134631fdee
Convert delete expunge to use Spring Batch ( #2697 )
...
* prepare to add $delete-expunge operation that will create a spring batch job
* Add operation
* Wire up jpa provider. Begin with failing test.
* Copy/paste bulk import job as a starting point.
FIXME with proposed design
* delete expunge job parameter validation with test
* implemented reader
stubbed processor, writer
* wip for master merge
* started implementing reader
* started implementing reader
* working with stubs
* happy path batch delete expunge is done
* Provider done but test not passing. Guessing batch infrastructure not running in that test.
* IT test works now
* add reader test
* Converted delete _expunge=true to use new batch job
* DeleteExpungeDaoTest passes
* Fix test
* Change batch size to integer
* rename search count to batch size
* Make delete expunge partition aware
* updated docs
* pre-review cleanup
* change log
* add partition id to SystemRequestDetails
* Make RequestPartitionId serializable
* Change delete expunge provider to use partition id instead of tenant name
* fix tests
* test pointcut gets called
* assert on pointcut calls
* Add resource type to STORAGE_PARTITION_SELECTED pointcut
* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants
* bump hapi-fhir version
* copyrights
* restore deleteexpungeservice for mdm
* restore deleteexpungeservice for mdm
* fix test
* public constants
* convert instant to date
* Moved expunge constants to ProviderConstants
* final review
* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run
* fix tests
* fix tests
* fix tests
* fix tests
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* improve logging
* bump version
* version bump
* recovering from failed merge
* unzip RequestListJson per Gary's suggestion. I didn't want to do it at first, but as usual Gary was right.
* fix serialization
2021-06-15 10:36:05 -04:00
376a84d213
Version bump
2021-06-14 13:12:34 -04:00
b934abb297
Impropve transaction Performance ( #2717 )
...
* Work on changes
* Work on perf
* Work on testing
* Work on perf
* Work on perf
* Work on fix
* Work on perf
* Ongoing work
* Add changelog
* Additional docs
* Test fixes
* Address review comments
* Test fix
2021-06-14 13:08:19 -04:00
48eea5a7cc
Prepare changelog for 5.4.1 release
2021-06-14 09:13:41 -04:00
474cca877a
Merge branch 'rel_5_4_2'
2021-06-14 09:07:26 -04:00
14070914ae
Add test
2021-06-14 05:53:22 -04:00
3ee05b5a62
Refactor transaction processing
2021-06-13 19:42:26 -04:00
a3fd23e70a
Merge branch 'rel_5_4_2'
2021-06-13 19:36:11 -04:00
39d7d4ad03
Use pageSize variable to hold page size ( #2719 )
...
* Use pageSize variable to hold page size as previously used variable has other function, so not always hols intended value required for previous link
* Adjust test to standards and use RestfulServerExtension instead of own server
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-06-11 17:29:14 -04:00
8e807c1436
Bump jetty_version from 9.4.39.v20210325 to 9.4.42.v20210604 ( #2722 )
...
Bumps `jetty_version` from 9.4.39.v20210325 to 9.4.42.v20210604.
Updates `jetty-http` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-servlets` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-io` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-continuation` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `jetty-security` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-servlet` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-server` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-util` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-webapp` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-xml` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `websocket-api` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `websocket-client` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `websocket-server` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `jetty-maven-plugin` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
---
updated-dependencies:
- dependency-name: org.eclipse.jetty:jetty-http
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-servlets
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-io
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-continuation
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-security
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-servlet
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-server
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-util
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-webapp
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-xml
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty.websocket:websocket-api
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty.websocket:websocket-client
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty.websocket:websocket-server
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-maven-plugin
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-06-11 15:57:58 -04:00
090dc9a2e2
Docs
2021-06-11 15:55:35 -04:00
c4b96d6dc7
Bump jetty_version from 9.4.39.v20210325 to 9.4.42.v20210604 ( #2722 )
...
Bumps `jetty_version` from 9.4.39.v20210325 to 9.4.42.v20210604.
Updates `jetty-http` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-servlets` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-io` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-continuation` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `jetty-security` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-servlet` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-server` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-util` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-webapp` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `jetty-xml` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
Updates `websocket-api` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `websocket-client` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `websocket-server` from 9.4.39.v20210325 to 9.4.42.v20210604
Updates `jetty-maven-plugin` from 9.4.39.v20210325 to 9.4.42.v20210604
- [Release notes](https://github.com/eclipse/jetty.project/releases )
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.39.v20210325...jetty-9.4.42.v20210604 )
---
updated-dependencies:
- dependency-name: org.eclipse.jetty:jetty-http
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-servlets
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-io
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-continuation
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-security
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-servlet
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-server
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-util
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-webapp
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-xml
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty.websocket:websocket-api
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty.websocket:websocket-client
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty.websocket:websocket-server
dependency-type: direct:production
update-type: version-update:semver-patch
- dependency-name: org.eclipse.jetty:jetty-maven-plugin
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-06-11 15:54:48 -04:00
fcb32eacb6
Add support for loinc 2.70 ( #2721 )
...
* Add support for loinc 2.70
* Add changelog
2021-06-11 15:15:22 -04:00
3863e82a59
Fixed bug with choice children ( #2714 )
2021-06-08 08:24:13 -04:00
dc627dc019
Add bulk export authorization layer ( #2712 )
...
* Add bulk export authorization layer
* Add docs
* Version bump
* Authorize any
* Add bulk export - all
* Address lgtm issue
2021-06-06 20:47:43 -04:00
4f1f09abb1
Merge branch 'master' of github.com:hapifhir/hapi-fhir
2021-06-04 20:40:51 -04:00
3e4522be86
Add logging
2021-06-04 20:40:40 -04:00
0143e83156
Added another try-with-resources local variable based on a lgtm.com report. ( #2711 )
2021-06-04 15:17:27 -04:00
4f6c1eaedb
Add license header
2021-06-04 14:50:10 -04:00
899caa1913
Update transaction service visibility
2021-06-04 14:18:19 -04:00
62be623cf5
Add support for ICD-10-CM ( #2702 )
...
* Add support for ICD-10-CM
* Have this working
* Fix LGTM issues
* Test fix
2021-06-03 19:55:16 -04:00
94d6b15db9
_filter searchparam should not appear in cap stmt if disabled ( #2706 )
...
* issue reproduced and fixed
* changelog
* cleanup
2021-06-03 18:45:49 -04:00
c498522c78
search by source reported incorrect size ( #2705 )
...
* issue reproduced in test and fixed
* changelog
2021-06-03 18:19:43 -04:00
d574c4625b
Merge pull request #2704 from hapifhir/2703-@RequiresDocker-annotation-check-fails
...
Fix DockerRequiredCondition check.
2021-06-03 15:58:38 -04:00
473de64ddc
Fix DockerRequiredCondition check.
...
Add @RequiresDocker annotation to two tests.
2021-06-03 14:14:47 -04:00
73afed86d7
Merge pull request #2701 from hapifhir/1811-generalize-request-tracing
...
Expose tracing code for sharing.
2021-06-03 09:10:59 -04:00
4d6c35ac12
Hide constructor for static helper
2021-06-03 09:09:54 -04:00
80266a20a2
Pull request tracing out for sharing
2021-06-02 21:25:06 -04:00
9401ecaf95
Merge branch 'master' of github.com:hapifhir/hapi-fhir
2021-06-02 16:47:12 -04:00
a0366befc4
Forward port fix
2021-06-02 16:47:02 -04:00
1d2b47c9fb
Update endpoint validation interceptors ( #2698 )
2021-06-02 05:39:01 -04:00
fe763dd2d6
Upgrade deps ( #2695 )
...
* Upgrade deps
* Fix build error
* Branch tweak
* Build fix
* Build fix
* Undo bump
* Test fixes
2021-06-01 12:03:29 -04:00
f5c75e80de
Credit for #2693
2021-06-01 10:53:53 -04:00
dfde993f2d
Allow lower case error message to also trigger retry ( #2693 )
...
* Allow lower case error message to also trigger retry
* similar data integrity exception on different table
Co-authored-by: Hedman, Bruno <bruno.hedman@rmp.uhn.ca>
2021-06-01 10:50:06 -04:00
05ac88bc21
Add initiate bulk export pointcut ( #2692 )
...
* Add initiate bulk export pointcut
* Add changelog
* Test fixes
2021-05-31 16:05:09 -04:00
94bd2400e3
Merge pull request #2689 from me-d4l/fix/update-chaelog-for-2682
...
Add CHANGELOG entry for ticket 2682
2021-05-31 12:16:13 +02:00
b9931dfb03
Add CHANGELOG entry for ticket 2682
2021-05-31 08:43:23 +02:00
a2950324ef
Avoid SQL based transaction dupe check ( #2688 )
...
* Avoid SQL based transaction dupe check
* Add changelog
* Test fixes
* Test fixes
2021-05-30 20:26:36 -04:00
786112284b
Bump spring version ( #2687 )
2021-05-30 19:04:14 -04:00
8d377fbf76
Add bulk import instrumentation ( #2685 )
...
* Add batch job instrumentation
* Add bulk import instrumentation
* Fix build
2021-05-30 11:47:51 -04:00
f34dd7ecd8
Merge pull request #2683 from me-d4l/feature/ignore-package-id-case
...
Make package ID handling case-insensitive (#2682 )
2021-05-29 17:12:43 +02:00
9aaf5ec5d8
Add logging to the test server
2021-05-28 11:23:57 -04:00
1703568840
Merge branch 'master' of github.com:hapifhir/hapi-fhir
2021-05-28 05:42:03 -04:00
5b93affca1
Add logging to test server
2021-05-28 05:41:53 -04:00
24b3f0f30d
Enable mass ingestion mode ( #2681 )
...
* Work on fixes
* Work on counts
* Enable mass ingestion mode
* Add changelog
* Test fix
* Test fix
* Test fixes
* Fixes
* Test fix
* Test fix
2021-05-27 18:43:51 -04:00
d70bbad6f1
Expand access
2021-05-27 12:15:37 -04:00
52ce8e35a7
Merge pull request #2679 from hapifhir/2678_mdm_identifier
...
Updated identifier matcher to only match on non-empty values
2021-05-27 09:35:07 -04:00
69d3e3f3ca
Add further test for non-matching IDs
2021-05-27 15:18:45 +02:00
cbfca6a560
Make package ID handling case-insensitive
2021-05-27 14:57:07 +02:00
8636e4f155
Test fix
2021-05-27 07:30:09 -04:00
Ken Stevens
jamesagnew
jmarchionatto
dependabot[bot]
Nick Goupinets
Kevin Dougan SmileCDR
juan.marchionatto
michaelabuckley
Michael Buckley
rbhman
Patrick Werner
morten.ernebjerg