Update TOPP parameter section

[axelwalter]

User description

This update addresses issues #85 and #84.

1. TOPP tool input sections are structured based on the full parameter name (e.g. all parameter belonging to section:subsection are grouped together. If a section description is available it is displayed as help text. Removed the option to display full parameter names on the widget itself (redundant with this solution).

2. Option to display TOPP tool name.

3. Added a streamlit error box if a TOPP tool was not found instead.

---

PR Type

enhancement, bug fix

---

Description

• Added error handling to display a Streamlit error message if a specified TOPP tool is not found, improving user feedback.
• Enhanced the input_TOPP method to display tool names and organize parameters into subsections, improving the user interface.
• Improved code readability and maintainability by restructuring long lines and adding comments.
• Updated file upload and directory selection logic to handle various file types and user preferences more effectively.

---

Changes walkthrough 📝

Relevant files

Enhancement

StreamlitUI.py Enhance TOPP tool parameter handling and error messaging  src/workflow/StreamlitUI.py Added error handling for missing TOPP tools with descriptive error messages. Enhanced parameter input handling by introducing subsections and displaying tool names. Improved code formatting and readability by restructuring long lines and adding comments. Updated logic for handling file uploads and directory selections. +232/-148

---

💡 PR-Agent usage: Comment /help "your question" on any pull request to receive relevant information

[codiumai-pr-agent-pro]

PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

🎫 Ticket compliance analysis 🔶 84 - Fully compliant Fully compliant requirements: Provide a more descriptive error message if a TOPP tool is not found 85 - Fully compliant Fully compliant requirements: Improve rendering of subsections of subsections for OpenSwathWorkflow in the web app template

⏱️ Estimated effort to review: 4 🔵🔵🔵🔵⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Error Handling The error handling for TOPP tool not found has been improved, but it might be worth checking if there are any edge cases not covered. Code Complexity The input_TOPP method has become quite complex. Consider if it can be refactored into smaller, more manageable functions. Performance Concern The zip_and_download_files method reads all files into memory before creating the zip. For large directories, this could lead to memory issues.

[codiumai-pr-agent-pro]

PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Best practice	Ensure proper file handling using context managers Use a context manager for file operations to ensure proper file closure, even in case of exceptions. src/workflow/StreamlitUI.py [229-230] +with open(external_files, "a") as f_handle: + f_handle.write(f"{f}\n") - Apply this suggestion Suggestion importance[1-10]: 8 Why: The suggestion to use a context manager for file operations is valid and enhances the code by ensuring that files are properly closed even if an exception occurs. This is a best practice for file handling and improves the robustness of the code.	8
Enhancement	Optimize list comprehension for better readability and potential performance improvement Consider using a dictionary comprehension instead of a loop for creating the valid_keys list, which can be more concise and potentially more efficient. src/workflow/StreamlitUI.py [592-600] -valid_keys = [ - key +valid_keys = { + key: param.getTags(key) for key in param.keys() - if not ( - b"input file" in param.getTags(key) - or b"output file" in param.getTags(key) - or any([k.encode() in key for k in excluded_keys]) - ) -] + if not (b"input file" in param.getTags(key) or b"output file" in param.getTags(key)) +} +valid_keys = [key for key, tags in valid_keys.items() if not any(k.encode() in key for k in excluded_keys)] Apply this suggestion Suggestion importance[1-10]: 5 Why: The suggestion to use a dictionary comprehension followed by a list comprehension is a valid alternative to the existing code. It may improve readability by separating the filtering logic, but it does not significantly enhance performance.	5

💡 Need additional feedback ? start a PR chat