copySubstitute {Biobase} | R Documentation

## Copy Between Connections or Files with Configure-Like Name-Value Substitution

### 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")

[Package Biobase version 2.40.0 Index]