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7075 Commits

Author SHA1 Message Date
jamesagnew 4d441ad7f2 Version bump to 5.2.0 2020-11-18 06:30:20 -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
Tadgh d15a300486
Merge pull request #2174 from jamesagnew/feature/2172-update-tag-docs 
Feature/2172 update tag docs
 2020-11-13 17:43:09 -05:00
jamesagnew 1db0944243 Improve logging for terminology ingestion 2020-11-13 17:25:14 -05:00
Tadgh 1048df4d87
Update rest_operations.md 2020-11-13 15:54:43 -05:00
Tadgh 8f95ad4c0f fix typo :) 2020-11-13 15:35:06 -05:00
Tadgh 16003162fd Address #2172 2020-11-13 15:27:58 -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
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 40c34a4518 Truncate package descriptions that are longer than 200 characters. 2020-11-09 16:36:37 -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
jamesagnew 22fe9420ac Add tests 2020-11-06 09:10:47 -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
Nick Goupinets 382c0f2119
Merge pull request #2156 from jamesagnew/2155-Incorrect_EMPI_normalized_score_calculation 
Fixed score calculation to use selected bits in the vector. Addresses…
 2020-11-03 14:40:07 -05:00
Nick Goupinets 4c01025934 Updated based on code review feedback 2020-11-03 13:10:16 -05:00
Nick Goupinets 52e8761701 Added rule count for proper scoring implementation 2020-11-02 17:15:39 -05:00
Nick Goupinets 296b193bb5 Fixed score calculation to use selected bits in the vector. Addresses #2155 2020-11-02 09:22:00 -05:00
nvg-smile 590d3c468b
Merge pull request #2149 from jamesagnew/EMPI_-_Patient_matching_using_MPI_-_return_mode,_score,_and_grade 
#2148 Initial implementation
 2020-10-28 17:43:20 -04:00
Nick Goupinets 954fbf054f Fixed implementation based on the feedback. 2020-10-28 15:09:15 -04:00
James Agnew 5e8ec8d6f3
Resolve crash in InMemory SP resolver for empty source (#2150) 
* Resolve crash in InMemory SP resolver for empty source

* Add changelog
 2020-10-28 14:30:32 -04:00
jamesagnew 6ccb7c8312 Bump HTTPClient version 2020-10-28 10:28:04 -04:00
Nick Goupinets 170cf245cc #2184 Initial implementation 2020-10-27 15:50:29 -04:00
jamesagnew 53c23b8d9b Add method to stringutil 2020-10-27 11:29:16 -04:00
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
jamesagnew 137e215003 Docs fixes 2020-10-26 07:36:46 -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
jamesagnew 0fdff3e052 Credit for #2142 2020-10-23 10:33:49 -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 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