## Configure LyX and Sweave Automatically under Windows, Mac and Ubuntu
## Author: Yihui Xie <http://yihui.name>
## License: GPL-3
## URL: http://yihui.name/en/2010/10/how-to-start-using-pgfsweave-in-lyx-in-one-minute
## This script comes with ABSOLUTELY NO WARRANTY. Please use it at your own risk.

if (compareVersion(paste(R.version$major, R.version$minor, sep='.'), '2.12.0') < 0) {
    (if (.Platform$OS.type == 'windows') winDialog else warning)(message = 'This script expects at least R 2.12.0; please update your R first.')
}

## the three lines below are nasty (force you to install and update) but they can remove lots of puzzles
if (!require("pgfSweave")) install.packages("pgfSweave", Sys.getenv('R_LIBS_USER'))
if (!require("xtable")) install.packages("xtable", Sys.getenv('R_LIBS_USER'))
if (class(x <- try(update.packages(ask = FALSE, repos = 'http://cran.r-project.org'))) == 'try-error') {
	warning('Unable to update all the packages. You have to run this script with system admin.')
	try(update.packages(Sys.getenv('R_LIBS_USER'), ask = FALSE, repos = 'http://cran.r-project.org'))
}

owd = setwd(tempdir())

## download Sweave.sty and related files
url.prefix = 'http://gitorious.org/yihui/lyx-sweave/blobs/raw/master/texmf/'
tex.files = c("bibtex/bib/RJournal.bib", "bibtex/bib/Rnews.bib", "bibtex/bst/jss.bst", "tex/latex/jss.cls", "tex/latex/omsaer.fd", "tex/latex/omsaett.fd", "tex/latex/omscmtt.fd", "tex/latex/Rd.sty", "tex/latex/Sweave.sty", "tex/latex/ts1aer.fd", "tex/latex/ts1aett.fd", "tex/latex/upquote.sty")
sapply(unique(dirname(tex.files)), dir.create, showWarnings=FALSE, recursive=TRUE)
sapply(tex.files, function(f) download.file(paste(url.prefix, f, sep=''), f))
tex.files = c('bibtex', 'tex')

layout.files = c("ctex-article-sweave.layout", "ctex-article.layout", "ctex-book-sweave.layout",
"ctex-book.layout", "ctex-report-sweave.layout", "ctex-report.layout",
"literate-article.layout", "literate-book.layout", "literate-report.layout",
"literate-scrap.inc", "literate-jss.layout", "literate-beamer.layout")

sapply(layout.files, function(f) download.file(paste("http://gitorious.org/yihui/lyx-sweave/blobs/raw/master/lyx/layouts/", f, sep = ""), f))
download.file('http://gitorious.org/yihui/lyx-sweave/blobs/raw/master/lyx-sweave-exec.R', 'lyx-sweave-exec.R')

## update the preferences file
updatePref = function(){
	dir.create(lyxscripts <- file.path(dirname(lyxpref), 'scripts'), showWarnings=FALSE)
	file.copy('lyx-sweave-exec.R', lyxscripts, overwrite = TRUE)
	xx = c("\\format \"r\" \"R\" \"R/S code\" \"\" \"\" \"\" \"document\"",
"\\format \"literate\" \"Rnw\" \"Sweave\" \"\" \"\" \"\" \"document\"",
"\\converter \"literate\" \"r\" \"R CMD Stangle $$i\" \"\"",
"\\converter \"literate\" \"latex\" \"Rscript %s%s/lyx-sweave-exec.R%s %sUTF-8%s %spgfSweave%s $$r $$p $$i > $$i.log 2>&1\" \"\"",
"\\converter \"literate\" \"pdflatex\" \"Rscript %s%s/lyx-sweave-exec.R%s %sUTF-8%s %spgfSweave%s $$r $$p $$i > $$i.log 2>&1\" \"\"")
	xx[4] = sprintf(xx[4], quote.char, lyxscripts, quote.char, quote.char, quote.char, quote.char, quote.char)
	xx[5] = sprintf(xx[5], quote.char, lyxscripts, quote.char, quote.char, quote.char, quote.char, quote.char)
	roa = function(pattern, value) {
		idx = grep(pattern, x)
		if (!length(idx)) append(x, value) else {
			x[idx] = value
			x
		}
	}
	if (file.exists(lyxpref)) {
		x = readLines(lyxpref)
		x = roa('\\\\format "r".*', xx[1])
		x = roa('\\\\format "literate".*', xx[2])
		x = roa('\\converter "literate" "r".*', xx[3])
		x = roa('\\converter "literate" "latex".*', xx[4])
		x = roa('\\converter "literate" "pdflatex".*', xx[5])
		writeLines(x, lyxpref)
	} else {
		writeLines(xx, lyxpref)
	}
	message('LyX preferences updated')
	flush.console()
}

if (.Platform$OS.type == 'windows') {

	## make sure you have installed R and LyX/MikTeX; this R script will
	## take care of the gory details which nobody wants to know except hackers
	## it was tested under Win Server 2003, Win Vista and Win 7

	miktex = length(grep('MiKTeX', system('latex --version', intern = TRUE))) > 0
	if (miktex) {
		## install an additional required LaTeX package
		system("mpm --install mptopdf")
		system("mpm --install fancyvrb")
		system("mpm --install ae")
		system("mpm --install ms")
		system("mpm --install xcolor")
		system("mpm --install pgf")
		if (length(grep('Chinese', Sys.getlocale()))) {
			system("mpm --install ctex")
			## if you are in the Chinese locale, you have to set the locale in order to call R in LyX
			Rprofile = file.path(Sys.getenv('HOME'), '.Rprofile')
			if (!file.exists(Rprofile) || !length(grep('Sys\\.setlocale', readLines(Rprofile)))) cat('if (.Platform$OS.type == "windows" && !interactive()) invisible({
	Sys.setlocale(, "Chinese (Simplified)_People\'s Republic of China.936")
	})\n', file = Rprofile, append = TRUE)
		}

		## a tricky way to get the User's directory for MikTeX
		mikreport = system("initexmf --report", intern = TRUE)
		mikpath = sub("^UserInstall: ", "", grep("^UserInstall: ", mikreport, value = TRUE))
		if (!length(mikpath)) {
			mikpath = sub("^UserData: ", "", grep("^UserData: ", mikreport, value = TRUE))
		}
		## create some directories in the 'Application Data' directory
		dir.create(mikpath, showWarnings = FALSE, recursive = TRUE)
		file.copy(tex.files, mikpath, recursive = TRUE)
		## update LaTeX filename database
		if (system("initexmf --admin --update-fndb -v") != 0) {
			system("initexmf --update-fndb -v")
		}
	} else {
		## you are probably using TeXLive
		texpath = file.path(Sys.getenv('USERPROFILE'), 'texmf')
		dir.create(texpath, showWarnings = FALSE, recursive = TRUE)
		file.copy(tex.files, texpath, recursive = TRUE)
		try(system(sprintf('texhash %s', shQuote(normalizePath(texpath)))), TRUE)
	}
	message('required LaTeX packages installed')
	flush.console()

	lyxpath = head(grep('.*(lyx)([0-9]+)$', list.files(Sys.getenv("APPDATA"), full.names=TRUE), ignore.case=TRUE, value=TRUE), 1)
	if (!length(lyxpath)) lyxpath = file.path(Sys.getenv("APPDATA"), "LyX16")
	try(file.remove(file.path(lyxpath, list.files(lyxpath, '\\.lst$'))), silent=TRUE)
	dir.create(file.path(lyxpath, 'layouts'), showWarnings = FALSE, recursive = TRUE)
	file.copy(layout.files, file.path(lyxpath, 'layouts'), overwrite=TRUE)
	message('required LyX layouts installed')

	## configure LyX
	lyxpref = file.path(lyxpath, 'preferences')
	quote.char = "\\\""
	updatePref()

	## put R's bin path to the system PATH variable
	if (shell('R --version') != 0) {
		system(paste('setx PATH "', normalizePath(file.path(R.home(), 'bin')), ';', Sys.getenv('PATH'), '"', sep = ''))
	}

	## try really hard to find where is LyX in your system
	if (!inherits(try({
			lyxinstall = readRegistry("LyX.Document\\Shell\\open\\command", "HCR")
		}, silent = TRUE), "try-error")) {
		    lyxinstall = dirname(gsub("(^\"|\" \"%1\"$)", "", lyxinstall[[1]]))
		    lyxbin = file.path(lyxinstall, 'LyX.exe')
	} else {
		lyxbin = file.path(grep('LyX', list.files(Sys.getenv('ProgramFiles'),
			full.names=TRUE), value=TRUE), 'bin', 'LyX.exe')
	}

	while (!file.exists(lyxbin)) {
		winDialog('ok', 'Oh my Gosh, I really cannot find where you installed LyX... Please select the folder containing "LyX.exe" in the next diaglog box.')
		lyxbin = file.path(choose.dir(Sys.getenv('ProgramFiles'), 'Where is LyX?'), 'bin', 'LyX.exe')
	}

	message('Please restart LyX after you see the message "The system has been reconfigured"')
	## setwd(lyxpath)
	## system(paste(shQuote(normalizePath(file.path(lyxbin, c('../../python/python.exe', '../../Resources/scripts/TeXFiles.py')))), collapse=' '))
	system(paste(shQuote(normalizePath(lyxbin)), '-x reconfigure'))
	## done! yeah!! Thank you, Microsoft Windows!
} else if (Sys.info()["sysname"] == "Linux") {
	## configuration under Ubuntu is a piece of cake
	oowd = setwd(Sys.getenv('HOME'))
	dir.create('texmf', showWarnings=FALSE)
	file.copy(file.path(oowd, tex.files), 'texmf/', recursive=TRUE)
	message('required LaTeX packages installed')
	dir.create('.lyx/layouts', showWarnings=FALSE, recursive=TRUE)
	file.copy(file.path(tempdir(), layout.files), '.lyx/layouts', overwrite=TRUE)
	message('required LyX layouts installed')
	try(file.remove(list.files('.lyx/', '\\.lst$', full.names=TRUE)), TRUE)
	lyxpref = file.path(getwd(), '.lyx/preferences')
	quote.char = "'"
        setwd(oowd)
	updatePref()
	system('lyx -x reconfigure')
} else  if (Sys.info()["sysname"] == "Darwin") {
	oowd = setwd(Sys.getenv('HOME'))
	dir.create('Library/texmf', showWarnings=FALSE)
	file.copy(file.path(oowd, tex.files), 'Library/texmf', recursive=TRUE)
	message('required LaTeX packages installed')
	lyxpath = tail(grep('^LyX', list.files('Library/Application Support', full.names=TRUE), value=TRUE), 1)
	if (!length(lyxpath)) lyxpath = 'Library/Application Support/LyX-1.6'
	lyxpath = file.path(getwd(), lyxpath)
	dir.create(file.path(lyxpath, 'layouts'), showWarnings=FALSE, recursive=TRUE)
	file.copy(file.path(tempdir(), layout.files), file.path(lyxpath, 'layouts'), overwrite=TRUE)
	message('required LyX layouts installed')
	try(file.remove(file.path(lyxpath, list.files(lyxpath, '\\.lst$'))), TRUE)
	lyxpref = file.path(lyxpath, 'preferences')
	quote.char = "'"
        setwd(oowd)
	updatePref()
	## Done! Thank you, Mac OS!
} else {
	message('I really have no idea about your OS. Sorry.')
}

setwd(owd)