Commit Graph

412 Commits

Author SHA1 Message Date
Ken Stevens f92c2bb5f9 ensure only one @PostConstruct method to make order explicit 2019-11-29 11:46:03 -05:00
Ken Stevens 37eef4e3e4 rename schedule interface methods 2019-11-29 11:04:35 -05:00
Ken Stevens 6f9cd56c81 moved scheduler up to hapi-server 2019-11-20 14:30:24 -05:00
Ken Stevens 8fca468e1f remove boolean from scheduling API 2019-11-19 10:13:22 -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 c8801f1977 Fix public erver 2019-10-30 09:08:13 -04:00
James Agnew 4a751cbfc5
Integrate Bulk Export (#1487)
* Start working on subscription processor

* Work on new scheduler

* Test fixes

* Scheduler refactoring

* Fix test failure

* One more test fix

* Updates to scheduler

* More scheduler work

* Tests now all passing

* Ongoing work on export

* Ongoing scheduler work

* Ongoing testing

* Work on export task

* Sync master

* Ongoing work

* Bump xml patch version

* Work on provider

* Work on bulk

* Work on export scheduler

* More test fies

* More test fixes

* Compile fix

* Reduce logging

* Improve logging

* Reuse bulk export jobs

* Export provider

* Improve logging in bulk export

* Work on bulk export service

* One more bugfix

* Ongoing work on Bulk Data

* Add changelog
2019-09-17 16:01:35 -04:00
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 31e374ded8 Credit for #1220 2019-08-12 13:35:27 -04:00
James Agnew 0c9e5ec1ea
Support GraphQL for R3/4/5 (#1424)
* Work on grpahql enhanbcements

* Add some more chars to the sanitizer function

* Add changelog
2019-08-12 08:24:32 -04:00
James Agnew 60eab3ad70
Add support for R5 resources (#1416)
* Work so far on R5 support

* Add support for R5

* Docs changes
2019-08-06 17:30:31 -04:00
James Agnew a4ca5374ec
Add terminology delta operations (#1401)
* Start work on delta operations

* Add changelog

* Some build fixes

* Move upload terminology command to CodeSystem resource

* Updates

* Some test fixes

* Add changelog

* Some test fixes

* More test fixes

* Test fix

* Add additional tests

* Transaction boundary fixes
2019-07-29 17:46:42 -04:00
James Agnew 55c0d5b604
Add binary storage for Attachments (#1386)
* Have this working now

* Add utility method

* Build fixes

* Add changelog
2019-07-17 18:31:17 -04:00
James Agnew 120b93f204
Use HL7 FHIR Core Structures (#1382)
* Ongoing work on core structures suport

* Ongoing work on this merge

* Ongoing work to clean up structures

* Credit for #1179

* Address compile issues

* Latest changes

* Work on parallel execution

* Work on getting tests passing

* Add H2 to migrator

* Test fix
2019-07-14 10:16:40 -04:00
James Agnew 1fd99dac63
Enable optional cascading deletes on JPA server (#1363)
* Start working on cascading deleets

* WOrk on cascading deletes

* Work on cascading deletes

* Enable cascading deletes

* Cascade deletes almost working

* FIx test

* Test fix
2019-06-28 17:32:39 -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 cb8634f26f
Ja interceptor callback fix (#1308)
* Interceptor callback fix

* Ensure that interceptor methods are called after a transaction
2019-05-14 18:47:11 -04:00
jamesagnew f5732d321d Enable websockets on the public server 2019-05-04 18:24:08 -04:00
James Agnew 9353ea5b06 Enable websockets on public HAPI server 2019-05-04 10:06:10 -04:00
James Agnew 8c7f065440 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-29 14:49:56 -04:00
James Agnew 37b9e1a42c Improve validation of enableWhen questionnaires 2019-04-29 14:43:42 -04:00
Ken Stevens 0feb3f5932 register subscription interceptors on uhn test server 2019-04-29 14:38:58 -04:00
Ken Stevens 381f422e98 enable subscriptions 2019-04-29 09:58:17 -04:00
Ken Stevens 130e879d04
Delete performance (#1286)
* move expunge out

* move to prototype

* turns parameters into fields

* cleanup control flow

* moved transactions outside of loops

* add expungeeverything

* moved daos out

* add expungeThreadCount

* add expungeBatchSize

* added partition runner to run in separate threads

* all done.  just need to consolidate test code.

* Moar tests

* consolidated pointcutlatch into hapi-fhir-jpaserver-model

* final cleanup

* update javadoc

* change log

* failing test

* added delete
also @Transactional

* remove unused parameter

* fix compile

* race condition

(cherry picked from commit e1940d2fb20838859a205f2b96c833b0ce9f05eb)

# Conflicts:
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/PartitionRunnerTest.java

* ja feedback

* ja feedback
2019-04-25 15:38:37 -04:00
James Agnew 738c2c1797
Interceptor framework refactoring (#1287)
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
James Agnew a8c76450e5 Re-enable contains searches on the public HAPI FHIR server and improve
message formatting in HapiLocalizer
2019-03-14 13:19:26 -04:00
James Agnew 00a8f8c759 Fix broken build 2019-03-12 13:13:13 -04:00
James Agnew 48c10bddc5
Narrative Generator refactoring (#1219)
* Starting work on this

* Working on narrative templates

* Work on new narrative system

* Account for some failing tests due to refactoring of narrative mode

* Another test fix

* More test fixes

* One more test fix

* Work on searches

* Address review comments
2019-02-27 14:59:57 -05:00
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
James Agnew e401ec86e4
Enhanced elements (#1192)
Squashed merge: Add elements exclude mode

* Start working on elements enhancement

* Work on elements projection

* Work on elements filter

* Feature is now working

* Just some cleanup

* Address compile issues
2019-02-03 16:41:33 -05:00
James Agnew 415ed80522 Get public HAPI FHIR server building again 2019-01-09 15:04:58 -05:00
James Agnew d091665ab6 Test fix 2019-01-09 14:40:43 -05:00
Ken Stevens 84a34eb3c9
Subscription module support (#1147)
* Reorganizing packages and dependencies to support standalone subscription running within a CDR container where all hapi modules are on the classpath.

Moved Subscription registry out of interceptor and introduced SubscriptionLoader

* Created ActiveSubscription and moved cache bits into it

* Moved ExecutorQueue stuff out into its own class

* Add test and supporting code to validate SubscriptionConstants.EXT_SUBSCRIPTION_RESTHOOK_DELIVER_LATEST_VERSION behaviour

* Added SubscriptionCheckingSubscriber

* Moved a few beans to @ComponentScan

* Replaced use of beanFactory with concrete factory classes

* Switched test to use subscribablechannel

* Added SubscriptionLoaderFhirClientTest

* Confirm that our SubscriptionProviderFhirClient works with a live fhir client

* Register interceptors with DaoConfig instead of RestServer.
Also, Rename @VisibleForTesting methods with ForUnitTest

* Fix triggering service so it uses new subscriptionmatcherinterceptor

* Renamed "Database" classes to "Dao"

* processing -> matching naming change
2018-12-18 13:09:06 -05:00
Ken Stevens 6baee4dc3f
Standalone subscription (#1125) 2018-11-30 17:19:16 -05:00
James Agnew b2179b1696 Syntax fixes for the JPA migrator 2018-11-30 12:39:37 -05:00
James Agnew b41c222880 Require explicit declaration of authorizationinterceptor operation rules
on whether the response is authorized or not
2018-11-23 14:25:46 -05:00
James Agnew 1de0ef405c Clean up test compile and reenable GraphQL on hapi.fhir.org 2018-11-16 11:15:44 +01:00
James Agnew 75210d614b Bump to 3.7.0-SNAPSHOT 2018-11-12 22:37:52 -05:00
James Agnew 63af04a7b4 Prepare for 3.6.0 release 2018-11-12 05:40:55 -05:00
James Agnew 5d5ee78873 API cleanup following JPA search performance enhancements 2018-10-03 07:43:01 -04:00
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
jamesagnew 5d60b90b81 Update refererence server to avoid long calls 2018-09-17 08:29:47 -04:00
James Agnew daef975734 Version bump to 3.5.0 2018-09-08 07:22:21 +08:00
James Agnew 6511545d25 Don't re-activate already active identical subscriptions 2018-08-17 11:56:33 -04:00
James Agnew acfe442cf9 Add equivalency flag to reverse lookup 2018-08-11 09:55:28 -04:00
James Agnew 03e7b018a6 Add skeleton for the $process-message operation in JPA erver 2018-07-12 17:52:24 -04:00
James Agnew bb637c5433 Work on presence API 2018-06-29 14:32:08 -04:00
James Agnew 32ddfff191 Improve indexing 2018-06-27 18:33:04 -04:00
James Agnew f0da7a33de Fix expunge transaction boundaries 2018-06-25 10:22:49 -04:00
James Agnew dd9031de32 Updates 2018-06-16 14:10:15 -04:00
Diederik Muylwyk 0e2c57fa60 Bumping version. 2018-05-28 17:44:38 -04:00
Diederik Muylwyk 2871920734 Preparing release. 2018-05-28 10:45:47 -04:00
James Agnew 2f2900e837 Improve indexing on JPA server in anticipation of a new indexing
strategy in HAPI FHIR 3.5.0
2018-05-23 08:09:57 -04:00
jamesagnew 7e83fc78cf Disable user resource and weaken validation on the public server 2018-05-21 19:04:37 -04:00
jamesagnew e8139192e0 FIx test issues 2018-05-21 13:07:11 -04:00
jamesagnew aa2d278520 Update vonk address 2018-05-16 21:46:09 -04:00
jamesagnew 4d62120a18 Fix issues reported by errorprone 2018-05-15 08:44:15 -04:00
James Agnew a3ff08d9ec
Replace phloc with ph for #775 (#930)
* Replace phloc with ph

* Enable schematron tests

* Make HAPI-FHIR ph-schematron on OSGI

* Work on getting tests passing

* Another test fix

* Fix up transaction handling for DSTU2

* Add changelog

* Avoid double transaction

* Dont use readonly

* One more test fix

* Update to snapshow build

* Resolve a circular dependency

* Try to fix tests

* Solve recurring NPE in DSTU2 tests

* Fix one more test

* Test fix

* More test threading fixes

* One more attempt to get tests passing

* Refactoring for tests

* Refactoring for tests
2018-05-14 17:38:40 -04:00
James Agnew f1ba0016b2 Improve the error message thrown by JPA server 2018-05-11 17:03:48 -04:00
Diederik Muylwyk d97fb8f5cf
709 the conceptmap operation called translate needs to be implemented (#923)
The ConceptMap operation $translate has been implemented.
2018-05-10 10:52:56 -04:00
James Agnew 8bfd7913c8 More work on loinc loader 2018-04-15 17:19:34 -04:00
James Agnew b6232b5683 loinc updates 2018-04-02 21:28:31 -04:00
jamesagnew 673a3d6272 Bump to JDK8 2018-03-30 08:54:04 -04:00
jamesagnew 180336e076 Sync to master 2018-03-29 06:54:24 -04:00
jamesagnew 53c2d8a38d Merge branch 'master' into loinc_loader_update 2018-03-29 06:21:55 -04:00
jamesagnew 418e82032f Prep for 3.3.0 2018-03-29 05:48:13 -04:00
jamesagnew 4ba56d5021 Reorganize the OSGI projects a bit 2018-03-28 06:15:28 -04:00
jamesagnew e5903f79f0 A bit of test cleanup 2018-03-23 07:15:22 -04:00
James Agnew 45a16fe066 More loinc work 2018-03-22 07:16:16 -04:00
James Agnew 6359f7f8a1 More work on loinc 2018-03-19 08:51:02 -04:00
James Agnew 81305fb17f Don't deliver subscription results for deleetd resource 2018-02-19 20:58:55 -05:00
James Agnew e52f582769 An experimental interceptor called VersionedApiConverterInterceptor has been added, which automaticaly converts response payloads to a client-specified version according to transforms built into FHIR. 2018-01-29 12:10:05 -06:00
James Agnew 16038ece26 Version bump to 3.3.0-SNAPSHOT 2018-01-23 10:31:01 -05:00
James Agnew 4dcce4e582 Fix #832 - Correctly normalize text with Korean characters 2018-01-21 14:55:14 +08:00
James Agnew 6468ca474a Verion bump to 3.2.0 2018-01-13 02:14:33 -05:00
James Agnew f58a03dacf Add some tests 2018-01-11 09:26:28 -05:00
jamesagnew ae9ab6c109 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2017-12-04 22:35:43 -05:00
jamesagnew 4de1f2cd90 Point test server at hapi.fhir.org 2017-12-04 22:35:24 -05:00
James Agnew 3e296f9d1b Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2017-11-25 17:53:01 -05:00
James Agnew 6afe6804db Fix #796 - Correctly escape spaces in generated URLs 2017-11-25 17:52:12 -05:00
jamesagnew 5b909b4746 Version bump to 3.2.0-SNAPSHOT 2017-11-24 13:32:47 -05:00
jamesagnew 42dd34252d Version bump to 3.1.0 2017-11-23 13:27:21 -05:00
jamesagnew aaed0c5876 Add some logging 2017-11-13 21:02:39 -05:00
James Agnew 49f4ac4fc5
Merge branch 'master' into analyzer-def-using-search-mapping 2017-11-13 13:32:40 -05:00
James Agnew 7c1ab11b02 Clean up places where CORS headers are declared - Related to #718 2017-10-30 16:37:47 -04:00
James d461567433 Allow cache-control to be used with CORS 2017-10-26 09:08:10 -04:00
James 0959156a4a Faster processing for mandatory count searches 2017-10-17 14:11:05 -04:00
James Agnew 290894557d Optionally require JPA server to collect count information even for
large searches
2017-10-13 06:31:37 -04:00
Jiajing LIANG 86fb1de3ae rename file 2017-10-09 18:34:49 +02:00
Jiajing LIANG 65c3a316f2 move out the analysers definitions from entity classes 2017-10-09 18:34:03 +02:00
James Agnew bacd0bfbbb Squashed commit of the following:
commit 7ff895de77
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Oct 6 15:25:06 2017 -0400

    More test fixes

commit c9fee23e48
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Oct 6 15:14:52 2017 -0400

    More tests work

commit c796e19458
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Oct 6 15:00:26 2017 -0400

    Get tests passing

commit eb2787d30c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Oct 6 14:08:23 2017 -0400

    Add an optimistic lock to the ResourceTable

commit ff85503acb
Author: James <jamesagnew@gmail.com>
Date:   Fri Oct 6 08:56:35 2017 -0400

    Add a test
2017-10-06 15:33:24 -04:00
James Agnew 87383ad802 Version bump to 3.1.0-SNAPSHOT 2017-09-27 21:23:34 -04:00
James 49bdaa1a45 Version bump to 3.0.0 2017-09-23 17:31:39 -04:00
James be07ebc4ef Subscription refactoring 2017-09-21 08:33:20 -04:00
James Agnew e94d639d29 Refactor websockets to use queuing mechanism 2017-09-14 21:29:57 -05:00