d320b78ae1
Improve synthea ingest performance ( #3033 )
...
* Improve synthea ingest performance
* Tweaks
* Fix param splitting
* Update to test
* Add changelog
* Test fix
* Add some runtime checks
* Remove useless test
* Test fix
2021-10-04 05:46:06 -04:00
eca725afa4
Improve versioned URL support for ValueSet expansion ( #2994 )
...
* Add test
* Test fixes
* Work on expansion errors
* Fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Test fixes
* Work on fix
* Test fixes
* Test fixes
* Test fix
* Cleanup
* Test fixes
* Remove accidental commit
* Test fixes
* Version bump
* Add changelog
* Fixes
* Test fix
* Fix conflicts
2021-10-03 19:47:23 -04:00
cd1a4154c1
Merge branch 'remove-parallel-non-gets' of github.com:hapifhir/hapi-fhir into remove-parallel-non-gets
2021-09-28 09:55:13 -04:00
072c030c2d
Remove modifications, defaults work
2021-09-28 09:55:06 -04:00
ad05a5ec09
Merge branch 'master' into remove-parallel-non-gets
2021-09-28 09:43:01 -04:00
dde0529b07
Remove extra semicolon
2021-09-27 15:36:17 -04:00
0c123384c7
add test for failing batch bug, remove bounding on queue
2021-09-27 15:34:19 -04:00
d121f6eff1
Merge branch 'master' into 3020_Add_documentation_for_$partition-management-create-partition
2021-09-27 15:10:19 -04:00
2dec5f0821
Add explicit brackets
2021-09-27 13:47:23 -04:00
b4343a9823
Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning
2021-09-27 09:48:15 -04:00
00ceb3f35d
Add tests
2021-09-27 09:47:05 -04:00
5ee5b08b50
Merge branch 'master' into mb-fix-NoFt-tests
2021-09-24 16:38:05 -04:00
b1dd40fdba
Try commenting out clearAllStaticFieldsForUnitTest to see what happens ( #3034 )
...
* Try commenting out clearAllStaticFieldsForUnitTest to see what happens
* Rename clearAllStaticFieldsForUnitTest to randomizeLocaleAndTimezone and only do that
2021-09-24 16:01:28 -04:00
d03f9cb35b
Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning
2021-09-24 15:40:22 -04:00
eb9f29b3f3
Simplify code
2021-09-24 15:05:06 -04:00
d067586607
[3020] add documentation/changelog
2021-09-24 14:49:07 -04:00
11c5f7ee87
Some configs don't publish and FullText service at all. Make it optional.
2021-09-24 14:32:34 -04:00
79e2800f3e
Fix cut-n-paste glitch in dstu2 NoFt
2021-09-24 13:48:01 -04:00
8c145d1212
Merge branch 'master' into 3020_Add_documentation_for_$partition-management-create-partition
2021-09-24 13:01:38 -04:00
6431ae4401
[3020] fix implementation/add tests
2021-09-24 13:00:05 -04:00
db55837c3c
Make our NoFt tests actually run without Ft.
...
Hibernate search was always configured with a lucene heap engine in all JPA tests.
Added a new config param - hapi_test.enable_lucene - to disable with config params on the NoFt tests.
2021-09-24 12:05:16 -04:00
4ab60e2f9b
Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology
2021-09-24 08:59:15 -04:00
0db40c6118
support non-jpa batch
2021-09-24 00:39:15 -04:00
53c7476dae
hapi storage ( #3024 )
...
* first pass moving core storage classes to storage-api
* move term service apis
* nearly done
* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor
* rename hapi-fhir-storage-api to hapi-fhir-storage and move transaction processor
* create new SearchConstants class to store platform independent search constants
* move a couple of subscription services
* move transaction processor adapter to storage
* version bump
* move searchparam
* fix test
* fix compile includes
* fix text
* fix docs
2021-09-23 22:04:46 -04:00
8bd14ae024
[3020] add $partition-management-lists-partitions
2021-09-23 16:08:56 -04:00
91d9101785
Merge branch 'master' into issue-3017-remove-loincxml-file-from-application-used-as-fallback-when-loading-loinc-terminology
2021-09-23 13:45:28 -04:00
d1e9c23c13
Remove loinc.xml file from application. Now it required as input for loinc upload.
2021-09-23 13:43:27 -04:00
9c8fd26692
Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning
2021-09-23 11:56:44 -04:00
751c5d0d05
Implement revision suggestions. Add changelog.
2021-09-23 11:55:50 -04:00
ad9e0f1c9a
Merge branch 'master' into 3014-prevent-delete-expunge-cascade
2021-09-23 09:33:04 -04:00
2436f748aa
fix test
2021-09-22 14:38:53 -04:00
f9796b9e2a
fix test
2021-09-22 12:52:28 -04:00
26ac649946
changelog
2021-09-22 11:11:10 -04:00
9a18422173
fix review
2021-09-22 11:09:50 -04:00
48f73fa1d1
typo
2021-09-22 10:25:57 -04:00
c913707599
added header check
2021-09-22 10:15:22 -04:00
81a4f0c78f
Rename method for clarity. Increase test coverage.
2021-09-22 09:40:25 -04:00
fdf639d353
Merge branch 'master' into issue-2851-upload-terminology-valueset-parallel-versioning
2021-09-22 09:25:48 -04:00
ad5297b714
fix for issue #3014
2021-09-21 13:09:08 -07:00
060791aeb4
hapi-fhir-storage-api ( #3006 )
...
* rename hapi-fhir-jpaserver-migrate to hapi-fhir-sql-migrate and move hapi-tasks into jpaserver-persistence
* rename hapi-fhir-jpaserver-api to hapi-fhir-storage-api
* move bulk import apis
* create hapi-fhir-jpa
* create hapi-fhir-jpa
* move CircularQueueCaptureQueriesListener to japi-fhir-jpa
* move mdm logs to storage-api
* move gziputil to storage-api
* move quartz scheduling to hapi-fhir-jpa
* move default subscription channel factory to storage-api
* consolidated batch constants
* correct accidental Logs change
* remove dependency of cdr-api on cdr-persistence
* fix javadoc
* pom descriptions
* review feedback
2021-09-21 15:36:08 +00:00
371484a4ea
Fix test to add now required id to loinc CodeSystem creation
2021-09-20 17:19:31 -04:00
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
James Agnew
Tadgh
Tadgh
katie_smilecdr
juan.marchionatto
michaelabuckley
Ken Stevens
Michael Buckley
jmarchionatto
Jimmy Deng
Justin Dar
Johnson Lu
Jaison B
jdar8
Dušan Markovič
Jason Roberts
Kevin Dougan SmileCDR
leif stawnyczy
Jari Maijenburg
Nick Goupinets
Vadim Karantayer
Frank Tao
VK-SMILECDR