Commit Graph

69 Commits

Author SHA1 Message Date
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -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
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
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 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 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 2068372998 Version bump 2021-05-07 17:43:54 -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 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
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
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
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
James Agnew 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
Diederik Muylwyk b720c32c1d Version bump 2021-03-29 18:23:16 -04:00
James Agnew dc41d5ad61
Add terminology mapping and display population interceptors (#2488)
* Start work on code mapping interceptors

* Work on generation

* Add terminology mapping and display population interceptors

* Add changelog

* License header updates

* Test fixes

* Fix typo

* Interceptor fixes

* License header update

* Test fixes

* Mapping fixes

* Version bump

* License header updates

* Add null tests

* Add null guard

* Intermittent fix
2021-03-21 12:03:57 -04:00
hdconradi 8c4d522f11
Remove the trailing ,' from some of the schemata (#2413)
Co-authored-by: Heinz-Dieter Conradi <heinz-dieter.conradi@icw.de>
2021-02-23 13:46:10 -05:00
James Agnew 3eda19c65a
Version bump (#2400)
* Version bump

* Docs changes

* Docs tweaks

* Docs tweak

* Spelling fixes

* Docs tweaks
2021-02-18 11:07:49 -05:00
jamesagnew 919c1dbddc Version bump to 5.3.0 2021-02-17 07:10:13 -05:00
Bill Denton 84d9854e24
OSGi manifest maintenance (#2217)
* manifest cleanup and delete Fragment-Host

* make hapi-fhir-server-empi into an OSGi bundle
2020-12-18 16:48:44 -05:00
jamesagnew 0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew 4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -05:00
jamesagnew 92718c7ef2 Version bump to 5.2.0-SNAPSHOT 2020-08-12 10:23:46 -04:00
jamesagnew 5fb7bd5156 Version bump to 5.1.0 2020-08-11 17:43:24 -04:00
jamesagnew 52c8e3551c Version bump to 5.1.0-SNAPSHOT 2020-05-15 14:43:32 -04:00
jamesagnew fe0e07a313 Bump to 5.0.1 2020-05-15 05:47:01 -04:00
jamesagnew 1d13e29ac0 Version bump to 5.1.0-SNAPSHOT 2020-05-12 20:04:20 -04:00
jamesagnew d631ecff4a Prepare for 5.0.0 2020-05-12 11:49:18 -04:00
James Agnew 0c13a65871
Bump to latest Core version (#1841)
* Start working on bumping core

* Work on tests

* Work on tests

* Bump core definitions

* Bump R5 defs

* Tweak changelog

* Test fix
2020-05-11 12:37:16 -04:00
James Agnew 9d8bd0d51e
Bump R4 definitions to 4.0.1 (#1837)
* Bump R4 definitions to 4.0.1

* Add changelog

* Test fixes
2020-05-08 19:34:13 -04:00
James Agnew 22413911bf
Validation api changes (#1719)
* Validation enhancements

* Work on validation api reworking

* Keep working on validation API

* Keep working on new term API

* Work on validation api

* Ongoing work on validation

* Work on integrating validation

* Work on validation API

* Add to validation API

* Work on validation

* Work on API

* Work on validation

* Work on validation API

* Work on validation API

* Work on validation api

* Work on validation API

* Work on validation api

* Validation API changes

* Work on API

* More work on validationo API

* Work on validation API

* FIxes

* WOrk on validation api

* Work on validation API

* Tests passing!

* More cleanup

* More validation API changes

* Fix intermittent test failure

* Package reorg

* Validation API work

* Work on doocumentation

* Work on API

* More work on new validation API

* Fix errorprone-reported error

* Test fixes

* Documentation updates

* Documentation tweaks

* Work on API

* Bean name adjustments

* Build fixes

* Some test fixes
2020-03-17 13:28:59 -04:00
jamesagnew ddc7b601ee Version bump to 4.3.0-SNAPSHOT 2020-02-16 19:23:22 -05:00
jamesagnew 4fd80cfca7 Bump to 4.2.0 2020-02-16 19:00:15 -05:00
James Agnew 497a96ae68 Version bump for next round of development 2019-11-12 22:09:21 -05:00
jamesagnew f99ad981b5 Version bump to 4.1.0 2019-11-12 16:08:20 -05:00
James Agnew aa0301084b
Don't succeed validation on unknown codesystem (#1575)
* Don't succeed validation on unknown codesystem

* Test fixes

* Work on error messages

* Work on code validation API

* work on tests

* Work on validation

* Test fix

* Update DSTU3 validation reources

* Upgrade structures

* Test fixes
2019-11-12 14:35:49 -05:00
jamesagnew e1b43d811f Version bump to 4.1.0-SNAPSHOT 2019-08-14 14:06:06 -04:00
jamesagnew 3f22456b0f Bump version to 4.0.0 2019-08-14 11:06:26 -04:00
James Agnew 50a8c66bf5 Version bump to 4.0.0-SNAPSHOT 2019-05-30 17:13:03 -04:00
jamesagnew 73aa53be8f Release 3.8.0 2019-05-30 16:50:04 -04:00
James Agnew 0f8c8d18e2 Bump version to 3.8.0-SNAPSHOT 2019-02-06 20:02:28 -05:00
jamesagnew 207015c3af Version bump to 3.7.0 2019-02-05 21:36:38 -05:00
jamesagnew b3c9b32db4 Credit for #1065 and forward-port fix to R4 provider 2019-01-09 07:19:55 -05:00
James Agnew 14a132a937 Squashed commit of the following:
commit 9659655830
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Dec 27 17:54:25 2018 -0500

    Finish sync

commit 70da25b76f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Dec 27 10:32:51 2018 -0500

    Work on RI4 sync
2018-12-27 17:58:47 -05:00
jamesagnew cc57bacab8 Version bump to 3.7.0-SNAPSHOT 2018-11-12 10:07:28 -05:00
James Agnew 63af04a7b4 Prepare for 3.6.0 release 2018-11-12 05:40:55 -05:00
James Agnew 3e445faf47 Squashed commit of the following:
commit df641506885e09e63f80efc6c658d01a1a3a8142
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sat Sep 29 13:47:22 2018 -0400

    Shrink validation resources

commit 4c1550eafa26f4235b4b8804741aecc03276b5c6
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Sep 28 22:45:28 2018 -0400

    Updates to get R4 working

commit 8332f15291006691ed9b07ead3e3524b0fc85510
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Fri Sep 28 09:02:13 2018 -0400

    Ongoing work on gettign R4 working

commit f7146cab7aed937bb625a8aec95744d76db00041
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Sep 28 05:21:01 2018 -0400

    More work on sync

commit f48de4a10b1bab2584fee813017d9b27b237bfa9
Merge: 9e4f3cc722 aacb78b779
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:11:29 2018 -0400

    Merge branch 'sync_r4' of github.com:jamesagnew/hapi-fhir into sync_r4

commit 9e4f3cc722668aae31a77b19bf9b032af3ae01b0
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:11:19 2018 -0400

    Fix compile error

commit 7ec29e0ceda8f9013cbabb95767cbe15b4b81303
Merge: 23f7517325 002c4b3ff7
Author: James Agnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:04:23 2018 -0400

    Merge branch 'master' into sync_r4

commit aacb78b7793ab2c71e0a2a774240ee2b5d3f9e7f
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Sep 27 20:01:42 2018 -0400

    Keep working on getting R4 building

commit 4950de46d99897e74d41dfdb10d3d8a3435cb0c9
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Tue Sep 25 13:11:27 2018 -0400

    Ongoing work to get R4 working

commit 819d69c20e112dd3c72569ec50114ddb8263c300
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Sep 20 08:15:36 2018 -0400

    Work on getting build working

commit 2c61b6cd1205ced5d7b822cf10942c69272ea078
Merge: 16b5bb06c8 dfb4de86f1
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Thu Sep 20 05:16:53 2018 -0400

    Merge branch 'master' into sync_r4

commit 16b5bb06c8cdaf8d67c3b80f5aa9be9fccd99aef
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Mon Sep 17 05:30:39 2018 -0400

    Work on R4 sync

commit 23f7517325a14dd2ca1eb5641296ead2776634ae
Author: James Agnew <jamesagnew@gmail.com>
Date:   Sun Sep 16 10:19:00 2018 -0400

    Work on sync

commit 6cc413c1f1dea538295aa4c16c21a5677494ac4c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Sep 14 17:28:28 2018 -0400

    Work on R$ sync

commit df6f6ad2ce783b07ccc383134705d874bc5d2cf1
Author: jamesagnew <jamesagnew@gmail.com>
Date:   Fri Sep 14 08:33:07 2018 -0400

    Work on R4
2018-09-29 13:48:35 -04:00
James Agnew 706e004b9d Bump to 3.6.0-SNAPSHOT 2018-09-19 10:24:48 -04:00