64aa0feb5d
Fix for issue of persisting blob data types to MS SQL databases.
2020-06-09 11:06:01 -04:00
122bd97344
Changes recommended during code review.
2020-06-09 09:59:03 -04:00
278a1070ae
:Merge branch 'master' into spring-batch-integration
2020-06-08 17:16:11 -07:00
25fa0377df
tidying
2020-06-08 17:02:37 -07:00
864c9c2cb8
Add task executor to partition step
2020-06-08 16:35:15 -07:00
44aa688a20
Final config layout of Bulk Export Batch job
2020-06-08 15:59:08 -07:00
c86e46b196
Add documentation and remove requirement for max parameter (defaulted to 1 now).
2020-06-08 18:08:02 -04:00
30dd858f17
Add close method for Elasticsearch service. Fix the partial code match.
2020-06-08 15:07:02 -04:00
4982e67a0f
Merge remote-tracking branch 'remotes/origin/master' into im_2020601_lastn_code_text_filter
2020-06-08 09:26:55 -04:00
56cbc5149b
Add support for partial code description matching.
2020-06-08 09:24:09 -04:00
4405e50db9
wip
2020-06-05 15:53:06 -07:00
558f419955
Empi 54 not duplicate ( #1900 )
...
add operation to unduplicate persons
2020-06-05 12:21:09 -04:00
5483c99e00
License header updates
2020-06-05 05:47:20 -04:00
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
7ed65b0080
partially done writer, working out size-based chunking
2020-06-04 20:58:06 -07:00
549993886d
Fix merge conflicts.
2020-06-04 17:57:38 -04:00
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
eb7b8e816b
Empi 58 no match create person ( #1898 )
2020-06-04 16:07:50 -04:00
0a2f9d2697
Changes per code review plus fix for possible intermittent JUnit failures.
2020-06-04 15:24:41 -04:00
9696af5dc0
Changed observation indexing to bypass hibernate search and removed Observation index tables.
2020-06-04 13:20:42 -04:00
6e507bf642
Changed observation indexing to bypass hibernate search and removed Observation indexing tables.
2020-06-04 13:10:06 -04:00
7d46b3cc10
Partitioning Based on resource type complete. Still no threading
2020-06-03 14:58:42 -07:00
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
8d5232bced
Merge remote-tracking branch 'remotes/origin/master' into im_2020601_lastn_code_text_filter
2020-06-02 21:28:10 -04:00
e8970bce46
Running batch job
2020-06-02 16:08:19 -07:00
75a74bdd38
License headers
2020-06-02 18:20:56 -04:00
31b7e862d4
Remove extra beans
2020-06-02 15:00:56 -07:00
bb863f26fa
Initial run through the first part of batch integration
2020-06-02 13:44:23 -07:00
bfc5f93ec8
Enable filtering $lastn operation by Observation effective date.
2020-06-02 16:39:06 -04:00
2e709a50c0
Enable filtering $lastn operation by Observation effective date.
2020-06-02 16:37:07 -04:00
f8d699e13b
Initial working commit passing jobs to spring batch
2020-06-01 15:51:09 -07:00
0fc2e04e65
wip
2020-06-01 12:13:55 -07:00
aa7d1cbcb7
Wip getting tasks built
2020-06-01 11:32:36 -07:00
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
a4811f1508
Changes per code review.
2020-05-29 23:47:44 -04:00
a306825625
moving dependencies around. Get non-persisted batch working
2020-05-28 12:10:52 -07:00
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
81d5ff8f5a
Add schema initialization
2020-05-27 17:06:52 -07:00
22af36ae7b
Conditional update on Partitioned Server fails ( #1870 )
...
* Fix #1869
* Remove FIXME
* Test fix
* Test fix
2020-05-27 10:40:29 -04:00
5cc77b78d4
Fixed problems with results of chunked queries being incorrectly sorted.
2020-05-26 18:09:54 -04:00
5482367e37
Remove redundant index - Already covered by FK
2020-05-26 08:54:00 -04:00
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
1e554731bb
Additional cleanup and test fixes.
2020-05-25 18:25:25 -04:00
6ed724e01b
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
2020-05-25 17:40:53 -04:00
2bcfe7cdaa
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2020-05-25 13:20:59 -04:00
bf550f9c27
License header updates
2020-05-25 13:20:32 -04:00
535bf88efe
Fixes to diff operation ( #1866 )
2020-05-25 13:16:58 -04:00
ee87a2e2d0
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
2020-05-25 11:37:34 -04:00
816f409a8a
Re-factor lastn entities to locate them is same package as other Search Parameter entities.
2020-05-25 11:37:01 -04:00
3807640347
Resolve merge conflict
2020-05-24 11:38:52 -04:00
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
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
35b75f8ffb
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
2020-05-23 15:54:23 -04:00
e780a8402e
Use R5 snapshot generator ( #1862 )
...
* Use R5 snapshot generator
* Snapshot generator reworking
2020-05-23 12:54:19 -04:00
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
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
a1a3d9de38
Merge branch 'master' into im_20200520_cascade_delete
2020-05-22 16:11:38 -04:00
d1b963321a
MVP EMPI implementation ( #1857 )
...
EMPI Initial Implementation (still plenty of known gaps)
2020-05-22 15:03:20 -04:00
b501a601b7
Some final cleanup minor updates.
2020-05-22 13:36:08 -04:00
a60e5809b2
Changes to enable adjusting limits on delete conflict handling through configuration.
2020-05-22 10:15:04 -04:00
5ba7f1525f
Test fix
2020-05-21 20:38:11 -04:00
63ff0ede9c
Make diff operation work securely ( #1859 )
...
* Make diff operation work securely
* Build tweak
* FIx tests
2020-05-21 19:20:48 -04:00
ce5ade53d9
Fix #1855 - StructureDefinition search not working ( #1858 )
2020-05-21 09:35:37 -04:00
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
b044d05332
Add a disabled test
2020-05-20 17:26:24 -04:00
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
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
3b7f106052
Fixed latest merge conflicts.
2020-05-19 16:34:05 -04:00
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
6a27192a96
Fixed sorting with chunked and paged queries.
2020-05-19 14:48:26 -04:00
cc92bd7b07
Revert "Start working on FHIRPatch"
...
This reverts commit b3f6e7d521
2020-05-17 11:56:50 -04:00
b3f6e7d521
Start working on FHIRPatch
2020-05-17 11:44:06 -04:00
52c8e3551c
Version bump to 5.1.0-SNAPSHOT
2020-05-15 14:43:32 -04:00
fe0e07a313
Bump to 5.0.1
2020-05-15 05:47:01 -04:00
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
529e1e1f5e
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
2020-05-14 12:09:24 -04:00
eb1d1c2b27
Changes to better support chunking of queries and paging of results for lastn operation and to monitor performance.
2020-05-14 12:08:55 -04:00
1d13e29ac0
Version bump to 5.1.0-SNAPSHOT
2020-05-12 20:04:20 -04:00
d631ecff4a
Prepare for 5.0.0
2020-05-12 11:49:18 -04:00
0c13a65871
Bump to latest Core version ( #1841 )
...
* Start working on bumping core
* Work on tests
* Work on tests
* Bump core definitions
* Bump R5 defs
* Tweak changelog
* Test fix
2020-05-11 12:37:16 -04:00
9d8bd0d51e
Bump R4 definitions to 4.0.1 ( #1837 )
...
* Bump R4 definitions to 4.0.1
* Add changelog
* Test fixes
2020-05-08 19:34:13 -04:00
8fcdc78077
Fix issues resulting from latest merge.
2020-05-08 09:31:05 -04:00
e56cb049f7
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
2020-05-08 09:19:44 -04:00
c290fa3493
Fixes to enable $lastn to return more than 32K records.
2020-05-08 09:19:14 -04:00
6cc07b6689
Make binary storage work for bulk export ( #1836 )
...
* Make binary storage work for bulk export
* Add changelog
* Build fixes
* Test fix
* Test fix
* Test fix
2020-05-07 19:20:22 -04:00
b67509d7ff
Transaction write performance fix ( #1832 )
...
* Performance fix for transactions
* Test fix
* Fixes
* Add docs
* Test fixes
2020-05-07 10:56:41 -04:00
4cced40b54
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
2020-05-05 17:19:32 -04:00
4db5beeabf
Additional changes to enable processing of lastn operations with large numbers of parameters.
2020-05-05 16:53:47 -04:00
a77aa6a28e
Multitenancy Ticket 2 - #1813 ( #1821 )
...
* Work on multitenancy
* Second ticket started
* More multitenancy work
* Work on tenancy security
* Work on multitenancy
* Test fixes
* Add docs
* cs tweak
* Multitenancy fixes
* Add debug log
* Fix build
* Add headers
* Add partition selection interceptor hook
* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Account for review comments
* Resolve FIXMES
* Work on tests
* Test fixes
* A bit more cleanup
* Work on multitenancy
* Update hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientExamples.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Allow disabling text modifier indexing
* Add changelog
* Docs fixes
* Address review comment
* Resolve merge conflicts
* Merge master
* Compile fix
* Test fix
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-05-05 15:12:15 -04:00
35c2b7a2c1
Allow disabling text modifier indexing ( #1831 )
...
* Allow disabling text modifier indexing
* Add changelog
* Address review comment
* Resolve merge conflicts
2020-05-05 12:16:55 -04:00
dada217966
Clean up hash code calculation ( #1830 )
...
* Clean up hash code calculation
* Test fixes
* Test fix
* Test fixes
* Compile fix
* Test fix
2020-05-05 11:11:24 -04:00
91147cf6b0
Scope tag search to correct resource type ( #1829 )
...
* failing _tag tests
* cleanup
* Scope tag query to correct resource type
* Changelog
* Test fix
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-05-05 11:09:46 -04:00
41056092ed
License header updates
2020-04-30 18:24:07 -04:00
8f8a8a3dc2
Merge branch 'master' into date-match-bug
2020-04-29 16:17:50 -07:00
e439891ea2
Add test
2020-04-29 15:21:54 -04:00
3e49e5615f
Fixing merge conflicts after merge from Master.
2020-04-25 22:14:55 -04:00
dd749791db
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
2020-04-24 16:55:45 -04:00
0e45db0ba9
More cleanup and test fixes.
2020-04-24 16:23:59 -04:00
e219c1774b
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2020-04-24 05:45:26 -04:00
ededcc18d2
Add Partitioning / Multitenancy ( #1807 )
...
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* Add columns
* Work on multitenancy
* Work on muiltitenancy
* Work on multitenancy
* Work on uniques
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* More work on multitenancy
* Work on multitenancy
* Multitenancy work
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* Work on multitenancy
* Work on docs
* Work on multitenancy
* Work on docs
* DOcs work
* Tenancy docs
* Work on docs
* Finish docs
* Add changelog
* Rename config
* Add migration tasks
* Fix typo
* Migration fix
* One more migration fix
* A couple more migration fixes
* Docs cleanup
* Work on docs
* Bump boot version
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Work on review comments
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/partitioning.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
Co-Authored-By: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Compile fx
* Test fixes
* One more bugfix
* Update operation name
* Add one more constant
* Roll back a change that was causing test failures
* Test fixes
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-04-24 05:45:11 -04:00
ianmarshall
Tadgh
Ken Stevens
jamesagnew
Martin Zacho Grønhøj
Jacob Stampe Mikkelsen
IanMMarshall
Tadgh