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6649 Commits

Author SHA1 Message Date
Ken Stevens 50ae07acaa
stub out all migrations if an empty schema was initialized (#1975) 2020-07-09 20:18:54 -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
jamesagnew c40d15294d Credit for #1966 2020-07-08 10:44:52 -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
Ken Stevens 1e2505e548
change migration to correct table. (#1970) 
* change migration to correct table.

QUESTION: Do we need to stub this migration and add new ones?

* fix variable name
 2020-07-07 05:45:39 -04:00
Ken Stevens 79862c449a
add migration cutpoint (#1968) 2020-07-06 16:12:44 -04:00
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 2f11a673e3 change test name 2020-07-06 11:53:40 -07:00
Tadgh be429299de Change string name 2020-07-06 11:46:20 -07:00
Tadgh 84da932187 fix test 2020-07-06 11:36:47 -07:00
jamesagnew b786006183 Credit for #1878 2020-07-06 13:46:30 -04:00
Joel Schneider (NMDP) 1266619e37
quick fix to avoid including duplicate copies of hapi-fhir-testpage-overlay classes (#1878) 2020-07-06 13:43:51 -04:00
jamesagnew 11ad41d472 Credit for #1893 2020-07-06 05:52:40 -04:00
Alexander Lukyanchikov df133d10f2
#1892 Add support for :of-type Token Modifier (#1893) 2020-07-06 05:50:44 -04:00
jamesagnew 9813c6915c Merge branch 'ConsultingMD-atlas-grand-rounds' 2020-07-06 05:45:35 -04:00
jamesagnew 2b5c834d96 Merge branch 'atlas-grand-rounds' of https://github.com/ConsultingMD/hapi-fhir into ConsultingMD-atlas-grand-rounds 2020-07-06 05:45:19 -04:00
Sumeet Chhetri 4c883cf741
Added an entry for Ohum/FHIR (#1930) 2020-07-06 05:43:20 -04:00
James Agnew 4b1546f002
Add support for ISO 3166 to validator (#1967) 
* Add ISO 3166 support

* Add support for ISO-3166

* Add changelog

* Test fixes
 2020-07-06 05:29:48 -04:00
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
jamesagnew 9e19b87e67 Fix build 2020-07-04 19:32:40 -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
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
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
IanMMarshall 0e885064ce
Merge pull request #1958 from jamesagnew/im_20200630_code_system_load 
Im 20200630 code system load
 2020-07-03 13:06:42 -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
jamesagnew aa1e46fdb0 Fix public hapi test server 2020-07-02 13:09:49 -04:00
jamesagnew ef86d26357 License header updates 2020-07-02 12:07:02 -04:00
jamesagnew a59b25c8c0 Fix startup failure on hapi.fhir.org 2020-07-02 12:06:33 -04:00
ianmarshall 557f732e17 Cleanup and improved Unit tests. 2020-07-02 12:03:15 -04:00
dependabot[bot] fb0029cc4b
Bump mysql-connector-java (#1956) 
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 18:30:07 -04:00
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
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 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