Commit Graph

4868 Commits

Author SHA1 Message Date
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 fa80223d57 Fix invalid xml 2019-06-28 15:25:11 -04:00
James Agnew 8acaafed36 Credit for #1354 2019-06-28 15:24:43 -04:00
Stig Rohde Døssing d25e882d9a Issue-1351: Add a BOM POM for HAPI FHIR 2019-06-28 15:18:06 -04:00
James Agnew 05d004803f Credit for #1330 2019-06-28 15:15:51 -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 6d8465abe6 Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-06-27 18:23:54 -04:00
jamesagnew 5910131319 License header updates 2019-06-27 18:23:45 -04:00
James Agnew 53b47ed580 Ensure that parsed reesource is available to interceptors 2019-06-27 18:23:10 -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
James Agnew c14f5c1520 Credit for #1361 2019-06-25 18:31:25 -04:00
Gary Teichrow 5509e5c1df Tweaked a couple POM files for 2 sub-projects to stop the IDE from complaining on the builds. After these changes, the build went flawlessly.
The first change to hapi-fhir-testpage-overlay/pom.xml was to remove a redundant dependency to javax.annotation.
The second change to hapi-fhir-test-utilities/pom.xml was to add a <relativePath> tag to the <parent> tag so that the project could build.
2019-06-25 18:28:23 -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
jamesagnew 3274693576 FIx a test 2019-06-22 16:31:55 -04:00
jamesagnew 95876ec3cb Merge branch 'master' of github.com:jamesagnew/hapi-fhir 2019-06-22 16:24:07 -04:00
jamesagnew 638cb976fd Fix #1250 - Don't include Bundle.entry.response on search results 2019-06-22 16:23:32 -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 c7798fee48 Test fix 2019-06-18 05:40:00 -04:00
jamesagnew 9e9be00088 License eader updates 2019-06-17 21:59:03 -04:00
James Agnew 36ff58a320 Add docs 2019-06-17 17:46:28 -04:00
James Agnew 6724fd0348
Implement the $subsumes operation (#1344)
* Implement the $subsumes operation

* Fix #976
2019-06-17 17:31:24 -04:00
James Agnew 8bef3eddf9 Credit for #1347 2019-06-17 16:50:51 -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
James Agnew f6504ffc44 Credit for #1336 2019-06-14 15:40:28 -07:00
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
jpoth c59238cf11 Fix hapi-fhir Karaf feature 2019-06-11 18:11:21 +02:00
Ken Stevens dd203ae28f Credit for #1337 2019-06-10 11:14:52 -04:00
Stig Døssing f032916776 Issue-1337: Fix unstable concurrent code in PointcutLatch, fix subscription tests getting latch exceptions due to missing expectations, make hapi-fhir-jpaserver-subscription tests load StructureDefinitions outside latch timers, as this can be slow on busy machines (#1338) 2019-06-10 11:05:05 -04:00
jamesagnew a952663dc3 Disable OSGI mdule for now# 2019-06-09 23:51:41 -04:00
jamesagnew 3dbfb47411 Fix bad dependency 2019-06-09 21:11:13 -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 9500f6e6fe Roll back derby version for now 2019-06-07 16:27:19 -04:00