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3387 Commits

Author SHA1 Message Date
Tadgh 77c99e47c1 TIL that anyString() wont match nulls in Mockito, but any() will 2021-08-19 15:15:51 -04:00
markiantorno 367b338d85 Updating HAPI to use latest core lib changes. 2021-08-18 11:06:14 -04:00
Tadgh cf917d0f82 Version Bump 2021-08-15 16:54:38 -04:00
Tadgh 669cf05b30 Modify SearchParameterMap toNormalizedQueryString to include value of _contained parameter 2021-08-12 14:25:12 -04:00
Tadgh 41ec1e03c0
Merge pull request #2880 from hapifhir/weird-contained-issue 
Contained Issue
 2021-08-11 08:27:54 -04:00
Tadgh e311835e8d Revert test 2021-08-10 18:44:42 -04:00
Tadgh a5c850b119 Pre-review cleaning 2021-08-10 17:37:24 -04:00
Tadgh daa3bc773e remove dummy test 2021-08-10 16:46:03 -04:00
Tadgh fe98162616 Add changelog 2021-08-10 14:59:03 -04:00
Tadgh 71ed25b77c Add commetn for juan 2021-08-10 14:58:47 -04:00
Tadgh 1cb6f490d6 Add dummy test. NOTE, remove before merge 2021-08-10 14:58:38 -04:00
Tadgh 2f42391ba8 wip 2021-08-10 14:58:30 -04:00
Tadgh e402804049 Add test json files 2021-08-10 14:58:24 -04:00
Tadgh 8f200c1819 Add a failing test 2021-08-10 14:58:17 -04:00
Tadgh 35afa8bbfa tidy 2021-08-10 14:57:51 -04:00
Tadgh 4c154951e2 Fully fleshed test, partial refactor 2021-08-10 14:56:57 -04:00
Tadgh 0a303a0e11 Add MDM expansion by golden pid 2021-08-06 13:22:08 -04:00
Michael Buckley e8e49f3ffa Pick d85a4e5ec2 for release branch 2021-08-04 16:34:48 -04:00
juan.marchionatto cb68c59fb5 Remove validation in code which will never reached for the conditions. 2021-08-03 15:39:02 -04:00
juan.marchionatto 45549d2bb9 Fix broken ITs. 
Add error message for non-snapshot upload with current version = false combination.
 2021-08-03 14:11:14 -04:00
juan.marchionatto 1ff1954cba Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control 2021-07-30 11:20:23 -04:00
juan.marchionatto 4e8b1719f3 Add test for fixed use case 2021-07-30 10:48:10 -04:00
Ken Stevens f5dfc3a5ed
New reindex spring batch operation (#2845) 
* first sweep to add new $reindex job

* first cut done.  next up integration test.

* start roughing out reindex everything

* Failing test

* test passes

* add BundleUtil helper method

* rough in processEverything

* rough in processEverything

* fix mock test

* merge master

* Make BaseJpaTest.mySrd lenient.

* fix test

* reindex everything works with FIXMEs

* reindex everything more tests

* moar tests

* moar tests

* fix test

* fix test

* fix regression and fix test

* fix test cycle

* fixme

* fix test

* test provider layer

* reindex everything partition aware

* yay last fixme!

* run reindex in partitioned threads

* add fixmes for areas that require extra testing

* added transaction and log message

* manual integration testing

* changelog

* reindex all partitions

* bump hapi version

* fix test

* moar test

* pre-review cleanup

* fix javadoc

* review feedback

* review feedback

* review feedback

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2845-reindex-operation.yaml

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* review feedback

* review feedback

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

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

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/IDeleteExpungeJobSubmitter.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
 2021-07-29 19:18:49 -04:00
juan.marchionatto 264dfee099 Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control 2021-07-29 16:21:56 -04:00
juan.marchionatto 1fcb36d84a Fix implementation to work also for use case where version is being updated. 
Use property instead of parameter.
 2021-07-29 15:54:00 -04:00
James Agnew f957661dda
Patient ID Partition Mode should support conditional create (#2828) 
* Fixes

* Test fix

* Add changelog

* Test fixes

* Test fixes

* Docs tweak

* Partitioning fixes

* Import fix

* Fix test data
 2021-07-26 14:18:58 -04:00
Ken Stevens 6bbb403fd1
When Client Id Strategy is set to NOT_ALLOWED, permit system requests to create resources (#2827) 
* resolved 2826

* fix regression
 2021-07-23 19:10:19 -04:00
juan.marchionatto ad6f7a204c Fix changelog syntax. Merge current master. 2021-07-22 10:49:16 -04:00
jamesagnew a5e6674e84 Version bump to 5.5.0-PRE7-SNAPSHOT 2021-07-22 08:41:16 -04:00
James Agnew d78fef6732
Fix NPE in IdHelperService (#2819) 2021-07-22 08:34:28 -04:00
IanMMarshall 8b8db82666
Enable Package Loader when partitioning is enabled with unnamed partitions (#2808) 
* Enable Package Loader when partitioning is enabled with unnamed partitions.

* Enable Package Loader when partitioning is enabled with unnamed partitions.

* Additional package loading problems found with partitioning.

* Additional package loading problems found with partitioning.

Co-authored-by: ianmarshall <ian@simpatico.ai>
 2021-07-22 05:17:17 -04:00
James Agnew 6d37749be8
Add non unique combo search params (#2809) 
* Start work on nonunique combo search params

* Work on SQL

* Version bump

* A fix

* Test fixes

* Fixes

* Undo version bump

* Test fixes

* Resolve fixme
 2021-07-21 19:14:14 -04:00
James Agnew 6af022062f
Fix issue with partitioning in patient ID compartment mode (#2810) 
* Fix issue with partitioning in patient ID compartment mode

* Add changelog
 2021-07-21 17:21:23 -04:00
juan.marchionatto e0e52c666c Add current-version parameter to upload-terminology command. 2021-07-21 16:18:35 -04:00
Michael Buckley cbb9a4355a Add details when we fail to load an element of a package definition. 2021-07-19 17:59:54 -04:00
Frank Tao 64f1643046
Added LOINC linguistic variants support (#2803) 
* Added linguistic variants for LOINC uploader

* Using static class

* Added the changelog
 2021-07-19 14:17:56 -04:00
Frank Tao 946080d709
Added ConsumerName to the loinc loader. (#2800) 
* Added ConsumerName to the loinc loader.

* Added extra test for coverage

* Added the changelog for LOINC CONSUMER NAME support
 2021-07-16 13:30:42 -04:00
James Agnew 0235296ba7
Add support for bulk export of multiple types (#2797) 
* Add support for bulk export of multiple types

* Add changelog
 2021-07-15 14:01:10 -04:00
Nick Goupinets ac31000377 Updated docs 2021-07-15 09:13:03 -04:00
Nick Goupinets 520cec1e15 Fixed link resolution 2021-07-14 11:30:09 -04:00
jamesagnew 6d4c2ef8f0 Expand access to SqlQuery 2021-07-08 16:16:27 -04:00
James Agnew d762a07817
Partition patient interceptor (#2766) 
* Start work on interceptor

* Implemented

* Add interceptor and docs

* Add docs

* Compile fix

* Test fixes

* Test cleanup

* Test fixes

* Test fixes

* Improve error message

* Add broken tests

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2766-add-patient-id-compartment-interceptor.yaml

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

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptor.java

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

* Address review comments

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2021-07-05 09:15:20 -04:00
jamesagnew 6bb5cbf764 Cleanup logging 2021-07-04 15:31:10 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
Tadgh a770d577cb Initial quick implementation of paging with tests 2021-06-29 17:46:03 -04:00
Ken Stevens 795fb31a3a
fixed mdm rules (#2764) 
* fixed mdm rules

* changelog

* review feedback jetbrains

* review feedback
 2021-06-28 23:24:37 -04:00
Ken Stevens 5565bf9930
fixed an issue with matching compartments to lists of ids (#2761) 
* fixed an issue with matching compartments to lists of ids

* change log
 2021-06-26 20:24:28 -04:00
Ken Stevens ea98e62656
collapse multiple owners for same compartment into shared compartment (#2760) 
* collapse multiple owners for same compartment into shared compartment

* changelog

* fix regression

* fix regression

* pre-review cleanup

* pre-review cleanup
 2021-06-26 11:48:47 -04:00
michaelabuckley 110173dafb
Merge pull request #2757 from hapifhir/2091-MemoryCacheService-confused-expiry 
Fix units on cache expiry
 2021-06-25 14:29:43 -04:00
Michael Buckley b31e464a90 Found bad growing cache scenario 2021-06-25 11:01:41 -04:00