ARCHIVE-NIHOCC(1)

💖 ARCHIVE-NIHOCC(1) 💖

okay bestie, welcome to archive-nihocc, straight out of the NCBI Entrez Direct User's Manual. she's a little script with big main character energy, and by the end of this page you two are gonna be besties. no cap. 🫶

✨ NAME ✨

archive-nihocc — the girl who maintains a local NIH Open Citation Collection archive. that's it, that's the job. 💅

🌸 SYNOPSIS 🌸

archive-nihocc [[-]daily|[-][re]index] [[-]clean|[-]clear|[-]scrub|
[-]scour|[-]scratch|[-]erase] [-ftp|-http[s]]

like, look at her. so many moods. pick one, or honestly, stack a couple — she can handle it. 😌

🦋 DESCRIPTION 🦋

so here's the tea: archive-nihocc gets a directory all cute and ready to hold a local NIH Open Citation Collection archive, then goes and downloads a full database dump and organizes the whole thing into an rchive(1) trie. it's giving prepared. it's giving organized. it's giving downloaded a whole entire database dump and didn't even complain once. 🔥

👑 OPTIONS 👑

• [-]daily — oh, you want the extra credit? this also produces or updates an inverted index on top of everything else. lowkey the overachiever option. ⭐
• [-][re]index — full reindex, bestie. and yes, it comes complete with an inverted index, because we don't do half measures around here. periodt. 💅
• [-]clean, [-]clear, [-]scrub, [-]scour, [-]scratch, [-]erase — six whole names for one job: delete Scratch directories. she has range, she has synonyms, she has a villain arc for your temp files. pick whichever one vibes with you, they all do the same thing. 💀
• -ftp — download the needed data over FTP. this is the default, so if you do nothing, you get this. she's the moment. 😌
• -http[s] — download the needed data over HTTPS instead. for when you're feeling ✨secure✨ and slightly more modern about it. 🌈

🌈 ENVIRONMENT 🌈

• EDIRECT_LOCAL_ARCHIVE — the local archive directory to use. it's expected to hold an absolute path, so no relative-path shenanigans, bestie, she will not be charmed by them. 🎀
• EDIRECT_LOCAL_WORKING — the directory that holds intermediate subtrees. also expected to hold an absolute path. when it's not set, it defaults to the local archive directory. so like, if you don't tell her where to do the messy work, she just does it in the archive. relatable tbh. 🫶

💜 SEE ALSO 💜

go follow the whole friend group, they're all iconic:

archive-nlmnlp(1), archive-nmcds(1), archive-pids(1), archive-pmc(1), archive-pubmed(1), archive-taxonomy(1), nquire(1), pm-clean(1), pm-prepare(1), pm-setup(1), rchive(1), xfetch(1), xfilter(1), xinfo(1), xlink(1), xsearch(1), xtract(1).

⚠️ quick vibe check: the clean / clear / scrub / scour / scratch / erase situation is deleting directories. that's a real delete. so be a little careful with your paths, okay? ily but she will not undo it for you. 😭

and that's the whole page, bestie. brought to you by NCBI, dated 2025-05-26. go forth and archive responsibly. mwah. 💖✨🎀🦋🌸💅🫶👑