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8096 Commits

Author SHA1 Message Date
Tadgh c64269054b
Merge pull request #2752 from hapifhir/2751-jv-bump-bulk-export-job-request-length 
Increase bulk export job request length
 2021-06-25 09:03:35 -04:00
Josiah 914cf53b62 Merge branch 'master' into 2751-jv-bump-bulk-export-job-request-length 2021-06-24 15:56:05 -04:00
Tadgh 8a2ad8dad2
Merge pull request #2755 from hapifhir/fix-test-bug 
Swap to URI instead of token for test
 2021-06-24 15:55:18 -04:00
Tadgh 8dcb6053a4 Swap to URI instead of token 2021-06-24 15:48:51 -04:00
Josiah a9208a88da Revert "Version bump" 
This reverts commit 1f5fa70fb6.
 2021-06-24 11:48:31 -04:00
Josiah 1f5fa70fb6 Version bump 2021-06-24 11:22:35 -04:00
Josiah 2cc27d9b4f Forgot changelog 2021-06-24 10:19:45 -04:00
Josiah eb0e2e20d7 Bump bulk export request length 2021-06-24 10:17:44 -04:00
Josiah 1ab3d0a159 Bump bulk export request length 2021-06-24 10:10:10 -04:00
jamesagnew 9bc4859761 Add test 2021-06-23 20:55:22 -04:00
jamesagnew 59653759ed Update tests 2021-06-23 15:58:14 -04:00
Nick Goupinets 6feaa12593
Merge pull request #2747 from hapifhir/2746_npe_in_mdm_utils 
Added null checks
 2021-06-23 09:51:53 -04:00
jamesagnew e3158045aa License header 2021-06-22 23:25:36 -04:00
James Agnew 068de6a708
Test cleanup (#2749) 
* Start work on tag mode 3

* Add changelog

* Test fix

* Test cleanup
 2021-06-22 23:09:03 -04:00
James Agnew 8379392e16
Add inline tag mode (#2748) 
* Start work on tag mode 3

* Add changelog

* Test fix
 2021-06-22 23:08:09 -04:00
Nick Goupinets 9caa5e68fc Added changelog 2021-06-22 15:52:21 -04:00
Nick Goupinets 5c9f2617da Code review 2021-06-22 15:23:03 -04:00
Nick Goupinets 95012623f6 Added null checks 2021-06-22 15:12:10 -04:00
Josiah 912b44c3fa
Merge pull request #2734 from hapifhir/2732-bump-conceptmap-group-element-display-storage-size 
Address #2732
 2021-06-21 08:33:36 -04:00
James Agnew 0d0a0fd6a2
Add transaction write semaphore interceptor (#2744) 
* Add transaction write semaphore interceptor

* Add changelog

* Test fix

* Two missing commits on TransactionConcurrencySemaphoreInterceptor

* License header
 2021-06-21 05:38:53 -04:00
jamesagnew f0cfb5ad1b License headers 2021-06-21 05:29:02 -04:00
James Agnew 6ea1438f1d
Add transaction write semaphore interceptor (#2743) 
* Add transaction write semaphore interceptor

* Add changelog

* Test fix
 2021-06-20 12:55:49 -04:00
Ken Stevens 0b05c730fb
don't create a channel if subscriptions are disabled. (#2733) 
* don't create a channel if subscriptions are disabled.

* review feedback

* fix test

* fix intermittent

* fix intermittent
 2021-06-19 00:00:16 -04:00
Ken Stevens 32ac16e2aa
add a limit to mdm candidate searches (#2742) 
* done

* verbal review feedback

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2739-max-mdm-matches.yaml

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

* review feedback

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2021-06-18 20:48:34 -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
Ken Stevens 097a2f70b3
add partition support to $evaluate-measure (#2736) 
* Finished adding partition support to $evaluate-measure

* review feedback
 2021-06-18 14:22:57 -04:00
Josiah 164e684d7c Merge branch 'master' into 2732-bump-conceptmap-group-element-display-storage-size 2021-06-17 15:14:05 -04:00
jamesagnew 5d246bcca8 License header 2021-06-17 14:40:00 -04:00
Josiah 324201b105 Make change 2021-06-17 11:28:02 -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
Kevin Dougan SmileCDR 6f680af3ce
SearchBuilder NPE (#2726) 
* Add failing test first.

* Fixed the NPE and enhanced the test.

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2021-06-15 11:50:18 -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
James Agnew 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
jamesagnew 48eea5a7cc Prepare changelog for 5.4.1 release 2021-06-14 09:13:41 -04:00
jamesagnew 474cca877a Merge branch 'rel_5_4_2' 2021-06-14 09:07:26 -04:00
jamesagnew 14070914ae Add test 2021-06-14 05:53:22 -04:00
jamesagnew 3ee05b5a62 Refactor transaction processing 2021-06-13 19:42:26 -04:00
jamesagnew a3fd23e70a Merge branch 'rel_5_4_2' 2021-06-13 19:36:11 -04:00
jmarchionatto 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
dependabot[bot] 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
jamesagnew 090dc9a2e2 Docs 2021-06-11 15:55:35 -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 fcb32eacb6
Add support for loinc 2.70 (#2721) 
* Add support for loinc 2.70

* Add changelog
 2021-06-11 15:15:22 -04:00
Nick Goupinets 3863e82a59
Fixed bug with choice children (#2714) 2021-06-08 08:24:13 -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
jamesagnew 4f1f09abb1 Merge branch 'master' of github.com:hapifhir/hapi-fhir 2021-06-04 20:40:51 -04:00
jamesagnew 3e4522be86 Add logging 2021-06-04 20:40:40 -04:00
Kevin Dougan SmileCDR 0143e83156
Added another try-with-resources local variable based on a lgtm.com report. (#2711) 2021-06-04 15:17:27 -04:00
jamesagnew 4f6c1eaedb Add license header 2021-06-04 14:50:10 -04:00