Commit Graph

9900 Commits

Author SHA1 Message Date
volodymyr-korzh 93a41559b5
Reindex Batch Jobs stuck in QUEUED status after SearchParameter update (#5043)
* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - test added

* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix

* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - fix test

* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - send BatchJobWorkNotification after commit

* Reindex Batch Jobs stuck in QUEUED status after SearchParameter update - changelog fix

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

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-06-29 14:29:37 -04:00
James Agnew 6e0651e261
Bulk export partitioning fixes (#5039)
* Work

* Bulk export partitioning fixes

* Changelog fixes

* cleanup

* Compile fixes

* Test fix

* Add JIRA note

* Version bump

* Drop unneeded tag
2023-06-29 08:34:32 -04:00
jmarchionatto ed04dd2498
Issue 5004 make bundleutil also accept name prev for previous links (#5042)
* Add test

* Fix

* Changelog

* Small details to reset build pipe

* Reformat

* Make definition animal-sniffer (check-android-26-compliance) compliant

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-06-28 15:46:54 -04:00
TipzCM ce04e897cf
5033 fk indexing round2 (#5040)
* updated query to find more results and be simpler

* updating query in fhir

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-28 15:37:45 -04:00
jmarchionatto 17eeb07c58
Issue 5032 gateway pagination throws NPE when targets use usehttppostforallsearches true (#5036)
* Allow PageMethodBinding to bind also for POST

* Add changelog

* Adjust test

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-06-28 12:58:51 -04:00
Tadgh 9fb718820d
Complete change, changelog, test (#5035)
* Complete change, changelog, test

* whitespace

* Update hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/StorageSettings.java

Co-authored-by: James Agnew <jamesagnew@gmail.com>

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-06-28 14:14:22 +00:00
StevenXLi 73d6997d21
fixed batch jobs on Postgres (#5022)
* fixed issue

* fixed pipeline issue

* review changes

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-06-23 09:06:38 -04:00
volodymyr-korzh 1f44ac1092
GenericClient POST paging support (#5013)
* GenericClient POST paging support - implementation and test

* GenericClient POST paging support - fixes

* GenericClient POST paging support - fixes

* GenericClient POST paging support - failed tests fix

* GenericClient POST paging support - HAPI version bump
2023-06-22 15:28:47 -04:00
LalithE a59eb1ace3
Partitioning: creating two partitions with the same ID overwrites the first (#5012)
* Added unit test and bug fix to ensure no two partitions with the same ID can be created.

* Added changelogs, and changed the equals operator.

* Made required changes to ensure updating of partition is not affected

* Changed unit test and its location to ensure functionality.

* changing for loop to findById to avoid iteration over all partitions.

* Only allows findById when list is not empty, deals with that edge case.

* Replaced null with isPresent in if statement to fix issues regarding the creation of links on different partitions

* Removed the findAll command within the function. To avoid searching twice.

* Edited the changelogs to properly describe the issue that we have at hand

* Edited the changelogs to properly describe the issue that we have at hand pt 2, wording changes.
2023-06-22 11:23:39 -04:00
TipzCM d7bdabb91b
nickname svc refatoring (#5006)
* nickname svc refatoring

* moving things around

* cleanup

* gitignore

* removing factory

* added changelog

* version bump

* fixing test

* fix test

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-22 08:26:47 -04:00
Tadgh 20a9ad0985
Make Partition ID non-mandatory during partition creation. (#5016)
* closes #5014, fix, changelog, docs

* documentationf fixes

* checkstyle fix
2023-06-21 21:19:12 -04:00
James Agnew ddf3b72f2d
Encode non-resource types (#5003)
* Encode non-resource types

* Add changelog

* Compile fix
2023-06-21 13:02:40 -04:00
jdar8 ee3c59a3bc
4968 mdm throws nonsensical error when updating resources after mdm clear (#4975)
* log specific error message + test

* changelog

* remove draft tests

* remove another comment i left behind

* update issue number in changelog

* update error location

* update error location

* update test

* change to exception

* address review comments: add test with submit and also update change log

* format test nicer

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-06-20 14:41:22 -04:00
Ken Stevens 8eec285611
revinclude order (#5009)
* start building tests

* add test

* merge master

* fix bug

* fix regression

* changelog

* documentation

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-06-20 07:54:20 -04:00
TynerGjs ac9eaf9d89
4959 loadsynchronousupto will affect searchforids when set to small value (#4966)
* Implemented fixes, created test for JPA side

* Added test and getter for test for register listener

* refactored test names to make them more descriptive

* Modified tests

* resolved comments

* created changlog

* changed test to use MAX_MANAGED_PARAM_COUNT, and created the corresponding getter
2023-06-19 09:54:39 -04:00
volodymyr-korzh 6296884583
Error when expanding task code ValueSet resource (#4974)
* Error when expanding task-code ValueSet resource - tests

* Error when expanding task-code ValueSet resource - fix valuesets.xml for R4 and R4B

* Error when expanding task-code ValueSet resource - throw exception in case of Not found CodeSystem

* Error when expanding task-code ValueSet resource - added changelog

* Error when expanding task-code ValueSet resource - fixed changelog

* Error when expanding task-code ValueSet resource - fixes

* Error when expanding task-code ValueSet resource - fixes

* Error when expanding task-code ValueSet resource - fixes and tests

* Error when expanding task-code ValueSet resource - added tests for TermCodeSystemVersionDao methods

* Error when expanding task-code ValueSet resource - added comments to valuesets.xml

* Error when expanding task-code ValueSet resource - test fixes
2023-06-19 09:31:05 -04:00
Tadgh a544a546ec
Raw sql revincludes (#5001)
* start building tests

* add test

* Basic test and fix bug

* remove tests, fix existing test

* fix up tests

* fix up tests

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-06-17 05:52:10 -04:00
Luke deGruchy e5699bcbfc
Add auto-generated headers to Java files. (#4999) 2023-06-16 13:53:20 -04:00
TipzCM 65ae1785e8
mdm-clear will now use batch-size parameter (#4985)
* using delete expunge service

* test fixing

* update version

* review points

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-15 20:32:21 -04:00
Luke deGruchy f79ac1992e
First commit: Patch bad implementation of RuleBulkExportImpl to fix … (#4986)
* First commit:  Patch bad implementation of RuleBulkExportImpl to fix this use case.

* Fix changelog.  Fix comments on unit tests.

* Fix TODO with correct issue number.
2023-06-15 15:34:00 +00:00
jmarchionatto 048c1f99bb
issue-4987-searchbundle-parts-are-labeled-by-default-as-include-instead-of-match (#4988)
* Default search mode to MATCH when creating SearchBundleEntryParts

* Add changelog

* Use enum name instead of explicit constant

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-06-15 10:03:45 -04:00
TipzCM c87ff96d5c
4976 adding indexes to foreign keys (#4980)
* adding test and initial migrations

* indexing and verifying foreign keys

* connection with resources

* fixing migration for oracle

* adding change log

* updates and cleanup

* cleanup

* fixing broken tests

* remove unique constraints

* debug code

* cleanup

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-14 13:20:53 +00:00
dotasek 49c3a18c0a
Bump core to 6.0.15 (#4972)
* Bump core to 6.0.14

* Bump core to 6.0.15
2023-06-09 11:25:24 -04:00
volodymyr-korzh 737238b97d
validate code on remote terminology service returns nullpointerexception (#4958)
* validate-code on remote-terminology service returns NullPointerException - tests

* validate-code on remote-terminology service returns NullPointerException - fixed

* validate-code on remote-terminology service returns NullPointerException - added changelog

* validate-code on remote-terminology service returns NullPointerException - tests readability improvement and fixes

* validate-code on remote-terminology service returns NullPointerException - fixes
2023-06-08 12:47:39 -04:00
TynerGjs fddea8db92
Resolve 4952 PUT requests for resources that don't exist get created in sequential format rather than abiding by the ResourceServerIdStrategy (#4953)
* Test implemented, issue resolved

* fixed a logical bug in the previous change

* modified comment

* added tests for Dstu2&3 resources

* Adding afterEach constructions to reset spring context beans.

* resolved comments

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-06-08 12:38:24 -04:00
volodymyr-korzh e28398fc4c
4888 Add validation for composite SearchParameter components types (#4909)
* Added unit tests for composite SearchParameter validator

* Added validation for composite SearchParameter components

* validation for composite SearchParameter components - fixes

* Modified tests

* fixed string in setDefinition

* validation for composite SearchParameter components - fixed validation and Unit tests

* validation for composite SearchParameter components - added method getActiveSearchParameterByComponentDefinition and unit tests

* validation for composite SearchParameter components - minor fixes

* validation for composite SearchParameter components - remove getActiveSearchParameterByComponentDefinition method

* validation for composite SearchParameter components - optimise import

* validation for composite SearchParameter components - fix changelog

* validation for composite SearchParameter components - improved validation logic

* validation for composite SearchParameter components - improved validation logic (remove unused lines)

* validation for composite SearchParameter components - improved validation logic

* validation for composite SearchParameter components - improved validation logic

* validation for composite SearchParameter components - fixed validation logic

* validation for composite SearchParameter components - added test for uri and number combo search

* validation for composite SearchParameter components - added test for uri and number combo search

* validation for composite SearchParameter components - validation logic fix

* validation for composite SearchParameter components - fixes

* validation for composite SearchParameter components - fixes

* validation for composite SearchParameter components - test fixes

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-06-08 11:00:27 -04:00
Luke deGruchy e37edfcf84
Ensure StepExecutor only logs a stack trace and error if the retries have been exhausted. Otherwise, just log a debug. (#4961)
* Ensure StepExecutor only logs a stack trace and error if the retries have been exhausted.  Otherwise, just log a debug.

* Accept code reviewer suggestion to amend log message

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

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-06-07 09:05:08 -04:00
TipzCM 0a7f97adb7
4917 refactor nicknaming hapi with version bump (#4955)
* refactoring 1

* refactoring step 2

* refactoring matches

* cleanup

* fixing some tests

* fixing more tests

* remove dbugcode

* adding the nickname factory

* code review fixes

* review fixes

* put default to prevent breaking

* refactor review fixes

* more review points

* more review points

* review points

* review points

* more review changes

* review points

* review points

* adding bean

* updating version

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-06 09:00:14 -04:00
Tadgh 6c03a512f5
Revert "refactoring nickname matching (#4918)" (#4954)
This reverts commit 7a18f17a01.
2023-06-02 19:40:50 +00:00
TipzCM 7a18f17a01
refactoring nickname matching (#4918)
* refactoring 1

* refactoring step 2

* refactoring matches

* cleanup

* fixing some tests

* fixing more tests

* remove dbugcode

* adding the nickname factory

* code review fixes

* review fixes

* put default to prevent breaking

* refactor review fixes

* more review points

* more review points

* review points

* review points

* more review changes

* review points

* review points

* adding bean

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-06-02 14:04:30 -04:00
michaelabuckley 9838f8a19a
Delete dead code now that Hapi has merged. (#4946) 2023-06-01 17:27:14 -07:00
StevenXLi 83411e585b
4570 add support for warning messages to the batch framework (#4571)
* added failing test

* added support for warning messages to batch2

* added change log

* fixed errors from merge, made warning work with new batch2

* fixed message parse, changed interface method to default, formatting changes

* added changelog

* code review changes

* code review change

* added new implementation for warning message processing, fixed migration

* changed column to lob, as text is not well supported

* code review changes

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-06-01 13:16:44 -04:00
Tadgh 6c314edee9
add Adi (#4939)
* add Adi

* Name typo
2023-05-31 21:34:14 +00:00
Tadgh 08a0844c12 Touch codeowners 2023-05-30 15:54:08 -07:00
dependabot[bot] 8288ebabcf
Bump snakeyaml from 1.33 to 2.0 in /hapi-fhir-docs (#4928)
Bumps [snakeyaml](https://bitbucket.org/snakeyaml/snakeyaml) from 1.33 to 2.0.
- [Commits](https://bitbucket.org/snakeyaml/snakeyaml/branches/compare/snakeyaml-2.0..snakeyaml-1.33)

---
updated-dependencies:
- dependency-name: org.yaml:snakeyaml
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-05-30 15:52:58 -07:00
Luke deGruchy 4d90719552
Delete methods deleted in previous release. (#4944) 2023-05-30 15:21:20 -04:00
volodymyr-korzh 31ae8d8f27
4934 validation doesn't consider loaded ig immediately (#4935)
* Unit tests for validation after install and uninstall IG

* Fix validation result cached after install and uninstall IG

* Fix validation result cached after install and uninstall IG - updated changelog

* Fix validation result cached after uninstalling IG - updated changelog

* Fix validation result cached after uninstalling IG - fixed unit tests

* Fix validation result cached after uninstalling IG - fixed changelog

* Fix validation result cached after uninstalling IG - test fixes
2023-05-30 14:02:14 -04:00
dotasek 34f4c90eb9
Bump org.hl7.fhir.core dependency to 6.0.8 (#4942)
* Bump core, fix compilation errors

* Match pattern in kindling for use of version

Match the pattern used by Grahame in this update of kindling: f765642470

* Bump core, fix compilation errors

* Match pattern in kindling for use of version

Match the pattern used by Grahame in this update of kindling: f765642470

* Bump core to 6.0.5, fix compilation errors

* Bump to core version 6.0.8

* Individual message code for exception

* Bump core to 6.0.10

* Fix test message
2023-05-30 09:36:40 -04:00
Etienne Poirier e068a2f32b
4799 searching on paramname profile with and missing modifier does not match resources (#4840)
* initial test

* Adding changelog

* Updated to remove the discarding of search params starting with an underscore

* test commit

* Updated handling of search parameters with underscores

* Revert work in progress

* Updated storage settings with new property for inline tag storage mode

* Updated storage settings to tell when inline tag storage mode is set

* simplified test failure

* Added tests for _tag and _system

* Add PreviousVersion service with tests (#4902)

* started writing PreviousVersionReader

* started writing PreviousVersionReader

* moar tests

* add partitioning to the test

* switch subscription to use previous version reader

---------

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

* Updated logic to be less confusing

* Bumping version to 6.7.4

* Reverted hapi bump, added improve logic for handling missing search params

* updates

* Updated failing tests

* remove redundant tests

* more updates

* Adding Jira number.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: David Raeside <davidraeside@smilecdr.com>
Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
Co-authored-by: David Raeside <david.raeside@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-30 07:12:53 -04:00
yueshi9988 e6367f03fd
change $mdm-link-history param to resourceId (#4945) 2023-05-29 12:18:24 -04:00
Ken Stevens b84e8c0bcc
Canonicalize R4 topic subscriptions (#4913)
* WIP

* add canonicalizer for R4 topic subscriptions

* test R4 topic subscription registration

* Add support for R4 Subscription Topic Backport

* FIXME

* add filter matching support

* add simpler signature

* add resource type matching to filter

* review feedback

* fixed

* changelog

* test both ways

* add bundle test

* change how toplevel is detected since in some contexts the parent state can be a non-null pre-resource state

* added logs

* changelog

* fix v2 issues

* Clean up WIP comments

* Switch to in-memory event numbers (instead of always 1)

* Final WIP cleanup

* Msg.code

* review feedback

* review feedback

* review feedback

* review feedback

* back out import changes

* back out import changes

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-29 05:32:22 +00:00
James Agnew 46857711c9
Delete expunge with cascade (#4931)
* Delete expunge with cascade

* Work

* Workgin

* Version bump hibernate

* Start working on delete cascade

* Work on delete expunge

* Test fixes

* Test fixes

* Add changelog

* Work on cascade

* Fixes

* Test work

* Test fixes
2023-05-27 11:07:59 -04:00
William Denton f8548c5d7b
let schematron use hapi-fhir-base classloader (#4366) 2023-05-26 19:05:16 -04:00
James Agnew a04a49cb68
Schema migrator returns status (#4937)
* Migrator should return status

* Cleanup

* Add changelog

* Delete unused

* Test fix
2023-05-24 19:31:39 -04:00
Tadgh c98c4a4dca
Implement codeowners (#4938)
* Initial run through codeowners

* Remove dead action

* Add consent intercept and auth interceptor
2023-05-24 21:48:55 +00:00
Tadgh d9530a9aff
Bump snake yaml (#4929)
* Bump snakeyaml

* Bump jackson to be compatible with new snakeyaml
2023-05-23 21:39:38 -07:00
Nathan Doef 3b9a9c6193
Oracle Testcontainers and Test Data (#4897)
* OracleEmbeddedDatabase + test data
2023-05-23 18:59:41 -04:00
Nathan Doef 970befad90
Fixes broken Oracle migration (#4933) 2023-05-23 17:06:27 -04:00
Tadgh 93a4a7bb33
Bump deps (#4926) 2023-05-23 09:53:52 -07:00
Tadgh 32a4ee056c
Bump snake yaml (#4929)
* Bump snakeyaml

* Bump jackson to be compatible with new snakeyaml
2023-05-23 09:32:55 -07:00