Fix sample-type visibility and AST commit crash (#14018, #14156, #14124)

[roldy]

Fixes #14018 #14156 #14124

Summary by CodeRabbit

• Bug Fixes
  • Updated sample/material visibility rules so “Clinical Sample / Other” is available for all diseases and peritoneal fluid is no longer hidden for Luxembourg.
  • Prevented an empty drug susceptibility form from being saved when no value is present, reducing form-related errors.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 38230260-e522-4ea8-8b53-67253deab201

📥 Commits

Reviewing files that changed from the base of the PR and between 87d0496 and 280ba79.

📒 Files selected for processing (1)

• sormas-ui/src/main/java/de/symeda/sormas/ui/therapy/DrugSusceptibilityForm.java

🚧 Files skipped from review as they are similar to previous changes (1)

• sormas-ui/src/main/java/de/symeda/sormas/ui/therapy/DrugSusceptibilityForm.java

---

📝 Walkthrough

Walkthrough

Updates SampleMaterial visibility metadata for two specimen types, adjusts one inline specimen comment, adds a null guard to DrugSusceptibilityForm.commit(), and makes a formatting-only edit in ImiSectionComponent.

Changes

Sample Material Visibility

Layer / File(s)	Summary
SampleMaterial annotation and comment updates sormas-api/src/main/java/de/symeda/sormas/api/sample/SampleMaterial.java	Removes the disease hide restriction from CLINICAL_SAMPLE, removes the Luxembourg hide restriction from PERITONEAL_FLUID, and adjusts the PLEURAL_FLUID SNOMED-CT export comment.

UI Form Fixes

Layer / File(s)	Summary
DrugSusceptibilityForm commit null guard sormas-ui/src/main/java/de/symeda/sormas/ui/therapy/DrugSusceptibilityForm.java	Overrides commit() to return early without calling super.commit() when the form value is null.

Estimated code review effort: 2 (Simple) | ~10 minutes

Possibly related PRs

• SORMAS-Foundation/SORMAS-Project#13945: Both PRs modify SampleMaterial behavior around CLINICAL_SAMPLE.
• SORMAS-Foundation/SORMAS-Project#13962: Both PRs modify SampleMaterial visibility rules, including country-specific specimen behavior.
• SORMAS-Foundation/SORMAS-Project#14114: Both PRs adjust SampleMaterial annotation metadata for specimen visibility.

Suggested reviewers: KarnaiahPesula, raulbob

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (2 warnings)

Check name	Status	Explanation	Resolution
Linked Issues check	⚠️ Warning	The PR does not add the Giardia-specific sample list for #14018; it mainly changes other sample visibility rules and a null guard.	Implement the Giardia-specific sample list (Stool, Duodenum fluid, Biopsy) in the web app and verify the case-specific sample selection flow.
Out of Scope Changes check	⚠️ Warning	It includes unrelated changes for #14156/#14124 and a formatting-only edit, which are outside the provided #14018 objective.	Remove or split unrelated fixes and cleanup into separate PRs, or expand the linked issue scope to cover them explicitly.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title matches the main changes: sample visibility updates and the commit-crash fix, and it names the relevant issue numbers.
Description check	✅ Passed	The description satisfies the template's Fixes line and references the issue numbers needed for this PR.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch bugfix-14018-14156-14124-sample-types-ast-binding

---

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.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}

[coderabbitai]

🧹 Nitpick comments (1)

sormas-ui/src/main/java/de/symeda/sormas/ui/therapy/DrugSusceptibilityForm.java (1)

351-358: 📐 Maintainability & Code Quality | 🔵 Trivial | 💤 Low value

Null guard looks correct given existing clear-on-hide behavior.

Skipping super.commit() when getValue() is null avoids the crash while the form is unbound/inapplicable. Since updateFieldsVisibility() already clears field values whenever the disease/test-type combination doesn't apply or the DTO is null before this state, no user-entered data should be silently dropped by this guard.

One nit: a short comment on why the null check is needed (e.g., referencing the crash it prevents) would help future maintainers avoid removing it by mistake.

📝 Optional: document rationale

 	`@Override`
 	public void commit() {
+		// Guard against committing when no DrugSusceptibilityDto is bound (e.g. form hidden/inapplicable);
+		// calling super.commit() in that state previously caused a crash.
 		if (getValue() == null) {
 			return;
 		}
 		super.commit();
 	}

🤖 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/therapy/DrugSusceptibilityForm.java`
around lines 351 - 358, Add a brief inline comment in
DrugSusceptibilityForm.commit() next to the getValue() null guard explaining
that super.commit() is skipped because the form can be unbound/inapplicable and
this prevents the crash; keep the existing null check and reference the
clear-on-hide behavior/updateFieldsVisibility logic so the intent is obvious to
future maintainers.

🤖 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.

Nitpick comments:
In
`@sormas-ui/src/main/java/de/symeda/sormas/ui/therapy/DrugSusceptibilityForm.java`:
- Around line 351-358: Add a brief inline comment in
DrugSusceptibilityForm.commit() next to the getValue() null guard explaining
that super.commit() is skipped because the form can be unbound/inapplicable and
this prevents the crash; keep the existing null check and reference the
clear-on-hide behavior/updateFieldsVisibility logic so the intent is obvious to
future maintainers.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 1d030d1a-823b-464f-85c7-9a13349828d6

📥 Commits

Reviewing files that changed from the base of the PR and between a4846f6 and 87d0496.

📒 Files selected for processing (3)

• sormas-api/src/main/java/de/symeda/sormas/api/sample/SampleMaterial.java
• sormas-ui/src/main/java/de/symeda/sormas/ui/samples/diseasesection/ImiSectionComponent.java
• sormas-ui/src/main/java/de/symeda/sormas/ui/therapy/DrugSusceptibilityForm.java

💤 Files with no reviewable changes (1)

• sormas-ui/src/main/java/de/symeda/sormas/ui/samples/diseasesection/ImiSectionComponent.java