7069 Commits

Author SHA1 Message Date
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
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
jamesagnew
7903b2b577 License headers 2020-10-13 11:43:09 -04:00
James Agnew
aa3da9b05f
Bump bootstrap version (#2128)
* Bump bootstrap version

* Add changelog

* Resolve fixme

* Rmove test code
2020-10-12 20:47:14 -04:00
jamesagnew
7d150858dc Credit for #2118 2020-10-12 20:45:02 -04:00
jamesagnew
90016b25a2 Credit for #2059 2020-10-12 17:45:01 -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
Joel Schneider (NMDP)
a32397d993
add CorsInterceptorTest (#2126)
* add simple CorsInterceptorTest

* add relevant exposedHeaders to custom CorsConfiguration

* use SLF4J Logger.info() instead of System.err.println(), and run the test assertions first

* Add logback-classic dependency to test scope, to enable SLF4J logging within unit tests.  (SLF4J defaults to NOP binding if no binding found on classpath, see also http://www.slf4j.org/codes.html#StaticLoggerBinder)
2020-10-12 17:38:31 -04:00