organize_excel_files.md

Used by the gen-excel Makefile target. No tool.poetry.scripts alias in the pyproject.toml file.

This Python script is designed to organize Excel files based on the categorization derived from a MIxS schema. It sorts files into directories corresponding to different schema classifications such as Checklists and Extensions. Here's a breakdown of the script's operations and structure:

1. Imports and Setup:

   • Imports necessary modules including os for directory manipulations, shutil for file operations, defaultdict from collections for data aggregation, SchemaView from linkml_runtime for schema operations, and logging and argparse for logging and command-line interface management.

2. Class Definition: MIxSExcelFileOrganizer:

   • A class is defined to encapsulate all functionality related to file organization based on a MIxS schema.
   • Constructor (__init__):
     • Takes paths to the MIxS schema file, the source directory containing Excel files, and the base destination folder.
     • Initializes a logger for the class.
   • Method: setup_logger:
     • Configures and returns a logger object for logging information and warnings.
   • Method: organize_files:
     • Loads the schema using SchemaView and identifies classes categorized as "Checklist" and "Extension".
     • Organizes classes by their type and associations into a results dictionary.
     • For each extension class, attempts to copy its corresponding Excel file from the source directory to a new ' extensions_only' directory.
     • For each checklist class, copies its associated Excel files and those of any related classes into categorized directories.
     • Logs warnings for any Excel files that are expected but not found in the source directory.

3. Command-Line Interface Setup:

   • Uses argparse to create a CLI that requires users to specify paths for the schema file, source directory, and destination folder.
   • Provides a default path for the schema file and makes the source and destination folder paths required arguments, ensuring that the user provides these essential inputs.

4. Script Execution:

   • The script is designed to be run from the command line. It parses arguments provided by the user and creates an instance of MIxSExcelFileOrganizer with these inputs.
   • Calls the organize_files method to perform the file organization based on the schema-defined classifications.

Detailed Observations:

• Effective Use of Libraries: The script effectively utilizes Python's built-in libraries and external modules to handle file and directory operations, logging, and command-line interactions.
• Structured and Modular Code: By encapsulating functionality within a class and using methods for specific tasks, the script maintains a clean and modular code structure that enhances readability and maintainability.
• Advanced File Management: Demonstrates complex file management tasks including conditional file copying based on schema-derived logic, and dynamic directory creation based on schema categories.

Overall Analysis:

• The script is well-organized and serves a specific functional purpose of categorizing and organizing Excel files based on a schema classification. It provides robust error handling and user interaction through command-line arguments, making it a practical tool for managing dataset files according to a predefined schema structure.