Commit Graph

223 Commits

Author SHA1 Message Date
Nick Goupinets a2aa2ca1c3 2849 Added new parameter to MDM processing 2021-07-29 15:52:27 -04:00
Ken Stevens 92ec113775
fixed bug (#2824) 2021-07-23 16:58:53 -04:00
Tadgh a4fb72975d
Merge pull request #2767 from hapifhir/2765-mdm-paging
Paging implementation for MDM query links operation
2021-07-01 23:16:47 -04:00
Tadgh cfcc939caa Fix broken tests, add license 2021-07-01 18:28:29 -04:00
Tadgh 1eb82d633d Rip out pagingprovider requirement 2021-06-30 18:41:18 -04:00
Michael Buckley fa750d209e $mdm-submit operation was only submitting 100 resources and then stopping.
It now correctly submits all requested resources.
2021-06-30 14:48:28 -04:00
Tadgh 8f3cbb0a7f Refactor docs 2021-06-30 14:48:13 -04:00
Tadgh 61260dd1b1 Slightly more portable solution for paging 2021-06-30 11:54:59 -04:00
Tadgh a770d577cb Initial quick implementation of paging with tests 2021-06-29 17:46:03 -04:00
Nick Goupinets 95012623f6 Added null checks 2021-06-22 15:12:10 -04:00
James Agnew 6ea1438f1d
Add transaction write semaphore interceptor (#2743)
* Add transaction write semaphore interceptor

* Add changelog

* Test fix
2021-06-20 12:55:49 -04:00
Ken Stevens 32ac16e2aa
add a limit to mdm candidate searches (#2742)
* done

* verbal review feedback

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2739-max-mdm-matches.yaml

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

* review feedback

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-06-18 20:48:34 -04:00
Ken Stevens a4856bba17
fix iBundleProvider.getResources(from,to) throwing a NPE (#2632)
* fix iBundleProvider.getResources(from,to) throwing a NPE

* change log

* review feedback

* rename test to IT that has concurrency failures
2021-05-05 21:50:51 -04:00
Nick Goupinets 1f10a15c35 Merge branch 'master' into 2515_MDM_survivorship_rules 2021-04-19 17:33:53 -04:00
Tadgh 99e10de5fb
Merge pull request #2487 from hapifhir/mdm-expansion-interceptor
MDM Expansion Interceptor (poc)
2021-04-09 11:23:04 -04:00
James Agnew b617c7690d
Search Parameter Infrastructure Cleanup (#2522)
* Search param service cleanup

* Work on collapsing search param

* Search param cleanup

* Work on build

* Test fix

* Test fixes

* Ongoing work

* Test fix

* Compile fix

* Test fixes

* Test fix

* Test fix

* License header updates

* Remove fixme

* Cleanup

* Cleanup
2021-04-05 17:40:10 -04:00
Nick Goupinets d05b585426 Added a test for survivorship svc invocation 2021-04-01 19:38:53 -04:00
Nick Goupinets 9629aceff0 Removed obsolete test and added more control to replace fields in TU 2021-04-01 15:52:52 -04:00
Nick Goupinets 6b4d6702c1 Merge branch 'master' into 2515_MDM_survivorship_rules 2021-03-31 16:07:45 -04:00
Nick Goupinets ab8505dfc4 Removed deprecated TerserUtil 2021-03-31 16:07:21 -04:00
Tadgh 74be6761b1 Merge remote-tracking branch 'origin/master' into mdm-expansion-interceptor 2021-03-31 09:47:57 -04:00
Tadgh 007ce8fc6f add a test forthe case where there are no mdm links 2021-03-30 23:40:20 -04:00
Tadgh 8b69d161bd Update docs 2021-03-30 17:12:55 -04:00
Tadgh 419a5829ea This shockingly works 2021-03-30 12:39:37 -04:00
James Agnew 049097e5b4
Improve CapabilityStatement Generation (#2511)
* Start work

* Work on testing

* Version bump

* Test fix

* Compile fix

* Test Fixes

* Test fix

* Test fix

* Compile fix

* Tst fix

* Test fix

* Test fix

* Test fix
2021-03-30 05:48:03 -04:00
Tadgh a15ded7140 Interceptor now correctly intercepts at the right point 2021-03-29 21:12:03 -04:00
Nick Goupinets 7a9514b94a Initial fix 2021-03-29 20:43:43 -04:00
Tadgh 9f13225aa5 WIP interceptor using reference param modifier 2021-03-26 17:57:38 -04:00
Tadgh e6cfb77c79 Wip 2021-03-23 18:11:39 -04:00
Tadgh 6226ae02d5 Add basic skeleton of MDM expansion 2021-03-18 23:16:45 -04:00
Nick Goupinets c5342c116f Fixed orphaned channel setup 2021-02-12 14:06:44 -05:00
Tadgh 96b4e5ab38
Merge pull request #2324 from hapifhir/single-threading-mdm
Ensure Single threading mdm
2021-01-29 10:01:56 -05:00
Tadgh c572575412 Remove mutator 2021-01-25 09:55:31 -05:00
Tadgh aa37884b2e Worked on #2317, force single consumer 2021-01-25 09:51:50 -05:00
Nick 82e52750e7 Merge branch 'master' into ng_20201218_survivorship_poc 2021-01-21 09:00:28 -05:00
jamesagnew 078a94f1a6 Fix nonnull annotations 2021-01-21 08:47:44 -05:00
Nick f8c1591d21 post CDR review fixes 2021-01-20 16:44:48 -05:00
Nick 0cb6d56348 Code review followup 2021-01-19 11:33:39 -05:00
Nick f10785ed43 Code review updates 2021-01-15 14:07:14 -05:00
Nick 6cc40b134e Pre-review commit 2021-01-14 20:35:09 -05:00
Nick 759f06ce48 Added optional manual override to link update 2021-01-14 14:24:59 -05:00
Nick 8a5651093b Renamed method param 2021-01-14 11:16:17 -05:00
Nick 07be675484 Reverted active flag check on golden resource 2021-01-14 11:10:34 -05:00
Nick e6f484cefd Added tests 2021-01-14 10:52:28 -05:00
Nick 6781718702 Survivorship 7 2021-01-12 19:08:54 -05:00
Nick 5aa85c7e17 Survivorship 6 2021-01-11 17:22:06 -05:00
Nick 9338a4e73e Survivorship 5 2021-01-08 19:25:25 -05:00
Nick bec056cf9d Survivorship 4 2021-01-07 17:36:04 -05:00
Nick 19341a17b7 Survivorship 3 2021-01-06 18:02:04 -05:00
Nick 51064ca6c0 Merge remote-tracking branch 'origin/master' into ng_20201218_survivorship_poc 2021-01-06 09:37:25 -05:00
Nick a4a173d5c7 Survivorship 2 2021-01-05 17:59:26 -05:00
Tadgh efc6809ea6
Replacing Hibernate Search 5 with Hibernate Search 6 (#2190)
* Beginning work on converting to hibernate search 6
* replace all out of date properties
* replace all POM references to old versions
* remove the shaded ES jars as HS6 supports 7.9
* Convert "Bridges" to RoutingBinder and RoutingBridge
* Modernize all indexing annotations
* Begin refactoring of search queries (wip)

* Fix spatial API changes, work on BaseTermReadSvcImpl

* Most of the way through the various filter property conversions

* Finished i think with BaseTermReadSvcImpl

* Compiling, but definitely broken

* Start test compilation failures

* All tests compiling (i think)

* remove suggest keywords operation

* Fix bootstrap errors, still have to deal with transient fields

* Rollback CR

* More refactoring, got IDs baked back into docs

* Fix coord util, fix a few more fields which require projection

* merge fixes

* begin refactor of valuesetexpansion tests

* fix another test

* Update tests

* remove todos, add TestContainers

* Fix descendant in

* Add testcontainers, fix another test

* fix more tests, replace embedded es

* Rip out embedded elastic, replace with TestContainer

* merge conflicts for new analyzers

* Bump to CR2 for hibernate search 6. Add forgotten CLI dep. Add backwards compatible codecs

* Remove dead deps, update testcontainer

* Remove java-hamcrest

* Pull asserts up, refactor tests to pass in RP tests

* Update V2 check

* Remove suggest keyword tests

* Split line for testing

* Fix perhaps one of the dumbest programming mistakes in my career so far

* Refactor tests which no longer rely on a strict known order

* Fix up test config, disable log test temporarily

* Remove log4j from being transitively pulled in. re-enable test

* Update log4j exclusions with new bridge. Update test to check for core class

* Move dependency to root pom in dep management section

* Update changelog, add changelog for HS6 with ES requirements. Remove dead comment

* update testst, remove todos

* Add hibernate props provider method, add elastic regexp query

* Add todo for high level client builder

* Modify ElasticsearchRestClientFactory to support HTTPS hosts

* Remove protocol extraction from rest url

* do we even need to index this...?

* remove purge of non-indexed resources

* Add longer timeout to testcontainers

* Add task to add docker CLI to azure pipeline via task, for testcontainers

* WIP remove this

* Dont update version

* Add test for duplicate termconcepts

* Use real hibernate ORM methods

* merge issues

* Add partitionsettigns bean to match master

* Trying to debug testcontainers on azure...

* Trying to debug testcontainers on azure...

* Run even on previous failure

* Fix testcontainer port binds

* Add full text logs attaching, and test reporting

* I love yaml

* Remove comment

* Refactor delta remove to not do a once-over traversal and flatten all children pre-delete. Resolves transaction commit boundary issue

* Modify TX beheaviour

* wip

* Rework to use config and mocked beans for partition-aware lastN

* rework to not use beans and just inject vars i need for test, keps test envs cleaner

* update azure pipeline to only copy test results

* Remove erroneous publish

* Always get test logs

* Make it so indexing works,

* Add todos

* revert deleteByPid

* Work on test fixes

* Test fixes

* Test fixes

* Another test fix

* Test fix

* Work on tests

* Test fixes

* All tests passing locally

* Fix test failure

* FIx build error

* Rename usages of HibernateDialectProvider -> HibernatePropertiesProvider

* Update ngram of token filters

* Tidying

* subvert the purpose of hibernate elastic props builder to inject template

* dead space

* Rename changed class

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-01-05 17:56:59 -05:00
Nick f4cf4bf54a Survivorship 2021-01-04 17:09:31 -05:00
jamesagnew cbb16ce3af License header updates 2021-01-01 16:40:46 -05:00
jamesagnew f30999b053 License header updates 2021-01-01 15:07:23 -05:00
Tadgh e79114e2ec
Un-revert the MDM changes, now that issues have been addressed (#2226)
* Backward compatibility changes

* Revert "Revert "Remove all references to Person from EMPI.""

* Updated docs

* Removed mdm channel references

* Initial implementation

* fix coarseness bug. Fix tests. reinitialize silly bean

* Add forgotten json file

* Generic provider PoC

* Refactored provider to use BundleBuilder

* Removed version-specific MDM providers

* Addressed code review comments

* Fixed after merge

* Fixed docs

* MDM SVG for Update Use Cases

* Removed obsolete docs

Co-authored-by: Nick <nick.goupinets@smilecdr.com>
Co-authored-by: Nick Goupinets <73255752+nvg-smile@users.noreply.github.com>
2020-12-17 10:12:53 -05:00
Tadgh 0938d72b51
Revert "Remove all references to Person from EMPI." 2020-12-09 14:57:00 -05:00
Nick b3a9ab20dc Updated wording assertion in exception tracing 2020-12-08 19:05:21 -05:00
Nick 4c7b597983 Addressed more code review comments 2020-12-08 15:32:01 -05:00
Nick efb429b319 Fixed todos and reverted FK check in the test 2020-12-08 13:00:02 -05:00
Nick b503d50b67 Addressed failures 2020-12-07 19:18:58 -05:00
Nick fd90eb699f Review updates 2020-12-07 18:03:56 -05:00
Nick 5c40afb0c9 Updated doc headers 2020-12-03 16:11:10 -05:00
Nick 4352e0a61f Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-12-03 11:28:21 -05:00
Nick Goupinets 6d74f4f398 Fixed alert 2020-12-02 21:00:49 -05:00
Nick Goupinets ffee7a894f Removed person refs 2020-12-02 17:41:42 -05:00
Nick Goupinets db28a94eee Resolved alerts 2020-11-30 09:09:38 -05:00
Nick Goupinets dc2a9e55c5 Renamed sourceResource to goldenResource 2020-11-27 16:53:47 -05:00
Nick Goupinets 36ce84335a Renamed sourceResource to goldenResource 2020-11-27 16:53:21 -05:00
Nick Goupinets 8a7dc4e80b EMPI to MDM 2020-11-27 15:12:21 -05:00
Nick Goupinets 03643a7b3c Fix for bean scope inconsistenices 2020-11-25 17:37:37 -05:00
Nick Goupinets b44ae49dd2 Removed hardcoded references to the supported MDM types 2020-11-19 13:37:45 -05:00
Tadgh 3209faf2fb Rename package and module 2020-11-18 21:55:29 -05:00