Commit Graph

9198 Commits

Author SHA1 Message Date
Mark Iantorno 908c1de536 Adding full test run to Release Pipeline 2022-06-29 16:25:35 -04:00
michaelabuckley 9aac4f9ba8
Introduce memory-matcher based rules (#3677)
Extend rules with filters.

New rule extension, and consent service for post-query filtering.

Co-authored-by: josie <josie.vandewetering@smilecdr.com>
Co-authored-by: Jason Roberts <jason.roberts@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-06-29 18:23:12 +00:00
Mark Iantorno b54b7b133e Removing all triggers from release pipeline. 2022-06-29 13:27:57 -04:00
Mark Iantorno f3b4268bb6 Update release-pipeline.yml for Azure Pipelines 2022-06-29 13:25:13 -04:00
Ken Stevens 069f20a5f7
batch2 management operations api (#3742)
* first test passes.  onto the next one

* two down two to go

* three down one to go

* licenses

* basic admin-json plumbing confirmed with IT

* FIXME

* FIXME

* FIXME

* FIXME

* changelog

* bump hapi version to 6.1.0-PRE6-SNAPSHOT

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-28 23:02:17 -04:00
jmarchionatto 84fe58cc86
Hsearch namespace consolidation (#3733)
* Initial implementation

* Implement job cancellation

* Works for date and token. Cleanup required.

* Works for string and quantity.Cleanup pending.

* Works for reference and perform cleanup.

* Cleanup configuration and add missing tests

* Eliminate sort property registry (no go for a cluster) for a static property map.

* Missed in previous commit

* Implement HSearch number parameter

* Implement HSearch number sorting

* Unify different hibernate search names (HibernateSearch, Freetext and Lucene) to HSearch

* Move analysis configures for lucene and elastic to same file to enforce the need to keep them in synch

* Use new defined constant

* Rename package too

* Rename additional elastic references

* bump version to 6.1.0-PRE5-SNAPSHOT

* Restore Hap prefix to hapi configurers

* fixing hapi version of new maven module

* fix pom

* fix pom

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-28 18:38:05 -04:00
Ken Stevens f4629822f1
make mdm-clear partition aware (#3741)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-26 14:32:00 -04:00
Ken Stevens c3f34099fb
only register mdm clear job definition if it is not registered yet (#3740)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-26 14:10:42 -04:00
Ken Stevens 49d298dba1
mdm clear move to batch2 (#3671)
* begin with failing test

* continue building out

* continue building out

* reworking chunk api

* replace ChunkId zippers with proper iterator

* progressing test

* yay test passes!

* switch to idchunk interface

* fixmes

* compiles

* fixme

* fixme

* rename classes

* rename json classes with json suffix

* work towards homogeneous chunks

* fixme

* fixme

* unit test

* fixme

* fixme

* pull out builder

* moar tests

* moar tests

* preserve order

* moar test

* moar test

* fixme

* fixme -> wip to start ci

* msg code

* msg code fix test

* fixme

* change provider implementation

* final WIPs

* IT failing

* IT passes

* java 11

* fix test

* fix test

* fix test

* changelog

* use batch size if provided

* last WIP

* fix test

* fix test

* fix test

* whitespace change to trigger new build

* fix test

* bumping hapi version

* bumping hapi version

* fix test

* review feedback

Co-authored-by: Ken Stevens <ken@Kens-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-25 20:26:44 -04:00
Mark Iantorno fe99c36d97 Update release-pipeline.yml for Azure Pipelines 2022-06-23 13:53:49 -04:00
Mark Iantorno febd40c4ff Adding release pipeline.
[skip ci]
2022-06-23 09:54:03 -04:00
jdar8 ac006ba7d7
Unknown resource type error message contains plain providers (#3711)
* fix and test

* change stream

* change variable name

* modify test

* changlog

* changlog

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>
2022-06-22 14:26:15 -04:00
jmarchionatto e7ce41e5b8
Freetext search sort (#3695)
* Works for date and token. Cleanup required.

* Works for string and quantity.Cleanup pending.

* Works for reference and perform cleanup.

* Cleanup configuration and add missing tests

* Eliminate sort property registry (no go for a cluster) for a static property map.

* Missed in previous commit

* Implement HSearch number parameter

* Implement HSearch number sorting

* Replicate new normalizer configuration from HapiElasticsearchAnalysisConfigurer to HapiLuceneAnalysisConfigurer.
Replace deprecated word filter factory

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-06-22 10:31:01 -04:00
Qingyixia dce330eb01
Fix to the issue (#3723) 2022-06-21 16:29:35 +00:00
TipzCM 48c28997e6
3662 batch2 reduction step (#3681)
* adding a bunch of stuff

* most of the steps are working now

* writing more tests

* adding more tests

* updated the batch2 coordinators

* updating version

* some minor test tweaks

* added a new test

* adding more tests

* blah

* blah

* review fixes 1

* fixing tests and refactoring

* review points

* updated for code review

* review fixes

* updated

* step 1 on review step 5

* final touches

* blah

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-20 18:59:01 +00:00
imageRAD 46fdc03151
Update points.json (#3718)
imageRAD HealthChain project record has been added.
2022-06-20 09:59:30 -04:00
Ken Stevens 427bdf330e
fix 403 on updates when version submitted without rewrite header (#3716)
* fix 403 on updates when version submitted without rewrite header

* change log

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2022-06-17 19:51:47 +00:00
JasonRoberts-smile a18c83ae13
replace UNION with UNION ALL in chained search query (#3715) 2022-06-17 16:10:21 +00:00
Tadgh 4fbbf4366c
Add impl test and changelog (#3713) 2022-06-16 21:11:15 -04:00
JasonRoberts-smile cedeaa04f1
add support for in and not-in qualifiers (#3680)
* add support for in and not-in qualifiers

* fix failing test

* fix broken test

* fix broken tests

* code review comments

* Make dependency on IValidationSupport optional

* create IValidationSupport dependency only if needed

* small design improvements

* changelog

* rework validation support initialization

* Update hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/InMemoryResourceMatcher.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-06-16 20:17:57 +00:00
James Agnew ac8f4f1e56
Apply fix from #3270 (#3712)
* Apply fix from #3270

* Rework compare method
2022-06-16 15:46:14 -04:00
kateryna-mironova 93b89b2bd7
3702 mpi link add index (#3708)
* 3702 - added index to mpi_link

* added changelog file
2022-06-16 13:23:23 -04:00
StevenXLi 3da39aeda3
3658 adding updating with history rewrite feature (#3659)
* Updating With History Rewrite implementation

* Missed new files

* Updated changelog and documentation

* Fixed test failures and doc

* minor fix

* lgtm code refactor

* Fixed test to clear DaoConfig

* Removed unused class

* Code review changes

* Simplified updateHistoryRewrite's fluent, combining with normal update's, also changed logic on custom header error checking, updated tests

* refactored method to extracted common code

* removed `updateHistoryRewrite()` and replaced with `update()`, updated tests accordingly

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-06-15 12:40:58 -04:00
Tadgh bf2f126c91
Add changelog, add test, add implementation to short-circuit logic in group export (#3701) 2022-06-15 11:22:42 -04:00
Martin Ashby e2effc65b8
Upgrade okhttp_version to 4.9.3. (#3683)
* Upgrade okhttp_version to 4.9.3.

Remove dependency on okhttp.internal package.

Fixes https://github.com/hapifhir/hapi-fhir/issues/3682

* Include "okhttp/" before the okhttp version in the user agent.

Fixup GenericClientDstu3IT test expectation for the new okhttp version.

Fixes https://github.com/hapifhir/hapi-fhir/pull/3683#issuecomment-1151492939

* Remove the okhttp version from the user-agent.

For consistency with the apache-based client, also simplifies upgrade (tests won't fail).

Fixes https://github.com/hapifhir/hapi-fhir/pull/3683#issuecomment-1151589776
2022-06-14 09:59:02 -04:00
Tadgh 1eeb6112f6
Fix Patch in bundle to return Response Entry (#3678)
* Refactor test to cause failure

* Handle patch for entry response building

* add changelog

* Update hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-06-13 19:11:18 +00:00
StevenXLi 9336af4b0f
3684 subscription for delivering delete events formatted wrong (#3685)
* Fixed issue with delivering delete events Subscriptions

* Extracted deliverer class name to a constant, now shared across tests and interceptor class

* Added change log and doc changes

* moved the constant to a more appropriate place

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-06-13 18:04:49 +00:00
Etienne Poirier 05cb6c241c
3668 fhir patch operation returning 500 when patching in a transaction with a resource query in property request.url (#3675)
* Initial test exerting the issue.

* Providing fix and changelog

* Providing fix and changelog

* Providing a searchUrl or matchUrl based on the requestUrl.

* Providing fix and changelog

* Modification on test

* Modification on test

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: qingyixia <cherry.xia@smilecdr.com>
2022-06-13 09:15:09 -04:00
Tadgh 2c580dfa2f
Make a unique log folder name on publish (#3688) 2022-06-12 06:57:29 +00:00
Tadgh 10f49d862d Attribution for #3673 2022-06-08 08:53:18 -04:00
Patrick Werner 1b25a32567
set h2 to latest version to fix #3673 (#3676)
closes #3673
2022-06-08 08:50:11 -04:00
Etienne Poirier 868a7e5c40
3637 encapsulation of synchronous query execution capabilities into a new service for reuse (#3638)
* Adding test reproducing the issue.

* Providing implementation fixing the issue and strengthening integrated test.

* Cleaning up commended code.

* Preparing code for review.

* Adding test class SynchronousSearchSvcImplTest.

* Addressing first code review comments.

* Addressing first code review comments.

* Forcing one extra processing step to ensure exit condition is met.

* Adding tests

* Clean up in preparation of second code review.

* Addition of setting page size if required.

* Grouping synch test in nested test class.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2022-06-05 20:38:53 -04:00
longma1 1a90c7e9ce
added fix for subscription in default partition when default partitio… (#3670)
* added fix for subscription in default partition when default partition's id is null

* added changelog

Co-authored-by: Long Ma <long@smilecdr.com>
2022-06-03 18:54:54 +00:00
michaelabuckley 72823b730d
Add upgrade notes for upgrading SearchParameter indexing offline (#3666)
Add upgrade notes to support upgrading SearchParameter database indexing.
2022-06-02 15:46:34 +00:00
Ken Stevens a3de219a1e
replace search by example. (it caused a cryptic hibernate session error) (#3665) 2022-06-01 19:46:44 +00:00
michaelabuckley 92acd9b001
Avoid unsupported features during migrations on MSSQL (#3652)
Avoid unsupported ONLINE index operations on MSSQL Standard
2022-05-31 18:44:42 +00:00
Mark Iantorno 82e9a0d427 Updated GPG keys for signing. 2022-05-30 11:23:53 -04:00
Ken Stevens 4f4032d892
Issue 3648 fix mdm log messages (#3649)
* fix log messages

* fix log messages

* fix log messages

* fix log messages

* fix log messages

* fix log messages

* review feedback and fix log messages

* improved logging

* improved logging
2022-05-26 18:50:17 +00:00
jmarchionatto ad3294f8e8
Freetext search lastupdated param support (#3630)
* Initial implementation

* Implement job cancellation

* Handle uri, _tag, _security and _profile freetext search parameters

* Fix combined 'and' and 'or' clauses and add tests
Use collection instead of typed array to eliminate warnings

* Eliminate predicate nesting level

* Implement _source freetext search

* Implement _lastUpdated freetext search

* add ITestDataBuilder.withLastUpdated(String theIsoDate) method

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-26 18:41:12 +00:00
jmarchionatto 464a07e284
Freetext search tag types support (#3622)
* Handle uri, _tag, _security and _profile freetext search parameters

* Fix combined 'and' and 'or' clauses and add tests
Use collection instead of typed array to eliminate warnings

* Eliminate predicate nesting level

* Add changelog

* Implement revision suggestions

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-26 15:59:39 +00:00
Tadgh 6f5eea81b7
Jpaserver changes (#3632)
* Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider

* wip

* wip

* wip fix test

* move to override in test class

* Test fixes

* Add failsafe to other projects which have ITs

* Fix test

* Fix test to use transaction

* Move subscription loading

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-05-26 02:52:05 +00:00
Ken Stevens 66b3fa680b
fix fast-tracked job record count reporting (#3645) 2022-05-25 22:53:45 +00:00
jmarchionatto 4eb099b900
Freetext search source parameter support (#3641)
* Handle uri, _tag, _security and _profile freetext search parameters

* Fix combined 'and' and 'or' clauses and add tests
Use collection instead of typed array to eliminate warnings

* Eliminate predicate nesting level

* Implement _source freetext search

* Implement suggestions

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-05-25 20:07:29 +00:00
Ken Stevens fb6e5cf6ce
Batch 2 Maintenance refactor (#3631)
* SRP refactor maintenance

* SRP refactor maintenance

* cache jobDefinition in jobInstance when processing (rather than looking it up in a bunch of different places)

* begin with failing test

* test passes

* tests pass.  still need to add a few more tests

* add comment to trigger new ci

* added positive and negative tests for new behaviour

* fix IJ warnings

* change log

* change log

* fix test race condition

* resolved feedback

* review feedback
2022-05-25 04:16:58 +00:00
Tadgh a19c1ec996
Group Bulk Export rules exiting too early. (#3643)
* Implementation, test, changelog

* Add jira link
2022-05-25 00:14:36 +00:00
jamesagnew 5b7add9b81 License header 2022-05-24 15:56:31 -04:00
Ken Stevens df76b0f8f1
improve nickname matcher (#3628)
* improve nickname matcher

* change log

* review feedback and fix test
2022-05-24 17:13:09 +00:00
JasonRoberts-smile 1c70e97087
fix build failure (#3639)
* fix build failure

* add missing cleanup
2022-05-24 16:24:08 +00:00
JasonRoberts-smile b9579313ef
Jr 20220519 expunge config params (#3627)
* fix config settings for system-level expunge

* clean up expunge everything interface

* extract common system provider

* changelog

* version bump

* touch changelog to force a fresh pipeline

* re-enable publishing of checkstyle

* back out Gary's Sonatype change entirely
2022-05-23 18:55:42 -04:00
Tadgh bf6f763691
20220520 mdm test failure (#3629)
* wip fix test

* move to override in test class

* Test fixes

* Add failsafe to other projects which have ITs

* Fix test

* Fix test to use transaction

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2022-05-20 19:56:27 -04:00