nm.unzip: Unzip function for zipped PsN output

In qPharmetra/qpToolkit: qPharmetra R Tools

Unzip function for zipped PsN output

Description

Many large files like XML output and covariance matrices are zipped by (qPharmetra's tweaked version of) PsN. To enable the parsing function of the nm.xxx domain to operate well this function unzips these files. The unzip call is pulled from the system environment variable UNZIP_CALL on startup, or defaulted as stated below. the %s in the call is replaced with the basename (no extension) of the file to unzip. The unzip call can be modified by changing the option unzip.call. Paths are specified relative to the current directory.

Usage

nm.unzip(
  run,
  extension = ".xml",
  filename = paste(run, extension, sep = ""),
  path = file.path(getOption("nmDir", ""), run),
  tmpdir = tempfile("subdir"),
  temp = FALSE,
  outdir = ifelse(temp, tmpdir, path),
  zip.filename = file.path(path, filename),
  zip.call = getOption("unzip.call"),
  command = paste0(sprintf(zip.call, gsub(" ", "\\\\ ", zip.filename)), " -o",
    gsub(" ", "\\\\ ", outdir)),
  target = file.path(outdir, filename),
  quiet = TRUE,
  ...
)

Arguments

run	run rootname (e.g. run1)
extension	file extension of the file to unzip. Could be ".xml", or ".cov", or ".cor" or anything else that has been zipped
filename	file name (excluding path) of the filename to extract. Is automatically populated with qP workflow defaults
path	directory where run resides
tmpdir	directory to use if temp is true
temp	if true, unzip to a unique temporary file path
outdir	location for unzipped file
zip.filename	filename of the zip file to extract. Is automatically populated with qP workflow defaults
zip.call	full OS call to zip utility for unzipping. Defaults to "c:/progra~1/7-zip/7z e %s.7z" on windows. Option "-o" is currently appended by nm.unzip().
command	zip.call with filename substituted; passes to system
target	path for expected result; possibly identical to zip.filename
quiet	whether to suppress process messages
...	ignored arguments

Value

(invisible) path to the unzipped file: especially useful if temp is true.

Examples

file.exists( file.path(getOption("qpExampleDir"),"example1"))
file.exists( file.path(getOption("qpExampleDir"),"example1/example1.cov"))
nm.unzip(run = "example1", extension = ".cov",
path = file.path(getOption("qpExampleDir"),"example1"),quiet = FALSE)
file.exists( file.path(getOption("qpExampleDir"),"example1/example1.cov"))
file.remove( file.path(getOption("qpExampleDir"),"example1/example1.cov"))
file.exists('c:/progra~1/7-zip/7z.exe')
# If the above does not exist, consider:
# options(unzip.call = 'C:/my-zip-path/7z e %s.7z') # or similar
tmp <- nm.unzip(
  run = "example1", 
  extension = ".cov",
  path = file.path(
    getOption("qpExampleDir"),
    "example1"
  ),
 temp = TRUE
)
file.exists( file.path(getOption("qpExampleDir"),"example1/example1.cov"))
file.exists(tmp)

qPharmetra/qpToolkit documentation built on May 24, 2023, 8:52 a.m.