Commit Graph

9665 Commits

Author SHA1 Message Date
longma1 b350337531 add changelog for 6.10.3 2024-01-17 13:31:31 -07:00
longma1 46b5de79bf added bunch of license stuff 2024-01-16 13:35:50 -07:00
Ken Stevens 05a416ac4f backport mdm duplicate identifier fix 2024-01-16 13:08:06 -07:00
markiantorno c1039ea1cd Updating version to: 6.10.3 post release. 2023-12-24 03:25:45 +00:00
Tadgh 882e7a33ef
Fix fixed migration (#5571)
* Fix bad migration, prep for 6.10.2

* spotless

* Version bump
2023-12-23 05:51:01 +00:00
longma1 4b885a7363 move to non snapshot version 2023-12-18 16:44:49 -07:00
Michael Buckley cc294505cc
Merge the fhir_id copy migration with the fhir_id fix to avoid traversing hfj_resource twice. (#5552)
Turn off the original migration ForceIdMigrationCopyTask.
Fix it anyway so nobody copies bad code.
Also add another migration ForceIdMigrationFixTask 
that fixes the bad data, as well as fills in the fhir_id column for new migrations.
2023-12-14 18:27:52 -05:00
Michael Buckley 71b0987fc2
Fix bad resource id migration (#5548)
* Fix bad migration of fhir id.

Fix the original migration ForceIdMigrationCopyTask.
Also add another migration ForceIdMigrationFixTask to trim
the fhir id to correct the data.

* Bump to 6.10.1-SNAPSHOT
2023-12-14 01:18:56 +00:00
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