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14 November 2023, 18:36:22 UTC
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d9dc25c Tadgh 18 September 2022, 18:32:27 UTC add test 18 September 2022, 18:32:27 UTC
c3339f3 Tadgh 15 September 2022, 22:18:32 UTC Rel 6 1 2 mergeback (#4033) * Bump for CVE (#3856) * Bump for CVE * Bump spring-data version * Fix compile * Cut over to spring bom * Bump to RC1 * remove RC * do not contrain reindex for common SP updates (#3876) * only fast-track jobs with exactly one chunk (#3879) * 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 * Fixed the issue (#3845) * Fixed the issue * Changelog modification * Changelog modification * 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 * Subscription sending delete events being skipped (#3888) * fixed bug and added test * refactor * Update for CVE (#3895) * 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> * 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905) * Add test and implementation * Add changelog * 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> * 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> * 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 * 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> * 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> * 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 * 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> * Version bump * fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <ken@smilecdr.com> * 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> * Offset interceptor now only works for external calls * Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup. * do not reindex searchparam jobs on startup * Fix oracle non-enterprise attempting online index add (#3925) * 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> * add index * Fix up colun grab * Revert offset mode change * Revert fix for null/system request details checks for reindex purposes * Fix bug and add test for SP Validating Interceptor (#3930) * wip * Fix uptests * Fix index online test * Fix SP validating interceptor logic * Updating version to: 6.1.1 post release. * fix compile error * 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 * wip * Revert version enum * Updating version to: 6.1.1 post release. * Add test, changelog, and implementation * Add backport info * Create failing test * Implemented the fix, fixed existing unit tests * added changelog * added test case for no filter, exclude 1 patient * wip * Add backport info * Add info of new version * Updating version to: 6.1.2 post release. * bump info and backport for 6.1.2 * Bump for hapi * Implement bug fixes, add new tests (#4022) * Implement bug fixes, add new tests * tidy * Tidy * refactor for cleaning * More tidying * Lower logging * Split into nested tests, rename, add todos * Typo * Code review * add backport info * Tidy versionenum * Fix import * Remove files that were repackaged Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> 15 September 2022, 22:18:32 UTC
ae3faaf TipzCM 14 September 2022, 13:29:16 UTC change search method for missing parameter names (#3982) * handle changing in missing parameters * added changelog * refactor step1 * refactor step 2 * refactor step 3 * refactor step 3 * more code review fixes * tra lala * tra lala * blah * more changes * review fixes * review point * more review points * blah Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 14 September 2022, 13:29:16 UTC
1a3de51 alackerbauer 14 September 2022, 11:55:35 UTC removed library immunizationCQLLibrary (#4024) * removed library immunizationCQLLibrary * deleted unused resource file Co-authored-by: Anna <anna@MacBook-Pro.local> 14 September 2022, 11:55:35 UTC
8fdfcaa alackerbauer 14 September 2022, 11:54:24 UTC #3738 renamed patient parameter to subject (#4019) * #3738 renamed patient parameter to subject to be R4 compliant * #3738 removed accidental STU3 rename Co-authored-by: Anna <anna@MacBook-Pro.local> 14 September 2022, 11:54:24 UTC
6021a09 James Agnew 13 September 2022, 20:25:15 UTC Avoid NPE when run in IJ (#4018) * Avoid NPE when run in IJ * Add changelog 13 September 2022, 20:25:15 UTC
ad57ebf jmarchionatto 13 September 2022, 17:56:31 UTC Add disabled test reproducing open bug (#3994) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 13 September 2022, 17:56:31 UTC
6c0c730 James Agnew 12 September 2022, 10:48:56 UTC ForcedOffsetSearchModeInterceptor should not modify the search when it is already manually marked as synchronous (#4016) * ForcedOffsetSearchModeInterceptor should not modify the search when it is already manually marked as synchronous * Add changelog 12 September 2022, 10:48:56 UTC
cb3cc1f Tadgh 09 September 2022, 23:24:06 UTC Iam opensearch auth (#4011) * Bump HS version, add support for credential provider * License files * Use index settings file instead of injecting a template at boot * Changelog * Typo * fix logs * Add javadoc 09 September 2022, 23:24:06 UTC
4226cae Tadgh 09 September 2022, 23:18:30 UTC Broken bulk export (#4012) * Implement test * wip * Fixed a bug in bulk export * add changelog * typo * Switch out to debug logs 09 September 2022, 23:18:30 UTC
306bb8b Qingyixia 08 September 2022, 15:44:41 UTC Handling unexpected response status code of import-poll-status operation (#3939) * Handling unexpected response status code when executing import-poll-status operation * Handling unexpected response status code 08 September 2022, 15:44:41 UTC
6d9a199 Tadgh 08 September 2022, 14:38:42 UTC Rel 6 1 1 mergeback (#4004) * Bump for CVE (#3856) * Bump for CVE * Bump spring-data version * Fix compile * Cut over to spring bom * Bump to RC1 * remove RC * do not contrain reindex for common SP updates (#3876) * only fast-track jobs with exactly one chunk (#3879) * 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 * Fixed the issue (#3845) * Fixed the issue * Changelog modification * Changelog modification * 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 * Subscription sending delete events being skipped (#3888) * fixed bug and added test * refactor * Update for CVE (#3895) * 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> * 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905) * Add test and implementation * Add changelog * 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> * 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> * 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 * 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> * 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> * 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 * 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> * Version bump * fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <ken@smilecdr.com> * 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> * Offset interceptor now only works for external calls * Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup. * do not reindex searchparam jobs on startup * Fix oracle non-enterprise attempting online index add (#3925) * 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> * add index * Fix up colun grab * Revert offset mode change * Revert fix for null/system request details checks for reindex purposes * Fix bug and add test for SP Validating Interceptor (#3930) * wip * Fix uptests * Fix index online test * Fix SP validating interceptor logic * Updating version to: 6.1.1 post release. * fix compile error * 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 * wip * Revert version enum * Updating version to: 6.1.1 post release. * Add test, changelog, and implementation * Add backport info * Create failing test * Implemented the fix, fixed existing unit tests * added changelog * added test case for no filter, exclude 1 patient * wip * Add backport info * Add info of new version * Fix bad mergback * Added a couple of missing imports to a unit test. Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: Kevin SmileCDR <kevinsmilecdr@Kevins-MacBook-Pro-2.local> 08 September 2022, 14:38:42 UTC
d22651a alackerbauer 08 September 2022, 12:16:16 UTC 3984 rework immunization cql unit test (#4005) * 3984 added test resources * 3984 added unit test for ontario immunization POC * #3084 reworking unit tests to showcase immunization evaluation POC Co-authored-by: Anna <anna@MacBook-Pro.local> 08 September 2022, 12:16:16 UTC
002a7dc jmarchionatto 07 September 2022, 19:52:38 UTC Issue 3419 elastic search exception while pre expanding valueset with more than 10 000 concepts (#3991) * Add test reproducing bug * Refactor ValueSet expansion hsearch queries to use scroll. * Use void method for never used return value. * Execute action when transaction is active * Update tests query counts as the CodeSystemVersion.pid is always queried now * Enable test after reproduced bug fix. Add changelog. * Implement suggestions Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 07 September 2022, 19:52:38 UTC
9b50b33 Nathan Doef 07 September 2022, 15:52:37 UTC :nickname Qualifier Support for Custom SearchParameters (#3969) * - add failing test * 4977 Allow any search parameter to have a nickname qualifier. * IT test to ensure nickname expansion is working on custom SearchParameters * capture log output in tests * changelog * code review changes Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com> Co-authored-by: kylejule <kyle.jule@smilecdr.com> 07 September 2022, 15:52:37 UTC
cc183c7 Tadgh 07 September 2022, 15:35:57 UTC Ensure HS before attempting fulltext reindex. (#3995) * Do not attempt fulltext reindex if disabled. Validate enabled before using any operation * attribute 07 September 2022, 15:35:57 UTC
c647154 jdar8 07 September 2022, 10:44:36 UTC Everything operation with type param code review fixes (#3926) * check for valid resource type * add test and refactor test class * refactor auto get method name * introduce parameter object to patient everything methods * introduce parameter object to patient everything methods * change record to class * add hapi error code * refactor * refactor * change code num * refactor getmethodname to util method * add docs and rename fields to conform to fhir standard * typo * version bump * resolving merge conflicts. * Bumping version * Bumping version to 6.2.0-PRE5-SNAPSHOT * Encapsulating parameters in a PatientEverythingParameters object. Co-authored-by: Justin_Dar <justin.dar@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> 07 September 2022, 10:44:36 UTC
ec5a6ad Ken Stevens 06 September 2022, 18:05:15 UTC update azure-pipelines.yml to match projects that have tests (#3993) 06 September 2022, 18:05:15 UTC
f3e6837 Qingyixia 06 September 2022, 15:40:03 UTC Fixed the issue of bulk export returning the wrong path if "Fixed Value for Endpoint Base URL" is set (#3958) * Fixed the issue of bulk export returning the wrong path if "Fixed Value for Endpoint Base URL" is set * Minor modifications according to the suggestions * Modify the msg code number * Modify the tests to be parameterized test * Modifications according to review suggestions * Update the msg code 06 September 2022, 15:40:03 UTC
dd5c49a Kai Kewley 06 September 2022, 13:11:45 UTC Add support for ICD-10 International Version (Fixes #3734) (#3849) * Update CLI upload examples for R4. * Fixes #3734 Add support for ICD-10 (International) Include all concept properties in ICD-10 loader. Remove newlines and tabs from ICD Rubrics. * Bump Msg code and use in Term Loader. * Added a changelog entry for this addition. * Update icd10-dummy-test-en.xml * Added a default impl to the new interface method to avoid breaking upstream projects. Co-authored-by: Kevin Dougan <kevin.dougan@smilecdr.com> Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com> Co-authored-by: Kevin SmileCDR <kevinsmilecdr@Kevins-MacBook-Pro-2.local> 06 September 2022, 13:11:45 UTC
100b8f9 Ken Stevens 05 September 2022, 04:04:54 UTC batch2 rework (#3964) * consolidated Batch2Helper check status in assert before running maintenance ignore illegal job instance state transition * Fix mock tests * rename intermittent to IT * extra logging * into to debug * review feedback * added more logging * removed fasttracking. replaced with support for triggering a maintenance run * fixed tests * fixed tests * add asserts * licenses * snakeyaml cve version bump * data migration * merge origin/master * merge origin/master * fix test (support triggering jobs when scheduling is disabled) * add counter to abort potential infinite loop after 100000 calls * compile error * move multipartition mdm tests out to a separate IT update mongo job instance creation with new logic * fix race condition * back out infinite loop circuit breaker. it breaks terminology tests that depend on this loop running > 100000 times. * fix test (triggered job key was missing group) * revert saveAllDeferred * Almost finished getting JpaPersistenceR4IT to pass * testBulkExportDeleteForOnGoingJob still not passing * testBulkExportDeleteForOnGoingJob still not passing * Removed method `fetchInstanceAndMarkInProgress`. It was clobbering other state transitions like CANCELLED. * undo rename of cancelled to cancelRequested. Thymeleaf depends on the old name * ExpandResourcesStep requires a synchronous search * Tests are passing but man testBulkExportDeleteForOnGoingJob is a flakey test * fix test * fix test * change log * allow ERRORED -> FAILED state transition * add a timeout to saveAllDeferred() * improve error message on timeout message * fix tests * added more logging * added more logging * fix semaphore issue * Msg.code * fix test * javadoc * switch all batch loggers to batch troubleshooting log * add unit test, improve logging * move TimeoutManager to its own class. Add tests. * fix tests * comment cleanup * test race condition * review feedback Co-authored-by: Ken Stevens <ken@smilecdr.com> 05 September 2022, 04:04:54 UTC
a4a7fd9 StevenXLi 02 September 2022, 20:53:52 UTC 3987 group bulk export does not apply typefilter searches to members of the group (#3988) * Create failing test * Implemented the fix, fixed existing unit tests * added changelog * added test case for no filter, exclude 1 patient Co-authored-by: Steven Li <steven@smilecdr.com> 02 September 2022, 20:53:52 UTC
21cce44 jdar8 02 September 2022, 17:58:57 UTC 3962 import csv to conceptmap needs status element (#3963) * wip * test * refactor * doc change and changelog * add test cases * edit msg.code * fix msg code Co-authored-by: Justin_Dar <justin.dar@smilecdr.com> 02 September 2022, 17:58:57 UTC
9fd0add Tadgh 01 September 2022, 18:00:48 UTC Add test, changelog, and implementation (#3981) 01 September 2022, 18:00:48 UTC
68c3439 Ken Stevens 01 September 2022, 02:46:17 UTC jpa test split (#3959) * create fhir-version specific hapi-fhir-jpaserver-test projects * moved dstu2 tests out to dstu2 test project. * moved dstu2 tests out to dstu2 test project. * finished moving dstu2 tests out to dstu2 test project. * finished moving dstu2 tests out to dstu2 test project. * dstu3 test project compiles * start moving dstu3 resources * letting azure pileine know about the new modules * finished moving dstu3 resources. this might pass * OK this one should pass for sure * OK this one should pass for sure * change test poms to test scope * move the rest of R4 test classes * move the rest of R4 test classes * moar r4 moves * moar r4 moves * moar r4 moves * finished with r4 * finished with r4 * started r5 * started r5 * Cache busting based on source branch name * Fix other cache key * cache pegged to SHa1 * test cleanup Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> 01 September 2022, 02:46:17 UTC
d9134fc Tadgh 01 September 2022, 01:03:43 UTC Permit uplift (#3978) * Add test and implementation for permitting uplifts * Add new code paths, error code * Add license * Modify to support arbitrary urls * Modify to support arbitrary urls 01 September 2022, 01:03:43 UTC
26ca950 Ken Stevens 31 August 2022, 02:15:32 UTC Checkstyle Abstract Class Name (#3966) * init rev * checkstyle enforce abstract classes start with "Base" (and vice versa) * checkstyle enforce abstract classes start with "Base" (and vice versa) Co-authored-by: Ken Stevens <ken@smilecdr.com> 31 August 2022, 02:15:32 UTC
7d478f0 Tadgh 30 August 2022, 19:10:47 UTC Fix logging when there are no jobs to start (#3971) 30 August 2022, 19:10:47 UTC
65d4fe8 StevenXLi 30 August 2022, 15:30:03 UTC 3947 support http delete for operation $export poll status (#3961) * Added failing test, and the methods that are necessary to not break the build * Implemented solution to cancel jobs via delete request for poll status * change log added * change log name change to pass test * Changed implementation to work with existing infrastructure * code review changes Co-authored-by: Steven Li <steven@smilecdr.com> 30 August 2022, 15:30:03 UTC
bd39d65 Kunjan Patel 30 August 2022, 12:39:42 UTC Update points.json (#2516) Co-authored-by: James Agnew <jamesagnew@gmail.com> 30 August 2022, 12:39:42 UTC
b9caec1 Tadgh 30 August 2022, 02:29:02 UTC Rel 6 0 mb 3 (#3933) * adding version.yaml, updating version in pom.xml * It is possible to write to a resource in a partition the user is not authorized to. (#3397) * fixed * remove sout * add msg.code * fix failed tests * fix equal sign * update msg code * extract method * Fix up code numbers * Clean changelog Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Revert final artifact version * add graphql test (#3585) * added graphql birthdate test * fix variable name * typo * 3506 mdm log enhancement (#3543) * Providing Fixme's to be reworked at a later time. * Adding // FIXME Anna to assist our Austrian friend. * Adding logging test as a first step in addressing issue #2822. * hapifhir#3506 part 2: enhance logging for (un)successful MDM matching hapifhir#3506 part 2: enhance logging for (un)successful MDM matching * Update MdmMatchLinkSvc.java #3506 move "narrowed down" log to different place * #3506 added scores and tests #3506 added scores and tests * #3506 formatting #3506 formatting * #3506 create changelog file #3506 create changelog file * #3506 fix typo #3506 fix typo * #3506 fix part 3, minor formatting #3506 fix part 3, minor formatting * #3506 fix tests #3506 fix tests Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com> Co-authored-by: Anna <anna@MacBook-Pro.local> * mdm matching (#3579) * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328 * Update HapiFhirJpaMigrationTasks.java Corrected ordering * Update HapiFhirJpaMigrationTasks.java Moving index status to be last operation * Revert "Update HapiFhirJpaMigrationTasks.java" This reverts commit 37bfd3e66e4f4dc76de135c1fe108ccbf9e3690c. * Moved to bottom Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> * begin with failing test * fixed * changelog * add jira tag * Update to 6 1 (#3582) * added changelog folder, upped version * version enum * add a few more unit tests to assert proper NO_MATCH exclusion * revert merge master doh! bad reflexes * revert merge origin master * unrevert revert. ugh what a pain * merge recovery. fix poms. * merge recovery. more reverting * merge recovery. more reverting * merge recovery. more reverting * Revert "merge recovery. fix poms." This reverts commit ae6e0ddb06bdcb424f9c4637eb0a987bc112b115. * more revert revert reversions * more revert revert reversions * pre-review cleanup Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> Co-authored-by: Mark Iantorno <markiantorno@gmail.com> * Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586) * When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller. * License * Ks 20220508 log colour (#3592) * don't use colours when output is redirected to a file * change log * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594) * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328 * Update HapiFhirJpaMigrationTasks.java Corrected ordering * Update HapiFhirJpaMigrationTasks.java Moving index status to be last operation * Revert "Update HapiFhirJpaMigrationTasks.java" This reverts commit 37bfd3e66e4f4dc76de135c1fe108ccbf9e3690c. * Moved to bottom Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> * 3584 case sensitive string elasticsearch (#3596) * Fix for case-sensitive search with newer elasticsearch * Test and fix ascii normalization too * more test cases * comments * Docs update empi usecase (#3598) * Update diagram for use case 5 * Add new page for database support * Licnese * Mb norm fix (#3604) * Normalize query since wildcard searches aren't normalized in elastic * Handle batch2 job cancellation (#3603) * Handle batch2 job cancellation * Add CANCELLED status * Remove unuseful test Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Add batch2 interfaces to obtain recent instances (#3601) Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * changelog folder * Documentation change, added warning log and change log for ticket (#3609) Co-authored-by: Steven Li <steven@smilecdr.com> * fix ne for lastUpdated search param (#3589) * init/wip * add implementation, add tests * add checks and some refactoring * refactor and simplify tests * refactor * get rid of some of the warnings * add changelog * remove my todos * redo ne logic to account for less precise dates * add tests * refactoring * rename to follow convention Co-authored-by: Justin_Dar <justin.dar@smilecdr.com> * Version bump * Add skip of checkstyle to upload * Typo * upping version enum, upping version number, 6.0.1 * Group Bulk Export rules exiting too early. (#3643) * Implementation, test, changelog * Add jira link * adding backport in yaml for 3642 * adding folder for 6.0.1 release * pom changes to publish checkstyle to sonatype * bad version in pom file * Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider * AUtomcplete error code * updating comment indicating final erorr code * Bump error code * fixing version enum so release docs generate correctly, adding additional changelog for 3650 * 3684 subscription for delivering delete events formatted wrong (#3685) * Fixed issue with delivering delete events Subscriptions * Extracted deliverer class name to a constant, now shared across tests and interceptor class * Added change log and doc changes * moved the constant to a more appropriate place Co-authored-by: Steven Li <steven@smilecdr.com> * Version bump * Add version enum * Version enum and folder * adding release pipeline yml file fo azure * Adding autoclose for sonatype publishing (#3797) * Add impl test and changelog (#3713) * fix up changelog, new version * Version bump * Updating version to: 6.0.4 post release. * reverting 6.0.4 commit * Updating version to: 6.0.4 post release. * removing double entry from preious release * Add support for DSTU3 delete subscrion events, add test * Add changelogP * Add version enum * Remove notnull * Add test for DSTU2 * Updating version to: 6.0.5 post release. * Fix up * wip * Adding solution and changeLog file. * Adding failing test. * fix up * Version bump Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com> Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com> Co-authored-by: Anna <anna@MacBook-Pro.local> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: StevenXLi <stevenli_8118@hotmail.com> Co-authored-by: Steven Li <steven@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Justin_Dar <justin.dar@smilecdr.com> 30 August 2022, 02:29:02 UTC
506966e Tadgh 29 August 2022, 22:55:12 UTC cache pegged to SHa1 (#3968) 29 August 2022, 22:55:12 UTC
5509bd0 James Agnew 29 August 2022, 13:42:10 UTC Move partition interceptor (#3907) * Add license headers * Move partition interceptor * More cleanup * One more tweak * Headers * Add changelog * Test logging enhancement * Test fix * Test fixes * Add test method 29 August 2022, 13:42:10 UTC
d9f7c7d Ken Stevens 25 August 2022, 18:10:10 UTC back out hl7 version bump (#3955) * back out hl7 version bump * bump fhir core to 55 Co-authored-by: Ken Stevens <ken@smilecdr.com> 25 August 2022, 18:10:10 UTC
caf370d Mark Iantorno 24 August 2022, 16:55:00 UTC Azure Pipelines Overhaul (#3948) This PR changes the way HAPI is built by Azure pipelines. Instead of a FIFO queue for all tests in the project, the entire project is quickly built and cached without testing, then the individual modules are built and tested in separate jobs which can be run in parallel from each other. Each of these jobs then uploads the test coverage for that module as a build artifact. Finally, a last stage downloads all the archived tests results and aggregates them using jacoco so they can be uploaded to codecov. This has two key benefits: If there is a failing test because of an intermittent, the individual failing module can be re-run instead of having to re-run the whole project build. The build time is decreased substantially (90min -> 45min). This is the first run at this, I will be iterating to further reduce build times going forward. 24 August 2022, 16:55:00 UTC
b5f5cd3 Etienne Poirier 22 August 2022, 12:23:35 UTC 3937 searching for resources with a target resource parameter in include fail (#3938) * Adding failing test. * Adding solution and changeLog file. Co-authored-by: peartree <etienne.poirier@smilecdr.com> 22 August 2022, 12:23:35 UTC
e7a4c49 Tadgh 19 August 2022, 00:21:27 UTC Rel 6 1 mergeback (#3927) * Bump for CVE (#3856) * Bump for CVE * Bump spring-data version * Fix compile * Cut over to spring bom * Bump to RC1 * remove RC * do not contrain reindex for common SP updates (#3876) * only fast-track jobs with exactly one chunk (#3879) * 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 * Fixed the issue (#3845) * Fixed the issue * Changelog modification * Changelog modification * 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 * Subscription sending delete events being skipped (#3888) * fixed bug and added test * refactor * Update for CVE (#3895) * 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> * 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905) * Add test and implementation * Add changelog * 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> * 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> * 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 * 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> * 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> * 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 * 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> * Version bump * fix $mdm-submit output (#3917) Co-authored-by: Ken Stevens <ken@smilecdr.com> * 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> * Offset interceptor now only works for external calls * Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup. * do not reindex searchparam jobs on startup * Fix oracle non-enterprise attempting online index add (#3925) * 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> * add index * Fix up colun grab * Bump Version for non-breaking purposes * Fix broken test * bump error code * revert internal logic * Revert offset mode change * wip * Revert fix for null/system request details checks for reindex purposes * Fix bug and add test for SP Validating Interceptor (#3930) * wip * Fix uptests * Fix index online test * Fix SP validating interceptor logic Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com> Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com> Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> 19 August 2022, 00:21:27 UTC
7f7b7d6 Jose Arturo Garcia 15 August 2022, 17:45:43 UTC Update points.json (#3919) * Update points.json * Update points.json 15 August 2022, 17:45:43 UTC
dad1e42 dotasek 12 August 2022, 19:01:07 UTC 3764 Fix NullPointer on validator meta extension (#3910) * Failing test * Failing test * Add necessary package load to test * WIP add minimum code for passing test * Use PrePopulatedValidationSupport binaryMap in NpmPackage * Rename test * Add test for non-CachingValidationSupport * Rename Tests + InvalidExtensionValue test * Revert change to ValidateDirectory * Gentle reformat * Fix typo * Test CachingValidationSupport fetchBinary * Test for NpmPackageValidationSupport * Refactor * Check for nulls when adding Binary * Test PrePopulatedValidationSupport addBinary * Test ValidationSupportChain * Move ValidationSupportChainTest to proper package * Remove FIXME in VersionSpecificWorkerContextWrapper * Test VersionSpecificWorkerContextWrapper * Add example in docs Co-authored-by: dotasek <david.otasek@smilecdr.com> 12 August 2022, 19:01:07 UTC
64e1f4d MykolaMedynskyiSCDR 11 August 2022, 23:37:12 UTC Fixing response message when deleting non-existing or deleted resource. (#3898) * Fixing response message when deleting non-existing or deleted resource. * Changed names of properties. * The full ID shown in message, not just IdPart 11 August 2022, 23:37:12 UTC
f4a0397 James Agnew 09 August 2022, 21:30:10 UTC Add test for #3890 (#3891) * Add test for #3890 * Remove unneeded import * Add changelog 09 August 2022, 21:30:10 UTC
60a879c michaelabuckley 07 August 2022, 07:09:12 UTC Renable elasticsearch tests (#3850) * Renable elasticsearch tests Limit elasticsearch container to 512MB instead of the default 4GB. 07 August 2022, 07:09:12 UTC
a5c4b07 jmarchionatto 05 August 2022, 16:39:00 UTC Fallback direct resource HSearch to JPA when resources are not found … (#3823) * Fallback direct resource HSearch to JPA when resources are not found in index * Use specific exception instead of identifying it by the message * Add Message code to exception Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 05 August 2022, 16:39:00 UTC
ebac65c jmarchionatto 05 August 2022, 14:48:37 UTC Add simple local implementation of UCUM temperature canonicalization … (#3872) * Add simple local implementation of UCUM temperature canonicalization for Celsius and Fahrenheit * Adjust conversion to not increase precision, as it matter when finding ranges * Simplify test variables Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 05 August 2022, 14:48:37 UTC
2e1f4c2 jmarchionatto 04 August 2022, 22:19:06 UTC Make sure that direct resource load path is only executed for synchro… (#3833) * Make sure that direct resource load path is only executed for synchronous searches * Remove unneeded mockito extension * Only allow for resource loading from fulltext index when advanced search (indexed parameters) is also enabled Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 04 August 2022, 22:19:06 UTC
9324c6a michaelabuckley 04 August 2022, 21:10:10 UTC Use released version of core so we have javadoc. (#3880) 04 August 2022, 21:10:10 UTC
7010ddd jmarchionatto 04 August 2022, 16:30:20 UTC Allow hsearch sorted offset searches (#3864) * 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 * Allow hsearch sorted offset searches * Add changelog Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 04 August 2022, 16:30:20 UTC
b026ac1 Patrick Werner 03 August 2022, 20:12:59 UTC Bump fhir.core to latest version (#3593) * adding version.yaml, updating version in pom.xml * It is possible to write to a resource in a partition the user is not authorized to. (#3397) * fixed * remove sout * add msg.code * fix failed tests * fix equal sign * update msg code * extract method * Fix up code numbers * Clean changelog Co-authored-by: Tadgh <garygrantgraham@gmail.com> * Revert final artifact version * add graphql test (#3585) * added graphql birthdate test * fix variable name * typo * 3506 mdm log enhancement (#3543) * Providing Fixme's to be reworked at a later time. * Adding // FIXME Anna to assist our Austrian friend. * Adding logging test as a first step in addressing issue #2822. * hapifhir#3506 part 2: enhance logging for (un)successful MDM matching hapifhir#3506 part 2: enhance logging for (un)successful MDM matching * Update MdmMatchLinkSvc.java #3506 move "narrowed down" log to different place * #3506 added scores and tests #3506 added scores and tests * #3506 formatting #3506 formatting * #3506 create changelog file #3506 create changelog file * #3506 fix typo #3506 fix typo * #3506 fix part 3, minor formatting #3506 fix part 3, minor formatting * #3506 fix tests #3506 fix tests Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com> Co-authored-by: Anna <anna@MacBook-Pro.local> * mdm matching (#3579) * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328 * Update HapiFhirJpaMigrationTasks.java Corrected ordering * Update HapiFhirJpaMigrationTasks.java Moving index status to be last operation * Revert "Update HapiFhirJpaMigrationTasks.java" This reverts commit 37bfd3e66e4f4dc76de135c1fe108ccbf9e3690c. * Moved to bottom Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> * begin with failing test * fixed * changelog * add jira tag * Update to 6 1 (#3582) * added changelog folder, upped version * version enum * add a few more unit tests to assert proper NO_MATCH exclusion * revert merge master doh! bad reflexes * revert merge origin master * unrevert revert. ugh what a pain * merge recovery. fix poms. * merge recovery. more reverting * merge recovery. more reverting * merge recovery. more reverting * Revert "merge recovery. fix poms." This reverts commit ae6e0ddb06bdcb424f9c4637eb0a987bc112b115. * more revert revert reversions * more revert revert reversions * pre-review cleanup Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> Co-authored-by: Mark Iantorno <markiantorno@gmail.com> * Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586) * When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller. * License * added support for OO.issue.details from Java RI Validator * remove duplicated Msg.code * Ks 20220508 log colour (#3592) * don't use colours when output is redirected to a file * change log * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594) * Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328 * Update HapiFhirJpaMigrationTasks.java Corrected ordering * Update HapiFhirJpaMigrationTasks.java Moving index status to be last operation * Revert "Update HapiFhirJpaMigrationTasks.java" This reverts commit 37bfd3e66e4f4dc76de135c1fe108ccbf9e3690c. * Moved to bottom Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> * 3584 case sensitive string elasticsearch (#3596) * Fix for case-sensitive search with newer elasticsearch * Test and fix ascii normalization too * more test cases * comments * Docs update empi usecase (#3598) * Update diagram for use case 5 * Add new page for database support * Licnese * Mb norm fix (#3604) * Normalize query since wildcard searches aren't normalized in elastic * removed duplicated dependency with wrong version * fixed test file(added a Base64 string) * fixed tests * fixed test: history?_since is an instant * removing time from date-strings in examples * fixed more instant strings * changed filtering of messages to messageId * fixed messageId filter on missing profiles * changed messageID system string to Grahames preferred String * updated MsgIds of unsupported methods * removed fixed commons-codec version as fhir.core uses commons-codec:1.15 This will introduce issues with the android built. * fixed GraphQL Test * fixing test issue caused by different message string, switch to details code assertion * fixing test issue caused by different message string, switch to details code assertion * updated Msg.codes * updated Msg.codes * fixed duplicated Msg.codes * setErrorOnInvalidValue set to false in test * reverted date precision test changes * updated r5 resources to latest build version * updated to latest snapshot, https://github.com/hapifhir/org.hl7.fhir.core/issues/884 causes test failures. * Try to fix message codes * Test fixes * Checkstyle fix * Test fix * Try to avoid CME Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com> Co-authored-by: Tadgh <garygrantgraham@gmail.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com> Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com> Co-authored-by: Anna <anna@MacBook-Pro.local> Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com> Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com> Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com> Co-authored-by: James Agnew <jamesagnew@gmail.com> 03 August 2022, 20:12:59 UTC
a6c2e58 jmarchionatto 03 August 2022, 19:44:10 UTC Fix range calculation for number or quantity search parameters (#3871) * Fix range calculation for number or quantity search parameters * Unify clause building for prefixed numeric parameters. Fix range tests for quantity. Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> 03 August 2022, 19:44:10 UTC
71a3fa9 jmarchionatto 03 August 2022, 15:51:34 UTC Fix range calculation for number or quantity search parameters (#3870) by: juan.marchionatto <juan.marchionatto@smilecdr.com> 03 August 2022, 15:51:34 UTC
eae1c0f TipzCM 03 August 2022, 14:50:51 UTC 3846 migrate bulk import pull to batch2 (#3853) * still fixing tests * migrated a bulk import pull job t obatch 2 * changelog * cleanup * review fixes * minor tweaks * cleaningup * tra la la * blah * blah * updating msg Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> 03 August 2022, 14:50:51 UTC
dcfaf42 Tadgh 03 August 2022, 04:46:20 UTC add new version enum, bump version, new folder 03 August 2022, 04:46:20 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
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