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3387 Commits

Author SHA1 Message Date
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
James Agnew 3015438a0c
Avoid query cache poisoning (#2647) 
* Avoid query cache poisoning

* Test fixes

* Add changelog
 2021-05-11 08:39:38 -04:00
James Agnew 43631d4937
Account for NOPs in Auto-Versioned References (#2643) 
* Account for NOPs in auto-versioned references

* Add docs

* Add tests
 2021-05-08 18:09:50 -04:00
jamesagnew 0cebbf4fa8 Merge branch 'master' of github.com:hapifhir/hapi-fhir 2021-05-07 17:44:27 -04:00
jamesagnew 2068372998 Version bump 2021-05-07 17:43:54 -04:00
James Agnew 5a9f499fbf
Resolve weakness in history operation (#2642) 
* Address DOS issue in History operation

* Work on history caching

* Add docs

* Add changelog

* Resolve test failures

* Test fixes

* Test fix

* Test fixes
 2021-05-07 12:04:59 -04:00
Tadgh cf864c2078 Merge remote-tracking branch 'origin/master' into issue-2634-increase-src-path-length 2021-05-06 09:10:48 -04:00
James Agnew 1424d48912
Avoid NPE in concept mapping (#2637) 2021-05-06 05:25:38 -04:00
Ken Stevens a4856bba17
fix iBundleProvider.getResources(from,to) throwing a NPE (#2632) 
* fix iBundleProvider.getResources(from,to) throwing a NPE

* change log

* review feedback

* rename test to IT that has concurrency failures
 2021-05-05 21:50:51 -04:00
Tadgh 4031968357
Calls with zero request details and non-partitionable resource automatically go to default now. This updates the test to pass in servletrequest details, simulating a user request (#2636) 2021-05-05 16:57:12 -04:00
Tadgh bf37d1db74 Fix test 2021-05-05 15:36:20 -04:00
Tadgh e15825b336 Increase length, add test 2021-05-05 15:29:02 -04:00
Tadgh 0fb0419a67 If null, return default partition during create 2021-05-04 16:22:01 -04:00
Tadgh fcc662da79 Fix not sending request details 2021-05-04 16:18:34 -04:00
KevinIsAProgrammer 75c74a22db
Merge pull request #2619 from hapifhir/2590_preserve_the_ID_value_of_the_resources_in_the_package_loader 
2590 preserve the id value of the resources in the package loader
 2021-05-03 15:39:14 -04:00
Kevin Hartmann 320e8379b3 Now convert pure numeric ids to "npm-<id>". 2021-05-03 12:55:17 -04:00
James Agnew 172ea770b8
Fix transaction references (#2627) 2021-05-03 12:25:51 -04:00
jamesagnew 8be50641e5 License header 2021-05-03 08:45:54 -04:00
Hanan Awwad 871914bd3b
Concept properties are not being saved while using the operation apply-codesystem-delta-add (#2577) 
* fix issue #2280

* revert the indentation back.

* revert-back untouched changes.

* saving concept properties using the operation apply-codesystem-delta-add

* fix test cases; add check for null properties

* fix test; expected file descriptors
 2021-05-03 08:02:20 -04:00
Jari Maijenburg 6dc12603bb
Fixed GraphQL token parameter matching bug (#2623) 2021-05-02 17:18:51 -04:00
James Agnew 0cea403800
Fix vulnerability warning on maven plugin (#2621) 
* Fix vulnerability warning on maven plugin

* Compile fixes

* Fix bootstrap dep

* Test fix

* Fix tests

* FIx deps
 2021-05-02 12:14:32 -04:00
James Agnew 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
Tuomo Ala-Vannesluoma fbca9f8060
Offset query fixes (#2579) 
* Fix new searchbuilder limit similar to legacy searchbuilder

* Fix returning includes when using offset query

* Add unit tests for offset query with include

* Only use count param if offset is given (sometimes we want to search synchronously more if DAO is used directly)

* Throw if offset is tried to use with everything operations

* Do not offer offset paging for everything operations and fix tests to assert that
 2021-04-30 19:01:27 -04:00