Fix TypeError when protein description is not a string

[t0mdavid-m]

Handle cases where protein description values may be non-string types (e.g., NaN, float) by explicitly converting to string before truncation. This prevents "TypeError: object of type 'float' has no len()" errors when parsing FLASHTnT results.

Summary by CodeRabbit

• Bug Fixes
  • Improved robustness of protein description handling to safely process and truncate descriptions regardless of input data type.

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Walkthrough

A lambda function for truncating protein descriptions in src/parse/tnt.py is updated to coerce input values to strings before performing slicing and length checks, improving type safety and preventing potential failures when non-string types are present.

Changes

Cohort / File(s)	Summary
Description truncation type safety src/parse/tnt.py	Lambda function updated to wrap input with str() before slicing and length validation: lambda x: str(x)[:50] + '...' if len(str(x)) > 50 else str(x)

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~5 minutes

• Single file with a focused, straightforward logic tweak
• Type coercion pattern is clear and direct
• No structural or control flow changes to verify

Poem

🐰 A string so unsure of its form,
Now safely coerced to the norm!
No more type despair,
With str() care,
Descriptions truncated with charm! ✨

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run @coderabbitai generate docstrings to improve docstring coverage.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and specifically describes the main functional change—fixing a TypeError caused by non-string protein descriptions.

✨ Finishing touches

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🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/tnt-protein-description-type-error

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/parse/tnt.py (1)

36-38: String coercion in description truncation correctly fixes the TypeError

Casting x to str before slicing/len is the right fix and will prevent the "object of type 'float' has no len()" error when descriptions are NaN/floats, while keeping the original truncation behavior. Looks good.

If you want to tighten this up a bit, you could (optionally) avoid repeated str(x) calls and make the NA handling explicit via a small helper:

-    protein_df['description'] = protein_df['description'].apply(
-        lambda x: str(x)[:50] + '...' if len(str(x)) > 50 else str(x)
-    )
+    def _truncate_description(x):
+        # Treat missing values as empty; everything else is stringified
+        if pd.isna(x):
+            s = ""
+        else:
+            s = str(x)
+        return s[:50] + "..." if len(s) > 50 else s
+
+    protein_df['description'] = protein_df['description'].apply(_truncate_description)

This keeps the bug fix, improves readability, and avoids rendering missing values as the literal strings "nan"/"None".

If you adopt this, please re-run a small sample through parseTnT to confirm the UI/reporting still shows descriptions as expected, especially for NaN/missing descriptions.

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 2a74955 and 05aa44a.

📒 Files selected for processing (1)

• src/parse/tnt.py (1 hunks)

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