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hapi-fhir
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6676 Commits

Author SHA1 Message Date
Tadgh 6a5b96d05f Start with broken test for #1996 2020-07-23 15:52:12 -07:00
jamesagnew 296ed963cc Fix sentence fragment 2020-07-23 12:57:46 -04:00
Ken Stevens 08cbac59cc
fix tests (#1993) 2020-07-23 11:01:54 -04:00
James Agnew a6fd6254db
Speed up loinc ingestion (#1991) 
* Speed up loinc ingestion

* Add some logging
 2020-07-23 09:20:33 -04:00
Ken Stevens 160778d3fd
Empi docs (#1989) 
* Remove lines from image edges.  Thanks Max!

* fix case 4 docs
only mark possible match as eid if it was via an eid match
 2020-07-21 13:07:49 -04:00
jamesagnew 5f1078ac13 Cleanup of package installer 2020-07-21 11:43:57 -04:00
jamesagnew c44c1ff11f Wrap NPM loader in a try-catch 2020-07-21 09:57:10 -04:00
jamesagnew 4c4d46008b Credit for #1848 2020-07-21 05:40:41 -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 05735900fd
Fixes to interceptor in order to prevent zombie listeners on restart (#1988) 
* Fixes to interceptor in order to prevent zombie listeners on restart

* Add test

* Add license header

* Test fixes
 2020-07-20 14:03:46 -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
jamesagnew c13e17b4e6 Add changelog and bump Jetty 2020-07-17 11:50:45 -04:00
dependabot[bot] dbe171d658
Bump jetty_version from 9.4.24.v20191120 to 9.4.29.v20200521 (#1890) 
Bumps `jetty_version` from 9.4.24.v20191120 to 9.4.29.v20200521.

Updates `jetty-http` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-servlets` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-io` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-continuation` from 9.4.24.v20191120 to 9.4.29.v20200521

Updates `jetty-security` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-servlet` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-server` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-util` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-webapp` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `jetty-xml` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

Updates `websocket-api` from 9.4.24.v20191120 to 9.4.29.v20200521

Updates `websocket-client` from 9.4.24.v20191120 to 9.4.29.v20200521

Updates `websocket-server` from 9.4.24.v20191120 to 9.4.29.v20200521

Updates `jetty-maven-plugin` from 9.4.24.v20191120 to 9.4.29.v20200521
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.24.v20191120...jetty-9.4.29.v20200521)

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-07-17 11:47:06 -04:00
jamesagnew b57681da59 License header updates 2020-07-17 08:54:20 -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
jamesagnew 49c08f31d8 Credit for #1896 2020-07-16 09:26:41 -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
jamesagnew 962055e092 Undo extra logging in tests 2020-07-15 13:47:19 -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 063bf4237c
Allow ConceptMap with no explicit group source/target (#1983) 
* Allow ConceptMap with no explicit group source/target

* Add changelog
 2020-07-15 12:57:10 -04:00
James Agnew 29bf6b8171
Fix a bug validating ValueSets (#1981) 
* Fix a buig validating ValueSets

* Test fix
 2020-07-15 09:25:34 -04:00
jamesagnew addcdc9269 Make method transactional 2020-07-14 19:12:40 -04:00
jamesagnew d6f6ec2d66 License headers 2020-07-13 16:57:24 -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
James Agnew 5c14a6c217
Revert pointless SQL optimization (#1977) 
* Revert pointless SQL optimization

* Fix tests
 2020-07-09 22:14:25 -04:00
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