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.