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361 Commits

Author SHA1 Message Date
Tadgh 66a0115340 Missed a space 2020-09-30 11:13:40 -04:00
Tadgh ca52268249 Rename accessors, fix whitespace 2020-09-30 11:11:56 -04:00
Ken Stevens 09d09233ff
empi bugfixes and enhancements (#2104) 2020-09-29 17:27:43 -04:00
James Agnew 072e63be5a
Avoid a crash on double date chains (#2097) 
* Avoid a crash on double date chains

* Add changelog

* Address coverage warning
 2020-09-21 15:43:07 -04:00
Tadgh 45775c8660 Reuse constant 2020-09-16 15:29:04 -04:00
Tadgh ddfac72e8d Clean spacing 2020-09-16 15:27:03 -04:00
Tadgh 9d3a97a46f Default for int 2020-09-16 15:24:09 -04:00
Tadgh 558f7a5ccf Minor cleanup 2020-09-16 15:21:49 -04:00
Tadgh 4c5051a5d9 More refactor for custom headers and top level attributes 2020-09-16 15:05:44 -04:00
Tadgh 666113696b add attributes to HapiHeaders. Turns out deserialization makes a best guess, and doesnt respect types in Map<String,Object> 2020-09-16 14:06:54 -04:00
Tadgh cdc195bd0b Change to use long type for failure timestamps 2020-09-16 13:13:43 -04:00
Tadgh 74bba9dbcc Rename to ResourceOperationMessage 2020-09-15 18:57:55 -04:00
Tadgh ea64bea1b0 Refactor to use concrete class instead of parent 2020-09-15 15:27:21 -04:00
Tadgh a9fb849d49 Moved more into parent class, added javadocs for transactionId 2020-09-14 16:44:50 -04:00
Tadgh 6e0ef035e9 Rename constants. Remove dead comment 2020-09-14 15:35:58 -04:00
Tadgh f20c42a8bd Remove license claims, remove dead class 2020-09-14 13:48:44 -04:00
Tadgh 9a09a8abf3 Update todos 2020-09-14 13:41:11 -04:00
Tadgh 3e324355f2 Add javadocs 2020-09-14 13:28:36 -04:00
Tadgh 2e1f2a662a Move class to top level, add tests 2020-09-14 13:20:01 -04:00
Tadgh c3ddf59d6f Add HapiMessageHeaders to BaseJsonMessage class 2020-09-14 13:02:32 -04:00
Tadgh 28a9a53917 Rework to keep several things in subscription 2020-09-10 16:05:56 -04:00
Tadgh 2229233749 Move subscription models to legacy, except the ones that are subscription specific 2020-09-09 15:58:41 -04:00
jamesagnew 190f0ccb22 Add test for #2063 2020-09-01 14:12:57 -04:00
James Agnew 63ef2ce006
Fix #2012 - Always filter total from search results when consent interceptor in use (#2020) 
* consent bug test

* Fix #2012 - Always filter total from search results when consent
interceptor in use

* Add changelog

* Address coverage issues

Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
Co-authored-by: jvi <jvi@trifork.com>
 2020-08-07 09:16:02 -04:00
Tadgh 3b9f9e6cc3 Rename operation 2020-08-03 21:35:12 -07:00
Tadgh da30772a01 Remove dead methods, constants, and add a javadoc 2020-08-01 13:19:52 -07:00
Tadgh e67ee36492 Renamed and modified reset constant for better naming 2020-08-01 11:36:14 -07:00
Tadgh 90e96c1fb4 Fix bug caused by Persons with >1 historical version 2020-07-23 14:35:28 -07:00
Tadgh 9491a3e499 Add DSTU3 clear operation 2020-07-23 09:37:11 -07:00
Tadgh de9621602b Update provider and create test skeletons for empi batch run 2020-07-18 18:18:21 -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 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
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 c3b89b4ad5 Get basic tests running 2020-07-09 15:56:41 -07:00
Tadgh f82a53e6f9 Merge branch 'master' into batch-empi-job 2020-07-06 13:12:20 -07:00
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 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
jamesagnew 34c68e15af Add license headers 2020-06-14 19:10:36 -04:00
Ken Stevens d164e2d450
Empi 28 matchers (#1918) 
* adding matchers

* reorganize resource matching api

* added precision sensitive date matcher

* stricter rules validation

* validate thresholds

* validate paths.  with FIXMES

* validate searchparams

* fix merge compile error

* add soundex, validate no duplicate names

* add normalize substring

* add exact field to matcher

* EXACT -> STRING, exact=true

* cleanup test method

* match test passes with fixmes

* fixed vector matching

* fixed vector matching

* updating documentation and fixing tests

* updated rules documentation with latest matchers

* updated rules documentation with latest matchers

* created eid page

* eid documentation

* pre-review cleanup

* clean up beans

* disentangling beans

* checkstyle

* noop to trigger CI

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_details.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_empi/empi_rules.md

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* review feedback

* review feedback

* review feedback

* review feedback

* review feedback

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2020-06-14 17:15:56 -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
Ken Stevens 558f419955
Empi 54 not duplicate (#1900) 
add operation to unduplicate persons
 2020-06-05 12:21:09 -04:00
Ken Stevens 33753881e2
Empi 55 deactivate merged (#1883) 2020-06-03 13:12:01 -04:00
James Agnew 86ef0ec0e2
Correct transaction processing in multitenant server (#1884) 
* Correct transaction processing in multitenant server

* # d codethe npm registry for updates every day (weekdays)
 2020-06-03 10:37:47 -04:00
James Agnew c374383b37
Allow AuthorizationInterceptor to properly authorize GraphQL statements (#1864) 
* Allow AuthorizationInterceptor to properly authorize GraphQL statements

* Add changelog
 2020-05-22 20:40:37 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857) 
EMPI Initial Implementation (still plenty of known gaps)
 2020-05-22 15:03:20 -04:00
James Agnew 63ff0ede9c
Make diff operation work securely (#1859) 
* Make diff operation work securely

* Build tweak

* FIx tests
 2020-05-21 19:20:48 -04:00
James Agnew ce5ade53d9
Fix #1855 - StructureDefinition search not working (#1858) 2020-05-21 09:35:37 -04:00
James Agnew 5b2181a563
Implement FHIR Patch (#1850) 
* Start working on FHIRPatch

* More work on fhirpatch

* Work on FHIR Patch

* Add patch

* Test fixes

* Test fixes

* Get tests fixed

* Chnage to trigger a build

* Compile fix

* Dependency version fixes

* Test fix

* COmpile fix

* Try to fix build

* Test fix attempt

* Another build attempt

* Another build tweak

* Cleanup
 2020-05-20 19:43:55 -04:00