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3409 Commits

Author SHA1 Message Date
jamesagnew a5e6674e84 Version bump to 5.5.0-PRE7-SNAPSHOT 2021-07-22 08:41:16 -04:00
James Agnew d78fef6732
Fix NPE in IdHelperService (#2819) 2021-07-22 08:34:28 -04:00
IanMMarshall 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
James Agnew 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
James Agnew 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
juan.marchionatto e0e52c666c Add current-version parameter to upload-terminology command. 2021-07-21 16:18:35 -04:00
Michael Buckley cbb9a4355a Add details when we fail to load an element of a package definition. 2021-07-19 17:59:54 -04:00
Frank Tao 64f1643046
Added LOINC linguistic variants support (#2803) 
* Added linguistic variants for LOINC uploader

* Using static class

* Added the changelog
 2021-07-19 14:17:56 -04:00
Frank Tao 946080d709
Added ConsumerName to the loinc loader. (#2800) 
* 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
James Agnew 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
Nick Goupinets ac31000377 Updated docs 2021-07-15 09:13:03 -04:00
Nick Goupinets 520cec1e15 Fixed link resolution 2021-07-14 11:30:09 -04:00
jamesagnew 6d4c2ef8f0 Expand access to SqlQuery 2021-07-08 16:16:27 -04:00
James Agnew d762a07817
Partition patient interceptor (#2766) 
* 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
jamesagnew 6bb5cbf764 Cleanup logging 2021-07-04 15:31:10 -04:00
Tadgh f66f9b992e Bump pre-version as this will break downstream implementations 2021-06-30 15:37:19 -04:00
Tadgh a770d577cb Initial quick implementation of paging with tests 2021-06-29 17:46:03 -04:00
Ken Stevens 795fb31a3a
fixed mdm rules (#2764) 
* fixed mdm rules

* changelog

* review feedback jetbrains

* review feedback
 2021-06-28 23:24:37 -04:00
Ken Stevens 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
Ken Stevens 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
michaelabuckley 110173dafb
Merge pull request #2757 from hapifhir/2091-MemoryCacheService-confused-expiry 
Fix units on cache expiry
 2021-06-25 14:29:43 -04:00
Michael Buckley b31e464a90 Found bad growing cache scenario 2021-06-25 11:01:41 -04:00
James Agnew 7185089c9d
Add forced offset search JPA interceptor (#2756) 
* 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
Michael Buckley 1367e61c93 changelog 2021-06-24 19:13:54 -04:00
Michael Buckley e74dec1fa6 Fix units on cache expiry 
Added a test to abuse Caffeine
 2021-06-24 19:04:41 -04:00
Josiah 914cf53b62 Merge branch 'master' into 2751-jv-bump-bulk-export-job-request-length 2021-06-24 15:56:05 -04:00
Tadgh 8dcb6053a4 Swap to URI instead of token 2021-06-24 15:48:51 -04:00
Josiah a9208a88da Revert "Version bump" 
This reverts commit 1f5fa70fb6.
 2021-06-24 11:48:31 -04:00
Josiah 1f5fa70fb6 Version bump 2021-06-24 11:22:35 -04:00
Josiah eb0e2e20d7 Bump bulk export request length 2021-06-24 10:17:44 -04:00
Josiah 1ab3d0a159 Bump bulk export request length 2021-06-24 10:10:10 -04:00
jamesagnew 9bc4859761 Add test 2021-06-23 20:55:22 -04:00
jamesagnew 59653759ed Update tests 2021-06-23 15:58:14 -04:00
James Agnew 068de6a708
Test cleanup (#2749) 
* Start work on tag mode 3

* Add changelog

* Test fix

* Test cleanup
 2021-06-22 23:09:03 -04:00
James Agnew 8379392e16
Add inline tag mode (#2748) 
* Start work on tag mode 3

* Add changelog

* Test fix
 2021-06-22 23:08:09 -04:00
Josiah 912b44c3fa
Merge pull request #2734 from hapifhir/2732-bump-conceptmap-group-element-display-storage-size 
Address #2732
 2021-06-21 08:33:36 -04:00
James Agnew 0d0a0fd6a2
Add transaction write semaphore interceptor (#2744) 
* Add transaction write semaphore interceptor

* Add changelog

* Test fix

* Two missing commits on TransactionConcurrencySemaphoreInterceptor

* License header
 2021-06-21 05:38:53 -04:00
jamesagnew f0cfb5ad1b License headers 2021-06-21 05:29:02 -04:00
James Agnew 6ea1438f1d
Add transaction write semaphore interceptor (#2743) 
* Add transaction write semaphore interceptor

* Add changelog

* Test fix
 2021-06-20 12:55:49 -04:00
Ken Stevens 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
James Agnew 8b205b23d0
Fix history paging (#2741) 
* Fix history paging

* Add changelog

* Add license header
 2021-06-18 17:47:51 -04:00
Ken Stevens 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
Josiah 164e684d7c Merge branch 'master' into 2732-bump-conceptmap-group-element-display-storage-size 2021-06-17 15:14:05 -04:00
jamesagnew 5d246bcca8 License header 2021-06-17 14:40:00 -04:00
Josiah 324201b105 Make change 2021-06-17 11:28:02 -04:00
James Agnew 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
Kevin Dougan SmileCDR 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
Ken Stevens 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
jamesagnew 376a84d213 Version bump 2021-06-14 13:12:34 -04:00
James Agnew b934abb297
Impropve transaction Performance (#2717) 
* 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
jamesagnew 14070914ae Add test 2021-06-14 05:53:22 -04:00
jamesagnew 3ee05b5a62 Refactor transaction processing 2021-06-13 19:42:26 -04:00
jamesagnew 090dc9a2e2 Docs 2021-06-11 15:55:35 -04:00
James Agnew fcb32eacb6
Add support for loinc 2.70 (#2721) 
* Add support for loinc 2.70

* Add changelog
 2021-06-11 15:15:22 -04:00
James Agnew 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
jamesagnew 4f1f09abb1 Merge branch 'master' of github.com:hapifhir/hapi-fhir 2021-06-04 20:40:51 -04:00
jamesagnew 3e4522be86 Add logging 2021-06-04 20:40:40 -04:00
Kevin Dougan SmileCDR 0143e83156
Added another try-with-resources local variable based on a lgtm.com report. (#2711) 2021-06-04 15:17:27 -04:00
jamesagnew 899caa1913 Update transaction service visibility 2021-06-04 14:18:19 -04:00
James Agnew 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
Ken Stevens 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
Ken Stevens c498522c78
search by source reported incorrect size (#2705) 
* issue reproduced in test and fixed

* changelog
 2021-06-03 18:19:43 -04:00
juan.marchionatto 473de64ddc Fix DockerRequiredCondition check. 
Add @RequiresDocker annotation to two tests.
 2021-06-03 14:14:47 -04:00
jamesagnew 9401ecaf95 Merge branch 'master' of github.com:hapifhir/hapi-fhir 2021-06-02 16:47:12 -04:00
jamesagnew a0366befc4 Forward port fix 2021-06-02 16:47:02 -04:00
James Agnew 1d2b47c9fb
Update endpoint validation interceptors (#2698) 2021-06-02 05:39:01 -04:00
James Agnew 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
rbhman 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
James Agnew 05ac88bc21
Add initiate bulk export pointcut (#2692) 
* Add initiate bulk export pointcut

* Add changelog

* Test fixes
 2021-05-31 16:05:09 -04:00
James Agnew 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
James Agnew 8d377fbf76
Add bulk import instrumentation (#2685) 
* Add batch job instrumentation

* Add bulk import instrumentation

* Fix build
 2021-05-30 11:47:51 -04:00
Patrick Werner f34dd7ecd8
Merge pull request #2683 from me-d4l/feature/ignore-package-id-case 
Make package ID handling case-insensitive (#2682)
 2021-05-29 17:12:43 +02:00
James Agnew 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
morten.ernebjerg 69d3e3f3ca
Add further test for non-matching IDs 2021-05-27 15:18:45 +02:00
morten.ernebjerg cbfca6a560
Make package ID handling case-insensitive 2021-05-27 14:57:07 +02:00
James Agnew 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
James Agnew 7a83c76e65
Add validation suppression mode (#2675) 
* Add validation suppression mode

* Add changelog

* Compile fix
 2021-05-26 17:41:48 -04:00
Ken Stevens af44b9c7a0
Ks 20210526 accurate total (#2677) 
* begin with failing test

* fixed

* changelog
 2021-05-26 12:20:49 -04:00
Kevin Dougan SmileCDR 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
James Agnew 2c722e64c2
Add support for including qualified star syntax (#2672) 
* Add support for including qualified star syntax

* Add changelog

* Add docs

* Build fix
 2021-05-23 16:50:37 -04:00
jamesagnew ff2698d4d1 Merge branch 'rel_5_4' 2021-05-19 09:22:11 -04:00
James Agnew 2badae2097
Avoid contained resource in conditional create (#2665) 
* Work on unexpected contained resources

* Avoid contained on conditional create

* Add changelog
 2021-05-19 07:49:59 -04:00
jamesagnew b463b072c8 Test fixes 2021-05-18 21:32:13 -04:00
jamesagnew de56f440cb Version bump 2021-05-18 17:14:14 -04:00
jamesagnew e02bfca610 Add logging 2021-05-18 12:33:02 -04:00
Tadgh 9d039e095b Fix copy paste error. shame. 2021-05-18 11:12:59 -04:00
Tadgh 5b6f76e2dc Address review comments 2021-05-18 11:05:56 -04:00
Tadgh 143474225e Add test. Add fix 2021-05-18 09:58:58 -04:00
jamesagnew c725d1453f Add logs 2021-05-18 09:22:29 -04:00
jamesagnew 926bf393d3 Merge branch 'rel_5_4' 2021-05-17 09:10:58 -04:00
James Agnew 40ecafcd31
Don't unescape plus in match URLs (#2658) 
* 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
Tadgh 57bb11797e fix 2021-05-13 15:46:26 -04:00
Tadgh 15ea4fb555 Tidy test 2021-05-13 10:47:26 -04:00
Tadgh 3428d71023 Add toggle. Add test. Add changelog. add docs 2021-05-13 10:29:07 -04:00
Ken Stevens 316e7e0d6d
Ks 20210512 value set expansion id (#2654) 
* tested and fixed

* changelog
 2021-05-12 21:38:29 -04:00
James Agnew b64346ba1e
Add shcheduled task enablement config (#2652) 
* Add shcheduled task enablement config

* Add changelog

* Test fix

* Cleanup
 2021-05-12 14:38:30 -04:00
Tadgh d6252526c3 Move member variable 2021-05-11 10:53:10 -04:00
jamesagnew 31ef476efe Test fix 2021-05-11 10:12:27 -04:00
jamesagnew e9ff2fd3ae Test fix 2021-05-11 09:26:23 -04:00
jamesagnew 5c4fcac530 Merge branch 'rel_5_4' 2021-05-11 08:40:09 -04:00