instrument-data-to-allotrope

# Instrument Data to Allotrope Converter

Convert instrument files into standardized Allotrope Simple Model (ASM) format for LIMS upload, data lakes, or handoff to data engineering teams.

> **Note: This is an Example Skill**
>
> This skill demonstrates how skills can support your data engineering tasks—automating schema transformations, parsing instrument outputs, and generating production-ready code.
>
> **To customize for your organization:**
> - Modify the `references/` files to include your company's specific schemas or ontology mappings
> - Use an MCP server to connect to systems that define your schemas (e.g., your LIMS, data catalog, or schema registry)
> - Extend the `scripts/` to handle proprietary instrument formats or internal data standards
>
> This pattern can be adapted for any data transformation workflow where you need to convert between formats or validate against organizational standards.

## Workflow Overview

1. **Detect instrument type** from file contents (auto-detect or user-specified)
2. **Parse file** using allotropy library (native) or flexible fallback parser
3. **Generate outputs**:
   - ASM JSON (full semantic structure)
   - Flattened CSV (2D tabular format)
   - Python parser code (for data engineer handoff)
4. **Deliver** files with summary and usage instructions

> **When Uncertain:** If you're unsure how to map a field to ASM (e.g., is this raw data or calculated? device setting or environmental condition?), ask the user for clarification. Refer to `references/field_classification_guide.md` for guidance, but when ambiguity remains, confirm with the user rather than guessing.

## Quick Start

```python
# Install requirements first
pip install allotropy pandas openpyxl pdfplumber --break-system-packages

# Core conversion
from allotropy.parser_factory import Vendor
from allotropy.to_allotrope import allotrope_from_file

# Convert with allotropy
asm = allotrope_from_file("instrument_data.csv", Vendor.BECKMAN_VI_CELL_BLU)
```

## Outpu