download-pmc

name	download-pmc
description	Use when bulk-downloading PubMed Central OA tarballs across the standard PMC sections with the EDirect helper script.
disable-model-invocation	true
user-invocable	true

download-pmc

Quick Start

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

When To Use This Tool

• Mirror the PMC OA bulk XML archives in batch.
• Pull baseline and incremental tarballs from oa_comm, oa_noncomm, and oa_other.
• Retry failed downloads and verify tarball contents before keeping them.

Common Patterns

# 1) Use the default FTP-backed download mode
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/download-pmc

# 2) Force HTTPS retrieval instead of FTP-style listing
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/download-pmc -https

Recommended Workflow

1. Run it from a directory where bulk PMC tarballs are supposed to accumulate.
2. Pick -ftp or -https deliberately; FTP-style mode is the default.
3. Let the script finish its full pass over baseline and incr tarballs in all three OA sections.
4. Review stderr for retries or invalid-content deletions before treating the mirror as complete.

Guardrails

• This is a bulk operational downloader, not a one-file fetcher and not a safe probe.
• The script iterates all of oa_comm, oa_noncomm, and oa_other for both baseline and incr; there is no fine-grained selector for one archive family.
• It depends on nquire, xtract, and skip-if-file-exists being available on PATH.
• Files that download empty or fail XML verification are deleted and retried; a missing file after the run can reflect repeated validation failure, not just an interrupted transfer.