Gdr 3331

[bczech]

Description

What changed?

• add support for D300 files without mapping file
  Related JIRA issue: GDR-3331

Why was it changed?

Checklist for sustainable code base

• I added tests for any code changed/added
• I added documentation for any code changed/added
• I made sure naming of any new functions is self-explanatory and consistent

Logistic checklist

• Package version bumped
• Changelog updated

Screenshots (optional)

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly enhances the data import capabilities of the gDRimport package. It introduces greater flexibility for D300 file processing by making the metadata mapping file optional and expands the EnVision_new results loading function to seamlessly handle Excel files, alongside CSVs. These changes aim to streamline data ingestion and improve the overall robustness of the import functionalities.

Highlights

• D300 File Import Flexibility: The import_D300 function now supports D300 files without requiring a separate metadata mapping file, making the import process more flexible.
• EnVision New Results Loading Enhanced: The load_results_EnVision_new function has been updated to support both CSV and XLSX file formats, including handling multiple sheets within Excel files, and improved robustness in parsing data matrices and plate barcodes.
• XML Parsing Robustness: Improved the parsing of D300 XML files by adding checks for NULL nodes and handling missing unit information, making the process more resilient to variations in XML structure.

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[gemini-code-assist]

Code Review

This pull request updates the gDRimport package to version 1.9.9, adding support for D300 files without a mapping file and enhancing the load_results_EnVision_new function to handle both CSV and XLSX formats. Key changes include making the metadata_file parameter optional in import_D300, improving the extraction and handling of plate dimensions and drug information from D300 XML files, and making the parsing of EnVision data more robust against varied input structures and missing barcodes. All review comments were descriptive and validating, and thus no actionable feedback was identified.

[j-smola]

Please, make lintr happy.

Then add a set of test data in the new format and tests that verify that the code works as expected.

[j-smola]

Please, make lintr happy.

Where has you added a set of test data in the new format?