Gdr 3299

[bczech]

Description

What changed?

Added support for multi-plate new envision format
Related JIRA issue: GDR-3299

Why was it changed?

To support multi-plate format

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 @bczech, 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 upgrades the gDRimport package's ability to process EnVision new format CSV files. The primary goal was to enable the ingestion of files containing data from multiple plates and to make the data parsing more resilient to varied or malformed readout values, ensuring a more reliable and flexible import process for experimental data.

Highlights

• Multi-plate EnVision Format Support: The load_results_EnVision_new function has been enhanced to correctly parse EnVision files containing data for multiple plates, dynamically identifying and processing each plate's data matrix.
• Robust Data Parsing and Coercion: Improved logic for extracting plate barcodes and dynamically determining plate dimensions. The ReadoutValue parsing now includes comprehensive sanitization to handle non-numeric values (e.g., 'OVR', empty strings) by coercing them to NA, preventing errors and ensuring data integrity.
• New Test Coverage: Dedicated test cases were added to validate the new multi-plate parsing capabilities and the robust handling of various ReadoutValue formats in EnVision files.

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Changelog

• DESCRIPTION
  • Updated package version from 1.9.7 to 1.9.8 and updated the release date.
• NEWS.md
  • Added a new entry for version 1.9.8, documenting support for multi-plate new EnVision format.
• R/load_files.R
  • Modified load_results_EnVision_new to iterate through multiple data matrices within a single file, supporting multi-plate EnVision format.
  • Implemented dynamic row counting for each plate to handle varying plate sizes (e.g., 96-well, 384-well).
  • Enhanced barcode extraction logic to robustly find plate barcodes, including fallback mechanisms.
  • Added explicit colClasses = 'character' and lapply(.SD, as.character) to fread to prevent data type inference issues during melting.
  • Introduced comprehensive sanitization for ReadoutValue to correctly handle and coerce non-numeric strings (like 'OVR', empty strings, 'NA', 'NAN', 'INF') to NA.
• tests/testthat/test-load_files.R
  • Added a new test_that block for load_results_EnVision_new to verify multi-plate parsing and robust ReadoutValue handling.
  • Included test cases for two plates in a single file, validating correct barcode identification and data extraction.
  • Verified that non-numeric ReadoutValue entries (e.g., 'OVR', empty strings) are correctly coerced to NA.
  • Added a test case to ensure proper error handling when a data matrix header is not found.

Activity

• The author has confirmed that tests were added for all changed/added code.
• The author has confirmed that documentation was added for all changed/added code.
• The author has confirmed that naming conventions for new functions are self-explanatory and consistent.
• The author has confirmed that the package version has been bumped.
• The author has confirmed that the changelog has been updated.

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[gemini-code-assist]

Code Review

This pull request adds support for multi-plate new Envision format files. The implementation is a significant improvement, making parsing more robust by dynamically detecting plate boundaries, barcodes, and plate dimensions. It also includes a very thorough sanitization of readout values. The new functionality is well-covered by unit tests.

My review found a couple of potential issues in edge cases which could lead to errors. I've provided specific suggestions to address these points. Overall, this is a great enhancement.

[gladkia]

Please check these two majors identified by Copilot. Otherwise LGTM. GJ!