cb68c59fb5
Remove validation in code which will never reached for the conditions.
2021-08-03 15:39:02 -04:00
45549d2bb9
Fix broken ITs.
...
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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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
...
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
...
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"
...
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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* Fix history paging
* Add changelog
* Add license header
2021-06-18 17:47:51 -04:00
097a2f70b3
add partition support to $evaluate-measure ( #2736 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* Add support for loinc 2.70
* Add changelog
2021-06-11 15:15:22 -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
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 )
...
* 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 )
...
* issue reproduced and fixed
* changelog
* cleanup
2021-06-03 18:45:49 -04:00
c498522c78
search by source reported incorrect size ( #2705 )
...
* issue reproduced in test and fixed
* changelog
2021-06-03 18:19:43 -04:00
473de64ddc
Fix DockerRequiredCondition check.
...
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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* 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 )
...
* Add validation suppression mode
* Add changelog
* Compile fix
2021-05-26 17:41:48 -04:00
af44b9c7a0
Ks 20210526 accurate total ( #2677 )
...
* begin with failing test
* fixed
* changelog
2021-05-26 12:20:49 -04:00
6167fb2415
2669 - Cache-Control no-store returns excessive resources ( #2671 )
...
* 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
juan.marchionatto
Ken Stevens
James Agnew
IanMMarshall
Michael Buckley
Frank Tao
Nick Goupinets
Tadgh
michaelabuckley
Josiah
Josiah
Kevin Dougan SmileCDR
rbhman
Patrick Werner
morten.ernebjerg