Commit Graph

9343 Commits

Author SHA1 Message Date
nathaniel.doef bbc7418d51 maintenance pass 2023-02-08 02:19:34 -05:00
Nathan Doef 70f49a2e6f
shorten test 2023-02-08 01:01:16 -05:00
nathaniel.doef 1e7a96a0fb Merge branch 'rel_6_4' into nd-4123-bulk-export-stuck-in-finalize-state 2023-02-07 23:46:15 -05:00
Tadgh e724040c14 New line:: 2023-02-07 17:22:36 -08:00
Nathan Doef a4068b40ca
Increase timeout limit to match BulkExportUseCaseTest 2023-02-07 18:51:13 -05:00
nathaniel.doef 0ee3434669 version bump 2023-02-07 17:27:31 -05:00
nathaniel.doef 1f66d87b2f code review comments 2023-02-07 17:21:33 -05:00
nathaniel.doef 1280367593 Merge branch 'rel_6_4' into nd-4123-bulk-export-stuck-in-finalize-state 2023-02-07 17:18:50 -05:00
Isaac Wen 85ecbf181e
Unable to Expunge CodeSystem (#4507)
* changes for GL-3943

* changes for GL-3943

---------

Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
2023-02-07 15:26:10 -05:00
Tadgh ca21abf0f8
4516 create hapi fhir cli command to clear stale lock entries (#4517)
* Initial implementation

* better tests

* Add changelog and docs

* Forgotten files

* Code review comments

* Fix checkstyle
2023-02-07 11:37:52 -08:00
Tadgh d08995a5e6
Add check in scanner (#4518) 2023-02-07 10:13:29 -08:00
nathaniel.doef 7da52ef537 clean up 2023-02-07 10:33:08 -05:00
nathaniel.doef 34e27c4313 decrease test time 2023-02-06 22:57:42 -05:00
nathaniel.doef 43b3dd468a tweak 2023-02-06 22:03:50 -05:00
nathaniel.doef 19128fcd0d tweak 2023-02-06 21:17:52 -05:00
nathaniel.doef 6ca50687b4 add method to IJobPersistence to use a Stream 2023-02-06 20:39:42 -05:00
Tadgh e160325af6
CVE resolutions (#4513)
* Bump Postgres for CVE

* Bump jetty

* Verison bump

* Remove comments

* Revrt bump
2023-02-06 13:44:52 -08:00
samguntersmilecdr 33f6ed3d32
Change bulk import test for valueUri type (#4503)
* change tests

* suggested test change
2023-02-06 09:19:21 -08:00
Luke deGruchy 2a963acde2
Scheduled batch 2 bulk export job and binary delete (#4492)
* First commit:  Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.

* Refine solution and add a concrete unit test but still work to do.

* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.

* Unit tests complete.  New Msg code for new IJobPersistence.fetchInstances() method.  Cleanup TODOs and add others.

* Finish final touches on implementation.

* Add changelog.

* Various cleanup.

* Code review feedback.

* Small tweak to changelog.

* Last code review tweak.

* Address more code review comments.

* Reverse changes to consider work chunks.  Add a constant for write-to-binary.
2023-02-06 09:04:04 -05:00
nathaniel.doef 22c05268c2 tweak 2023-02-05 20:55:31 -05:00
nathaniel.doef 2cbea97ed0 fix + changelog 2023-02-05 13:02:26 -05:00
nathaniel.doef 87df691fc2 Merge branch 'rel_6_4' into nd-4123-bulk-export-stuck-in-finalize-state 2023-02-03 23:31:37 -05:00
TipzCM 0996124778
fix batch2 reduction step (#4499)
* fix bug where FINALIZE jobs are not cancellable

* moved reduction step to message hander

* moving reduction step to queue

* addingchangelog

* cleaning up

* review fixes

* review fix'

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-02-03 14:00:29 -05:00
Tadgh 7d554d56fd License 2023-02-03 10:25:19 -08:00
Tadgh df83d05fbb Merge branch 'rel_6_4' of github.com:hapifhir/hapi-fhir into rel_6_4 2023-02-02 15:22:28 -08:00
Tadgh a855af576d Loosen rules for id helper 2023-02-02 15:11:32 -08:00
Mark Iantorno c64285394f core version fix 2023-02-02 17:40:13 -05:00
Mark Iantorno 740fec9554 Revert "cleaning up checkstyle files (#4470)"
This reverts commit efae3b5d5f.
2023-02-02 17:24:34 -05:00
nathaniel.doef 832c540036 failing test 2023-02-02 16:37:32 -05:00
jmarchionatto 0a213a52d6
Issue 4486 mdm inconsistent possible match score values (#4487)
* Extract method for readability

* Save always normalized score values in POSSIBLE_MATCH links.

* Avoid setting properties to null values. Adjust test.

* Simplify fix

* Fix test. Add RangeTestHelper.

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-02-02 11:42:38 -08:00
dotasek b1770abb85
Bump core to 5.6.881 (#4496)
* Bump core to 5.6.881-SNAPSHOT

* Work on fixing tests

* Work on fixing tests 2

* Bump to core release

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>
2023-02-02 09:52:04 -05:00
Mark Iantorno efae3b5d5f
cleaning up checkstyle files (#4470)
* cleaning up checkstyle files

* One more fix for #4467 (#4469)

* added exlusions for files at base project level so checkstyle doesn't error out

* duplicate error code from merge

* changing lifecycle goal for all module checkstyle check

* moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code

* wip

* trying to figure out why pipeline cannot copy files

* removing modules that don't actually need to be built.

* I messed up the version

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-02-01 18:00:45 -05:00
Etienne Poirier dd8c8a3b24
Reindex batch job fails when processing deleted resources. (#4482)
* adding changelog.

* Providing solution and adding changelog.

* Adding new test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-02-01 08:15:33 -05:00
Luke deGruchy 67ace43492
Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484)
* First commit:  Make SubscriptionValidatingInterceptor aware of which Pointcut is being called.  In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED.   Fix resulting compile errors in various unit tests.

* Fix/enhance unit tests.  Mark methods as deprecated instead of deleting them.  Add proper error code.  Complete changelog.

* Remove erroneous TODOs and tweak the validation logic.

* Enhance unit tests and fix changelog.
2023-01-31 15:42:39 -05:00
Nathan Doef 882f22fdb0
Change visibility of migration method (#4471)
* change migration visibility

* add empty migration method for 640

---------

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2023-01-31 10:19:25 -05:00
Etienne Poirier 40508a00e3
Provide the capability to request that the name of the subscription matching channel be unqualified (#4464)
* Adding initial test.

* Adding initial solution implementation.

* Adding change log and code clean up.

* addressing comments from 1st code review.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-01-30 11:07:09 -05:00
Etienne Poirier 1a9b749b5a
Enabling massIngestionMode causes incomplete resource deletion (#4476)
* Adding initial test.

* Adding fix and subsequent test.

* Adding changelog.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
2023-01-30 07:34:50 -05:00
James Agnew 078dcd9c0d One more fix for #4467 2023-01-27 08:30:28 -08:00
michaelabuckley 10060bef7f
Batch option processing cleanup (#4466)
* BulkDataExportOptions null safety
2023-01-26 11:50:45 -05:00
James Agnew 8c287f0269
Terser cloneInto doesn't work for contained resources (#4467)
* Add fix

* Add docs
2023-01-26 14:55:19 +00:00
James Agnew 69f64269cf
Port #4444 to master (#4465)
* Port #4444 to master

* Add operation

* Add developer credit
2023-01-25 14:37:16 -05:00
James Agnew d46f6d635e
Web Admin Console Improvements (#4456)
* Testpage improvements

* Work on tests

* Split fragment out

* Reformat command buttons

* Work on web admin console

* Work on testpage

* Fixes

* Fix

* Test fixes

* Improve examples

* Test fixes

* Address review comment
2023-01-25 09:27:12 -05:00
Tadgh 456cc81b32
Rel 6 2 5 mergeback (#4459)
* jm wrong bundle entry url (#4213)

* Bug test

* here you go

* Generate relative URIs for bundle entry.request.url, as specified

* Point jira issue in changelog

* Adjust tests to fixes

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* improved logging (#4217)

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

* Rel 6 1 3 mergeback (#4215)

* Bump for CVE (#3856)

* Bump for CVE

* Bump spring-data version

* Fix compile

* Cut over to spring bom

* Bump to RC1

* remove RC

* do not contrain reindex for common SP updates (#3876)

* only fast-track jobs with exactly one chunk (#3879)

* Fix illegalstateexception when an exception is thrown during stream response (#3882)

* Finish up changelog, minor refactor

* reset buffer only

* Hack for some replacements

* Failure handling

* wip

* Fixed the issue (#3845)

* Fixed the issue

* Changelog modification

* Changelog modification

* Implemented seventh character extended code and the corresponding dis… (#3709)

* Implemented seventh character extended code and the corresponding display

* Modifications

* Changes on previous test according to modifications made in ICD10-CM XML file

* Subscription sending delete events being skipped (#3888)

* fixed bug and added test

* refactor

* Update for CVE (#3895)

* updated pointcuts to work as intended (#3903)

* updated pointcuts to work as intended

* added changelog

* review fixes

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

* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)

* Add test and implementation

* Add changelog

* 3899 code in limits (#3901)

* Add implementation, changelog, test

* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* 3884 overlapping searchparameter undetected rel 6 1 (#3909)

* Applying all changes from previous dev branch to current one pointing to rel_6_1

* Fixing merge conflict related to Msg.code value.

* Fixing Msg.code value.

* Making checkstyle happy.

* Making sure that all tests are passing.

* Passing all tests after fixing Msg.code

* Passing all tests.

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

* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)

* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete

* created unit test for skip of delete operation while processing duplicating create entries

* moved unit test to FhirSystemDaoR4Test

* 3379 mdm fixes (#3906)

* added MdmLinkCreateSvcimplTest

* fixed creating mdm-link not setting the resource type correctly

* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on

* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java

Change order of tests such that assertEquals takes expected value then actual value

Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* added changelog, also changed a setup function in test to beforeeach

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* Fix to the issue (#3855)

* Fix to the issue

* Progress

* fixed the issue

* Addressing suggestions

* add response status code to MethodOutcome

* Addressing suggestions

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

* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)

* Respect caching in bullk export, fix bug with completed date on empty jobs

* add changelog

* Add impl

* Add breaking test

* Complete failing test

* more broken tests

* Fix more tests'

* Fix paging bug

* Fix another brittle test

* 3915 do not collapse rules with filters (#3916)

* do not attempt to merge compartment permissions with filters

* changelog

* Rename to IT for concurrency problems

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Version bump

* fix $mdm-submit output (#3917)

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

* Gl3407 bundle offset size (#3918)

* begin with failing test

* fixed

* change log

* rollback default count change and corresponding comments

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

* Offset interceptor now only works for external calls

* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.

* do not reindex searchparam jobs on startup

* Fix oracle non-enterprise attempting online index add (#3925)

* 3922 delete expunge large dataset (#3923)

* lower batchsize of delete requests so that we do not get sql exceptions

* blah

* fix test

* updated tests to not fail

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

* add index

* Fix up colun grab

* Revert offset mode change

* Revert fix for null/system request details checks for reindex purposes

* Fix bug and add test for SP Validating Interceptor (#3930)

* wip

* Fix uptests

* Fix index online test

* Fix SP validating interceptor logic

* Updating version to: 6.1.1 post release.

* fix compile error

* Deploy to sonatype (#3934)

* adding sonatype profile to checkstyle module

* adding sonatype profile to tinder module

* adding sonatype profile to base pom

* adding final deployToSonatype profile

* wip

* Revert version enum

* Updating version to: 6.1.1 post release.

* Add test, changelog, and implementation

* Add backport info

* Create failing test

* Implemented the fix, fixed existing unit tests

* added changelog

* added test case for no filter, exclude 1 patient

* wip

* Add backport info

* Add info of new version

* Updating version to: 6.1.2 post release.

* bump info and backport for 6.1.2

* Bump for hapi

* Implement bug fixes, add new tests (#4022)

* Implement bug fixes, add new tests

* tidy

* Tidy

* refactor for cleaning

* More tidying

* Lower logging

* Split into nested tests, rename, add todos

* Typo

* Code review

* add backport info

* Updating version to: 6.1.3 post release.

* Updating version to: 6.1.3 post release.

* removed duplicate mention of ver 6.1.3 in versionEnum

* backport pr 4101

* mdm message key (#4111)

* begin with failing test

* fixed 2 tests

* fix tests

* fix tests

* change log

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

* backport 6.1.3 docs changes

* fixed typo on doc backport message

* fix test breaking

* Updating version to: 6.1.4 post release.

* wip

Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@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: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>

* pin okio-jvm for kotlin vuln (#4216)

* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)

* First commit:  Failing unit test and a TODO with a vague idea of where the bug happens.

* Don't escape "+" in a URL GET parameter if it starts with "application".

* Remove unnecessary TODO.

* Add changelog.

* Code review feedback on naming.  Also, make logic more robust by putting plus and should escape boolean && in parens.

* Ks 20221031 migration lock (#4224)

* started design

* complete with tests

* changelog

* cleanup

* tyop

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

* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)

* Added test

* Added solution

* Changelog

* Changes made based on comments

* Fix bug with MDM submit

* fix

* Version bump

* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)

* Add constant for interceptor

* add test, changelog

* Allow Batch2 transition from ERRORED to COMPLETE (#4242)

* Allow Batch2 transition from ERRORED to COMPLETE

* Add changelog

* Test fix

Co-authored-by: James Agnew <james@jamess-mbp.lan>

* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)

* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.

* Update test case.

* Cleaned up changelog.

* Added test case for multiple resource types.

* Added failing test case for not returning Binary resource.

* Refactor solution.

Co-authored-by: kylejule <kyle.jule@smilecdr.com>

* Add next version

* bulk export permanently reusing cached results (#4249)

* Add test, fix bug, add changelog

* minor refactor

* Fix broken test

* Smile 4892 DocumentReference Attachment url (#4237)

* failing test

* fix

* increase test Attachment url size to new max

* decrease limit to 500

* ci fix

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Overlapping SearchParameter with the same code and base are not allowed (#4253)

* Overlapping SearchParameter with the same code and base are not allowed

* Fix existing tests according to changes

* Cleanup dead code and remove related tests

* Version Bump

* ignore misfires in quartz

* Allowing Failures On Index Drops (#4272)

* Allowing failure on index drops.

* Adding changeLog

* Modification to changelog following code review.

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

* Revert "ignore misfires in quartz"

This reverts commit 15c74a46bc.

* Ignore misfires in quartz (#4273)

* Reindex Behaviour Issues (#4261)

* fixmes for ND

* address FIXME comments

* fix tests

* increase max retries

* fix resource id chunking logic

* fix test

* add modular patient

* change log

* version bump

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

* Set official Version

* license

* Fix up numbers

* Fix up numbers

* Update numbers

* wip

* fix numbers

* Fix test:

* Fix more tests

* TEMP FIX FOR BUILD

* wip

* Updating version to: 6.2.1 post release.

* Add a whack of logging

* wip

* add implementation

* wip and test

* wip

* last-second-fetch

* expose useful method

* remove 10000 limit

* Strip some logging

* Fix up logging

* Unpublicize method

* Fix version

* Make minor changes

* once again on 6.2.1

* re-add version enum

* add folder

* fix test

* DIsable busted test

* Disable more broken tests

* Only submit queued chunks

* Quiet log

* Fix wrong pinned version

* Updating version to: 6.2.2 post release.

* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https… (#4291)

* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https://github.com/hapifhir/hapi-fhir/issues/4276

* Credit for #4291

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

* backport and changelog for 6.2.2

* Updating version to: 6.2.3 post release.

* fix https://simpaticois.atlassian.net/browse/SMILE-5781

* Version bump to 6.2.3-SNAPSHOT

* Auto retry on MDM Clear conflicts (#4398)

* Auto-retry mdm-clear on conflict

* Add changelog

* Build fix

* Disable failing test

* Update to 6.2.3 again

* Update license dates

* Dont fail on batch2 double delivery (#4400)

* Don't fail on Batch2 double delivery

* Add changelog

* Update docker for release ppipeline

* Updating version to: 6.2.4 post release.

* Add test and implementation to fix potential NPE in pre-show resources (#4388)

* Add test and implementation to fix potential NPE in pre-show resources

* add test

* WIP getting identical test scenario

* More robust solution

* Finalize Code

* Add changelog, move a bunch of changelogs

* Remove not needed test

* Minor refactor and reporting

* Fix up megeback

* update backport info

* update backport info

* Updating version to: 6.2.5 post release.

* Prevent chunk from returning to in-progress unless it is errorred, in-progress, or queued

* changelog

* Update logger

* Indicate backport

* Add version and upgrade info. add backport

* hapi-fhir side done

* cdr side

* add assert

* add test

* Fix import

* prevent multiple reduction step runs in maintenance run (#4423)

* setting job to inprog to prevent multiple maintenance passes from running reduction steps

* added a new status

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* Add backport info

* Fix up tests

* Fix discrepancies

* Fix test

* Version bump

* bump ips

Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@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: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
2023-01-24 17:38:35 -08:00
Luke deGruchy 1755eb46e6
Introduce new logical AND boolean in CachingValidationSupport that influences Coding validation in VersionSpecificWorkerContextWrapper (#4433)
* Failing unit test with a combination of both communication language types plus two passing tests with each language type individually.

* Failing unit test with a combination of both communication language types plus two passing tests with each language type individually.

* Change patient name and birhdate.

* Latest unit test enhancements.

* Preliminary solution that seems to fix the bug and not break module unit tests.  Instead of VersionSpecificWorkerContextWrapper.validateCode() returning immediately upon the first OK validation, collect all the OKs and return the first if all codings are OK.

* Try another solution to output the correct error message without breaking other tests.

* Try a solution focused on a ValueSet with a languages URI.

* Working but messy config to toggle the AND/OR behaviour in VersionSpecificWorkerContextWrapper.validateCode().  Need to do a lot of cleanup, unit/integration tests and possibly documentation.

* Working but messy solution to toggle the AND/OR behaviour in VersionSpecificWorkerContextWrapper.validateCode().  Need to do a lot of cleanup, unit/integration tests and possibly documentation.

* Reverse changes that are not needed for the final solution.  Also, add a convenient method to ValidationSupportContext and call it.

* Update FhirInstanceValidatorR4Test to set the new logical AND flag.  Rename all references to the new flag.

* Revert all classes to master that were changed to call the new constructor.  Add new changelog.

* Revert other false param constructor calls.

* Add code reuse to ValidationSupportConfigUtil and increase test coverage for CachingValidationSupportTest.

* Code review feedback:  Clarify property description.  Fix parameter names.  Add extra check for empty codings.
2023-01-24 14:40:28 -05:00
KGJ-software 527a948285
Added SearchRequest.requester to Patient/everything (#4462)
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
2023-01-24 13:28:19 -05:00
James Agnew d584e14048
Add IPS Generator (#4438)
* Begin IPS refactor

* Commit work so far

* Fix test bug

* Fix typo

* Fix typo

* Narrative generator cleanup

* Narrative generator working

* Add test for bad reference in narrative

* Tests passing

* Start docs

* Tests passing

* Cleanup

* Update cyangelog

* Doc tweaks

* Version bump

* Address review comments

* Address review comments

* Build fix

* Cleanup

* Compile fix

* Test fix

* Test fix

* Version bump

* Build update

* Test fix

* Test fix

* Add one utility method

* Add doc
2023-01-24 12:07:36 -05:00
Nathan Doef 320a0d895f
Fix ConceptMap processing in transaction (#4442)
* failing test

* fix

* only store ConceptMap once

* remove new myPreliminaryTransactionWrite flag and use thePerformIndexing

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
2023-01-24 10:58:11 -05:00
jmarchionatto c2b5ae6436
Improve doc title formatting (#4460)
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
2023-01-23 21:09:06 +00:00
ivagulin 758c8f12dd
fix ValueSet$expand?includeHierarchy=true with fts disabled (#4449)
* fix ValueSet$expand?includeHierarchy=true

* add test for valuset$expand with hierarchy without hibernate search

* move testExpandValueSet_PreExpandedWithHierarchyNoHibernateSearch to FhirResourceDaoR4ValueSetTest, add javadoc

* Add credit

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-01-23 10:25:24 -05:00
Ken Stevens 5dda16d467
Reduce postconstruct use (#4445) 2023-01-21 00:37:58 -05:00