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14 November 2023, 18:36:22 UTC
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Revision Author Date Message Commit Date
2baa190 Tadgh 18 August 2022, 17:36:35 UTC Revert version enum 18 August 2022, 17:36:35 UTC
7985fa0 Tadgh 18 August 2022, 17:35:51 UTC wip 18 August 2022, 17:35:51 UTC
ce57c1c Mark Iantorno 18 August 2022, 17:33:46 UTC Deploy to sonatype (#3934) * adding sonatype profile to checkstyle module * adding sonatype profile to tinder module * adding sonatype profile to base pom * adding final deployToSonatype profile 18 August 2022, 17:33:46 UTC
4937fb4 Ken Stevens 18 August 2022, 14:07:24 UTC fix compile error 18 August 2022, 14:07:24 UTC
0ec984e markiantorno 18 August 2022, 06:39:36 UTC Updating version to: 6.1.1 post release. 18 August 2022, 06:39:36 UTC
f43edb2 Tadgh 18 August 2022, 01:06:36 UTC Fix SP validating interceptor logic 18 August 2022, 01:06:36 UTC
7e609a7 Tadgh 17 August 2022, 23:57:49 UTC Fix index online test 17 August 2022, 23:57:49 UTC
695f43d Tadgh 17 August 2022, 22:23:37 UTC Fix uptests 17 August 2022, 22:23:37 UTC
40bcf65 Tadgh 17 August 2022, 22:14:17 UTC wip 17 August 2022, 22:14:17 UTC
290bf96 Tadgh 17 August 2022, 21:23:47 UTC Merge branch 'rel_6_1' of github.com:hapifhir/hapi-fhir into rel_6_1 17 August 2022, 21:23:47 UTC
28b09a7 Tadgh 17 August 2022, 21:23:41 UTC Fix bug and add test for SP Validating Interceptor (#3930) 17 August 2022, 21:23:41 UTC
117cb57 Tadgh 17 August 2022, 21:19:31 UTC Revert fix for null/system request details checks for reindex purposes 17 August 2022, 21:19:31 UTC
8732469 Tadgh 17 August 2022, 17:23:06 UTC Revert offset mode change 17 August 2022, 17:23:06 UTC
0d16fa8 Tadgh 16 August 2022, 21:42:55 UTC Fix up colun grab 16 August 2022, 21:42:55 UTC
cc3e7d4 Tadgh 16 August 2022, 20:46:10 UTC add index 16 August 2022, 20:46:10 UTC
9e354af TipzCM 16 August 2022, 20:37:48 UTC 3922 delete expunge large dataset (#3923) * lower batchsize of delete requests so that we do not get sql exceptions * blah * fix test * updated tests to not fail Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 16 August 2022, 20:37:48 UTC
d53035c Tadgh 16 August 2022, 19:17:27 UTC Fix oracle non-enterprise attempting online index add (#3925) 16 August 2022, 19:17:27 UTC
a6ae9f9 Ken Stevens 16 August 2022, 14:30:39 UTC do not reindex searchparam jobs on startup 16 August 2022, 14:30:39 UTC
c08c359 Ken Stevens 15 August 2022, 19:53:00 UTC Merge remote-tracking branch 'origin/rel_6_1' into rel_6_1 15 August 2022, 19:53:00 UTC
b071b96 Ken Stevens 15 August 2022, 19:52:17 UTC Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup. 15 August 2022, 19:52:17 UTC
bdef499 Tadgh 15 August 2022, 18:23:50 UTC Offset interceptor now only works for external calls 15 August 2022, 18:23:50 UTC
ca8c6e7 Ken Stevens 15 August 2022, 17:13:05 UTC Gl3407 bundle offset size (#3918) * begin with failing test * fixed * change log * rollback default count change and corresponding comments Co-authored-by: Ken Stevens <ken@smilecdr.com> 15 August 2022, 17:13:05 UTC
e057820 Ken Stevens 14 August 2022, 23:35:48 UTC fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <ken@smilecdr.com> 14 August 2022, 23:35:48 UTC
94db12f Tadgh 13 August 2022, 17:36:29 UTC Version bump 13 August 2022, 17:36:29 UTC
5267183 JasonRoberts-smile 13 August 2022, 11:35:38 UTC 3915 do not collapse rules with filters (#3916) * do not attempt to merge compartment permissions with filters * changelog * Rename to IT for concurrency problems Co-authored-by: Tadgh <garygrantgraham@gmail.com> 13 August 2022, 11:35:38 UTC
a6e0a91 Tadgh 13 August 2022, 01:24:40 UTC Fix for caching appearing broken in batch2 for bulkexport jobs (#3912) * Respect caching in bullk export, fix bug with completed date on empty jobs * add changelog * Add impl * Add breaking test * Complete failing test * more broken tests * Fix more tests' * Fix paging bug * Fix another brittle test 13 August 2022, 01:24:40 UTC
231b9ef Qingyixia 13 August 2022, 00:07:04 UTC Fix to the issue (#3855) * Fix to the issue * Progress * fixed the issue * Addressing suggestions * add response status code to MethodOutcome * Addressing suggestions Co-authored-by: Ken Stevens <ken@smilecdr.com> 13 August 2022, 00:07:04 UTC
f49073d longma1 12 August 2022, 18:20:42 UTC 3379 mdm fixes (#3906) * added MdmLinkCreateSvcimplTest * fixed creating mdm-link not setting the resource type correctly * fixed a bug where ResourcePersistenceId was being duplicated instead of passed on * Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java Change order of tests such that assertEquals takes expected value then actual value Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> * added changelog, also changed a setup function in test to beforeeach Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> 12 August 2022, 18:20:42 UTC
27659c6 kateryna-mironova 12 August 2022, 15:59:22 UTC 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746) * 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete * created unit test for skip of delete operation while processing duplicating create entries * moved unit test to FhirSystemDaoR4Test 12 August 2022, 15:59:22 UTC
89ce87e Etienne Poirier 11 August 2022, 21:11:20 UTC 3884 overlapping searchparameter undetected rel 6 1 (#3909) * Applying all changes from previous dev branch to current one pointing to rel_6_1 * Fixing merge conflict related to Msg.code value. * Fixing Msg.code value. * Making checkstyle happy. * Making sure that all tests are passing. * Passing all tests after fixing Msg.code * Passing all tests. Co-authored-by: peartree <etienne.poirier@smilecdr.com> 11 August 2022, 21:11:20 UTC
f1b5f94 Tadgh 11 August 2022, 19:52:35 UTC 3899 code in limits (#3901) * Add implementation, changelog, test * Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> 11 August 2022, 19:52:35 UTC
d47c958 Tadgh 11 August 2022, 17:31:37 UTC 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905) * Add test and implementation * Add changelog 11 August 2022, 17:31:37 UTC
d8dd5d7 TipzCM 11 August 2022, 14:39:11 UTC updated pointcuts to work as intended (#3903) * updated pointcuts to work as intended * added changelog * review fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 11 August 2022, 14:39:11 UTC
7032ab9 Tadgh 10 August 2022, 12:08:10 UTC Update for CVE (#3895) 10 August 2022, 12:08:10 UTC
686c606 Tadgh 08 August 2022, 17:37:28 UTC Subscription sending delete events being skipped (#3888) * fixed bug and added test * refactor 08 August 2022, 17:37:28 UTC
e95a929 Qingyixia 08 August 2022, 17:33:19 UTC Implemented seventh character extended code and the corresponding dis… (#3709) * Implemented seventh character extended code and the corresponding display * Modifications * Changes on previous test according to modifications made in ICD10-CM XML file 08 August 2022, 17:33:19 UTC
a60a624 Qingyixia 08 August 2022, 17:33:07 UTC Fixed the issue (#3845) * Fixed the issue * Changelog modification * Changelog modification 08 August 2022, 17:33:07 UTC
131e3de Tadgh 06 August 2022, 16:56:12 UTC Fix illegalstateexception when an exception is thrown during stream response (#3882) * Finish up changelog, minor refactor * reset buffer only * Hack for some replacements * Failure handling * wip 06 August 2022, 16:56:12 UTC
7e1a7e2 JasonRoberts-smile 04 August 2022, 22:12:59 UTC only fast-track jobs with exactly one chunk (#3879) 04 August 2022, 22:12:59 UTC
6634234 JasonRoberts-smile 04 August 2022, 16:43:18 UTC do not contrain reindex for common SP updates (#3876) 04 August 2022, 16:43:18 UTC
fef8a14 Tadgh 04 August 2022, 14:35:33 UTC remove RC 04 August 2022, 14:35:33 UTC
1939d74 Tadgh 03 August 2022, 17:57:22 UTC Bump to RC1 03 August 2022, 17:57:22 UTC
9dafbc8 Tadgh 03 August 2022, 17:55:52 UTC Bump for CVE (#3856) * Bump for CVE * Bump spring-data version * Fix compile * Cut over to spring bom 03 August 2022, 17:55:52 UTC
5f1c50a jdar8 03 August 2022, 03:51:37 UTC everything operation with type param (#3842) * wip+test * wip, rough implementation * clean up * clean up * clean up unused methods * Completing implementation. * Removing TODO. * Replacing toList() with Collectors.toList() * support other fhir versions and everything instance * tests wip * tests for instance * Adding default methods in interface * add testsss * Removing @Deprecated. * fix spacing * changelog * reword changelog * Removing default methods from interface. * Bumping version to 6.1.0-PRE28-SNAPSHOT * Adding parameter to method call following interface modification. * Fixing documentation and parameter order for consistency. * Bumping version to PRE30. * Providing backward compatibility. * fix pom * licences * Fixing pom dependencies. * Fixing more pom dependencies. * Fixing dependencies for test-utilities. Co-authored-by: Justin_Dar <justin.dar@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> 03 August 2022, 03:51:37 UTC
e2bed96 Nathan Doef 02 August 2022, 13:27:02 UTC 3776 add https support for hapi fhir cli using tls (#3777) * wip functional TODO - add tests - look at adding TLS to other RestfulClientFactory classes (FhirwebRestfulClientFactory, JaxRsRestfulClientFactory, OkHttpRestfulClientFactory) * move BaseRestServerHelper to Hapi-Fhir * - add TLS support for JaxRsClient and OkHttpClient - add tests * - to use resources and files * - ci fixes * - ci fixes * - ci fixes * - ci fixes * - refactor and tests * - ci fixes * - tests * - tests * - tests / refactor * - clean up * - changelog * - remove OkHttpClient HTTPS support * - ci * - Ken's code review changes * - Ken's code review: method renaming * - Ken's code review: javadoc * - Code coverage * - Create HapiFhirCliRestfulClientFactory to encapsulate new HTTPS functionality. Remove modifications to the FhirContext API. * - version bump * - fix unable to bind port errors by using Jetty functionality to assign random ports * Revert "- version bump" This reverts commit cfce82576aad0c64e181eb8f9baa4f7bfc433bb8. * - version bump Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> 02 August 2022, 13:27:02 UTC
8740c10 David 29 July 2022, 17:05:55 UTC Fix 3840 broken test (#3862) * added a paging api to ijobcoordinator * adding changelog * moved location * added a comment * Added Sort parameter to JobInstanceFetchRequest * Bump HAPI-FHIR version * Updated JPA api to include sort * Add changelog * Fix test Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: David Chen <david.chen@smilecdr.com> 29 July 2022, 17:05:55 UTC
be0b6f1 David 29 July 2022, 15:12:53 UTC 3840 add sort parameter to fetching jobs (#3861) * added a paging api to ijobcoordinator * adding changelog * moved location * added a comment * Added Sort parameter to JobInstanceFetchRequest * Bump HAPI-FHIR version * Updated JPA api to include sort * Add changelog Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: David Chen <david.chen@smilecdr.com> 29 July 2022, 15:12:53 UTC
f933ff3 longma1 29 July 2022, 14:58:40 UTC 2878 mdm mongo support (#3748) * small refactor * refactored MDM module to use iterface IMDMLink, refactored MDMLink to use ResourcePersistenceId wrapper rather than pid as long * removing IJpaIdHelperService and refactor IIdHelperService * fixed bugs for GoldenResourceMergerSvcImpl and FindCandidateByExampleSvc * changes to IIdHelperService * move MdmSearchParamSvc and MdmSubmitSvcImpl out of jpaserver-mdm * moved JpaResourceLoader to hapi-fhir-storage, renamed to ResourceLoaderImpl * added error Msg code, removed Fixme * fixed error code, update last used code in Msg.java to 2083 * fixed accidentally throwing unprocessableentityException * added MdmLinkExpandSvc interface * build adding license to files * MdmLinkdao refactor * fix build * mdm config refactoring * MdmStorageInterceptor and IExpungeEverythingService changes * fix bug where a pid is converted to ResourcePersistenceId twice * minor refactor to IMdmLink, change id from long to ResourcePersistenceId * changed PageImpl to Page interface * refactor MdmSearchExpandingInterceptor to use interface * fixed missed refactor where the resourcePersistenceId is still assumed to be long * resolve test failures resulting from merging master * changed conflicting exception code * fixed issue with bulk export wrapping resourcePid inside resourcePersistenceId * added IMdmLinkImpl to MdmSettings * fixed missing import in IdHelperService from merging master * fixed MdmLinkDaoSvcTest importing wrong MdmLinkTuple * restored JpaIdHelperService and added changelog * modified msg.code to non-duplicate * code review changes * refactored some bulk export batch 2 files to accomodate change in beans being exported * fixed jpa bulk export failing tests * removed duplicate bean declaration of MdmLinkImplFactory in BaseMdmR4Test * merged master and bump version to pre25 * extracted expungeEverythingByType to IExpungeEverythingService * fixed wiring issue * messed up merging pom with master * fixed broken changelog Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: Samuel Lee <samuel.lee@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> 29 July 2022, 14:58:40 UTC
8346c02 jmarchionatto 29 July 2022, 13:23:34 UTC Issue 3804 application fails to start 610 pre14 snapshot with beandefinitionoverrideexception invalid bean definition with name loadidsstep (#3819) * shared steps * Add changelog * Rename as suggested * Remove unnecessary bean * Add missing imports * Remove parent class not used anymore Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 29 July 2022, 13:23:34 UTC
5586b32 jmarchionatto 28 July 2022, 23:09:31 UTC Issue 3857 elastic lucene search returns only 50 results when offset0 and count100 (#3858) * Add logback definition to project to stop debugging all output * Fix limit definition to include _offset=0 case * Move test required resources from previous test module * Add changelog Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 28 July 2022, 23:09:31 UTC
d5a69d8 Etienne Poirier 28 July 2022, 20:07:58 UTC 3859 hapi fhir doc snippet link referring a file as opposed to classpath (#3860) * Using snippet type of classpath as opposed to file. * Modifying documentation. Co-authored-by: peartree <etienne.poirier@smilecdr.com> 28 July 2022, 20:07:58 UTC
9a1d6f3 TipzCM 27 July 2022, 18:50:42 UTC 3821 term code system batch jobs (#3826) * step one * blah * no working test * updated existing tests * delete code system version and code system jobs * trying to get terminology fixed * updating tests * need to have some movement * added completion handler * added clearing code for failsafe * review points * fixing tests * fixing tests * more test fixes * fixing more tests * review fixes * todo Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 27 July 2022, 18:50:42 UTC
d405fa1 Etienne Poirier 27 July 2022, 12:45:59 UTC 3792 providing capability to alter source resource content before mdm matching (#3802) * Solution baseline. * Adding integration test. * Parameterizing the test * Adding to documentation. * Modification following code review. * Modification following code review. * Adding documentation. * Adding documentation specific to MDM customization with pointcut. * Modifications following second code review. * Code review modifications. Co-authored-by: peartree <etienne.poirier@smilecdr.com> 27 July 2022, 12:45:59 UTC
59540ce TipzCM 26 July 2022, 17:29:37 UTC 3813 paging job coordinator (#3814) * added a paging api to ijobcoordinator * adding changelog * moved location * added a comment * blah Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 26 July 2022, 17:29:37 UTC
533019f Ken Stevens 25 July 2022, 22:41:01 UTC Response Terminology Wiring (#3807) * cleaned up response terminology wiring * jpa is failing atm * bump pom versions * double build RAM * bump hapi version to PRE-22 * license headers * re-bump to PRE-22 * tag intermittent Co-authored-by: Ken Stevens <ken@smilecdr.com> 25 July 2022, 22:41:01 UTC
f01e4a7 Ken Stevens 25 July 2022, 15:47:31 UTC Remote Terminology support refactor (#3822) * Revert "test passes with a lot of copy/paste" This reverts commit f2f28e22ef467f0c7dd512152ee68d73385f3b75. * make translateOutcomeToResults public * double RAM * final consolidation. move shared code out to static utility methods * revert azure memory disable jacoco on jpaserver test prokect * bump hapi version * rebump hapi to PRE-21 * licenses Co-authored-by: Ken Stevens <ken@smilecdr.com> 25 July 2022, 15:47:31 UTC
611c1d9 Ken Stevens 25 July 2022, 06:59:49 UTC enable partition-aware subscription activation (#3844) Co-authored-by: Ken Stevens <ken@smilecdr.com> 25 July 2022, 06:59:49 UTC
6d9bbbe Tadgh 22 July 2022, 19:24:59 UTC Add support for deletes to stu3/dstu2 subscriptions. (#3836) * Add support for DSTU3 delete subscrion events, add test * Add changelogP 22 July 2022, 19:24:59 UTC
cbcf3f1 Nathan Doef 22 July 2022, 17:12:07 UTC 3829 Fix Subscriptions created with package installer and partitioning enabled bug (#3830) * - failing test + increase existing code coverage * - fix: use RequestPartitionId.defaultPartition() to handle malformed default partitions * - changelog * - typo 22 July 2022, 17:12:07 UTC
d2fd098 Etienne Poirier 22 July 2022, 15:55:44 UTC 3820 Providing an exception for search request with invalid or incomplete tokenParam (#3825) * Creating an exception to be raised when searching for _tag/_provide/_security where the associated tokenParam is not properly formatted. * Adding changelogs. * Adding integration test. * Rewording ChangeLog. * Rewording exception message. * Addressing code review comments. * Addressing code review comments. * Bumping hapi-fhir version to 6.1.0-PRE20-SNAPSHOT * Modifications to pass checkstyle. Co-authored-by: peartree <etienne.poirier@smilecdr.com> 22 July 2022, 15:55:44 UTC
0a1e782 Tadgh 22 July 2022, 01:56:27 UTC 3817 enhance subscription before message delivery (#3824) * Add changelog * implementation and changes * collection implementation * tidy 22 July 2022, 01:56:27 UTC
f5697e1 JasonRoberts-smile 21 July 2022, 19:26:15 UTC 3755 use batch2 job after search parameter change (#3806) * broke some tests * invoke batch 2 reindex * changelog * fix compile error after merge * fix failing test * hook up partition support * fix some failing tests * deprecate the old reindex service * fix more failing tests * fix broken test 21 July 2022, 19:26:15 UTC
85384fe Ken Stevens 21 July 2022, 17:12:19 UTC separate elastic tests into their own project (#3827) * move elastic tests out into their own project in the hopes it solves ci memory issues * move elastic tests out into their own project in the hopes it solves ci memory issues * disable elastic tests temporarily Co-authored-by: Ken Stevens <ken@smilecdr.com> 21 July 2022, 17:12:19 UTC
e5cc727 jmarchionatto 20 July 2022, 17:24:49 UTC Document the need to reindex when enabling full resource storage with indexed resources. (#3815) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 20 July 2022, 17:24:49 UTC
599f513 Ken Stevens 20 July 2022, 14:40:37 UTC fix checkstyle 20 July 2022, 14:40:37 UTC
f2f28e2 Ken Stevens 20 July 2022, 01:02:16 UTC test passes with a lot of copy/paste 20 July 2022, 01:02:16 UTC
67e67bb jmarchionatto 19 July 2022, 14:00:28 UTC Issue 3804 application fails to start 610 pre14 snapshot with beandefinitionoverrideexception invalid bean definition with name loadidsstep (#3805) * shared steps * Add changelog Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 19 July 2022, 14:00:28 UTC
5921907 Qingyixia 18 July 2022, 01:26:34 UTC Implement patch in mongo db (#3781) * Not the final version * Support PATCH operation * minor modifications * minor modifications * Final version * Final version * Version Bump * bump version again Co-authored-by: Ken Stevens <ken@smilecdr.com> 18 July 2022, 01:26:34 UTC
8ed0a18 TipzCM 17 July 2022, 21:49:03 UTC 3531 implement bulk processors (#3566) * base batch2 bulk export steps - unimplemented * added the basic steps * adding tests * we have added the tests * added tests for bulk export stages * implementing jpa * 3531 adding the jpabukexportprocessorimplementation * 3531 first step for mongo bulk export * jpa stuff updated * 3531 hapi fhir stuff * trying to fix up tests * fixing test * fixed most tests in batch export * deprecate * need some more guidance here * fixing some tests * some steps taken * blah * stashing * test * fixing tests round 1 * many a changes * updating version * small updates * merging in mster again * fixing up serialization * added the permission checkers * cleanup and sonarkube crap * some more tests * updating adding tests * crimes * blah * updatingmsg number again * removal of commented code * cleanup * merge confflicts * fixing msg * review fixes round 1 * more review fixes * merging in master * fixing poms * review points * test fix * test fix * fix test race condition * truncate error * add stack trace to error * rename to IT * fix race condition in test * finally fixed race condition in test. this time I'm optimistic hapi ci will finally pass * fix mock test. not a fan of mock tests like this. * any job definition with a reducer step must be gated. * fixed common batch bean wiring * fix test * lazy init ResponseTerminologyTranslationSvc * change the way we lazy init ResponseTerminologyTranslationSvc * change the way we lazy init ResponseTerminologyTranslationSvc (for the third time. this is super tricky!) * disabling testGoldenResourceWithCircularReferenceCanBeCleared for now Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Ken Stevens <ken@smilecdr.com> 17 July 2022, 21:49:03 UTC
398ed99 jmarchionatto 15 July 2022, 18:04:12 UTC Hsearch no scroll queries (#3799) * Avoid scrolling result for not-asynchronous searches * Adjust deprecated properties * Add changelog Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 15 July 2022, 18:04:12 UTC
0c64427 TipzCM 15 July 2022, 16:42:46 UTC 3770 fix batch2 failure loop (#3779) * 3770 fixing error handling * some updates to error handling * changelog * blah * bumping version * fix test failures * code review points * review points * add retry test * assert counts in the test * test fixes Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Ken Stevens <ken@smilecdr.com> 15 July 2022, 16:42:46 UTC
ab4d957 Tadgh 15 July 2022, 16:29:16 UTC Make patch `add` actually add instead of replace. (#3800) * Fix some patch problems * Changelog 15 July 2022, 16:29:16 UTC
e0169fa Mark Iantorno 15 July 2022, 15:10:26 UTC Adding autoclosing for sonatype publishing (#3798) 15 July 2022, 15:10:26 UTC
98cce2a jmarchionatto 14 July 2022, 19:21:43 UTC 3664 fast elastic load (#3769) * Start direct HSearch path * Support no HSearch * Spike out the direct resource query * Implement hsearch fast load * Fix last master merge in issues * Implement revision requests * Test direct resources (no IDs query) sorting * Use mock to count freetext searches to avoid implementing interface in test * Remove fixme * Make listener optional as it is used only for tests * Provide new dependency * Widen fast path test scope and fix previously untested configurations * Make method transactional as it can be called from outside a TX (at least testObservationLastNAllParamsPopulated does) * Update test validation Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 14 July 2022, 19:21:43 UTC
5575e72 jdar8 14 July 2022, 18:41:36 UTC 3788 FHIR patch on soft deleted resource undeletes resource (#3789) * failing test * fix * refactor * refactor * changelog * changelog * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3788-fix-fhir-patch-on-soft-deleted-resources.yaml Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: Justin_Dar <justin.dar@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> 14 July 2022, 18:41:36 UTC
05ebf02 Tadgh 14 July 2022, 16:01:44 UTC 3790 remove legacy search builder (#3791) * Remove legacy SB * Add changelog * Fix more messages * Fix missed hapi message * Fix up more messages 14 July 2022, 16:01:44 UTC
94a1cda michaelabuckley 13 July 2022, 17:32:40 UTC Fix sort in hsearch - use full millis (#3787) Fix sort in hsearch - use full millis 13 July 2022, 17:32:40 UTC
1785c07 michaelabuckley 13 July 2022, 15:51:24 UTC Mb implement token :not inmemory (#3784) Implement token :not and fix :not-in in InMemoryMatcher Both `:not` and `:not-in` require that NONE of the values in an OR-list match, so we need some machinery to do a none-match instead of any-match. 13 July 2022, 15:51:24 UTC
6ba84e1 jamesagnew 12 July 2022, 20:01:18 UTC Changelog 12 July 2022, 20:01:18 UTC
31034dd dependabot[bot] 12 July 2022, 19:59:00 UTC Bump jetty-http from 9.4.44.v20210927 to 9.4.48.v20220622 (#3766) Bumps [jetty-http](https://github.com/eclipse/jetty.project) from 9.4.44.v20210927 to 9.4.48.v20220622. - [Release notes](https://github.com/eclipse/jetty.project/releases) - [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.44.v20210927...jetty-9.4.48.v20220622) --- updated-dependencies: - dependency-name: org.eclipse.jetty:jetty-http dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 12 July 2022, 19:59:00 UTC
b7c316f jamesagnew 12 July 2022, 19:57:26 UTC Credit for #3619 12 July 2022, 19:57:26 UTC
4684dde Gjergj Sheldija 12 July 2022, 19:54:29 UTC add `displayLanguage` to the `ValueSet/$expand` (#3619) * add `displayLanguage` to the `ValueSet/$expand` * fix tests * fix tests 12 July 2022, 19:54:29 UTC
f0decbf Tadgh 12 July 2022, 18:09:02 UTC Mergeback 2022 07 08 2 (#3772) * 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 * Bump hapi version to 5.6.3 * Add version enum * Add changelog folder and version.yaml * Patch vulnerability, add changelog * AuthorizationInterceptor concurrency failure (#3528) * Fix #3256 - AuthorizationInterceptor concurrency failure * Test fixes * Add backport info * Fix test for lang level 8 * Bump hapi * License updates * Add release pipeline * remove checkstyle from old version * swap jdk for build * Couple removals for arbitrary failures * disabling tests for this next 5_6 release because we shoot from the hip here * Updating version to: 5.6.5 post release. * add new folder * fix versionenum * remove unreleased versions * Bring back into line 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> Co-authored-by: James Agnew <jamesagnew@gmail.com> Co-authored-by: markiantorno <markiantorno@gmail.com> 12 July 2022, 18:09:02 UTC
57ee932 Tadgh 12 July 2022, 18:08:46 UTC Mergeback 2022 07 08 (#3771) * fix handling of common search parameters * Revert "fix handling of common search parameters" This reverts commit 89c45eebdc31c3dd9533570d9c709ecc7ed5a7a6. * Fix implementation, add test (#3378) * Fix implementation, add test * Tighten test * Rip out dead modules * Add changelog * 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 * Issue 3357 * Version bump * Fixed null pointer exception for re-loading subscription on cdr restart and when there's no partition id in the request, and added tests * added changelogs for this fix * Fix broken changelog file * 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> * Make migration donothing as it was added in error * Remove ehcache * Add version.yaml: * Add to sources/javadocs for dist * Fix typo * fix up pom * wip test removing checkstyle plugin from deployable pom * remove test pom changes, instead just dont deploy to sonatype * typo * Version bump * Add implementation, testing, and changelog * Add backport info, make aware of 6_0_0 * add jira ref * Fix test * Add versionenum * Bump dep for spring, add changelog, add versionenum, add changelog folder * Actually do the version bump * 3654 postgres lobs (#3656) * Implementation, test, changelog * Modify changelog * Fix changelog * Add upgrade.md file * Modify to yaml changes * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_3/3654-lob-problems.yaml Co-authored-by: Ken Stevens <khstevens@gmail.com> * tidy * more work Co-authored-by: Ken Stevens <khstevens@gmail.com> * Fix bad yaml indent * Version bump * Back out the reindex changes introduced in 5.7.3 * update changelog * version bump * added fix for subscription in default partition when default partition's id is null * added changelog * Add version info and changelog folder * adding release pipeline yml file fo azure * Fix parameter count limitation on MSSQL/Oracle large transactions (#3075) * Fix parameter count limitation on MSSQL/Oracle large transactions * Changelog fix * Move changelog * Force a change to trigger CI * Test refactoring * Backport oracle fix * Fix backport * upping version to 5.7.5 for release * add versionenum * Updating version to: 5.7.6 post release. * Add query-chunk-aware code * Add new folder * Fix up versionenum * Remove imports Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com> Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Mark Iantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Olivia You <46392181+oliviayou@users.noreply.github.com> Co-authored-by: olivia-you <olivia.you@smilecdr.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> 12 July 2022, 18:08:46 UTC
2bc6c91 StevenXLi 12 July 2022, 16:24:15 UTC 3719 enable map response terminology for bulk export (#3735) * added failing test for Map Response Terminology for bulk export * moved logic for terminology translation out of the interceptor to svc, added translation logic to bulk export file writer, added more tests * added changelog * Wip refactor dependency fix * wip terminology translation code refactor * terminology translation code refactor * refactor clean up * Remove circular dependency * Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3719-enable-map-response-terminology-for-bulk-export.yaml * bump version of hapi to 6.1.0-PRE7-SNAPSHOT * doc update * fix issue when search param registry doesn't contain search param for the resource type * fix beans * hapi version bump from PRE7 to PRE10 * doc update * add ResponseTerminologyTranslationSvc as a constructor variable to the interceptor * fixed ResponseTerminologyInterceptorLoaderTest, added IT for cdr side * version bump to PRE13 * removed unused import Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> 12 July 2022, 16:24:15 UTC
3d4556b Qingyixia 11 July 2022, 14:56:22 UTC Move PATCH to hapi-fhir-storage (#3763) * Not the final version * Support PATCH operation * minor modifications * minor modifications * Final version * Final version 11 July 2022, 14:56:22 UTC
0526da0 Ken Stevens 09 July 2022, 21:25:55 UTC 3757 move delete expunge to batch2 (#3759) * begin with failing test * begin with failing test * remove unused Spring Batch classes. convert service classes * move provider * just one test left to fix * fix test * msg.code * change log * bumping hapi to PRE12 * fix test * review feedback * license update * fix intermittent and status update atomicity * restore url-level partition selection * fix tests Co-authored-by: Ken Stevens <ken@smilecdr.com> 09 July 2022, 21:25:55 UTC
839a1b5 Ken Stevens 09 July 2022, 12:51:04 UTC fix batch intermittent and status update atomicity (#3773) * fix intermittent and status update atomicity * change log Co-authored-by: Ken Stevens <ken@smilecdr.com> 09 July 2022, 12:51:04 UTC
61d34ab James Agnew 07 July 2022, 21:22:38 UTC Add license headers (#3765) 07 July 2022, 21:22:38 UTC
7cf447c michaelabuckley 07 July 2022, 16:15:17 UTC Implement query filter auth via tester (#3758) Use tester instead of new subclass to implement fhir filtering. The subclass was too complicated to be trusted for authorization. 07 July 2022, 16:15:17 UTC
835ec1b alackerbauer 06 July 2022, 07:19:39 UTC #3729 renaming patient-list to subject-list (#3730) * #3729 renaming patient-list to subject-list * #3729 adding changelog * #3729 updating changelog * #3729 renaming patient to subject * #3729 fixing tests Co-authored-by: Anna <anna@MacBook-Pro.local> 06 July 2022, 07:19:39 UTC
616a126 michaelabuckley 06 July 2022, 02:08:45 UTC Change the IAuthRuleTester api to a parameter object. (#3756) * Try using tester to implement fhir filtering. 06 July 2022, 02:08:45 UTC
b68ccb3 Nathan Doef 05 July 2022, 16:37:25 UTC 3693 Search by id is returning a deleted resource with a client-generated id (#3694) - Added functionality to optionally filter out deleted resources when resolving forced ids to persistent ids - Bumps version Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> 05 July 2022, 16:37:25 UTC
3a28920 Ken Stevens 05 July 2022, 03:27:58 UTC Add error-handler callback and ensure batch2 completion handler can't be called twice (#3752) * rename field that drives everything includes * discovered design flaw in completion * fix intermittent * ensure batch2 completion handler can't be called twice * changelog * changelog * javadoc * bump hapi version * licences * Batch2 job definitions can now optionally provide an error handler callback that will be called when a job instance fails, errors or is cancelled. * Changed error handler and completion handler to take a "read-only" copy of an instance instead of just certain fields. * comment * javadoc * fix test * change step execution context from taking instance id to instance * review feedback * fix test * replace 20 or so jetbrains annotations * fixed a few incorrect @NotNull annotations Co-authored-by: Ken Stevens <ken@smilecdr.com> 05 July 2022, 03:27:58 UTC
a13f241 michaelabuckley 04 July 2022, 22:18:29 UTC Implement direct HSearch search path (#3727) * Start direct HSearch path * Support no HSearch * Spike out the direct resource query * Implement hsearch fast load * Fix last master merge in issues * Implement revision requests * Test direct resources (no IDs query) sorting * Use mock to count freetext searches to avoid implementing interface in test Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 04 July 2022, 22:18:29 UTC
bf85195 Tadgh 04 July 2022, 21:13:18 UTC Add implementation, test, and changelog (#3753) 04 July 2022, 21:13:18 UTC
fb4dce7 Tadgh 30 June 2022, 23:51:21 UTC Add unique run number to the published artifact (#3751) 30 June 2022, 23:51:21 UTC
c073c0e JasonRoberts-smile 30 June 2022, 23:42:14 UTC ConformanceStatement generation for DSTU3 is out of date (#3737) * add system SPs to resource * populate include list * wip * wip * Tighten test * Chaneglog * Use old-style collectors Co-authored-by: Tadgh <garygrantgraham@gmail.com> 30 June 2022, 23:42:14 UTC
4ec4d36 michaelabuckley 30 June 2022, 21:29:25 UTC Doc link fix (#3750) * Doc link fix * Whitespace to trigger a build 30 June 2022, 21:29:25 UTC
cc841e1 alackerbauer 30 June 2022, 07:11:20 UTC #3728 passing on practitioner parameter (#3731) * #3728 passing on practitioner parameter * #3728 adding changelog Co-authored-by: Anna <anna@MacBook-Pro.local> 30 June 2022, 07:11:20 UTC
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