archive-pubmed(1)

NAME

archive-pubmed - maintain a local NCBI PubMed archive

SYNOPSIS

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.