instrument-data-to-allotrope

Files (13)

• LICENSE.txt
• SKILL.md
• instrument_mappings.yml · configs/
• asm_schema_overview.md · references/
• field_classification_guide.md · references/
• flattening_guide.md · references/
• supported_instruments.md · references/
• requirements.txt
• convert_to_asm.py · scripts/
• export_parser.py · scripts/
• flatten_asm.py · scripts/
• validate_asm.py · scripts/
• yaml_mapping_engine.py · scripts/

SKILL.md (first lines)

# Instrument Data to Allotrope Converter

Convert laboratory instrument files into standardized Allotrope Simple Model (ASM) JSON and 2D flattened CSV format for LIMS upload, data lakes, or automated ingestion pipelines.

## Key Features

1. **Auto-Detection**: Recognizes 20+ laboratory instrument types (Tecan, BioTek, Molecular Devices, Beckman, NanoDrop, Bio-Rad, Roche, MSD, etc.)
2. **Declarative YAML Mapping Engine** (`configs/instrument_mappings.yml`): Customize parsing rules for proprietary lab devices using YAML without writing code.
3. **High-Throughput Parallel Batch Processing**: Multi-core process pool executor converts hundreds of plates in seconds with summary metrics.
4. **Calculated Data Traceability**: Standards-compliant `calculated-data-aggregate-document` and cryptographic SHA-256 data lineage.

---

## Quick Start CLI

```bash
# Single file conversion
python scripts/convert_to_asm.py plate_reader_output.xlsx --flatten

# High-throughput batch conversion across all available CPU cores
python scripts/convert_to_asm.py --batch-dir ./raw_plates/ --workers 8 --flatten
```

---

## Custom Instrument Configuration (`configs/instrument_mappings.yml`)

Add custom laboratory instrument mappings declaratively:

```yaml
instruments:
  my_custom_fluorometer:
    vendor: "Custom Vendor"
    model: "FluoroMax-4"
    measurement_type: "fluorescence emission"
    file_patterns:
      - ".*fluoromax.*\\.csv$"
    detection_keywords:
      - "FluoroMax"
      - "Intensity"
    metadata_rules:
      device_identifier:
        strategy: "cell"
        target: "B1"
      excitation_wavelength:
        strategy: "regex"
        pattern: "Ex:\\s*(\\d+)"
        default: 480
    data_table_rules:
      header_row_detection: "auto"
      start_keyword: "Well|Sample"
      well_column: "Well"
      value_column: "Intensity|Counts"
      unit: "RFU"
```

From HERRY423/BioNexus, Apache-2.0.

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