R/lyxutils.r
In jefferis/paperutils: Support preparation of journal articles from LyX/pdflatex output
Defines functions
linked_from_lyx
current_lyx_tempfile
lyxexport
lyxbin
lyx
lyxhtml2html
lyx_citekeys
Documented in
current_lyx_tempfile
linked_from_lyx
lyx_citekeys
lyxexport
lyxhtml2html
#' Return all the files linked from a LyX file
#'
#' @details by default make paths absolute using normalizePath
#' @param x Path to LyX file
#' @inheritParams linked_from_ai
#' @examples
#' \dontrun{
#' linked_from_lyx('/GD/LMBD/Papers/2012fruLHNs/lyx/main.lyx')
#' linked_from_lyx(system.file('tests','testthat','testdata','lyx','test.lyx',package='paperutils'))
#' }
#' @author jefferis
#' @export
#' @family LyX,linked_from
linked_from_lyx<-function(x,AbsolutePaths=TRUE,mustWork=NA){
ll=readLines(x)
lf=grep('filename',value=TRUE,ll,useBytes=TRUE)
ff=sub("^\\s*filename\\s+(.*)","\\1",lf)
if(AbsolutePaths){
owd=setwd(dirname(x))
on.exit(setwd(owd))
ff=normalizePath(ff,mustWork=mustWork)
}
ff
}
#' Full path to most recent temporary PDF previewed by LyX
#'
#' Can also return e.g. aux file or containing directory.
#' @details Uses the modification date of the tex file in the directory to
#' choose LyX dir in case of ambiguity => last previewed file.
#' @param ftype Type of file (or 'dir' for enclosing directory)
#' @param lyxfile Optional stem or full name of LyX file
#' @param tmproot Optional path to temporary directory containing LyX tempdir
#' @return Path to current LyX temporary directory /pdf
#' @author jefferis
#' @export
#' @family LyX
#' @examples
#' \dontrun{
#' # current lyx pdf
#' current_lyx_tempfile()
#' # current lyx directory
#' current_lyx_tempfile('pdf')
#' # make sure the file is main.lyx
#' current_lyx_tempfile(lyxfile='main.lyx')
#' }
current_lyx_tempfile<-function(ftype=c('pdf','aux','dir','tex','lof'),lyxfile=NULL,tmproot=NULL){
ftype=match.arg(ftype)
# Two up from R's temp directory is place to start looking
if(is.null(tmproot)) tmproot=dirname(dirname(tempdir()))
patt="\\.tex$"
if(!is.null(lyxfile)){
# be more specific if we can
patt=paste(sub("\\.(lyx|pdf)","",lyxfile),patt,sep='')
}
cand_files<-dir(tmproot,pattern=patt,full.names=TRUE,recursive=TRUE)
# if(length(cand_files)==0) return(NA)
if(length(cand_files)>1){
# sort by mtime
df=file.info(cand_files)
cand_files=rownames(df[order(df$mtime,decreasing=TRUE)[1],])
}
res <- if(ftype=='dir') dirname(cand_files)
else sub('tex$',ftype,cand_files)
if(!length(res) || !file.exists(res))
stop("Unable to find requested LyX temp file. Please preview in LyX")
res
}
#' Export a LyX file to another format (by default xhtml)
#'
#' @param x The input file
#' @param outfile Path to output file (defaults to <infilestem>.<format>)
#' @param format The LyX shortname for the format (see details)
#' @details Look in Tools->Preferences->File Handling->File Formats->Short Name
#' to see which parameter (which differs from the format name in the
#' File->Export menu) should be passed as format.
#' @export
#' @family LyX
lyxexport <-function(x, outfile=NULL, format="xhtml") {
if(is.null(outfile)) {
outfile=paste(tools::file_path_sans_ext(x),sep=".", format)
}
rval=lyx(c("-batch","--export-to", format, shQuote(outfile), shQuote(x)))
if(rval!=0) stop("error running lyxexport")
invisible(outfile)
}
# Find lyx binary
lyxbin<-function() {
lyx=if(Sys.info()[['sysname']] == "Darwin") {
"/Applications/LyX.app/Contents/MacOS/lyx"
} else {
Sys.which('lyx')[[1]]
}
if(!nzchar(lyx) || !file.exists(lyx)) stop("Can't find lyx binary!")
lyx
}
# Call lyx command line tool
lyx<-function(args, ...) {
system2(lyxbin(), args, ...)
}
#' Convert a LyXHTML file to an html file that can be opened by Word
#'
#' LyXHTML is currently (LyX 2.1 series) the highest quality html export
#' available by default. However, it cannot be opened by word immediately
#' because it interposes a small xml type header before the html content. This
#' function removes that header and renames the file with a .html extension by
#' default.
#' @param infile path to xhtml file
#' @param outfile path to output html file (defaults to <infilestem>.<html>)
#' @family LyX
#' @export
#' @importFrom XML xmlParse saveXML xmlChildren
#' @examples
#' \dontrun{
#' lyxfile=system.file('tests/testthat/testdata/lyx/test.lyx', package='paperutils')
#' lyxhtml=tempfile(pattern = basename(lyxfile), fileext = '.xhtml')
#' lyxexport(lyxfile, outfile=lyxhtml)
#' lyxhtml2html(lyxhtml)
#' }
lyxhtml2html<-function(infile, outfile=NULL){
if(is.null(outfile))
outfile=paste0(tools::file_path_sans_ext(infile), ".html")
x=XML::xmlParse(infile)
# cut off the header
saveXML(xmlChildren(x)[[2]], file = outfile)
}
#' List the bibtex citekeys for a LyX document
#'
#' Uses latex \code{.aux} file to extract citation keys
#'
#' @details The required input is not the LyX file itself, but rather the
#' auxfile produced by a latex/bibtex run (note this is also produced by
#' biblatex). When \code{auxfile=NULL} the \code{\link{current_lyx_tempfile}}
#' is used to determine the appropriate auxfile.
#'
#' auxfiles do seem to have a variety of different formats for recording the
#' citekey list - this function has been tested for files processed using
#' \code{natbib} + \code{bibdesk}.
#'
#' @param auxfile Path to a latex aux file (see details for default behaviour)
#' @export
#' @family LyX
#' @family bib
#' @return A character vector of citation keys in the order in which they are
#' cited in the LyX document.
lyx_citekeys<-function(auxfile=NULL) {
if(is.null(auxfile)) {
auxfile=paste0(tools::file_path_sans_ext(current_lyx_tempfile()), ".aux")
}
ll=readLines(auxfile)
citel=ll[grepl('cite{', ll, fixed = T)]
citekeys=sub(".*cite\\{(.*?)\\}.*", "\\1", citel)
citekeys
}
jefferis/paperutils documentation built on Sept. 20, 2019, 10:20 a.m.
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Defines functions linked_from_lyx current_lyx_tempfile lyxexport lyxbin lyx lyxhtml2html lyx_citekeys
Documented in current_lyx_tempfile linked_from_lyx lyx_citekeys lyxexport lyxhtml2html
#' Return all the files linked from a LyX file
#'
#' @details by default make paths absolute using normalizePath
#' @param x Path to LyX file
#' @inheritParams linked_from_ai
#' @examples
#' \dontrun{
#' linked_from_lyx('/GD/LMBD/Papers/2012fruLHNs/lyx/main.lyx')
#' linked_from_lyx(system.file('tests','testthat','testdata','lyx','test.lyx',package='paperutils'))
#' }
#' @author jefferis
#' @export
#' @family LyX,linked_from
linked_from_lyx<-function(x,AbsolutePaths=TRUE,mustWork=NA){
ll=readLines(x)
lf=grep('filename',value=TRUE,ll,useBytes=TRUE)
ff=sub("^\\s*filename\\s+(.*)","\\1",lf)
if(AbsolutePaths){
owd=setwd(dirname(x))
on.exit(setwd(owd))
ff=normalizePath(ff,mustWork=mustWork)
}
ff
}
#' Full path to most recent temporary PDF previewed by LyX
#'
#' Can also return e.g. aux file or containing directory.
#' @details Uses the modification date of the tex file in the directory to
#' choose LyX dir in case of ambiguity => last previewed file.
#' @param ftype Type of file (or 'dir' for enclosing directory)
#' @param lyxfile Optional stem or full name of LyX file
#' @param tmproot Optional path to temporary directory containing LyX tempdir
#' @return Path to current LyX temporary directory /pdf
#' @author jefferis
#' @export
#' @family LyX
#' @examples
#' \dontrun{
#' # current lyx pdf
#' current_lyx_tempfile()
#' # current lyx directory
#' current_lyx_tempfile('pdf')
#' # make sure the file is main.lyx
#' current_lyx_tempfile(lyxfile='main.lyx')
#' }
current_lyx_tempfile<-function(ftype=c('pdf','aux','dir','tex','lof'),lyxfile=NULL,tmproot=NULL){
ftype=match.arg(ftype)
# Two up from R's temp directory is place to start looking
if(is.null(tmproot)) tmproot=dirname(dirname(tempdir()))
patt="\\.tex$"
if(!is.null(lyxfile)){
# be more specific if we can
patt=paste(sub("\\.(lyx|pdf)","",lyxfile),patt,sep='')
}
cand_files<-dir(tmproot,pattern=patt,full.names=TRUE,recursive=TRUE)
# if(length(cand_files)==0) return(NA)
if(length(cand_files)>1){
# sort by mtime
df=file.info(cand_files)
cand_files=rownames(df[order(df$mtime,decreasing=TRUE)[1],])
}
res <- if(ftype=='dir') dirname(cand_files)
else sub('tex$',ftype,cand_files)
if(!length(res) || !file.exists(res))
stop("Unable to find requested LyX temp file. Please preview in LyX")
res
}
#' Export a LyX file to another format (by default xhtml)
#'
#' @param x The input file
#' @param outfile Path to output file (defaults to <infilestem>.<format>)
#' @param format The LyX shortname for the format (see details)
#' @details Look in Tools->Preferences->File Handling->File Formats->Short Name
#' to see which parameter (which differs from the format name in the
#' File->Export menu) should be passed as format.
#' @export
#' @family LyX
lyxexport <-function(x, outfile=NULL, format="xhtml") {
if(is.null(outfile)) {
outfile=paste(tools::file_path_sans_ext(x),sep=".", format)
}
rval=lyx(c("-batch","--export-to", format, shQuote(outfile), shQuote(x)))
if(rval!=0) stop("error running lyxexport")
invisible(outfile)
}
# Find lyx binary
lyxbin<-function() {
lyx=if(Sys.info()[['sysname']] == "Darwin") {
"/Applications/LyX.app/Contents/MacOS/lyx"
} else {
Sys.which('lyx')[[1]]
}
if(!nzchar(lyx) || !file.exists(lyx)) stop("Can't find lyx binary!")
lyx
}
# Call lyx command line tool
lyx<-function(args, ...) {
system2(lyxbin(), args, ...)
}
#' Convert a LyXHTML file to an html file that can be opened by Word
#'
#' LyXHTML is currently (LyX 2.1 series) the highest quality html export
#' available by default. However, it cannot be opened by word immediately
#' because it interposes a small xml type header before the html content. This
#' function removes that header and renames the file with a .html extension by
#' default.
#' @param infile path to xhtml file
#' @param outfile path to output html file (defaults to <infilestem>.<html>)
#' @family LyX
#' @export
#' @importFrom XML xmlParse saveXML xmlChildren
#' @examples
#' \dontrun{
#' lyxfile=system.file('tests/testthat/testdata/lyx/test.lyx', package='paperutils')
#' lyxhtml=tempfile(pattern = basename(lyxfile), fileext = '.xhtml')
#' lyxexport(lyxfile, outfile=lyxhtml)
#' lyxhtml2html(lyxhtml)
#' }
lyxhtml2html<-function(infile, outfile=NULL){
if(is.null(outfile))
outfile=paste0(tools::file_path_sans_ext(infile), ".html")
x=XML::xmlParse(infile)
# cut off the header
saveXML(xmlChildren(x)[[2]], file = outfile)
}
#' List the bibtex citekeys for a LyX document
#'
#' Uses latex \code{.aux} file to extract citation keys
#'
#' @details The required input is not the LyX file itself, but rather the
#' auxfile produced by a latex/bibtex run (note this is also produced by
#' biblatex). When \code{auxfile=NULL} the \code{\link{current_lyx_tempfile}}
#' is used to determine the appropriate auxfile.
#'
#' auxfiles do seem to have a variety of different formats for recording the
#' citekey list - this function has been tested for files processed using
#' \code{natbib} + \code{bibdesk}.
#'
#' @param auxfile Path to a latex aux file (see details for default behaviour)
#' @export
#' @family LyX
#' @family bib
#' @return A character vector of citation keys in the order in which they are
#' cited in the LyX document.
lyx_citekeys<-function(auxfile=NULL) {
if(is.null(auxfile)) {
auxfile=paste0(tools::file_path_sans_ext(current_lyx_tempfile()), ".aux")
}
ll=readLines(auxfile)
citel=ll[grepl('cite{', ll, fixed = T)]
citekeys=sub(".*cite\\{(.*?)\\}.*", "\\1", citel)
citekeys
}
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