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2613 Commits

Author SHA1 Message Date
Ken Stevens 558f419955
Empi 54 not duplicate (#1900) 
add operation to unduplicate persons
 2020-06-05 12:21:09 -04:00
jamesagnew 5483c99e00 License header updates 2020-06-05 05:47:20 -04:00
James Agnew 21330a0a22
Transaction create performance improvement (#1899) 
* Work on perf issue

* Improve write performance for large bundles with tags

* Add changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1899-improve-write-xact-perf-with-tags.yaml

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Test fix

* Test fixes

* Test fixes

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
 2020-06-05 05:26:06 -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
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
jamesagnew 75a74bdd38 License headers 2020-06-02 18:20:56 -04:00
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
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
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
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
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 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 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
jamesagnew 52c8e3551c Version bump to 5.1.0-SNAPSHOT 2020-05-15 14:43:32 -04:00
jamesagnew fe0e07a313 Bump to 5.0.1 2020-05-15 05:47:01 -04:00
James Agnew 79a064dfd9
Optimize chain sql paths (#1844) 
* Start cleanup

* Almost workinf

* Possibly working!!

* Fixes

* Test fix

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootStack.java

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

* Address review comments

* Add changelog

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-05-15 05:36:12 -04:00
ianmarshall 529e1e1f5e Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch 2020-05-14 12:09:24 -04:00