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2778 Commits

Author SHA1 Message Date
James Agnew 5c14a6c217
Revert pointless SQL optimization (#1977) 
* Revert pointless SQL optimization

* Fix tests
 2020-07-09 22:14:25 -04:00
James Agnew 1449b9cb0a
Install NPM resources correctly (#1972) 
* Install NPM resources correctly

* Fix tests
 2020-07-09 18:37:55 -04:00
James Agnew c949349a41
Correctly validate ISO 3166 codes (#1967 update) (#1973) 
* Add tests

* Test fixes

* Fix tests

* Test fix

* One more test fix
 2020-07-09 18:34:26 -04:00
Ibrohim Kholilul Islam 7a44fa3eb3
Fix GraphQL Array of Argument should be ORed (#1966) 
* provide IQueryParameterOr instead of IQueryParameterType to params.add

* add tests
 2020-07-08 10:38:50 -04:00
Tadgh 86f2761580 Merge branch 'master' into batch-empi-job 2020-07-07 07:52:42 -07:00
Tadgh 5b402de581 Add EmpiTargetType to link 2020-07-07 07:51:41 -07:00
Tadgh f82a53e6f9 Merge branch 'master' into batch-empi-job 2020-07-06 13:12:20 -07:00
Tadgh 3081df3cbd
Merge pull request #1969 from jamesagnew/empi-interceptor-bug 
EMPI Storage interceptor bug fix
 2020-07-06 13:10:39 -07:00
jamesagnew 489bd77dd4 Make constraint name comparisons case insensitive 2020-07-06 14:58:03 -04:00
Tadgh 84da932187 fix test 2020-07-06 11:36:47 -07:00
James Agnew 6fb6675b1e
Resolve validation errors to ValueSet with UCUM (#1948) 
* Add tests for validation errors

* Work on validation errors

* Bump core version

* Fix validation errors

* Test fixes

* Add changelog

* Test fix

* Test fix

* Test fix
 2020-07-05 19:59:21 -04:00
James Agnew f356c7c385
Migrate to JUnit5 (#1952) 
* Work on junit

* Work on junit 5

* Work on junit 5

* Bump errorprone vcersion

* Work on tests

* Junit 5 tweaks

* Fixes

* Work on tests

* Work on junit5

* Work on tests

* Test fixes

* Work on junit5

* Test work

* Get junit5 working

* Test fix

* Work on tests

* WOrk on tests

* Work on tests

* fixes

* Compile fix

* One more tweak

* Compile fix

* Add changelog

* Fix compile error

* Compile fix
 2020-07-04 18:28:16 -04:00
Tadgh 25d8668f55 Add Basic provider method, skeleton of tests 2020-07-03 15:21:32 -07:00
James Agnew 290577ff3e
Remove unnecessary type predicate (#1963) 
* Remove unnecessary type predicate

* Add changelog
 2020-07-03 17:54:25 -04:00
IanMMarshall e23e222f80
Merge pull request #1960 from jamesagnew/im_20200630_code_system_load 
Accidentally merged pull request before pushing changes from code review
 2020-07-03 16:29:34 -04:00
Tadgh 6259eada3c Fix parameter names. These are not partitions 2020-07-03 13:18:48 -07:00
ianmarshall b1ff6cbe37 Changes from code review 2020-07-03 14:25:24 -04:00
Tadgh 63bf9cca1b
Merge pull request #1961 from jamesagnew/bulk-intermittent 
Bulk intermittent bug
 2020-07-03 11:19:51 -07:00
Tadgh 4ff63e2493 Remove unnecessary logging. Spring batch already logs this 2020-07-03 10:21:04 -07:00
Tadgh d09f410b4d Tidy logging, increase timeout to 120 because clocks 2020-07-03 10:15:57 -07:00
Tadgh a84a41643d Increase awaitility timeout for bulk export of ALL resources 2020-07-03 10:08:34 -07:00
ianmarshall 4e5ca2ee15 Changes from code review 2020-07-03 13:08:11 -04:00
Tadgh 38cb526696 Add logging 2020-07-03 09:40:52 -07:00
ianmarshall 46abdfafe0 Merge remote-tracking branch 'remotes/origin/master' into im_20200630_code_system_load 2020-07-02 13:29:17 -04:00
ianmarshall 557f732e17 Cleanup and improved Unit tests. 2020-07-02 12:03:15 -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
ianmarshall 0788e79d51 Fix to address deferred save of TermConcept when code system version changes prior to save. 2020-06-30 15:07:14 -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 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 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 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 b31b6652a9 Add async to the job launcher, fix test to reflect this 2020-06-26 11:51:01 -07:00
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 06e1368388 Re-add comment 2020-06-24 21:00:45 -07:00
Tadgh 3da4ad280b undoes merge issues 2020-06-24 20:00:52 -07:00
ianmarshall 55ff15d039 Merge remote-tracking branch 'remotes/origin/master' into im_20200619_mariadb_expand_valueset_fix 2020-06-24 17:43:34 -04:00
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 a7740922f9 Specify version 2020-06-24 11:02:52 -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 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 ce0cb8916e Improve tests. 2020-06-22 17:22:21 -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
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