6ea58f74d1
Code review
2021-08-23 10:55:09 -04:00
8670f107b5
Updated link expansion
2021-08-17 13:17:44 -04:00
4cfe11a221
Merge branch 'master' into 2849_add_new_mdm_param
2021-08-16 13:33:57 -04:00
d5fe1eeef7
Move test out of IT
2021-08-09 16:13:47 -04:00
4fadc62066
Bump Hapi Version
2021-08-06 13:44:04 -04:00
891a6304d0
WIP
2021-08-04 11:06:14 -04:00
d467c1c79b
yMerge branch 'master' into 2849_add_new_mdm_param
2021-07-30 11:18:33 -04:00
0d34fe61c8
Adding tests
2021-07-30 11:17:56 -04:00
f5dfc3a5ed
New reindex spring batch operation ( #2845 )
...
* 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
a2aa2ca1c3
2849 Added new parameter to MDM processing
2021-07-29 15:52:27 -04:00
a5e6674e84
Version bump to 5.5.0-PRE7-SNAPSHOT
2021-07-22 08:41:16 -04:00
6d37749be8
Add non unique combo search params ( #2809 )
...
* 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
a4fb72975d
Merge pull request #2767 from hapifhir/2765-mdm-paging
...
Paging implementation for MDM query links operation
2021-07-01 23:16:47 -04:00
cfcc939caa
Fix broken tests, add license
2021-07-01 18:28:29 -04:00
86519a892a
Add tests for link builder
2021-07-01 09:43:53 -04:00
b963520c98
Fix bug in link builder
2021-07-01 09:33:19 -04:00
0893ba0039
Fix up operation param types, fix bug in link builder
2021-06-30 23:17:04 -04:00
1eb82d633d
Rip out pagingprovider requirement
2021-06-30 18:41:18 -04:00
950096d42f
remove demand for paging provider
2021-06-30 18:21:08 -04:00
9f3b262d6d
Add alternate caller methods
2021-06-30 17:54:09 -04:00
f66f9b992e
Bump pre-version as this will break downstream implementations
2021-06-30 15:37:19 -04:00
d407501071
More docs
2021-06-30 15:04:05 -04:00
883337a9f4
Tidying
2021-06-30 14:55:57 -04:00
fa750d209e
$mdm-submit operation was only submitting 100 resources and then stopping.
...
It now correctly submits all requested resources.
2021-06-30 14:48:28 -04:00
8f3cbb0a7f
Refactor docs
2021-06-30 14:48:13 -04:00
61260dd1b1
Slightly more portable solution for paging
2021-06-30 11:54:59 -04:00
a770d577cb
Initial quick implementation of paging with tests
2021-06-29 17:46:03 -04:00
5c9f2617da
Code review
2021-06-22 15:23:03 -04:00
95012623f6
Added null checks
2021-06-22 15:12:10 -04:00
32ac16e2aa
add a limit to mdm candidate searches ( #2742 )
...
* done
* verbal review feedback
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2739-max-mdm-matches.yaml
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
* review feedback
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-06-18 20:48:34 -04:00
8b205b23d0
Fix history paging ( #2741 )
...
* Fix history paging
* Add changelog
* Add license header
2021-06-18 17:47:51 -04:00
134631fdee
Convert delete expunge to use Spring Batch ( #2697 )
...
* 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
dc627dc019
Add bulk export authorization layer ( #2712 )
...
* 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
dc89a4abd7
Updated identifier matcher to only match on non-empty values
2021-05-26 15:13:43 -04:00
2068372998
Version bump
2021-05-07 17:43:54 -04:00
970a9884f0
Avoid tag definition constraint ( #2620 )
...
* Avoid tag definition constraint failure
* Version bumps
* Add changelog
* Avoid guava issue
* Test fix
* Test fix
* Bump pom
2021-05-01 17:16:15 -04:00
ac7c684437
Refactor to support all new tests
2021-04-29 17:01:19 -04:00
95d7ba6fa8
Streamline Search SQLs ( #2576 )
...
* Streamline SQL queries
* SQL query tidying
* Add changelog
* Test fixes
* Tests passing
* Ongoing work
* Test fixes
* Test fixes
* Build fix
* Cleanup
* Fixes
2021-04-28 10:29:09 -04:00
2ba1005762
OpenAPI Support ( #2560 )
...
* Start work on OpenAPI
* Fixes
* Work on OpenAPI
* Cleanup
* Cleanup
* More swagger work
* Build fix
* More work
* More work
* Add documentation
* Docs fixes
* Add changelog
* License updates
* Add API
* Cleanup
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
* Work on scripts
* Add docs
* Compile fix
* Work on fixes
* Fix tests
* Test fix
* Test fix
* Build fix
* Tests
* Build fix
* Work on pipeline
* Version bump
* Test fix
* Version bump
* Test fix attempts
* Test fix
* Test fix
* Remove accidentally committed files
* Fixes
* Tets fixes
* Test fix
* Test fix
* Test fix
* Test fixes
* Test fixes
* Test fixes
* License header updates
* test fix
* Test fixes
* Test fix
* Test fixes
* Test fix
* Checkstyle bump
Co-authored-by: patrick-vachon-smilecdr <81274188+patrick-vachon-smilecdr@users.noreply.github.com>
2021-04-25 15:40:50 -04:00
4e266462ec
Bumped up version due to breaking changes
2021-04-20 16:17:27 -04:00
1f10a15c35
Merge branch 'master' into 2515_MDM_survivorship_rules
2021-04-19 17:33:53 -04:00
b294f7d208
License headers
2021-04-14 18:00:52 -04:00
ca2088f3ad
Add framework for Bulk Import ( #2538 )
...
* Start work on bul;k import
* Work on bulk import
* Have batch working
* Working
* Working
* More work
* More work on bulk export
* Address fixmes
* License header updates
* Test fixes
* License header updates
* Test fix
* Test fix
* Version bumps
* Work on config
* Test cleanup
* One more version bump
* Version bump
* CLeanup
* A few additions
* Test fixes
* Test fix
* Test fix
* Migration fix
* Test fix
* Test fix
2021-04-14 17:41:32 -04:00
550602b2f1
added numeric matcher ( #2547 )
...
* added numeric matcher
* changelog
* performance optimization
* fix test
2021-04-14 13:15:30 -04:00
a6cbf7eebd
Add support for hierarchycal valueset expansion ( #2525 )
...
* Add support for hierarchycal valueset expansion
* Add changelog
* Add tests
* Cleanup
* Test fix
* Test fixes
2021-04-06 17:36:54 -04:00
b617c7690d
Search Parameter Infrastructure Cleanup ( #2522 )
...
* Search param service cleanup
* Work on collapsing search param
* Search param cleanup
* Work on build
* Test fix
* Test fixes
* Ongoing work
* Test fix
* Compile fix
* Test fixes
* Test fix
* Test fix
* License header updates
* Remove fixme
* Cleanup
* Cleanup
2021-04-05 17:40:10 -04:00
ab8505dfc4
Removed deprecated TerserUtil
2021-03-31 16:07:21 -04:00
4feda13d7f
License header update
2021-03-30 06:02:32 -04:00
7a9514b94a
Initial fix
2021-03-29 20:43:43 -04:00
b720c32c1d
Version bump
2021-03-29 18:23:16 -04:00
644885e91a
Fixed typo in the docs
2021-03-25 18:32:08 -04:00
caaa040def
removed identifierSystem from extensionMatcher and removed related test
2021-03-23 13:21:32 -06:00
de0399da23
Merge branch 'master' into 2478_add_extension_mdm_matcher
2021-03-22 09:34:32 -04:00
dc41d5ad61
Add terminology mapping and display population interceptors ( #2488 )
...
* Start work on code mapping interceptors
* Work on generation
* Add terminology mapping and display population interceptors
* Add changelog
* License header updates
* Test fixes
* Fix typo
* Interceptor fixes
* License header update
* Test fixes
* Mapping fixes
* Version bump
* License header updates
* Add null tests
* Add null guard
* Intermittent fix
2021-03-21 12:03:57 -04:00
6c41ded507
fixed based on pull request comments, added tests
2021-03-18 13:59:07 -06:00
989e9e7903
refactored terserUtil, added equals function in ExtensionUtil
2021-03-17 13:02:59 -06:00
660777f855
Merge branch 'master' of https://github.com/hapifhir/hapi-fhir into 2478_add_extension_mdm_matcher
2021-03-17 10:01:56 -06:00
55f49b1b65
changed rules json from resourcePath to fhirPath
2021-03-16 14:28:24 -06:00
9d9e0d5429
added extension mdm matcher
2021-03-16 12:07:42 -06:00
b5da1068a2
Removed CDR from the text literal
2021-03-10 15:32:48 -05:00
ccb5b1aaad
Addresses #2449
2021-03-08 17:40:16 -05:00
57c7d4f3eb
Support MDM expansion in group bulk export, re-add capability to use _typeFilter in Bulk Export
2021-03-03 15:02:41 -05:00
b2b0462154
Skip loading a FHIRPath object if we are older than STU3 ( #2416 )
...
* Skip loading a FHIRPath object if we are older than STU3
* Change log level
2021-02-23 18:04:53 -05:00
04b36d9e0a
Readd forgotten file
2021-02-22 18:47:34 -05:00
0bcf421fb2
add forgotten files
2021-02-22 18:32:27 -05:00
18b61f21d0
re-add only relevant code
2021-02-22 18:23:03 -05:00
3eda19c65a
Version bump ( #2400 )
...
* Version bump
* Docs changes
* Docs tweaks
* Docs tweak
* Spelling fixes
* Docs tweaks
2021-02-18 11:07:49 -05:00
919c1dbddc
Version bump to 5.3.0
2021-02-17 07:10:13 -05:00
96b4e5ab38
Merge pull request #2324 from hapifhir/single-threading-mdm
...
Ensure Single threading mdm
2021-01-29 10:01:56 -05:00
c572575412
Remove mutator
2021-01-25 09:55:31 -05:00
10382c4915
Added a few more tests
2021-01-22 16:46:18 -05:00
d783229406
updated docs
2021-01-22 13:28:24 -05:00
cdda12ef8e
Added empty matcher
2021-01-21 17:42:28 -05:00
f8c1591d21
post CDR review fixes
2021-01-20 16:44:48 -05:00
f10785ed43
Code review updates
2021-01-15 14:07:14 -05:00
6cc40b134e
Pre-review commit
2021-01-14 20:35:09 -05:00
759f06ce48
Added optional manual override to link update
2021-01-14 14:24:59 -05:00
8a5651093b
Renamed method param
2021-01-14 11:16:17 -05:00
6781718702
Survivorship 7
2021-01-12 19:08:54 -05:00
5aa85c7e17
Survivorship 6
2021-01-11 17:22:06 -05:00
9338a4e73e
Survivorship 5
2021-01-08 19:25:25 -05:00
bec056cf9d
Survivorship 4
2021-01-07 17:36:04 -05:00
19341a17b7
Survivorship 3
2021-01-06 18:02:04 -05:00
a4a173d5c7
Survivorship 2
2021-01-05 17:59:26 -05:00
f4cf4bf54a
Survivorship
2021-01-04 17:09:31 -05:00
d20b07c78e
Update license headers
2021-01-01 15:50:24 -05:00
f30999b053
License header updates
2021-01-01 15:07:23 -05:00
84d9854e24
OSGi manifest maintenance ( #2217 )
...
* manifest cleanup and delete Fragment-Host
* make hapi-fhir-server-empi into an OSGi bundle
2020-12-18 16:48:44 -05:00
e79114e2ec
Un-revert the MDM changes, now that issues have been addressed ( #2226 )
...
* Backward compatibility changes
* Revert "Revert "Remove all references to Person from EMPI.""
* Updated docs
* Removed mdm channel references
* Initial implementation
* fix coarseness bug. Fix tests. reinitialize silly bean
* Add forgotten json file
* Generic provider PoC
* Refactored provider to use BundleBuilder
* Removed version-specific MDM providers
* Addressed code review comments
* Fixed after merge
* Fixed docs
* MDM SVG for Update Use Cases
* Removed obsolete docs
Co-authored-by: Nick <nick.goupinets@smilecdr.com>
Co-authored-by: Nick Goupinets <73255752+nvg-smile@users.noreply.github.com>
2020-12-17 10:12:53 -05:00
0938d72b51
Revert "Remove all references to Person from EMPI."
2020-12-09 14:57:00 -05:00
b3a9ab20dc
Updated wording assertion in exception tracing
2020-12-08 19:05:21 -05:00
4b610801fa
Added header
2020-12-08 16:47:19 -05:00
4c7b597983
Addressed more code review comments
2020-12-08 15:32:01 -05:00
fd90eb699f
Review updates
2020-12-07 18:03:56 -05:00
51b3fb0525
Synced Provider impl bw R4 and Dstu3
2020-12-04 11:57:40 -05:00
5c40afb0c9
Updated doc headers
2020-12-03 16:11:10 -05:00
4352e0a61f
Merge remote-tracking branch 'origin/master' into gg_20201105-remove-person-references
2020-12-03 11:28:21 -05:00
ffee7a894f
Removed person refs
2020-12-02 17:41:42 -05:00
db28a94eee
Resolved alerts
2020-11-30 09:09:38 -05:00
da3df49089
Fixed build failures
2020-11-27 18:00:24 -05:00
c64ca81373
Removed obsolete tests
2020-11-27 17:11:52 -05:00
36ce84335a
Renamed sourceResource to goldenResource
2020-11-27 16:53:21 -05:00
8a7dc4e80b
EMPI to MDM
2020-11-27 15:12:21 -05:00
03643a7b3c
Fix for bean scope inconsistenices
2020-11-25 17:37:37 -05:00
953b662827
Merge branch '2161-refactor-empi' into gg_20201105-remove-person-references
2020-11-19 14:24:51 -05:00
3ad0fa8fda
Merge branch 'gg_20201105-remove-person-references' of github.com:jamesagnew/hapi-fhir into gg_20201105-remove-person-references
2020-11-19 14:23:50 -05:00
f11f8a38ac
Add licenses
2020-11-19 14:23:47 -05:00
b44ae49dd2
Removed hardcoded references to the supported MDM types
2020-11-19 13:37:45 -05:00
3209faf2fb
Rename package and module
2020-11-18 21:55:29 -05:00
Nick Goupinets
Tadgh
Ken Stevens
jamesagnew
Tadgh
Michael Buckley
Diederik Muylwyk
long
Bill Denton