archive-nihocc

name	archive-nihocc
description	Use when maintaining a local NIH Open Citation Collection archive for offline citation-link lookups in EDirect workflows.
disable-model-invocation	true
user-invocable	true

archive-nihocc

Quick Start

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

When To Use This Tool

• Build a local NIH Open Citation Collection snapshot for offline PMID citation-link lookups.
• Refresh local CITED / CITES posting files after the upstream OCC bundle changes.
• Keep citation data in the standard EDirect archive layout instead of managing ad hoc zip downloads by hand.
• Rebuild index, invert, merge, and posting layers when downstream local search commands need updated citation edges.

Common Patterns

# 1) Download or refresh the local OCC archive
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-nihocc

# 2) Incrementally rebuild index and invert layers after new data arrives
archive-nihocc daily

# 3) Rebuild the full local search/postings structures
archive-nihocc -index

Recommended Workflow

1. Set EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable before invoking the script.
2. Make sure the supporting EDirect helpers and a local Go toolchain are available.
3. Run archive-nihocc to refresh the downloaded OCC bundle in the archive tree.
4. Follow with daily or -index as a separate command, depending on whether you need only incremental rebuilds or a full postings refresh.
5. Review the DWN, IDX, INV, MRG, and PST timing lines before trusting the local archive.

Guardrails

• --help and --version are not metadata-only here; they still enter archive setup logic and fail if prerequisites are missing.
• The script requires EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and a working local go compiler.
• Cleaning and indexing are mutually exclusive in one invocation; run cleanup commands separately from daily / -index.
• The cleanup aliases (clean, scrub, scour, scratch, erase) remove local scratch material and should be treated as destructive maintenance.
• The OCC zip download is large and the script warns it can take hours; do not treat this like a lightweight helper command.