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prep_dat <- function(rebuild=FALSE, overwrite, pkgdir) {
cat("\n")
# if 'pkgdir' argument is unspecified, assume it is the current working directory
if (missing(pkgdir)) {
pkgdir <- normalizePath(".")
cat("Package root directory:", pkgdir, "\n\n")
}
# check if package root directory actually exists and that it has
# a DESCRIPTION file with "Package: metadat" in the first line
if (dir.exists(pkgdir)) {
if (!file.exists(paste0(pkgdir, "/DESCRIPTION")))
stop("No DESCRIPTION file in the package root directory.")
if (readLines(paste0(pkgdir, "/DESCRIPTION"), n=1) != "Package: metadat")
stop("DESCRIPTION file in the package root directory is not for the 'metadat' package.")
} else {
stop("Specified 'pkgdir' directory does not exist.")
}
data_raw.dir <- paste0(pkgdir, "/data-raw/")
data.dir <- paste0(pkgdir, "/data/")
man.dir <- paste0(pkgdir, "/man/")
# check that directories actually exist
if (!dir.exists(data_raw.dir))
stop("Cannot find 'data-raw' directory.")
if (!dir.exists(data.dir))
stop("Cannot find 'data' directory.")
if (!dir.exists(man.dir))
stop("Cannot find 'man' directory.")
# load .rfiles.txt (if it exists)
if (file.exists(paste0(data_raw.dir, ".rfiles.txt"))) {
.rfiles <- read.table(paste0(data_raw.dir, ".rfiles.txt"), header=FALSE, as.is=TRUE)[[1]]
} else {
.rfiles <- NULL
}
# try running Rscript
tmp <- try(suppressWarnings(system2("Rscript", args="-e 1", stdout=TRUE, stderr=TRUE)), silent=TRUE)
if (inherits(tmp, "try-error"))
stop("Cannot run 'Rscript'. Make sure that Rscript/Rscript.exe is on the system path.")
# get names of all data preparation scripts (.r/.R files) in the 'data-raw' directory
rfiles <- list.files(path=data_raw.dir, pattern=".[rR]$")
# paste header for output
cat("File", paste0(rep(" ", max(nchar(rfiles))-4), collapse=""), "new ", "rda ", "build ", "Rd ", "create", "\n")
cat(paste0(rep("-", max(nchar(rfiles))+29), collapse=""), "\n")
# process all data preparation scripts
for (i in seq_along(rfiles)) {
# paste name of the data preparation script (and enough space to align everything)
cat(rfiles[i], paste0(rep(" ", max(nchar(rfiles))-nchar(rfiles[i])+1), collapse=""))
# check if the data preparation file is already in .rfiles.txt
rfile.exists <- rfiles[i] %in% .rfiles
# [new]: paste T/F if it is a new script or not
cat(ifelse(!rfile.exists, "T ", "F "))
# get 'root' name of the data preparation script (remove .r/.R extension)
root <- substr(rfiles[i], 1, nchar(rfiles[i])-2)
# get names of all .rda files in the 'data' directory
rda.files <- list.files(path=data.dir, pattern=".rda$")
# grep names of all <root>.<anything>.rda files (could be one or multiple)
rda.files <- grep(paste0("^", root, ".*.rda"), rda.files, value=TRUE)
# check if <root>.<anything>.rda files already exist
rda.files.exist <- ifelse(length(rda.files) > 0, TRUE, FALSE)
# [rda]: paste T/F if the rda files already exist or not
cat(ifelse(rda.files.exist, "T ", "F "))
# if rebuild=TRUE or if the rda files do not exist, try running the data preparation script
# [build]: paste T/F if the data processing script was run (without error)
if (rebuild || !rda.files.exist) {
#rfilerun <- try(source(paste0(data_raw.dir, rfiles[i])), silent=TRUE)
#if (inherits(rfilerun, "try-error")) {
# run each script in its own independent process
cmd <- paste0(data_raw.dir, rfiles[i])
out <- suppressWarnings(system2("Rscript", cmd, stdout=TRUE, stderr=TRUE))
if (isTRUE(attributes(out)$status == 1)) {
warning("Error while running ", rfiles[i], ".", call.=FALSE)
cat("F ")
} else {
cat("T ")
}
} else {
cat("F ")
}
# list all files in the 'data' directory (possibly includes non-.rda files)
data.files <- list.files(path=data.dir)
# check if there are now any non-.rda files in 'data'; if so, throw an error
if (any(tools::file_ext(data.files) != "rda"))
stop("\n\nThere are non-.rda files in the 'data' directory.\nData preparation scripts must create only .rda files.")
# check if <root>.Rd file exists in 'man' directory
rd.exists <- file.exists(paste0(man.dir, root, ".Rd"))
# [Rd]: paste T/F if <root>.Rd file exists or not
if (rd.exists) {
cat("T ")
} else {
cat("F ")
}
# if it doesn't exist or if it is in 'overwrite' vector, create template <root>.Rd file
# [create]: paste T/F if template <root>.Rd file is created
if (!rd.exists || !missing(overwrite) && paste0(root, ".Rd") %in% overwrite) {
cat("T ")
.rd_generator(root, pkgdir, overwrite)
} else {
cat("F ")
}
cat("\n")
}
# make sure every .rda file in 'data' is lower case
for (data.file in data.files) {
file.rename(paste0(data.dir, data.file), paste0(data.dir, tolower(data.file)))
}
# write updated .rfiles.txt file to 'data-raw' directory
write.table(rfiles, file=paste0(data_raw.dir, ".rfiles.txt"), row.names=FALSE, col.names=FALSE)
cat("\n")
}
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