Commit Graph

1945 Commits

Author SHA1 Message Date
James Agnew 4f7d4aa8d2 Two test fixes 2019-07-04 09:54:26 -04:00
James Agnew 886f3f442b Moving testloggingutil into test utilities 2019-07-04 09:00:30 -04:00
James Agnew f1848fb1ad Include version ID in response for deleted resource 2019-07-03 14:44:12 -04:00
James Agnew 56aaef641c Add request ID 2019-07-02 21:32:28 -04:00
James Agnew 1faf7785c4 Dont filter constraints from the event broadcast - this was not needed
after all
2019-07-02 09:21:15 -04:00
jamesagnew 7b7136e3ab Ensure test coverage of JPA entities 2019-07-02 08:37:48 -04:00
jamesagnew 491776a7b8 Fixes to cascading delete 2019-07-02 05:41:38 -04:00
jamesagnew 742389642d Add tests for delete conflicts and authorizationinterceptor 2019-07-01 10:49:38 -04:00
jamesagnew ccf491b3ae Add parent pom to BOM 2019-06-29 13:50:43 -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
Joel Schneider 5c55133275 quick hack to pass unit test (handle files located in subdirectories of zipfile) 2019-06-28 15:11:16 -04:00
Joel Schneider 557c9b66c2 add TerminologyLoaderSvcImgthlaTest 2019-06-28 15:11:16 -04:00
Joel Schneider 5d113c2e8b Remove allele_id property. (If needed, a CodeSystem supplement could define it. Defining a separate allele_id CodeSystem, and related ConceptMap, may also be a reasonable option.) Trying to keep the list of concept properties as straightforward as possible for now. 2019-06-28 15:11:16 -04:00
Joel Schneider 1f5cbc36b3 add stub for HLA nomenclature terminology upload 2019-06-28 15:11:16 -04:00
jamesagnew 5910131319 License header updates 2019-06-27 18:23:45 -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
James Agnew 2bfbea4e6b Remove duplicate test class 2019-06-26 09:24:36 -04:00
James Agnew ce0c84db03
JPA server can't use OR list on _tag:not (#1362)
* Add a failing test for :not tags

* Add changelog and fix issue
2019-06-26 08:44:56 -04:00
jamesagnew e76b1dacb3 License header updates 2019-06-22 18:31:16 -04:00
jamesagnew 8bb010bb18 Test fixes 2019-06-22 17:42:02 -04:00
jamesagnew 3ba194acbe Reject subscriptions in JPA server if status field is not set 2019-06-22 17:03:22 -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 58e6b7f6aa Fix #1011 - Was resolved in #1355 2019-06-22 16:03:35 -04:00
jamesagnew 989e26fdb4 Fix #1355 - Failed to call access method: java.lang.NullPointerException in case of bundle entry without resource 2019-06-22 15:51:56 -04:00
James Agnew 2543f27697 Add a test 2019-06-21 15:38:16 -04:00
Diederik Muylwyk 266384b536 Evaluation of PartTypeName in LoincRsnaPlaybookHandler is not case insensitive. 2019-06-21 15:36:51 -04:00
jamesagnew 9e9be00088 License eader updates 2019-06-17 21:59:03 -04:00
James Agnew 6724fd0348
Implement the $subsumes operation (#1344)
* Implement the $subsumes operation

* Fix #976
2019-06-17 17:31:24 -04:00
jvi 8b4ceb8d5f changed json patch framework to slightly more maintained fork 2019-06-17 16:45:17 -04:00
James Agnew b2e99cf035
Add support for conditional patch (#1348)
* Add support for conditional patch

* Add changelog

* Test fix
2019-06-17 16:12:05 -04:00
jamesagnew 087c53286c License header updates 2019-06-14 18:43:55 -04:00
Stig Rohde Døssing b56f59542a Move JettyUtil to new module 2019-06-14 18:34:45 -04:00
Stig Rohde Døssing aab7bb6b64 Issue-1325: Let OS assign random ports to servers during testing, and let tests get the port of the running server once the OS has assigned a port. Delete PortUtil and similar utilities. 2019-06-14 18:34:45 -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
jamesagnew b72f1c4555 Roll back derby upgrade 2019-06-08 09:27:28 -04:00
James Agnew 517b68882c Fix derby dependencies for tests 2019-06-07 11:11:25 -04:00
Ken Stevens 5752a6e2b3 reported issue with proposed fix that breaks tests (#1243)
* reported issue with proposed fix that breaks tests

* Fix spelling

* Merge my changes into this

* Correctly check referential integrity on deletes

* Add one more test
2019-06-04 20:40:20 -04:00
James Agnew be06c2ee19 Correctly index timing events 2019-05-31 16:42:45 -04:00
James Agnew f6c7ff1dbb Modify expunge everything to use small batches of deletes 2019-05-31 11:05:17 -04:00
James Agnew 95af87f658 Test fix 2019-05-30 21:46:05 -04:00
James Agnew f2be9f47a0 Add 4.0.0 version enum 2019-05-30 20:59:23 -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
James Agnew d4d3178621 A couple of test fixes 2019-05-11 15:04:44 -04:00
James Agnew 444730373b Fix an NPE in validation 2019-05-10 12:49:34 -04:00
James Agnew 92bd2c7173 Fix regression in validator when validating codesystems explicitly
defined in the JPA database
2019-05-10 12:08:40 -04:00
James Agnew 6b37525f2d
Clean up redundant dependencies (#1306)
* Remove a bunch of unneedd deps

* Test fix

* Disable useless test
2019-05-09 12:51:13 -04:00
James Agnew 702ffd631d Fix #1299 - Return an HTTP 201 when creating a previously deleted
resource
2019-05-06 16:33:23 -04:00
James Agnew 61902da527 Tweak to validator 2019-05-06 10:18:55 -04:00
James Agnew 64f57b9736 Fix broken R4 serrver 2019-05-05 09:12:26 -04:00
James Agnew 7a320729a0 One more test fix 2019-05-04 14:57:18 -04:00
James Agnew 9353ea5b06 Enable websockets on public HAPI server 2019-05-04 10:06:10 -04:00
Ken Stevens b860269eb9 fix broken test 2019-04-29 11:12:08 -04:00
Ken Stevens 10f7eb31eb fixed delete reference error message 2019-04-29 10:20:45 -04:00
jamesagnew ddf12e7c28 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-28 11:17:18 -04:00
jamesagnew c1bf6d0b3c License headers 2019-04-28 10:46:52 -04:00
James Agnew 828df1528f Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-26 11:24:00 -04:00
James Agnew 685adf7754 Revert Jetty upgrade, and improve patch error messages 2019-04-26 11:23:22 -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
jamesagnew abd53c0cbe License header updates 2019-04-24 21:20:11 -04:00
James Agnew c8c81c2ebc FIx invalid patch syntax 2019-04-24 15:00:03 -04:00
James Agnew da962b8c10 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-24 14:33:28 -04:00
James Agnew 738c2c1797
Interceptor framework refactoring (#1287)
Interceptor framework overhaul
2019-04-24 14:32:30 -04:00
James Agnew f2e382a132 Swap JSON Patch provider 2019-04-24 14:10:21 -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 311246e5f0
Merge pull request #1255 from jamesagnew/addFetchValueSet
added fetchValueSet to IValidationSupport and made it public
2019-04-15 17:03:56 -04:00
James Agnew 1e4a497181 Add some tests 2019-04-15 14:44:25 -04:00
jamesagnew a9cfce3615 Header updates 2019-04-15 12:31:11 -04:00
James Agnew f7ad0bc0d8 Fix a test regression 2019-04-15 11:34:13 -04:00
James Agnew 0848fdf1eb Fix broken test 2019-04-15 10:29:55 -04:00
James Agnew c8f2e4bbc9 Return HTTP 400 for missing body on POST and PUT 2019-04-14 12:32:09 -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
Ken Stevens bb98ded1fa
Websocket improvements (#1272)
* subscription loader now only pulls active subscriptions
only allow websocket connections to subscriptions of type websocket

* Added a "flag for deletion" to ActiveSubscription in the SubscriptionRegistry to handle the race condition of a scheduled sync overlapping with a subscription creation.  We could have used a package-scoped semaphore or a pre-remove FHIR read, but this seemed like the safest, simplest and most performant way to handle it.

* ActiveSubscriptionCacheTest

* WebsocketConnectionValidatorTest

* fix compile error in jpa example
2019-04-12 08:36:49 -04:00
jamesagnew ca8b6acdf9 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-07 07:52:40 -04:00
jamesagnew 884b80c1d7 Improve ability to select active resources 2019-04-07 07:52:21 -04:00
James Agnew 706af5d579 Don't update modified time when performing NOOP update in JPA 2019-04-05 14:36:18 -04:00
Ken Stevens 5299479143 fix broken test 2019-04-04 10:26:09 -04:00
jamesagnew 859bc7d71b Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-03 20:15:19 -04:00
jamesagnew 54e3c50ad7 FIx a build failure 2019-04-03 20:15:07 -04:00
Ken Stevens 1d5f648070 fixed second expunge bug reported by FMCNA 2019-04-03 13:32:10 -04:00
Ken Stevens de4cc89568 bug fixed 2019-04-03 12:20:49 -04:00
Ken Stevens 28ea97ee9a reproduced failure reported by FMCNA 2019-04-03 11:42:21 -04:00
James Agnew 767a84bddb Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-04-02 10:56:43 -04:00
James Agnew 8065f0f5fc Revert one accidental change 2019-04-02 10:56:26 -04:00
jamesagnew 8b5143f436 License header updates 2019-04-02 10:44:41 -04:00
James Agnew 588082aee2 Fix broken test 2019-04-02 10:00:56 -04:00
James Agnew 90d163a4e9 Merge branch 'ja_interceptor_jpa_queries' of github.com:jamesagnew/hapi-fhir into ja_interceptor_jpa_queries 2019-04-02 09:33:22 -04:00
James Agnew 7359b77d99 Address review comments 2019-04-02 09:33:01 -04:00
jamesagnew 835b89f449 Build fixes 2019-04-01 18:55:55 -04:00
James Agnew 3eeca4a8fd Merge branch 'master' into ja_interceptor_jpa_queries 2019-04-01 09:59:03 -04:00
patrick-werner 1aeb54e94e added all fetchValueSet Implementations 2019-03-30 21:02:24 +01:00
jamesagnew 8791ed5793 Test tweaks 2019-03-29 17:13:41 -04:00
Ken Stevens b1d41a8211 named interceptor registries 2019-03-29 14:29:36 -04:00
James Agnew cf7cd40336 Make sure we properly scope reference queries on external URLs 2019-03-27 13:10:24 -04:00
James Agnew e85bec2858
Ja inline references (#1252)
* Use a single IN clause for OR reference searches

* Add changelog

* One more attempt at getting the free port util to actually work... sigh

* One more tweak to free ports

* Bundle fix
2019-03-26 10:42:42 +01:00
Ken Stevens 9a54d7086e Fix a couple of bugs (#1251)
* might keep this

* might keep this

* undoing start in interface

* fixed bug that only supported resources with ResourceType/id prefixes

* added standalone subscription support for Dstu2.  untested.

* failing test

* fixed cannonicalsubscription.equals for email

* final cleanup
2019-03-26 10:39:40 +01:00
James Agnew 87c0b3778b More work on threadlocal interceptors 2019-03-22 09:54:02 -04:00
James Agnew c701de2861 Create a performance interceptor framework for HAPI FHIR 2019-03-22 01:06:03 +01:00
James Agnew d1667487c2 Clean up unique composite search params 2019-03-21 21:57:38 +01:00
James Agnew 8d49b4e6d2 Add a test (currently ignored) 2019-03-21 15:59:59 +01:00
jamesagnew 037ed27497 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-03-17 14:09:37 -04:00
jamesagnew 3e57fdb491 Improvements to PortUtil to avoid reusing ports 2019-03-17 14:09:21 -04:00
James Agnew 08c7afb804 Reduce logging in JPA server 2019-03-14 17:42:13 -04:00
jamesagnew 6ff92abecc License header 2019-03-14 13:32:32 -04:00
James Agnew e15afbc4f0 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-03-14 13:32:03 -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
jamesagnew a1046f7729 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-03-12 17:46:03 -04:00
jamesagnew 7b1950aeed License headers 2019-03-12 17:45:51 -04:00
James Agnew ed4da7c414 Add setting to disable resource type target validation in JPA 2019-03-12 17:45:19 -04:00
James Agnew 6597a928d5 Fix broken test 2019-03-12 15:45:53 -04:00
James Agnew 00a8f8c759 Fix broken build 2019-03-12 13:13:13 -04:00
James Agnew f934f76c96
Several JPA search fixes (#1231)
* Search fixes

* Add some tests

* CHangelog

* Some cleanup of the query tracker

* FIx XML issue in changelog

* Test fixes

* SOme test fixes

* Address review comments

* Fix test breakage
2019-03-11 15:49:34 -04:00
Ken Stevens dcfacfea49
Has param no in (#1232) 2019-03-10 20:50:24 -04:00
James Agnew 5dccf93506 Fix broken test 2019-03-06 17:15:30 -05:00
James Agnew f8b8f2d1b0 Move process-message to the correct level 2019-03-06 16:12:43 -05:00
Ken Stevens a2d4c93922 Subscription matcher transactions (#1229)
* fix bug in ResourceIndexSearchParamQuantity
Move transaction boundary around SubscriptionMatcherInterceptor so it can be overridden in subclass
Lots of CRLF changes from a mvn -P DIST

* FIXME
2019-03-06 16:12:04 -05:00
James Agnew fd401165a9 Fix an occassional failure in the stress test 2019-03-06 09:32:37 -05:00
James Agnew 9bc0f6784d
Search paging timeout with 1500 < n < 2000 results (#1221)
* Avoid paging links when offset is artificially set very high

* Ongoing fixes

* Adding logging and clean up transaction processing

* Add changelog

* More work on queries

* Keep working on getting tests passing

* More test fixes

* More work on tests

* More test works

* One more test attempt

* Ongoing fixes

* One more change

* FIxes to search algorithm

* Add changelog

* Clean up for review

* Fixed NPE in token matcher when system is not null and value is null

* test opposite (null system not null value)

* added null protection to all matchers

* Address review comments

* Address broken test

* Trying to resolve DB ordering issues
2019-03-06 05:45:05 -05:00
James Agnew 7896887f67 Updates to transaction processing 2019-02-28 12:23:48 -05:00
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 94f9ffa977 Avoid paging links when offset is artificially set very high 2019-02-25 20:44:22 -05:00
James Agnew fb06664f70 Clean up paging query 2019-02-25 19:05:19 -05:00
James Agnew 820a3d2296 Collapse conditional UPDATES as well in JPA transactions 2019-02-22 13:49:38 -05:00
James Agnew 43c07077be Automatically remove duplicate conditional creates in JPA 2019-02-22 12:57:07 -05:00
James Agnew 89b08cd627
Improve SQL IN(..) queries (#1214)
* First attempt, probably has compile issues

* Fix qualified searches

* Another test fix

* More test fixes

* Add changelog

* Two more fixes

* Revert SQL logging
2019-02-20 16:38:51 -05:00
James Agnew 28b4b812ac Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-02-20 15:07:08 -05:00
James Agnew e7b7ba1a6d Add caching test 2019-02-20 11:18:02 -05:00
Ken Stevens 01568ab0b5 Fix test race condition. 2019-02-19 21:14:11 -05:00
Ken Stevens 3af0bc7206 changes needed to support different number of consumers in matching vs delivery 2019-02-17 15:23:01 -05:00
James Agnew c6fcb4fcbf Allow canonical subscription to hold multiple extensions with the same
URL
2019-02-16 15:28:39 -05:00
jamesagnew 1311ded7de Fix compile issue 2019-02-15 14:55:25 -05:00
James Agnew c0970ed46d Fix typo in test 2019-02-15 14:30:38 -05:00
James Agnew a35f30b18e
Merge pull request #1208 from jamesagnew/reuse-subscription-channels
Reuse subscription channels
2019-02-15 13:42:54 -05:00
James Agnew 485335e975 Allow terminology service to work without having Lucene enabled for
simple ValueSet expansions
2019-02-14 20:47:28 -05:00
Ken Stevens ffc5966aa3 Merge branch 'master' into reuse-subscription-channels
# Conflicts:
#	src/changes/changes.xml
2019-02-14 19:42:00 -05:00
James Agnew 10c348d44f Tweak to elements parametr support 2019-02-14 19:30:10 -05:00
Ken Stevens 508e15956e added a couple of subscription tests and un@Ignored another 2019-02-14 15:30:25 -05:00
Ken Stevens 7b3fedc642 sonar 2019-02-13 20:41:11 -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
James Agnew a5e10740c0
Merge pull request #1194 from jamesagnew/ja_more_subscription_logger
More subscription logger work
2019-02-09 11:45:25 -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
Ken Stevens 52c62884fb Merge branch 'master' into reuse-subscription-channels 2019-02-08 10:39:00 -05:00
James Agnew ce840ecb6e Fix broken test 2019-02-07 17:48:08 -05:00
James Agnew 810f1ad969 Improvements to elements parameter as well as adding attributes to
RequestDetails
2019-02-07 16:45:59 -05:00
Ken Stevens b3e80f8da7 Merge branch 'master' into reuse-subscription-channels 2019-02-07 10:10:10 -05:00