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8366 Commits

Author SHA1 Message Date
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 29545d9adc
Merge pull request #2879 from hapifhir/mail_cleanup 
fix SimpleJavaMail configuration username and password handling
 2021-08-10 10:48:56 -04:00
Vadim Karantayer f68040aae9 fix SimpleJavaMail configuration username and password handling 2021-08-10 10:45:30 -04:00
Tadgh 3edb59475c
Merge pull request #2877 from hapifhir/2876-npe-mdm-resource-util 
NPE in MdmResourceUtil
 2021-08-10 08:13:19 -04:00
Tadgh 97f88202eb Fix Changelog typo 2021-08-10 08:12:54 -04:00
Tadgh 1dfaf73066 Merge branch 'master' into 2876-npe-mdm-resource-util 2021-08-09 19:21:58 -04:00
Tadgh bfd9dffdbe Allow jira field in changelog 2021-08-09 19:09:40 -04:00
Tadgh 293bbe2a40
Merge pull request #2878 from hapifhir/backport-mdm-resource-util-npe 
Backport mdm resource util npe
 2021-08-09 18:53:50 -04:00
Tadgh 2d203302da Remove changelog as it will eventually create a duplicate 2021-08-09 16:20:46 -04:00
Tadgh 966e451587 Backport fix 2021-08-09 16:19:38 -04:00
Tadgh d5fe1eeef7 Move test out of IT 2021-08-09 16:13:47 -04:00
Tadgh 416a52c679 Add changelog, fix code 2021-08-09 16:02:19 -04:00
VK-SMILECDR 1e0f843d6c
2852 - Simplify java mail code (#2874) 
* testing

* [2852] adding SimpleJavaEmail

* [2852] refactor email sender code

* [2852] dependency cleanup

* [2852] add missing dependency

* [2852] add missing spring framework test dependency

* [2852] add change log

* [2852] add change log

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2852-simplify-java-mail-code.yaml

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

* [2852] minor test code cleanup

* [2852] add more tests

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2021-08-09 15:59:47 -04:00
Tadgh a7f0929405
Merge pull request #2875 from hapifhir/bump-version-5-6-0 
Bump version to 5.6.0-PRE1-SNAPSHOT
 2021-08-09 10:19:32 -04:00
Tadgh fa2b4ea0d7 Add version number 2021-08-06 14:08:10 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -04:00
Tadgh 0a303a0e11 Add MDM expansion by golden pid 2021-08-06 13:22:08 -04:00
Frank Tao 3c598e2ff8
Fix loinc designation issue with FormalName (#2865) 
* Fix loinc designation issue with FormalName

* Changed Loinc designation name to 'FullySpecifiedName'
 2021-08-06 10:59:01 -04:00
Kevin Dougan SmileCDR 35d3e3689b
2829 - Add DSTU3 Support To UploadTerminologyCommand (#2832) 2021-08-05 13:07:50 -04:00
michaelabuckley 1df270c9b9
Merge pull request #2864 from hapifhir/mb-20210804-ioob-pick-to-release 
Pick d85a4e5ec2 for release branch
 2021-08-04 16:41:07 -04:00
Michael Buckley e8e49f3ffa Pick d85a4e5ec2 for release branch 2021-08-04 16:34:48 -04:00
Nick Goupinets 4be3334f6f WIP after persistence checked 2021-08-04 16:33:59 -04:00
michaelabuckley 67682a86fb
Merge pull request #2862 from hapifhir/mb-20210804-combo-index-ioob 
Hack to fix a weird IOOB error we can't reproduce.
 2021-08-04 16:24:47 -04:00
Michael Buckley d85a4e5ec2 Hack to fix a weird IOOB error we can't reproduce. 2021-08-04 16:08:38 -04:00
Nick Goupinets 2bc024fef9 Merge remote-tracking branch 'origin/master' into 2849_add_new_mdm_param 2021-08-04 11:06:35 -04:00
Nick Goupinets 891a6304d0 WIP 2021-08-04 11:06:14 -04:00
jmarchionatto 66e1f10f5f
Merge pull request #2821 from hapifhir/issue-2786-upload-terminology-command-add-explicit-current-version-control 
Issue 2786 upload terminology command add explicit current version control
 2021-08-03 16:55:49 -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
Nick Goupinets d467c1c79b yMerge branch 'master' into 2849_add_new_mdm_param 2021-07-30 11:18:33 -04:00
Nick Goupinets 0d34fe61c8 Adding tests 2021-07-30 11:17:56 -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
Nick Goupinets a2aa2ca1c3 2849 Added new parameter to MDM processing 2021-07-29 15:52:27 -04:00
Tadgh 1b9761c91b
Merge pull request #2840 from hapifhir/issue-2835-cve-jetty 
bump Jetty for CVEs
 2021-07-28 10:51:59 -04:00
Tadgh e076b30eef bump Jetty for CVEs 2021-07-27 15:49:00 -04:00
Tadgh 7c1d87b662
Merge pull request #2834 from hapifhir/issue-2833-commons-compress-cve 
Bump commons-compress version
 2021-07-27 11:00:19 -04:00
Tadgh 07cb3ff427 Bump commons-compress version 2021-07-27 09:14:05 -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
Ken Stevens 92ec113775
fixed bug (#2824) 2021-07-23 16:58:53 -04:00
michaelabuckley 91bbebad27
Merge pull request #2830 from hapifhir/mb-docker-mac-m1-arm 
Upgrade net.java.dev.jna dependency to support Mac M1 ARM architecture.
 2021-07-23 16:50:31 -04:00
Michael Buckley 2539f49662 Add detail to changelog 2021-07-23 15:07:36 -04:00
Michael Buckley d99f94e665 changelog 2021-07-23 15:00:48 -04:00
Michael Buckley 0a256fef77 Upgrade net.java.dev.jna dependency to support Mac M1 ARM architecture. 2021-07-23 14:58:10 -04:00
Ken Stevens 6f7f787813
fixed migration (#2822) 2021-07-22 14:07:10 -04:00