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109 Commits

Author SHA1 Message Date
James Agnew 201ec34db4
Fix expunge issue when no tags present (#1671) 
* Fix expunge issue when no tags present

* Add changelog

* Try to clean up POMs that are failing CI

* Rework dependencies

* Roll back change that did not work
 2020-01-15 14:47:22 +08:00
James Agnew 1390ea3c06
Update FHIR R5 structures to 4.2.0 version (#1665) 
* Work on upgrading core

* Work on R5 updates

* Work on core updates

* Test fix

* Update model version properties file for R5

* Bump core version

* Test fixes

* Add 4.2.0-SNAPSHOT version to versions page in docs
 2020-01-14 10:27:01 +08:00
jamesagnew 9c7f5e1b9b License header updates 2020-01-12 10:15:08 -05:00
jamesagnew 6fc0bdb88f Add licene headers 2019-12-16 11:14:17 -05:00
Ken Stevens 2f89f10c64 allow users to set default group 2019-12-04 17:23:51 -05:00
Ken Stevens f29118fa9c move clustered quartz from cm db to pers db 2019-12-02 14:32:34 -05:00
Ken Stevens 993d8220d1 review feedback 2019-12-02 11:18:52 -05:00
Ken Stevens 959dba7611 pre review cleanup 2019-12-01 16:51:01 -05:00
Ken Stevens 321790f6bf standardized job names and how they're scheduled 2019-11-29 10:12:13 -05:00
Ken Stevens a0e363171d replace FireAtInterval class with an interface for now 2019-11-29 09:21:20 -05:00
Ken Stevens f450cea9a5 disable gap time for now 2019-11-28 17:57:52 -05:00
Ken Stevens 6f9cd56c81 moved scheduler up to hapi-server 2019-11-20 14:30:24 -05:00
Ken Stevens 8fca468e1f remove boolean from scheduling API 2019-11-19 10:13:22 -05:00
James Agnew 74159dcb26
Work on refactoring how PIDs work (#1580) 
* Start work on refactoring how PIDs work

* Some test fixes

* Test fixes

* Test fixes

* Restore accidentally deleted line

* One more tweak

* Rework resource link extraction

* Test fix

* Split out transaction processor

* Updates

* Test fix

* Test fixes

* Test fixes

* Clean up LGTM warning

* Fix compile failure

* One more test fix

* Fix LGTM issue

* Add spot for metadata

* Add test logging

* Remove testing code

* More test logging

* Add some test logging

* Attempty to fix intermittent test failure

* Improve exception tracking

* Work on simplifying search param registry

* Fix compile

* Fix compile errors

* Fix two test bugs
 2019-11-17 14:35:19 -05:00
James Agnew b90f285218 Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-30 08:41:14 -04:00
James Agnew 007cfaf00e
Don't error out on missing CS (#1570) 
* Don't error out on mi9ssing CS

* Add tests

* Add a bit of test coverage

* One more test
 2019-10-30 08:38:39 -04:00
James Agnew 817f9ae36e Merge branch 'master' into ja_20190928_rationalize_search_param_extractor 2019-10-27 17:25:20 -04:00
James Agnew 6580c98ed7 Work on extractor 2019-10-26 16:56:12 -04:00
James Agnew 385a885abf Add ability for resource source to be specified by header 2019-10-24 08:32:52 -04:00
James Agnew 464c6c5b45
Upgrade dependencies and addess Semmle issues (#1554) 
* Version bumps

* FIx build issues

* Address a few Semmle issues

* Work on tests

* Some test fixes

* Test fix

* Fix deletions

* Test fix

* Fix intermittent test failure

* One more dependency bump

* Add some test logging

* Remove bad import

* Add some tests

* Test updates
 2019-10-22 17:10:58 -04:00
James Agnew 8b2ab51bc6
Handle canonical questionnaire refs in validator (#1544) 
* Handle canonical questionnaire refs in validator

* FIx changelog

* Fix canonical reference

* Build tweak

* Change to trigger a build
 2019-10-15 20:27:53 -04:00
James Agnew bf476b9c32 Handle null returns from search cache methods 2019-10-15 16:25:21 -05:00
James Agnew e656863a73
Correct bugs reported by LGTM (#1533) 
* Correct bugs reported by LGTM

* Add some tests

* A few more updates

* YAML update

* Test fixes

* One more test fix

* Test fix
 2019-10-09 19:26:57 -05:00
James Agnew a3b9db1363 Clean up a few unused methods and move test classes into test project 2019-10-03 14:58:02 -04:00
James Agnew ac08f632ae Increase visibility of constant 2019-10-03 12:31:31 -04:00
James Agnew b5e7e305c1 Remove a few unused methods 2019-10-03 08:35:11 -04:00
James Agnew 260cee023a Account for longer resource type names 2019-10-02 10:00:45 -04:00
James Agnew a1bf50685d Work on cleanup 2019-09-30 21:40:41 -04:00
jamesagnew 6475146bc9 Add license headers 2019-09-19 18:08:21 -04:00
James Agnew 2be63a1650 Test fixes 2019-09-19 09:45:07 -04:00
James Agnew 4a751cbfc5
Integrate Bulk Export (#1487) 
* Start working on subscription processor

* Work on new scheduler

* Test fixes

* Scheduler refactoring

* Fix test failure

* One more test fix

* Updates to scheduler

* More scheduler work

* Tests now all passing

* Ongoing work on export

* Ongoing scheduler work

* Ongoing testing

* Work on export task

* Sync master

* Ongoing work

* Bump xml patch version

* Work on provider

* Work on bulk

* Work on export scheduler

* More test fies

* More test fixes

* Compile fix

* Reduce logging

* Improve logging

* Reuse bulk export jobs

* Export provider

* Improve logging in bulk export

* Work on bulk export service

* One more bugfix

* Ongoing work on Bulk Data

* Add changelog
 2019-09-17 16:01:35 -04:00
Ken Stevens 1ca0e7bd53 anylist r5 support 
also added another accessor
 2019-09-04 21:15:08 -04:00
jamesagnew 8b09b3f3eb Rename config enum for consistency 2019-09-03 07:01:36 -04:00
James Agnew 9428430822
Add support for Resource.meta.source (#1438) 
* Work on indexing source

* Work on tests

* Refactor query count tests

* Unit test fixes

* Add some tests

* DAO fix

* Fix compile error

* Unit test fix

* Cleanup

* Test fix

* Fix compile error

* One more test fix
 2019-08-21 11:17:43 -04:00
jamesagnew 3e95ff3ca0 Licence header updates 2019-08-08 16:22:08 -04:00
James Agnew 2518d4e0be Add some tests 2019-08-08 15:23:55 -04:00
Ken Stevens f1d3fc2307 Changed Stopwatch getThroughput param from int to long 
Added FhirVersion accessor to AnyListResource
 2019-08-01 06:32:09 -04:00
James Agnew a4ca5374ec
Add terminology delta operations (#1401) 
* Start work on delta operations

* Add changelog

* Some build fixes

* Move upload terminology command to CodeSystem resource

* Updates

* Some test fixes

* Add changelog

* Some test fixes

* More test fixes

* Test fix

* Add additional tests

* Transaction boundary fixes
 2019-07-29 17:46:42 -04:00
Ken Stevens 8d86e34bcf Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
 2019-07-23 09:12:08 -04:00
jamesagnew 60ea922e8d Add license headers 2019-07-23 05:38:10 -04:00
James Agnew 7e3d062d15
Switch default client to JSON (#1392) 
* Start work on changing over

* Update tests

* More test fixes

* Work on generalizing binary access provider a bit

* Add expunge capability to binary storage, and also support actual binary
resources

* Work on binary provider

* Get the DB bound binary storage service working

* Test fixes

* Compile fix

* Fix compile error

* Test fix

* Test tweak

* Trying to figure out an intermittent failure

* Work on tests

* More work on tests

* Another test fix
 2019-07-22 21:27:10 -04:00
Ken Stevens 72aa4932d6 Merge remote-tracking branch 'remotes/origin/master' into expunge-resource-hook 2019-07-18 10:12:15 -04:00
jamesagnew 7488047686 Add license headers 2019-07-17 18:53:23 -04:00
James Agnew 55c0d5b604
Add binary storage for Attachments (#1386) 
* Have this working now

* Add utility method

* Build fixes

* Add changelog
 2019-07-17 18:31:17 -04:00
Ken Stevens fe21dba4a6 Added Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE. 
Also added a couple of tests.
 2019-07-17 13:26:50 -04:00
James Agnew 120b93f204
Use HL7 FHIR Core Structures (#1382) 
* Ongoing work on core structures suport

* Ongoing work on this merge

* Ongoing work to clean up structures

* Credit for #1179

* Address compile issues

* Latest changes

* Work on parallel execution

* Work on getting tests passing

* Add H2 to migrator

* Test fix
 2019-07-14 10:16:40 -04:00
James Agnew ba4bb005bc
Switch JPA unit tests to use H2 (#1381) 
* Start working on this

* Ongoing fixes to H2 branch

* Work on fixing tests

* Updated fixes

* Some test fixes

* More work on H2 migration

* Fixes to try and get the H2 migration building

* Test seem to be passing!

* Tweaks to locale randomization

* Add changelog
 2019-07-13 17:22:43 -04:00
James Agnew 4bd60a8447 Roll back one dependency 2019-07-07 11:02:08 -04:00
jamesagnew dff2fdd3cf GET RID OF TRAILING LICENSE HEADER SPACES ONCE AND FOR ALL 
YESSSSSSSSSSSSS
 2019-07-05 11:19:51 -04:00
jamesagnew cdb0006a5b Correct version of license plugin 2019-07-05 09:38:31 -04:00