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6802 Commits

Author SHA1 Message Date
Tadgh 249f5e5947 Add two new tests. Fix non-jupiter-tests 2020-07-21 08:51:18 -07:00
jamesagnew 5f1078ac13 Cleanup of package installer 2020-07-21 11:43:57 -04:00
Tadgh 4ec2be4ff5 Merge branch 'master' into batch-empi-job 2020-07-21 07:54:18 -07:00
Tadgh e82451533f Move provider logic. Fix tests to reflect. Remove now-dead methods 2020-07-21 07:52:51 -07:00
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
Tadgh de9621602b Update provider and create test skeletons for empi batch run 2020-07-18 18:18:21 -07:00
Tadgh b79ed21672 Add forgotten bean 2020-07-18 13:36:31 -07:00
Tadgh 62b5221c3f Move Empi Batch work to the BaseHapiResourceProvider, allowing manual EMPI runs on a server/type/ID basis. 2020-07-18 13:36:14 -07:00
Tadgh 4fa4dd1c48 Update Javadocs 2020-07-17 13:39:39 -07:00
Tadgh fec50686ec Forgot to unregister interceptor 2020-07-17 13:18:27 -07:00
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
Tadgh e540e4b0a2 Minor addition to PointcutLatch to support an inline runnable 2020-07-17 12:06:19 -07:00
Tadgh aebdef1e3f Fix import issues 2020-07-17 09:36:08 -07:00
Tadgh 1e12c740f6 Merge branch 'master' into batch-empi-job 2020-07-17 09:28:10 -07:00
Tadgh 92461b6346 wip 2020-07-17 09:00:15 -07:00
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
Tadgh 6bb92717f5 Merge branch 'master' into batch-empi-job 2020-07-16 11:00:32 -07:00
Tadgh 31e9f140ad Fix operation name. Remove unnecessary beans 2020-07-16 09:48:58 -07:00
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
Tadgh acd881ca76 Adds queue submitter class, for simplicity of manual triggers of Empi Runs 2020-07-15 15:20:26 -07:00
Tadgh f965b26f0d add more tests for criteria conversion 2020-07-15 14:03:27 -07:00
Tadgh 80b59599fc wip 2020-07-15 12:27:49 -07:00
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
Tadgh 9d7df0cdda wip 2020-07-14 14:49:16 -07:00
jamesagnew d6f6ec2d66 License headers 2020-07-13 16:57:24 -04:00
Tadgh 677bc5577b wip 2020-07-13 12:00:19 -07:00
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
Tadgh c3b89b4ad5 Get basic tests running 2020-07-09 15:56:41 -07:00
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
Tadgh 5a7e1de367 Flesh out tests 2020-07-07 10:15:38 -07:00
Tadgh 57f5c10bca Add migration for MPI Score/TargetType 2020-07-07 07:56:43 -07:00
Tadgh 86f2761580 Merge branch 'master' into batch-empi-job 2020-07-07 07:52:42 -07:00