download-pubmed

name	download-pubmed
description	Use when you need to bulk-download PubMed baseline or update files from NCBI's FTP server for local offline analysis.
disable-model-invocation	true
user-invocable	true

download-pubmed

Quick Start

• Command: download-pubmed [-ftp|-https] [section...]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/download-pubmed
• Full reference: See references/help.md

When To Use This Tool

• Mirror PubMed XML baselines and daily update files into local storage.
• Seed a local PubMed archive before running archive-pubmed, fetch-pubmed, or custom text-mining pipelines.
• Refresh a PubMed mirror incrementally by targeting updatefiles after an initial baseline sync.

Common Patterns

# 1) Download the default PubMed mirror set: baseline + updatefiles
download-pubmed

# 2) Use HTTPS explicitly
download-pubmed -https

# 3) Download only one section
download-pubmed baseline
download-pubmed updatefiles

Recommended Workflow

1. Run this from a clean target directory because all downloaded .xml.gz files land in the current working directory.
2. Use the no-argument form once to fetch both baseline and updatefiles, or target sections explicitly when refreshing an existing mirror.
3. Let the wrapper finish its retry and validation cycle before deciding a file is broken.
4. Feed the validated archive into local indexing or parsing workflows instead of repeatedly querying PubMed live.

Guardrails

• With no arguments, this command downloads both baseline and updatefiles, which is large.
• The local wrapper validates XML payloads and deletes bad downloads before retrying, so interrupted runs can leave partial work that must be retried.
• Output is written into the current directory; keep PubMed mirrors isolated from unrelated files.
• This script does not expose a normal --help mode in practice, so rely on the captured reference rather than probing it with arbitrary flags.