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 )
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* 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 )
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* 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 )
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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 )
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* 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
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Truncate package descriptions that are longer than 200 characters.
2020-11-10 12:01:53 -05:00
James Agnew
63b7b379c2
Improve ValueSet filtering ( #2162 )
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* 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
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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
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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
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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 )
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Added delete _expunge=true
2020-10-20 17:21:50 -04:00
James Agnew
9e8e98b6fb
Rework scheduler to use Spring factory ( #2134 )
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* 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 )
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* 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 )
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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 )
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* 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
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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 )
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* 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
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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
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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
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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
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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
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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
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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
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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
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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
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Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-09-29 14:17:19 -04:00
IanMMarshall
ebb3fa0ca1
Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ConceptMapTest.java
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Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-09-29 14:16:56 -04:00
IanMMarshall
10620a8bb4
Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCodeSystemDstu3.java
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Co-authored-by: Diederik Muylwyk <diederik.muylwyk@gmail.com>
2020-09-29 14:16:13 -04:00
ianmarshall
9d8664ccd8
Additional tests and updates.
2020-09-27 21:09:06 -04:00
ianmarshall
e86d9deaac
Additional tests.
2020-09-27 17:45:15 -04:00
ianmarshall
732624bfaf
Fix broken JUnit test.
2020-09-25 22:55:01 -04:00
ianmarshall
1dc4a533d6
Fixes to terminology loader.
2020-09-25 21:43:15 -04:00
ianmarshall
47244c54dc
Merge remote-tracking branch 'origin/feature_2020_09_02_term_multi_version_support' into im_20200728_term_multi_version_support
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# Conflicts:
# hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
# hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
# hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
2020-09-25 09:10:07 -04:00
ianmarshall
6f9874468a
Merge remote-tracking branch 'origin/master' into feature_2020_09_02_term_multi_version_support
2020-09-25 08:54:17 -04:00
ianmarshall
2bceacd9a6
Update loader to ensure that ConceptMap and ValueSet Ids are unique for each version loaded.
2020-09-25 08:51:53 -04:00
ianmarshall
5fe46be41c
Validate code changes and new tests.
2020-09-24 18:51:47 -04:00
ianmarshall
e5daea17b7
Additional cleanup and migration tasks.
2020-09-23 17:17:07 -04:00
ianmarshall
dffc02a126
Missing fixes for DSTU3 and R5.
2020-09-23 16:51:18 -04:00
ianmarshall
640ee94c5c
Merge remote-tracking branch 'origin/master' into im_20200728_term_multi_version_support
2020-09-23 16:43:22 -04:00
ianmarshall
ceb5ec6384
Use canonical identifiers for code systems rather than specifying version separately.
2020-09-23 16:42:29 -04:00
Frank Tao
3d3d013d72
Changed import of IdType to r5.
2020-09-23 09:19:06 -04:00
Frank Tao
b6d86dc5f2
Added fail(); in the invalid test cases
2020-09-22 20:39:20 -04:00
Frank Tao
20661c7a2b
Removed unused import
2020-09-22 20:19:43 -04:00
Frank Tao
673274a966
Added invalid test cases for CodeSystem/$validate-code R3
2020-09-22 20:18:18 -04:00
ianmarshall
b32c4f01a8
Fixed lookupCode implementation in InMemoryTerminologyServerValidationSupport.
2020-09-22 18:46:16 -04:00
ianmarshall
4216cee8c6
Added and enhanced tests plus fixes arising from tests.
2020-09-22 14:44:32 -04:00
James Agnew
ef4f3df945
Don't install draft package contents ( #2099 )
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* Don't install draft package contents
* Add changelog
* Add changelog
2020-09-22 09:44:36 -04:00
James Agnew
072e63be5a
Avoid a crash on double date chains ( #2097 )
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* Avoid a crash on double date chains
* Add changelog
* Address coverage warning
2020-09-21 15:43:07 -04:00
ianmarshall
f9f8bf6515
Merge remote-tracking branch 'origin/master' into im_20200728_term_multi_version_support
2020-09-20 22:02:08 -04:00
ianmarshall
302bbca8fd
Changes to support multi-versioning in ValueSet $expand operation.
2020-09-20 22:01:21 -04:00
Frank Tao
8f692a4776
CodeSystem/$validate-code not supported for DSTU2, DSTU3
2020-09-19 22:54:39 -04:00
Frank Tao
a3a032584b
Made Transactional
2020-09-19 15:18:28 -04:00
Frank Tao
01d88a665d
Added CodeSystem/$validate-code for R5
2020-09-19 14:13:07 -04:00
Frank Tao
7db9f7475b
Changed fetch size to 1 for CodeSystem $validate-code
2020-09-19 12:52:18 -04:00
Frank Tao
05de0c5031
Added more test cases for R4
2020-09-19 12:36:14 -04:00
Frank Tao
64f2bae2e7
Impl CodeSystem $validate-code for R4 with basic test cases
2020-09-18 22:30:59 -04:00
Ken Stevens
3189819dd5
limit transaction size config ( #2087 )
2020-09-16 14:13:03 -04:00
jamesagnew
b64e982ec3
Credit for #2083
2020-09-16 09:07:33 -04:00