viewCache: Examining and modifying the cache

In reproducible: Enhance Reproducibility of R Code

Examining and modifying the cache

Description

These are convenience wrappers around DBI package functions. They allow the user a bit of control over what is being cached.

Usage

clearCache(
  x,
  userTags = character(),
  after = NULL,
  before = NULL,
  ask = getOption("reproducible.ask"),
  useCloud = FALSE,
  cloudFolderID = getOption("reproducible.cloudFolderID", NULL),
  drv = getDrv(getOption("reproducible.drv", NULL)),
  conn = getOption("reproducible.conn", NULL),
  verbose = getOption("reproducible.verbose"),
  ...
)

## S4 method for signature 'ANY'
clearCache(
  x,
  userTags = character(),
  after = NULL,
  before = NULL,
  ask = getOption("reproducible.ask"),
  useCloud = FALSE,
  cloudFolderID = getOption("reproducible.cloudFolderID", NULL),
  drv = getDrv(getOption("reproducible.drv", NULL)),
  conn = getOption("reproducible.conn", NULL),
  verbose = getOption("reproducible.verbose"),
  ...
)

cc(secs, ..., verbose = getOption("reproducible.verbose"))

showCache(
  x,
  userTags = character(),
  after = NULL,
  before = NULL,
  drv = getDrv(getOption("reproducible.drv", NULL)),
  conn = getOption("reproducible.conn", NULL),
  verbose = getOption("reproducible.verbose"),
  ...
)

## S4 method for signature 'ANY'
showCache(
  x,
  userTags = character(),
  after = NULL,
  before = NULL,
  drv = getDrv(getOption("reproducible.drv", NULL)),
  conn = getOption("reproducible.conn", NULL),
  verbose = getOption("reproducible.verbose"),
  ...
)

keepCache(
  x,
  userTags = character(),
  after = NULL,
  before = NULL,
  ask = getOption("reproducible.ask"),
  drv = getDrv(getOption("reproducible.drv", NULL)),
  conn = getOption("reproducible.conn", NULL),
  verbose = getOption("reproducible.verbose"),
  ...
)

## S4 method for signature 'ANY'
keepCache(
  x,
  userTags = character(),
  after = NULL,
  before = NULL,
  ask = getOption("reproducible.ask"),
  drv = getDrv(getOption("reproducible.drv", NULL)),
  conn = getOption("reproducible.conn", NULL),
  verbose = getOption("reproducible.verbose"),
  ...
)

Arguments

x	A simList or a directory containing a valid Cache repository. Note: For compatibility with Cache argument, cachePath can also be used instead of x, though x will take precedence.
userTags	Character vector. If used, this will be used in place of the after and before. Specifying one or more userTag here will clear all objects that match those tags. Matching is via regular expression, meaning partial matches will work unless strict beginning (^) and end ($) of string characters are used. Matching will be against any of the 3 columns returned by showCache(), i.e., artifact, tagValue or tagName. Also, if length(userTags) > 1, then matching is by and. For or matching, use | in a single character string. See examples.
after	A time (POSIX, character understandable by data.table). Objects cached after this time will be shown or deleted.
before	A time (POSIX, character understandable by data.table). Objects cached before this time will be shown or deleted.
ask	Logical. If FALSE, then it will not ask to confirm deletions using clearCache or keepCache. Default is TRUE
useCloud	Logical. If TRUE, then every object that is deleted locally will also be deleted in the cloudFolderID, if it is non-NULL
cloudFolderID	A googledrive dribble of a folder, e.g., using drive_mkdir(). If left as NULL, the function will create a cloud folder with name from last two folder levels of the cachePath path, : paste0(basename(dirname(cachePath)), "_", basename(cachePath)). This cloudFolderID will be added to options("reproducible.cloudFolderID"), but this will not persist across sessions. If this is a character string, it will treat this as a folder name to create or use on GoogleDrive.
drv	if using a database backend, drv must be an object that inherits from DBIDriver e.g., from package RSQLite, e.g., SQLite
conn	an optional DBIConnection object, as returned by dbConnect().
verbose	Numeric, -1 silent (where possible), 0 being very quiet, 1 showing more messaging, 2 being more messaging, etc. Default is 1. Above 3 will output much more information about the internals of Caching, which may help diagnose Caching challenges. Can set globally with an option, e.g., ⁠options('reproducible.verbose' = 0) to reduce to minimal⁠
...	Other arguments. Currently, regexp, a logical, can be provided. This must be TRUE if the use is passing a regular expression. Otherwise, userTags will need to be exact matches. Default is missing, which is the same as TRUE. If there are errors due to regular expression problem, try FALSE. For cc, it is passed to clearCache, e.g., ask, userTags. For showCache, it can also be sorted = FALSE to return the object unsorted.
secs	Currently 3 options: the number of seconds to pass to clearCache(after = secs), a POSIXct time e.g., from Sys.time(), or missing. If missing, the default, then it will delete the most recent entry in the Cache.

Details

If neither after or before are provided, nor userTags, then all objects will be removed. If both after and before are specified, then all objects between after and before will be deleted. If userTags is used, this will override after or before.

cc(secs) is just a shortcut for clearCache(repo = currentRepo, after = secs), i.e., to remove any cache entries touched in the last secs seconds. Since, secs can be missing, this is also be a shorthand for "remove most recent entry from the cache".

clearCache

remove items from the cache based on their userTag or times values.

keepCache

remove all cached items except those based on certain userTags or times values.

showCache

display the contents of the cache.

By default the return of showCache is sorted by cacheId. For convenience, a user can optionally have it unsorted (passing sorted = FALSE), which may be noticeably faster when the cache is large (⁠> 1e4⁠ entries).

Value

Will clear all objects (or those that match userTags, or those between after or before) from the repository located at cachePath of the sim object, if sim is provided, or located in cachePath. Invisibly returns a data.table of the removed items.

Note

If the cache is larger than 10MB, and clearCache is used, there will be a message and a pause, if interactive, to prevent accidentally deleting of a large cache repository.

See Also

mergeCache(). Many more examples in Cache().

Examples

data.table::setDTthreads(2)

tmpDir <- file.path(tempdir(), "reproducible_examples", "Cache")
try(clearCache(tmpDir, ask = FALSE), silent = TRUE) # just to make sure it is clear

# Basic use
ranNumsA <- Cache(rnorm, 10, 16, cachePath = tmpDir)

# All same
ranNumsB <- Cache(rnorm, 10, 16, cachePath = tmpDir) # recovers cached copy
ranNumsD <- Cache(quote(rnorm(n = 10, 16)), cachePath = tmpDir) # recovers cached copy

# Any minor change makes it different
ranNumsE <- Cache(rnorm, 10, 6, cachePath = tmpDir) # different

## Example 1: basic cache use with tags
ranNumsA <- Cache(rnorm, 4, cachePath = tmpDir, userTags = "objectName:a")
ranNumsB <- Cache(runif, 4, cachePath = tmpDir, userTags = "objectName:b")
ranNumsC <- Cache(runif, 40, cachePath = tmpDir, userTags = "objectName:b")

showCache(tmpDir, userTags = c("objectName"))
showCache(tmpDir, userTags = c("^a$")) # regular expression ... "a" exactly

# Fine control of cache elements -- pick out only the large runif object, and remove it
cache1 <- showCache(tmpDir, userTags = c("runif")) # show only cached objects made during runif
toRemove <- cache1[tagKey == "object.size"][as.numeric(tagValue) > 700]$cacheId
clearCache(tmpDir, userTags = toRemove, ask = FALSE)
cacheAfter <- showCache(tmpDir, userTags = c("runif")) # Only the small one is left

data.table::setDTthreads(2)
tmpDir <- file.path(tempdir(), "reproducible_examples", "Cache")
try(clearCache(tmpDir, ask = FALSE), silent = TRUE) # just to make sure it is clear

Cache(rnorm, 1, cachePath = tmpDir)
thisTime <- Sys.time()
Cache(rnorm, 2, cachePath = tmpDir)
Cache(rnorm, 3, cachePath = tmpDir)
Cache(rnorm, 4, cachePath = tmpDir)
showCache(x = tmpDir) # shows all 4 entries
cc(ask = FALSE, x = tmpDir)
showCache(x = tmpDir) # most recent is gone
cc(thisTime, ask = FALSE, x = tmpDir)
showCache(x = tmpDir) # all those after thisTime gone, i.e., only 1 left
cc(ask = FALSE, x = tmpDir) # Cache is
cc(ask = FALSE, x = tmpDir) # Cache is already empty

reproducible documentation built on Nov. 22, 2023, 9:06 a.m.