Commit Graph

7140 Commits

Author SHA1 Message Date
IanMMarshall fd46d0965f
Merge pull request #2141 from jamesagnew/im_20201020_package_installer_enhancements
Enable package installer to load non-Conformance resources
2020-10-21 18:28:15 -04:00
ianmarshall 115b09e4d4 Throw exception if any resources in package have no url and no identifier. 2020-10-21 17:23:40 -04:00
ianmarshall 830ad70089 Add changelog for package installer enhancement. 2020-10-21 16:18:10 -04:00
ianmarshall 756432e61a Enable package installer to load resources other than conformance resources. 2020-10-21 15:47:31 -04:00
jamesagnew 9b4c1a58a6 License header updates 2020-10-21 12:58:29 -04:00
Ken Stevens 3b91873b7c
delete expunge (#2131)
Added delete _expunge=true
2020-10-20 17:21:50 -04:00
jamesagnew 3738297354 Test fix 2020-10-19 20:13:31 -04:00
James Agnew 9e8e98b6fb
Rework scheduler to use Spring factory (#2134)
* Rework scheduler to use Spring factory

* Add test
2020-10-19 10:33:12 -04:00
ianmarshall 76416998ce Merge remote-tracking branch 'origin/master' into im_20201015_loinc_versioned_resourceids 2020-10-16 16:48:32 -04:00
ianmarshall 6e0754da98 restore maven-wrapper.properties file inadvertently deleted. 2020-10-16 16:47:19 -04:00
ianmarshall 3d041febce restore maven-wrapper.properties file inadvertently deleted. 2020-10-16 16:40:54 -04:00
ianmarshall 3cfeff89bf restore maven-wrapper.properties file inadvertently deleted. 2020-10-16 16:39:48 -04:00
ianmarshall f3639ee1ce Changes to terminology loader to support preserving the original resource IDs for LOINC even when multiple versions are loaded. 2020-10-16 16:30:37 -04:00
jamesagnew a25aa37e6a Update to #1607 2020-10-16 14:52:40 -04:00
jamesagnew 66e36378c1 Add hardcoded anchor name to docs 2020-10-13 12:11:58 -04:00
jamesagnew 7903b2b577 License headers 2020-10-13 11:43:09 -04:00
James Agnew aa3da9b05f
Bump bootstrap version (#2128)
* Bump bootstrap version

* Add changelog

* Resolve fixme

* Rmove test code
2020-10-12 20:47:14 -04:00
jamesagnew 7d150858dc Credit for #2118 2020-10-12 20:45:02 -04:00
jamesagnew 90016b25a2 Credit for #2059 2020-10-12 17:45:01 -04:00
Tuomo Ala-Vannesluoma 1435540320
Improve synchronous searching by providing offset & limit support (#2059)
* Improve synchronous searching by providing offset & limit support

Add support for offset querying which leverages paging at the query level
Add configuration for search default page size and search maximum page size
If using offset, always use synchronous searching to avoid extra database insert/update etc.
When using offset, only calculate count if it's wanted
Validate params closer to provider and handle size if search returned "all" (or last)

* Review and test fixes

Comment _offset as nonstandard parameter
Make synchronous search always count the total value (for now)
Fix issue with FulltextSearchSvcImpl mutating param map
Dirty fix for BaseJpaTest (not sure how to fix the including resources issue)

* Remove temporary count querying fix for synchronous loads

* Fix offsetting of everything operations, do not drop zero offset

* Fix jpa test default and maximum page size, add some fixmes to tests before resolved

* Ignore one failing test, fix others

* Fix Dereferenced variable may be null

* Fix everything paging in R4 by adding DISTINCT if synchronous load is used

Also fix assertion of size when hitting fetchSizeDefaultMaximum

* Add documentation about offset annotation and paging

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2020-10-12 17:42:03 -04:00
Joel Schneider (NMDP) a32397d993
add CorsInterceptorTest (#2126)
* add simple CorsInterceptorTest

* add relevant exposedHeaders to custom CorsConfiguration

* use SLF4J Logger.info() instead of System.err.println(), and run the test assertions first

* Add logback-classic dependency to test scope, to enable SLF4J logging within unit tests.  (SLF4J defaults to NOP binding if no binding found on classpath, see also http://www.slf4j.org/codes.html#StaticLoggerBinder)
2020-10-12 17:38:31 -04:00
vedion e4214a4cbe
Exposing hasIncludes PersistedJpaBundleProvider (#2047)
Co-authored-by: ahn <anders.havn@systematic.com>
2020-10-12 17:37:12 -04:00
jamesagnew bd6feec2f4 Initial credit for #2118 2020-10-12 17:19:15 -04:00
Josh Collins 844624b6dd
RDF Support in HAPI FHIR (#2118)
* RDF Support in HAPI FHIR

* Ability to read/write FHIR resources as RDF (turtle serialization)
* Test suite to test roundtrip-ability of RDF parser

* Add null checks to appease LGTM

* Correct null check logic
2020-10-12 17:16:00 -04:00
Oliver Egger 3297e50815
make invoke available for derived classes (#2125) 2020-10-12 17:07:27 -04:00
jamesagnew 3ba80de717 Add to date equals comparison 2020-10-11 15:35:28 -04:00
jamesagnew 81d7a1eae1 Credit for #2112 2020-10-11 15:29:06 -04:00
Oliver Egger 8294b8ddb6
add namespace, prefix for attributes (xml:lang) (#2112) 2020-10-11 15:25:37 -04:00
jamesagnew 576f6efc39 Credit for #1607 2020-10-09 11:58:00 -04:00
abrsystematic cad3ba5a66
Fix gettimezone performanceissue (#1607)
* [(release_3_7_SSE)] cache timezone since timezone.gettimezone is static synchronized and performs poorly

* [(fixgettimezoneperformanceissue)] fiximport
2020-10-09 11:51:50 -04:00
Tadgh d5b533c73c
Merge pull request #2123 from jamesagnew/gg_20201008_baddeps
Update hibernate core and validator
2020-10-09 09:06:38 -04:00
jamesagnew e8d844f4f3 Merge branch 'master' into gg_20201008_baddeps 2020-10-09 07:53:19 -04:00
James Agnew 2134d40f1c
Account for timezones in lastUpdated search (#2113)
* Add test

* Fix

* Add changelog

* Test fixes

* Test fix

* Test fixes

* Resolve fixme

* Test fixes

* Remove debug logs

* Try to get CI tests passing again
2020-10-09 07:52:46 -04:00
Tadgh cbfadd427f Merge branch 'master' into gg_20201008_baddeps 2020-10-08 18:40:44 -04:00
Tadgh 375552ac49 Update hibernate core and validator 2020-10-08 14:15:57 -04:00
IanMMarshall a44037daf3
Merge pull request #2122 from jamesagnew/im_20201007_conceptmap_sourcesystemversion
Fixed loader so that it now sets source system version for ConceptMap…
2020-10-08 14:04:49 -04:00
James Agnew d2aae361bf
Rewrite deferred interceptor callback framework (#2121)
* Rewrite deferred interceptor callback framework

* Improve deferred handling

* Null guard

* Test fix
2020-10-07 20:08:18 -04:00
ianmarshall 476eba676e Fixed loader so that it now sets source system version for ConceptMap resources. 2020-10-07 15:07:25 -04:00
IanMMarshall ebbdafb107
Merge pull request #2120 from jamesagnew/im_20201005_loincpartlink_fix
Im 20201005 loincpartlink fix
2020-10-07 12:07:23 -04:00
Tadgh f85f7c0237
Merge pull request #2117 from jamesagnew/gg_20201006_dep_update
Update dependencies
2020-10-07 11:13:45 -04:00
ianmarshall 46b2fde1db Fixed tests to accommodate suggested changes from code review. 2020-10-07 11:07:34 -04:00
IanMMarshall 1bac646dc3
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/LoadedFileDescriptors.java
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-10-07 11:01:54 -04:00
IanMMarshall e24e233ec6
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/LoadedFileDescriptors.java
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-10-07 11:01:47 -04:00
ianmarshall 0f39eeb0e9 Bug fix and test improvements. 2020-10-06 21:22:09 -04:00
Tadgh f347f95f85 rollback elastic 2020-10-06 19:04:10 -04:00
Tadgh 47207e11d1 Merge branch 'gg_20201006_dep_update' of github.com:jamesagnew/hapi-fhir into gg_20201006_dep_update 2020-10-06 17:20:33 -04:00
Tadgh 5a29fd9945 rollback the elastic changes 2020-10-06 17:20:11 -04:00
ianmarshall f044f9c47e Merge remote-tracking branch 'origin/master' into im_20201005_loincpartlink_fix 2020-10-06 14:55:57 -04:00
ianmarshall d9841e59ac Restore ability to load LOINC PartLink data from a single file for pre-2.68 versions. 2020-10-06 14:36:23 -04:00
Tadgh bac43d480f Update dependencies 2020-10-06 14:14:17 -04:00