Commit Graph

285 Commits

Author SHA1 Message Date
James Agnew 8b2ab51bc6
Handle canonical questionnaire refs in validator (#1544)
* Handle canonical questionnaire refs in validator

* FIx changelog

* Fix canonical reference

* Build tweak

* Change to trigger a build
2019-10-15 20:27:53 -04:00
James Agnew 1618ccc14c FIx compile error 2019-10-15 20:06:11 -04:00
James Agnew fdcf5f5d73 Add a test 2019-10-15 18:16:22 -04:00
James Agnew 836fac9a30 Ensure that JPA PRESHOW interceptor broadcasts don't include expunged
resources
2019-10-03 15:49:03 -04:00
Ken Stevens 98c76a4d49 Test passes 2019-10-03 12:03:38 -04:00
James Agnew a1bf50685d Work on cleanup 2019-09-30 21:40:41 -04:00
James Agnew c0eb662a21 Rationalize search param extractor 2019-09-28 19:23:21 -04:00
James Agnew 8657afb01e
Fix intermittent test failures regarding search (#1509)
* Add some logging

* Add more test logging

* Work on some test logging

* Fix compile error

* Work on codecov

* Work on codecov

* Remove test debug messages
2019-09-25 20:15:21 -04:00
jamesagnew 473fa3456e Work on adding codecov 2019-09-25 14:12:42 -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
Ken Stevens c974e9283b added search % now test 2019-09-10 10:11:09 -04:00
Ken Stevens abef4455eb done 2019-09-09 17:22:07 -04:00
Ken Stevens 7cfbf710fe Merge remote-tracking branch 'remotes/origin/master' into ks-in-memory-date-compare
# Conflicts:
#	src/changes/changes.xml
2019-09-09 14:46:25 -04:00
Ken Stevens 9e83f1d40a changelog 2019-09-09 14:22:42 -04:00
Ken Stevens cdbe527456 date comparison for in-memory matcher works now 2019-09-09 11:44:44 -04:00
Ken Stevens 02b8e14a7a first part of test passes now 2019-09-07 10:24:18 -04:00
Ken Stevens 15098109c8 start with failing test 2019-09-06 18:33:33 -04:00
James Agnew 718fcb28a5 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-09-06 14:58:03 -04:00
James Agnew 722c7a8211 Work on GraphQL updates 2019-09-06 14:56:17 -04:00
Ken Stevens fa62ab9c9e Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache
# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	src/changes/changes.xml
2019-09-04 13:31:00 -04:00
James Agnew f59bdc4afe Reuse FHIRPath across JPA requests 2019-08-29 14:13:31 -04:00
James Agnew 956bb39327 Resolve an inefficient regex expression 2019-08-29 13:59:31 -04:00
James Agnew 84836aed84 Fix accidental typo 2019-08-20 08:39:46 -04:00
James Agnew ce879b3863 Fix versioned API incompatibility with GraphQL 2019-08-20 08:35:27 -04:00
jamesagnew 54657214de FIx issue uploading US Core resources 2019-08-17 18:11:52 -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 6aa7916ba7
Merge pull request #1415 from jamesagnew/ks-inmemory-id-match
in-memory id match
2019-08-07 08:31:38 -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
Ken Stevens f9e86b5c83 revert public method 2019-08-06 15:38:23 -04:00
Ken Stevens 15e549f345 Add remaining cases to test 2019-08-06 15:25:22 -04:00
Ken Stevens c11d719957 Fix bug when in-memory matcher compares long id to string id 2019-08-06 15:17:09 -04:00
Ken Stevens 13a83567ae Start with failing test. 2019-08-06 15:04:27 -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 642e62a563 Improve toString method 2019-07-11 18:17:13 -04:00
jamesagnew dff2fdd3cf GET RID OF TRAILING LICENSE HEADER SPACES ONCE AND FOR ALL
YESSSSSSSSSSSSS
2019-07-05 11:19:51 -04:00
James Agnew 2a473d1825 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-07-05 09:03:23 -04:00
James Agnew 2a6436af23 Rename columns in code mapping 2019-07-05 09:03:03 -04:00
Ken Stevens 2b1ed16f68 Apply the same fix we used for Dstu3 2019-07-04 13:58:20 -04:00
James Agnew 10d969c514
Add Consent Service (#1359)
* Initial consent svc

* Ongoing consent svc work

* Add docs

* Ongoing consent service work

* Work on consent service

* More work on consent svc

* License header updates

* Ongoing consent svc work

* Some test fixes

* Some test fixes

* More work on consent svc

* Tests working

* Test fix

* Propagate RequestDetails to everything in JPA server

* More interceptor tweaks

* Fix compile error

* One more tweak to captured SQL

* Ongoing interceptor tweaks

* Ongoing interceptor tweaks

* More interceptor tweaks

* Interceptor tweaks

* Tweaks to tests

* Fix tests

* Test fix

* Raise warnings when encoding extensions with missing values

* Consent service work

* More interceptor tweaks

* Consent interceptor tweaks

* Add logging to test
2019-06-27 16:35:29 -04:00
jamesagnew e76b1dacb3 License header updates 2019-06-22 18:31:16 -04:00
jamesagnew 0fbde2a4e5 Fix #1352 - Don't fail to create observation with a value type of
SampledData
2019-06-22 16:43:25 -04:00
James Agnew 4ad1808da3
Propagate RequestDetails to everything in JPA server (#1358) 2019-06-22 15:18:06 -05:00
jamesagnew 087c53286c License header updates 2019-06-14 18:43:55 -04:00
Ken Stevens 19dd7ebc2e try excluding stress tests from build 2019-06-13 15:21:03 -04:00
Ken Stevens 2bf680509b
DeleteConflict hook, SearchableHashMapResourceProvider, and in-memory searching (#1341)
* Make IBundle list interface more flexible

* Make matchResourceLinks visible

* Make matchResourceLinks visible

* Pull in-memory matching functionality out of subscription module into dedicated classes in searchparam module

* Added more accessors to version independent resource classes

* improved forcedid matching (needs to be verified by James)
filter out nulls from HashMapProvider.searchAll() (hopefully no tests depend on this)

* add AnyComposition

* cleanup of Any classes

* create searchparam config so people can use that module without using subscriptions

* create searchparam config so people can use that module without using subscriptions

* fix broken test

* added derivedFrom

* renamed daoRegistry.getResourceDaoIfExists to getResourceDaoOrNull
also added method to add a new dao to the registry and retrieve registered types

* TokenParam.equals

* add error check to searchable hashmap resource provider

* added support for R4

* add successor to measure

* delete conflict hook
start with failing test

* test passes.
hook is called.

* added delete conflict hook
all delete conflict tests pass

* added javadoc

* Performance test

* test bad interceptor case

* typo

* rename criteria matcher

* added support for multiple topics

* fix method name

* add effective period

* Temporarily excluding StressTest from build to try to get Travis under time limit

* change log

* review feedback

* review feedback

* review feedback
2019-06-13 13:59:51 -04:00
James Agnew c2aec5c1a9 Respect the _total parameter for all JPA searches 2019-06-09 05:44:49 -04:00
James Agnew be06c2ee19 Correctly index timing events 2019-05-31 16:42:45 -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 9e9a1ed06d ndle special params correctly 2019-04-25 13:25:57 -04:00
James Agnew b8e24ed01c Refactoring the registry a bit 2019-04-25 10:19:51 -04:00
jamesagnew abd53c0cbe License header updates 2019-04-24 21:20:11 -04:00
James Agnew 738c2c1797
Interceptor framework refactoring (#1287)
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
Ken Stevens a57e50317d
Websocket cleanup (#1275)
* fix bug in websocket subscription (It wasn't destroying the channel when there are no subscribers)

* add support for removing channel.  Also synchronize removal (there was a race condition between sync and queue)

* keep deprecated method for backwards compatibility

* make websocket endpoint configurable

* make websocket context path configurable

* make websocket context path configurable

* trying mvn clean test instead of mvn clean install to see if the build goes faster

* that didn't work at all.  reverting.

* change log
2019-04-17 15:03:35 -04:00
jamesagnew 08a9844066 Work on #1280 2019-04-17 09:10:17 -04:00
James Agnew 380644d19d Add a bit of logging for search parameters when they can't be found 2019-04-14 12:32:09 -04:00
James Agnew 87c0b3778b More work on threadlocal interceptors 2019-03-22 09:54:02 -04:00
James Agnew d1667487c2 Clean up unique composite search params 2019-03-21 21:57:38 +01:00
Ken Stevens be4863133e
Pointcut parameters and Retrier log (#1236)
* Fixed a pointcut parameter list and log an exception that was being swallowed by Retrier

* Documentation clarification
2019-03-11 17:31:03 -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 14e04085ae Try for a test fix and a bit of cleanup 2019-02-16 16:11:33 -05:00
James Agnew 09920ad545 Reduce thread contention during tests 2019-02-15 14:18:34 -05:00
Ken Stevens f34926bb18
fixed a bug matching long ids in searchparams (#1203)
* fixed a bug matching long ids in searchparams
2019-02-09 13:45:51 -05:00
Ken Stevens f40614a1aa fixed bug in in-memory matching for reference id when searchparam has two components 2019-02-08 16:37:08 -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
jamesagnew d4af1ee2a3 Add tests and license headers 2019-02-04 16:34:39 -05:00
Ken Stevens 9280cde491
Subscription only registers active (#1189)
* Fixed a bug in standalone subscription subscriber:  It was adding REQUESTED subscriptions to the active subscription registry.  (Only ACTIVE subscriptions should be added.)
2019-02-01 10:14:46 -05:00
jamesagnew 503d1d8aff Subscription NPE fix 2019-01-26 18:42:01 -05:00
James Agnew 38d03ea99a
Invalid ids in subscription queue (#1175)
* Start work on this

* Work on interceptors

* Attempt fix

* Avoid environment dependency

* Test fixes

* One more test fix

* One more build tweak

* Lots of cleanup

* A bit more cleanup

* Still more cleanup

* Some test fixes

* Add legacy methods temporarily

* Don't auto-scan interceptor beans

* One more test fix

* rsolve merge conflicts

* Address review comments
2019-01-23 21:17:47 -05:00
James Agnew 3e84173180 Merge branch 'master' into ja-subscription-interceptors 2019-01-18 17:52:23 -05:00
jamesagnew a584e15251 Add headers 2019-01-14 14:58:27 -05:00
Ken Stevens 4f5640e541
Resilient searchparamregistry (#1165)
SearchParamRegistry and SubscriptionRegistry now both poll retrying connection to the server. This will help in particular in the scenario where the subscriptions are managed in a standalone server that depends on a FHIR Server being available to pull search parameters and subscriptions from.
2019-01-14 11:39:28 -05:00
James Agnew 8beccab9ab Merge branch 'master' into test-openjdk-11 2019-01-09 10:48:57 -05:00
jamesagnew 98d93df12a License header updates 2019-01-04 16:22:15 -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 4599a10180 Merge branch 'master' into test-openjdk-11 2018-12-23 14:19:59 -05:00
jamesagnew f0eda57048 Add missing dependency to search param project 2018-12-21 07:06:32 -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
James Agnew f978bc3039 Always apply new search params to any resource reindexing 2018-12-14 13:43:25 -05:00
jamesagnew 3a3b81a6a8 Preparing things for OpenJDK 11 2018-12-08 17:52:48 -05:00
James Agnew cbaa39fd63
Try to reuse index rows in JPA server (#1133)
* Try to reuse index rows in JPA server

* Address review comments

* One more test fix

* One more test
2018-12-05 19:25:59 -05:00
jamesagnew 82f40f0423 License header updates 2018-12-03 05:22:10 -05:00
Ken Stevens 6baee4dc3f
Standalone subscription (#1125) 2018-11-30 17:19:16 -05:00