Add convenience function for retrieving parameters

[t0mdavid-m]

Summary by CodeRabbit

• New Features
  • Enhanced parameter management for TOPP tools with automatic merging of default settings from configuration files with user-specified parameters.

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[coderabbitai]

📝 Walkthrough

Walkthrough

Added a new public method to ParameterManager that retrieves merged TOPP tool parameters by loading defaults from an ini file, extracting tool-specific parameters, and overlaying user-provided JSON values to produce a consolidated parameter dictionary.

Changes

Cohort / File(s)	Summary
TOPP Parameter Retrieval src/workflow/ParameterManager.py	Added get_topp_parameters(tool: str) method that loads ini file defaults for a specified TOPP tool, extracts parameters matching the tool-specific prefix pattern (tool:1:...), merges with user-provided JSON overrides, and returns the consolidated parameter dictionary. Returns empty dict if ini file is absent.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 A parameter manager, wise and keen,
Now gathers TOPP defaults unseen,
Merges ini files with user's say,
Creating harmony in every way!
Default and override, hand in hand—
Configuration magic across the land! ✨

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Add convenience function for retrieving parameters' accurately summarizes the main change: a new public method get_topp_parameters() was added to ParameterManager for convenient parameter retrieval.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch add_parameter_convenience

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[coderabbitai]

Actionable comments posted: 1

📜 Review details

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 546e091 and 4c4fdd2.

📒 Files selected for processing (1)

• src/workflow/ParameterManager.py

🔇 Additional comments (2)

src/workflow/ParameterManager.py (2)

101-114: LGTM! Clear method signature with defensive check.

The method signature, docstring, and defensive check for ini file existence are well-implemented. The documentation clearly explains the purpose and return behavior.

---

120-133: LGTM! Merge logic correctly implemented.

The implementation correctly:

• Extracts parameters with the tool-specific prefix
• Handles both bytes and string keys from the pyopenms API
• Merges user overrides on top of defaults using update()

The logic is consistent with the existing parameter handling patterns in save_parameters().

[coderabbitai]

⚠️ Potential issue | 🟠 Major

Add error handling for corrupted ini files.

The ParamXMLFile().load() call lacks error handling for corrupted or malformed ini files, which could raise an unhandled exception and disrupt the application. Compare this with get_parameters_from_json() (lines 94-99), which includes a try-except block to handle invalid JSON files gracefully.

🔎 Proposed fix with error handling

     # Load defaults from ini file
     param = poms.Param()
-    poms.ParamXMLFile().load(str(ini_path), param)
+    try:
+        poms.ParamXMLFile().load(str(ini_path), param)
+    except Exception:
+        st.error(f"**ERROR**: Failed to load ini file for tool '{tool}'. File may be corrupted.")
+        return {}

🤖 Prompt for AI Agents

In src/workflow/ParameterManager.py around lines 116-118, the
poms.ParamXMLFile().load(...) call lacks error handling for malformed/corrupted
ini files; wrap that load call in a try/except block (matching the pattern used
in get_parameters_from_json at lines 94-99), catch parsing/file exceptions
(catch Exception as e if no specific poms exception is available), log the error
including exception details (using the module logger or logging.exception), and
then fall back to an empty/default poms.Param() or return/continue gracefully so
the application does not crash.