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2903 Commits

Author SHA1 Message Date
James Agnew 228e75b501
Bump core to latest versions (#2154) 
* Bump core to latest versions

* Compile fix

* Bump to non snapshot core library
 2020-11-03 15:43:37 -05:00
jamesagnew 783cbb3cf8 Bump postgres driver version 2020-10-26 19:34:50 -04:00
James Agnew 72294fc0a0
Suport typeFilter parameter for bulk export (#2147) 
* Cleanup

* Fix tests

* Work on bulk export

* Work on export

* Test fixes

* Add changelog

* Address review comments

* Address review comments
 2020-10-26 12:28:07 -04:00
James Agnew 8000d2d0cf
SQL Join Rework (#2086) 
* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* switched to adding annotations.  Just did a test with Token, but the sql looks clean.

* added the other six index links

* trying different annotations

* Start testing

* Update resources on package install

* Add changelog

* Join rework

* CLean up SQL builder

* Add docs

* SP rework

* Join work

* Work on params

* Work on refactor

* Work on chains

* Work on joins

* Rework queries

* Work on queries

* Many more tests passing

* Refs test

* Work on sorting

* Work on tests

* More joins work

* Work on tests

* Work on queries

* Tests passing

* More test fixes

* Test fixes

* Work on SQL

* Tests passing

* Add some tests

* Add some tests

* License headers

* Use entity manager to get datasourcd

* One more fix

* Model cleanup

* Ongoing work

* Fixes

* Fixes

* Work on joins

* Ongoing fixes

* Merge conflict

* Cleanup

* clean up unused fields

* Work on join

* COmpile fix

* Rework querying

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernateDialectProvider.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* Address review comments

* Resolve fixmes

* Test fix

* Test fixes

* Test fix

Co-authored-by: Ken Stevens <khstevens@gmail.com>
 2020-10-26 05:24:26 -04:00
James Agnew 4a5f5199b5
Add custom partition interceptor examples (#2145) 
* Add custom partition interceptor examples

* Add documentation

* Test fixes

* Remove outdated test

* Test modification
 2020-10-25 19:19:40 -04:00
blangley28 d468183edd
Validate theSearchParamRegistry is not null (#2142) 2020-10-23 10:29:55 -04:00
IanMMarshall 1c9e4dcc81
Merge pull request #2135 from jamesagnew/im_20201015_loinc_versioned_resourceids 
Im 20201015 loinc versioned resourceids
 2020-10-22 19:01:31 -04:00
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