| name | archive-pubmed |
| description | Use when maintaining a local PubMed XML archive for offline literature search, indexing, or bulk processing. |
| disable-model-invocation | true |
| user-invocable | true |
archive-pubmed
Quick Start
- Command:
archive-pubmed [download|verify|missing|index]
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/archive-pubmed
- Full reference: See references/help.md for detailed documentation
When To Use This Tool
- Maintain a local PubMed XML archive for offline literature search, text mining, or batch analysis.
- Backfill missing baseline/update files after interrupted refreshes.
- Verify downloaded gzip packages before rebuilding the search/posting layers.
- Rebuild local PubMed postings after the archive content changes.
Common Patterns
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-pubmed
archive-pubmed -missing
archive-pubmed -index
Recommended Workflow
- Set
EDIRECT_LOCAL_ARCHIVE and confirm the archive root is writable before starting.
- Make sure the required helper commands for drive setup and versioned-record refresh are present.
- Run
archive-pubmed to download new files and populate the archive.
- Use
-verify or -missing if the refresh was interrupted or you suspect archive gaps.
- Run
-index only after the data files are stable, then inspect the timing summary before using the local archive with other EDirect tools.
Guardrails
--help and --version are not safe inspection switches; they still run archive setup and can emit real helper/env failures.- The script requires
EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and pm-refresh.
-clean, -scrub, -scour, -erase, and -zap are destructive maintenance modes and must be run separately from -index.- Mixed-year archive states can force a cleanup path before reindexing; the script explicitly tells you to
-zap or -scour in some stale-data scenarios.
-stem and -strict change how text is normalized and indexed, so record them in reproducible workflows.
