improve data_prep.R file loading approach with config file to specify…

[Neilmagi]

… which files to read in every ecoregion

Summary by Sourcery

Enhance the data loading approach in the data_prep.R script by using a configuration file to specify the files to read for each ecoregion, allowing for more dynamic and customizable data processing.

Enhancements:

• Introduce a configuration file (config.yml) to specify which files to read for each ecoregion, improving flexibility and maintainability.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request improves the data loading approach in the prep_data.R file by introducing a configuration file (YAML) to specify which files to read for each ecoregion. The changes make the data processing more flexible and configurable.

Class diagram for updated data processing in prep_data.R

classDiagram
    class process_ecoregion_data {
        -ecoregion
        -config
        +process_ecoregion_data(ecoregion, config)
    }
    class YAMLConfig {
        +load_file(path)
        +get_config_for_ecoregion(ecoregion)
    }
    class DataList {
        +lapply(names, function)
        +remove_null_entries()
    }
    process_ecoregion_data --> YAMLConfig : uses
    process_ecoregion_data --> DataList : creates

Loading

File-Level Changes

Change	Details	Files
Introduce YAML configuration for file loading	Add yaml library Create config_path variable Load YAML configuration file Update process_ecoregion_data function to accept config parameter Implement config-based file loading logic	data-raw/prep_data.R
Implement dynamic file loading based on configuration	Replace hardcoded file reading with dynamic approach Add error handling for missing configuration Add warning for missing files Implement file existence check Remove NULL entries for files not found	data-raw/prep_data.R
Update main processing loop	Modify map function call to include config parameter Return data_list instead of hardcoded list	data-raw/prep_data.R

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[sourcery-ai]

Hey @Neilmagi - I've reviewed your changes and found some issues that need to be addressed.

Blocking issues:

• Update function call to match new process_ecoregion_data signature (link)

Overall Comments:

• Consider implementing more robust error handling and logging, especially for missing files or configuration errors. The current approach of warning and continuing execution could lead to silent failures.
• The function signature change for process_ecoregion_data might break existing code. Consider maintaining backward compatibility or clearly documenting this breaking change.

Here's what I looked at during the review

• 🔴 General issues: 1 blocking issue, 1 other issue
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[sourcery-ai]

suggestion: Enhance error handling and logging for missing data files

Consider adding more detailed logging, such as which ecoregion and file type is missing. This would help in debugging and data completeness verification.

if (!file.exists(file_path)) {
  log_message <- sprintf("File not found for ecoregion '%s', file type '%s': %s", 
                         ecoregion, file_key, file_path)
  warning(log_message)
  logging::logwarn(log_message)

[sourcery-ai]

issue (bug_risk): Update function call to match new process_ecoregion_data signature

The process_ecoregion_data function now expects two arguments, but it's being called with only one. This will cause an error. Update the map call to pass both ecoregions and all_config.