2190 Commits

Author SHA1 Message Date
ianmarshall
6f9874468a Merge remote-tracking branch 'origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-25 08:54:17 -04:00
Tadgh
74bba9dbcc Rename to ResourceOperationMessage 2020-09-15 18:57:55 -04:00
ianmarshall
3add1320b7 Merge remote-tracking branch 'remotes/origin/im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:52:02 -04:00
ianmarshall
539ef63fc0 Merge branch 'im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 16:24:47 -04:00
Tadgh
ea64bea1b0 Refactor to use concrete class instead of parent 2020-09-15 15:27:21 -04:00
ianmarshall
7b15f85fa1 Merge remote-tracking branch 'remotes/origin/feature_20200830_term_multi_version_support' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:35:31 -04:00
ianmarshall
087c9e3c3b Merge remote-tracking branch 'remotes/origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-15 12:34:11 -04:00
Tadgh
28a9a53917 Rework to keep several things in subscription 2020-09-10 16:05:56 -04:00
ianmarshall
d00db11586 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-09-09 17:38:24 -04:00
Frank Tao
5410042643 Multi-version supported for ConceptMap $translate operation 2020-09-07 10:43:58 -04:00
Frank Tao
1ecec0abc9 Fixed duplicate ConceptMap URL only 2020-09-06 15:23:26 -04:00
jamesagnew
2d7c808326 Localizer refactor 2020-09-05 15:47:10 -04:00
ianmarshall
5f005120c9 Initial changes to support multi-version ValueSets 2020-09-03 22:36:15 -04:00
ianmarshall
1c55d87b10 Problem found in LOINC loader. 2020-08-30 17:11:48 -04:00
ianmarshall
dc786eaff9 Refine model for storing multiple code versions. 2020-08-21 10:16:10 -04:00
ianmarshall
2126c5c556 Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-18 11:15:09 -04:00
James Agnew
eab828f47a
Add transactionbuilder (#2041)
* Add transactionbuilder

* Add changelog

* Add creates
2020-08-17 07:47:40 -04:00
ianmarshall
bd94ff96cc Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support 2020-08-16 21:38:41 -04:00
jamesagnew
92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew
5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
jamesagnew
90ebaf8549 Add one more test for #2023 2020-08-11 08:54:03 -04:00
James Agnew
e61b39fc30
Force a flush of the SearchParameter cache sooner when SPs change (#2030)
* Force a flush of the SearchParameter cache sooner when SPs change

* Add changelog

* Test fixes
2020-08-09 19:30:59 -04:00
ianmarshall
d39348d7bd Initial changes to support multiple versions for code system. 2020-08-09 11:49:04 -04:00
James Agnew
0de0b88aa0
Fix TestpageOverlay XSS Vulnerability (#2027)
* Resolve XSS vulnerability

* Add changelog
2020-08-09 07:06:11 -04:00
James Agnew
5d9d4070fb
Fix an issue with binary storage not updating correctly if a retry (#2014)
interceptor is present
2020-08-05 09:14:40 -04:00
jamesagnew
a35c97e13d Add utility method to XmlUtil 2020-07-26 17:54:45 -04:00
christian ohr
1c27726055
#1817: fix problem with missing resource references when extensions are used (#1848)
Co-authored-by: Christian Ohr <christian.ohr@icw.de>
2020-07-21 05:36:25 -04:00
James Agnew
5db90d3e6e
Address issues when importing US Core (#1986)
* Work on US Core import

* Work on US Core

* Resolve issues with US Core import

* Test fix
2020-07-17 15:28:16 -04:00
Ken Stevens
ebd6ca4b64
Empi 3 ruleset version (#1978)
* add rule version

* add rule version

* Rough in model for Golden Record.

* Test Link Rule Version

* add eid match boolean

* added new fields to EmpiLink to provide more information about how the link was created

* add logging to check an edge case

* all tests pass

* wip with failing tests

* tests pass

* FIXME

* optimize imports

* test score in provider output

* FIXME

* FIXME

* Fix jpa test app context

* fix migration string length

* review feedback param name

* review feedback javadoc

* review feedback javadoc

* bean config reorganization for cdr

* add more tests
2020-07-17 08:31:15 -04:00
jamesagnew
f5222f3105 License headeer update 2020-07-17 08:27:10 -04:00
Ibrohim Kholilul Islam
5a79304893
Implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation (#1896)
* implement GraphQLQueryBodyParameter and GraphQLQueryBody annotation

* GraphQLQueryBodyParameter to recognize application/graphql

* fix 500 error on method without @GraphQLQueryBody

* refactor to processGraphQlGetRequest and processGraphQlPostRequest

* add testGraphPostContentTypeJson and testGraphPostContentTypeGraphql to GraphQLR4RawTest

* fix imports
2020-07-16 09:25:26 -04:00
James Agnew
077ee02771
Fix validation for enumerated ValueSets (#1982)
* Allow code validation against enumerated VS

* Work on validation

* Work on this

* Work on tests

* Work on validation

* Work on tests

* Work on validation

* Test fixes

* Add changelog

* For a change

* Test fixes
2020-07-15 13:38:14 -04:00
James Agnew
baba4cc240
Avoid version conflicts on current writes (#1971)
* Add auto retry of transactions

* Experiment in Maven build

* Transaction autoretry

* Work on transaction retries

* Work on transaction retry

* Work on transaction retry

* Fix tests

* Avoid version conflicts

* Add changelog

* Resolve LGTM issue

* FIx transaction scope error

* Test fixes

* Test fix

* Test fixes

* Test fix

* Test fixes
2020-07-13 08:51:13 -04:00
Ken Stevens
e565b1c948
done (#1976) 2020-07-10 15:08:50 -04:00
Alexander Lukyanchikov
df133d10f2
#1892 Add support for :of-type Token Modifier (#1893) 2020-07-06 05:50:44 -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
jamesagnew
ef86d26357 License header updates 2020-07-02 12:07:02 -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
349c752860 License headers 2020-06-30 15:13:38 -04:00
jamesagnew
2cdef055aa Missed commit on #1951
Squashed commit of the following:

commit f820135996bf25d13483012074b38878085e2384
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 14:29:24 2020 -0400

    Address review comments

commit 11c4f9defba581132a340a2e5f189a934e829b67
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:38:16 2020 -0400

    Fix LGTM warning

commit b650fdb9ea7d09bdc1f9f811727e6d23bbf153ce
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Jun 30 09:20:52 2020 -0400

    Test fix

commit 6ebcceeb5ca314313c197ff8543a87343e82a7a1
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:49:01 2020 -0400

    Add changelog

commit 4a1d7383b0c7d119acf0f97866be902c61cff0f5
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 18:46:52 2020 -0400

    Bundle transmission

commit 88bd4abf0cf105765e622a2fedd18b265ec8fbbe
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 7cde945281890ce34023a1e954a24503f2741809
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 17:10:33 2020 -0400

    Work on seed bundles

commit ed2e62752efc828c16e0ca772c76ca1428610777
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Jun 29 09:39:10 2020 -0400

    Work on subscriptions

commit 52addcff5916ee3f32b245f464dfa13f4e1c6ac8
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 64a9eaa4de38b5b16c0b5d8f3727634c897f06de
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Wed Jun 17 18:32:17 2020 -0400

    Start work

commit f74eba5397d40f948970c0fc77ef721b021de46a
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
Tadgh
bb7a773f41 Merge branch 'master' into spring-batch-integration 2020-06-23 16:02:41 -07:00
James Agnew
f88298a1fb
Remote terminology service enhancements (#1934)
* Remote terminology service enhancements

* Add changelog
2020-06-23 11:35:26 -04:00
jamesagnew
4119cbb0c4 Terser should create correct Enumeration on create 2020-06-17 18:32:27 -04:00
Tadgh
a9c704c06e Merge branch 'master' into spring-batch-integration 2020-06-10 12:24:19 -07:00
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
278a1070ae :Merge branch 'master' into spring-batch-integration 2020-06-08 17:16:11 -07:00
Tadgh
44aa688a20 Final config layout of Bulk Export Batch job 2020-06-08 15:59:08 -07:00
Diederik Muylwyk
eda806babd Fix typo. 2020-06-08 13:48:44 -04:00