Check an install against a lockfile, and optionally reinstall what drifted

Reads a lockfile written by taxify_lock() and reports, for each backbone and enrichment it pins, whether the currently installed asset matches – by version and byte-identity (content id) – or has drifted, or is missing.

Usage

taxify_restore(file, install = FALSE, verbose = TRUE)

Arguments

file

Path to a lockfile written by taxify_lock(), or the lock list it returned.

install

Logical. FALSE (default) verifies and reports only. TRUE downloads and activates the pinned build of every asset that does not already match.

verbose

Logical. Default TRUE.

Value

A data.frame with one row per pinned asset, columns: component, type ("backbone"/"enrichment"), locked_version, installed_version, locked_content_id and installed_content_id (short), and status ("ok", "version_drift", "content_drift", "missing", or "unverified" when what the lock pinned cannot be compared against this install). With install = TRUE the statuses describe the install afterwards, a restored column records which rows were fetched, and a pinned column which rows are now pinned (every row whose status is "ok").

Details

With install = TRUE it also fetches the exact build each row pins, from the immutable copy published beside the rolling asset, and makes it the active one: the recorded run is put back in place in a single call. The build each pinned build replaces is kept on disk under its own content id, so restoring a lockfile is reversible. Every build that matches the lock afterwards is pinned, including one that already matched and needed no download, so the next session's version check does not refresh it away from the lock. Release a pin with taxify_pin().

A build published before taxifydb began uploading an immutable copy cannot be recovered – the re-cut replaced it in place – and its row keeps reporting drift after the install pass.

See also

taxify_lock(), taxify_pin() to pin or release an installed build without a lockfile, taxify_store() for the builds on disk, taxify_download_enrichment() to fetch a single build by content id.

Examples

# Runs offline against the bundled example database.
old <- options(taxify.data_dir = taxify_example_data())

res  <- taxify("Quercus robur", backbone = "wfo", verbose = FALSE)
lock <- taxify_lock(res)
taxify_restore(lock, verbose = FALSE)

options(old)