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1835 Commits

Author SHA1 Message Date
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