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902 Commits

Author SHA1 Message Date
markiantorno 3fdb7c8408 conversion issues fixed, validation issues next 2021-08-19 13:48:59 -04:00
Tadgh e92fd47b16 Bump core ver 2021-08-17 18:07:23 -04:00
Tadgh cf917d0f82 Version Bump 2021-08-15 16:54:38 -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
Tadgh e076b30eef bump Jetty for CVEs 2021-07-27 15:49:00 -04:00
Tadgh 07cb3ff427 Bump commons-compress version 2021-07-27 09:14:05 -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
jamesagnew a5e6674e84 Version bump to 5.5.0-PRE7-SNAPSHOT 2021-07-22 08:41:16 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
jamesagnew 59653759ed Update tests 2021-06-23 15:58:14 -04:00
James Agnew 8b205b23d0
Fix history paging (#2741) 
* Fix history paging

* Add changelog

* Add license header
 2021-06-18 17:47:51 -04:00
James Agnew 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
Ken Stevens 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
jamesagnew 376a84d213 Version bump 2021-06-14 13:12:34 -04:00
dependabot[bot] 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
James Agnew 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
James Agnew 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
jamesagnew f5c75e80de Credit for #2693 2021-06-01 10:53:53 -04:00
James Agnew 786112284b
Bump spring version (#2687) 2021-05-30 19:04:14 -04:00
James Agnew 8d377fbf76
Add bulk import instrumentation (#2685) 
* Add batch job instrumentation

* Add bulk import instrumentation

* Fix build
 2021-05-30 11:47:51 -04:00
James Agnew 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
jamesagnew ff2698d4d1 Merge branch 'rel_5_4' 2021-05-19 09:22:11 -04:00
jamesagnew 994f09e125 Version bump 2021-05-18 21:05:50 -04:00
jamesagnew de56f440cb Version bump 2021-05-18 17:14:14 -04:00
James Agnew 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
jamesagnew 2068372998 Version bump 2021-05-07 17:43:54 -04:00
jamesagnew 63c4b22cd3 Undo bump 2021-05-07 17:42:50 -04:00
jamesagnew 17e41520a4 Version bump 2021-05-07 17:41:39 -04:00
dependabot[bot] 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
dependabot[bot] 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
jamesagnew 5db01f3139 Build fixes 2021-05-03 05:57:45 -04:00
James Agnew 593230f6bf
Fix openapi redirect (#2624) 
* Fix redirect for openapi

* FIx deps
 2021-05-03 05:32:34 -04:00
James Agnew 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
James Agnew 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
James Agnew 292b350f2c
Bump Junit for to avoid OWASP flag (#2618) 2021-04-30 14:39:16 -04:00
Tadgh 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
Tadgh 78271a2931 Create tests for all possiblye use cases 2021-04-29 15:25:11 -04:00
Kevin Dougan SmileCDR 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
JP 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
James Agnew 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
jamesagnew 1d054054c7 Test fixes 2021-04-27 07:03:24 -04:00
jamesagnew 987264b271 Version bump JENA 2021-04-25 17:38:04 -04:00
James Agnew 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
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -04:00
dependabot[bot] 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
dependabot[bot] 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
dependabot[bot] 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
James Agnew 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
jamesagnew 7cf061d76b Jetty version bump 2021-04-06 21:15:11 -04:00
James Agnew 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