3d5c863276
Revert creation of test utility class finally not needed
2021-09-20 17:18:45 -04:00
9c790a7374
Revert creation of test utility class finally not needed
2021-09-20 17:18:11 -04:00
8a1d95f348
Add service to get CodeSystem from its forcedId without forcing rollback by ResourceNotFoundException in case not found
2021-09-20 17:14:42 -04:00
f1f9c672ad
3110 zh disallow unknown extensions ( #3009 )
...
* Added allowKnownExtensionsOnly() method such which calls setAnyExtensionsAllowed() to set myAnyExtensionsAllowed to false and modified changelogs to add entry for this ticket.
* Modified docs to remove description for .allowAnyExtensions() and included it within a description for .allowKnownExtensionsOnly() and also added test for .allowKnownExtensionsOnly()
* refactored allowKnownExtensionsOnly() to rejectUnknownExtensions()
2021-09-20 15:40:56 -04:00
1492b9220a
Add test comment
2021-09-20 11:15:53 -04:00
d706caf949
merge master in
2021-09-20 11:08:17 -04:00
d372371f36
Make sure a loinc CodeSystem always has a ForcedId
2021-09-20 08:51:51 -04:00
3b1bf7aa09
Merge branch 'master' into 2849_add_new_mdm_param
2021-09-17 13:27:09 -04:00
8bb9aca8df
Merge branch 'master' into 2849_add_new_mdm_param
2021-09-17 10:18:24 -06:00
115056800c
Merge branch 'master' into issue-2995-valuesetcomposeincludeversion-is-not-set-when-uploading-terminology
2021-09-17 11:32:18 -04:00
18e3ed68eb
Revert loinc.xml deletion until current work gets completed
2021-09-16 15:14:43 -04:00
fbd23498fc
Adjust test data and fix all test cases implemented so far
2021-09-16 13:41:05 -04:00
c9162cba6d
Merge in fix for ISSUE-2995
2021-09-16 13:20:00 -04:00
0dfc716a82
Adjust code validation to properly obtain CodeSystem's current version
2021-09-16 13:18:49 -04:00
a56c85f780
Eliminate Search Coordinator ThreadPool ( #2991 )
...
* Add test
* Remove search coordinator thread pool
* Add changelog
* Add docs
* Test fixes
* Test fixes
* Test fixes
* Test fix
2021-09-16 16:37:34 +00:00
3d3bab5102
merge master into branch
2021-09-16 11:02:17 -04:00
16e329e40c
Add version to ValueSet.compose.include when uploading terminology
2021-09-15 14:40:21 -04:00
724e4b37da
Fix up test to actually match
2021-09-15 11:24:01 -04:00
171f0f8724
fix rulebuilder
2021-09-15 09:04:45 -04:00
a0c8cc4279
fix test
2021-09-15 01:23:43 -04:00
8f0e8b9e51
remove useless DB calls
2021-09-14 18:44:55 -04:00
9bb1558b71
Update query count ttest
2021-09-14 17:45:09 -04:00
bb5e04e706
Fix broken test
2021-09-14 17:22:25 -04:00
b25bdc1169
Remove crazy double encoding
2021-09-14 13:48:37 -04:00
9771210553
Prefer non-lazy outcomes in map
2021-09-14 13:40:53 -04:00
49debec36a
Fix problem with null conditionals
2021-09-14 10:48:56 -04:00
bd456dfff2
Enhance test by adding operations use cases. Improve test data with more version differentiators.
2021-09-14 10:00:15 -04:00
8288d12e97
Obtain current CodeSystem from null-pointed ForcedId, as done for ValueSet
2021-09-14 09:58:32 -04:00
9d982c5e08
Merge branch 'master' into conditional-bug
2021-09-14 08:51:58 -04:00
1ca313f8ad
lower logging
2021-09-13 21:27:05 -04:00
b4e2679872
Remove jetbrains
2021-09-13 21:15:23 -04:00
a0cd83398b
Bump test java to 16
2021-09-13 20:52:14 -04:00
3ccadd636e
Merge branch 'master' into 2958-consistent-error-handling
2021-09-13 19:38:57 -04:00
876768718d
Remove log
2021-09-13 11:29:36 -07:00
3ca73f1067
Merge remote-tracking branch 'origin/2958-consistent-error-handling' into 2958-consistent-error-handling
2021-09-13 11:26:39 -07:00
46936e1704
Fixed code formatting and better way of fixing issue
2021-09-13 11:26:21 -07:00
5f86370c98
Merge branch 'master' into conditional-bug
2021-09-13 13:04:10 -04:00
59c8765e6a
Add implementation to validate conditional URLs post-transaction
2021-09-13 13:03:44 -04:00
eee7d7e455
code cleanup ( #2986 )
...
* failed attempt to get it to work
* Use simplified FhirContext.forCached methods
* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2021-09-13 03:09:18 +00:00
5554431146
Avoid dead SearchParameter links in CapabilityStatement ( #2790 )
...
* Avoid dead SearchParameter links in CapabilityStatement
* Resolve fixmes
* Build fix
* Test fix
* Test fix
* Test fix
* Work on metadata
* Fixes
* Test fixes
* Test fix
* Test fix
* Test fixes
* Test fix
* Work on test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fix
* Fix params
* Resolve fixme
* Adjust changelogs
* Version bump to 5.6.0-PRE7
* Add license header
* Bump version to 5.6.0-PRE5-SNAPSHOT
2021-09-11 18:27:18 -04:00
94f157a4ac
Start refactoring of basetransactionprocessor
2021-09-11 15:13:05 -04:00
b224463d35
add broken test
2021-09-10 22:46:35 -04:00
a02a9e0254
Merge branch 'master' into 2958-consistent-error-handling
2021-09-10 17:02:31 -07:00
2163e6e548
Fixed error that previous fix caused
2021-09-10 12:36:11 -07:00
77845d66f7
Improved code formatting
2021-09-10 10:54:33 -07:00
5b6ac3e6d6
Refactor to eliminate duplication
2021-09-10 11:22:04 -04:00
d6d862015b
Address concerns in review for issue 2975
2021-09-10 15:46:27 +02:00
d7fde3f984
Simplify implementation. Add tests.
2021-09-10 09:32:47 -04:00
cfc0c7e6b3
Add test for validation of multiple hosts in ElasticsearchHibernatePropertiesBuilder
2021-09-10 11:44:15 +02:00
032a9155f0
Merge branch 'master' of https://github.com/hapifhir/hapi-fhir into issue_2975
2021-09-10 09:11:06 +02:00
836948010f
Fixes issue ( #2958 ) where Procedure?patient caused inconsistent results and ensured that such requests gave http 400
2021-09-09 16:10:09 -07:00
ed325e9e11
Enable multiple hosts in ElasticsearchHibernatePropertiesBuilder
2021-09-10 00:14:21 +02:00
a4ba65a9fd
Don't wrap known errors
2021-09-09 12:27:34 -04:00
d5f3b5db18
Merge branch 'master' into fix-batch-pool-breaking
2021-09-09 11:28:44 -04:00
41d5e2b8e7
Add failing test, implementation
2021-09-09 10:50:54 -04:00
661ca02a6a
revert clobbered code
2021-09-09 09:28:01 -04:00
c6aa21b915
Enable empty username and password in ElasticsearchHibernatePropertiesBuilder
2021-09-09 12:55:04 +02:00
5bc571d97d
fix test
2021-09-09 01:00:12 -04:00
519244a2ea
unit test passes
2021-09-08 19:14:50 -04:00
0ccd71faf8
Merge pull request #2963 from hapifhir/custom-elastic-index
...
Custom elastic index
2021-09-08 14:29:58 -04:00
fbf6b35d2e
Merge branch 'master' into custom-elastic-index
2021-09-08 08:49:26 -04:00
5d5c45e357
Add whitespace
2021-09-08 08:49:19 -04:00
f04cf02be7
Merge branch 'master' into issue-2901-npe-in-bundle-transaction
2021-09-08 08:45:47 -04:00
c2414d2cae
Throw error if misconfigured
2021-09-07 18:35:59 -04:00
436c74616b
Merge branch 'master' into custom-elastic-index
2021-09-07 18:19:35 -04:00
34075911ce
Merge branch 'master' into jr-20210831-contained-chained-search
2021-09-07 17:28:24 -04:00
207558dba3
code review feedback
2021-09-07 17:27:22 -04:00
2dcc4f534f
Resolve Search Causing JOINs on HFJ_RESOURCE Checking RES_TYPE and RES_DELETED_AT Columns ( #2964 )
2021-09-07 19:38:08 +00:00
a3743fbcca
Add utility method
2021-09-07 14:21:50 -04:00
3ec47cb0ba
Bump version as we break the localcontainerentitymanagerfactory bean constructors args
2021-09-07 13:58:22 -04:00
6a2a5d5097
Merge branch 'master' into custom-elastic-index
2021-09-07 13:56:56 -04:00
eabe3e7c74
Merge branch 'master' into custom-elastic-index
2021-09-07 13:56:44 -04:00
ecd93c9e8a
Add changelog
2021-09-07 13:54:28 -04:00
16752f393c
Finalize implementation
2021-09-07 13:33:03 -04:00
4d7f53851c
issue-2901 cleanup of code/imports
2021-09-07 12:08:32 -04:00
69287b6bc3
issue-2901 review fixes - moving methods to idhelperservice
2021-09-07 11:52:11 -04:00
d3d7c6e97e
Merge branch 'master' into npe_fix
2021-09-07 17:36:05 +02:00
35aaa98431
Merge branch 'master' into 2849_add_new_mdm_param
2021-09-07 11:27:49 -04:00
ca2a1ff9df
Add HsTest replicating boot failure
2021-09-07 10:08:17 -04:00
190ca7a2b5
tests for longer chains
2021-09-07 09:40:49 -04:00
ad5d56172a
Return 2 unused beans
2021-09-07 09:11:48 -04:00
a1733ed3eb
cleanup
2021-09-06 13:55:19 -04:00
4281648a33
extract some methods for readability
2021-09-06 13:52:10 -04:00
ea153334fb
extract some methods for readability
2021-09-06 13:50:09 -04:00
710fb3bd89
wip
2021-09-05 00:04:13 -04:00
f0a8659653
Fix template and setup static prefix as sample
2021-09-04 23:55:03 -04:00
cdb7ffb0d3
Fixed NPE in PidToIBaseResourceProcessor
2021-09-04 01:44:07 +02:00
c63a503841
Updated link processing for MDM events
2021-09-03 16:29:26 -04:00
64270a51e0
issue-2901 review fixes
2021-09-03 15:36:42 -04:00
0dad28fb33
tidy up
2021-09-03 15:02:19 -04:00
346e29920a
Issue 2927 convert mdm clear to spring batch ( #2929 )
...
* initial roughout of mdm clear batch job
* still roughing out classes
* finished first draft of reader
* most tests passing now
* all tests pass. now FIXMEs
* FIXMEs done. Time for regression.
* fix test
* changelog and docs
* fix test
* pre-review cleanup
* version bump
* move spring autowire deps for cdr
* move spring autowire deps for cdr
* finally got beans working phew
* rearrange method calls so persistence module can perform clear operation on its own
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* review feedback
* review feedback
* Remove inheritance
* fix beans
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2021-09-03 14:58:19 -04:00
8a9e4e4328
force the resource table to be the root of the query if we might be traversing a contained reference
2021-09-03 11:26:46 -04:00
b29a61df40
update TestUtil to test Embeddable classes, not just Entity classes
2021-09-03 10:40:54 -04:00
78c71ce761
issue-2901 fix tests
2021-09-03 08:38:19 -04:00
5604cabbe8
add tests for qualifiers
2021-09-03 07:45:57 -04:00
0edf77d214
clean up a bit
2021-09-03 07:31:49 -04:00
fed755523f
Resolve - Avoid JOINs on HFJ_RESOURCE Checking RES_TYPE and RES_DELETED_AT Columns ( #2944 )
...
* Added the start of a new Unit Test.
* Renamed the Unit Test.
* Fleshed out the Unit Test with additional Resource properties.
* Tweaked the Unit Test more but it is still not working as desired so more changes will be needed to replicate the specific scenario...
* More Unit Test tweaks...
* More Unit Test tweaks.
* More tweaks...
* Reproduced the problem.
* Finally, a Failing Unit Test that exposes the problem.
* Fixed the Unit Test by changing how SearchBuilder manipulates underscore params.
* Added another test scenario.
* Added a third search test.
* Removed the third search example since it was not effective.
* Test fix
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-09-03 05:28:04 -04:00
2ed7019a6c
Add another test
2021-09-03 00:08:12 -04:00
8651990cac
Fixed class cast issue
2021-09-02 23:04:30 -04:00
56890dba93
Reformatted the code
2021-09-02 22:26:55 -04:00
be96adb694
Merge branch 'poc-chained-not-bug' into ft-search-with-not-modifier
...
# Conflicts:
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
# hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderSearchModifierR4Test.java
2021-09-02 22:07:22 -04:00
b81a61e465
Fixed :not modifier issue for the resource
2021-09-02 21:52:37 -04:00
39f18e1897
Merge branch 'master' into 2948
2021-09-02 17:24:15 -04:00
c28f5e75b3
update TestUtil to recursively scan down into subpackages
2021-09-02 15:35:40 -04:00
9fd2746113
fixed the double chain with contained resource second case
2021-09-02 14:38:30 -04:00
26ff15f939
Revert "Fix search of :not modifier"
2021-09-02 14:33:30 -04:00
6c700f9432
Add POC for failure
2021-09-02 13:33:27 -04:00
6f82e3568c
issue-2901 remove debug code
2021-09-02 13:20:38 -04:00
49124c298d
issue-2901 fixing test
2021-09-02 13:15:24 -04:00
ff7433edd7
issue-2901 cleaning up test contexts
2021-09-02 11:43:12 -04:00
cbfcc02a92
issue-2901 removing cruft and cleaning up
2021-09-02 11:07:06 -04:00
1a7b101d03
Merge branch 'master' into issue-2901-npe-in-bundle-transaction
2021-09-02 10:13:04 -04:00
0286eb5278
issue-2901 updated some documentation and added support for autocreated placeholder / autoversioned references at paths when in transactios and have not been created yet
2021-09-02 09:15:39 -04:00
b1d192637d
Merge pull request #2928 from hapifhir/ft-search-with-not-modifier
...
Fix search of :not modifier
2021-09-02 08:41:16 -04:00
6e389d6f59
Merge branch 'memorycacheservicefix' of https://github.com/theGOTOguy/hapi-fhir into memorycacheservicefix
2021-09-01 15:05:32 -04:00
0724e652bb
Refactor to prevent adding additional signatures to expungeEverythingByType.
2021-09-01 15:04:31 -04:00
3789bc0f75
Merge branch 'master' into memorycacheservicefix
2021-09-01 13:55:03 -04:00
2e2048ce52
Add more test cases, not passing
2021-09-01 13:37:45 -04:00
453ef7ec1c
Merge branch 'master' into 2935_Search_with_trailing_percent_sign
2021-09-01 11:33:26 -04:00
7001272e4b
Clear out the memory cache whenever we call the ExpungeEverythingService.
2021-09-01 01:26:47 -04:00
444bc5f330
Merge branch 'master' into memorycacheservicefix
2021-08-31 20:26:31 -04:00
51fe5ec5e7
Remove extra update from test.
2021-08-31 20:16:22 -04:00
44b0d3e9e7
Fixed $lookup with displayLanguage caching issue ( #2932 )
...
* Fixed $lookup with displayLanguage caching issue
* Added changelog and optimized the test cases
2021-08-31 22:18:40 +00:00
28e3265b6c
Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning
2021-08-31 15:52:24 -04:00
a1fbeeacaa
[2935] Escape "%" in like expression
2021-08-31 15:11:06 -04:00
c1dc342659
more logs
2021-08-31 15:06:51 -04:00
ef4adda527
failing tests
2021-08-31 14:53:05 -04:00
d75af14d29
Merge branch 'master' into double-conditionalCreateIssue
2021-08-31 14:25:51 -04:00
765b18013c
Merge branch 'master' into fix-intermittent-in-tests
2021-08-31 14:22:22 -04:00
710343a599
Use ForcedId to get current ValueSet version
2021-08-31 13:33:39 -04:00
825ac1e81c
Chnge privacy
2021-08-31 12:58:00 -04:00
b1515b5963
Lazy load executor so that tests work safely.
2021-08-31 12:57:45 -04:00
c9f5dfd6d3
Swap to SyncTaskExecutor
2021-08-31 11:33:06 -04:00
2f6d8c7b35
Revert logging
2021-08-31 10:56:31 -04:00
0f6ae50105
Fix bug in hashToSearchMap
2021-08-31 10:47:23 -04:00
a38b791141
issue-2901 added db access method for existence and setting the version to 1 if createplaceholders is true and object does not exist in db
2021-08-31 10:12:40 -04:00
7534ab58f3
Add failing test
2021-08-31 09:58:38 -04:00
f04ff3fd0a
Adds failing test for expunging and recreating a Patient with a profile in its meta field.
2021-08-31 02:04:27 -04:00
e7c6ce920d
issue-2901 checkin to test
2021-08-30 10:29:59 -04:00
3f128be34d
Update the code
2021-08-28 13:29:00 -04:00
88d535c608
Update the comment
2021-08-28 13:27:40 -04:00
9bdef1a9fa
Fix search of :not modifier
2021-08-28 13:24:09 -04:00
513bc387e9
Remove essentially duplicate bean definition
2021-08-27 13:20:29 -04:00
faf4dfd056
fix other test class
2021-08-27 12:04:56 -04:00
c2c6e0b440
Force the caller to run the bundle task if we are operating with <= 1 pool size
2021-08-27 12:01:10 -04:00
f63f12e976
Use boolean parameter as DAO misinterprets RequestDetails
2021-08-27 10:57:06 -04:00
3fbae63968
Merge master
2021-08-26 13:09:11 -04:00
0304ea2d62
Add requested test
2021-08-26 12:03:00 -04:00
426315f589
Consider last stored ValueSet not necessarily current version anymore.
2021-08-26 10:40:10 -04:00
99cd865174
test
2021-08-26 08:47:45 -04:00
646592b1b7
issue-2901 some refactoring
2021-08-25 15:56:55 -04:00
090a8b0821
Impl displayLanguage for $lookup ( #2908 )
...
* Impl displayLanguage for $lookup - first cut
* Added original lookupCode method
* Added original lookupCode method to IFhirResourceDaoCodeSystem
* Added more test cases and changelog
2021-08-25 14:47:10 -04:00
b51c722755
stashing minor refactors
2021-08-25 10:41:58 -04:00
37ad73a422
Bump PRE version so we don't conflict downstream
2021-08-23 15:42:18 -04:00
1acaf325c5
Merge branch 'master' into rel_5_5_0
2021-08-23 14:50:29 -04:00
ee9c630228
Merge branch 'master' into issue-2901-npe-in-bundle-transaction
2021-08-23 12:05:31 -04:00
3ebb374059
Avoid redundant resource type selector in _id query ( #2909 )
...
* Fixed
* Add more tests
* Test fixes
2021-08-23 09:04:51 -04:00
4c2ae513d8
Process bundle batch in parallel ( #2905 )
...
* Process batch in parallel
* Added a test case
* Added more test cases
* Default the bundle batch to single thread.
* Tried transaction before multi-thread.
* Updated the test cases
* Update based on review comments and add changelog
* Updated the changelog
* Restore QueueCapacity
2021-08-20 21:14:08 -04:00
3135e82ea7
Strip jetbrains annotations
2021-08-20 18:48:34 -04:00
35440d3b1b
Merge pull request #2900 from hapifhir/bump-hapi-core-for-5-5-0
...
Bump hapi core for 5 5 0
2021-08-20 18:03:29 -04:00
f3fe7130c0
flipped case for code validation test
2021-08-20 14:36:37 -04:00
3cfc41f840
updating all convertor calls to not failfast
2021-08-20 14:11:20 -04:00
770b773761
JPA conversion lib fixes
2021-08-20 11:08:14 -04:00
c2e3401185
Move display name
2021-08-19 17:25:51 -04:00
3556299332
Add another failing Test
2021-08-19 17:25:15 -04:00
77c99e47c1
TIL that anyString() wont match nulls in Mockito, but any() will
2021-08-19 15:15:51 -04:00
19d181989c
Add another failing test
2021-08-19 14:52:48 -04:00
85517c47e2
Include includes on revincludes ( #2902 )
...
* Include includes on revincludes
2021-08-19 12:31:29 -04:00
07937e4431
Start with failing test
2021-08-19 10:35:14 -04:00
367b338d85
Updating HAPI to use latest core lib changes.
2021-08-18 11:06:14 -04:00
1f7fb52d91
set version map to check all partitions
2021-08-17 16:45:12 -04:00
cf917d0f82
Version Bump
2021-08-15 16:54:38 -04:00
4920f0a15d
Don't create designation of all components are empty ( #2891 )
...
* Don't create designation of all components are empty
* Fixed typo
2021-08-13 11:01:50 -04:00
669cf05b30
Modify SearchParameterMap toNormalizedQueryString to include value of _contained parameter
2021-08-12 14:25:12 -04:00
fb855620da
Save version collections also when version is not made current.
...
Add test covering bug.
2021-08-11 12:49:54 -04:00
41ec1e03c0
Merge pull request #2880 from hapifhir/weird-contained-issue
...
Contained Issue
2021-08-11 08:27:54 -04:00
e311835e8d
Revert test
2021-08-10 18:44:42 -04:00
a5c850b119
Pre-review cleaning
2021-08-10 17:37:24 -04:00
daa3bc773e
remove dummy test
2021-08-10 16:46:03 -04:00
fe98162616
Add changelog
2021-08-10 14:59:03 -04:00
71ed25b77c
Add commetn for juan
2021-08-10 14:58:47 -04:00
1cb6f490d6
Add dummy test. NOTE, remove before merge
2021-08-10 14:58:38 -04:00
2f42391ba8
wip
2021-08-10 14:58:30 -04:00
e402804049
Add test json files
2021-08-10 14:58:24 -04:00
8f200c1819
Add a failing test
2021-08-10 14:58:17 -04:00
35afa8bbfa
tidy
2021-08-10 14:57:51 -04:00
4c154951e2
Fully fleshed test, partial refactor
2021-08-10 14:56:57 -04:00
1e0f843d6c
2852 - Simplify java mail code ( #2874 )
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* testing
* [2852] adding SimpleJavaEmail
* [2852] refactor email sender code
* [2852] dependency cleanup
* [2852] add missing dependency
* [2852] add missing spring framework test dependency
* [2852] add change log
* [2852] add change log
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2852-simplify-java-mail-code.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* [2852] minor test code cleanup
* [2852] add more tests
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-08-09 15:59:47 -04:00
4fadc62066
Bump Hapi Version
2021-08-06 13:44:04 -04:00
0a303a0e11
Add MDM expansion by golden pid
2021-08-06 13:22:08 -04:00
3c598e2ff8
Fix loinc designation issue with FormalName ( #2865 )
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* Fix loinc designation issue with FormalName
* Changed Loinc designation name to 'FullySpecifiedName'
2021-08-06 10:59:01 -04:00
e8e49f3ffa
Pick d85a4e5ec2 for release branch
2021-08-04 16:34:48 -04:00
d85a4e5ec2
Hack to fix a weird IOOB error we can't reproduce.
2021-08-04 16:08:38 -04:00
cb68c59fb5
Remove validation in code which will never reached for the conditions.
2021-08-03 15:39:02 -04:00
45549d2bb9
Fix broken ITs.
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Add error message for non-snapshot upload with current version = false combination.
2021-08-03 14:11:14 -04:00
1ff1954cba
Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control
2021-07-30 11:20:23 -04:00
4e8b1719f3
Add test for fixed use case
2021-07-30 10:48:10 -04:00
f5dfc3a5ed
New reindex spring batch operation ( #2845 )
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* first sweep to add new $reindex job
* first cut done. next up integration test.
* start roughing out reindex everything
* Failing test
* test passes
* add BundleUtil helper method
* rough in processEverything
* rough in processEverything
* fix mock test
* merge master
* Make BaseJpaTest.mySrd lenient.
* fix test
* reindex everything works with FIXMEs
* reindex everything more tests
* moar tests
* moar tests
* fix test
* fix test
* fix regression and fix test
* fix test cycle
* fixme
* fix test
* test provider layer
* reindex everything partition aware
* yay last fixme!
* run reindex in partitioned threads
* add fixmes for areas that require extra testing
* added transaction and log message
* manual integration testing
* changelog
* reindex all partitions
* bump hapi version
* fix test
* moar test
* pre-review cleanup
* fix javadoc
* review feedback
* review feedback
* review feedback
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2845-reindex-operation.yaml
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* review feedback
* review feedback
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantBatchOperationR4Test.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/ResourceSearch.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
* Update hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/IDeleteExpungeJobSubmitter.java
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-07-29 19:18:49 -04:00
264dfee099
Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control
2021-07-29 16:21:56 -04:00
1fcb36d84a
Fix implementation to work also for use case where version is being updated.
...
Use property instead of parameter.
2021-07-29 15:54:00 -04:00
f957661dda
Patient ID Partition Mode should support conditional create ( #2828 )
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* Fixes
* Test fix
* Add changelog
* Test fixes
* Test fixes
* Docs tweak
* Partitioning fixes
* Import fix
* Fix test data
2021-07-26 14:18:58 -04:00
6bbb403fd1
When Client Id Strategy is set to NOT_ALLOWED, permit system requests to create resources ( #2827 )
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* resolved 2826
* fix regression
2021-07-23 19:10:19 -04:00
ad6f7a204c
Fix changelog syntax. Merge current master.
2021-07-22 10:49:16 -04:00
a5e6674e84
Version bump to 5.5.0-PRE7-SNAPSHOT
2021-07-22 08:41:16 -04:00
d78fef6732
Fix NPE in IdHelperService ( #2819 )
2021-07-22 08:34:28 -04:00
8b8db82666
Enable Package Loader when partitioning is enabled with unnamed partitions ( #2808 )
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* Enable Package Loader when partitioning is enabled with unnamed partitions.
* Enable Package Loader when partitioning is enabled with unnamed partitions.
* Additional package loading problems found with partitioning.
* Additional package loading problems found with partitioning.
Co-authored-by: ianmarshall <ian@simpatico.ai>
2021-07-22 05:17:17 -04:00
6d37749be8
Add non unique combo search params ( #2809 )
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* Start work on nonunique combo search params
* Work on SQL
* Version bump
* A fix
* Test fixes
* Fixes
* Undo version bump
* Test fixes
* Resolve fixme
2021-07-21 19:14:14 -04:00
6af022062f
Fix issue with partitioning in patient ID compartment mode ( #2810 )
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* Fix issue with partitioning in patient ID compartment mode
* Add changelog
2021-07-21 17:21:23 -04:00
e0e52c666c
Add current-version parameter to upload-terminology command.
2021-07-21 16:18:35 -04:00
cbb9a4355a
Add details when we fail to load an element of a package definition.
2021-07-19 17:59:54 -04:00
64f1643046
Added LOINC linguistic variants support ( #2803 )
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* Added linguistic variants for LOINC uploader
* Using static class
* Added the changelog
2021-07-19 14:17:56 -04:00
946080d709
Added ConsumerName to the loinc loader. ( #2800 )
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* Added ConsumerName to the loinc loader.
* Added extra test for coverage
* Added the changelog for LOINC CONSUMER NAME support
2021-07-16 13:30:42 -04:00
0235296ba7
Add support for bulk export of multiple types ( #2797 )
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* Add support for bulk export of multiple types
* Add changelog
2021-07-15 14:01:10 -04:00
ac31000377
Updated docs
2021-07-15 09:13:03 -04:00
520cec1e15
Fixed link resolution
2021-07-14 11:30:09 -04:00
6d4c2ef8f0
Expand access to SqlQuery
2021-07-08 16:16:27 -04:00
d762a07817
Partition patient interceptor ( #2766 )
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* Start work on interceptor
* Implemented
* Add interceptor and docs
* Add docs
* Compile fix
* Test fixes
* Test cleanup
* Test fixes
* Test fixes
* Improve error message
* Add broken tests
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2766-add-patient-id-compartment-interceptor.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptor.java
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* Address review comments
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-07-05 09:15:20 -04:00
6bb5cbf764
Cleanup logging
2021-07-04 15:31:10 -04:00
f66f9b992e
Bump pre-version as this will break downstream implementations
2021-06-30 15:37:19 -04:00
a770d577cb
Initial quick implementation of paging with tests
2021-06-29 17:46:03 -04:00
795fb31a3a
fixed mdm rules ( #2764 )
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* fixed mdm rules
* changelog
* review feedback jetbrains
* review feedback
2021-06-28 23:24:37 -04:00
5565bf9930
fixed an issue with matching compartments to lists of ids ( #2761 )
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* fixed an issue with matching compartments to lists of ids
* change log
2021-06-26 20:24:28 -04:00
ea98e62656
collapse multiple owners for same compartment into shared compartment ( #2760 )
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* collapse multiple owners for same compartment into shared compartment
* changelog
* fix regression
* fix regression
* pre-review cleanup
* pre-review cleanup
2021-06-26 11:48:47 -04:00
110173dafb
Merge pull request #2757 from hapifhir/2091-MemoryCacheService-confused-expiry
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Fix units on cache expiry
2021-06-25 14:29:43 -04:00
b31e464a90
Found bad growing cache scenario
2021-06-25 11:01:41 -04:00
7185089c9d
Add forced offset search JPA interceptor ( #2756 )
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* Add support for offset searches
* Tests working
* Add changelog
* Test fixes
* Test fix
* More test fixes
* Add commit counter
2021-06-25 10:40:39 -04:00
1367e61c93
changelog
2021-06-24 19:13:54 -04:00
e74dec1fa6
Fix units on cache expiry
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Added a test to abuse Caffeine
2021-06-24 19:04:41 -04:00
914cf53b62
Merge branch 'master' into 2751-jv-bump-bulk-export-job-request-length
2021-06-24 15:56:05 -04:00
8dcb6053a4
Swap to URI instead of token
2021-06-24 15:48:51 -04:00
a9208a88da
Revert "Version bump"
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This reverts commit 1f5fa70fb6
2021-06-24 11:48:31 -04:00
1f5fa70fb6
Version bump
2021-06-24 11:22:35 -04:00
eb0e2e20d7
Bump bulk export request length
2021-06-24 10:17:44 -04:00
1ab3d0a159
Bump bulk export request length
2021-06-24 10:10:10 -04:00
9bc4859761
Add test
2021-06-23 20:55:22 -04:00
59653759ed
Update tests
2021-06-23 15:58:14 -04:00
068de6a708
Test cleanup ( #2749 )
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* Start work on tag mode 3
* Add changelog
* Test fix
* Test cleanup
2021-06-22 23:09:03 -04:00
8379392e16
Add inline tag mode ( #2748 )
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* Start work on tag mode 3
* Add changelog
* Test fix
2021-06-22 23:08:09 -04:00
912b44c3fa
Merge pull request #2734 from hapifhir/2732-bump-conceptmap-group-element-display-storage-size
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Address #2732
2021-06-21 08:33:36 -04:00
0d0a0fd6a2
Add transaction write semaphore interceptor ( #2744 )
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* Add transaction write semaphore interceptor
* Add changelog
* Test fix
* Two missing commits on TransactionConcurrencySemaphoreInterceptor
* License header
2021-06-21 05:38:53 -04:00
f0cfb5ad1b
License headers
2021-06-21 05:29:02 -04:00
6ea1438f1d
Add transaction write semaphore interceptor ( #2743 )
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* Add transaction write semaphore interceptor
* Add changelog
* Test fix
2021-06-20 12:55:49 -04:00
0b05c730fb
don't create a channel if subscriptions are disabled. ( #2733 )
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* don't create a channel if subscriptions are disabled.
* review feedback
* fix test
* fix intermittent
* fix intermittent
2021-06-19 00:00:16 -04:00
8b205b23d0
Fix history paging ( #2741 )
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* Fix history paging
* Add changelog
* Add license header
2021-06-18 17:47:51 -04:00
097a2f70b3
add partition support to $evaluate-measure ( #2736 )
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* Finished adding partition support to $evaluate-measure
* review feedback
2021-06-18 14:22:57 -04:00
164e684d7c
Merge branch 'master' into 2732-bump-conceptmap-group-element-display-storage-size
2021-06-17 15:14:05 -04:00
5d246bcca8
License header
2021-06-17 14:40:00 -04:00
324201b105
Make change
2021-06-17 11:28:02 -04:00
659efa786c
ValueSet Expansion Should Preserve Order ( #2724 )
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* Add test
* FIxed
* Add changelog
* Add test
* Intermittent test failure fix
* Build fix
* Build fix
* Test fix
* Test fixes
* Fix checkstyle issue
* Test fix
* Add test logging
2021-06-16 07:20:59 -04:00
6f680af3ce
SearchBuilder NPE ( #2726 )
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* Add failing test first.
* Fixed the NPE and enhanced the test.
* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2021-06-15 11:50:18 -04:00
134631fdee
Convert delete expunge to use Spring Batch ( #2697 )
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* prepare to add $delete-expunge operation that will create a spring batch job
* Add operation
* Wire up jpa provider. Begin with failing test.
* Copy/paste bulk import job as a starting point.
FIXME with proposed design
* delete expunge job parameter validation with test
* implemented reader
stubbed processor, writer
* wip for master merge
* started implementing reader
* started implementing reader
* working with stubs
* happy path batch delete expunge is done
* Provider done but test not passing. Guessing batch infrastructure not running in that test.
* IT test works now
* add reader test
* Converted delete _expunge=true to use new batch job
* DeleteExpungeDaoTest passes
* Fix test
* Change batch size to integer
* rename search count to batch size
* Make delete expunge partition aware
* updated docs
* pre-review cleanup
* change log
* add partition id to SystemRequestDetails
* Make RequestPartitionId serializable
* Change delete expunge provider to use partition id instead of tenant name
* fix tests
* test pointcut gets called
* assert on pointcut calls
* Add resource type to STORAGE_PARTITION_SELECTED pointcut
* bump hapi-fhir version
move expunge provider parameters from JpaConstants to ProviderConstants
* bump hapi-fhir version
* copyrights
* restore deleteexpungeservice for mdm
* restore deleteexpungeservice for mdm
* fix test
* public constants
* convert instant to date
* Moved expunge constants to ProviderConstants
* final review
* disabling InMemoryResourceMatcherR5Test.testNowNextMinute() to see if I can get a clean test run
* fix tests
* fix tests
* fix tests
* fix tests
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* review feedback
* improve logging
* bump version
* version bump
* recovering from failed merge
* unzip RequestListJson per Gary's suggestion. I didn't want to do it at first, but as usual Gary was right.
* fix serialization
2021-06-15 10:36:05 -04:00
376a84d213
Version bump
2021-06-14 13:12:34 -04:00
b934abb297
Impropve transaction Performance ( #2717 )
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* Work on changes
* Work on perf
* Work on testing
* Work on perf
* Work on perf
* Work on fix
* Work on perf
* Ongoing work
* Add changelog
* Additional docs
* Test fixes
* Address review comments
* Test fix
2021-06-14 13:08:19 -04:00
14070914ae
Add test
2021-06-14 05:53:22 -04:00
3ee05b5a62
Refactor transaction processing
2021-06-13 19:42:26 -04:00
090dc9a2e2
Docs
2021-06-11 15:55:35 -04:00
fcb32eacb6
Add support for loinc 2.70 ( #2721 )
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* Add support for loinc 2.70
* Add changelog
2021-06-11 15:15:22 -04:00
dc627dc019
Add bulk export authorization layer ( #2712 )
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* Add bulk export authorization layer
* Add docs
* Version bump
* Authorize any
* Add bulk export - all
* Address lgtm issue
2021-06-06 20:47:43 -04:00
4f1f09abb1
Merge branch 'master' of github.com:hapifhir/hapi-fhir
2021-06-04 20:40:51 -04:00
3e4522be86
Add logging
2021-06-04 20:40:40 -04:00
0143e83156
Added another try-with-resources local variable based on a lgtm.com report. ( #2711 )
2021-06-04 15:17:27 -04:00
899caa1913
Update transaction service visibility
2021-06-04 14:18:19 -04:00
62be623cf5
Add support for ICD-10-CM ( #2702 )
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* Add support for ICD-10-CM
* Have this working
* Fix LGTM issues
* Test fix
2021-06-03 19:55:16 -04:00
94d6b15db9
_filter searchparam should not appear in cap stmt if disabled ( #2706 )
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* issue reproduced and fixed
* changelog
* cleanup
2021-06-03 18:45:49 -04:00
c498522c78
search by source reported incorrect size ( #2705 )
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* issue reproduced in test and fixed
* changelog
2021-06-03 18:19:43 -04:00
473de64ddc
Fix DockerRequiredCondition check.
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Add @RequiresDocker annotation to two tests.
2021-06-03 14:14:47 -04:00
9401ecaf95
Merge branch 'master' of github.com:hapifhir/hapi-fhir
2021-06-02 16:47:12 -04:00
a0366befc4
Forward port fix
2021-06-02 16:47:02 -04:00
1d2b47c9fb
Update endpoint validation interceptors ( #2698 )
2021-06-02 05:39:01 -04:00
fe763dd2d6
Upgrade deps ( #2695 )
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* Upgrade deps
* Fix build error
* Branch tweak
* Build fix
* Build fix
* Undo bump
* Test fixes
2021-06-01 12:03:29 -04:00
dfde993f2d
Allow lower case error message to also trigger retry ( #2693 )
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* Allow lower case error message to also trigger retry
* similar data integrity exception on different table
Co-authored-by: Hedman, Bruno <bruno.hedman@rmp.uhn.ca>
2021-06-01 10:50:06 -04:00
05ac88bc21
Add initiate bulk export pointcut ( #2692 )
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* Add initiate bulk export pointcut
* Add changelog
* Test fixes
2021-05-31 16:05:09 -04:00
a2950324ef
Avoid SQL based transaction dupe check ( #2688 )
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* Avoid SQL based transaction dupe check
* Add changelog
* Test fixes
* Test fixes
2021-05-30 20:26:36 -04:00
8d377fbf76
Add bulk import instrumentation ( #2685 )
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* Add batch job instrumentation
* Add bulk import instrumentation
* Fix build
2021-05-30 11:47:51 -04:00
f34dd7ecd8
Merge pull request #2683 from me-d4l/feature/ignore-package-id-case
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Make package ID handling case-insensitive (#2682 )
2021-05-29 17:12:43 +02:00
24b3f0f30d
Enable mass ingestion mode ( #2681 )
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* Work on fixes
* Work on counts
* Enable mass ingestion mode
* Add changelog
* Test fix
* Test fix
* Test fixes
* Fixes
* Test fix
* Test fix
2021-05-27 18:43:51 -04:00
69d3e3f3ca
Add further test for non-matching IDs
2021-05-27 15:18:45 +02:00
cbfca6a560
Make package ID handling case-insensitive
2021-05-27 14:57:07 +02:00
c8c596aff4
Fix date search on period with no end ( #2676 )
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* Add test
* Working test
* Update test
* Account for date fixes
* Add changelog
* Add setting
* Test fixes
* Test fix
2021-05-26 21:03:53 -04:00
7a83c76e65
Add validation suppression mode ( #2675 )
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* Add validation suppression mode
* Add changelog
* Compile fix
2021-05-26 17:41:48 -04:00
af44b9c7a0
Ks 20210526 accurate total ( #2677 )
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* begin with failing test
* fixed
* changelog
2021-05-26 12:20:49 -04:00
6167fb2415
2669 - Cache-Control no-store returns excessive resources ( #2671 )
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* First attempt at a Unit Test.
* Removed sample test data.
* Added failing Unit Test - now to find out why.
* Added a _count param to more exactly match the provided customer scenario.
* Added a possible fix for this sceanrio.
* Work on this
* Have a working fix, not yet fully tested
* Test fix
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2021-05-25 08:49:25 -04:00
2c722e64c2
Add support for including qualified star syntax ( #2672 )
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* Add support for including qualified star syntax
* Add changelog
* Add docs
* Build fix
2021-05-23 16:50:37 -04:00
ff2698d4d1
Merge branch 'rel_5_4'
2021-05-19 09:22:11 -04:00
2badae2097
Avoid contained resource in conditional create ( #2665 )
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* Work on unexpected contained resources
* Avoid contained on conditional create
* Add changelog
2021-05-19 07:49:59 -04:00
b463b072c8
Test fixes
2021-05-18 21:32:13 -04:00
de56f440cb
Version bump
2021-05-18 17:14:14 -04:00
e02bfca610
Add logging
2021-05-18 12:33:02 -04:00
9d039e095b
Fix copy paste error. shame.
2021-05-18 11:12:59 -04:00
5b6f76e2dc
Address review comments
2021-05-18 11:05:56 -04:00
143474225e
Add test. Add fix
2021-05-18 09:58:58 -04:00
c725d1453f
Add logs
2021-05-18 09:22:29 -04:00
926bf393d3
Merge branch 'rel_5_4'
2021-05-17 09:10:58 -04:00
40ecafcd31
Don't unescape plus in match URLs ( #2658 )
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* Don't unescape plus in match URLs
* Perf improvements
* Add changelog
* Test fix
* Work on tests
* Fixes
* Test fix
2021-05-16 21:51:23 -04:00
57bb11797e
fix
2021-05-13 15:46:26 -04:00
15ea4fb555
Tidy test
2021-05-13 10:47:26 -04:00
3428d71023
Add toggle. Add test. Add changelog. add docs
2021-05-13 10:29:07 -04:00
316e7e0d6d
Ks 20210512 value set expansion id ( #2654 )
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* tested and fixed
* changelog
2021-05-12 21:38:29 -04:00
b64346ba1e
Add shcheduled task enablement config ( #2652 )
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* Add shcheduled task enablement config
* Add changelog
* Test fix
* Cleanup
2021-05-12 14:38:30 -04:00
d6252526c3
Move member variable
2021-05-11 10:53:10 -04:00
juan.marchionatto
Johnson Lu
Tadgh
Jaison B
jmarchionatto
James Agnew
Tadgh
Justin Dar
Ken Stevens
jdar8
Dušan Markovič
Jason Roberts
Kevin Dougan SmileCDR
leif stawnyczy
Jari Maijenburg
Nick Goupinets
Vadim Karantayer
Frank Tao
VK-SMILECDR
Ben Li-Sauerwine
katie_smilecdr
Frank Tao
markiantorno
Michael Buckley
IanMMarshall
michaelabuckley
Josiah
Josiah
rbhman
Patrick Werner
morten.ernebjerg