NAME¶

archive-pubmed - maintain a local NCBI PubMed archive

SYNOPSIS¶

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

DESCRIPTION¶

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

OPTIONS¶

[-]download

Download the dump but perform no further processing.

[-]verify

Verify that all downloaded files are in good shape.

[-]missing

Check for missing downloads.

[-]daily

Additionally produce or update an inverted index.

[-][re]index

Fully reindex, complete with an inverted index.

[-]clean|[-]clear

Delete Indices contents and Increment files.

[-]scrap

Delete Postings directories.

[-]scrub

Delete Indices contents, Increment files, and Postings directories.

[-]scour

Delete Indices contents, Increment files, and Postings, Data, Archive, and Sentinel directories.

[-]erase

Delete Indices contents, Increment files, Postings, Data, Archive, and Sentinel directories, and Extras directory contents.

[-]zap

Delete entire archive.

-info

Check whether the archive is complete and up to date; report what's wrong if it isn't.

-ftp

Download needed data via FTP (default).

-http[s]

Download needed data via HTTPS.

[-path] dir

Place the local archive in dir.

[-temp|-work[ing]] dir

Place intermediate subtrees in dir.

ENVIRONMENT¶

EDIRECT_LOCAL_ARCHIVE

Local archive directory to use; expected to hold an absolute path.

EDIRECT_LOCAL_WORKING

Directory to hold intermediate subtrees; expected to hold an absolute path. Defaults to the local archive directory when not set.

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).