ARCHIVE-PUBMED(1)

💾 ARCHIVE-PUBMED(1) 💾

okay bestie, welcome to the NCBI Entrez Direct User's Manual page for archive-pubmed — yes that's the manual name, we're not copying the header line, we're folding it in like a lil name tag at the party 🎀

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✨ NAME ✨

archive-pubmed — bestie, it maintains a local NCBI PubMed archive. that's it, that's the whole job 💅

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🌸 SYNOPSIS 🌸

archive-pubmed [[-]download] [[-]verify] [[-]missing] [[-]daily|
[-][re]index] [[-]stem[med]] [[-]clean|[-]clear|[-]scrap|[-]scrub|
[-]scour|[-]erase|[-]zap] [-info] [-ftp|-http[s]]

like, look at all those brackets. it's giving "choose your own adventure" 😭

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🦋 DESCRIPTION 🦋

so here's the vibe: archive-pubmed prepares a directory to hold a local PubMed archive, then it goes and downloads a full database dump and auxiliary vocabulary data from NCBI's servers, then it organizes the dump into an rchive(1) trie, and then it refreshes the versioned records.

setup ➡️ download ➡️ organize ➡️ refresh. main character pipeline energy, no cap 👑

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💅 OPTIONS 💅

• [-]download — just download the dump, bestie. no further processing, we're not doing extra credit today.
• [-]verify — double-check that every single downloaded file is in good shape. vibe check on your files fr fr ✨
• [-]missing — hunt for downloads that are missing. where did they go 😭
• [-]daily — on top of everything else, produce or update an inverted index. lil daily routine 🍓
• [-][re]index — do a full reindex, inverted index and all. the whole thing. periodt.
• [-]clean | [-]clear — deletes Indices contents and Increment files. poof 🫶
• [-]scrap — deletes Postings directories. bye 👋
• [-]scrub — deletes Indices contents, Increment files, and Postings directories. it's escalating 💀
• [-]scour — deletes Indices contents, Increment files, and Postings, Data, Archive, and Sentinel directories. okay this one has range.
• [-]erase — deletes Indices contents, Increment files, Postings, Data, Archive, and Sentinel directories, and Extras directory contents. literally nothing is safe 😭
• [-]zap — delete the entire archive. absolutely unhinged. icon behaviour. ⚡

⚠️ heads up bestie: clean/clear, scrap, scrub, scour, erase, and zap are all destructive. each one deletes more than the last. zap takes the whole archive. read twice, run once, no cap 🙈

• -info — check whether the archive is complete and up to date, and if it isn't, report exactly what's wrong. your honest bestie 💖
• -ftp — download the needed data via FTP. this is the default, iykyk.
• -http[s] — download the needed data via HTTPS instead. secure girlie behaviour 🔥
• [-path] dir — put the local archive in dir. choose your home 🏡
• [-temp|-work[ing]] dir — put intermediate subtrees in dir. the lil in-between zone 🧚

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🌈 ENVIRONMENT 🌈

• EDIRECT_LOCAL_ARCHIVE — the local archive directory to use. it's expected to hold an absolute path. no relative nonsense pls.
• EDIRECT_LOCAL_WORKING — the directory to hold intermediate subtrees. also expected to hold an absolute path. when it's not set, it defaults to the local archive directory. cute, it just stays home 🫶

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👑 SEE ALSO 👑

archive-nihocc(1), archive-nlmnlp(1), archive-nmcds(1), archive-pids(1), archive-pmc(1), archive-taxonomy(1), cit2pmid(1), custom-index(1), download-ncbi-data(1), download-pubmed(1), edict(1), expand-current(1), nquire(1), pm-clean(1), pm-collect(1), pm-prepare(1), pm-refresh(1), pm-setup(1), rchive(1), ref2pmid(1), xfetch(1), xfilter(1), xinfo(1), xlink(1), xsearch(1). xtract(1).

the whole friend group, assembled 💜 (yes, that period before xtract(1) is canon, we keep the facts exactly as they are ✨)

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that's the whole page bestie, go forth and archive responsibly 🌸

NCBI · 2025-05-26 — mwah, love u, bye 💖🎀🦋