Manage the persistent annotation cache

build_glyanno_cache() is the magic that makes glyanno fast. It precalculates database views and annotation indexes from the installed glydb. You will only need to call this function once on your computer. When glydb is updated, you'll also need to call this function to update the cache. But don't worry. We'll remind you then.

• build_glyanno_cache() reuses a valid cache unless force = TRUE.

• glyanno_cache_info() inspects it without building it, and

• clear_glyanno_cache() removes it and clears the session cache.

Usage

build_glyanno_cache(force = FALSE)

glyanno_cache_info()

clear_glyanno_cache()

Arguments

force

Rebuild even when the cache is current.

Value

build_glyanno_cache() invisibly returns the cache file path. glyanno_cache_info() returns a list with path, status (one of "missing", "outdated", "unreadable", or "ready"), size_bytes, expected, and stored version metadata. clear_glyanno_cache() invisibly returns NULL.

Details

The cache lives in tools::R_user_dir("glyanno", "cache"). Set the glyanno.cache_dir option to use another directory. Only an explicit call to build_glyanno_cache() writes persistent data. Without a disk cache, annotation builds the required views in memory for the current session.

On interactive attachment, a startup message reminds you to build a missing, outdated, or unreadable cache. No computation or questions block attachment. The cache is invalidated by a changed glydb version, glyrepr or igraph version, R major/minor version, collation locale, or internal cache schema. Restart R after updating dependencies. Development data changes without a version bump require force = TRUE.

Cached data include concrete/generic compositions, intact/topological structures, confidence ranks, exact and compatible composition indexes, residue counts, species/type membership, floating-structure flags, masses for all built-in dictionaries, and local GlyTouCan accession keys. Structure vectors retain their parsed graphs. Arbitrary structure matching still uses glymotif at query time. Custom databases are never persisted.

A complete replacement is written before the previous cache is replaced; failed builds preserve the previous file. Only one completed cache is kept. Metadata inspection reads a small file header and checks the file size. The compressed annotation payload is loaded and validated on first use. Use force = TRUE to repair a damaged payload whose header is still valid.

Examples

glyanno_cache_info()
#> $path
#> [1] "/home/runner/.cache/R/glyanno/annotation-v1.rds"
#> 
#> $status
#> [1] "missing"
#> 
#> $size_bytes
#> [1] 0
#> 
#> $expected
#> $expected$schema
#> [1] 2
#> 
#> $expected$glydb
#> [1] "0.7.0"
#> 
#> $expected$glyrepr
#> [1] "1.1.0"
#> 
#> $expected$igraph
#> [1] "2.3.3"
#> 
#> $expected$R
#> [1] "4.6"
#> 
#> $expected$collation
#> [1] "C"
#> 
#> 
#> $stored
#> NULL
#>