## file lyx-pgfsweave.R
## This file is part of LyX, the document processor.
## Licence details can be found in the file COPYING.

## author Yihui Xie

## Full author contact details are available in file CREDITS

## Rscript $$s/scripts/lyx-pgfsweave.R $$p $$i $$o $$r $$e
## arguments in order:
## 1: $$p the path of the output (temp dir)
## 2: $$i the file name of the input Rnw
## 3: $$o the tex output
## 4: $$r path to the original input file (the lyx document)
## 5: $$e encoding (e.g. 'UTF-8')

.cmdargs = commandArgs(TRUE)
message('options passed from LyX:')
print(.cmdargs)

if (is.null(getOption('lyx.use.encoding')) || isTRUE(getOption('lyx.use.encoding')))
    options(encoding = .cmdargs[5])

## the working directory is the same with the original .lyx file; you
## can put your data files there and functions like read.table() can
## work correctly without specifying the full path
setwd(.cmdargs[4])
## copy Sweave.sty and friends to $$p if kpsewhich cannot find it
if (length(system("kpsewhich Sweave.sty", intern = TRUE, ignore.stderr = TRUE)) == 0) {
    file.copy(list.files(file.path(R.home('share'), 'texmf', 'tex', 'latex'),
                         full.names = TRUE), .cmdargs[1])
}

.Rnw.basename = sub('\\.Rnw$', '', .cmdargs[2])

if (!require('pgfSweave')) {
    ## install pgfSweave if not available
    install.packages('pgfSweave', repos='http://cran.r-project.org')
    library(pgfSweave)
}

## set the dictionary to a fixed place, otherwise each time you open
## the LyX document and re-run pgfSweave you will have to generate a
## new dictionary, which is time-consuming
options(tikzMetricsDictionary = file.path(.cmdargs[4],
                                          paste('tikzDict', '-', .Rnw.basename, sep = '')),
        tikzDocumentDeclaration = grep('^\\\\documentclass',
                                       readLines(file.path(.cmdargs[1], .cmdargs[2])),
                                       value = TRUE)[1]
        )
## copy the Rnw file to the current working directory
file.copy(file.path(.cmdargs[1], .cmdargs[2]), '.', overwrite = TRUE)
## run pgfSweave() without directly generating the PDF output (tex only)
pgfSweave(.cmdargs[2], graphics.only = TRUE)
## in case users have changed the working directory in their Sweave code
setwd(.cmdargs[4])
.tex.file = .cmdargs[3]

.doc = readLines(.tex.file)

## before the tex file is passed back to LyX, we need to comment out
## these lines because otherwise a new makefile will be generated in
## the temporary dir and the cache work which has been done previously
## in the working directory will be in vain; this is a nasty trick to
## preserve the nice cache mechanism in pgfSweave
.idx = grep('^\\\\usetikzlibrary\\{external\\}|^\\\\tikzexternalize\\[mode=list and make\\]|^\\\\tikzsetnextfilename\\{|^\\\\tikzexternalfiledependsonfile\\{|^\\\\tikzset\\{external/system call=\\{xelatex', .doc)
.doc[.idx] = paste('%%', .doc[.idx])

## another nasty trick to cache graphics and tune the styles
.begin.center = .end.center = ''
if (isTRUE(getOption('lyx.graphics.center'))) {
    .begin.center = '\\begin{center}\n'
    .end.center = '\n\\end{center}'
}
.idx = grep('^\\\\input\\{.*\\.tikz\\}', .doc)
if (length(.idx)) {
    .idx2 = !grepl('{\\tikzexternaldisable', .doc[.idx-1], fixed = TRUE)
    .doc[.idx] = ifelse(.idx2,
        paste(.begin.center, '\\includegraphics', getOption('lyx.graphics.width'), '{',
              gsub('^\\\\input\\{(.*)\\.tikz\\}', '\\1', .doc[.idx]), '}', .end.center,
              sep = ''),
        paste(.begin.center, .doc[.idx], .end.center, sep = ''))
    .doc = gsub('^\\{\\\\tikzexternaldisable', '{', .doc)
}

## put the tweaked tex file to the temporary dir for LyX to compile
message('Sweave is done; now handing the tex output over to LyX')
writeLines(.doc, file.path(.cmdargs[1], .tex.file))
unlink(.cmdargs[2])

## if $$r contains spaces (strongly not recommended!!), we have to
## copy all possible R output to $$p (typically graphics output); this
## is very conservative, but we really do not know which of these
## files are needed by LaTeX
if (grepl('[[:space:]]', .cmdargs[4])) {
    warning('your working directory contains spaces: ', .cmdargs[4],
            ', but we highly recommend you not to use a directory that contains spaces')
    .files = list.files()
    .files = .files[!grepl('\\.(lyx|Rnw|tex|lyx~)$', .files)]
    message('copying these files to LyX temporary directory: ',
            paste(.files, collapse = '\n'))
    file.copy(.files, .cmdargs[1], overwrite = TRUE, recursive = TRUE)
}