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
e076b30eef
bump Jetty for CVEs
2021-07-27 15:49:00 -04:00
07cb3ff427
Bump commons-compress version
2021-07-27 09:14:05 -04:00
0a256fef77
Upgrade net.java.dev.jna dependency to support Mac M1 ARM architecture.
2021-07-23 14:58:10 -04:00
a5e6674e84
Version bump to 5.5.0-PRE7-SNAPSHOT
2021-07-22 08:41:16 -04:00
f66f9b992e
Bump pre-version as this will break downstream implementations
2021-06-30 15:37:19 -04:00
59653759ed
Update tests
2021-06-23 15:58:14 -04:00
8b205b23d0
Fix history paging ( #2741 )
...
* Fix history paging
* Add changelog
* Add license header
2021-06-18 17:47:51 -04:00
659efa786c
ValueSet Expansion Should Preserve Order ( #2724 )
...
* Add test
* FIxed
* Add changelog
* Add test
* Intermittent test failure fix
* Build fix
* Build fix
* Test fix
* Test fixes
* Fix checkstyle issue
* Test fix
* Add test logging
2021-06-16 07:20:59 -04:00
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
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
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
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
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
2c722e64c2
Add support for including qualified star syntax ( #2672 )
...
* Add support for including qualified star syntax
* Add changelog
* Add docs
* Build fix
2021-05-23 16:50:37 -04:00
ff2698d4d1
Merge branch 'rel_5_4'
2021-05-19 09:22:11 -04:00
994f09e125
Version bump
2021-05-18 21:05:50 -04:00
de56f440cb
Version bump
2021-05-18 17:14:14 -04:00
b31bb945ad
Add include clause to MSSQL forcedid table index ( #2659 )
...
* Add include clause to MSSQL forcedid table index
* Add changelog
* Test fix
* Bump MSSQL version
2021-05-16 19:14:51 -04:00
2068372998
Version bump
2021-05-07 17:43:54 -04:00
63c4b22cd3
Undo bump
2021-05-07 17:42:50 -04:00
17e41520a4
Version bump
2021-05-07 17:41:39 -04:00
9e61136c2d
Bump greenmail from 1.5.11 to 1.6.3 ( #2626 )
...
Bumps [greenmail](https://github.com/greenmail-mail-test/greenmail ) from 1.5.11 to 1.6.3.
- [Release notes](https://github.com/greenmail-mail-test/greenmail/releases )
- [Commits](https://github.com/greenmail-mail-test/greenmail/compare/release-1.5.11...release-1.6.3 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-05-03 17:31:03 -04:00
91fa23b11a
Bump fhir_core_version from 5.3.10 to 5.3.11 ( #2625 )
...
Bumps `fhir_core_version` from 5.3.10 to 5.3.11.
Updates `org.hl7.fhir.utilities` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.convertors` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.validation` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.dstu2` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.dstu2016may` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.dstu3` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.r4` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.r4` from 5.3.10 to 5.3.11
Updates `org.hl7.fhir.r5` from 5.3.10 to 5.3.11
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-05-03 07:58:55 -04:00
5db01f3139
Build fixes
2021-05-03 05:57:45 -04:00
593230f6bf
Fix openapi redirect ( #2624 )
...
* Fix redirect for openapi
* FIx deps
2021-05-03 05:32:34 -04:00
0cea403800
Fix vulnerability warning on maven plugin ( #2621 )
...
* Fix vulnerability warning on maven plugin
* Compile fixes
* Fix bootstrap dep
* Test fix
* Fix tests
* FIx deps
2021-05-02 12:14:32 -04:00
970a9884f0
Avoid tag definition constraint ( #2620 )
...
* Avoid tag definition constraint failure
* Version bumps
* Add changelog
* Avoid guava issue
* Test fix
* Test fix
* Bump pom
2021-05-01 17:16:15 -04:00
292b350f2c
Bump Junit for to avoid OWASP flag ( #2618 )
2021-04-30 14:39:16 -04:00
983d811af6
Merge pull request #2587 from hapifhir/issue-2585-enhance-placeholder-targets-logic
...
Issue 2585 enhance placeholder targets logic
2021-04-30 12:55:27 -04:00
78271a2931
Create tests for all possiblye use cases
2021-04-29 15:25:11 -04:00
646faa10e1
2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.10 ( #2545 )
...
* 2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.9.
* 2540 - Updated the Unit Test messages due to the upgraded dependencies.
* 2540 - Fixed some additional Unit Test message checks.
* 2540 - Updated the POM to refer to fhir_core_version 5.3.10-SNAPSHOT so a FULL Pipeline Build can run to verify that everything is fixed now.
* 2540 - Added some DEBUG Sysout logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...
* 2540 - Added some more logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...
* 2540 - Updated a Unit Test to account for a newly returned search param.
* 2540 - Updated a Unit Test to account for a newly returned search param and removed some debug output.
2021-04-29 15:00:37 -04:00
239d2496ea
CQL hardening and Dstu3 unit tests ( #2450 )
...
* WIP for elm caching
* Bug fixes and a working DSTU3 unit test
* More tests, Address review feedback, add initial docs
* Update to cql-evaluator 1.2.0
* Fixes for documentation
2021-04-29 14:52:13 -04:00
95d7ba6fa8
Streamline Search SQLs ( #2576 )
...
* Streamline SQL queries
* SQL query tidying
* Add changelog
* Test fixes
* Tests passing
* Ongoing work
* Test fixes
* Test fixes
* Build fix
* Cleanup
* Fixes
2021-04-28 10:29:09 -04:00
1d054054c7
Test fixes
2021-04-27 07:03:24 -04:00
987264b271
Version bump JENA
2021-04-25 17:38:04 -04:00
2ba1005762
OpenAPI Support ( #2560 )
...
* Start work on OpenAPI
* Fixes
* Work on OpenAPI
* Cleanup
* Cleanup
* More swagger work
* Build fix
* More work
* More work
* Add documentation
* Docs fixes
* Add changelog
* License updates
* Add API
* Cleanup
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
* Work on scripts
* Add docs
* Compile fix
* Work on fixes
* Fix tests
* Test fix
* Test fix
* Build fix
* Tests
* Build fix
* Work on pipeline
* Version bump
* Test fix
* Version bump
* Test fix attempts
* Test fix
* Test fix
* Remove accidentally committed files
* Fixes
* Tets fixes
* Test fix
* Test fix
* Test fix
* Test fixes
* Test fixes
* Test fixes
* License header updates
* test fix
* Test fixes
* Test fix
* Test fixes
* Test fix
* Checkstyle bump
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
2021-04-25 15:40:50 -04:00
4e266462ec
Bumped up version due to breaking changes
2021-04-20 16:17:27 -04:00
d94611edf6
Bump junit_version from 5.7.0 to 5.7.1 ( #2554 )
...
Bumps `junit_version` from 5.7.0 to 5.7.1.
Updates `junit-jupiter` from 5.7.0 to 5.7.1
- [Release notes](https://github.com/junit-team/junit5/releases )
- [Commits](https://github.com/junit-team/junit5/compare/r5.7.0...r5.7.1 )
Updates `junit-jupiter-api` from 5.7.0 to 5.7.1
- [Release notes](https://github.com/junit-team/junit5/releases )
- [Commits](https://github.com/junit-team/junit5/compare/r5.7.0...r5.7.1 )
Updates `junit-jupiter-engine` from 5.7.0 to 5.7.1
- [Release notes](https://github.com/junit-team/junit5/releases )
- [Commits](https://github.com/junit-team/junit5/compare/r5.7.0...r5.7.1 )
Updates `junit-jupiter-params` from 5.7.0 to 5.7.1
- [Release notes](https://github.com/junit-team/junit5/releases )
- [Commits](https://github.com/junit-team/junit5/compare/r5.7.0...r5.7.1 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-04-15 08:23:30 -04:00
05b1323638
Bump jarchivelib from 1.0.0 to 1.1.0 ( #2553 )
...
Bumps [jarchivelib](https://github.com/thrau/jarchivelib ) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/thrau/jarchivelib/releases )
- [Commits](https://github.com/thrau/jarchivelib/compare/v1.0.0...v1.1.0 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-04-15 08:21:33 -04:00
9a67f3ee0c
Bump spring_boot_version from 2.4.1 to 2.4.4 ( #2550 )
...
Bumps `spring_boot_version` from 2.4.1 to 2.4.4.
Updates `spring-boot-starter-test` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-test` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-maven-plugin` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-dependencies` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-autoconfigure` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Updates `spring-boot-configuration-processor` from 2.4.1 to 2.4.4
- [Release notes](https://github.com/spring-projects/spring-boot/releases )
- [Commits](https://github.com/spring-projects/spring-boot/compare/v2.4.1...v2.4.4 )
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-04-14 20:09:37 -04:00
ca2088f3ad
Add framework for Bulk Import ( #2538 )
...
* Start work on bul;k import
* Work on bulk import
* Have batch working
* Working
* Working
* More work
* More work on bulk export
* Address fixmes
* License header updates
* Test fixes
* License header updates
* Test fix
* Test fix
* Version bumps
* Work on config
* Test cleanup
* One more version bump
* Version bump
* CLeanup
* A few additions
* Test fixes
* Test fix
* Test fix
* Migration fix
* Test fix
* Test fix
2021-04-14 17:41:32 -04:00
7cf061d76b
Jetty version bump
2021-04-06 21:15:11 -04:00
a6cbf7eebd
Add support for hierarchycal valueset expansion ( #2525 )
...
* Add support for hierarchycal valueset expansion
* Add changelog
* Add tests
* Cleanup
* Test fix
* Test fixes
2021-04-06 17:36:54 -04:00
b617c7690d
Search Parameter Infrastructure Cleanup ( #2522 )
...
* Search param service cleanup
* Work on collapsing search param
* Search param cleanup
* Work on build
* Test fix
* Test fixes
* Ongoing work
* Test fix
* Compile fix
* Test fixes
* Test fix
* Test fix
* License header updates
* Remove fixme
* Cleanup
* Cleanup
2021-04-05 17:40:10 -04:00
8759cdae00
Additional cleanup
2021-03-30 08:20:14 -04:00
b720c32c1d
Version bump
2021-03-29 18:23:16 -04:00
Ken Stevens
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dependabot[bot]
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JP
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