caching: Utilities for caching of workflow data.

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Utilities for caching of workflow data.

Description

Several utility functions for caching workflow data. The most important function is clearCache; other functions are primarily for internal use.

Usage

makeHash(..., checkDT = TRUE)

makeFileHash(..., length = Inf)

loadCacheData(category, hashes, dbArg = NULL, simplify = TRUE, fixDTs = TRUE)

saveCacheData(category, data, hash, dbArg = NULL)

clearCache(what = NULL, file = NULL, vacuum = TRUE)

Arguments

...	Arguments/objects to be used for hashing.
checkDT	logical, set to TRUE with (a list with) data.tables to ensure reproducible hashing. Otherwise can be set to FALSE to improve performance.
length	Maximum file length to hash. Passed to digest.
category	The category of the object to be cached.
hashes	A character with one more hashes (e.g. obtained with makeHash) of the objects to be loaded.
dbArg	Alternative connection to database. Default is NULL and uses the cache options as defined by patRoon.cache.fileName. Mainly used internally to improve performance.
simplify	If TRUE and length(hashes)==1 then the returned data is returned directly, otherwise the data is in a list.
fixDTs	Should be TRUE if cached data consists of (nested) data.tables. Otherwise can be FALSE to speed up loading.
data	The object to be cached.
hash	The hash string of the object to be cached (e.g. obtained with makeHash).
what	This argument describes what should be done. When what = NULL this function will list which tables are present along with an indication of their size (database rows). If what = "all" then the complete file will be removed. Otherwise, what should be a character string (a regular expression) that is used to match the table names that should be removed.
file	The cache file. If NULL then the value of the patRoon.cache.fileName option is used.
vacuum	If TRUE then the VACUUM operation will be run on the cache database to reduce the file size. Setting this to FALSE might be handy to avoid long processing times on large cache databases.

Details

makeHash Make a hash string of given arguments.

makeFileHash Generates a hash from the contents of one or more files.

loadCacheData Loads cached data from a database.

saveCacheData caches data in a database.

clearCache will either remove one or more tables within the cache sqlite database or simply wipe the whole cache file. Removing tables will VACUUM the database (unless vacuum=FALSE), which may take some time for large cache files.

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.