Commit Graph

2913 Commits

Author SHA1 Message Date
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
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
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
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