allotrope-tier1-native-parsing-preferred

name	allotrope-tier1-native-parsing-preferred
description	Sub-skill of instrument-data-allotrope: Tier 1: Native allotropy parsing (PREFERRED) (+2).
version	1.0.0
category	science
type	reference
scripts_exempt	true

Tier 1: Native allotropy parsing (PREFERRED) (+2)

Tier 1: Native allotropy parsing (PREFERRED)

Always try allotropy first. Check available vendors directly:

from allotropy.parser_factory import Vendor

# List all supported vendors
for v in Vendor:
    print(f"{v.name}")

# Common vendors:
# AGILENT_TAPESTATION_ANALYSIS  (for TapeStation XML)
# BECKMAN_VI_CELL_BLU
# THERMO_FISHER_NANODROP_EIGHT
# MOLDEV_SOFTMAX_PRO
# APPBIO_QUANTSTUDIO
# ... many more

When the user provides a file, check if allotropy supports it before falling back to manual parsing. The scripts/convert_to_asm.py auto-detection only covers a subset of allotropy vendors.

Tier 2: Flexible fallback parsing

Only use if allotropy doesn't support the instrument. This fallback:

• Does NOT generate calculated-data-aggregate-document
• Does NOT include full traceability
• Produces simplified ASM structure

Use flexible parser with:

• Column name fuzzy matching
• Unit extraction from headers
• Metadata extraction from file structure

Tier 3: PDF extraction

For PDF-only files, extract tables using pdfplumber, then apply Tier 2 parsing.