Commit Graph

9706 Commits

Author SHA1 Message Date
Ken Stevens 216c6ed4f1
fix surefire config (#5049)
* relegate surefire config to parent pom pluginManagement

* back out build fix to see if stack trace now shows up in logs

* back out the backed out fix.

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-07-04 14:08:44 -04:00
Thomas Papke 754bd49781
#5023 Unexpected usage of awssdk StringUtils in hapi 6.6 jpa migration (#5024)
task

Replace usage of awssdk
2023-07-03 17:42:07 -04:00
Yusuf Daniju 39ee86d0fe
fix: typo in 'opposed' (#5051) 2023-07-02 15:48:20 -04:00
Tadgh a73b74869d
5014 only positive ints (#5050)
* limit ints, add test and changelog

* changelog
2023-07-01 17:02:52 +00:00
Ken Stevens 2c6cd60526
bundle paging cleanup (#5044)
* extracted ResponseBundleBuilder and started writing unit tests.  Currently at 71% coverage.

* asert bundle entries

* assert first entry id

* unknown size

* coverage up to 78%

* test filter nulls

* test null id check

* up to 91% test coverage

* 96% test coverage

* 98% test coverage.  this is final state

* fix cyclic dep

* switch to record

* split up large method

* split up large method

* consolidate params

* consolidate params

* IntelliJ Warnings

* cleanup

* cleanup

* extract methods

* extract methods

* param names

* variable name

* formatting

* extract method

* cleanup

* javadoc

* upstream consolidation

* parameter names

* TODO

* TODO

* review feedback

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-07-01 04:23:32 +00:00
Luke deGruchy ad71755c2b
Resolve 5029 Token params with system and value longer than maximum length should be created and searched differently (#4998)
* Partial implementation after this has been paused:  Move trimming of value and system from BaseSearchParamExtractor to ResourceIndexedSearchParamToken.  Do not throw Exceptions in TokenPredicateBuilder.  Ensure that the hash computing in the search param token takes the 200+ token value into account.  Other search param tokens are not yet implemented.

* in ResourceIndexedSearchParamToken,changed hardcoded length to constant MAX_LENGTH;
in BaseSearchParamExtractor, added check in createTokenIndexIfNotBlank so that the return value is null if system or value is blank.

* added test for TokenPredicateBuilder to verify that long values exceeds the max length does not cause exception.

added test in FhirSystemDaoR4SearchTest to verify searchParamToken with longer system and value than max length can be created successfully. And hash value will be calculated before truncation

* fixed a logical error in previous commits

* changed existing tests to accommodate for the changes

* modified existing tests

* added changelog

* changed truncation method name and added comments

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

* modified changelog

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

* combined redundant tests

---------

Co-authored-by: tyner <tyner.guo@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-06-30 10:48:33 -04:00
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