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6426 Commits

Author SHA1 Message Date
ianmarshall 6ed724e01b Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-25 17:40:53 -04:00
jamesagnew 2bcfe7cdaa Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-05-25 13:20:59 -04:00
jamesagnew bf550f9c27 License header updates 2020-05-25 13:20:32 -04:00
James Agnew 535bf88efe
Fixes to diff operation (#1866) 2020-05-25 13:16:58 -04:00
ianmarshall ee87a2e2d0 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-25 11:37:34 -04:00
ianmarshall 816f409a8a Re-factor lastn entities to locate them is same package as other Search Parameter entities. 2020-05-25 11:37:01 -04:00
jamesagnew 3807640347 Resolve merge conflict 2020-05-24 11:38:52 -04:00
jamesagnew 6a4f5b9b3a Credit for #1826 2020-05-24 09:32:44 -04:00
Martin Zacho Grønhøj 9bde517540
Install external ig package at startup (#1826) 
* Do not use deprecated methods in structures-r4 test

* beginning development of feature Implementation Guide installer

* fetch IG, generate snapshots of SDs of and persist conformance resources to db

Missing initialization, error-handling and handling of NameSystems and Subscriptions

* Refactor IgInstaller and implement support for R4 and R5

* Error handling and removed logic for invoking IG installation

IgInstaller should be invoked by applications

* Implement pull request comments in IgInstaller

1) Renamed IgInstaller -> IgInstallerSvc for consistency
2) Use field autowiring and @PostConstruct for consistency
3) Use exceptions instead of boolean flags for success indication
4) Use IValidationSuport to generate snapshots of StructureDefinitions
in a version independent way (less maintenance) instead of SnapshotGenerator.java
5) Read IGs for tests from src/main/resources instead of external URL

* IG installation: Wrap exceptions during resource creation in custom class

* IG installation: Improved logging

* IG installation: Search for existing resources in a version independent way
 2020-05-24 09:25:46 -04:00
jamesagnew c97ef7adfc A bit more contributors cleanup 2020-05-23 19:45:00 -04:00
jamesagnew 3bf0628436 Updatyes to devs list 2020-05-23 19:17:33 -04:00
jamesagnew d24f075cdb Update some orgs 2020-05-23 17:22:59 -04:00
jamesagnew b60404dbb8 Credit for #1849 2020-05-23 17:18:37 -04:00
Craig Appl 098c3ad737
Fixing a typo in the performance.md server_jpa doc (#1849) 2020-05-23 17:17:51 -04:00
jamesagnew 9192d41448 Credit for #1637 2020-05-23 17:16:19 -04:00
Jacob Stampe Mikkelsen 262a964a31
Add index on CONCEPT_PID on TRM_CONCEPT_PROPERTY to optimize a full-reindex of lucene index which can be needed when running in a docker container where the lucene files are discarded on redeploy. (#1637) 
Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-05-23 17:11:21 -04:00
ianmarshall 35b75f8ffb Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-23 15:54:23 -04:00
James Agnew e780a8402e
Use R5 snapshot generator (#1862) 
* Use R5 snapshot generator

* Snapshot generator reworking
 2020-05-23 12:54:19 -04:00
James Agnew c374383b37
Allow AuthorizationInterceptor to properly authorize GraphQL statements (#1864) 
* Allow AuthorizationInterceptor to properly authorize GraphQL statements

* Add changelog
 2020-05-22 20:40:37 -04:00
ianmarshall 4d378ee0ed Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
#	hapi-fhir-jpaserver-base/pom.xml
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java
 2020-05-22 17:04:01 -04:00
IanMMarshall 12f80b3da5
Merge pull request #1863 from jamesagnew/im_20200520_cascade_delete 
Im 20200520 cascade delete
 2020-05-22 16:17:08 -04:00
IanMMarshall a1a3d9de38
Merge branch 'master' into im_20200520_cascade_delete 2020-05-22 16:11:38 -04:00
jamesagnew 056721829d License header updates 2020-05-22 15:56:14 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857) 
EMPI Initial Implementation (still plenty of known gaps)
 2020-05-22 15:03:20 -04:00
IanMMarshall 612fb215d6
Update hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java 
Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-05-22 13:50:42 -04:00
IanMMarshall 51604dab2c
Update hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java 
Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-05-22 13:50:35 -04:00
IanMMarshall 44869856da
Update hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java 
Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-05-22 13:50:24 -04:00
ianmarshall 6a5c23c36b Adding a proposed change log. 2020-05-22 13:45:17 -04:00
ianmarshall b501a601b7 Some final cleanup minor updates. 2020-05-22 13:36:08 -04:00
ianmarshall a60e5809b2 Changes to enable adjusting limits on delete conflict handling through configuration. 2020-05-22 10:15:04 -04:00
jamesagnew e22549e0c4 Bump MySQL JDBC driver version 2020-05-21 21:21:13 -04:00
jamesagnew 5ba7f1525f Test fix 2020-05-21 20:38:11 -04:00
jamesagnew 8ff7d5407a Bump core version 2020-05-21 19:22:28 -04:00
Ken Stevens 2360ed4abe
fix build (#1861) 2020-05-21 19:22:08 -04:00
James Agnew 63ff0ede9c
Make diff operation work securely (#1859) 
* Make diff operation work securely

* Build tweak

* FIx tests
 2020-05-21 19:20:48 -04:00
James Agnew ce5ade53d9
Fix #1855 - StructureDefinition search not working (#1858) 2020-05-21 09:35:37 -04:00
James Agnew e07e071130
Avoid deserialization issues in subscription delivery (#1856) 
* Avoid deserialization issues in subscription delivery

* Add changelog
 2020-05-21 05:47:39 -04:00
James Agnew 5b2181a563
Implement FHIR Patch (#1850) 
* Start working on FHIRPatch

* More work on fhirpatch

* Work on FHIR Patch

* Add patch

* Test fixes

* Test fixes

* Get tests fixed

* Chnage to trigger a build

* Compile fix

* Dependency version fixes

* Test fix

* COmpile fix

* Try to fix build

* Test fix attempt

* Another build attempt

* Another build tweak

* Cleanup
 2020-05-20 19:43:55 -04:00
jamesagnew b044d05332 Add a disabled test 2020-05-20 17:26:24 -04:00
James Agnew 9aaf5ccd63
Fix expunge when using unique search param (#1854) 
* Fix expunge when using unique search param

* Add chaneglog
 2020-05-20 15:58:53 -04:00
jamesagnew 8ab80e3529 Credit for #1853 2020-05-20 10:54:38 -04:00
Tue Toft Nørgård 2f48c7d7fe
Make @Interceptor @Inherited so InterceptorService.determineOrder accepts Spring proxies of @Interceptor annotated classes. (#1853) 
See https://groups.google.com/forum/#!topic/hapi-fhir/7Z_FKDBTJSE
 2020-05-20 10:52:56 -04:00
James Agnew c9c90b327c
Allow no read interceptor for partition (#1851) 
* Allow no read interceptor for partition

* Add changelog

* Test fix
 2020-05-19 17:06:56 -04:00
ianmarshall 645a0d3681 Removing extra file that was mistakenly committed. 2020-05-19 16:37:40 -04:00
ianmarshall 3b7f106052 Fixed latest merge conflicts. 2020-05-19 16:34:05 -04:00
ianmarshall d2b54d6203 Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
 2020-05-19 15:20:06 -04:00
ianmarshall 6a27192a96 Fixed sorting with chunked and paged queries. 2020-05-19 14:48:26 -04:00
jamesagnew f3c023bb6f Tweak to test data builder 2020-05-19 09:18:59 -04:00
jamesagnew cc92bd7b07 Revert "Start working on FHIRPatch" 
This reverts commit b3f6e7d521.
 2020-05-17 11:56:50 -04:00
jamesagnew b3f6e7d521 Start working on FHIRPatch 2020-05-17 11:44:06 -04:00