#13948 sample & test form changes#13967
Merged
Merged
Conversation
…al messages survey
…ake "Add pathogen test" administrator-configurable
…ake "Add pathogen test" administrator-configurable
…ake "Add pathogen test" administrator-configurable
…ake "Add pathogen test" administrator-configurable
…al messages survey
…n-config for required tests / add new test
|
Caution Review failedPull request was closed or merged during review No actionable comments were generated in the recent review. 🎉 ℹ️ Recent review info⚙️ Run configurationConfiguration used: defaults Review profile: CHILL Plan: Pro Run ID: 📒 Files selected for processing (1)
📝 WalkthroughWalkthroughThis PR introduces a server-side feature configuration framework alongside sample lab field enhancements. It adds two feature toggles for lab workflows ( ChangesFeature Configuration and Sample Lab Workflow
Estimated code review effort🎯 4 (Complex) | ⏱️ ~45 minutes Possibly related issues
Possibly related PRs
Suggested reviewers
Poem
🚥 Pre-merge checks | ✅ 3 | ❌ 2❌ Failed checks (2 warnings)
✅ Passed checks (3 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing Touches🧪 Generate unit tests (beta)
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 2
🧹 Nitpick comments (3)
sormas-backend/src/test/java/de/symeda/sormas/backend/sample/SampleFacadeEjbTest.java (1)
1233-1235: ⚡ Quick winConsider verifying
performedByReferenceLaboratory's default value.The comment on line 1234 states that
performedByReferenceLaboratoryis "unset" initially, but there's no assertion to validate this. OnlyretestRequestedis checked. For comprehensive default-value coverage, consider adding an assertion forperformedByReferenceLaboratoryas well.📋 Suggested addition
SampleDto sample = creator.createSample(caze.toReference(), user.toReference(), rdcf.facility); // New samples default retestRequested to false and leave performedByReferenceLaboratory unset. + assertNull(getSampleFacade().getSampleByUuid(sample.getUuid()).getPerformedByReferenceLaboratory()); assertEquals(Boolean.FALSE, getSampleFacade().getSampleByUuid(sample.getUuid()).getRetestRequested());🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@sormas-backend/src/test/java/de/symeda/sormas/backend/sample/SampleFacadeEjbTest.java` around lines 1233 - 1235, The test creates a SampleDto via creator.createSample and currently only asserts retestRequested; add an assertion that the returned SampleDto's performedByReferenceLaboratory is unset (null) to match the comment. Locate the call using SampleDto sample = creator.createSample(...) and the fetch via getSampleFacade().getSampleByUuid(sample.getUuid()), then add an assertNull (or assertEquals(null, ...)) against getPerformedByReferenceLaboratory() on that fetched SampleDto to verify the default.sormas-ui/src/main/java/de/symeda/sormas/ui/samples/AbstractSampleForm.java (1)
192-219: ⚡ Quick winRemove now-unused disease fetch logic after unconditional sample-source hiding.
Lines 192-200 no longer influence behavior because Line 218 always hides
SAMPLE_SOURCE. Keeping this block adds unnecessary facade calls during form initialization.Proposed cleanup
- Disease disease = null; - final CaseReferenceDto associatedCase = getValue().getAssociatedCase(); - if (associatedCase != null && UiUtil.permitted(UserRight.CASE_VIEW)) { - disease = FacadeProvider.getCaseFacade().getCaseDataByUuid(associatedCase.getUuid()).getDisease(); - } else { - final ContactReferenceDto associatedContact = getValue().getAssociatedContact(); - if (associatedContact != null && UiUtil.permitted(UserRight.CONTACT_VIEW)) { - disease = FacadeProvider.getContactFacade().getByUuid(associatedContact.getUuid()).getDisease(); - } - } - // The sample source dropdown is no longer shown for any disease (`#13948` issue `#13959`); the field is // kept bound so existing values still round-trip and appear in exports. getField(SampleDto.SAMPLE_SOURCE).setVisible(false);🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@sormas-ui/src/main/java/de/symeda/sormas/ui/samples/AbstractSampleForm.java` around lines 192 - 219, Remove the now-unused disease lookup block: delete the local variable "Disease disease = null;" and the conditional block that reads associated case/contact using getValue().getAssociatedCase(), CaseReferenceDto/ContactReferenceDto and FacadeProvider.getCaseFacade()/getContactFacade() since SAMPLE_SOURCE is unconditionally hidden via getField(SampleDto.SAMPLE_SOURCE).setVisible(false) and those facade calls only cause unnecessary work; after removal, ensure any imports or references exclusively used by that block (e.g., Disease, CaseReferenceDto, ContactReferenceDto, FacadeProvider calls) are cleaned up.sormas-backend/src/main/java/de/symeda/sormas/backend/feature/FeatureConfigurationFacadeEjb.java (1)
357-360: ⚡ Quick winAlign initial creation with entity-scoped server feature contracts.
Line 358 currently creates a single row when none exists. If a server feature supports multiple entity types, this can persist an incomplete configuration set and diverge from the entity-aware creation contract already used in
FeatureConfigurationService.createMissingFeatureConfigurations.Proposed adjustment
List<FeatureConfiguration> configurations = service.getServerFeatureConfigurationsByType(featureType); if (configurations.isEmpty()) { - FeatureConfiguration configuration = FeatureConfiguration.build(featureType, enabled); - configuration.setProperties(featureType.getSupportedPropertyDefaults()); - service.ensurePersisted(configuration); + if (featureType.getEntityTypes() != null) { + for (DeletableEntityType entityType : featureType.getEntityTypes()) { + FeatureConfiguration configuration = FeatureConfiguration.build(featureType, enabled); + configuration.setEntityType(entityType); + configuration.setProperties(featureType.getSupportedPropertyDefaults()); + service.ensurePersisted(configuration); + } + } else { + FeatureConfiguration configuration = FeatureConfiguration.build(featureType, enabled); + configuration.setProperties(featureType.getSupportedPropertyDefaults()); + service.ensurePersisted(configuration); + } } else {🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@sormas-backend/src/main/java/de/symeda/sormas/backend/feature/FeatureConfigurationFacadeEjb.java` around lines 357 - 360, When no configurations exist (the configurations.isEmpty() branch in FeatureConfigurationFacadeEjb), do not create a single generic row via FeatureConfiguration.build; instead create per-entity configurations to match the entity-scoped contract used by FeatureConfigurationService.createMissingFeatureConfigurations. Replace the single-feature creation with logic that iterates the featureType's supported entity types (or delegate to FeatureConfigurationService.createMissingFeatureConfigurations) and call service.ensurePersisted for each generated FeatureConfiguration (using FeatureConfiguration.build and setting properties via featureType.getSupportedPropertyDefaults()) so all required entity-specific rows are created.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@sormas-api/src/main/java/de/symeda/sormas/api/sample/SampleDto.java`:
- Around line 140-141: migrateAttributesOfPhysicalSample and buildReferralDto
currently omit the performedByReferenceLaboratory and retestRequested flags,
causing them to be lost during referral creation; update
migrateAttributesOfPhysicalSample to copy
sampleDto.getPerformedByReferenceLaboratory() and sampleDto.getRetestRequested()
into the target/referral DTO, and ensure buildReferralDto sets those same fields
on the new SampleDto (or copies the source SampleDto fields) so both
performedByReferenceLaboratory and retestRequested are preserved during referral
migration.
In `@sormas-backend/src/main/resources/sql/sormas_schema.sql`:
- Around line 16307-16312: The migration currently adds a nullable boolean
column retestrequested and only backfills existing rows, allowing future NULLs;
change the migration to enforce a DB-level default and NOT NULL so new rows
default to FALSE. Specifically, for both samples and samples_history ensure you:
(1) ALTER TABLE ... ADD COLUMN IF NOT EXISTS retestrequested boolean DEFAULT
false; (2) UPDATE ... SET retestrequested = false WHERE retestrequested IS NULL;
and (3) ALTER TABLE ... ALTER COLUMN retestrequested SET NOT NULL; reference the
tables samples and samples_history and the column name retestrequested when
making these changes.
---
Nitpick comments:
In
`@sormas-backend/src/main/java/de/symeda/sormas/backend/feature/FeatureConfigurationFacadeEjb.java`:
- Around line 357-360: When no configurations exist (the
configurations.isEmpty() branch in FeatureConfigurationFacadeEjb), do not create
a single generic row via FeatureConfiguration.build; instead create per-entity
configurations to match the entity-scoped contract used by
FeatureConfigurationService.createMissingFeatureConfigurations. Replace the
single-feature creation with logic that iterates the featureType's supported
entity types (or delegate to
FeatureConfigurationService.createMissingFeatureConfigurations) and call
service.ensurePersisted for each generated FeatureConfiguration (using
FeatureConfiguration.build and setting properties via
featureType.getSupportedPropertyDefaults()) so all required entity-specific rows
are created.
In
`@sormas-backend/src/test/java/de/symeda/sormas/backend/sample/SampleFacadeEjbTest.java`:
- Around line 1233-1235: The test creates a SampleDto via creator.createSample
and currently only asserts retestRequested; add an assertion that the returned
SampleDto's performedByReferenceLaboratory is unset (null) to match the comment.
Locate the call using SampleDto sample = creator.createSample(...) and the fetch
via getSampleFacade().getSampleByUuid(sample.getUuid()), then add an assertNull
(or assertEquals(null, ...)) against getPerformedByReferenceLaboratory() on that
fetched SampleDto to verify the default.
In `@sormas-ui/src/main/java/de/symeda/sormas/ui/samples/AbstractSampleForm.java`:
- Around line 192-219: Remove the now-unused disease lookup block: delete the
local variable "Disease disease = null;" and the conditional block that reads
associated case/contact using getValue().getAssociatedCase(),
CaseReferenceDto/ContactReferenceDto and
FacadeProvider.getCaseFacade()/getContactFacade() since SAMPLE_SOURCE is
unconditionally hidden via getField(SampleDto.SAMPLE_SOURCE).setVisible(false)
and those facade calls only cause unnecessary work; after removal, ensure any
imports or references exclusively used by that block (e.g., Disease,
CaseReferenceDto, ContactReferenceDto, FacadeProvider calls) are cleaned up.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: defaults
Review profile: CHILL
Plan: Pro
Run ID: 97623fea-8d9d-42a2-9acf-9cc1c4760ad1
📒 Files selected for processing (29)
sormas-api/src/main/java/de/symeda/sormas/api/feature/FeatureConfigurationFacade.javasormas-api/src/main/java/de/symeda/sormas/api/feature/FeatureType.javasormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.javasormas-api/src/main/java/de/symeda/sormas/api/i18n/Strings.javasormas-api/src/main/java/de/symeda/sormas/api/sample/SampleDto.javasormas-api/src/main/java/de/symeda/sormas/api/sample/SampleExportDto.javasormas-api/src/main/resources/captions.propertiessormas-api/src/main/resources/enum.propertiessormas-api/src/main/resources/strings.propertiessormas-backend/src/main/java/de/symeda/sormas/backend/externalmessage/ExternalMessageFacadeEjb.javasormas-backend/src/main/java/de/symeda/sormas/backend/externalmessage/ExternalMessageService.javasormas-backend/src/main/java/de/symeda/sormas/backend/feature/FeatureConfigurationFacadeEjb.javasormas-backend/src/main/java/de/symeda/sormas/backend/feature/FeatureConfigurationService.javasormas-backend/src/main/java/de/symeda/sormas/backend/sample/PathogenTestFacadeEjb.javasormas-backend/src/main/java/de/symeda/sormas/backend/sample/Sample.javasormas-backend/src/main/java/de/symeda/sormas/backend/sample/SampleFacadeEjb.javasormas-backend/src/main/resources/sql/sormas_schema.sqlsormas-backend/src/test/java/de/symeda/sormas/backend/externalmessage/ExternalMessageFacadeEjbUnitTest.javasormas-backend/src/test/java/de/symeda/sormas/backend/feature/FeatureConfigurationFacadeEjbTest.javasormas-backend/src/test/java/de/symeda/sormas/backend/sample/PathogenTestFacadeEjbTest.javasormas-backend/src/test/java/de/symeda/sormas/backend/sample/SampleFacadeEjbTest.javasormas-ui/src/main/java/de/symeda/sormas/ui/configuration/AbstractConfigurationView.javasormas-ui/src/main/java/de/symeda/sormas/ui/configuration/featureconfiguration/FeatureConfigurationView.javasormas-ui/src/main/java/de/symeda/sormas/ui/samples/AbstractSampleForm.javasormas-ui/src/main/java/de/symeda/sormas/ui/samples/PathogenTestController.javasormas-ui/src/main/java/de/symeda/sormas/ui/samples/PathogenTestForm.javasormas-ui/src/main/java/de/symeda/sormas/ui/samples/components/TestResultComponent.javasormas-ui/src/main/java/de/symeda/sormas/ui/samples/diseasesection/PathogenTestFormConfig.javasormas-ui/src/main/java/de/symeda/sormas/ui/samples/humansample/SampleController.java
…migration & Enforce a DB-level default/constraint for retestrequested
KarnaiahPesula
approved these changes
Jun 9, 2026
raulbob
approved these changes
Jun 9, 2026
Re-sequence schema versions after development renumbered the tail: the sample-form "reference laboratory + retest indicators" migration moves from 638 to 637. Revert ExternalMessage* changes (schema JSONB->JSON / config-key rename block and the countDistinct(...get(ID)) Java fixes).
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes #13953 #13954 #13958 #13959
Summary by CodeRabbit