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3344 Commits

Author SHA1 Message Date
Tadgh ac8e012892 wip 2021-04-09 13:07:15 -04:00
Tadgh 99e10de5fb
Merge pull request #2487 from hapifhir/mdm-expansion-interceptor 
MDM Expansion Interceptor (poc)
 2021-04-09 11:23:04 -04:00
Tadgh 8f30f7b0f2 Vague skeleton of pointcut 2021-04-09 11:08:47 -04:00
James Agnew edfe1ae8e6
Add lastupdated to capabilitystatement (#2530) 
* Add lastupdated to capabilitystatement

* Test fix

* Test fix
 2021-04-08 13:23:21 -04:00
James Agnew f70648484a
Avoid a deadlock uploading terminology in postgres (#2529) 
* Fix #2493

* Try to fix intermittent test failure
 2021-04-08 12:28:42 -04:00
James Agnew 462d9bc6c4
Fix compartment defs for R5 (#2528) 
* Fix compartment defs for R5

* Add changelog

* Test fix
 2021-04-08 05:59:05 -04:00
James Agnew a6cbf7eebd
Add support for hierarchycal valueset expansion (#2525) 
* Add support for hierarchycal valueset expansion

* Add changelog

* Add tests

* Cleanup

* Test fix

* Test fixes
 2021-04-06 17:36:54 -04:00
James Agnew fcffb04c7b
Allow unknown code systems during validation (#2523) 
* Allow unknown code systems during validation

* Add changelog

* Test fix
 2021-04-05 20:59:59 -04:00
James Agnew b617c7690d
Search Parameter Infrastructure Cleanup (#2522) 
* Search param service cleanup

* Work on collapsing search param

* Search param cleanup

* Work on build

* Test fix

* Test fixes

* Ongoing work

* Test fix

* Compile fix

* Test fixes

* Test fix

* Test fix

* License header updates

* Remove fixme

* Cleanup

* Cleanup
 2021-04-05 17:40:10 -04:00
James Agnew 0bf746f23b
Add support for revincludes to CapabilityStatement generator (#2521) 
* Add support for revincludes to CapabilotyStatement generator

* Add changelog

* Fixes

* Test fix

* Test fixes

* Test fix

* Test fix

* More fixes to CS cache

* Test fix

* Test fix

* Test fix
 2021-04-05 08:29:04 -04:00
Tadgh 961c996ea9 Remove foolish local bind 2021-04-01 17:32:14 -04:00
Tadgh 696982ce1e Fix bean name. Update docs 2021-03-31 13:45:40 -04:00
Tadgh 74be6761b1 Merge remote-tracking branch 'origin/master' into mdm-expansion-interceptor 2021-03-31 09:47:57 -04:00
Tadgh 8b69d161bd Update docs 2021-03-30 17:12:55 -04:00
Tadgh 419a5829ea This shockingly works 2021-03-30 12:39:37 -04:00
jamesagnew 4eb9508e28 One more fix to interceptor 2021-03-30 11:47:03 -04:00
jamesagnew 8759cdae00 Additional cleanup 2021-03-30 08:20:14 -04:00
jamesagnew 4feda13d7f License header update 2021-03-30 06:02:32 -04:00
James Agnew 049097e5b4
Improve CapabilityStatement Generation (#2511) 
* Start work

* Work on testing

* Version bump

* Test fix

* Compile fix

* Test Fixes

* Test fix

* Test fix

* Compile fix

* Tst fix

* Test fix

* Test fix

* Test fix
 2021-03-30 05:48:03 -04:00
Tadgh a15ded7140 Interceptor now correctly intercepts at the right point 2021-03-29 21:12:03 -04:00
Tadgh ab143e34cb Merge remote-tracking branch 'origin/master' into mdm-expansion-interceptor 2021-03-29 19:27:37 -04:00
Tadgh 838ac890d3 wip 2021-03-29 19:19:37 -04:00
Tadgh 5f42743f48 wip 2021-03-29 19:16:26 -04:00
Diederik Muylwyk e3be7cc6fb Fix build 2021-03-29 18:39:51 -04:00
Diederik Muylwyk b720c32c1d Version bump 2021-03-29 18:23:16 -04:00
Tadgh 432579c591 Fix test error 2021-03-29 15:00:20 -04:00
Tadgh 19810db65d Test refactor. address review comments 2021-03-29 14:55:41 -04:00
Tadgh c46617fefa Use dynamic projection 2021-03-29 11:38:52 -04:00
Tadgh 002d3fcf3c Migrate constant 2021-03-29 11:07:23 -04:00
Tadgh e9e20988c9 Partial moving of presearch regsitered pointcut 2021-03-29 10:49:58 -04:00
Tadgh 9f13225aa5 WIP interceptor using reference param modifier 2021-03-26 17:57:38 -04:00
Tadgh e8f49f2fba More docs 2021-03-26 16:01:29 -04:00
Tadgh a3fbd3e1a1 Hotter docs 2021-03-26 16:00:06 -04:00
Tadgh bee33f763a Refactors, tidying. Improving docs 2021-03-26 15:54:27 -04:00
Tadgh f7eee5985e Add some logging to figure out CI failure 2021-03-26 11:58:52 -04:00
Tadgh a1a3e65106 remove dead whitespace 2021-03-26 10:20:41 -04:00
Tadgh cc1861e876 Update test. 2021-03-25 15:48:03 -04:00
Tadgh 4d3b021f12 Add annotating processor and composite processor 2021-03-25 13:53:41 -04:00
Tadgh 315dc3fcb7 start with failing test 2021-03-24 12:50:29 -04:00
Tadgh 6f669f9ccd wip 2021-03-23 19:29:22 -04:00
Tadgh 8a8eb84fe6 Works on #2496, start with failing test 2021-03-23 18:14:06 -04:00
Tadgh e6cfb77c79 Wip 2021-03-23 18:11:39 -04:00
Kevin Dougan SmileCDR d1c2d839d1
2491 - Fix NullPointerException when performing cascade delete (#2492) 
* 2491 - Fix NullPointerException when performing cascade delete.
 2021-03-22 10:29:03 -04:00
James Agnew dc41d5ad61
Add terminology mapping and display population interceptors (#2488) 
* Start work on code mapping interceptors

* Work on generation

* Add terminology mapping and display population interceptors

* Add changelog

* License header updates

* Test fixes

* Fix typo

* Interceptor fixes

* License header update

* Test fixes

* Mapping fixes

* Version bump

* License header updates

* Add null tests

* Add null guard

* Intermittent fix
 2021-03-21 12:03:57 -04:00
Tadgh 659a877100 Add interceptor 2021-03-18 23:17:56 -04:00
Tadgh 6226ae02d5 Add basic skeleton of MDM expansion 2021-03-18 23:16:45 -04:00
michelgleeson 009f184ab4
fix refering to wrong view (#2486) 
Co-authored-by: Mike G <michel.gleeson@gmail.com>
 2021-03-18 17:47:46 -04:00
jamesagnew c9c13646f5 License header update 2021-03-18 10:42:46 -04:00
James Agnew d857048207
Preserve meta values in stored resources (#2481) 
* Fix #1731

* Test fix

* Test fixes

* Avoid intermittent failure
 2021-03-17 09:23:22 -04:00
michelgleeson 0a6c61372c
Parameterize term valueset concept view dao (#2477) 
* Generic the list type to accomidate different substring queries

* special subquery for Oracle

* change the conceptview dao depending on dialect

* address review comments

* remove generics

* no longer inherits

* copy paste from non Oracle version

* dang copy pasters

* changelog

Co-authored-by: Mike G <michel.gleeson@gmail.com>
 2021-03-16 16:26:19 -04:00
jamesagnew 72026811e6 Add passing test for #2015 2021-03-16 14:44:29 -04:00
jamesagnew beecb49d45 Add test 2021-03-16 08:34:43 -04:00
jamesagnew 14f12e7dab Missed commit for #2471 2021-03-15 08:52:46 -04:00
James Agnew 3a8881f913
Resolve NPE in group bulk export (#2476) 2021-03-14 13:12:58 -04:00
James Agnew 2e7eb972ff
Avoid NPE in ResourceVersionConflictResolutionStrategy for system request (#2471) 
* Avoid NPE in ResourceVersionConflictResolutionStrategy for system
request

* Add changelog
 2021-03-12 19:23:49 -05:00
James Agnew 0ad57c51bb
Fix resource reindexing on partitioned seerver (#2468) 
* Fix resource reindexing on partitioned seerver

* Add changelog

* Test fix

* Test fix

* Tets fix

* Test fix
 2021-03-12 14:14:39 -05:00
James Agnew 2633cbd141
Improve error message for invalid date param (#2466) 
* Improve error message for invalid date param

* Add changelog

* Test fixes
 2021-03-11 14:23:02 -05:00
Tadgh e09741cbf6 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-11 11:08:48 -05:00
Tadgh c8ed81d338 Fix up some mocks, fix empty search param maps being generated 2021-03-10 18:26:16 -05:00
Xiaocheng Luan f752e46e84
Make the search coordinator thread pool size configurable and set a (#2457) 
reasonable default value. The default was 1 and all searches were being
executed sequentially.
 2021-03-10 16:56:49 -05:00
Tadgh 126fc212a7 Reverting dumb changes 2021-03-10 15:43:51 -05:00
Tadgh b86eee5392 Add more validation of resource types 2021-03-10 15:40:18 -05:00
Tadgh 9e8af41b8b Add test for cache recency 2021-03-10 15:16:21 -05:00
Tadgh 75f756b49f Add changelog 2021-03-10 15:00:54 -05:00
Tadgh 412cf003b0 Add test for cache busting header 2021-03-10 14:52:53 -05:00
Tadgh 827ee33414 Add test for provider type validation pre-submission 2021-03-10 13:52:15 -05:00
Tadgh 420c4f8378 Rework pid translator to accept non-forced-ids 2021-03-10 13:34:04 -05:00
Tadgh 5323486d28 Validate tyepes 2021-03-10 12:48:54 -05:00
Tadgh 374a65db7d Fix bug 2021-03-10 12:03:52 -05:00
Tadgh 3e249d0261 Minor cleanup 2021-03-10 12:03:19 -05:00
Tadgh b7398cb6f2 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-10 10:33:24 -05:00
Tadgh bfb9d0bc36 Filter default resource types based on export style 2021-03-10 10:30:54 -05:00
jamesagnew 9f5786ba6c License header updates 2021-03-10 05:09:14 -05:00
Tadgh 30a48894cc Add another test 2021-03-09 22:54:51 -05:00
Tadgh e26d757ba3 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-09 22:54:24 -05:00
James Agnew 807d9d53f0
Improve performance for large transactions (#2462) 
* Performance tweaks

* Work on processing speed

* Disable no longer relevant tests

* Work on performance

* Work on tests

* Work on large transaction performance

* Add changelog

* Perf tweaks

* Test fixes

* Resolve FIXME

* Fixes

* Test cleanup

* Fix broken changelog entry
 2021-03-09 18:16:02 -05:00
Tadgh 1a1a5ee661 WIP supporting multiple type filters 2021-03-09 12:42:39 -05:00
James Agnew be50a46d76
Tweaks to contained searches (#2461) 
* Tweaks to contained searches

* Add changelog

* Build fix
 2021-03-09 11:51:30 -05:00
Frank Tao bf8e890a0c
Supported contained resource search (#2441) 
* POC for indexing on contained resource - test case may failed

* Test contained url

* Add a spt to handle contained flag

* Added search option for contained resource

* Impl contained resource search

* fixed typo

* Reworked on creating index based on the review comments

* Added changelog

* Added more test cases

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-03-09 06:50:23 -05:00
Diederik Muylwyk 6cc8a5ce4d
Fix HasParam#doGetQueryParameterQualifier() (#2460) 
* Fix HasParam#doGetQueryParameterQualifier(); add changelog entry

* Fix bad test in SearchParameterMapTest
 2021-03-09 06:28:40 -05:00
Tadgh 27952ab5e4 add patient export, partial rework for multiple _typeFilters 2021-03-09 00:56:49 -05:00
James Agnew 62df320ceb
Avoid a crash reading an unknown ID on partitioned server (#2451) 
* Avoid a crash reading an unknown ID on partitioned server. Fix #1953.

* Attempt 2 at fixing #1953
 2021-03-07 10:16:30 -05:00
Tadgh ccf5798634 Fix bug with ignored typeFilters 2021-03-05 14:20:15 -05:00
Diederik Muylwyk 120dc19a54 Merge branch 'master' into 2446-issues-with-placeholder-reference-targets-need-to-be-resolved 2021-03-05 12:34:49 -05:00
Diederik Muylwyk 2945cd9f74 Remove FIXME 2021-03-05 12:33:23 -05:00
Diederik Muylwyk a195eebdec Placeholder extension moved to resource body from meta; tests passing. 2021-03-05 12:09:17 -05:00
Tadgh 5b75ff2425 WIP working out bug in typefilters 2021-03-05 10:35:52 -05:00
Tadgh 9547048848 Add support for Patient export 2021-03-04 20:16:50 -05:00
Diederik Muylwyk bd85c0c362 Remove unnecessary failing test. 2021-03-04 19:38:09 -05:00
Diederik Muylwyk beab3522b9 Enhance isPlaceholder to check value of placeholder extension. 2021-03-04 19:33:00 -05:00
Diederik Muylwyk 96a2151542 Remove unnecessary FIXMEs. 2021-03-04 19:19:34 -05:00
Diederik Muylwyk e3ba4bd1b6 Set default for Populate Identifier in Auto-Created Placeholder Reference Targets to true; update javadocs accordingly 2021-03-04 18:54:04 -05:00
Diederik Muylwyk dfdcfa1365 Add failing tests. 2021-03-04 17:01:39 -05:00
Diederik Muylwyk 9a7bd0e775 Add failing tests. 2021-03-04 16:55:16 -05:00
Tadgh 6129194353 Merge remote-tracking branch 'origin/master' into issue-2445-support-patient-level-export 2021-03-04 16:53:20 -05:00
Tadgh 2f1518344b Add changelogs, add patientbulkredaer implementation 2021-03-04 16:53:05 -05:00
Tadgh c2877e84bb
Merge pull request #2439 from hapifhir/issue-2433-mdm-export 
Support MDM expansion in Group Bulk Export
 2021-03-04 16:49:19 -05:00
Tadgh ff1c6e4d27 Start with failling test and partial job config 2021-03-04 16:15:51 -05:00
Tadgh 8021396f4f Remove unused mdmlink functions 2021-03-04 14:17:02 -05:00
Diederik Muylwyk 5a952ad980 Add more FIXMEs as my understanding grows. 2021-03-04 14:16:14 -05:00
Tadgh 8eb9ebb797 Add space 2021-03-04 14:07:04 -05:00
Tadgh e5eacdddd6 Fixes bug with uninterpretable string expression in job parameter 2021-03-04 14:06:48 -05:00
Diederik Muylwyk e8c080bb12 Add initial FIXMEs. 2021-03-04 13:45:09 -05:00
Tadgh 94377c1159 Just use boolean 2021-03-04 13:02:17 -05:00
Tadgh f7153a609a Fix formatting error 2021-03-04 10:04:38 -05:00
Tadgh 3d628a4e9c Add test for exporting patients from group 2021-03-03 21:30:40 -05:00
Tadgh de09c7e2da Bit of logic tidying 2021-03-03 19:03:31 -05:00
Tadgh 7b663bfe99 Add constants, fix up some tests 2021-03-03 18:51:03 -05:00
Tadgh 02f38e9532 Fix up other tests for new data reality 2021-03-03 16:16:22 -05:00
Tadgh 3f3e252175 Extract a superclass 2021-03-03 15:48:28 -05:00
Tadgh 57c7d4f3eb Support MDM expansion in group bulk export, re-add capability to use _typeFilter in Bulk Export 2021-03-03 15:02:41 -05:00
Tue Toft Nørgård 70c2808ecd
Fix https://github.com/hapifhir/hapi-fhir/issues/2435 (#2436) 2021-03-03 08:51:27 -05:00
Tadgh 53598c3bdc Start with failing test 2021-03-02 13:18:43 -05:00
Tadgh 74066a81b6
Merge pull request #2420 from hapifhir/issue-2401-add-support-for-group-id-export 
Issue 2401 add support for group id export
 2021-02-26 10:23:42 -05:00
Ken Stevens 7d769e3b05
Issue 2332 create via put for implementationguide that references some placeholders (#2423) 
* begin with failing test

* fixed.  test passes.

* documentation and changelog

* added ConceptMap

* review feedback
 2021-02-26 09:44:48 -05:00
Tadgh 604b5d2060 Fix all broken tests 2021-02-25 19:11:18 -05:00
Tadgh 6c6b959cb5 fix test 2021-02-25 16:54:21 -05:00
Tadgh b0209fdaac Fix multi search parameter issue 2021-02-25 16:39:24 -05:00
Tadgh 1a5439fad5 Comment out unused mdm parameter 2021-02-25 16:27:57 -05:00
Tadgh 1663e367a6 Address review comments 2021-02-25 16:23:36 -05:00
Ken Stevens a2a3ffb7ec added failing test 2021-02-25 14:35:20 -05:00
Tadgh f6a913effe Fix NPE 2021-02-25 09:27:28 -05:00
Tadgh 8e060a05e0 remove fixme 2021-02-24 22:46:51 -05:00
Tadgh b725c51172 Change tests 2021-02-24 17:28:46 -05:00
Tadgh a56060a096 Tidy things from preliminary review 2021-02-24 17:16:54 -05:00
Tadgh 3937d2ef01 Remove some dead code 2021-02-24 15:57:55 -05:00
Tadgh 0033827f57 Minor refactor 2021-02-24 15:14:59 -05:00
Kevin Hartmann 26a385a595 Merge remote-tracking branch 'origin/master' into kh-20200222-search-list 2021-02-24 10:29:38 -05:00
Kevin Hartmann 1eab2caf9f Added _list as a valid parameter in MatchUrlService 
Wrote tests for and/or/both processing in FhirResourceDaoSearchListTest.
 2021-02-24 10:27:22 -05:00
Patrick Werner cf1f2f27db
added nullchecks to prevent NPE (#2417) 
* added nullchecks to prevent NPE
fixes #2171

* Add test from #2171 and changelog

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-02-24 10:09:04 -05:00
Ken Stevens 30905aeba7 Merge remote-tracking branch 'origin/master' into issue-2401-add-support-for-group-id-export 2021-02-24 09:38:59 -05:00
Kevin Hartmann 62bfa2cdbc Merge remote-tracking branch 'origin/master' into kh-20200222-search-list 2021-02-24 09:20:07 -05:00
Tadgh 627d2b9bd0 Tidy test 2021-02-23 18:53:18 -05:00
Tadgh 077225b87c Add chunking 2021-02-23 16:41:17 -05:00
Tadgh 7561889924 Partially complete groupbulkexportjob 2021-02-23 13:05:58 -05:00
Ken Stevens fb884f9f15 test infrastructure 2021-02-23 11:32:02 -05:00
Ken Stevens 330cafa83e initial implementation 2021-02-23 11:25:56 -05:00
Tadgh b5b8d27b39 Tidy code 2021-02-22 22:51:20 -05:00
Tadgh 66c2b456de Add more tests 2021-02-22 22:47:08 -05:00
James Agnew b108e43600
Allow partition date for non-partitionable resources (#2407) 
* Allow partition date for searchparam resources

* Cleanup

* Test fix

* Documentation update

* Docs tweak
 2021-02-22 20:49:09 -05:00
Tadgh a3c291336c partial add of new style of job 2021-02-22 17:00:01 -05:00
Ken Stevens 24efa97b17 begin with failing test 2021-02-22 11:37:32 -05:00
Tadgh d8ce476e99 Merge branch 'issue-2401-add-support-for-group-id-export' of github.com:jamesagnew/hapi-fhir into issue-2401-add-support-for-group-id-export 2021-02-22 10:25:26 -05:00
Tadgh d31b04ee65 wip 2021-02-22 10:25:24 -05:00
Ken Stevens 61a7f9ed6a added mdm flag 2021-02-19 20:51:52 -05:00
Ken Stevens 9bc051c193 added mdm flag 2021-02-19 20:47:43 -05:00
Ken Stevens 3de51103a3 fixed provider 2021-02-19 20:24:56 -05:00
Ken Stevens 1e0981b416 job call 2021-02-19 13:39:50 -05:00
Ken Stevens 00a8e3897a begin with failing test 2021-02-18 21:54:16 -05:00
Ken Stevens 70b2b83d1a begin with failing test 2021-02-18 21:47:43 -05:00
James Agnew 3eda19c65a
Version bump (#2400) 
* Version bump

* Docs changes

* Docs tweaks

* Docs tweak

* Spelling fixes

* Docs tweaks
 2021-02-18 11:07:49 -05:00
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
James Agnew 65ac0e80fb
Add CapabilityStatement customizer (#2387) 
* Add CapabilityStatement customizer

* Fix javadocs
 2021-02-15 14:58:34 -05:00
ianmarshall 88d820bf38 Make LOINC Top2000* files optional in terminology loader. 2021-02-11 09:12:08 -05:00
ianmarshall a383cb94fc Make LOINC Top2000* files optional in terminology loader. 2021-02-10 22:30:19 -05:00
Tadgh 2759db2a31
Merge pull request #2371 from hapifhir/config-error-on-url-protocol 
Throw ConfigurationError if you attempt to provide a Rest URL that contains a protocol.
 2021-02-09 20:25:14 -05:00
Tadgh 64878c23d3 Update text, add changelog 2021-02-09 19:03:09 -05:00
Tadgh 2e3712357f Throw configueration error when somebody tries to put a protocol in the rest URL 2021-02-09 18:59:11 -05:00
Ken Stevens 7f127f75f9
validate that Terminology beans are proxied so that @Transactional annotated methods are run within transactions (#2362) 2021-02-08 13:11:29 -05:00
Hanan Awwad 6384067e50
Customize concept display in value set expansion (#2282) 
* fix issue #2280

* revert the indentation back.

* revert-back untouched changes.
 2021-02-07 12:29:05 -05:00
James Agnew 92669b29da
Add elastic test (#2348) 
* Add elastic test

* Rework

* Add test
 2021-02-04 11:04:27 -05:00
James Agnew 0f31d106e5
Allow empty request details in JPA (#2343) 
* Allow empty request details in JPA

* Test fixes
 2021-02-02 11:00:14 -05:00
Mike G f61cb163ae refactor and modify for prefix and suffix 2021-02-01 12:11:11 -05:00
Frank Tao 1d835d82d6
Fixed Ucum Conversion NullPointerException issue (#2331) 
* Fixed Ucum Conversion NullPointerException issue

* Revoke:save value to the original table if it can't be normalized
 2021-01-30 19:30:12 -05:00
Ken Stevens ba63f65115
changed $expand filter matching from left-match to contains match (#2327) 
* changed $expand filter matching from left-match to contains match

* changelog

* pure substring match is too generous (a regression test checked for that).  Tightened the match up to word boundaries.

* CLean up to avoid intermittent test failure

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-01-29 12:37:54 -05:00
jamesagnew 8854f344b3 Add test 2021-01-28 16:22:36 -05:00
Nick Goupinets 3be480c9f0 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-27 16:47:40 -05:00
James Agnew 909d9f742c
Enable Auto-reference versions in JPA (#2323) 
* Automatic reference versions

* Auto reference versions

* resolve fixmes

* Add changelog

* Test fixes

* Test fixes

* Resolve fixmes

* Work on versioning

* Add support for _includes

* Update headers

* Change visibility

* One more tweak

* One more API tweak

* Fixes

* Account for review comments

* Fix errorprone reported issue

* Test fix

* Test fixes

* Test fixes
 2021-01-27 14:49:10 -05:00
Nick Goupinets 04db4ed229 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-26 09:18:20 -05:00
Ken Stevens 86ea0d60ef
reduce _count to the maximum page size rather than throwing an error. (#2319) 
* reduce _count to the maximum page size rather than throwing an error.

Also when setting the paging provider on a restful server, automatically set the default page size and max page sized of the restful server from the paging provider.

* reword log message

* fixing this paging issue has uncovered all sorts of interesting things, including this long hidden bug!

* fix tests in sub-optimal way

* fix NPE

* fix test

* fixed a couple of bugs in SearchCoordinatorSvcImpl that surfaced when i added a default page size to RestfulServer
 2021-01-25 08:19:29 -05:00
Frank Tao 1d1ebcf5e8
Improved DateQuery and removed 'OR' in the SQL (#2302) 
* improved DateQuery and removed 'OR' in the SQL

* improved DateQuery and removed 'OR' in the SQL

* Date handling cleanup (#2316)

* Date handling cleanup

* Fix codecov

* One more fix

* Fix tests

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2021-01-23 17:53:18 -05:00
Ken Stevens 749934d5f1
fixed name text indexing (#2309) 
* fixed name text indexing

* fixed name text indexing
 2021-01-22 15:39:26 -05:00
dependabot[bot] feff734736
Bump jaxb-runtime from 2.3.1 to 3.0.0 (#2289) 
* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

Signed-off-by: dependabot[bot] <support@github.com>

* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

Signed-off-by: dependabot[bot] <support@github.com>

* Add jakarta bindings

* Dependency cleanup

* More depndency cleanup

* Work on deps

* Replace transaction annotation

* Cleanup

* Another fix

* Build fix

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-01-22 11:24:23 -05:00
Nick cfc798cb2b Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-22 09:45:04 -05:00
Frank Tao 341eb404e6
Improved the performance for multiple _has by exclude previous pids (#2304) 
* Improved the performance for multiple _has by exclude prev pids

* Removed extra import

* Added test case for SQL contains RES_ID NOT IN ()
 2021-01-21 14:42:10 -05:00
Nick ed5727d795 Fixed missing imports 2021-01-21 10:04:16 -05:00
jamesagnew 7cf41a7e85 One more build fix (grrrrrr) 2021-01-21 09:24:42 -05:00
Nick 82e52750e7 Merge branch 'master' into ng_20201218_survivorship_poc 2021-01-21 09:00:28 -05:00
jamesagnew 078a94f1a6 Fix nonnull annotations 2021-01-21 08:47:44 -05:00
James Agnew 14b0688f69
Bump core version to 5.2.16 (#2308) 
* Bump core library version

* Test fix

* Build fixes

* Some test fixes

* One more bit of docs

* Build fix

* Test fix

* Test fix

* Docs fix
 2021-01-21 05:30:23 -05:00
Tadgh 3d5255d88c Bump ES version running in tests 2021-01-20 11:34:51 -05:00
Nick f5e2086cfd Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-19 09:35:31 -05:00
Tadgh edbc789a93 Add annotation to skip test classes which require docker if it is not found on the host 2021-01-18 21:49:43 -05:00
Tadgh 7c6c64bfb7 Remove dead import 2021-01-18 15:53:49 -05:00
Tadgh 5b2530a948 Remove dead beans 2021-01-18 14:55:33 -05:00
Tadgh 8f72970063 Add bean to config 2021-01-18 14:09:38 -05:00
Nick b00f47ef81 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-18 09:25:58 -05:00
James Agnew 66e1a51e01
Add validation options to RepositoryValidingInterceptor (#2294) 
* Add repository validating interceptor outcome to response

* Add a doc

* Add a test and some docs

* Rework validation
 2021-01-17 16:40:32 -05:00
dependabot[bot] 391a6d1a3f
Bump ph-schematron from 5.2.0 to 5.6.5 (#2184) 
* Bump ph-schematron from 5.2.0 to 5.6.5

Bumps [ph-schematron](https://github.com/phax/ph-schematron) from 5.2.0 to 5.6.5.
- [Release notes](https://github.com/phax/ph-schematron/releases)
- [Commits](https://github.com/phax/ph-schematron/compare/ph-schematron-parent-pom-5.2.0...ph-schematron-parent-pom-5.6.5)

Signed-off-by: dependabot[bot] <support@github.com>

* Fix compile error

* Build fix

* Add test logging

* Test fix

* Resolve classpath duplicates

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-01-17 14:27:26 -05:00
James Agnew 29cf20aac3
Add repo validation outcome to response (#2293) 
* Add repository validating interceptor outcome to response

* Add a doc

* Add a test and some docs
 2021-01-17 12:50:13 -05:00
vedion 99b646eed7
Mapping noExtensibleWarnings and noBindingMsgSuppressed between FhirInstanceValidator and InstanceValidator (#2054) 
Co-authored-by: ahn <anders.havn@systematic.com>
 2021-01-17 09:21:08 -05:00
James Agnew 1dc4fb2206
Make quantity indexes use double datatype (#2290) 
* Make quantity indexes use double datatype

* Add changelog

* Test fixes

* Test fixes

* Disable test
 2021-01-16 18:44:15 -05:00
Nick 1d7ec3cc13 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-15 14:18:27 -05:00
jamesagnew 4791c81aec Improve package loading logs 2021-01-15 06:19:57 -05:00
Nick 57662eedb3 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-12 09:22:38 -05:00
jamesagnew ef407d85bf Add logging 2021-01-12 08:56:12 -05:00
Ken Stevens 520400d6ea
added IPagingProvider.canSearchByOffset() (#2281) 
* init rev

* added IPagingProvider.canSearchByOffset()
consolidated parameters in bundle link methods

* fix refactoring error

* add @Nonnull to BundleLinks parameter

* null check

* fix test

* cleanup

* fix refactoring

* final cleanup

* review feedback

* review feedback

* review feedback
 2021-01-11 20:42:41 -05:00
Nick 5aa85c7e17 Survivorship 6 2021-01-11 17:22:06 -05:00
Nick 684b77d396 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-11 09:21:29 -05:00
Frank Tao f6d4a40388
UCUM Service Support (#2261) 
* Added UcumServiceUtil

* Removed ucum-essense.xml

* Added ucum service existing test cases passed

* Added more test cases

* Merge branch 'master' into ft-ucum-support

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

* Added back extractReferenceParamsAsQueryTokens

* Added changelog and migration script

* Added length for the string type

* Moved UCUM util to hapi-fhir-jpaserver-model

* Renamed UCUM support to Normalized Quantity Search Support

* Moved setNormalizedQuantitySearchNotSupported to AfterEach

* Changed migrate task to 530

* Removed comments

* Fixed in memory search issue and added more test cases

* Fixed the version order

* License header updates

* Updated based on review comments

* Updated the migration task based on review comments

* Fixed RES_TYPE with type String and length 100

* Changed myParamsQuantityNormalizedPopulated type to Boolean class
 2021-01-10 21:05:24 -05:00