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123 Commits

Author SHA1 Message Date
Tadgh 606b642b1e Turns out expunge atomic integer didn't do what I expected for historical versions... 2020-07-27 17:29:27 -07:00
Tadgh 82dcc395ec Merge branch 'master' into batch-empi-job 2020-07-27 14:59:27 -07:00
Tadgh fac14240c8 Add circular reference handling, and DeleteConflict handling 2020-07-27 14:18:40 -07:00
Tadgh 7e694ded3f Add failing test showing issue with related persons 2020-07-24 17:18:59 -07:00
Tadgh 7fd690f830 Add test in provider with different empi json rules 2020-07-24 10:42:21 -07:00
Tadgh 31d0ed3ac1 remove question, put in PR instead 2020-07-23 18:09:10 -07:00
Tadgh 698b18eb2f Fix NPE in iterator, fix empi-rules.json, add extra tests 2020-07-23 18:01:08 -07:00
Tadgh 2da64119bb Resolve issue with test 2020-07-23 17:28:20 -07:00
Tadgh 6a5b96d05f Start with broken test for #1996 2020-07-23 15:52:12 -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
Ken Stevens 08cbac59cc
fix tests (#1993) 2020-07-23 11:01:54 -04:00
Gary Graham e9adebc412 Move SearchBuilderFactory into EmpiSearchParamSvc to avoid module loading issues 2020-07-22 16:19:55 -07:00
Tadgh 60e5d9783e Narrowing catch by LGTM 2020-07-22 14:00:39 -07:00
Tadgh 198385a7b4 Dead space 2020-07-22 12:01:34 -07:00
Tadgh bbe6d5600e Address review comments 2020-07-22 11:58:08 -07:00
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
Tadgh 249f5e5947 Add two new tests. Fix non-jupiter-tests 2020-07-21 08:51:18 -07:00
Tadgh e82451533f Move provider logic. Fix tests to reflect. Remove now-dead methods 2020-07-21 07:52:51 -07:00
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
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
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
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
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
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
Tadgh c3b89b4ad5 Get basic tests running 2020-07-09 15:56:41 -07:00
Tadgh 5a7e1de367 Flesh out tests 2020-07-07 10:15:38 -07:00
Tadgh 86f2761580 Merge branch 'master' into batch-empi-job 2020-07-07 07:52:42 -07:00
Tadgh 5b402de581 Add EmpiTargetType to link 2020-07-07 07:51:41 -07:00
Tadgh b7e5705f57 Fix tests to cover other scenarios 2020-07-06 14:57:28 -07:00
Tadgh f82a53e6f9 Merge branch 'master' into batch-empi-job 2020-07-06 13:12:20 -07:00
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
Tadgh db127ab32f tidy test file 2020-07-06 11:01:53 -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
Tadgh 1b7e5b75f1 wip 2020-06-30 14:53:54 -07:00
Tadgh e365e643ba
Merge pull request #1906 from jamesagnew/spring-batch-integration 
Spring batch integration
 2020-06-28 16:10:43 -07:00
jamesagnew bf8de84801 License header 2020-06-26 19:25:36 -04:00
Ken Stevens 7322760f5d Merge remote-tracking branch 'origin/spring-batch-integration' into spring-batch-integration 2020-06-25 15:27:46 -04:00
Ken Stevens c11b6eeab6 back out Tx wrap 
use qualifier
 2020-06-25 15:27:31 -04:00
Tadgh 1d9641a736 fix empilinks 2020-06-25 10:28:03 -07:00
Ken Stevens 93da042d19 fix empi tests so they work with Spring Batch 
(all but one test fixed)
 2020-06-25 11:14:42 -04:00
Tadgh 3da4ad280b undoes merge issues 2020-06-24 20:00:52 -07:00
Tadgh 571589d00d Merge branch 'master' into spring-batch-integration 2020-06-24 13:46:13 -07:00
Ken Stevens 38a2b00663
Empi 69 and candidates (#1936) 
broaden empi blocking searches to support and searchparams as well as ors
 2020-06-24 09:12:56 -04:00
Tadgh 798fdb9cc2 Merge branch 'master' into spring-batch-integration 2020-06-15 09:10:41 -07:00
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
Tadgh 6fc5b753e5 Readding imports 2020-06-09 19:20:43 -07:00
Tadgh 942fc313ec Code review comments 2020-06-09 19:00:41 -07:00
Ken Stevens d6a5cee6ba
fix test (#1909) 2020-06-09 11:38:39 -04:00
Ken Stevens 82b4864d79
Empi 57 filter out inactive person (#1903) 
* begin with failing test

* test passes

* pre-review cleanup

* little fix

* fix intermittent
 2020-06-09 09:52:40 -04:00
Ken Stevens dd84846b94
Empi 56 link merged person (#1902) 2020-06-05 15:50:50 -04:00
Ken Stevens 558f419955
Empi 54 not duplicate (#1900) 
add operation to unduplicate persons
 2020-06-05 12:21:09 -04:00
James Agnew 21330a0a22
Transaction create performance improvement (#1899) 
* Work on perf issue

* Improve write performance for large bundles with tags

* Add changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1899-improve-write-xact-perf-with-tags.yaml

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>

* Test fix

* Test fixes

* Test fixes

Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
 2020-06-05 05:26:06 -04:00
Ken Stevens eb7b8e816b
Empi 58 no match create person (#1898) 2020-06-04 16:07:50 -04:00
Ken Stevens 9136231b3b
Empi 62 resource history (#1894) 2020-06-03 18:00:20 -04:00
Ken Stevens 33753881e2
Empi 55 deactivate merged (#1883) 2020-06-03 13:12:01 -04:00
Ken Stevens 61f1b57b2a
Empi merge persons fixes (#1882) 2020-06-02 12:41:26 -04:00
jamesagnew 056721829d License header updates 2020-05-22 15:56:14 -04:00
Tadgh d1b963321a
MVP EMPI implementation (#1857) 
EMPI Initial Implementation (still plenty of known gaps)
 2020-05-22 15:03:20 -04:00