feat: Add Intelliflex v2.2 flat CSV format support#1184
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Extends the SingleDatasetParser to handle the v2.2 Intelliflex export format which has 47 fixed columns (vs 7) and 11 metrics per analyte region (vs 3). Key changes: - Pattern-based analyte column detection (R##: RP# prefix) alongside the existing FIXED_INPUT_COLUMNS approach for backward compatibility - New metric words and section mappings: BACKGROUND, NET MEDIAN, NET NORMALIZED MEDIAN, REPLICATE %CV, ANALYTE NAME, REGION - Analyte columns renamed from region prefixes (R25: RP1) to real names (HPV6) using ANALYTE NAME metadata columns - REGION values used as bead identifiers in Units section - DILUTION column mapped to dilution factor setting - Per-well data (well type/status, acquisition times, event counts) captured in measurement custom info - Calibration, verification, and fluidics metadata from v2.2 header columns flows through to custom info - Intelliflex structure now passes header custom_info to metadata Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Reduces diff noise in existing test files by aligning key ordering with main, making the actual content changes easy to review. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
stephenworlow
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Apr 20, 2026
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nathan-stender
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Apr 22, 2026
## Summary - Real-world Intelliflex v2.2 CSV exports include a `--DOCUMENT SIGNATURE--` footer block (serial number, data signature hashes) that was missing from the test fixture added in #1184 - These footer rows lack a `WELL LOCATION` value, creating duplicate NaN index entries in the parsed DataFrames. When `Measurement.create` looks up a location, `df.loc[location]` returns a DataFrame instead of a Series, causing `pd.isna()` to crash with "truth value of a Series is ambiguous" - Fix: strip footer lines starting at `--DOCUMENT SIGNATURE--` before passing to `read_csv`, so pandas never sees them and dtype inference stays clean - Updated the v2.2 test CSV to include a representative document signature footer ## Test plan - [x] All 773 tests pass - [x] Lint + mypy clean - [x] Verified against real-world `CO026755_P5_INTELLIFLEX (1).csv` that previously crashed 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
R##: RP#prefix) to distinguish analyte columns from fixed metadata columns, with backward-compatible fallback to theFIXED_INPUT_COLUMNSlist for older formatsANALYTE NAMEcolumns and region-based bead identifiers fromREGIONcolumnsData captured from v2.2 format
Files changed
src/allotropy/parsers/luminex_xponent/constants.py— New metric words and calculated data sectionssrc/allotropy/parsers/luminex_xponent/luminex_xponent_reader.py— ExtendedSingleDatasetParserwith pattern-based column detection, analyte renaming, section mappingssrc/allotropy/parsers/luminex_xponent/luminex_xponent_structure.py— Per-well metadata keys in count datasrc/allotropy/parsers/luminex_intelliflex/luminex_intelliflex_structure.py— Pass headercustom_infoto metadataTest plan
🤖 Generated with Claude Code