Commit Graph

10024 Commits

Author SHA1 Message Date
Tadgh c75dd41a45
6 8 cves ()
* bump

* Update deps

* reduce thymeleaf

* Remove dead import
2023-07-19 21:58:31 +00:00
jdar8 675699a177
5092 results ordering for mdm link history is incorrect ()
* update docs to be more specific

* fix ordering when client assigned id doesn't match pid

* remove fix ordering when client assigned id doesn't match pid

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>
2023-07-19 16:57:21 -04:00
jmarchionatto cd3c4d2076
Issue 5102 mdm link history ordering is incorrect when client assigned id and pid are different ()
* Failing test

* Add some self-assigned Patient IDs

* Sort after client-selected ID is interpolated into the result

* spotless

* changelog

* Keep DAO level ordering enforced by tests

* Filter out non-client-provider ids from test as they are unpredictable in build pipeline

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-07-19 15:35:51 -04:00
TipzCM cf8c70994f
fixing bug in findcandidatebyexamplesvc ()
* fixing build

* cleanup

* review fix

* review changes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-07-19 08:26:05 -04:00
Justin McKelvy d6fae7c673
fix bug on hapifhirdal searchbyurl to account for version ()
* fix bug on hapifhirdal searchbyurl to account for version

* update return type to bundleIterable, update test to validate

* add clinical-reasoning 3.0.0-PRE5

* added test comments, updated search, explicit variables

* add example comment to search cases

* fix typo

* spotless apply edits

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
2023-07-14 14:17:13 -04:00
Kevin Dougan SmileCDR 633a2d156d
5097 - Fixed a couple of links in the javadocs for the IValidationSupport class. () 2023-07-14 17:34:32 +00:00
Tadgh 6178075448
wip () 2023-07-13 15:56:23 -07:00
TipzCM 2401b2339e
fixing a bug with duplicte golden resources being returned ()
* fixing a bug with duplicte golden resources being returned

* review points

* fixing tests

* blah

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-07-13 19:58:27 +00:00
TipzCM 906355dd65
adding block list for mdm ()
* using any/exact enum

* bluck rule evaluation svc

* adding blocklist

* adding documentation

* cleanup

* adding mdm blocking service and code cleanup

* review points

* another review point

* review points

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-07-13 13:59:02 +00:00
Ken Stevens c88662205d
implement cds hooks ()
* move json and interfaces to hapi

* move serialization over

* moar test move

* move prefetch service

* move service registry

* moved everything we can.  now just need to add a controller and controller test

* controller done

* IJ Warnings

* Move test

* licenses

* mvn spotless:apply

* checkstyle

* spotless

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-07-12 16:47:37 -04:00
Luke deGruchy 43694f378c
Ensure FhirContext loads custom resources in the list of resource names ()
* Fix bug by maintaining a separate list of resource types including the custom resources that will be used to validate the Bundle resources.

* Add custom resource types to resource types list and add conditional logic in ValidationDataInitializerSvcImpl to ensure there is no Exception when parsing a custom resource type.

* Add changelog.

* Remove unnecessary change.

* Address code review feedback.

* Address code review feedback.

* Add one more unit test.

* Bump to 6.7.14-SNAPSHOT.
2023-07-12 14:32:09 +00:00
Tadgh 52f3ef5992
New formatting rules and pre-commit hooks ()
* pre-apply spotless

* New pre-format checkpoint

* Once-over the repository

* Add pre-commit hook

* New github action

* excludes

* Revert "Once-over the repository"

This reverts commit 89334ba8d1.

* Once-over the repo

* do not inherit

* Revert "Once-over the repo"

This reverts commit 31ed8731ad.

* Add baisc license support to spotless

* Move license

* Fix inclusions

* Fix inclusions

* Fix licensing

* license fixes

* Remove dead file that is only a license

* Remove dead class

* remove dead file

* Tighten licensing

* Tighten licensing

* Tighten licensing

* Tighten licensing

* Remove specific package

* Make the precommit hook executable

* Fix ordering

* rollback license

* wip

* Add to deployable pom

* remove file

* Fix location

* Remove dead comment

* wipP

* Fix ratchet

* Fix up error

* Add pre-commit

* precommit fixes

* wip

* wip

* Autoformat

* remove dead pom parts

* replace internal hook with pre-commit

* Fix fetch-depth for checker action

* Remove ratchet and filter

* fix up

* rename

* Add comment check

* rework message

* First once-over of the repo

* wip

* format
2023-07-11 17:36:44 -07:00
Tadgh 1ce2043dcd
Add JPA_PERFTRACE_INFO invocation to Fulltext Searches ()
* Changelog

* basic test

* Api change for fulltext, add test

* Add javadocs

* Refactor to use a simpler method

* Review comments
2023-07-11 20:32:02 +00:00
Brenin Rhodes eb06b473b9
Update version of the Clinical Reasoning module ()
* Update version of the Clinical Reasoning module

* cleanup

* Add changelog

* Update snapshot

* Inc version
2023-07-07 10:05:10 -04:00
Steve Corbett 10af1434fc
Delete expunge fails with identical update timestamps ()
* 4759 - WIP unit test for this issue

* WIP updating unit test for ResourceIdListStep

* WIP candidate fix for ResourceIdListStep batch size problem

* Enhance unit test with ArgumentCaptor.

* WIP Parameterized the ResourceIdListStepTest and added assertions

* Adding changelog for this issue

* Updating changelog message for 5055

* Code formatting and import cleanup

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
2023-07-06 11:59:56 -04:00
JasonRoberts-smile a87321a227
add instantiateBackboneElement method to TerserUtil ()
* add instantiateBackboneElement method to TerserUtil

* changelog
2023-07-05 21:57:19 +00:00
James Agnew a93d06c25f
Restrict bulk export download to specific user ()
* Work

* Bulk export partitioning fixes

* Changelog fixes

* cleanup

* Work on security

* Compile fixes

* Work

* Test fix

* Work

* Add changelog

* License header changes

* Test fix

* Test fix

* Fixes

* Version bump

* Test fix

* Fix accidental change
2023-07-05 12:48:15 -04:00
Ken Stevens 9a6288c363
fix hapi paging regression ()
* fix regression

* change log

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-07-04 18:43:43 +00:00
Ken Stevens 216c6ed4f1
fix surefire config ()
* 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
Unexpected usage of awssdk StringUtils in hapi 6.6 jpa migration ()
task

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

* changelog
2023-07-01 17:02:52 +00:00
Ken Stevens 2c6cd60526
bundle paging cleanup ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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. ()
* closes , fix, changelog, docs

* documentationf fixes

* checkstyle fix
2023-06-21 21:19:12 -04:00
James Agnew ddf3b72f2d
Encode non-resource types ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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. () 2023-06-16 13:53:20 -04:00
TipzCM 65ae1785e8
mdm-clear will now use batch-size parameter ()
* 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 … ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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 ()
* 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