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3746 Commits

Author SHA1 Message Date
juan.marchionatto 16e329e40c Add version to ValueSet.compose.include when uploading terminology 2021-09-15 14:40:21 -04:00
Tadgh 724e4b37da Fix up test to actually match 2021-09-15 11:24:01 -04:00
Tadgh 171f0f8724 fix rulebuilder 2021-09-15 09:04:45 -04:00
Tadgh a0c8cc4279 fix test 2021-09-15 01:23:43 -04:00
Tadgh 8f0e8b9e51 remove useless DB calls 2021-09-14 18:44:55 -04:00
Tadgh 9bb1558b71 Update query count ttest 2021-09-14 17:45:09 -04:00
Tadgh bb5e04e706 Fix broken test 2021-09-14 17:22:25 -04:00
Tadgh b25bdc1169 Remove crazy double encoding 2021-09-14 13:48:37 -04:00
Tadgh 9771210553 Prefer non-lazy outcomes in map 2021-09-14 13:40:53 -04:00
Tadgh 49debec36a Fix problem with null conditionals 2021-09-14 10:48:56 -04:00
juan.marchionatto bd456dfff2 Enhance test by adding operations use cases. Improve test data with more version differentiators. 2021-09-14 10:00:15 -04:00
juan.marchionatto 8288d12e97 Obtain current CodeSystem from null-pointed ForcedId, as done for ValueSet 2021-09-14 09:58:32 -04:00
Tadgh 9d982c5e08
Merge branch 'master' into conditional-bug 2021-09-14 08:51:58 -04:00
Tadgh 1ca313f8ad lower logging 2021-09-13 21:27:05 -04:00
Tadgh b4e2679872 Remove jetbrains 2021-09-13 21:15:23 -04:00
Tadgh a0cd83398b Bump test java to 16 2021-09-13 20:52:14 -04:00
Tadgh 3ccadd636e
Merge branch 'master' into 2958-consistent-error-handling 2021-09-13 19:38:57 -04:00
Justin Dar 876768718d Remove log 2021-09-13 11:29:36 -07:00
Justin Dar 3ca73f1067 Merge remote-tracking branch 'origin/2958-consistent-error-handling' into 2958-consistent-error-handling 2021-09-13 11:26:39 -07:00
Justin Dar 46936e1704 Fixed code formatting and better way of fixing issue 2021-09-13 11:26:21 -07:00
Tadgh 5f86370c98 Merge branch 'master' into conditional-bug 2021-09-13 13:04:10 -04:00
Tadgh 59c8765e6a Add implementation to validate conditional URLs post-transaction 2021-09-13 13:03:44 -04:00
Ken Stevens eee7d7e455
code cleanup (#2986) 
* failed attempt to get it to work

* Use simplified FhirContext.forCached methods

* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java

Co-authored-by: James Agnew <jamesagnew@gmail.com>

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2021-09-13 03:09:18 +00:00
James Agnew 5554431146
Avoid dead SearchParameter links in CapabilityStatement (#2790) 
* Avoid dead SearchParameter links in CapabilityStatement

* Resolve fixmes

* Build fix

* Test fix

* Test fix

* Test fix

* Work on metadata

* Fixes

* Test fixes

* Test fix

* Test fix

* Test fixes

* Test fix

* Work on test fixes

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Fix params

* Resolve fixme

* Adjust changelogs

* Version bump to 5.6.0-PRE7

* Add license header

* Bump version to 5.6.0-PRE5-SNAPSHOT
 2021-09-11 18:27:18 -04:00
Tadgh 94f157a4ac Start refactoring of basetransactionprocessor 2021-09-11 15:13:05 -04:00
Tadgh b224463d35 add broken test 2021-09-10 22:46:35 -04:00
jdar8 a02a9e0254
Merge branch 'master' into 2958-consistent-error-handling 2021-09-10 17:02:31 -07:00
Justin Dar 2163e6e548 Fixed error that previous fix caused 2021-09-10 12:36:11 -07:00
Justin Dar 77845d66f7 Improved code formatting 2021-09-10 10:54:33 -07:00
juan.marchionatto 5b6ac3e6d6 Refactor to eliminate duplication 2021-09-10 11:22:04 -04:00
Dušan Markovič d6d862015b Address concerns in review for issue 2975 2021-09-10 15:46:27 +02:00
juan.marchionatto d7fde3f984 Simplify implementation. Add tests. 2021-09-10 09:32:47 -04:00
Dušan Markovič cfc0c7e6b3 Add test for validation of multiple hosts in ElasticsearchHibernatePropertiesBuilder 2021-09-10 11:44:15 +02:00
Dušan Markovič 032a9155f0 Merge branch 'master' of https://github.com/hapifhir/hapi-fhir into issue_2975 2021-09-10 09:11:06 +02:00
Justin Dar 836948010f Fixes issue (#2958) where Procedure?patient caused inconsistent results and ensured that such requests gave http 400 2021-09-09 16:10:09 -07:00
Dušan Markovič ed325e9e11 Enable multiple hosts in ElasticsearchHibernatePropertiesBuilder 2021-09-10 00:14:21 +02:00
Tadgh a4ba65a9fd Don't wrap known errors 2021-09-09 12:27:34 -04:00
Tadgh d5f3b5db18 Merge branch 'master' into fix-batch-pool-breaking 2021-09-09 11:28:44 -04:00
Tadgh 41d5e2b8e7 Add failing test, implementation 2021-09-09 10:50:54 -04:00
Ken Stevens 661ca02a6a revert clobbered code 2021-09-09 09:28:01 -04:00
Dušan Markovič c6aa21b915 Enable empty username and password in ElasticsearchHibernatePropertiesBuilder 2021-09-09 12:55:04 +02:00
Ken Stevens 5bc571d97d fix test 2021-09-09 01:00:12 -04:00
Ken Stevens 519244a2ea unit test passes 2021-09-08 19:14:50 -04:00
Tadgh 0ccd71faf8
Merge pull request #2963 from hapifhir/custom-elastic-index 
Custom elastic index
 2021-09-08 14:29:58 -04:00
Tadgh fbf6b35d2e
Merge branch 'master' into custom-elastic-index 2021-09-08 08:49:26 -04:00
Tadgh 5d5c45e357 Add whitespace 2021-09-08 08:49:19 -04:00
Tadgh f04cf02be7
Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-08 08:45:47 -04:00
Tadgh c2414d2cae Throw error if misconfigured 2021-09-07 18:35:59 -04:00
Tadgh 436c74616b
Merge branch 'master' into custom-elastic-index 2021-09-07 18:19:35 -04:00
Jason Roberts 34075911ce Merge branch 'master' into jr-20210831-contained-chained-search 2021-09-07 17:28:24 -04:00
Jason Roberts 207558dba3 code review feedback 2021-09-07 17:27:22 -04:00
Kevin Dougan SmileCDR 2dcc4f534f
Resolve Search Causing JOINs on HFJ_RESOURCE Checking RES_TYPE and RES_DELETED_AT Columns (#2964) 2021-09-07 19:38:08 +00:00
jamesagnew a3743fbcca Add utility method 2021-09-07 14:21:50 -04:00
Tadgh 3ec47cb0ba Bump version as we break the localcontainerentitymanagerfactory bean constructors args 2021-09-07 13:58:22 -04:00
Tadgh 6a2a5d5097 Merge branch 'master' into custom-elastic-index 2021-09-07 13:56:56 -04:00
Tadgh eabe3e7c74 Merge branch 'master' into custom-elastic-index 2021-09-07 13:56:44 -04:00
Tadgh ecd93c9e8a Add changelog 2021-09-07 13:54:28 -04:00
Tadgh 16752f393c Finalize implementation 2021-09-07 13:33:03 -04:00
leif stawnyczy 4d7f53851c issue-2901 cleanup of code/imports 2021-09-07 12:08:32 -04:00
leif stawnyczy 69287b6bc3 issue-2901 review fixes - moving methods to idhelperservice 2021-09-07 11:52:11 -04:00
Jari Maijenburg d3d7c6e97e
Merge branch 'master' into npe_fix 2021-09-07 17:36:05 +02:00
Nick Goupinets 35aaa98431 Merge branch 'master' into 2849_add_new_mdm_param 2021-09-07 11:27:49 -04:00
Tadgh ca2a1ff9df Add HsTest replicating boot failure 2021-09-07 10:08:17 -04:00
Jason Roberts 190ca7a2b5 tests for longer chains 2021-09-07 09:40:49 -04:00
Tadgh ad5d56172a Return 2 unused beans 2021-09-07 09:11:48 -04:00
Ken Stevens a1733ed3eb cleanup 2021-09-06 13:55:19 -04:00
Ken Stevens 4281648a33 extract some methods for readability 2021-09-06 13:52:10 -04:00
Ken Stevens ea153334fb extract some methods for readability 2021-09-06 13:50:09 -04:00
Tadgh 710fb3bd89 wip 2021-09-05 00:04:13 -04:00
Tadgh f0a8659653 Fix template and setup static prefix as sample 2021-09-04 23:55:03 -04:00
Jari Maijenburg cdb7ffb0d3 Fixed NPE in PidToIBaseResourceProcessor 2021-09-04 01:44:07 +02:00
Nick Goupinets c63a503841 Updated link processing for MDM events 2021-09-03 16:29:26 -04:00
leif stawnyczy 64270a51e0 issue-2901 review fixes 2021-09-03 15:36:42 -04:00
Jason Roberts 0dad28fb33 tidy up 2021-09-03 15:02:19 -04:00
Ken Stevens 346e29920a
Issue 2927 convert mdm clear to spring batch (#2929) 
* initial roughout of mdm clear batch job

* still roughing out classes

* finished first draft of reader

* most tests passing now

* all tests pass.  now FIXMEs

* FIXMEs done.  Time for regression.

* fix test

* changelog and docs

* fix test

* pre-review cleanup

* version bump

* move spring autowire deps for cdr

* move spring autowire deps for cdr

* finally got beans working phew

* rearrange method calls so persistence module can perform clear operation on its own

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* review feedback

* review feedback

* Remove inheritance

* fix beans

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
 2021-09-03 14:58:19 -04:00
Jason Roberts 8a9e4e4328 force the resource table to be the root of the query if we might be traversing a contained reference 2021-09-03 11:26:46 -04:00
Vadim Karantayer b29a61df40 update TestUtil to test Embeddable classes, not just Entity classes 2021-09-03 10:40:54 -04:00
leif stawnyczy 78c71ce761 issue-2901 fix tests 2021-09-03 08:38:19 -04:00
Jason Roberts 5604cabbe8 add tests for qualifiers 2021-09-03 07:45:57 -04:00
Jason Roberts 0edf77d214 clean up a bit 2021-09-03 07:31:49 -04:00
Kevin Dougan SmileCDR fed755523f
Resolve - Avoid JOINs on HFJ_RESOURCE Checking RES_TYPE and RES_DELETED_AT Columns (#2944) 
* Added the start of a new Unit Test.

* Renamed the Unit Test.

* Fleshed out the Unit Test with additional Resource properties.

* Tweaked the Unit Test more but it is still not working as desired so more changes will be needed to replicate the specific scenario...

* More Unit Test tweaks...

* More Unit Test tweaks.

* More tweaks...

* Reproduced the problem.

* Finally, a Failing Unit Test that exposes the problem.

* Fixed the Unit Test by changing how SearchBuilder manipulates underscore params.

* Added another test scenario.

* Added a third search test.

* Removed the third search example since it was not effective.

* Test fix

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-09-03 05:28:04 -04:00
Tadgh 2ed7019a6c Add another test 2021-09-03 00:08:12 -04:00
Frank Tao 8651990cac Fixed class cast issue 2021-09-02 23:04:30 -04:00
Frank Tao 56890dba93 Reformatted the code 2021-09-02 22:26:55 -04:00
Frank Tao be96adb694 Merge branch 'poc-chained-not-bug' into ft-search-with-not-modifier 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderSearchModifierR4Test.java
 2021-09-02 22:07:22 -04:00
Frank Tao b81a61e465 Fixed :not modifier issue for the resource 2021-09-02 21:52:37 -04:00
VK-SMILECDR 39f18e1897
Merge branch 'master' into 2948 2021-09-02 17:24:15 -04:00
Vadim Karantayer c28f5e75b3 update TestUtil to recursively scan down into subpackages 2021-09-02 15:35:40 -04:00
Jason Roberts 9fd2746113 fixed the double chain with contained resource second case 2021-09-02 14:38:30 -04:00
Tadgh 26ff15f939
Revert "Fix search of :not modifier" 2021-09-02 14:33:30 -04:00
Tadgh 6c700f9432 Add POC for failure 2021-09-02 13:33:27 -04:00
leif stawnyczy 6f82e3568c issue-2901 remove debug code 2021-09-02 13:20:38 -04:00
leif stawnyczy 49124c298d issue-2901 fixing test 2021-09-02 13:15:24 -04:00
leif stawnyczy ff7433edd7 issue-2901 cleaning up test contexts 2021-09-02 11:43:12 -04:00
leif stawnyczy cbfcc02a92 issue-2901 removing cruft and cleaning up 2021-09-02 11:07:06 -04:00
leif stawnyczy 1a7b101d03 Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-09-02 10:13:04 -04:00
leif stawnyczy 0286eb5278 issue-2901 updated some documentation and added support for autocreated placeholder / autoversioned references at paths when in transactios and have not been created yet 2021-09-02 09:15:39 -04:00
Tadgh b1d192637d
Merge pull request #2928 from hapifhir/ft-search-with-not-modifier 
Fix search of :not modifier
 2021-09-02 08:41:16 -04:00
Ben Li-Sauerwine 6e389d6f59 Merge branch 'memorycacheservicefix' of https://github.com/theGOTOguy/hapi-fhir into memorycacheservicefix 2021-09-01 15:05:32 -04:00
Ben Li-Sauerwine 0724e652bb Refactor to prevent adding additional signatures to expungeEverythingByType. 2021-09-01 15:04:31 -04:00
Ben Li-Sauerwine 3789bc0f75
Merge branch 'master' into memorycacheservicefix 2021-09-01 13:55:03 -04:00
Jason Roberts 2e2048ce52 Add more test cases, not passing 2021-09-01 13:37:45 -04:00
katie_smilecdr 453ef7ec1c Merge branch 'master' into 2935_Search_with_trailing_percent_sign 2021-09-01 11:33:26 -04:00
Ben Li-Sauerwine 7001272e4b Clear out the memory cache whenever we call the ExpungeEverythingService. 2021-09-01 01:26:47 -04:00
Ben Li-Sauerwine 444bc5f330
Merge branch 'master' into memorycacheservicefix 2021-08-31 20:26:31 -04:00
Ben Li-Sauerwine 51fe5ec5e7 Remove extra update from test. 2021-08-31 20:16:22 -04:00
Frank Tao 44b0d3e9e7
Fixed $lookup with displayLanguage caching issue (#2932) 
* Fixed $lookup with displayLanguage caching issue

* Added changelog and optimized the test cases
 2021-08-31 22:18:40 +00:00
juan.marchionatto 28e3265b6c Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning 2021-08-31 15:52:24 -04:00
katie_smilecdr a1fbeeacaa [2935] Escape "%" in like expression 2021-08-31 15:11:06 -04:00
Ken Stevens c1dc342659 more logs 2021-08-31 15:06:51 -04:00
Ken Stevens ef4adda527 failing tests 2021-08-31 14:53:05 -04:00
Tadgh d75af14d29 Merge branch 'master' into double-conditionalCreateIssue 2021-08-31 14:25:51 -04:00
Tadgh 765b18013c
Merge branch 'master' into fix-intermittent-in-tests 2021-08-31 14:22:22 -04:00
juan.marchionatto 710343a599 Use ForcedId to get current ValueSet version 2021-08-31 13:33:39 -04:00
Tadgh 825ac1e81c Chnge privacy 2021-08-31 12:58:00 -04:00
Tadgh b1515b5963 Lazy load executor so that tests work safely. 2021-08-31 12:57:45 -04:00
Tadgh c9f5dfd6d3 Swap to SyncTaskExecutor 2021-08-31 11:33:06 -04:00
Tadgh 2f6d8c7b35 Revert logging 2021-08-31 10:56:31 -04:00
Tadgh 0f6ae50105 Fix bug in hashToSearchMap 2021-08-31 10:47:23 -04:00
leif stawnyczy a38b791141 issue-2901 added db access method for existence and setting the version to 1 if createplaceholders is true and object does not exist in db 2021-08-31 10:12:40 -04:00
Tadgh 7534ab58f3 Add failing test 2021-08-31 09:58:38 -04:00
Ben Li-Sauerwine f04ff3fd0a Adds failing test for expunging and recreating a Patient with a profile in its meta field. 2021-08-31 02:04:27 -04:00
leif stawnyczy e7c6ce920d issue-2901 checkin to test 2021-08-30 10:29:59 -04:00
Frank Tao 3f128be34d Update the code 2021-08-28 13:29:00 -04:00
Frank Tao 88d535c608 Update the comment 2021-08-28 13:27:40 -04:00
Frank Tao 9bdef1a9fa Fix search of :not modifier 2021-08-28 13:24:09 -04:00
Tadgh 513bc387e9 Remove essentially duplicate bean definition 2021-08-27 13:20:29 -04:00
Tadgh faf4dfd056 fix other test class 2021-08-27 12:04:56 -04:00
Tadgh c2c6e0b440 Force the caller to run the bundle task if we are operating with <= 1 pool size 2021-08-27 12:01:10 -04:00
juan.marchionatto f63f12e976 Use boolean parameter as DAO misinterprets RequestDetails 2021-08-27 10:57:06 -04:00
juan.marchionatto 3fbae63968 Merge master 2021-08-26 13:09:11 -04:00
Tadgh 0304ea2d62 Add requested test 2021-08-26 12:03:00 -04:00
juan.marchionatto 426315f589 Consider last stored ValueSet not necessarily current version anymore. 2021-08-26 10:40:10 -04:00
leif stawnyczy 99cd865174 test 2021-08-26 08:47:45 -04:00
leif stawnyczy 646592b1b7 issue-2901 some refactoring 2021-08-25 15:56:55 -04:00
Frank Tao 090a8b0821
Impl displayLanguage for $lookup (#2908) 
* Impl displayLanguage for $lookup - first cut

* Added original lookupCode method

* Added original lookupCode method to IFhirResourceDaoCodeSystem

* Added more test cases and changelog
 2021-08-25 14:47:10 -04:00
leif stawnyczy b51c722755 stashing minor refactors 2021-08-25 10:41:58 -04:00
Tadgh 37ad73a422 Bump PRE version so we don't conflict downstream 2021-08-23 15:42:18 -04:00
Tadgh 1acaf325c5 Merge branch 'master' into rel_5_5_0 2021-08-23 14:50:29 -04:00
Tadgh ee9c630228 Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-08-23 12:05:31 -04:00
James Agnew 3ebb374059
Avoid redundant resource type selector in _id query (#2909) 
* Fixed

* Add more tests

* Test fixes
 2021-08-23 09:04:51 -04:00
Frank Tao 4c2ae513d8
Process bundle batch in parallel (#2905) 
* Process batch in parallel

* Added a test case

* Added more test cases

* Default the bundle batch to single thread.

* Tried transaction before multi-thread.

* Updated the test cases

* Update based on review comments and add changelog

* Updated the changelog

* Restore QueueCapacity
 2021-08-20 21:14:08 -04:00
Tadgh 3135e82ea7 Strip jetbrains annotations 2021-08-20 18:48:34 -04:00
Tadgh 35440d3b1b
Merge pull request #2900 from hapifhir/bump-hapi-core-for-5-5-0 
Bump hapi core for 5 5 0
 2021-08-20 18:03:29 -04:00
markiantorno f3fe7130c0 flipped case for code validation test 2021-08-20 14:36:37 -04:00
markiantorno 3cfc41f840 updating all convertor calls to not failfast 2021-08-20 14:11:20 -04:00
markiantorno 770b773761 JPA conversion lib fixes 2021-08-20 11:08:14 -04:00
Tadgh c2e3401185 Move display name 2021-08-19 17:25:51 -04:00
Tadgh 3556299332 Add another failing Test 2021-08-19 17:25:15 -04:00
Tadgh 77c99e47c1 TIL that anyString() wont match nulls in Mockito, but any() will 2021-08-19 15:15:51 -04:00
Tadgh 19d181989c Add another failing test 2021-08-19 14:52:48 -04:00
James Agnew 85517c47e2
Include includes on revincludes (#2902) 
* Include includes on revincludes
 2021-08-19 12:31:29 -04:00
Tadgh 07937e4431 Start with failing test 2021-08-19 10:35:14 -04:00
markiantorno 367b338d85 Updating HAPI to use latest core lib changes. 2021-08-18 11:06:14 -04:00
Tadgh 1f7fb52d91 set version map to check all partitions 2021-08-17 16:45:12 -04:00
Tadgh cf917d0f82 Version Bump 2021-08-15 16:54:38 -04:00
Frank Tao 4920f0a15d
Don't create designation of all components are empty (#2891) 
* Don't create designation of all components are empty

* Fixed typo
 2021-08-13 11:01:50 -04:00
Tadgh 669cf05b30 Modify SearchParameterMap toNormalizedQueryString to include value of _contained parameter 2021-08-12 14:25:12 -04:00
juan.marchionatto fb855620da Save version collections also when version is not made current. 
Add test covering bug.
 2021-08-11 12:49:54 -04:00
Tadgh 41ec1e03c0
Merge pull request #2880 from hapifhir/weird-contained-issue 
Contained Issue
 2021-08-11 08:27:54 -04:00
Tadgh e311835e8d Revert test 2021-08-10 18:44:42 -04:00
Tadgh a5c850b119 Pre-review cleaning 2021-08-10 17:37:24 -04:00
Tadgh daa3bc773e remove dummy test 2021-08-10 16:46:03 -04:00
Tadgh fe98162616 Add changelog 2021-08-10 14:59:03 -04:00
Tadgh 71ed25b77c Add commetn for juan 2021-08-10 14:58:47 -04:00
Tadgh 1cb6f490d6 Add dummy test. NOTE, remove before merge 2021-08-10 14:58:38 -04:00
Tadgh 2f42391ba8 wip 2021-08-10 14:58:30 -04:00
Tadgh e402804049 Add test json files 2021-08-10 14:58:24 -04:00
Tadgh 8f200c1819 Add a failing test 2021-08-10 14:58:17 -04:00
Tadgh 35afa8bbfa tidy 2021-08-10 14:57:51 -04:00
Tadgh 4c154951e2 Fully fleshed test, partial refactor 2021-08-10 14:56:57 -04:00
VK-SMILECDR 1e0f843d6c
2852 - Simplify java mail code (#2874) 
* testing

* [2852] adding SimpleJavaEmail

* [2852] refactor email sender code

* [2852] dependency cleanup

* [2852] add missing dependency

* [2852] add missing spring framework test dependency

* [2852] add change log

* [2852] add change log

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2852-simplify-java-mail-code.yaml

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* [2852] minor test code cleanup

* [2852] add more tests

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2021-08-09 15:59:47 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -04:00
Tadgh 0a303a0e11 Add MDM expansion by golden pid 2021-08-06 13:22:08 -04:00
Frank Tao 3c598e2ff8
Fix loinc designation issue with FormalName (#2865) 
* Fix loinc designation issue with FormalName

* Changed Loinc designation name to 'FullySpecifiedName'
 2021-08-06 10:59:01 -04:00
Michael Buckley e8e49f3ffa Pick d85a4e5ec2 for release branch 2021-08-04 16:34:48 -04:00
Michael Buckley d85a4e5ec2 Hack to fix a weird IOOB error we can't reproduce. 2021-08-04 16:08:38 -04:00
juan.marchionatto cb68c59fb5 Remove validation in code which will never reached for the conditions. 2021-08-03 15:39:02 -04:00
juan.marchionatto 45549d2bb9 Fix broken ITs. 
Add error message for non-snapshot upload with current version = false combination.
 2021-08-03 14:11:14 -04:00
juan.marchionatto 1ff1954cba Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control 2021-07-30 11:20:23 -04:00
juan.marchionatto 4e8b1719f3 Add test for fixed use case 2021-07-30 10:48:10 -04:00
Ken Stevens f5dfc3a5ed
New reindex spring batch operation (#2845) 
* first sweep to add new $reindex job

* first cut done.  next up integration test.

* start roughing out reindex everything

* Failing test

* test passes

* add BundleUtil helper method

* rough in processEverything

* rough in processEverything

* fix mock test

* merge master

* Make BaseJpaTest.mySrd lenient.

* fix test

* reindex everything works with FIXMEs

* reindex everything more tests

* moar tests

* moar tests

* fix test

* fix test

* fix regression and fix test

* fix test cycle

* fixme

* fix test

* test provider layer

* reindex everything partition aware

* yay last fixme!

* run reindex in partitioned threads

* add fixmes for areas that require extra testing

* added transaction and log message

* manual integration testing

* changelog

* reindex all partitions

* bump hapi version

* fix test

* moar test

* pre-review cleanup

* fix javadoc

* review feedback

* review feedback

* review feedback

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2845-reindex-operation.yaml

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* review feedback

* review feedback

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/ResourceSearch.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/IDeleteExpungeJobSubmitter.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
 2021-07-29 19:18:49 -04:00
juan.marchionatto 264dfee099 Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control 2021-07-29 16:21:56 -04:00
juan.marchionatto 1fcb36d84a Fix implementation to work also for use case where version is being updated. 
Use property instead of parameter.
 2021-07-29 15:54:00 -04:00
James Agnew f957661dda
Patient ID Partition Mode should support conditional create (#2828) 
* Fixes

* Test fix

* Add changelog

* Test fixes

* Test fixes

* Docs tweak

* Partitioning fixes

* Import fix

* Fix test data
 2021-07-26 14:18:58 -04:00
Ken Stevens 6bbb403fd1
When Client Id Strategy is set to NOT_ALLOWED, permit system requests to create resources (#2827) 
* resolved 2826

* fix regression
 2021-07-23 19:10:19 -04:00
juan.marchionatto ad6f7a204c Fix changelog syntax. Merge current master. 2021-07-22 10:49:16 -04:00
jamesagnew a5e6674e84 Version bump to 5.5.0-PRE7-SNAPSHOT 2021-07-22 08:41:16 -04:00
James Agnew d78fef6732
Fix NPE in IdHelperService (#2819) 2021-07-22 08:34:28 -04:00
IanMMarshall 8b8db82666
Enable Package Loader when partitioning is enabled with unnamed partitions (#2808) 
* Enable Package Loader when partitioning is enabled with unnamed partitions.

* Enable Package Loader when partitioning is enabled with unnamed partitions.

* Additional package loading problems found with partitioning.

* Additional package loading problems found with partitioning.

Co-authored-by: ianmarshall <ian@simpatico.ai>
 2021-07-22 05:17:17 -04:00
James Agnew 6d37749be8
Add non unique combo search params (#2809) 
* Start work on nonunique combo search params

* Work on SQL

* Version bump

* A fix

* Test fixes

* Fixes

* Undo version bump

* Test fixes

* Resolve fixme
 2021-07-21 19:14:14 -04:00
James Agnew 6af022062f
Fix issue with partitioning in patient ID compartment mode (#2810) 
* Fix issue with partitioning in patient ID compartment mode

* Add changelog
 2021-07-21 17:21:23 -04:00
juan.marchionatto e0e52c666c Add current-version parameter to upload-terminology command. 2021-07-21 16:18:35 -04:00
Michael Buckley cbb9a4355a Add details when we fail to load an element of a package definition. 2021-07-19 17:59:54 -04:00
Frank Tao 64f1643046
Added LOINC linguistic variants support (#2803) 
* Added linguistic variants for LOINC uploader

* Using static class

* Added the changelog
 2021-07-19 14:17:56 -04:00
Frank Tao 946080d709
Added ConsumerName to the loinc loader. (#2800) 
* Added ConsumerName to the loinc loader.

* Added extra test for coverage

* Added the changelog for LOINC CONSUMER NAME support
 2021-07-16 13:30:42 -04:00
James Agnew 0235296ba7
Add support for bulk export of multiple types (#2797) 
* Add support for bulk export of multiple types

* Add changelog
 2021-07-15 14:01:10 -04:00
Nick Goupinets ac31000377 Updated docs 2021-07-15 09:13:03 -04:00
Nick Goupinets 520cec1e15 Fixed link resolution 2021-07-14 11:30:09 -04:00
jamesagnew 6d4c2ef8f0 Expand access to SqlQuery 2021-07-08 16:16:27 -04:00
James Agnew d762a07817
Partition patient interceptor (#2766) 
* Start work on interceptor

* Implemented

* Add interceptor and docs

* Add docs

* Compile fix

* Test fixes

* Test cleanup

* Test fixes

* Test fixes

* Improve error message

* Add broken tests

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2766-add-patient-id-compartment-interceptor.yaml

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptor.java

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Address review comments

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2021-07-05 09:15:20 -04:00
jamesagnew 6bb5cbf764 Cleanup logging 2021-07-04 15:31:10 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
Tadgh a770d577cb Initial quick implementation of paging with tests 2021-06-29 17:46:03 -04:00
Ken Stevens 795fb31a3a
fixed mdm rules (#2764) 
* fixed mdm rules

* changelog

* review feedback jetbrains

* review feedback
 2021-06-28 23:24:37 -04:00
Ken Stevens 5565bf9930
fixed an issue with matching compartments to lists of ids (#2761) 
* fixed an issue with matching compartments to lists of ids

* change log
 2021-06-26 20:24:28 -04:00
Ken Stevens ea98e62656
collapse multiple owners for same compartment into shared compartment (#2760) 
* collapse multiple owners for same compartment into shared compartment

* changelog

* fix regression

* fix regression

* pre-review cleanup

* pre-review cleanup
 2021-06-26 11:48:47 -04:00
michaelabuckley 110173dafb
Merge pull request #2757 from hapifhir/2091-MemoryCacheService-confused-expiry 
Fix units on cache expiry
 2021-06-25 14:29:43 -04:00
Michael Buckley b31e464a90 Found bad growing cache scenario 2021-06-25 11:01:41 -04:00
James Agnew 7185089c9d
Add forced offset search JPA interceptor (#2756) 
* Add support for offset searches

* Tests working

* Add changelog

* Test fixes

* Test fix

* More test fixes

* Add commit counter
 2021-06-25 10:40:39 -04:00
Michael Buckley 1367e61c93 changelog 2021-06-24 19:13:54 -04:00
Michael Buckley e74dec1fa6 Fix units on cache expiry 
Added a test to abuse Caffeine
 2021-06-24 19:04:41 -04:00
Josiah 914cf53b62 Merge branch 'master' into 2751-jv-bump-bulk-export-job-request-length 2021-06-24 15:56:05 -04:00
Tadgh 8dcb6053a4 Swap to URI instead of token 2021-06-24 15:48:51 -04:00
Josiah a9208a88da Revert "Version bump" 
This reverts commit 1f5fa70fb6.
 2021-06-24 11:48:31 -04:00
Josiah 1f5fa70fb6 Version bump 2021-06-24 11:22:35 -04:00
Josiah eb0e2e20d7 Bump bulk export request length 2021-06-24 10:17:44 -04:00
Josiah 1ab3d0a159 Bump bulk export request length 2021-06-24 10:10:10 -04:00
jamesagnew 9bc4859761 Add test 2021-06-23 20:55:22 -04:00
jamesagnew 59653759ed Update tests 2021-06-23 15:58:14 -04:00
James Agnew 068de6a708
Test cleanup (#2749) 
* Start work on tag mode 3

* Add changelog

* Test fix

* Test cleanup
 2021-06-22 23:09:03 -04:00
James Agnew 8379392e16
Add inline tag mode (#2748) 
* Start work on tag mode 3

* Add changelog

* Test fix
 2021-06-22 23:08:09 -04:00
Josiah 912b44c3fa
Merge pull request #2734 from hapifhir/2732-bump-conceptmap-group-element-display-storage-size 
Address #2732
 2021-06-21 08:33:36 -04:00
James Agnew 0d0a0fd6a2
Add transaction write semaphore interceptor (#2744) 
* Add transaction write semaphore interceptor

* Add changelog

* Test fix

* Two missing commits on TransactionConcurrencySemaphoreInterceptor

* License header
 2021-06-21 05:38:53 -04:00
jamesagnew f0cfb5ad1b License headers 2021-06-21 05:29:02 -04:00
James Agnew 6ea1438f1d
Add transaction write semaphore interceptor (#2743) 
* Add transaction write semaphore interceptor

* Add changelog

* Test fix
 2021-06-20 12:55:49 -04:00
Ken Stevens 0b05c730fb
don't create a channel if subscriptions are disabled. (#2733) 
* don't create a channel if subscriptions are disabled.

* review feedback

* fix test

* fix intermittent

* fix intermittent
 2021-06-19 00:00:16 -04:00
James Agnew 8b205b23d0
Fix history paging (#2741) 
* Fix history paging

* Add changelog

* Add license header
 2021-06-18 17:47:51 -04:00
Ken Stevens 097a2f70b3
add partition support to $evaluate-measure (#2736) 
* Finished adding partition support to $evaluate-measure

* review feedback
 2021-06-18 14:22:57 -04:00
Josiah 164e684d7c Merge branch 'master' into 2732-bump-conceptmap-group-element-display-storage-size 2021-06-17 15:14:05 -04:00
jamesagnew 5d246bcca8 License header 2021-06-17 14:40:00 -04:00
Josiah 324201b105 Make change 2021-06-17 11:28:02 -04:00
James Agnew 659efa786c
ValueSet Expansion Should Preserve Order (#2724) 
* Add test

* FIxed

* Add changelog

* Add test

* Intermittent test failure fix

* Build fix

* Build fix

* Test fix

* Test fixes

* Fix checkstyle issue

* Test fix

* Add test logging
 2021-06-16 07:20:59 -04:00
Kevin Dougan SmileCDR 6f680af3ce
SearchBuilder NPE (#2726) 
* Add failing test first.

* Fixed the NPE and enhanced the test.

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2021-06-15 11:50:18 -04:00
Ken Stevens 134631fdee
Convert delete expunge to use Spring Batch (#2697) 
* prepare to add $delete-expunge operation that will create a spring batch job

* Add operation

* Wire up jpa provider.  Begin with failing test.

* Copy/paste bulk import job as a starting point.
FIXME with proposed design

* delete expunge job parameter validation with test

* implemented reader
stubbed processor, writer

* wip for master merge

* started implementing reader

* started implementing reader

* working with stubs

* happy path batch delete expunge is done

* Provider done but test not passing.  Guessing batch infrastructure not running in that test.

* IT test works now

* add reader test

* Converted delete _expunge=true to use new batch job

* DeleteExpungeDaoTest passes

* Fix test

* Change batch size to integer

* rename search count to batch size

* Make delete expunge partition aware

* updated docs

* pre-review cleanup

* change log

* add partition id to SystemRequestDetails

* Make RequestPartitionId serializable

* Change delete expunge provider to use partition id instead of tenant name

* fix tests

* test pointcut gets called

* assert on pointcut calls

* Add resource type to STORAGE_PARTITION_SELECTED pointcut

* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants

* bump hapi-fhir version

* copyrights

* restore deleteexpungeservice for mdm

* restore deleteexpungeservice for mdm

* fix test

* public constants

* convert instant to date

* Moved expunge constants to ProviderConstants

* final review

* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run

* fix tests

* fix tests

* fix tests

* fix tests

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

* improve logging

* bump version

* version bump

* recovering from failed merge

* unzip RequestListJson per Gary's suggestion.  I didn't want to do it at first, but as usual Gary was right.

* fix serialization
 2021-06-15 10:36:05 -04:00
jamesagnew 376a84d213 Version bump 2021-06-14 13:12:34 -04:00
James Agnew b934abb297
Impropve transaction Performance (#2717) 
* Work on changes

* Work on perf

* Work on testing

* Work on perf

* Work on perf

* Work on fix

* Work on perf

* Ongoing work

* Add changelog

* Additional docs

* Test fixes

* Address review comments

* Test fix
 2021-06-14 13:08:19 -04:00
jamesagnew 14070914ae Add test 2021-06-14 05:53:22 -04:00
jamesagnew 3ee05b5a62 Refactor transaction processing 2021-06-13 19:42:26 -04:00
jamesagnew 090dc9a2e2 Docs 2021-06-11 15:55:35 -04:00
James Agnew fcb32eacb6
Add support for loinc 2.70 (#2721) 
* Add support for loinc 2.70

* Add changelog
 2021-06-11 15:15:22 -04:00
James Agnew dc627dc019
Add bulk export authorization layer (#2712) 
* Add bulk export authorization layer

* Add docs

* Version bump

* Authorize any

* Add bulk export - all

* Address lgtm issue
 2021-06-06 20:47:43 -04:00
jamesagnew 4f1f09abb1 Merge branch 'master' of github.com:hapifhir/hapi-fhir 2021-06-04 20:40:51 -04:00
jamesagnew 3e4522be86 Add logging 2021-06-04 20:40:40 -04:00
Kevin Dougan SmileCDR 0143e83156
Added another try-with-resources local variable based on a lgtm.com report. (#2711) 2021-06-04 15:17:27 -04:00
jamesagnew 899caa1913 Update transaction service visibility 2021-06-04 14:18:19 -04:00
James Agnew 62be623cf5
Add support for ICD-10-CM (#2702) 
* Add support for ICD-10-CM

* Have this working

* Fix LGTM issues

* Test fix
 2021-06-03 19:55:16 -04:00
Ken Stevens 94d6b15db9
_filter searchparam should not appear in cap stmt if disabled (#2706) 
* issue reproduced and fixed

* changelog

* cleanup
 2021-06-03 18:45:49 -04:00
Ken Stevens c498522c78
search by source reported incorrect size (#2705) 
* issue reproduced in test and fixed

* changelog
 2021-06-03 18:19:43 -04:00
juan.marchionatto 473de64ddc Fix DockerRequiredCondition check. 
Add @RequiresDocker annotation to two tests.
 2021-06-03 14:14:47 -04:00