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7089 Commits

Author SHA1 Message Date
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
Tadgh 702cc7762d
2185 doc updates for multitenancy (#2187) 
* update to docs to indicate requests to default partition

* update operation docs
 2020-11-20 11:08:19 -05:00
Tadgh 99d2bf1f0e
Merge pull request #2170 from jamesagnew/2169-docs-hapi-fhir-cli 
2169 - Fixed hapi-fhir-cli doc issues.
 2020-11-20 10:43:46 -05:00
Tadgh 8647502da1
update to docs to indicate requests to default partition (#2186) 2020-11-20 10:32:59 -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
dependabot[bot] 27cff8153b
Bump jetty_version from 9.4.30.v20200611 to 9.4.34.v20201102 (#2176) 
Bumps `jetty_version` from 9.4.30.v20200611 to 9.4.34.v20201102.

Updates `jetty-http` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-servlets` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-io` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-continuation` from 9.4.30.v20200611 to 9.4.34.v20201102

Updates `jetty-security` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-servlet` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-server` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-util` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-webapp` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `jetty-xml` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Updates `websocket-api` from 9.4.30.v20200611 to 9.4.34.v20201102

Updates `websocket-client` from 9.4.30.v20200611 to 9.4.34.v20201102

Updates `websocket-server` from 9.4.30.v20200611 to 9.4.34.v20201102

Updates `jetty-maven-plugin` from 9.4.30.v20200611 to 9.4.34.v20201102
- [Release notes](https://github.com/eclipse/jetty.project/releases)
- [Commits](https://github.com/eclipse/jetty.project/compare/jetty-9.4.30.v20200611...jetty-9.4.34.v20201102)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2020-11-19 20:20:01 -05:00
IanMMarshall 275b25c2cc
Merge pull request #2180 from jamesagnew/im_20201118_fix_package_load_when_no_desc 
Fixed NPE in package loader when package description is null
 2020-11-19 11:13:57 -05:00
ianmarshall eb0f5e1e5e Add changelog. 2020-11-19 09:37:34 -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
jamesagnew e8f2bca6ef Add 5.3.0 constant 2020-11-18 14:55:45 -05:00
jamesagnew 0c31741eec Version bump to 5.3.0-SNAPSHOT 2020-11-18 14:52:43 -05:00
jamesagnew 0336e59591 Add changelog 2020-11-18 14:26:37 -05:00
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
Kevin Dougan 50328abff1 2169 - Fixed hapi-fhir-cli doc issues. 2020-11-10 15:50:43 -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