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3610 Commits

Author SHA1 Message Date
leif stawnyczy b51c722755 stashing minor refactors 2021-08-25 10:41:58 -04:00
Tadgh 37ad73a422 Bump PRE version so we don't conflict downstream 2021-08-23 15:42:18 -04:00
Tadgh 1acaf325c5 Merge branch 'master' into rel_5_5_0 2021-08-23 14:50:29 -04:00
Tadgh ee9c630228 Merge branch 'master' into issue-2901-npe-in-bundle-transaction 2021-08-23 12:05:31 -04:00
James Agnew 3ebb374059
Avoid redundant resource type selector in _id query (#2909) 
* Fixed

* Add more tests

* Test fixes
 2021-08-23 09:04:51 -04:00
Frank Tao 4c2ae513d8
Process bundle batch in parallel (#2905) 
* Process batch in parallel

* Added a test case

* Added more test cases

* Default the bundle batch to single thread.

* Tried transaction before multi-thread.

* Updated the test cases

* Update based on review comments and add changelog

* Updated the changelog

* Restore QueueCapacity
 2021-08-20 21:14:08 -04:00
Tadgh 3135e82ea7 Strip jetbrains annotations 2021-08-20 18:48:34 -04:00
Tadgh 35440d3b1b
Merge pull request #2900 from hapifhir/bump-hapi-core-for-5-5-0 
Bump hapi core for 5 5 0
 2021-08-20 18:03:29 -04:00
markiantorno f3fe7130c0 flipped case for code validation test 2021-08-20 14:36:37 -04:00
markiantorno 3cfc41f840 updating all convertor calls to not failfast 2021-08-20 14:11:20 -04:00
markiantorno 770b773761 JPA conversion lib fixes 2021-08-20 11:08:14 -04:00
Tadgh c2e3401185 Move display name 2021-08-19 17:25:51 -04:00
Tadgh 3556299332 Add another failing Test 2021-08-19 17:25:15 -04:00
Tadgh 77c99e47c1 TIL that anyString() wont match nulls in Mockito, but any() will 2021-08-19 15:15:51 -04:00
Tadgh 19d181989c Add another failing test 2021-08-19 14:52:48 -04:00
James Agnew 85517c47e2
Include includes on revincludes (#2902) 
* Include includes on revincludes
 2021-08-19 12:31:29 -04:00
Tadgh 07937e4431 Start with failing test 2021-08-19 10:35:14 -04:00
markiantorno 367b338d85 Updating HAPI to use latest core lib changes. 2021-08-18 11:06:14 -04:00
Tadgh 1f7fb52d91 set version map to check all partitions 2021-08-17 16:45:12 -04:00
Tadgh cf917d0f82 Version Bump 2021-08-15 16:54:38 -04:00
Frank Tao 4920f0a15d
Don't create designation of all components are empty (#2891) 
* Don't create designation of all components are empty

* Fixed typo
 2021-08-13 11:01:50 -04:00
Tadgh 669cf05b30 Modify SearchParameterMap toNormalizedQueryString to include value of _contained parameter 2021-08-12 14:25:12 -04:00
juan.marchionatto fb855620da Save version collections also when version is not made current. 
Add test covering bug.
 2021-08-11 12:49:54 -04:00
Tadgh 41ec1e03c0
Merge pull request #2880 from hapifhir/weird-contained-issue 
Contained Issue
 2021-08-11 08:27:54 -04:00
Tadgh e311835e8d Revert test 2021-08-10 18:44:42 -04:00
Tadgh a5c850b119 Pre-review cleaning 2021-08-10 17:37:24 -04:00
Tadgh daa3bc773e remove dummy test 2021-08-10 16:46:03 -04:00
Tadgh fe98162616 Add changelog 2021-08-10 14:59:03 -04:00
Tadgh 71ed25b77c Add commetn for juan 2021-08-10 14:58:47 -04:00
Tadgh 1cb6f490d6 Add dummy test. NOTE, remove before merge 2021-08-10 14:58:38 -04:00
Tadgh 2f42391ba8 wip 2021-08-10 14:58:30 -04:00
Tadgh e402804049 Add test json files 2021-08-10 14:58:24 -04:00
Tadgh 8f200c1819 Add a failing test 2021-08-10 14:58:17 -04:00
Tadgh 35afa8bbfa tidy 2021-08-10 14:57:51 -04:00
Tadgh 4c154951e2 Fully fleshed test, partial refactor 2021-08-10 14:56:57 -04:00
VK-SMILECDR 1e0f843d6c
2852 - Simplify java mail code (#2874) 
* testing

* [2852] adding SimpleJavaEmail

* [2852] refactor email sender code

* [2852] dependency cleanup

* [2852] add missing dependency

* [2852] add missing spring framework test dependency

* [2852] add change log

* [2852] add change log

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2852-simplify-java-mail-code.yaml

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

* [2852] minor test code cleanup

* [2852] add more tests

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
 2021-08-09 15:59:47 -04:00
Tadgh 4fadc62066 Bump Hapi Version 2021-08-06 13:44:04 -04:00
Tadgh 0a303a0e11 Add MDM expansion by golden pid 2021-08-06 13:22:08 -04:00
Frank Tao 3c598e2ff8
Fix loinc designation issue with FormalName (#2865) 
* Fix loinc designation issue with FormalName

* Changed Loinc designation name to 'FullySpecifiedName'
 2021-08-06 10:59:01 -04:00
Michael Buckley e8e49f3ffa Pick d85a4e5ec2 for release branch 2021-08-04 16:34:48 -04:00
Michael Buckley d85a4e5ec2 Hack to fix a weird IOOB error we can't reproduce. 2021-08-04 16:08:38 -04:00
juan.marchionatto cb68c59fb5 Remove validation in code which will never reached for the conditions. 2021-08-03 15:39:02 -04:00
juan.marchionatto 45549d2bb9 Fix broken ITs. 
Add error message for non-snapshot upload with current version = false combination.
 2021-08-03 14:11:14 -04:00
juan.marchionatto 1ff1954cba Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control 2021-07-30 11:20:23 -04:00
juan.marchionatto 4e8b1719f3 Add test for fixed use case 2021-07-30 10:48:10 -04:00
Ken Stevens 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
juan.marchionatto 264dfee099 Merge branch 'master' into issue-2786-upload-terminology-command-add-explicit-current-version-control 2021-07-29 16:21:56 -04:00
juan.marchionatto 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
James Agnew 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
Ken Stevens 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
juan.marchionatto ad6f7a204c Fix changelog syntax. Merge current master. 2021-07-22 10:49:16 -04:00
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
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
Kevin Hartmann e8ac24b4df Test now passes. 2021-04-30 15:17:22 -04:00
Kevin Hartmann b3afe41de8 Added test to make sure we have loaded the expected package id. 2021-04-30 15:14:19 -04:00
Tadgh 983d811af6
Merge pull request #2587 from hapifhir/issue-2585-enhance-placeholder-targets-logic 
Issue 2585 enhance placeholder targets logic
 2021-04-30 12:55:27 -04:00
Tadgh ac7c684437 Refactor to support all new tests 2021-04-29 17:01:19 -04:00
Tadgh 78271a2931 Create tests for all possiblye use cases 2021-04-29 15:25:11 -04:00
Kevin Dougan SmileCDR 646faa10e1
2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.10 (#2545) 
* 2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.9.

* 2540 - Updated the Unit Test messages due to the upgraded dependencies.

* 2540 - Fixed some additional Unit Test message checks.

* 2540 - Updated the POM to refer to fhir_core_version 5.3.10-SNAPSHOT so a FULL Pipeline Build can run to verify that everything is fixed now.

* 2540 - Added some DEBUG Sysout logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...

* 2540 - Added some more logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...

* 2540 - Updated a Unit Test to account for a newly returned search param.

* 2540 - Updated a Unit Test to account for a newly returned search param and removed some debug output.
 2021-04-29 15:00:37 -04:00
Tadgh 3ff2ad37ff Start with failing test 2021-04-29 14:08:50 -04:00
James Agnew 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
Tadgh 9ecb390dae Move tests to proper class. Fix issue with version referencing 2021-04-26 13:40:11 -04:00
Tadgh b200c10ced Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-26 09:48:30 -04:00
James Agnew 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
Tadgh a5f81988fc Merge branch 'improve-bundle-builder' into issue-2534-new-tx-pointcut 2021-04-21 16:53:49 -04:00
Tadgh b7166735f9 Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-21 12:13:54 -04:00
Tadgh ad8921ac4e Add docs, enum, remove prints 2021-04-21 10:39:23 -04:00
Tadgh e997d49d42 Additional Tests 2021-04-20 18:25:45 -04:00
Tadgh 3dee0c8ab6 Working in-place bundle sort 2021-04-20 17:48:55 -04:00
Nick Goupinets 4e266462ec Bumped up version due to breaking changes 2021-04-20 16:17:27 -04:00
Tadgh ff2690b74e Add tests for transaction sorting 2021-04-20 14:12:25 -04:00
Tadgh 1670ed7202 Begin topological sort implementation 2021-04-19 20:01:02 -04:00
Tadgh 2ed4b01eb8 Remove notnull 2021-04-19 10:31:16 -04:00
Tadgh 014fa05271 Fix a present annotation 2021-04-19 09:17:35 -04:00
Tadgh 89e56ecb98 Remove jetbrains annotation 2021-04-19 09:14:12 -04:00
Tadgh c54862e772 Coding around at the speed of sound occasionally causes compilation failures 2021-04-18 18:03:37 -04:00
Tadgh 77e2768a14 Address code review comments. Create new static builder for all partitions SRD 2021-04-18 17:36:55 -04:00
Tadgh 3075a9b5e6 Still minor refactoring 2021-04-16 16:53:23 -04:00
Tadgh f91a4f9576 wip tidy implementaion 2021-04-16 14:18:01 -04:00
Tadgh fad32aa636 Partition management for expired jobs 2021-04-16 11:55:12 -04:00
Tadgh 8035d51e48 Refactor, comment 2021-04-16 11:31:43 -04:00
Tadgh efe5b7b140 Fix package cache usage 2021-04-16 11:24:42 -04:00
Tadgh 7cabcbd772 Fix partition selection for system request details 2021-04-16 11:12:40 -04:00
James Agnew 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
Ken Stevens 550602b2f1
added numeric matcher (#2547) 
* added numeric matcher

* changelog

* performance optimization

* fix test
 2021-04-14 13:15:30 -04:00
IanMMarshall 4cd0409bae
Merge pull request #2546 from hapifhir/2535_ignore_logical_structuredefinition_during_package_install 
2535 ignore logical structuredefinition during package install
 2021-04-14 10:54:37 -04:00
Kevin Dougan SmileCDR b45ddcc3da
2543 - Fix issue where versionned references are not being returned properly. (#2544) 
* 2543 - Fix issue where versionned references are not being returned properly.

* 2543 - Added changelog entries for this fix plus a previous fix for 2533.
 2021-04-14 08:45:49 -04:00
ianmarshall 5a3f2e3edf Change package loader to not generate snapshot for logical StructureDefinition resources. 2021-04-13 22:22:06 -04:00
Tadgh fcbfb11506 Merge remote-tracking branch 'origin/master' into issue-2534-new-tx-pointcut 2021-04-13 15:55:01 -04:00
Tadgh 3732698e01 Update a few more pointcuts 2021-04-13 13:50:53 -04:00
Tadgh de3d6cd36a Update pointcut invocations 2021-04-13 13:49:50 -04:00
Tadgh d695e35e59 Update test 2021-04-13 09:31:45 -04:00
Tadgh f61d52d199 Should have realized that transactiondetails is an object reference, so we can't change it effectively 2021-04-13 09:26:05 -04:00
Kevin Dougan SmileCDR 129df5dc14
2533 - Fix Issue with Reference Resources Not Being Returned In Search Queries (#2539) 
* 2533 - Initial commit to show how I might fix this Bug but not ready for merge at this time as it causes some other Unit Test failures in FhirResourceDaoR4VersionedReferenceTest.

* Fix up test

* 2533 - Cleaned up Unit Test to make it ready to merge.

Co-authored-by: jamesagnew <jamesagnew@gmail.com>
 2021-04-13 05:28:39 -04:00
jamesagnew 3637dfc60f License headers 2021-04-12 09:57:08 -04:00
Tadgh 8099b6634a wip 2021-04-09 18:21:15 -04:00
Tadgh ac8e012892 wip 2021-04-09 13:07:15 -04:00
Tadgh 99e10de5fb
Merge pull request #2487 from hapifhir/mdm-expansion-interceptor 
MDM Expansion Interceptor (poc)
 2021-04-09 11:23:04 -04:00
Tadgh 8f30f7b0f2 Vague skeleton of pointcut 2021-04-09 11:08:47 -04:00
James Agnew edfe1ae8e6
Add lastupdated to capabilitystatement (#2530) 
* Add lastupdated to capabilitystatement

* Test fix

* Test fix
 2021-04-08 13:23:21 -04:00
James Agnew f70648484a
Avoid a deadlock uploading terminology in postgres (#2529) 
* Fix #2493

* Try to fix intermittent test failure
 2021-04-08 12:28:42 -04:00
James Agnew 462d9bc6c4
Fix compartment defs for R5 (#2528) 
* Fix compartment defs for R5

* Add changelog

* Test fix
 2021-04-08 05:59:05 -04:00
James Agnew 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
James Agnew fcffb04c7b
Allow unknown code systems during validation (#2523) 
* Allow unknown code systems during validation

* Add changelog

* Test fix
 2021-04-05 20:59:59 -04:00
James Agnew 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
James Agnew 0bf746f23b
Add support for revincludes to CapabilityStatement generator (#2521) 
* Add support for revincludes to CapabilotyStatement generator

* Add changelog

* Fixes

* Test fix

* Test fixes

* Test fix

* Test fix

* More fixes to CS cache

* Test fix

* Test fix

* Test fix
 2021-04-05 08:29:04 -04:00
Tadgh 961c996ea9 Remove foolish local bind 2021-04-01 17:32:14 -04:00
Tadgh 696982ce1e Fix bean name. Update docs 2021-03-31 13:45:40 -04:00
Tadgh 74be6761b1 Merge remote-tracking branch 'origin/master' into mdm-expansion-interceptor 2021-03-31 09:47:57 -04:00
Tadgh 8b69d161bd Update docs 2021-03-30 17:12:55 -04:00
Tadgh 419a5829ea This shockingly works 2021-03-30 12:39:37 -04:00
jamesagnew 4eb9508e28 One more fix to interceptor 2021-03-30 11:47:03 -04:00
jamesagnew 8759cdae00 Additional cleanup 2021-03-30 08:20:14 -04:00
jamesagnew 4feda13d7f License header update 2021-03-30 06:02:32 -04:00
James Agnew 049097e5b4
Improve CapabilityStatement Generation (#2511) 
* Start work

* Work on testing

* Version bump

* Test fix

* Compile fix

* Test Fixes

* Test fix

* Test fix

* Compile fix

* Tst fix

* Test fix

* Test fix

* Test fix
 2021-03-30 05:48:03 -04:00
Tadgh a15ded7140 Interceptor now correctly intercepts at the right point 2021-03-29 21:12:03 -04:00
Tadgh ab143e34cb Merge remote-tracking branch 'origin/master' into mdm-expansion-interceptor 2021-03-29 19:27:37 -04:00
Tadgh 838ac890d3 wip 2021-03-29 19:19:37 -04:00
Tadgh 5f42743f48 wip 2021-03-29 19:16:26 -04:00
Diederik Muylwyk e3be7cc6fb Fix build 2021-03-29 18:39:51 -04:00
Diederik Muylwyk b720c32c1d Version bump 2021-03-29 18:23:16 -04:00
Tadgh 432579c591 Fix test error 2021-03-29 15:00:20 -04:00
Tadgh 19810db65d Test refactor. address review comments 2021-03-29 14:55:41 -04:00
Tadgh c46617fefa Use dynamic projection 2021-03-29 11:38:52 -04:00
Tadgh 002d3fcf3c Migrate constant 2021-03-29 11:07:23 -04:00
Tadgh e9e20988c9 Partial moving of presearch regsitered pointcut 2021-03-29 10:49:58 -04:00
Tadgh 9f13225aa5 WIP interceptor using reference param modifier 2021-03-26 17:57:38 -04:00
Tadgh e8f49f2fba More docs 2021-03-26 16:01:29 -04:00
Tadgh a3fbd3e1a1 Hotter docs 2021-03-26 16:00:06 -04:00
Tadgh bee33f763a Refactors, tidying. Improving docs 2021-03-26 15:54:27 -04:00