archive-pids

name	archive-pids
description	Use when maintaining a local PubMed-to-PMCID postings archive for offline identifier crosswalks in EDirect workflows.
disable-model-invocation	true
user-invocable	true

archive-pids

Quick Start

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

When To Use This Tool

• Build a local postings archive for the PubMed PMCID field.
• Support offline PMID-to-PMCID style lookups inside a populated local EDirect archive.
• Refresh the PMCID posting data after PubMed metadata updates.
• Keep this identifier crosswalk in the same archive layout used by the rest of the PubMed local-data tools.

Common Patterns

# 1) Refresh the local PMCID postings archive
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-pids

# 2) Rebuild incremental index and invert layers after a refresh
archive-pids daily

# 3) Rebuild merged postings for downstream local queries
archive-pids -index

Recommended Workflow

1. Set EDIRECT_LOCAL_ARCHIVE and verify the target archive tree is writable.
2. Confirm pm-setup, pm-prepare, and the local Go toolchain are available.
3. Run archive-pids to refresh the underlying PMCID data.
4. Follow with daily or -index as a separate maintenance command when you need refreshed postings.
5. Check the timing summary before assuming the archive is ready for local identifier lookups.

Guardrails

• --help and --version are not safe here; they still execute archive setup and prerequisite checks.
• The script depends on EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and a working local go compiler.
• Cleaning and indexing must be separate commands.
• Cleanup aliases remove local scratch content, so treat them as destructive maintenance.
• This tool is for building the local PMCID postings archive, not for extracting a one-off ID list from stdin.