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2824 Commits

Author SHA1 Message Date
ianmarshall
549993886d Fix merge conflicts. 2020-06-04 17:57:38 -04:00
ianmarshall
78b7f091ec Merge remote-tracking branch 'remotes/origin/master' into im_2020601_lastn_code_text_filter 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcMultipleObservationsIT.java
 2020-06-04 16:55:18 -04:00
Ken Stevens
eb7b8e816b
Empi 58 no match create person (#1898) 2020-06-04 16:07:50 -04:00
ianmarshall
0a2f9d2697 Changes per code review plus fix for possible intermittent JUnit failures. 2020-06-04 15:24:41 -04:00
ianmarshall
9696af5dc0 Changed observation indexing to bypass hibernate search and removed Observation index tables. 2020-06-04 13:20:42 -04:00
ianmarshall
6e507bf642 Changed observation indexing to bypass hibernate search and removed Observation indexing tables. 2020-06-04 13:10:06 -04:00
Tadgh
7d46b3cc10 Partitioning Based on resource type complete. Still no threading 2020-06-03 14:58:42 -07:00
James Agnew
86ef0ec0e2
Correct transaction processing in multitenant server (#1884) 
* Correct transaction processing in multitenant server

* # d codethe npm registry for updates every day (weekdays)
 2020-06-03 10:37:47 -04:00
ianmarshall
8d5232bced Merge remote-tracking branch 'remotes/origin/master' into im_2020601_lastn_code_text_filter 2020-06-02 21:28:10 -04:00
Tadgh
e8970bce46 Running batch job 2020-06-02 16:08:19 -07:00
jamesagnew
75a74bdd38 License headers 2020-06-02 18:20:56 -04:00
Tadgh
31b7e862d4 Remove extra beans 2020-06-02 15:00:56 -07:00
Tadgh
bb863f26fa Initial run through the first part of batch integration 2020-06-02 13:44:23 -07:00
ianmarshall
bfc5f93ec8 Enable filtering $lastn operation by Observation effective date. 2020-06-02 16:39:06 -04:00
ianmarshall
2e709a50c0 Enable filtering $lastn operation by Observation effective date. 2020-06-02 16:37:07 -04:00
Tadgh
f8d699e13b Initial working commit passing jobs to spring batch 2020-06-01 15:51:09 -07:00
Tadgh
0fc2e04e65 wip 2020-06-01 12:13:55 -07:00
Tadgh
aa7d1cbcb7 Wip getting tasks built 2020-06-01 11:32:36 -07:00
ianmarshall
f48214deda Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 
# Conflicts:
#	hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
 2020-05-29 23:54:11 -04:00
ianmarshall
a4811f1508 Changes per code review. 2020-05-29 23:47:44 -04:00
Tadgh
a306825625 moving dependencies around. Get non-persisted batch working 2020-05-28 12:10:52 -07:00
James Agnew
7f72305f57
Improve Period range indexing (#1873) 
* Fix #1871 - Handle period range searches better

* Add changelog

* FIx tests

* Add test logging

* Address review comments
 2020-05-28 08:56:43 -04:00
Tadgh
81d5ff8f5a Add schema initialization 2020-05-27 17:06:52 -07:00
James Agnew
22af36ae7b
Conditional update on Partitioned Server fails (#1870) 
* Fix #1869

* Remove FIXME

* Test fix

* Test fix
 2020-05-27 10:40:29 -04:00
ianmarshall
5cc77b78d4 Fixed problems with results of chunked queries being incorrectly sorted. 2020-05-26 18:09:54 -04:00
jamesagnew
5482367e37 Remove redundant index - Already covered by FK 2020-05-26 08:54:00 -04:00
James Agnew
6899604ae4
Correct validation of fragment codesystems (#1865) 
* Update validation for fragment codesystem

* Test fixes

* Add changelog

* Test fix
 2020-05-25 20:44:09 -04:00
ianmarshall
1e554731bb Additional cleanup and test fixes. 2020-05-25 18:25:25 -04:00
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
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
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
a1a3d9de38
Merge branch 'master' into im_20200520_cascade_delete 2020-05-22 16:11:38 -04:00
Tadgh
d1b963321a
MVP EMPI implementation (#1857) 
EMPI Initial Implementation (still plenty of known gaps)
 2020-05-22 15:03:20 -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
5ba7f1525f Test fix 2020-05-21 20:38:11 -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
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