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2824 Commits

Author SHA1 Message Date
ianmarshall
5bf1e94a23 Fix to accomodate MySQL and MariaDB. 2020-06-19 17:26:45 -04:00
James Agnew
46c00f4efb
Update for Loinc 2.68 (#1917) 
* Work on loinc updates

* Work on loinc upload

* Clean up CLI config

* Add changelog

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java

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

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java

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

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java

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

* Clean up imports

* LOINC fixes

* Loinc loader fixes

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
 2020-06-18 16:55:11 -04:00
James Agnew
b6540064ea
Improve TX scoping for validation (#1925) 
* Improve TX scoping for validation

* Test fix

* Test fix

* Some cleanup

* Test fixes

* Test fix
 2020-06-17 14:04:12 -04:00
Tadgh
d32ad74402 some renaming 2020-06-15 21:49:34 -07:00
Tadgh
9222fa3f59 change transaction call 2020-06-15 15:17:25 -07:00
Tadgh
eccd280d71 Fix test error 2020-06-15 11:24:39 -07:00
Tadgh
798fdb9cc2 Merge branch 'master' into spring-batch-integration 2020-06-15 09:10:41 -07:00
jamesagnew
ac0d8c0fe1 Test fixes 2020-06-14 15:32:50 -04:00
Tadgh
4270636d43 Merge branch 'master' into spring-batch-integration 2020-06-12 16:20:54 -07:00
Tadgh
928aafba1e Rename bean 2020-06-12 16:18:04 -07:00
Tadgh
0f469c1a56 Rework to allow for job creation inside of batch 2020-06-12 14:20:50 -07:00
James Agnew
622659cbb3
Add type parameter to resource reindexing operation (#1921) 
* Add type parameter to resource reindexing operation

* Add changelog

* CLean up reindexing
 2020-06-12 16:51:18 -04:00
Tadgh
a9c704c06e Merge branch 'master' into spring-batch-integration 2020-06-10 12:24:19 -07:00
Tadgh
4e42a59ad4 Add licenses 2020-06-10 11:52:45 -07:00
Tadgh
d698ad7180 Code review comments 2020-06-10 10:46:28 -07:00
jamesagnew
d521dc61cc Package fix 2020-06-10 11:59:37 -04:00
jamesagnew
7d6f8fe612 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2020-06-10 09:57:24 -04:00
jamesagnew
05df4f0827 Migration task updates 2020-06-10 09:56:49 -04:00
jamesagnew
0c100f1aca Test fixes 2020-06-10 08:09:10 -04:00
James Agnew
b8da4f0140
Add package support (#1911) 
* Begin rework of package management

* Work on NPM

* Work on package management

* Work on NPM

* NPM rework

* Work on NPM

* NPM package rework

* Updates

* Updates

* Add license

* Work on package server

* Work on package importing

* Work on package management

* Package rework

* Work on packages

* Work on package manager

* Work on pkgs

* NPM work

* NPM rework

* Work on package cache

* Work on NPM

* Work on NPM

* Package fixes

* Add tests

* Tweaks

* Test fixes

* Add changelog

* Avoid snapshot dep
 2020-06-10 05:30:20 -04:00
James Agnew
0d3ad622b5
Correct Validation Performance Regression (#1895) 
* Validation performance regression

* Optimize validation

* More cleanup

* Add changelog

* Test fixes

* Build fixes
 2020-06-10 05:26:21 -04:00
Tadgh
6e43c5348c Add missing imports from import reorganization 2020-06-09 19:27:16 -07:00
Tadgh
6fc5b753e5 Readding imports 2020-06-09 19:20:43 -07:00
Tadgh
c36e1d2899 More code review comments 2020-06-09 19:18:06 -07:00
Tadgh
942fc313ec Code review comments 2020-06-09 19:00:41 -07:00
Tadgh
d90987368a
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/JobExistsParameterValidator.java 
Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-06-09 16:29:15 -07:00
Tadgh
b7cea688f6
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/JobExistsParameterValidator.java 
Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-06-09 15:52:37 -07:00
Ken Stevens
7fdd0f1753 Merge remote-tracking branch 'remotes/origin/master' into spring-batch-integration 2020-06-09 15:52:54 -04:00
Ken Stevens
57f2002b84 organize imports 2020-06-09 15:49:11 -04:00
Tadgh
b1d2ab7619 Add invalid parameter validator 2020-06-09 11:02:37 -07:00
Tadgh
a25a1064f8 remove constant 2020-06-09 10:22:31 -07:00
Tadgh
4f59c38692 Remove comment 2020-06-09 10:20:41 -07:00
Tadgh
7273457ea7 Rework to read and process larger chunks 2020-06-09 09:55:10 -07:00
ianmarshall
0540c9e205 Merge remote-tracking branch 'remotes/origin/master' into im_20200605_db_blob_mssql 2020-06-09 12:43:05 -04:00
ianmarshall
97e6d967e9 Improve updated JUnit test. 2020-06-09 11:52:51 -04:00
ianmarshall
64aa0feb5d Fix for issue of persisting blob data types to MS SQL databases. 2020-06-09 11:06:01 -04:00
ianmarshall
122bd97344 Changes recommended during code review. 2020-06-09 09:59:03 -04:00
Tadgh
278a1070ae :Merge branch 'master' into spring-batch-integration 2020-06-08 17:16:11 -07:00
Tadgh
25fa0377df tidying 2020-06-08 17:02:37 -07:00
Tadgh
864c9c2cb8 Add task executor to partition step 2020-06-08 16:35:15 -07:00
Tadgh
44aa688a20 Final config layout of Bulk Export Batch job 2020-06-08 15:59:08 -07:00
ianmarshall
c86e46b196 Add documentation and remove requirement for max parameter (defaulted to 1 now). 2020-06-08 18:08:02 -04:00
ianmarshall
30dd858f17 Add close method for Elasticsearch service. Fix the partial code match. 2020-06-08 15:07:02 -04:00
ianmarshall
4982e67a0f Merge remote-tracking branch 'remotes/origin/master' into im_2020601_lastn_code_text_filter 2020-06-08 09:26:55 -04:00
ianmarshall
56cbc5149b Add support for partial code description matching. 2020-06-08 09:24:09 -04:00
Tadgh
4405e50db9 wip 2020-06-05 15:53:06 -07:00
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
Tadgh
7ed65b0080 partially done writer, working out size-based chunking 2020-06-04 20:58:06 -07:00