GuardedBy for fields which are not always locked by annotation object * Use same variable when checking and setting Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 21 January 2022, 19:29:24 UTC
3fa76a9 James Agnew 21 January 2022, 16:10:51 UTC Add support for of-type token modifier (#3309) * Add support for of-type token modifier * Add changelog * Clean up hash calculation logic * Test fix * Rework hash generation * Work on hash generation * Test fix * Avoid redundant hash calculations * Revert some useless changes * Cleanup * Test fixes 21 January 2022, 16:10:51 UTC
48caff3 JasonRoberts-smile 20 January 2022, 21:22:02 UTC Improve performance of chained queries into contained resources (#3312) * base restructuring of query * fix unit tests * suppress unnecessary resource type parameter * pass the resource type used to fetch the search param as part of the chain, so later we do not need to guess what it was * add query structure tests * changelog * fix test failures * got one of the branches wrong in the 3-reference case 20 January 2022, 21:22:02 UTC
283ff19 michaelabuckley 19 January 2022, 23:02:39 UTC Re-index lucene when reindexing hibernate, even if resource unchanged. (#3311) 19 January 2022, 23:02:39 UTC
3d4f8be Tadgh 19 January 2022, 22:09:40 UTC Revert bump to 11 (#3318) 19 January 2022, 22:09:40 UTC
71e959c Tadgh 19 January 2022, 16:24:59 UTC SERVER_OUTGOING_RESPONSE invocation on manualResponse operations (#3315) * Fix implementation so we can make the call anyhow * modify test to ensure that pointcut is invoked * Add changelog * Tighten tests * Add comment 19 January 2022, 16:24:59 UTC
80e4c3d James Agnew 19 January 2022, 16:14:14 UTC Bump HIbernate to 5.6.x (#3305) * Bump HIbernate to 5.6.x * Test fixes * Test fix * Dependency bump * Rollback change * Fix tests * One more fix * Avoid bump 19 January 2022, 16:14:14 UTC
0f0bf85 Tadgh 19 January 2022, 15:09:21 UTC Bump compiler plugin (#3313) * Bump compiler plugin * Bump jpaserver fhir test server version * Bump container for maven 19 January 2022, 15:09:21 UTC
cc2ca9e Jaison B 18 January 2022, 22:57:51 UTC Change token and reference search params to 'keyword' field type (#3310) 18 January 2022, 22:57:51 UTC
3062430 StevenXLi 18 January 2022, 19:56:10 UTC 2720 rest hook subscription with payload search criteria is not getting triggered (#3308) * Added IT for Payload Search REST HOOK subscription, fixed issue with null pointer exception * removed todo comment, added changelog Co-authored-by: Steven Li <steven@smilecdr.com> 18 January 2022, 19:56:10 UTC
f0a9b33 TipzCM 18 January 2022, 18:07:26 UTC 3283 delete will not return a 404 if resource is not found (#3284) * 3283 delete will not return a 404 if resource is not found * minor tweaks * checking if tests fail due to asynchronicity * 3283 added integration test * cleanup * review fixes * changed id names * cleanup Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 18 January 2022, 18:07:26 UTC
9f7c454 Tadgh 18 January 2022, 15:40:53 UTC Issue 2377 missing entry full url in document (#3304) * start with failing test * wip * add changelog * Add implementation * Fix DSTU3 impl * Fix DSTU2 and R5 18 January 2022, 15:40:53 UTC
b09b0f2 Tadgh 17 January 2022, 22:50:11 UTC Fix broken changelog 17 January 2022, 22:50:11 UTC
221d7ed TipzCM 17 January 2022, 16:46:32 UTC 3274 transactions with full request url should be rejected (#3280) * 3274 throw if url is full url * 3274 will throw on invalid urls * 3274 fixing the tests * 3274 cleanup * anonymize the data * review fixes * 3274 fixed for backward compatibility * added review fixes * fixing tests * some more test fixes * test fixes * 3274 fixing the check to only look for resource at begining * 3274 fixed test * test fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 17 January 2022, 16:46:32 UTC
456afa1 jmarchionatto 14 January 2022, 14:20:45 UTC 2681 member match fix method (#3281) * Disallow operation invocation by GET request * Add changelog Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 14 January 2022, 14:20:45 UTC
10dea07 Mark Iantorno 14 January 2022, 01:43:56 UTC JUnit jupiter fix for @Disabled tag order. (#3300) 14 January 2022, 01:43:56 UTC
e6fd5c9 IanMMarshall 13 January 2022, 17:06:27 UTC Fix batching of mdm-clear tasks (#3295) * Fix batching of mdm-clear tasks. * Fix batching of mdm-clear tasks. Co-authored-by: ianmarshall <ian@simpatico.ai> 13 January 2022, 17:06:27 UTC
55ad98d dependabot[bot] 12 January 2022, 00:35:37 UTC Bump h2 from 2.0.204 to 2.0.206 (#3285) * Bump h2 from 2.0.204 to 2.0.206 Bumps [h2](https://github.com/h2database/h2database) from 2.0.204 to 2.0.206. - [Release notes](https://github.com/h2database/h2database/releases) - [Commits](https://github.com/h2database/h2database/compare/version-2.0.204...version-2.0.206) --- updated-dependencies: - dependency-name: com.h2database:h2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Add to changelog Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: jamesagnew <jamesagnew@gmail.com> 12 January 2022, 00:35:37 UTC
fb453e1 Tadgh 10 January 2022, 23:56:13 UTC H2 CVE (#3291) * Bump h2 to address CVE-2021-42392 * update changes.yaml 10 January 2022, 23:56:13 UTC
7374099 jmarchionatto 06 January 2022, 18:29:01 UTC Issue 3251 terminology reindexing job is never triggered (#3271) * Run intended job * Add test ti validate right method is invoked by inner job * Add changelog * Make test fail with proper message instead of crash Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 06 January 2022, 18:29:01 UTC
2054ef6 Tadgh 06 January 2022, 18:21:25 UTC Rel 5 6 mergeback (#3282) * 3138 externalized binary packages (#3139) * Add test and impl * Add changelog * Fix test * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3138-support-externalized-binaries.yaml * add beans to test configs * Typo * Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * 3131 - Added support for the lookup operation in the Remote Terminology code (#3134) * Remove leading underscores from identifiers (#3146) * Version bump * License files * version.yaml * Add executeRawSql() method to Migrator (#3183) * Add implementation, add test * Add javadoc * Add another helper function * Bump version * 3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155) * 3153 updating the unknowncodesystemwarningvalidationsupport class * 3153 updating version for smile * 3153 update broken tests * 3153 adding log * 3153 cleanup * 3153 cleanup Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Add backport info * Avoid creating ResourcePersistentId for placeholder resources with null ID (#3158) * Add check before mapping storage ID to resource ID in TransactionDetails. * Add change log. * Changed to instead prevent creation of ResourcePersistentId with null ID value. * Changed to instead prevent ResourcePersistentId being created with null resource ID. Co-authored-by: ianmarshall <ian@simpatico.ai> * Fix bug loading packages in non-database mode (#3199) * Add implementation * Add changelog * Add backports * 3164 updating code review points (#3165) * 3164 updating code review points * 3164 updating code review points Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Add executeRawSqlStub (#3203) Co-authored-by: Joanne Mendoza <joanne@smilecdr.com> * Add new version * begin with failing test * fix bug * change log * change log * Add backport informationm * begin with failing test * fix issue * change log * code review * Add backport info. Add folder * fixed * Add test * Update test * Add backport info * Bump minor version * 3170 language portion of language code is case insensitive (#3171) * 3170 language portion of language code is case insensitive * 3170 adding changelog * 3170 house keeping Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Add backport info: * Add version enum * Remove worthless import Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com> Co-authored-by: ianmarshall <ian@simpatico.ai> Co-authored-by: Joanne Mendoza <joannemmendoza@gmail.com> Co-authored-by: Joanne Mendoza <joanne@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: katie_smilecdr <katie@smilecdr.com> 06 January 2022, 18:21:25 UTC
095b959 IanMMarshall 06 January 2022, 15:00:33 UTC Fix PatientIdPartitionInterceptor where patient ID has hashCode equal to Integer.MIN_VALUE. (#3275) * Fix PatientIdPartitionInterceptor for case where patient ID has hashCode equal to Integer.MIN_VALUE * Fix PatientIdPartitionInterceptor for case where patient ID has hashCode equal to Integer.MIN_VALUE Co-authored-by: ianmarshall <ian@simpatico.ai> 06 January 2022, 15:00:33 UTC
c38fdc4 James Agnew 06 January 2022, 13:40:51 UTC Fix inline resource migration (#3277) 06 January 2022, 13:40:51 UTC
2106631 jmarchionatto 05 January 2022, 21:53:46 UTC Disallow operation invocation by GET request (#3272) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 05 January 2022, 21:53:46 UTC
b148121 TipzCM 04 January 2022, 19:38:52 UTC 3242 search content param removed not readded (#3244) * 3242 initial changes and nonsense tests * 3242 added changelog * 3242 cleanup * cleanup * 3242 updated for review * cleanup * 3242 review fixes * review fixes * fix changelog file * review fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 04 January 2022, 19:38:52 UTC
aafc42f jamesagnew 04 January 2022, 18:37:10 UTC License header updates 04 January 2022, 18:37:10 UTC
d610d33 James Agnew 04 January 2022, 18:21:14 UTC Dependency bumps (#3264) * Bump a number of versions * Fixes * Work on version bump * Bump * Test fix * More version bumps * Build fixes * Test fixes * Fixes * Fixes * Test fix * Bump jacoco * Test fix * Test fix * Test fix * Build fix * Build fix * Remove versioned H2 * Build fix * Avoid memory issue in validation tests * JDK bump * Restore compile with errorprone * Force coloured output * Force jansi * Try again to force jansi * Fix for hardcoded date that just passed * Fixes to JPA * Improve changelog * Work on failing test * Test fix * Compile fix * One more version bump * Test fixes 04 January 2022, 18:21:14 UTC
d9820bf James Agnew 03 January 2022, 16:43:45 UTC Add inline resource mode (#3267) * Start work on inline resource text storage mode * Work on inlining * Add changelog * Test fixes * Fix for hardcoded date that just passed 03 January 2022, 16:43:45 UTC
216a3d3 Ken Stevens 29 December 2021, 21:38:22 UTC Merge remote-tracking branch 'origin/master' 29 December 2021, 21:38:22 UTC
fe77a23 Ken Stevens 29 December 2021, 21:36:17 UTC converted permissions to biconsumer 29 December 2021, 21:36:17 UTC
568d39d Ken Stevens 29 December 2021, 21:23:44 UTC fixed an error with concurrent validation (#3266) * fixed an error with concurrent validation * change log 29 December 2021, 21:23:44 UTC
1c318aa michaelabuckley 17 December 2021, 22:38:43 UTC Bypass jpa for lastn results (#3226) * Add flag in DaoConfig to enable storing resources in lucene index * Update loadResourceByPid to use ElasticSearch for loading observation resource and test added to check it * Added parsing to elastic search to parse inlined observation resources json to resource object 17 December 2021, 22:38:43 UTC
a41d79e Ken Stevens 17 December 2021, 02:35:23 UTC call delete expunge hook for pid list within delete expunge batch job (#3252) * call delete expunge hook for pid list within delete expunge batch job * review feedback 17 December 2021, 02:35:23 UTC
a078306 Ken Stevens 16 December 2021, 19:58:50 UTC merge master 16 December 2021, 19:58:50 UTC
6a333c0 Tadgh 16 December 2021, 09:49:28 UTC Fix badly built migrations and indexes 16 December 2021, 09:49:28 UTC
700b614 Tadgh 16 December 2021, 06:47:33 UTC Allow system request details to go through MDM 16 December 2021, 06:47:33 UTC
6d92d08 Patrick Werner 15 December 2021, 18:05:34 UTC log4j-to-slf4j -> 2.16.0 (#3248) logback -> 1.2.8 (https://jira.qos.ch/browse/LOGBACK-1591) 15 December 2021, 18:05:34 UTC
f3c1786 TipzCM 15 December 2021, 16:17:03 UTC 2521 delete subscription resource (#3235) * 2521 will set subscriptionst hat cant be initialized to error state to prevent infinite retries * 2521 add changelog * cleanup * fix issue in merge * fix bad merge * bad merge * 2521 review fixes and test fixes * 2521 review fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 15 December 2021, 16:17:03 UTC
9e20d62 Tadgh 15 December 2021, 06:53:26 UTC Issue 3237 delete expunge performance (#3239) * Initial test looking for bad deletes * Add indexes, add migration, add test' * Fix npe * Add provider test * fix up comments, tighten test * Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeProcessor.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Add changelog * Remove unnecessary migration Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> 15 December 2021, 06:53:26 UTC
ef83777 jmarchionatto 14 December 2021, 21:32:56 UTC Allow Subscription to be configured to send delete messages (#3245) * Allow Subscription to be configured to send delete messages * Add tests and implement MR suggestions Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 14 December 2021, 21:32:56 UTC
50a3005 Tadgh 14 December 2021, 19:20:03 UTC Fix flag name (#3247) * Fix flag name * Bump hapi version 14 December 2021, 19:20:03 UTC
a56603d longma1 13 December 2021, 15:45:30 UTC 2480 partition aware subscription (#3218) * some fixmes to start * Added some FIXMEs * added RequestPartitionId to reosurceDelivryMessage and ResourceModifiedMessage * ResourceDeliveryMessage and ResourceModifiedMessage tests * fixed issue with test missing partitionHelperSvc mocked bean * Added tests and implemented SubscriptionMatchingSubscriber for partition aware subscription * modified implementation of partitionId in CanonicalSubscription * Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID) * Revert "Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)" This reverts commit fe40fb97334e8cddb22037ff116f4a47f6024ddf. * Got added partitionId to subscriptions, added changes to make SubscriptionMatchingSubscriberTest work * added SubscriptionTriggering test, also added partition support to subscriptionLoader * Changed implementation for storing partition id of subscriptions from messages, refactored tests to new implementation * added all subscription systemRequestDetails with all partition to subscription reader * refactored a generic system request details with default all partition request * Added test for dao subscriptions, fixes to get the test working * added partition support for latest version delivery * added doc changes and changelog for multitenancy subscription * cleanup and added partitioned subscription manually trigger test * fixed mocked subscriptionDao * added package-info for subscription module * some code review changes * removed AllPartitionSystemRequestDetail, added new text for multitenant subscription * renamed method for code review * version bump to 5.7.0PRE7 Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Steven Li <steven@smilecdr.com> 13 December 2021, 15:45:30 UTC
d6e543a jmarchionatto 13 December 2021, 13:14:28 UTC Loop over new list to avoid ConcurrentModificationException in case a new hook is added while looping (#3233) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 13 December 2021, 13:14:28 UTC
4075c00 jamesagnew 12 December 2021, 23:09:38 UTC CHangelog for #3240 12 December 2021, 23:09:38 UTC
8e6785c Patrick Werner 12 December 2021, 23:07:13 UTC bumped log4j version to newest version (#3240) 12 December 2021, 23:07:13 UTC
d561577 Ken Stevens 12 December 2021, 00:29:52 UTC Ks 20211209 xml to java (#3236) * try xml -> json * Change from xml serialization to json serialization. Also fix a deadlock in how the validation cache is used. * changelog * back out logback change * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3236-change-validation-from-xml-to-java.yaml Co-authored-by: Tadgh <tadgh@cs.toronto.edu> Co-authored-by: Tadgh <tadgh@cs.toronto.edu> 12 December 2021, 00:29:52 UTC
bd89cf0 VK-SMILECDR 09 December 2021, 22:05:42 UTC Improve mail service (#3230) * move mail config to mail service constructor * update subscription email sender * added license text * [2669] bump HAPI version to 5.7.0-PRE6-SNAPSHOT * add changelog 09 December 2021, 22:05:42 UTC
9593b6b Tadgh 09 December 2021, 21:14:48 UTC Rel 5 6 1 mergeback (#3228) * 3138 externalized binary packages (#3139) * Add test and impl * Add changelog * Fix test * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3138-support-externalized-binaries.yaml * add beans to test configs * Typo * Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * 3131 - Added support for the lookup operation in the Remote Terminology code (#3134) * Remove leading underscores from identifiers (#3146) * Version bump * License files * version.yaml * Add executeRawSql() method to Migrator (#3183) * Add implementation, add test * Add javadoc * Add another helper function * Bump version * 3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155) * 3153 updating the unknowncodesystemwarningvalidationsupport class * 3153 updating version for smile * 3153 update broken tests * 3153 adding log * 3153 cleanup * 3153 cleanup Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Add backport info * Avoid creating ResourcePersistentId for placeholder resources with null ID (#3158) * Add check before mapping storage ID to resource ID in TransactionDetails. * Add change log. * Changed to instead prevent creation of ResourcePersistentId with null ID value. * Changed to instead prevent ResourcePersistentId being created with null resource ID. Co-authored-by: ianmarshall <ian@simpatico.ai> * Fix bug loading packages in non-database mode (#3199) * Add implementation * Add changelog * Add backports * 3164 updating code review points (#3165) * 3164 updating code review points * 3164 updating code review points Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Add executeRawSqlStub (#3203) Co-authored-by: Joanne Mendoza <joanne@smilecdr.com> * Add new version * begin with failing test * fix bug * change log * change log * Add backport informationm * begin with failing test * fix issue * change log * code review * Add backport info. Add folder * fixed * Add test * Update test * Add backport info * Add 5.5.4 * Remove jpaconstants Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com> Co-authored-by: ianmarshall <ian@simpatico.ai> Co-authored-by: Joanne Mendoza <joannemmendoza@gmail.com> Co-authored-by: Joanne Mendoza <joanne@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: katie_smilecdr <katie@smilecdr.com> 09 December 2021, 21:14:48 UTC
9753b66 Ken Stevens 08 December 2021, 20:18:54 UTC 2564 contained resource validation flag (#3225) * First cut at multithreading bundle validation * javadoc * change test to a red-green test * add daoconfig * move bundle concurrency config from validationsupport to request validator * Moved concurrent details from ValidationOptions to FhirValidator * Remove bundleValidationThreadCount (it's set by creating an appropriate executor) * validate threadpool prefixes * FIXME cleanup * reassign FIXMEs to JB * only create the threadpool if it will be used * Add the MdcTaskDectorator to all threadpools * Add bundle path to concurrently validated bundle resource validation messages. * Add test to check bundle entry path being added to validation messages * Threaded validation of contained resources initial checkin * FHIR validator refactored to maintain correct bundle path and async validation task * Refactored to use validation complete invoke callback to support raw string resource or resource object * switch from XML to JSON * # Conflicts: # hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java # hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java * Updated to use new HAPI-FHIR version * merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation * Updated to use new HAPI-FHIR version * Revert "Updated to use new HAPI-FHIR version" This reverts commit 910b7f676bd3b0bac6603abf758b09f6af819a55. * Revert "merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation" This reverts commit c7d60fc3e6a560d6263a39ca13469e51a8f5d155. * Revert "Updated to use new HAPI-FHIR version" This reverts commit aa8a7af45553f0b3f9ef0a697c0c88b8a8249f5a. # Conflicts: # hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java * Fix Test dependencies after reverting changes. * merge 'validate_contains_change' to 2564-contained-resource-validation-flag * Disable threadpool prefix name validate check. * merge master * fix thread regexp * pre-review cleanup * change log * fix test * revert to XML as default validation serialization * fix test * fix test Co-authored-by: Jaison B <jaisonb@gmail.com> 08 December 2021, 20:18:54 UTC
d481896 jamesagnew 07 December 2021, 20:38:36 UTC License header updates 07 December 2021, 20:38:36 UTC
90d05a9 jamesagnew 07 December 2021, 19:55:16 UTC Fix accidental commit 07 December 2021, 19:55:16 UTC
8aef580 jamesagnew 07 December 2021, 15:57:43 UTC Bump core library 07 December 2021, 15:57:43 UTC
d60d07b Mark Iantorno 06 December 2021, 16:25:00 UTC Validate contains change (#3209) * wip * The updated changes to the validator that were pulled in from the core dependencies are not backwards compat. Need to bump HAPI version. * pointing to stable core version * review feedback * Add changelog Co-authored-by: markiantorno <miantorno@pop-os.localdomain> 06 December 2021, 16:25:00 UTC
c4ec767 Ken Stevens 06 December 2021, 16:20:25 UTC Merge branch 'master' of github.com:hapifhir/hapi-fhir 06 December 2021, 16:20:25 UTC
3397bb6 Ken Stevens 06 December 2021, 16:19:50 UTC remove reflection from test. 06 December 2021, 16:19:50 UTC
2c2e31d jamesagnew 06 December 2021, 16:17:11 UTC Docs fix 06 December 2021, 16:17:11 UTC
66fa9e0 Ken Stevens 06 December 2021, 15:57:40 UTC merge master 06 December 2021, 15:57:40 UTC
0dc6339 Ken Stevens 06 December 2021, 13:55:47 UTC Merge branch 'master' of github.com:hapifhir/hapi-fhir 06 December 2021, 13:55:47 UTC
b7bf10c James Agnew 06 December 2021, 11:49:52 UTC Missed commits from #3214 (#3222) * Move graphql provider * Version bump * Moving things around * More reworking * Fix 06 December 2021, 11:49:52 UTC
7e04509 Ken Stevens 06 December 2021, 00:31:19 UTC add test for authorization 06 December 2021, 00:31:19 UTC
d072357 James Agnew 05 December 2021, 22:22:20 UTC Move graphql provider (#3214) * Move graphql provider * Version bump 05 December 2021, 22:22:20 UTC
2e72ec4 tommyyama2020 04 December 2021, 16:40:54 UTC Update points.json (#3213) added my entry for atlas 04 December 2021, 16:40:54 UTC
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