Commit Graph

9657 Commits

Author SHA1 Message Date
Long Ma 4bd186f106 added changelog, fix 6.10.0's version.yaml 2023-12-06 14:27:46 -07:00
Etienne Poirier f28011b6c2 CLI tool command migrate-database executing in dry-run mode insert entries into table FLY_HFJ_MIGRATION (#5487)
* initial test

* Solution with changelog.

* making spotless hapi

* addressing comments from code reviews

* making the test better.

* addressing code review comment and adding test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-12-06 14:16:26 -07:00
Ken Stevens 194e67c63b Oracle create index migration recovery (#5511) 2023-12-06 14:16:17 -07:00
markiantorno 5c949df315 Updating version to: 6.10.1 post release. 2023-11-17 06:41:14 +00:00
Tadgh f678747972 make release faster 2023-11-16 20:58:27 -08:00
Tadgh 3322e22524 Skip remorte nexus 2023-11-16 20:54:51 -08:00
Tadgh f75b279771 Fix pom 2023-11-16 20:54:41 -08:00
markiantorno fd77907297 Updating version to: 6.10.1 post release. 2023-11-17 01:48:59 +00:00
Tadgh 83dfe88f9e Ignored duplicate classes 2023-11-16 14:31:14 -08:00
Tadgh b6b130219a Pin Version 2023-11-16 10:38:34 -08:00
Tadgh fbea746f80 Bump jackson databind 2023-11-09 12:44:43 -08:00
Tadgh 42bf858b59 wip 2023-11-07 13:06:06 -08:00
TynerGjs 3062fad839
Fix for failing IT test in jpaserver-starter (#5435)
Co-authored-by: dotasek <dotasek.dev@gmail.com>
2023-11-07 18:30:27 +00:00
TynerGjs 0831e0f05e
Resolve We don't have guaranteed subscription delivery if a resource is too large (#5414)
* first fix

* - added the ability to handle null payload to SubscriptionDeliveringMessageSubscriber and SubscriptionDeliveringEmailSubscriber
- refactored code to reduce repeated code
- cleaned unnecessary comments and reformatted files

* Changed myResourceModifiedMessagePersistenceSvc to be autowired

* removed unused import

* added error handling when inflating the message to email and message subscriber

* reformatted code

* Fixing subscription tests with mocked IResourceModifiedMessagePersistenceSvc

* Changes by gary

* Reformatted file

* fixed failed tests

* implemented test for message and email delivery subscriber. Fixed logical error. Reformatted File.

* - implemented IT
- fixed logical error
- added changelog

* fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor

* fix for cdr tests, NOTE: this makes the assumption that we will always succeed for inflating the database in the tests that uses SynchronousSubscriptionMatcherInterceptor

* resolve code review comments

* reformatted files

* fixed tests
2023-11-06 17:12:06 -05:00
LalithE 7a25bfe847
5412 post bundle on partition incorrect response.link shown (#5413)
* Initial fix and unit test provided

* spottless check

* Made relevant changes to make solution version agnostic

* relevant logic changes made

* spotless changes made

* New logic added to fix failing test cases

* formatting

* New logic to make the function more robust

* spotless checks

* Left a trailing slash in the tests

* Made relevant test changes and changed logic

* spotless changes

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5412-during-partition-fullUrl-not-shown-in-response.yaml

changing changelog

Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>

* Formatting requirements

---------

Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
2023-11-06 11:16:35 -08:00
Tadgh 55ce4c4dce
CVEs for 6.10.0 (#5433)
* Bump jetty

* Bump okio-jvm

* 8.2.0 mysql connector

* Jena and elastic bumps

* Fix test
2023-11-05 12:53:46 -08:00
Martha Mitran 5318b24f0c
Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition (#5432)
* Fix VersionCanonicalizer conversion from R5 into DSTU2 for CapabilityStatement, Parameters and StructuredDefinition.

* Fix spotless issue
2023-11-05 12:53:26 -08:00
michaelabuckley 917f69c784
Review changes for new _pid SP. (#5430)
Change name to _pid to match our standard and add warning.
2023-11-03 15:07:05 -07:00
michaelabuckley 2ef2924b86
Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428)
Add a non-standard __pid SP.
2023-11-03 16:55:32 -04:00
jmarchionatto 33ca4e9b99
Make sure to return always a value for Boolean class return type. (#5424)
Implement change in a non-disruptive way for overriders

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-11-02 10:48:29 -04:00
dotasek 6b8f8a4ee6
Bump core to 6.1.2.2 (#5425)
* Bump core to 6.1.2.1

Patch release that uses https for primary org.hl7.fhir.core package server

* Bump core to 6.1.2.2
2023-11-02 09:10:22 -04:00
michaelabuckley f62e903a89
Use new FHIR_ID column for sorting (#5405)
* Sort `_id` using new FHIR_ID column.
* Fix old tests that put client-assigned ids first.

* Better indexing for sort
2023-11-02 09:01:27 -04:00
Tadgh 475b14864d
Revert "Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)" (#5423)
This reverts commit 4e295a59fb.

Co-authored-by: Nathan Doef <nathaniel.doef@smilecdr.com>
2023-11-01 19:46:04 +00:00
volodymyr-korzh 64cc704a40
If AutoInflateBinaries is enabled, binaries are created on the disk only for the first resource entry of the bundle (#5420)
* If AutoInflateBinaries is enabled, binaries created on disk by bundled requests are created only for the first resource entry - fix
2023-11-01 11:17:22 -06:00
jmarchionatto 4e295a59fb
Issue 5418 support Boolean class return type in BaseInterceptorService (#5421)
* Enable child classes to use Boolean class return type

* spotless

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-11-01 11:23:37 -04:00
TynerGjs 7131be758c
removed unused alias from SQL query of mdm-clear (#5416) 2023-10-31 12:08:08 -07:00
volodymyr-korzh 1c5fe61b38
Transaction fails if SearchNarrowingInterceptor is registered and Partitioning Enabled - fix cross-tenant requests failure (#5408)
* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - fix and tests added
2023-10-27 23:17:37 +00:00
Justin McKelvy 97fc5ca0dc
bump version of clinical reasoning (#5406) 2023-10-27 08:33:39 -06:00
michaelabuckley 757ef72279
Clean stale search results more aggressively. (#5396)
Use bulk DMA statements when cleaning the search cache.
The cleaner job now works as long as possible until a deadline based on the scheduling frequency.
2023-10-26 16:37:03 -04:00
michaelabuckley cf3cf2547d
Upgrade notes for the forced-id change (#5400)
Add upgrade notes for forced-id
2023-10-25 17:46:10 +00:00
Brenin Rhodes 69780a3445
Br 20231019 add cr settings for cds hooks (#5394)
* Add settings used in CR CDS Services.  Remove config dependency on Spring Boot.

* Add changelog

* Use String.format rather than concat strings

* spotless apply

* Add javadoc
2023-10-25 09:09:48 -07:00
TynerGjs a40adab882
Reverse Chaining searches returns an error when invoked with parameter _lastUpdated. (#5177)
* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* _source search parameter needs to support modifiers (#5095)

_source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers

* Fix HFQL docs (#5151)

* Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156)

* Initial failing test.

* Solution with changelog.

* fixing format.

* Addressing comment from code review.

* fixing failing test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* documentation update (#5154)

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

* Fix hsql jdbc driver deps (#5168)

Avoid non-included classes in jdbc driver dependencies.

* $delete-expunge over 10k resources will now delete all resources (#5144)

* First commit with very rough fix and unit test.

* Refinements to ResourceIdListStep and Batch2DaoSvcImpl.  Make LoadIdsStepTest pass.   Enhance Batch2DaoSvcImplTest.

* Spotless

* Fix checkstyle errors.

* Fix test failures.

* Minor refactoring.  New unit test.  Finalize changelist.

* Spotless fix.

* Delete now useless code from unit test.

* Delete more useless code.

* Test pre-commit hook

* More spotless fixes.

* Address most code review feedback.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Remove use of pageSize parameter and see if this breaks the pipeline.

* Fix the noUrl case by passing an unlimited Pegeable instead.  Effectively stop using page size for most databases.

* Deprecate the old method and have it call the new one by default.

* updating documentation (#5170)

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

* _source search parameter modifiers for Subscription matching (#5159)

* _source search parameter modifiers for Subscription matching - test, implementation and changelog

* first fix

* tests and preliminary fixes

* wip, commit before switching to release branch.

* adding capability to handle _lastUpdated in reverse search (_has)

* adding changelog

* applying spotless.

* addressing code review comments.

---------

Co-authored-by: tadgh <garygrantgraham@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>
Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
2023-10-25 08:47:07 -04:00
volodymyr-korzh 52bdc2693c
Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning (#5389)
* Transaction with conditional update fails if SearchNarrowingInterceptor is registered and Enabled Partitioning - Implementation
2023-10-23 14:26:25 -06:00
Martha Mitran edb01a891a
Change package installation behaviour such that it updates the existing SearchParameter base with remaining resources (#5376)
* Change package installation behavior such that it updates the existing SearchParameter base with remaining resources

* Change package installation behavior such that it updates the existing SearchParameter base with remaining resources

* Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable.

* Use resourceType in the package installer output to fix tests. Minor change with resourceType condition. Update changelog description to make it more readable.
2023-10-20 20:54:48 -07:00
michaelabuckley 0ba2e046c2
Allow cached search with consent active when safe (#5387)
Allow the search cache when using consent if safe
2023-10-21 00:10:38 +00:00
michaelabuckley 953f73529a
Review changes for #4803 (#5381)
review changes
2023-10-20 17:26:24 +00:00
michaelabuckley ee369269f8
Move forced-id to HFJ_RESOURCE - step 2 (#4803)
* First cut at forced-id step 2

Start using new fhir_id column in hfj_resource instead.

* demote fixme for build

* Start changelog

* Merge cleanups

* forced-id migration

various fixme cleanups

* checkstyle

* fix bad conversions to computeIfAbsent

* Ugh.  Lame checkstyle.

* Revert optimistic null assert

* missed import.

* Fixup broken tests

* Fix invalid test

* Add missing index annotation
2023-10-20 12:14:31 -04:00
TipzCM af1d46fb04
adding additional logging to resource modified submitter svc (#5370)
* adding additional logging to resource modified submitter svc

* s[otlestt

* review fixes

* spotless

* fixing test

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-10-20 09:56:32 -04:00
James Agnew 20c8109a32
Speed up subscription triggering (#5377)
* Improve subscription trigger speed

* Speed up subscription triggering

* Add changelogf

* Spotless

* Move changelog
2023-10-20 10:51:35 +00:00
michaelabuckley e2ca967fd9
Force _summary=false when fetching CodeSystems and ValueSets with remote terminology (#5372)
Force _summary=false when fetching CodeSystems and ValueSets with remote terminology
2023-10-19 09:18:01 -04:00
Tadgh 25ce7d0b8f fix broken version 2023-10-16 12:16:58 -07:00
Tadgh 90bfe05b9d
Fix version enum (#5352)
* Fix version enum

* Add license
2023-10-16 08:19:16 -04:00
Justin McKelvy c832cf0507
Hapi cr codecache (#5360)
* WIP code cache config

* WIP test

* Passing unit test

* cachelistener IT

* hardening cache listener tests

* cache listener fixes & tests, measureService migration, add reporter parameter to r4

* fix ELMCache listener to match on version, update test, remove reporter parameter

* edit inline notes

* changelog, version bump, spotless apply

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-10-11 11:47:52 -07:00
James Agnew 88e9780004
Add additional resource docs to generated OpenAPI documentation (#5359)
* Add additional resource docs to generated OpenAPI documentation

* Test fix
2023-10-11 00:36:33 +00:00
c-schuler 424f26b897
Removed helperSvc bean override from JpaConfig (#5350)
* Removed helperSvc bean override from JpaConfig

* Added change log entry
2023-10-10 11:13:21 -04:00
TynerGjs 02f25a9063
typo fix (#5358) 2023-10-06 20:30:44 +00:00
StevenXLi 12519bde9f
5353 iterate on revincludes and includes does not return correct resources when used with non iterate revincludes (#5354)
* added failing test

* implemented solution

* added doc generation

* added changelog

* fixed the order of includes and revincludes, based on what was implemented before

* fixed formatting

* fixed wording

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-10-06 11:54:26 -04:00
Etienne Poirier e5f700fc21
5344 $expunge operation fails when the operation is executed on a specific partition (#5347)
* initial failing test.

* solution with changelog

* fixing pom dependency version

* fixing pom circular dependency issue and making the new wrapper class generic.

* Fixing tests assertion.

* Moving test to solve dependency issues.

* addressing code review comments.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-10-05 12:40:16 -04:00
Brenin Rhodes 743e2c178b
Add Registries for CDS CR Services (#5342)
* Add registries for CdsCrServices and CrDiscoveryServices to allow registration of custom services

* Add changelog

* Fix broken find method

* Fix crDiscoveryServiceFactory
2023-10-03 07:15:32 -04:00
StevenXLi 4e9bd153cf
5339 bulk export errors when patient compartment searchparameter of the resource is not present (#5340)
* added failing test

* implemented solution, and fixed test

* added changelog

* fixed formatting

* fixed test not passing

* fixed test and formatting

* added warning for failing the active search param check

* code review change

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-10-02 11:32:58 -04:00