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3046 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
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
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
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
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
vedion
e4214a4cbe
Exposing hasIncludes PersistedJpaBundleProvider (#2047) 
Co-authored-by: ahn <anders.havn@systematic.com>
 2020-10-12 17:37:12 -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
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
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
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
IanMMarshall
5ec1284b8a
Apply suggestions from code review 
Edits per code review.

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-10-05 15:14:39 -04:00
ianmarshall
2258d37283 Documentation for terminology. 2020-10-05 09:02:00 -04:00
IanMMarshall
f1710fd0be
Merge pull request #2081 from jamesagnew/feature_2020_09_02_term_multi_version_support 
Feature 2020 09 02 term multi version support
 2020-10-01 12:24:40 -04:00
ianmarshall
90f1981817 Updated tests for missed dstu2 code coverage. 2020-09-30 18:10:57 -04:00
ianmarshall
dc3443665c Changes per code review. 2020-09-29 21:12:27 -04:00
ianmarshall
8e7b4e8437 Changes per code review. 2020-09-29 21:05:28 -04:00
Ken Stevens
09d09233ff
empi bugfixes and enhancements (#2104) 2020-09-29 17:27:43 -04:00
IanMMarshall
c593958d2c
Apply suggestions from code review 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 15:16:46 -04:00
IanMMarshall
d63c15ef09
Apply suggestions from code review 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:27:57 -04:00
IanMMarshall
43c16e1737
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:27:03 -04:00
IanMMarshall
43b6bd38ff
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:26:30 -04:00
IanMMarshall
2be47b5567
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:18:21 -04:00
IanMMarshall
b8531e599f
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:18:00 -04:00
IanMMarshall
3940e7526f
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:17:36 -04:00
IanMMarshall
6aa1a5ec3f
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:17:19 -04:00
IanMMarshall
ebb3fa0ca1
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ConceptMapTest.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:16:56 -04:00
IanMMarshall
10620a8bb4
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCodeSystemDstu3.java 
Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-09-29 14:16:13 -04:00
ianmarshall
9d8664ccd8 Additional tests and updates. 2020-09-27 21:09:06 -04:00
ianmarshall
e86d9deaac Additional tests. 2020-09-27 17:45:15 -04:00
ianmarshall
732624bfaf Fix broken JUnit test. 2020-09-25 22:55:01 -04:00
ianmarshall
1dc4a533d6 Fixes to terminology loader. 2020-09-25 21:43:15 -04:00
ianmarshall
47244c54dc Merge remote-tracking branch 'origin/feature_2020_09_02_term_multi_version_support' into im_20200728_term_multi_version_support 
# Conflicts:
#	hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
 2020-09-25 09:10:07 -04:00
ianmarshall
6f9874468a Merge remote-tracking branch 'origin/master' into feature_2020_09_02_term_multi_version_support 2020-09-25 08:54:17 -04:00
ianmarshall
2bceacd9a6 Update loader to ensure that ConceptMap and ValueSet Ids are unique for each version loaded. 2020-09-25 08:51:53 -04:00
ianmarshall
5fe46be41c Validate code changes and new tests. 2020-09-24 18:51:47 -04:00
ianmarshall
e5daea17b7 Additional cleanup and migration tasks. 2020-09-23 17:17:07 -04:00
ianmarshall
dffc02a126 Missing fixes for DSTU3 and R5. 2020-09-23 16:51:18 -04:00
ianmarshall
640ee94c5c Merge remote-tracking branch 'origin/master' into im_20200728_term_multi_version_support 2020-09-23 16:43:22 -04:00
ianmarshall
ceb5ec6384 Use canonical identifiers for code systems rather than specifying version separately. 2020-09-23 16:42:29 -04:00
Frank Tao
3d3d013d72 Changed import of IdType to r5. 2020-09-23 09:19:06 -04:00
Frank Tao
b6d86dc5f2 Added fail(); in the invalid test cases 2020-09-22 20:39:20 -04:00
Frank Tao
20661c7a2b Removed unused import 2020-09-22 20:19:43 -04:00