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3092 Commits

Author SHA1 Message Date
Nick Goupinets
dc2a9e55c5 Renamed sourceResource to goldenResource 2020-11-27 16:53:47 -05:00
jamesagnew
fbbba11417 Formatting only 2020-11-27 16:16:01 -05:00
IanMMarshall
722e24d80c
Merge pull request #2175 from jamesagnew/ft-fix-expend-filter-contains-issue 
Fixed expand filter issue
 2020-11-27 14:47:05 -05:00
ianmarshall
bbba4428ee Changed name for new tokenFilter to make it unique. 2020-11-27 11:38:24 -05:00
ianmarshall
be88a256d0 Changed name for new tokenFilter to make it unique. 2020-11-27 11:32:08 -05:00
Frank Tao
014e2ba9cb Rework on the expand issue replaced the EdgeAnalyzer 2020-11-26 20:37:51 -05:00
Frank Tao
a511543e77 Merge branch 'master' into ft-fix-expend-filter-contains-issue 
# Conflicts:
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
#	hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
 2020-11-26 18:47:10 -05:00
swagers
cb693afe25
Changed the names URIs and IDs of a few LOINC concept maps (#2197) 
Changed to match what LOINC uses for these concept maps

Co-authored-by: Steven Wagers <swagers@regenstrief.org>
 2020-11-26 10:06:17 -05:00
James Agnew
fb8658da70
Always apply vs filters correctly (#2195) 
* Always apply valueset filters correctly

* Test fix

* Testfix

* Test fix

* Add changelog

* Test fix
 2020-11-24 18:12:02 -05:00
Frank Tao
3d9e0aeac1 Added more test cases 2020-11-23 21:32:46 -05:00
Frank Tao
5a05513250 Revoked filter op to EQUAL and enabled NGramAnalyzer 2020-11-21 14:46:26 -05:00
Frank Tao
5b471602c6 Merge branch 'master' into ft-fix-expend-filter-contains-issue 2020-11-20 10:29:58 -05:00
James Agnew
a01f5ae906
Fix subsumption test direction (#2183) 
* Fix subsumption test direction

* Add changelog

* Test fixes
 2020-11-19 21:48:54 -05:00
James Agnew
8b65db0c98
Improve error message on unique constraint violation (#2182) 
* Improve error message on unique constraint violation

* Add changelog

* Test fixes

* Test fix
 2020-11-19 21:20:59 -05:00
Frank Tao
e551f1837e Updated based on review 2020-11-19 20:22:13 -05:00
Tadgh
953b662827 Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references 2020-11-19 14:24:51 -05:00
ianmarshall
d99db2dbcc Fixed NPE in package loader when package description is null. Also renamed tests that would have caught this problem sooner. 2020-11-18 22:37:35 -05:00
Frank Tao
878c22192e Added expand filter impl for R5 and dstu3, changed the filter logic 2020-11-18 22:26:21 -05:00
Frank Tao
f65fdb0d52 Merge branch 'master' into ft-fix-expend-filter-contains-issue 2020-11-18 19:54:01 -05:00
Tadgh
75c0c25d7b remove references to EMPI 2020-11-18 19:50:00 -05:00
jamesagnew
0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew
4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -05:00
Tadgh
805d5b1d6c Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references 2020-11-17 09:28:37 -05:00
IanMMarshall
7532313c0f
Change to not set ValueSet expansion component parameter id HibernateSearch not enabled. (#2178) 
Co-authored-by: ianmarshall <ian@simpatico.ai>
 2020-11-17 07:46:55 -05:00
Frank Tao
78f730c4ca Fixed expend filter issue 2020-11-15 22:39:14 -05:00
jamesagnew
1db0944243 Improve logging for terminology ingestion 2020-11-13 17:25:14 -05:00
IanMMarshall
ed953d82f8
Rename index that was recently changed. (#2173) 
* Restoring name of index that was changed in migration task.

* Rename TermValueSetConcept index that was recently changed.

Co-authored-by: ianmarshall <ian@simpatico.ai>
 2020-11-13 14:12:25 -05:00
Tadgh
f648d8ec2b renaming in personsvc 2020-11-13 09:44:15 -05:00
Nick Goupinets
2bbfb6dfaa WIP 2020-11-11 15:27:57 -05:00
Nick Goupinets
b0f449ff5e MergerSvcTest WIP 2020-11-11 10:17:03 -05:00
IanMMarshall
bf9e02bc16
Merge pull request #2164 from jamesagnew/im_20201029_ig_package_long_description 
Truncate package descriptions that are longer than 200 characters.
 2020-11-10 12:01:53 -05:00
James Agnew
63b7b379c2
Improve ValueSet filtering (#2162) 
* Improve filter search

* Filter improvements

* Tests passing

* Test fixes

* Fix transaction filter

* Add changelog

* Test fix

* Update hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Resolve FIXME

* Test fix

* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>

Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
 2020-11-10 11:01:13 -05:00
ianmarshall
881193cf24 Truncate package descriptions that are longer than 200 characters. 2020-11-09 16:19:05 -05:00
jamesagnew
4f6be9d9a7 Reduce test timeout 2020-11-09 14:46:15 -05:00
Nick Goupinets
4c0fab8cec Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references 2020-11-09 09:06:50 -05:00
jamesagnew
22fe9420ac Add tests 2020-11-06 09:10:47 -05:00
Tadgh
5797cd0682 * Add source_resource_id column 
* Add source_resource columm
Still need to depracate the old columns.
Reworked a Matcher to ignore Person
 2020-11-05 13:07:45 -05:00
Frank Tao
ce1caee9fa
Feature 2020 10 28 reverse chain (#2160) 
* Added test cases for multiple '_has'

* Fixed composite search for the new SearchBuilder

* Added more test cases
 2020-11-05 05:27:11 -05:00
IanMMarshall
38a975f09d
Im 20201028 fix versioned valueset expansions (#2151) 
* Fixes to ValueSet expansion for cases where CodeSystem is versioned.

* Fixes to ValueSet expansion for case where URL and filter parameters specified.

* Restore maven-wrapper.properties file inadvertently deleted from GitHub.

* Fix JUnit tests and ValueSet exclude.

Co-authored-by: ianmarshall <ian@simpatico.ai>
 2020-11-04 16:36:43 -05:00
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