Commit Graph

8788 Commits

Author SHA1 Message Date
James Agnew 80e4c3dd92
Bump HIbernate to 5.6.x (#3305)
* Bump HIbernate to 5.6.x

* Test fixes

* Test fix

* Dependency bump

* Rollback change

* Fix tests

* One more fix

* Avoid bump
2022-01-19 11:14:14 -05:00
Tadgh 0f0bf85f18
Bump compiler plugin (#3313)
* Bump compiler plugin

* Bump jpaserver fhir test server version

* Bump container for maven
2022-01-19 10:09:21 -05:00
Jaison B cc2ca9e491
Change token and reference search params to 'keyword' field type (#3310) 2022-01-18 22:57:51 +00:00
StevenXLi 3062430bc5
2720 rest hook subscription with payload search criteria is not getting triggered (#3308)
* Added IT for Payload Search REST HOOK subscription, fixed issue with null pointer exception

* removed todo comment, added changelog

Co-authored-by: Steven Li <steven@smilecdr.com>
2022-01-18 14:56:10 -05:00
TipzCM f0a9b33671
3283 delete will not return a 404 if resource is not found (#3284)
* 3283 delete will not return a 404 if resource is not found

* minor tweaks

* checking if tests fail due to asynchronicity

* 3283 added integration test

* cleanup

* review fixes

* changed id names

* cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-01-18 13:07:26 -05:00
Tadgh 9f7c454c6b
Issue 2377 missing entry full url in document (#3304)
* start with failing test

* wip

* add changelog

* Add implementation

* Fix DSTU3 impl

* Fix DSTU2 and R5
2022-01-18 10:40:53 -05:00
Tadgh b09b0f207b Fix broken changelog 2022-01-17 14:50:11 -08:00
TipzCM 221d7ed5b7
3274 transactions with full request url should be rejected (#3280)
* 3274 throw if url is full url

* 3274 will throw on invalid urls

* 3274 fixing the tests

* 3274 cleanup

* anonymize the data

* review fixes

* 3274 fixed for backward compatibility

* added review fixes

* fixing tests

* some more test fixes

* test fixes

* 3274 fixing the check to only look for resource at begining

* 3274 fixed test

* test fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-01-17 08:46:32 -08:00
jmarchionatto 456afa17e9
2681 member match fix method (#3281)
* Disallow operation invocation by GET request

* Add changelog

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-01-14 09:20:45 -05:00
Mark Iantorno 10dea0796a
JUnit jupiter fix for @Disabled tag order. (#3300) 2022-01-14 01:43:56 +00:00
IanMMarshall e6fd5c9807
Fix batching of mdm-clear tasks (#3295)
* Fix batching of mdm-clear tasks.

* Fix batching of mdm-clear tasks.

Co-authored-by: ianmarshall <ian@simpatico.ai>
2022-01-13 12:06:27 -05:00
dependabot[bot] 55ad98d061
Bump h2 from 2.0.204 to 2.0.206 (#3285)
* Bump h2 from 2.0.204 to 2.0.206

Bumps [h2](https://github.com/h2database/h2database) from 2.0.204 to 2.0.206.
- [Release notes](https://github.com/h2database/h2database/releases)
- [Commits](https://github.com/h2database/h2database/compare/version-2.0.204...version-2.0.206)

---
updated-dependencies:
- dependency-name: com.h2database:h2
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Add to changelog

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
2022-01-11 19:35:37 -05:00
Tadgh fb453e139d
H2 CVE (#3291)
* Bump h2 to address CVE-2021-42392

* update changes.yaml
2022-01-10 23:56:13 +00:00
jmarchionatto 737409955a
Issue 3251 terminology reindexing job is never triggered (#3271)
* Run intended job

* Add test ti validate right method is invoked by inner job

* Add changelog

* Make test fail with proper message instead of crash

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-01-06 13:29:01 -05:00
Tadgh 2054ef65a6
Rel 5 6 mergeback (#3282)
* 3138 externalized binary packages (#3139)

* Add test and impl

* Add changelog

* Fix test

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3138-support-externalized-binaries.yaml

* add beans to test configs

* Typo

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* 3131 - Added support for the lookup operation in the Remote Terminology code (#3134)

* Remove leading underscores from identifiers (#3146)

* Version bump

* License files

* version.yaml

* Add executeRawSql() method to Migrator (#3183)

* Add implementation, add test

* Add javadoc

* Add another helper function

* Bump version

* 3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155)

* 3153 updating the unknowncodesystemwarningvalidationsupport class

* 3153 updating version for smile

* 3153 update broken tests

* 3153 adding log

* 3153 cleanup

* 3153 cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Add backport info

* Avoid creating ResourcePersistentId for placeholder resources with null ID (#3158)

* Add check before mapping storage ID to resource ID in TransactionDetails.

* Add change log.

* Changed to instead prevent creation of ResourcePersistentId with null ID value.

* Changed to instead prevent ResourcePersistentId being created with null resource ID.

Co-authored-by: ianmarshall <ian@simpatico.ai>

* Fix bug loading packages in non-database mode (#3199)

* Add implementation

* Add changelog

* Add backports

* 3164 updating code review points (#3165)

* 3164 updating code review points

* 3164 updating code review points

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Add executeRawSqlStub (#3203)

Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>

* Add new version

* begin with failing test

* fix bug

* change log

* change log

* Add backport informationm

* begin with failing test

* fix issue

* change log

* code review

* Add backport info. Add folder

* fixed

* Add test

* Update test

* Add backport info

* Bump minor version

* 3170 language portion of language code is case insensitive (#3171)

* 3170 language portion of language code is case insensitive

* 3170 adding changelog

* 3170 house keeping

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Add backport info:

* Add version enum

* Remove worthless import

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
Co-authored-by: ianmarshall <ian@simpatico.ai>
Co-authored-by: Joanne Mendoza <joannemmendoza@gmail.com>
Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
2022-01-06 18:21:25 +00:00
IanMMarshall 095b959917
Fix PatientIdPartitionInterceptor where patient ID has hashCode equal to Integer.MIN_VALUE. (#3275)
* Fix PatientIdPartitionInterceptor for case where patient ID has hashCode equal to Integer.MIN_VALUE

* Fix PatientIdPartitionInterceptor for case where patient ID has hashCode equal to Integer.MIN_VALUE

Co-authored-by: ianmarshall <ian@simpatico.ai>
2022-01-06 10:00:33 -05:00
James Agnew c38fdc4c42
Fix inline resource migration (#3277) 2022-01-06 08:40:51 -05:00
jmarchionatto 2106631718
Disallow operation invocation by GET request (#3272)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2022-01-05 16:53:46 -05:00
TipzCM b148121ab3
3242 search content param removed not readded (#3244)
* 3242 initial changes and nonsense tests

* 3242 added changelog

* 3242 cleanup

* cleanup

* 3242 updated for review

* cleanup

* 3242 review fixes

* review fixes

* fix changelog file

* review fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2022-01-04 19:38:52 +00:00
jamesagnew aafc42fdd8 License header updates 2022-01-04 13:37:10 -05:00
James Agnew d610d33ac3
Dependency bumps (#3264)
* Bump a number of versions

* Fixes

* Work on version bump

* Bump

* Test fix

* More version bumps

* Build fixes

* Test fixes

* Fixes

* Fixes

* Test fix

* Bump jacoco

* Test fix

* Test fix

* Test fix

* Build fix

* Build fix

* Remove versioned H2

* Build fix

* Avoid memory issue in validation tests

* JDK bump

* Restore compile with errorprone

* Force coloured output

* Force jansi

* Try again to force jansi

* Fix for hardcoded date that just passed

* Fixes to JPA

* Improve changelog

* Work on failing test

* Test fix

* Compile fix

* One more version bump

* Test fixes
2022-01-04 13:21:14 -05:00
James Agnew d9820bfb89
Add inline resource mode (#3267)
* Start work on inline resource text storage mode

* Work on inlining

* Add changelog

* Test fixes

* Fix for hardcoded date that just passed
2022-01-03 11:43:45 -05:00
Ken Stevens 216a3d3878 Merge remote-tracking branch 'origin/master' 2021-12-29 16:38:22 -05:00
Ken Stevens fe77a23e39 converted permissions to biconsumer 2021-12-29 16:36:17 -05:00
Ken Stevens 568d39d13a
fixed an error with concurrent validation (#3266)
* fixed an error with concurrent validation

* change log
2021-12-29 21:23:44 +00:00
michaelabuckley 1c318aac1e
Bypass jpa for lastn results (#3226)
* Add flag in DaoConfig to enable storing resources in lucene index

* Update loadResourceByPid to use ElasticSearch for loading observation resource and test added to check it

* Added parsing to elastic search to parse inlined observation resources json to resource object
2021-12-17 22:38:43 +00:00
Ken Stevens a41d79ed22
call delete expunge hook for pid list within delete expunge batch job (#3252)
* call delete expunge hook for pid list within delete expunge batch job

* review feedback
2021-12-16 21:35:23 -05:00
Ken Stevens a078306a7d merge master 2021-12-16 14:58:50 -05:00
Tadgh 6a333c08bc Fix badly built migrations and indexes 2021-12-16 01:49:28 -08:00
Tadgh 700b614610 Allow system request details to go through MDM 2021-12-15 22:47:33 -08:00
Patrick Werner 6d92d08e6f
log4j-to-slf4j -> 2.16.0 (#3248)
logback -> 1.2.8 (https://jira.qos.ch/browse/LOGBACK-1591)
2021-12-15 13:05:34 -05:00
TipzCM f3c17865d7
2521 delete subscription resource (#3235)
* 2521 will set subscriptionst hat cant be initialized to error state to prevent infinite retries

* 2521 add changelog

* cleanup

* fix issue in merge

* fix bad merge

* bad merge

* 2521 review fixes and test fixes

* 2521 review fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2021-12-15 16:17:03 +00:00
Tadgh 9e20d62380
Issue 3237 delete expunge performance (#3239)
* Initial test looking for bad deletes

* Add indexes, add migration, add test'

* Fix npe

* Add provider test

* fix up comments, tighten test

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeProcessor.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Add changelog

* Remove unnecessary migration

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2021-12-15 06:53:26 +00:00
jmarchionatto ef83777115
Allow Subscription to be configured to send delete messages (#3245)
* Allow Subscription to be configured to send delete messages

* Add tests and implement MR suggestions

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-12-14 16:32:56 -05:00
Tadgh 50a3005c23
Fix flag name (#3247)
* Fix flag name

* Bump hapi version
2021-12-14 19:20:03 +00:00
longma1 a56603daa2
2480 partition aware subscription (#3218)
* some fixmes to start

* Added some FIXMEs

* added RequestPartitionId to reosurceDelivryMessage and ResourceModifiedMessage

* ResourceDeliveryMessage and ResourceModifiedMessage tests

* fixed issue with test missing partitionHelperSvc mocked bean

* Added tests and implemented SubscriptionMatchingSubscriber for partition aware subscription

* modified implementation of partitionId in CanonicalSubscription

* Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)

* Revert "Moved PartitionablePartitionId, and refactored all calls to getUserData(Constants.RESOURCE_PARTITION_ID) and setUserData(Constants.RESOURCE_PARTITION_ID)"

This reverts commit fe40fb9733.

* Got added partitionId to subscriptions, added changes to make SubscriptionMatchingSubscriberTest work

* added SubscriptionTriggering test, also added partition support to subscriptionLoader

* Changed implementation for storing partition id of subscriptions from messages, refactored tests to new implementation

* added all subscription systemRequestDetails with all partition to subscription reader

* refactored a generic system request details with default all partition request

* Added test for dao subscriptions, fixes to get the test working

* added partition support for latest version delivery

* added doc changes and changelog for multitenancy subscription

* cleanup and added partitioned subscription manually trigger test

* fixed mocked subscriptionDao

* added package-info for subscription module

* some code review changes

* removed AllPartitionSystemRequestDetail, added new text for multitenant subscription

* renamed method for code review

* version bump to 5.7.0PRE7

Co-authored-by: Michael Buckley <michael.buckley@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
2021-12-13 08:45:30 -07:00
jmarchionatto d6e543a478
Loop over new list to avoid ConcurrentModificationException in case a new hook is added while looping (#3233)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2021-12-13 08:14:28 -05:00
jamesagnew 4075c003f7 CHangelog for #3240 2021-12-12 18:09:38 -05:00
Patrick Werner 8e6785c2b4
bumped log4j version to newest version (#3240) 2021-12-12 18:07:13 -05:00
Ken Stevens d561577a9e
Ks 20211209 xml to java (#3236)
* try xml -> json

* Change from xml serialization to json serialization.  Also fix a deadlock in how the validation cache is used.

* changelog

* back out logback
change

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3236-change-validation-from-xml-to-java.yaml

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

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
2021-12-12 00:29:52 +00:00
VK-SMILECDR bd89cf022b
Improve mail service (#3230)
* move mail config to mail service constructor

* update subscription email sender

* added license text

* [2669] bump HAPI version to 5.7.0-PRE6-SNAPSHOT

* add changelog
2021-12-09 17:05:42 -05:00
Tadgh 9593b6b0b8
Rel 5 6 1 mergeback (#3228)
* 3138 externalized binary packages (#3139)

* Add test and impl

* Add changelog

* Fix test

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3138-support-externalized-binaries.yaml

* add beans to test configs

* Typo

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* 3131 - Added support for the lookup operation in the Remote Terminology code (#3134)

* Remove leading underscores from identifiers (#3146)

* Version bump

* License files

* version.yaml

* Add executeRawSql() method to Migrator (#3183)

* Add implementation, add test

* Add javadoc

* Add another helper function

* Bump version

* 3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155)

* 3153 updating the unknowncodesystemwarningvalidationsupport class

* 3153 updating version for smile

* 3153 update broken tests

* 3153 adding log

* 3153 cleanup

* 3153 cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Add backport info

* Avoid creating ResourcePersistentId for placeholder resources with null ID (#3158)

* Add check before mapping storage ID to resource ID in TransactionDetails.

* Add change log.

* Changed to instead prevent creation of ResourcePersistentId with null ID value.

* Changed to instead prevent ResourcePersistentId being created with null resource ID.

Co-authored-by: ianmarshall <ian@simpatico.ai>

* Fix bug loading packages in non-database mode (#3199)

* Add implementation

* Add changelog

* Add backports

* 3164 updating code review points (#3165)

* 3164 updating code review points

* 3164 updating code review points

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Add executeRawSqlStub (#3203)

Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>

* Add new version

* begin with failing test

* fix bug

* change log

* change log

* Add backport informationm

* begin with failing test

* fix issue

* change log

* code review

* Add backport info. Add folder

* fixed

* Add test

* Update test

* Add backport info

* Add 5.5.4

* Remove jpaconstants

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
Co-authored-by: ianmarshall <ian@simpatico.ai>
Co-authored-by: Joanne Mendoza <joannemmendoza@gmail.com>
Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
2021-12-09 16:14:48 -05:00
Ken Stevens 9753b66610
2564 contained resource validation flag (#3225)
* First cut at multithreading bundle validation

* javadoc

* change test to a red-green test

* add daoconfig

* move bundle concurrency config from validationsupport to request validator

* Moved concurrent details from ValidationOptions to FhirValidator

* Remove bundleValidationThreadCount (it's set by creating an appropriate executor)

* validate threadpool prefixes

* FIXME cleanup

* reassign FIXMEs to JB

* only create the threadpool if it will be used

* Add the MdcTaskDectorator to all threadpools

* Add bundle path to concurrently validated bundle resource validation messages.

* Add test to check bundle entry path being added to validation messages

* Threaded validation of contained resources initial checkin

* FHIR validator refactored to maintain correct bundle path and async validation task

* Refactored to use validation complete invoke callback to support raw string resource or resource object

* switch from XML to JSON

* # Conflicts:
#	hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Updated to use new HAPI-FHIR version

* merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation

* Updated to use new HAPI-FHIR version

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit 910b7f676b.

* Revert "merge 'validate_contains_change' into issue-3144-multi-threaded-bundle-validation"

This reverts commit c7d60fc3e6.

* Revert "Updated to use new HAPI-FHIR version"

This reverts commit aa8a7af455.

# Conflicts:
#	hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

* Fix Test dependencies after reverting changes.

* merge 'validate_contains_change' to 2564-contained-resource-validation-flag

* Disable threadpool prefix name validate check.

* merge master

* fix thread regexp

* pre-review cleanup

* change log

* fix test

* revert to XML as default validation serialization

* fix test

* fix test

Co-authored-by: Jaison B <jaisonb@gmail.com>
2021-12-08 15:18:54 -05:00
jamesagnew d481896d9b License header updates 2021-12-07 15:38:36 -05:00
jamesagnew 90d05a9ed4 Fix accidental commit 2021-12-07 14:55:16 -05:00
jamesagnew 8aef580aed Bump core library 2021-12-07 10:57:43 -05:00
Mark Iantorno d60d07b697
Validate contains change (#3209)
* wip

* The updated changes to the validator that were pulled in from the core dependencies are not backwards compat. Need to bump HAPI version.

* pointing to stable core version

* review feedback

* Add changelog

Co-authored-by: markiantorno <miantorno@pop-os.localdomain>
2021-12-06 11:25:00 -05:00
Ken Stevens c4ec767b9b Merge branch 'master' of github.com:hapifhir/hapi-fhir 2021-12-06 11:20:25 -05:00
Ken Stevens 3397bb6da3 remove reflection from test. 2021-12-06 11:19:50 -05:00
jamesagnew 2c2e31d7f4 Docs fix 2021-12-06 11:17:11 -05:00