copySubstitute: Copy Between Connections or Files with Configure-Like...

In Biobase: Biobase: Base functions for Bioconductor

Description

Copy files, directory trees or between connections and replace all occurences of a symbol by the corresponding value.

Usage

copySubstitute(src, dest, symbolValues, symbolDelimiter="@", allowUnresolvedSymbols=FALSE,
               recursive = FALSE, removeExtension = "\\.in$")

Arguments

src	Source, either a character vector with filenames and/or directory names, or a connection object.
dest	Destination, either a character vector of length 1 with the name of an existing, writable directory, or a connection object. The class of the dest argument must match that of the src argument.
symbolValues	A named list of character strings.
symbolDelimiter	A character string of length one with a single character in it.
allowUnresolvedSymbols	Logical. If FALSE, then the function will execute stop if it comes across symbols that are not defined in symbolValues.
recursive	Logical. If TRUE, the function works recursively down a directory tree (see details).
removeExtension	Character. Matches to this regular expression are removed from filenames and directory names.

Details

Symbol substitution: this is best explained with an example. If the list symbolValues contains an element with name FOO and value bar, and symbolDelimiter is @, then any occurrence of @FOO@ is replaced by bar. This applies both the text contents of the files in src as well as to the filenames. See examples.

If recursive is FALSE, both src and dest must be connection or a filenames. The text in src is read through the function readLines, symbols are replaced by their values, and the result is written to dest through the function writeLines.

If recursive is TRUE, copySubstitute works recursively down a directory tree (see details and example). src must be a character vector with multiple filenames or directory names, dest a directory name.

One use of this function is in createPackage for the automatic generation of packages from a template package directory.

Value

None. The function is called for its side effect.

Author(s)

Wolfgang Huber http://www.dkfz.de/mga/whuber

Examples

## create an example file
infile  = tempfile()
outfile = tempfile()

writeLines(text=c("We will perform in @WHAT@:",
  "So, thanks to @WHOM@ at once and to each one,",
  "Whom we invite to see us crown'd at @WHERE@."),
  con = infile)

## create the symbol table
z = list(WHAT="measure, time and place", WHOM="all", WHERE="Scone")

## run copySubstitute
copySubstitute(infile, outfile, z)

## display the results
readLines(outfile)



##--------------------------------------------------------------
## This is a slightly more complicated example that demonstrates
## how copySubstitute works on nested directories
##--------------------------------------------------------------
d = tempdir()
my.dir.create = function(x) {dir.create(x); return(x)}

unlink(file.path(d, "src"), recursive=TRUE)
unlink(file.path(d, "dest"), recursive=TRUE)

## create some directories and files:
src  = my.dir.create(file.path(d, "src"))
dest = file.path(d, "dest")
d1   = my.dir.create(file.path(src, "dir1.in"))
d2   = my.dir.create(file.path(src, "dir2@FOO@.in"))
d3   = my.dir.create(file.path(d2, "dir3"))
d4   = my.dir.create(file.path(d3, "dir4"))
d5   = my.dir.create(file.path(d4, "dir5@BAR@"))
writeLines(c("File1:", "FOO: @FOO@"),     file.path(d1, "file1.txt.in"))
writeLines(c("File2:", "BAR: @BAR@"),     file.path(d2, "file2.txt.in"))
writeLines(c("File3:", "SUN: @SUN@"),     file.path(d3, "file3.txt.in"))
writeLines(c("File4:", "MOON: @MOON@"),   file.path(d4, "@SUN@.txt"))

## call copySubstitute
copySubstitute(src, dest, recursive=TRUE,
               symbolValues = list(FOO="thefoo", BAR="thebar",
                                   SUN="thesun", MOON="themoon"))

## view the result
listsrc  = dir(src,  full.names=TRUE, recursive=TRUE)
listdest = dir(dest, full.names=TRUE, recursive=TRUE)
listsrc
listdest

cat(unlist(lapply(listsrc,  readLines)), sep="\n")
cat(unlist(lapply(listdest, readLines)), sep="\n")

Biobase documentation built on Nov. 8, 2020, 6:52 p.m.