5d540d9208
Query optimization in JPA
2019-01-27 20:03:48 -05:00
10c59fceeb
Subscription strategy tag ( #1178 )
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tests pass
2019-01-25 13:01:04 -05:00
f55be0b6d0
Test fix
2019-01-25 10:56:17 -05:00
38d03ea99a
Invalid ids in subscription queue ( #1175 )
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* 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
67eaeb8af1
Merge remote-tracking branch 'origin/windows-fixes' into windows-fixes
2019-01-23 17:14:51 -05:00
e819b83a94
Make busywait more clear
2019-01-23 16:21:13 -05:00
cfd67d88c7
Merge remote-tracking branch 'origin/windows-fixes' into windows-fixes
2019-01-23 16:17:48 -05:00
5c7907dfea
magic number
2019-01-23 16:17:41 -05:00
7d1d5a102c
Attempt to fix a weird lucene indexing issue
2019-01-23 16:14:53 -05:00
2c7eb39b29
final batch of windows fixes (to deal with jumpy windows clock)
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also added semaphore to PointcutLatch
2019-01-22 18:53:54 -05:00
6b22977d7c
fixing more tests for Windows
2019-01-21 22:28:48 -05:00
00320da9dc
Merge branch 'master' into windows-fixes
2019-01-21 20:34:01 -05:00
9cf64f78d0
Deprecate a bad setter on RetfulServer, fix a paging issue, and add a
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disabled unit test to the subscription matcher
2019-01-21 14:46:17 -05:00
29f483d7b4
Merge branch 'master' into windows-fixes
2019-01-21 11:06:42 -05:00
b4350bbdae
Working through failed tests. Consolidating sleep calls
2019-01-21 11:05:53 -05:00
17f03ac843
Allow null return type for interceptors
2019-01-20 19:44:18 -05:00
c3c7d156e9
Interceptor cleanup
2019-01-20 10:16:18 -05:00
b878925884
Try to avoid intermittent test failure
2019-01-19 18:44:09 -05:00
cd1e0e881c
Add headers
2019-01-19 18:31:17 -05:00
b0cbd52ae9
Interceptor cleanup
2019-01-19 18:01:00 -05:00
29c3cee287
Merge pull request #1172 from jamesagnew/ja-subscription-interceptors
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Ja subscription interceptors
2019-01-19 07:13:14 -06:00
3e84173180
Merge branch 'master' into ja-subscription-interceptors
2019-01-18 17:52:23 -05:00
3d07fc1c22
fixed null subscription id ( #1170 )
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* fixed null subscription id
2019-01-18 10:39:35 -05:00
5ce9d444e9
Work on interceptors
2019-01-18 09:04:45 -05:00
5fd084d7cf
Fix a couple of merge conflicts
2019-01-18 05:47:37 -05:00
432ad8e5bc
Subscription without Payload did not contain header.
2019-01-18 05:41:47 -05:00
66dc7f82d5
organize imports
2019-01-15 20:55:00 -05:00
19afcb7e09
all tests pass
2019-01-15 18:22:08 -05:00
a584e15251
Add headers
2019-01-14 14:58:27 -05:00
4f5640e541
Resilient searchparamregistry ( #1165 )
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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
4b48eebe8b
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-01-13 12:27:40 -06:00
63b8a70e8a
Allow storing ConceptMap with StructureDefinition as a source or target
2019-01-13 12:24:51 -06:00
068117138e
Merge branch 'master' into subscription-bugfix
2019-01-11 09:05:37 -06:00
860a8fb7a6
Emergency fix.
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Normally I'd write a test for this, but this startup behaviour is changing in my next PR.
2019-01-11 09:49:40 -05:00
aee7b2b882
Make sure that sub-request transaction searches and reads preserve HTTP
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headers
2019-01-10 07:26:04 -07:00
d091665ab6
Test fix
2019-01-09 14:40:43 -05:00
f241457bc1
Merge branch 'master' into test-openjdk-11
2019-01-09 13:42:50 -05:00
66dd6dc96c
updated documentation
2019-01-09 13:39:32 -05:00
cdf1cd9144
undoing inadvertent comment changes
2019-01-09 13:39:32 -05:00
3142ebb892
Fixed typo in class name
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Added channel extensions to CanonicalSubscription
2019-01-09 13:39:32 -05:00
d809569a2d
Added new DaoConfig parameter to control whether subscription matching happens on this server.
2019-01-09 13:39:32 -05:00
8beccab9ab
Merge branch 'master' into test-openjdk-11
2019-01-09 10:48:57 -05:00
62ae71c1c6
Allow authorizing delete operations via a transaction in
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AuthorizationInterceptor
2019-01-07 15:43:36 -05:00
a8a97ae6b2
Two test fixes
2019-01-07 09:18:11 -05:00
c104923855
Add an additional test for transaction processing
2019-01-07 09:17:19 -05:00
8f8385627f
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2019-01-05 11:33:08 -05:00
98d93df12a
License header updates
2019-01-04 16:22:15 -05:00
5b8fee869e
Add config options for default Prefer header and _total param on server
2019-01-04 16:12:45 -05:00
ba76492865
Another test fix
2019-01-04 14:04:26 -05:00
137d39e80f
Another test fix
2019-01-04 13:53:24 -05:00
051074d0bc
Work on tests
2019-01-04 13:05:39 -05:00
a1275874f8
Correct subscription delivery metadata
2019-01-04 10:56:21 -05:00
7ba07d9f02
Avoid search failure on Oracle when performing very large includes
2019-01-04 09:11:11 -05:00
31b8a392b7
Better CLI error handling for unit tests
2019-01-03 12:57:18 -05:00
14a132a937
Squashed commit of the following:
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commit 965965583070da25b76f
2018-12-27 17:58:47 -05:00
28218c9bba
Version bump for build JDK
2018-12-23 15:14:43 -05:00
fedc59a8d6
Subscription module startup changes ( #1154 )
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* Reorganizing packages and dependencies to support standalone subscription running within a CDR container where all hapi modules are on the classpath.
* EXPERIMENTAL: Moved Subscription registry out of interceptor and introduced ISubscriptionLoader that will be either a Database or FhirClient loader.
5 tests fail. Looks like we're getting too many matches--likely because there is now just one list of subscriptions instead of one list per interceptor.
* Created ActiveSubscription and moved cache bits into it
* Compiles. Next step is get app context to load.
* Application context loads. Now fix NullPointer.
* All subscription tests pass
* FIXME cleanup
* jpa-subscription tests
* fixed config so other module tests work
* MAJOR MILESTONE: All hapi-fhir tests pass.
updated READMEs in example projects
* Moved ExecutorQueue stuff out into its own class
* Organize Imports
* FIXME cleanup
* Null check -> Optional
* Add test and supporting code to validate SubscriptionConstants.EXT_SUBSCRIPTION_RESTHOOK_DELIVER_LATEST_VERSION behaviour
* Added SubscriptionCheckingSubscriber test that works without a database
* Moved a few beans to @ComponentScan
* Replaced use of beanFactory with concrete factory classes
* Switched test to use subscribablechannel
* Added SubscriptionLoaderFhirClientTest
* Undid changes that caused SearchParamProviderFhirClientTest to revert to the Database version. It's now calling the FhirClient version again. (oops)
* Confirm that our SubscriptionProviderFhirClient works with a live fhir client
* Organize imports
* Organize imports
* Register interceptors with DaoConfig instead of RestServer.
Also, Rename @VisibleForTesting methods with ForUnitTest
* Ready to go
* organize imports
* add processing queue
* Fixed interface implementation names
* Fix triggering service so it uses new subscriptionmatcherinterceptor
* fixed example
* Renamed "Database" classes to "Dao"
* Tightened up StoppableSubscriber API
* final code review
* processing -> matching naming change
* fix required by CDR
* oops
* Updated changes.xml
* Renamed subscriptioncheckingsubscriber to subscriptionmatchingsubscriber
* Renamed subscriptioncheckingsubscriber to subscriptionmatchingsubscriber
* CDR integration now works
* Changing subscribable channel abstraction layer in preparation for supporting more types of subscribable channels
* Add interface over both types of messages put on queues
* cosmetic change
* added subscription support for r4
* fixed again
* oops
* self code-review
2018-12-23 13:52:26 -05:00
9d3904ef3e
Fix #1142 - Upgrade Spring Boot to latest version
2018-12-23 13:10:03 -05:00
a0cb7edd08
Version bump a few dependencies
2018-12-22 20:13:03 -05:00
1311ef4157
Revert to JDK9 to build on travis temporarily
2018-12-21 09:26:19 -05:00
f5f9dff391
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-12-18 14:09:20 -05:00
bca958564f
Just a javadoc change
2018-12-18 14:09:11 -05:00
86b3e45a32
License header updates
2018-12-18 14:08:01 -05:00
84a34eb3c9
Subscription module support ( #1147 )
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* 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
dc1f48ffed
Test fix
2018-12-14 14:13:02 -05:00
f978bc3039
Always apply new search params to any resource reindexing
2018-12-14 13:43:25 -05:00
11b8304cb4
Fix case sensitivity issue
2018-12-13 08:31:35 -05:00
b442982310
Add media interceptor
2018-12-08 18:49:58 -05:00
5a80e70d93
Correctly reindex string indexes
2018-12-06 14:44:42 -05:00
a5b1f684f7
Try to prevent intermittent test failure
2018-12-05 19:28:37 -05:00
cbaa39fd63
Try to reuse index rows in JPA server ( #1133 )
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* 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
d150340d53
One more test fix
2018-12-04 19:55:14 -05:00
29af6160d6
Fix typo
2018-12-04 18:54:26 -05:00
1d3bcd9e8f
Fix indexing bug
2018-12-04 18:50:49 -05:00
d9ce0ebf7c
Unit test fix
2018-12-04 18:24:19 -05:00
8c7f249a21
Migrator enhancements and adjust reindexer to account for missing
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versions
2018-12-04 17:33:29 -05:00
c484c69664
Better error message for unqualified search parameter types
2018-12-03 13:14:10 -05:00
82f40f0423
License header updates
2018-12-03 05:22:10 -05:00
6baee4dc3f
Standalone subscription ( #1125 )
2018-11-30 17:19:16 -05:00
b2179b1696
Syntax fixes for the JPA migrator
2018-11-30 12:39:37 -05:00
364b6cc5fd
One more test fix
2018-11-22 18:40:39 -05:00
055478e1f1
Test fixes
2018-11-22 18:22:33 -05:00
ce3b7c82ce
Avoid issues when using subscription delivery in a serializing/queuing
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environment
2018-11-22 17:53:42 -05:00
d0b194f9d7
Fix two test failures
2018-11-22 08:41:12 -05:00
2e030eebaa
Make sure that reindexing happens correctly
2018-11-21 12:06:10 -05:00
e8482f5c87
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-11-20 13:59:51 -05:00
7cbad7f4e3
A bit of cleanup around subscription wiring following in-memory matcher
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landing
2018-11-20 13:59:31 -05:00
4c84b8fc89
Add a bit more test logging
2018-11-20 05:33:32 -05:00
03ebcafdf5
In-memory matcher ( #1116 )
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* Initial refactoring to move database matcher out into its own class
* MAJOR REFACTOR: Pulled indexing code out of BaseHapiFhirDao into a new class ResourceIndexedSearchParams
* Moved calculateHashes
* Replaced @Bean definitions in BaseConfig.java with @ComponentScan
Annotated bean classes with either @Service (if it's stateless) or @Component (if it's stateful). It doesn't really matter which annotation is used, but it's helpful to see at a glance whether a bean is stateful or stateless.
* Move services out of BaseHapiFhirDao
Moved services required by ResourceIndexedSearchParams out of BaseHapiFhirDao and into new classes called LogicalReferenceHelper, IdHelperService, MatchUrlService, and DaoProvider.
Converted SearchBuilder into Prototype Bean
Mark Spring components that depend on daos and entitymanagers with @Lazy so they aren't picked up by hapi-fhir-spring-boot-autoconfigure.
* Added SubscriptionMatcherInMemory
Moved static data out of BaseHapiFhirDao into ResourceMetaParams
Moved translateMatchUrl methods out of BaseHapiFhirDao into MatchUrlService bean
Simplified SubscriptionMatcherInMemory to not depend on entity or dao
Turned all subscribers into prototype beans
* Moved searchParam method out to mySearchParamProvider
Also removed dao and contest parameters from of myMatchUrlService methods
Moved code out of SearchBuilder into SearchParameterMap.clean() so it can be used by inMemoryMatcher
Introduced a new composite subscription matcher that tries to match in memory and if it finds a parameter in the criteria it doesn't support, it falls back to the database matcher.
* Added support for references
Also fixed a small bug in SearchParameterMap that was missing the ";" after "_has" when creating a normalized query from search params.
* Finished implementing all tests from FhirResourceDaoR4SearchNoFtTest
* Make in-memory matcher configurable, disabled by default
* Validate Subscription criteria when they're submitted
Send HTTP 422 UnprocessableEntityException if the criteria fail validation.
* fixed Sonar "Blocker" issues.
* Don't reload the resource before sending it out
Since we can always force a reload using restHookDetails.isDeliverLatestVersion
* Added tests to cover Custom Search param.
* Split ResourceIndexedSearchParam into separate state and service classes
* Cleaned up SearchBuilder.
Removed uses of myCallingDao as an injection mechanism.
Left // FIXME KHS cookie crumbs to clean up
* Reduced dependencies on BaseHapiFhirDao
Removed methods from IDao interface that were used for injection
* Updated change log
2018-11-19 16:19:52 -05:00
45a5db6fd8
One more fix
2018-11-19 13:31:01 -05:00
719339fc14
One more test fix
2018-11-19 10:27:16 -05:00
67dbc802be
Better detection of binary content in ResponseHighlighterInterceptor
2018-11-18 14:32:54 +01:00
fad53c6669
Fix a test
2018-11-16 13:15:14 +01:00
6a6451f694
Reduce number of queries on some DB operations
2018-11-16 12:41:50 +01:00
1de0ef405c
Clean up test compile and reenable GraphQL on hapi.fhir.org
2018-11-16 11:15:44 +01:00
84acafe3af
Streamline expunge operation
2018-11-15 11:37:16 +01:00
75210d614b
Bump to 3.7.0-SNAPSHOT
2018-11-12 22:37:52 -05:00
63af04a7b4
Prepare for 3.6.0 release
2018-11-12 05:40:55 -05:00
030b33a0f2
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-11-09 15:59:34 -05:00
4a0c45a494
License updates
2018-11-09 15:59:23 -05:00
c81a59bb9a
Only use FHIRPath to validate searchparameterr paths in R4
2018-11-09 15:57:34 -05:00
7f6f06dddf
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-11-09 15:47:22 -05:00
5834e6aa62
Test fixes
2018-11-09 15:32:55 -05:00
3942f1bb29
License header updates
2018-11-09 14:41:57 -05:00
f61df5c3fe
Use FHIRPath expression parser for custom SP validation
2018-11-09 14:41:20 -05:00
a3e79b5759
License updates only
2018-11-08 15:28:09 -05:00
3ae5f9a3b7
Build tweak
2018-11-08 14:04:21 -05:00
cca49425ae
Some work on collection processing
2018-11-08 08:56:51 -05:00
76cd3f6b47
Allow client assigned IDs to be purely numeric in JPA server if
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configured to do so
2018-11-07 18:25:50 -05:00
62145e1b74
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-11-07 11:02:02 +01:00
4b790eddb6
Add additional authorization test
2018-11-07 11:01:29 +01:00
896568c0f7
License updates
2018-11-04 16:06:53 -05:00
bc72093555
Add reindexing support based on table instead of column
2018-11-04 20:00:27 +01:00
b1283791ca
Allow JPA server to restore resources and link to them in a single
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transaction
2018-11-02 16:45:21 -04:00
1b877ac03e
Add licene headers
2018-11-01 09:15:51 -04:00
4315900ac0
Merge branch 'philips-3.6.0'
2018-11-01 09:15:27 -04:00
3bfdc61866
Fix a couple of test failures
2018-11-01 09:15:03 -04:00
3f6960d82b
Add multithreaded migrator tool
2018-11-01 05:42:51 -04:00
c8834cd29a
Merge branch 'philips-3.6.0' of github.com:jamesagnew/hapi-fhir into philips-3.6.0
2018-10-31 17:19:28 -04:00
041a4c4018
Fix SearchCoordinator tests
2018-10-31 12:36:27 -04:00
31ef4c68e1
Merge branch 'philips-3.6.0' of github.com:jamesagnew/hapi-fhir into philips-3.6.0
2018-10-31 05:51:13 -04:00
8955a9e54d
Add threading to migrator
2018-10-31 05:50:50 -04:00
7acba90d15
Update search logic
2018-10-30 22:43:16 -04:00
3d008aee5d
Make test observation lists thread safe ( #1105 )
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* Initial refactoring to move database matcher out into its own class
* MAJOR REFOACTOR: Pulled indexing code out of BaseHapiFhirDao into a new class ResourceIndexedSearchParams
* made observations lists thread safe to stop intermittent test failures
2018-10-29 15:56:47 -04:00
b66e01ce65
Allow plain server @Operation methods to declare a wildcard so that any
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opeeration invocations will be direected to them
2018-10-29 10:36:32 -04:00
794d9145e9
Move query count tests to consolidate them, and avoid an accidental
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rewrite of existing indexes in some conditions
2018-10-24 17:54:58 -03:00
f601b212ad
Performance enhancements to the JPA server and better retry logic in
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$trigger-subscription
2018-10-20 14:47:37 -04:00
c8db7fe035
Add a test
2018-10-18 15:12:22 -04:00
e00ff641b2
Increase visibility of two methods needed by the HSPC sandbox
2018-10-18 10:17:55 -04:00
da2763d8c8
Merge branch 'master' into philips-3.6.0
2018-10-17 22:38:27 -04:00
f571fc4f92
Rename DAO registry
2018-10-17 22:37:43 -04:00
b78aaea415
FIx up subscription processing
2018-10-17 21:23:52 -04:00
de76f37845
Try to fix an intermittent test failure
2018-10-17 15:49:26 -04:00
99cd4ce5f7
Allow for _total parameter
2018-10-17 09:47:35 -04:00
4b5dcce021
Add a bit of logging to subscription triggering
2018-10-17 08:32:57 -04:00
b220154e9c
Fix error in retriggeer logic
2018-10-17 07:02:51 -04:00
aa1f624132
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-17 05:53:46 -04:00
8130700d68
One more optimization to the subscription retriggering logic
2018-10-17 05:53:07 -04:00
d129d43635
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-16 21:51:50 -04:00
2c05d9c5db
Test cleanup
2018-10-16 21:51:33 -04:00
e2dfaa517f
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-16 20:38:21 -04:00
388bda1fec
Avoid transaction isolation level not supported by Oracle
2018-10-16 20:31:43 -04:00
47a5763fb5
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-16 20:25:12 -04:00
5d7142a972
Avoid intermittent test failures
2018-10-16 20:23:32 -04:00
1c1f601332
License header updates
2018-10-16 19:56:52 -04:00
0fbe897ca4
Add named beans to JPA config
2018-10-16 17:24:17 -04:00
755060f91e
Allow subscription triggering on a block of resources
2018-10-16 15:29:41 -04:00
ba6df6d55a
Handle unqualified ID in delete box for testpage overlay
2018-10-15 10:23:21 -04:00
93c545c42c
License header updates
2018-10-15 09:54:00 -04:00
483c9bff3a
Auto detect whether the appropriate dialect is selected
2018-10-15 09:53:04 -04:00
b44e96a5cd
Merge branch 'philips-3.6.0'
2018-10-15 08:37:00 -04:00
b75226914d
Fix intermittent test failure
2018-10-15 08:19:23 -04:00
6dc2dc1d6f
One more test fix
2018-10-15 07:11:10 -04:00
796b12e33e
Fix bug in $everything processing
2018-10-15 05:44:53 -04:00
8b46257423
Add warm cache module
2018-10-14 09:32:07 -04:00
51a69f0dc9
Fixes to migrator and count logic
2018-10-13 12:02:19 -04:00
a9fcfaf79a
Add a test
2018-10-10 19:11:57 -04:00
0837daecc2
One more recurring failure fix
2018-10-10 13:36:50 -04:00
e47cff2712
Fix an intermitttent test failure
2018-10-10 11:57:30 -04:00
8bd185acf2
Rename $retrigger-subscription to $trigger-subscription based on
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Diederik's suggestion
2018-10-10 10:49:50 -04:00
34bb70af65
Add validator test and allow migrator to be used for 3_3_0
2018-10-08 21:04:17 -04:00
34e943b49b
Fix bad counts when multiple parameters match
2018-10-05 13:11:09 -04:00
9c27e8e6dd
Fix an issue with the spring boot build
2018-10-04 15:12:21 -04:00
970c48ec37
A bit more test cleanup
2018-10-04 13:29:09 -04:00
8452f46b9b
More work on intermittent test failures
2018-10-04 13:16:50 -04:00
da3b4d4071
Try to fix an intermittent test failure
2018-10-04 13:07:52 -04:00
2464599a68
One more test fix
2018-10-04 09:36:10 -04:00
b265c0281b
Expand search range when searching by date
2018-10-03 21:31:01 -04:00
6ce9120132
Fix test failure in boot
2018-10-03 15:39:19 -04:00
5d5ee78873
API cleanup following JPA search performance enhancements
2018-10-03 07:43:01 -04:00
9d1e8aa246
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-10-01 21:36:52 -04:00
12b23fbf23
Make JPA searches more efficient by prefetching a much smaller number of
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resources
2018-10-01 21:36:10 -04:00
caf7c8b2e1
Header updates
2018-10-01 17:04:50 -04:00
d7abeb513b
Remove class that is failing the build and not used
2018-09-30 13:31:06 -04:00
62d6771814
Use a select count query for summary count searches in JPA server
2018-09-29 21:58:14 -04:00
9f7e21fec6
Improve logging for expunge operation
2018-09-29 18:38:27 -04:00
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 002c4b3ff7dfb4de86f1
2018-09-29 13:48:35 -04:00
002c4b3ff7
Add retrigger subscription operation
2018-09-27 20:03:01 -04:00
706e004b9d
Bump to 3.6.0-SNAPSHOT
2018-09-19 10:24:48 -04:00
3bfce11d2c
Add OSGI dependency for commons-text
2018-09-17 16:06:11 -04:00
a5de3f2ffd
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-09-17 05:31:23 -04:00
bb7fca19a3
Work on migrator
2018-09-14 08:34:39 -04:00
321e88c811
License header updates
2018-09-14 05:25:07 -04:00
640ee544c8
Clean up hamcrest dependency
2018-09-11 09:05:39 -04:00
9bf183f5b1
Fix depenedency on activation API
2018-09-11 08:53:45 -04:00
45dac5c5a8
A couple more test fixes
2018-09-11 08:47:00 -04:00
a26779de81
FIx compile error
2018-09-11 08:42:46 -04:00
261f2c73ab
Merge branch 'jpa_migration'
2018-09-11 08:09:15 -04:00
94eb12aca3
Add a retry to database expunge routines
2018-09-11 07:59:11 -04:00
0e75c8ed39
A few test fixes
2018-09-10 08:50:12 -04:00
29f324f8de
Merge branch 'master' into master
2018-09-07 23:25:49 -04:00
daef975734
Version bump to 3.5.0
2018-09-08 07:22:21 +08:00
f5d567cd00
Work on migrator
2018-09-08 03:30:35 +08:00
979b1287d0
Add ability to suspend scheduled reindexer
2018-09-05 16:22:09 +08:00
77305eb570
Work on migrator
2018-09-04 10:32:08 +08:00
0f7c4219cb
Merge branch 'master' into jpa_migration
2018-09-02 06:05:11 +08:00
bc270584d2
Work on terminology expansion
2018-09-01 22:56:42 +08:00
a4d8df3c6d
Test fixes
2018-09-01 17:19:21 +08:00
f4a21eadda
Fix this issue
2018-09-01 14:38:52 +08:00
fee0166800
Work on removing validstion cache
2018-08-28 05:26:06 -04:00
d0761ea604
Add a test
2018-08-27 08:58:10 -04:00
07cfed14b8
Work on migrator
2018-08-27 08:21:20 -04:00
54c07263b6
Increase code lengths
2018-08-26 12:32:35 -04:00
b2741dab0d
Fix crash in mapping
2018-08-23 16:51:35 -04:00
731658eef8
Remove accidental double initialization
2018-08-23 09:32:10 -04:00
f8c03a3c37
Prefetch subscriptions on app startup
2018-08-22 12:48:03 -04:00
bbe4de2842
Support for LOINC externally defined answerlists added
2018-08-20 09:38:44 -04:00
8ee701c934
License header update
2018-08-19 20:21:45 -04:00
fef105cfdb
More intermittent test failure fixes
2018-08-19 16:51:04 -04:00
77e35f5a56
Test fixes
2018-08-19 16:12:35 -04:00
6511545d25
Don't re-activate already active identical subscriptions
2018-08-17 11:56:33 -04:00
ddc4464552
Make constant public
2018-08-13 13:52:47 -04:00
9b61a8cdbe
Make constant public
2018-08-13 13:52:08 -04:00
bc1ee1f9dc
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-08-13 11:54:36 -04:00
8a19682ce3
Subscription cleanup trying to get tests passing again
2018-08-13 10:25:16 -04:00
6420e0e515
Merge pull request #1025 from jamesagnew/documentOperation
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$document operation added
2018-08-13 15:39:28 +02:00
39ef79ff2c
Subscription logic cleanup
2018-08-13 08:40:29 -04:00
fc03b1b1d4
switched myClient -> ourClient
2018-08-13 13:50:11 +02:00
b4001b7324
switched myClient -> ourClient
2018-08-13 13:29:42 +02:00
956cd093ed
fixed comments of merge request
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added JPAConstants Operation Names
2018-08-13 13:12:34 +02:00
89bdf40b55
Merge remote-tracking branch 'origin/master' into documentOperation
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# Conflicts:
# hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
# hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/r4/RestHookTestWithInterceptorRegisteredToDaoConfigR4Test.java
2018-08-13 13:05:09 +02:00
086b95013e
Add logging
2018-08-13 05:43:45 -04:00
5feec85662
Clean up subscription processing
2018-08-13 05:27:17 -04:00
5ef31a505c
One more test fix
2018-08-12 21:36:26 -04:00
f5d330dd03
Merge branch 'master' into 1053-lastupdate-shouldnt-apply-to-includes
2018-08-12 17:58:21 -04:00
d63cd267ab
Test fixes
2018-08-12 16:52:13 -04:00
52cfdb7b8b
Add some test logging
2018-08-12 13:43:31 -04:00
0a1ae541e6
Fix some test failures
2018-08-12 12:12:09 -04:00
ea70683604
Merge branch 'subscription_cleanup' of github.com:jamesagnew/hapi-fhir into subscription_cleanup
2018-08-12 11:13:24 -04:00
0f6188b73c
Improve error message for unknown UUIDs in transaction bundles
2018-08-12 09:58:34 -04:00
e0b188d574
Add test
2018-08-11 15:25:01 -04:00
6d10260d8f
Unit test cleanup
2018-08-11 15:12:33 -04:00
8284734a07
Fix failing test with new filter logic
2018-08-11 14:01:53 -04:00
ea1f17762e
Don't apply last updated to includes
2018-08-11 12:20:07 -04:00
acfe442cf9
Add equivalency flag to reverse lookup
2018-08-11 09:55:28 -04:00
98d794e30f
Bug fix in subscription processing
2018-08-10 13:07:06 -04:00
416054ddff
Fixes for issue #1048
2018-08-10 12:51:12 -04:00
ece0c9defe
Subscription cleanup
2018-08-10 09:07:55 -04:00
ec4604c498
Work on splitting subscriptions out into separate channels
2018-08-06 20:58:04 -04:00
d59a40d01a
Subscription cleanup started (won't build)
2018-08-06 19:03:30 -04:00
c98a1e0c62
Cleanup of subscription processing
2018-08-06 18:37:12 -04:00
0556dfa7af
Work on subscriptions
2018-08-03 11:56:06 -04:00
d07fd76d60
Dont keep resource bodies in the queue for JPA subscription delivery
2018-08-03 10:44:15 -04:00
cffe4c9df2
License header updates
2018-07-30 21:22:00 -04:00
d6293cf9b3
Merge branch 'client_enhancements'
2018-07-30 09:42:38 -04:00
518092cbd4
More updates
2018-07-29 17:10:26 -04:00
3399fa04de
Fixed issue
2018-07-27 17:47:27 +03:00
3a5556006b
Merge branch 'master' into master
2018-07-27 16:59:52 +03:00
9c39733aff
Fixed issues
2018-07-27 16:48:44 +03:00
f03d6b7c22
Allow configuration of default page size in SimpleBundleProvider
2018-07-27 18:34:12 +07:00
75a68a0332
Unit test fix
2018-07-26 18:58:23 +07:00
a4e4111376
Fix a unit test
2018-07-26 18:08:59 +07:00
3c80238f0e
Ongoing work on interceptors
2018-07-24 17:22:21 +07:00
23083a9283
Improvements to client and SP indexing in JPA server
2018-07-23 17:37:49 +09:00
8f2d3998f6
Merge branch 'master' into documentOperation
2018-07-19 17:44:46 -04:00
b4aa4c0e89
Add protection against HTML injection attacks
2018-07-19 08:56:22 -04:00
24b220ef5f
Fix expansions for ValueSet
2018-07-16 10:39:08 -04:00
4b3287c6a9
Code cleanup
2018-07-16 08:16:40 -04:00
401a4cd738
Clean up concept reindexing
2018-07-15 17:18:07 -04:00
116b9e335d
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-07-15 15:23:11 -04:00
43ac912033
Clean up terminology uploading
2018-07-15 15:22:52 -04:00
84b57f04d3
Fixed tests
2018-07-14 13:51:11 -04:00
738abc415c
Disable scheduled tasks during unit tests
2018-07-14 13:24:51 -04:00
36b4ed28e4
Header updates
2018-07-14 10:16:53 -04:00
81e8f77232
Work on indexes
2018-07-13 09:58:54 -04:00
e6ca408f67
Permissions for operations
2018-07-12 18:40:15 -04:00
03e7b018a6
Add skeleton for the $process-message operation in JPA erver
2018-07-12 17:52:24 -04:00
b275d20aba
added R4 document operation & merge master
2018-07-11 16:21:13 +02:00
68772f1e3a
removed unnecessary test
2018-07-10 16:02:39 +02:00
df7a9322e9
Merge branch 'master' into documentOperation
2018-07-10 14:35:51 +02:00
e992043a22
Fix ID
2018-07-06 09:43:43 -04:00
f03b1dec8e
Remove warning
2018-07-06 09:40:23 -04:00
60f57f2a6f
Fix property handler
2018-07-06 09:36:04 -04:00
1533746bbe
Add tests
2018-07-06 09:29:51 -04:00
c8f0e0047f
Test fixes
2018-07-05 19:17:06 -04:00
c9d7b88cab
Loinc updates
2018-07-05 18:52:19 -04:00
3b794a4f39
Fix a crash when reindexing deleted resources
2018-07-02 09:17:48 -04:00
6d83edabb6
License header updates
2018-07-01 20:59:04 -04:00
328541f537
Test fix
2018-07-01 12:57:05 -04:00
b929864873
Merge branch 'improve_jpa_indexes'
2018-07-01 12:08:03 -04:00
6ef34a8c5f
Merge pull request #1018 from jamesagnew/jpa_view
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Jpa view
2018-07-01 11:47:17 -04:00
495fd9f68e
Add support for patch in AuthorizationInterceptor
2018-07-01 11:46:11 -04:00
2c06a1437b
merged master to jpa_view
2018-06-30 22:16:30 -04:00
0ab15a05d6
Merge branch 'jpa_view' of https://github.com/jamesagnew/hapi-fhir.git into jpa_view
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Conflicts:
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceSearchView.java
2018-06-29 22:18:22 -04:00
ccf3c17f59
impl ResourceSearchView, reduce sql to db
2018-06-29 21:24:43 -04:00
af4b9f1c7b
impl ResourceSearchView, reduce sql to db
2018-06-29 21:24:02 -04:00
6afc2a7296
Improve indexing
2018-06-29 16:25:11 -04:00
bb637c5433
Work on presence API
2018-06-29 14:32:08 -04:00
03fc593cb9
Fix broken test
2018-06-28 18:11:19 -04:00
32fefefcd8
Allw successful deletion of concept maps
2018-06-28 18:01:00 -04:00
7b809f059a
Terminology updates
2018-06-27 18:48:36 -04:00
32ddfff191
Improve indexing
2018-06-27 18:33:04 -04:00
24beebe32f
Fix valueset URI for loinc groups
2018-06-27 13:15:37 -04:00
79ede4c5ee
Remove orphanremoval
2018-06-27 11:31:53 -04:00
4dca271735
Clean up concept deletion
2018-06-27 11:19:11 -04:00
050f9939ac
Merge branch 'master' into improve_jpa_indexes
2018-06-27 10:44:18 -04:00
2b992cfb3b
Fix compile issue
2018-06-27 10:34:06 -04:00
8c849b16a4
Merge pull request #1015 from jschneid-nmdp/resolve-term-upload-deferred-short-circuit
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avoid potential short circuit during saveDeferred processing of uploaded (e.g. LOINC) terminology
2018-06-27 10:33:06 -04:00
fb2976d0d2
Improve code system deletion from terminology service
2018-06-27 10:22:13 -04:00
b2853b3f9d
modify BaseHapiTerminologySvcImpl saveDeferred method to avoid short circuit that could potentially prevent processing of some deferred value sets and concept maps
2018-06-27 02:20:12 -05:00
52e3c9496e
Fix slow upload
2018-06-26 21:59:01 -04:00
74bca0562e
Merge branch 'improve_jpa_indexes' of github.com:jamesagnew/hapi-fhir into improve_jpa_indexes
2018-06-26 21:54:32 -04:00
a63205ecff
Merge branch 'master' into improve_jpa_indexes
2018-06-26 21:54:12 -04:00
f7029b9a0f
Update part code url for loinc
2018-06-26 17:17:31 -04:00
a77896ff2d
Add callback for resource deletion
2018-06-26 07:54:21 -04:00
f0da7a33de
Fix expunge transaction boundaries
2018-06-25 10:22:49 -04:00
e5cb609f4d
Performance improvements
2018-06-24 20:02:27 -04:00
9a880361b6
Merge branch 'master' into improve_jpa_indexes
2018-06-24 15:15:31 -04:00
2d57699066
Work on index improvements
2018-06-24 15:09:53 -04:00
f38f71cf0a
Merge remote-tracking branch 'origin/master' into
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1008_fix_jpa_sql_loop_issue
2018-06-22 15:34:56 -04:00
60ed0dab48
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-06-22 11:22:36 -04:00
e9fffd3cdc
Allow indexing in custom search params to descend into contained
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resources
2018-06-22 11:22:07 -04:00
d46b9b00be
Liinc updates
2018-06-22 09:59:54 -04:00
103b587ab5
#1008 : Fixed sql looping issue
2018-06-21 22:32:08 -04:00
cef4596211
Loinc updates
2018-06-21 19:23:23 -04:00
d6bfce4a1d
Make all loinc files mandatory
2018-06-21 18:30:57 -04:00
1b40188aab
FIx missing import
2018-06-21 14:48:39 -04:00
b3f7ab274d
License header updates
2018-06-21 14:44:34 -04:00
b9a4e1ae0f
Merge branch 'improve_jpa_indexes' of github.com:jamesagnew/hapi-fhir into improve_jpa_indexes
2018-06-21 13:48:27 -04:00
5b6cde8a9f
Merge branch 'master' into improve_jpa_indexes
2018-06-21 13:48:04 -04:00
ecc8e1eda0
More work on indexes
2018-06-21 13:42:34 -04:00
cc98f65500
Merge branch 'master' into valueset_expansion_fixes
2018-06-21 10:20:24 -04:00
2dc445fd10
ValueSet enhancements
2018-06-21 10:19:14 -04:00
e63604afc9
Merge pull request #1000 from rhausam/update-filenames
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Updated LOINC filenames to match 2.64 and future releases.
2018-06-21 10:18:36 -04:00
f9a19c4b1f
starting implementing check if only one Composition is returned
2018-06-20 16:12:58 +02:00
218937e425
Several fixes
2018-06-20 05:53:32 -04:00
6e7d67ba70
Update due to Spring version change
2018-06-19 20:16:27 -04:00
b76ad6870f
Merge remote-tracking branch 'origin/master' into documentOperation
2018-06-19 16:57:54 +02:00
0a8afb38ba
moved the BundleProvider -> DocumentBundle code from DAO to Service Layer
2018-06-19 15:20:35 +02:00
627491ad95
fixed Test if maxThreads >= 2
2018-06-19 14:50:04 +02:00
127efd55b0
Merge branch 'master' into 963_jpa_performance
2018-06-19 06:50:05 -04:00
299cf5b230
Changed retval to resource id instead of SearchResult in SearchResultDao
2018-06-16 22:37:12 -04:00
24ad8870cf
Add to indexes
2018-06-16 18:23:05 -04:00
d13d53c8ef
Add a bit of logging
2018-06-15 14:01:07 -04:00
215e224e3d
Updated terminology upload tests and artifacts to the new LOINC filenames.
2018-06-14 20:30:32 -05:00
99f80eef88
Performance enhancements to JPA searching
2018-06-15 01:13:44 +08:00
75c1b7baa8
Updated LOINC filenames to match 2.64 and future releases.
2018-06-14 11:33:35 -05:00
a46b4a4637
Reindexing shouldn't stop unexpectedly
2018-06-13 22:03:15 +08:00
c2b2a7eaa7
added missing CORS Headers for Test Setup
2018-06-11 11:09:23 +02:00
cc0e836680
Auth interceptor early checks ( #995 )
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* Validator fix
* Enhance AuthorizationInterceptor so that it tries to deny access earlier
for compartment searches that are outside the allowable compartment.
* FIx DSTU2 test that wasn't updated
* More test fixes
2018-06-10 17:48:20 -04:00
35991cd21b
#963 : renamed the parameter to 'the*'
2018-06-07 14:19:44 -04:00
903df68d2a
978 cli tools for importing exporting terminology mappings need to be fixed ( #988 )
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* Fixed export issue.
* Fixed import issue.
* Fixed tests.
* Fixed tests.
2018-06-07 10:22:41 -04:00
6bcddea416
Merge branch 'master' into documentOperation
2018-06-07 09:17:58 +02:00
6feb23896f
Hopefully fix #983
2018-06-06 15:51:23 -04:00
e7804b881c
Fix CI issue
2018-06-06 11:39:06 -04:00
583437d656
Prevent a crash if the application context has been set incorrectly in
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embedded deployments
2018-06-06 08:37:25 -04:00
49bdff1862
current state of $document
2018-06-05 18:32:59 +02:00
38b7b00f52
Merge branch 'master' into documentOperation
2018-06-04 17:34:39 +02:00
bd0682c2b2
Merge remote-tracking branch 'origin/master' into documentOperation
2018-06-04 13:53:02 +02:00
987679483a
Version bumps
2018-06-03 15:29:10 -04:00
jamesagnew
Ken Stevens
Volker Schmidt
Ken Stevens
Patrick Werner
Anthony Sute
Ana Maria Radu
anamariaradu10
frankjtao
Joel Schneider
Frank Tao
Rob Hausam
Diederik Muylwyk