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8289 Commits

Author SHA1 Message Date
Michael Buckley e8e49f3ffa Pick d85a4e5ec2 for release branch 2021-08-04 16:34:48 -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
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
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
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
juan.marchionatto ad6f7a204c Fix changelog syntax. Merge current master. 2021-07-22 10:49:16 -04:00
juan.marchionatto ae0665131b Fix syntax. 2021-07-22 09:41:16 -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
jamesagnew 9f77c57e5a Widen access for utility methods 2021-07-20 17:30:26 -04:00
michaelabuckley 0ebf274d36
Merge pull request #2806 from hapifhir/2805-improve-package-error-messages 
Add details when we fail to load an element of a package definition.
 2021-07-20 15:41:05 -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
Mad Mirrajabi 5f2a3af01e
Add Innovattic B.V. to HAPI FHIR Global Atlas (#2798) 2021-07-15 14:00:33 -04:00
Nick Goupinets ddf3df4209
Merge pull request #2795 from hapifhir/2794_res_links_not_resolved 
Fixed link resolution
 2021-07-15 10:38:26 -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
Tadgh 744a95ae58
Merge pull request #2792 from hapifhir/2791-increase-identifier-length 
2791 increase identifier length
 2021-07-14 09:49:33 -04:00
Tadgh 554685d142 Fix MDM documentation 2021-07-13 16:08:01 -04:00
Tadgh a7e6813510 Update string length. Add migration 2021-07-13 15:46:47 -04:00
Tadgh 0a27b08aad
Merge pull request #2783 from hapifhir/2777-hapi-fhir-cli-Add-option-to-pass-request-headers-to-target-server 
Add changelog. Address MR comments.
 2021-07-09 09:35:56 -04:00
jamesagnew b48b1884b8 Add license header 2021-07-08 19:19:02 -04:00
Tadgh 218325b385
Add backport info for full diff between 5.4.1 and 5.4.2 (#2784) 2021-07-08 16:25:18 -04:00
jamesagnew 6d4c2ef8f0 Expand access to SqlQuery 2021-07-08 16:16:27 -04:00
juan.marchionatto 1e9163c636 Add changelog. Address MR comments. 2021-07-08 14:52:19 -04:00
jmarchionatto ee1f1fb5b8
Merge pull request #2778 from hapifhir/2777-hapi-fhir-cli-Add-option-to-pass-request-headers-to-target-server 
Add header-passthrough option to hapi-fhir-cli commands which generate http requests(#2777)
 2021-07-07 16:47:28 -04:00