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feat: MSD Workbench - Update support for CSV format and Calc Conc CV handling#1157

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nathan-stender merged 1 commit into
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jleinas-msd-csv
Mar 26, 2026
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feat: MSD Workbench - Update support for CSV format and Calc Conc CV handling#1157
nathan-stender merged 1 commit into
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jleinas-msd-csv

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Changes:

  • Updated msd_workbench_reader.py to detect and handle both CSV formats:
    • Old format: Plate ID with trailing commas
    • New format: Plate ID without commas (line 1 = plate ID, line 2 = headers)
  • Added support for "Calc. Conc. CV" calculated data column
  • Improved column name handling to support both "Dilution Factor" and "Dilution"
  • "Calc. Conc. CV" now properly appears in calculated data documents
  • "Dilution" field now correctly consumed by dilution factor setting

… column

This commit adds support for a new MSD Workbench CSV format where the plate ID
appears on the first line without trailing commas (e.g., "Plate_TEST001" instead
of "Plate_TEST001,,,,,,,,,,,,,,,,").

Changes:
- Updated msd_workbench_reader.py to detect and handle both CSV formats:
  - Old format: Plate ID with trailing commas
  - New format: Plate ID without commas (line 1 = plate ID, line 2 = headers)
- Added support for "Calc. Conc. CV" calculated data column
- Improved column name handling to support both "Dilution Factor" and "Dilution"
- Added msd_workbench_test_2.csv test file with dummy data for new format
- Updated test_msd_workbench_xlsx.json to properly classify calculated data fields

Calculated Data Improvements:
- "Calc. Conc. CV" now properly appears in calculated data documents
- "Dilution" field now correctly consumed by dilution factor setting

All existing tests pass with full backwards compatibility maintained.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@james-leinas
james-leinas requested review from a team and slopez-b as code owners March 26, 2026 21:37
Comment thread src/allotropy/parsers/msd_workbench/msd_workbench_structure.py
@nathan-stender
nathan-stender merged commit 0fbfa21 into main Mar 26, 2026
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@nathan-stender
nathan-stender deleted the jleinas-msd-csv branch March 26, 2026 21:48
nathan-stender added a commit that referenced this pull request Mar 27, 2026
### Added

- MSD Workbench - Update support for CSV format and Calc Conc CV
handling (#1157)
- Add XLSX support to MSD Workbench parser (#1154)

### Fixed

- Thermo Skanit - Initialize plate_well_count to prevent
UnboundLocalError (#1156)
- AppBio QuantStudio Design & Analysis - Check for valid rq values
before setting r_sample and r_target (#1138)
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2 participants