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6608 Commits

Author SHA1 Message Date
dependabot[bot] ef4b79da7e
Bump mysql-connector-java in /hapi-fhir-jpaserver-migrate (#1955) 
Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 6.0.5 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/6.0.5...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-07-01 18:29:57 -04:00
dependabot[bot] d1ceb280fc
Bump mysql-connector-java (#1954) 
Bumps [mysql-connector-java](https://github.com/mysql/mysql-connector-j) from 5.1.40 to 8.0.16.
- [Release notes](https://github.com/mysql/mysql-connector-j/releases)
- [Changelog](https://github.com/mysql/mysql-connector-j/blob/release/8.0/CHANGES)
- [Commits](https://github.com/mysql/mysql-connector-j/compare/5.1.40...8.0.16)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-07-01 18:29:45 -04:00
Ken Stevens 714bd6216e
Empi 70 phonetic indexing (#1941) 
* start with failing test

* test passes with fixmes

* javadoc and config

* pre-review cleanup

* generalize encoding

* test passes, but indexing needs to be optimized

* test passes, but indexing needs to be optimized

* step 1 of optimization.  big refactor of all predicates

* step 2 of optimization: determine phonetic encoder at time of RuntimeSearchParam creation

* integrated new phonetic encoders into empi

* phonetic search implemented

* IT passes

* pre-review cleanup

* final pre-review cleanup

* final pre-review cleanup

* Fix compile error

Co-authored-by: James Agnew <jamesagnew@gmail.com>
 2020-06-30 17:36:54 -04:00
jamesagnew bb17688680 Add test for #1780 2020-06-30 17:03:16 -04:00
jamesagnew 349c752860 License headers 2020-06-30 15:13:38 -04:00
jamesagnew 2cdef055aa Missed commit on #1951 
Squashed commit of the following:

commit f820135996
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 14:29:24 2020 -0400

    Address review comments

commit 11c4f9defb
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:38:16 2020 -0400

    Fix LGTM warning

commit b650fdb9ea
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:20:52 2020 -0400

    Test fix

commit 6ebcceeb5c
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:49:01 2020 -0400

    Add changelog

commit 4a1d7383b0
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:46:52 2020 -0400

    Bundle transmission

commit 88bd4abf0c
Merge: 7cde945281 25fc747b9f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:31:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 7cde945281
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:10:33 2020 -0400

    Work on seed bundles

commit ed2e62752e
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 09:39:10 2020 -0400

    Work on subscriptions

commit 52addcff59
Merge: 64a9eaa4de bf8de84801
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Sat Jun 27 18:09:23 2020 -0400

    Merge branch 'master' into ja_20200617_subscription_send_bundles

commit 64a9eaa4de
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:32:17 2020 -0400

    Start work

commit f74eba5397
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:28:18 2020 -0400

    Terser should create correct Enumeration on create
 2020-06-30 14:31:40 -04:00
James Agnew fa4bbe3685
Allow search criteria as subscription delivery mechanism (#1951) 
* Terser should create correct Enumeration on create

* Start work

* Work on subscriptions

* Work on seed bundles

* Bundle transmission

* Add changelog

* Test fix

* Fix LGTM warning
 2020-06-30 14:29:09 -04:00
James Agnew cd69a140fc
Create codeql-analysis.yml 2020-06-30 11:58:29 -04:00
James Agnew 072f3a422a
Use read partition for finding update candidate on upsert (#1945) 
* Use read partition for finding update candidate on upsert

* Add changelog
 2020-06-29 18:22:27 -04:00
Tadgh 25fc747b9f
Merge pull request #1950 from jamesagnew/hotfix-test-import 
Hotfix test import
 2020-06-29 13:23:52 -07:00
jamesagnew bb7d889ca9 License header updates 2020-06-29 15:15:51 -04:00
Tadgh 8df0448f88 Fix import 2020-06-29 11:04:03 -07:00
Tadgh 4e789fbf42 Fix import error 2020-06-29 11:01:38 -07:00
Tadgh e365e643ba
Merge pull request #1906 from jamesagnew/spring-batch-integration 
Spring batch integration
 2020-06-28 16:10:43 -07:00
jamesagnew be23eb3cfc Move the flush into the existing transaction 2020-06-27 18:06:37 -04:00
jamesagnew bf8de84801 License header 2020-06-26 19:25:36 -04:00
jamesagnew dac516828e Move validation settings bean 2020-06-26 18:31:13 -04:00
Tadgh 16039af110 Fix up samlpe starters 2020-06-26 13:15:31 -07:00
Tadgh 8f6aee64b1 Fix batch project to now use an async task launcher 2020-06-26 12:22:23 -07:00
Tadgh b31b6652a9 Add async to the job launcher, fix test to reflect this 2020-06-26 11:51:01 -07:00
Tadgh 0b622597b4 Muck with initial loading to allow EMF and platformtransactionmanager to be available 2020-06-26 10:13:03 -07:00
IanMMarshall ceeff0ccf0
Merge pull request #1942 from jamesagnew/im_20200619_mariadb_expand_valueset_fix 
Im 20200619 mariadb expand valueset fix
 2020-06-25 20:05:24 -04:00
Tadgh 13bbdde458 pipeline fun 2020-06-25 15:38:15 -07:00
Tadgh 484f390db0 Fix batch test 2020-06-25 13:00:59 -07:00
Ken Stevens 7322760f5d Merge remote-tracking branch 'origin/spring-batch-integration' into spring-batch-integration 2020-06-25 15:27:46 -04:00
Ken Stevens c11b6eeab6 back out Tx wrap 
use qualifier
 2020-06-25 15:27:31 -04:00
Tadgh 21567fdc43 Tidy await 2020-06-25 11:42:17 -07:00
Tadgh ed155e7657 wip 2020-06-25 10:37:02 -07:00
Tadgh 1d9641a736 fix empilinks 2020-06-25 10:28:03 -07:00
Ken Stevens 93da042d19 fix empi tests so they work with Spring Batch 
(all but one test fixed)
 2020-06-25 11:14:42 -04:00
Tadgh e51c5b5263 change transactionmanager name so it doesnt shadow the batchprocessing one 2020-06-24 21:03:02 -07:00
Tadgh 06e1368388 Re-add comment 2020-06-24 21:00:45 -07:00
Tadgh 6875740178 Merge branch 'spring-batch-integration' of github.com:jamesagnew/hapi-fhir into spring-batch-integration 2020-06-24 20:15:47 -07:00
Tadgh 3da4ad280b undoes merge issues 2020-06-24 20:00:52 -07:00
Ken Stevens a69c1478a2 Merge remote-tracking branch 'remotes/origin/master' into spring-batch-integration 2020-06-24 22:07:38 -04:00
ianmarshall 55ff15d039 Merge remote-tracking branch 'remotes/origin/master' into im_20200619_mariadb_expand_valueset_fix 2020-06-24 17:43:34 -04:00
ianmarshall 053094f2a6 Apply recent fixes for MySQL migration tasks to MariaDB as well. 2020-06-24 17:42:46 -04:00
Tadgh 571589d00d Merge branch 'master' into spring-batch-integration 2020-06-24 13:46:13 -07:00
Tadgh 64dbd038c9 Increase min thread count for batch. Add new which waits for all bulkexport jobs to be done 2020-06-24 13:16:11 -07:00
ianmarshall 5e3e7c46a8 Changes to support valueset expansion with Elasticsearch. 2020-06-24 15:48:06 -04:00
Tadgh 99fe66bb58 Fix pom to use project.version 2020-06-24 11:52:05 -07:00
Tadgh a7740922f9 Specify version 2020-06-24 11:02:52 -07:00
Tadgh 59659b2802 Move order of modules 2020-06-24 10:11:30 -07:00
Tadgh 2bd17806c4 Update changelog 2020-06-24 09:46:56 -07:00
Ken Stevens 38a2b00663
Empi 69 and candidates (#1936) 
broaden empi blocking searches to support and searchparams as well as ors
 2020-06-24 09:12:56 -04:00
Tadgh 4cccc9804b nop for CI 2020-06-23 16:29:36 -07:00
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