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6763 Commits

Author SHA1 Message Date
Tadgh bb7a773f41 Merge branch 'master' into spring-batch-integration 2020-06-23 16:02:41 -07:00
James Agnew e65c264927
Support double _has expressions (#1939) 
* Support nested _has queries

* Add changelog
 2020-06-23 17:58:47 -04:00
James Agnew 6825d2fcf0
Reduce DB roundtrips for revincludes (#1937) 
* Reduce DB roundtrips for revincludes

* Add changelog
 2020-06-23 16:26:04 -04:00
James Agnew f88298a1fb
Remote terminology service enhancements (#1934) 
* Remote terminology service enhancements

* Add changelog
 2020-06-23 11:35:26 -04:00
James Agnew 67d363f9e1
Add setting to allow validation of reference targets (#1932) 
* Add setting to allow validation of reference targets

* Add changelog

* Add changelog

* License headers

* Plugin version bump

* Experiment with Maven build
 2020-06-23 11:35:10 -04:00
Diederik Muylwyk e849ff2cbc
Merge pull request #1933 from jamesagnew/dm-20200622-fix-valueset-expand-with-offset-and-count 
Fix ValueSet$expand with offset and count parameters.
 2020-06-22 18:30:22 -04:00
Diederik Muylwyk ce0cb8916e Improve tests. 2020-06-22 17:22:21 -04:00
Diederik Muylwyk ced376f7ba Add changelog entry; fix typo. 2020-06-22 17:02:08 -04:00
Diederik Muylwyk 314df43091 BaseValidationSupportWrapper.expandValueSet(...) and ValidationSupportChain.expandValueSet(...) were incorrectly replacing expansion options (i.e. offset and count) with null. 2020-06-22 16:52:52 -04:00
ianmarshall 5bf1e94a23 Fix to accomodate MySQL and MariaDB. 2020-06-19 17:26:45 -04:00
Tadgh 0e86732599 Add changelog 2020-06-19 14:03:22 -07:00
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
jamesagnew 4119cbb0c4 Terser should create correct Enumeration on create 2020-06-17 18:32:27 -04:00
IanMMarshall abf0a0053d
Merge pull request #1928 from jamesagnew/im_20200615_mysql_migration_syntax 
Im 20200615 mysql migration syntax
 2020-06-17 14:21:17 -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
ianmarshall 5b120ee71e Removed unused code and import statement. 2020-06-17 11:57:37 -04:00
ianmarshall 5d22af45bf Added tests for cases where a renamed column is used in a Foreign Key constraint. 2020-06-17 11:56:20 -04:00
ianmarshall eb990e9a68 Enhance added JUnit test. 2020-06-17 09:05:53 -04:00
ianmarshall cc7ed1b036 Cleanup JUnit test. 2020-06-16 17:21:17 -04:00
ianmarshall 2d857f484c Fix broken JUnit. 2020-06-16 17:13:00 -04:00
ianmarshall 0bd8084b5e Additional fixes to migration tasks for MySQL. 2020-06-16 16:05:10 -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 0d4e12fe58 Undo accidentally committed file with a weird name 2020-06-15 09:17:52 -04:00
jamesagnew 34c68e15af Add license headers 2020-06-14 19:10:36 -04:00
Ken Stevens d164e2d450
Empi 28 matchers (#1918) 
* adding matchers

* reorganize resource matching api

* added precision sensitive date matcher

* stricter rules validation

* validate thresholds

* validate paths.  with FIXMES

* validate searchparams

* fix merge compile error

* add soundex, validate no duplicate names

* add normalize substring

* add exact field to matcher

* EXACT -> STRING, exact=true

* cleanup test method

* match test passes with fixmes

* fixed vector matching

* fixed vector matching

* updating documentation and fixing tests

* updated rules documentation with latest matchers

* updated rules documentation with latest matchers

* created eid page

* eid documentation

* pre-review cleanup

* clean up beans

* disentangling beans

* checkstyle

* noop to trigger CI

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_rules.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2020-06-14 17:15:56 -04:00
jamesagnew db4b749436 License updates 2020-06-14 15:44:33 -04:00
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
IanMMarshall 4f45c2c25d
Merge pull request #1920 from jamesagnew/im_20200611_mysql_rename 
Enable rename table column migration task for MySQL.
 2020-06-12 13:04:54 -04:00
ianmarshall 1ed65f2e03 Enable rename table column migration task for MySQL. 2020-06-12 09:01:46 -04:00
jamesagnew 756602183b Add changelog for https://github.com/hapifhir/org.hl7.fhir.core/pull/237 2020-06-11 14:03:20 -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