archive-taxonomy

name	archive-taxonomy
description	Use when maintaining a local NCBI Taxonomy archive for offline lineage and taxon lookups in EDirect workflows.
disable-model-invocation	true
user-invocable	true

archive-taxonomy

Quick Start

• Command: archive-taxonomy [daily|-index]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/archive-taxonomy
• Full reference: See references/help.md for detailed usage

When To Use This Tool

• Build a local NCBI Taxonomy archive for offline taxon, lineage, and rank lookups.
• Refresh taxonomy records after the upstream taxdump changes.
• Rebuild postings so local EDirect searches can query taxonomy fields without going back to NCBI.
• Use this when you want taxonomy data to live inside the same EDirect local-archive structure as other databases.

Common Patterns

# 1) Refresh the local taxonomy archive
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-taxonomy

# 2) Rebuild only the incremental index and invert layers
archive-taxonomy daily

# 3) Rebuild the full local taxonomy postings set
archive-taxonomy -index

Recommended Workflow

1. Set EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable.
2. Make sure the required EDirect helpers and local Go toolchain are available.
3. Run archive-taxonomy to download the taxdump and populate the local archive.
4. Follow with daily or -index as a separate command when you need refreshed search/posting layers.
5. Check the DAT, DWN, POP, IDX, INV, COL, MRG, and PST timing blocks before relying on the rebuilt archive.

Guardrails

• --help and --version are not metadata-only; they still run real archive setup logic.
• The script depends on EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and a working local go compiler.
• Cleaning and indexing must be run as separate invocations.
• The cleanup ladder (-clean, -scrub, -scour, -erase, -zap) is destructive and removes progressively more of the local taxonomy archive.
• Default FTP mode may try Aspera-backed transfer; pick -https or -ftp explicitly if transport behavior matters.