##run this to update. The current working directory needs to be the
 ##top-level directory of the SVN checkout

 
 #########################################################
 ## PLEASE READ
 ##########################################################
 # When building a new version of gstruct/gmap, remove the
 # "--disable-maintainer-mode" argument passed in src/Makefile to the
 # respective configure scripts. This was added to avoid regenerating
 # autotools artifacts on user machines (the timestamp protection fails

 # through svn).

 ##########################################################
 

 enableMaintainerMode = function() {

     mkfile = file.path("src/Makefile")
     txt = readLines(mkfile)
     txt2 = gsub("(--disable-maintainer-mode.*)", "\\\\ # \\1;", txt)
     writeLines(txt2, con = mkfile)
 }
 

 disableMaintainerMode = function() {

     mkfile = file.path("src/Makefile")
     txt = readLines(mkfile)
     txt2 = gsub("\\\\ # (.*);", "\\1", txt)
     writeLines(txt2, con = mkfile)
 }
 

 updateGMAPSrc <- function() {

 
     mkfile = 
     gmapSVNProj <-

     "http://resscm/bioinfo/projects/gmap/releases/internal-2013-10-01"

   extractDirGmap <- file.path(getwd(), "src/gmap")

   .bootstrapAndExtract(projectSVNURL=gmapSVNProj, extractDir=extractDirGmap,

                        program="gmap", bootstrap = "bootstrap.gsnaptoo")

   
 }
 updateGSTRUCTSrc <- function() {

   #gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/releases/internal-2014-04-09"

     gstructSVNProj <- "http://resscm/bioinfo/projects/gstruct/trunk"

   extractDirGstruct <- file.path(getwd(), "src/gstruct")
   .bootstrapAndExtract(projectSVNURL=gstructSVNProj,
                        extractDir=extractDirGstruct,

                        program="gstruct",
                        bootstrap = "bootstrap.Rdist")

   .copySamflagsHeader(extractDirGstruct, file.path(getwd(), "src/gmap"))

 }

 
 ###################
 ###helper functions
 ###################
 

 .bootstrapAndExtract <- function(projectSVNURL, extractDir, program,
                                  bootstrap.script)
 {

   startingDir <- getwd()
   on.exit(setwd(startingDir))

   if (file.exists(extractDir)) {
     unlink(extractDir, recursive=TRUE)
   }

   dir.create(extractDir, recursive=TRUE)

   svnCheckoutDir <- .getSVNProj(projectSVNURL, extractDir)
   on.exit(unlink(svnCheckoutDir, recursive=TRUE), add=TRUE)
   setwd(svnCheckoutDir)

   .bootstrapSVNCheckout(bootstrap.script)
   samtoolsPath <- file.path(startingDir, "src", "samtools")
   .configureSrc(program, samtoolsPath)

   .makeDist()
   .extractDistTarballIntoSrcDirectory(extractDir)
   invisible(TRUE)
 }
 
 .copySamflagsHeader <- function(extractDirGstruct, extractDirGmap) {
   ##gstruct needs samflags.h. Copying from the gmap src
   gstructSamflagsLoc <- file.path(extractDirGstruct, "src/samflags.h")
   if (!file.exists(gstructSamflagsLoc)) {
     
     gmapSamflagsLoc <- file.path(extractDirGmap, "src/samflags.h")  
     if (!file.exists(gmapSamflagsLoc)) {
       stop("Could not find the samflags.h file in the gmap src code")
     }
     
     file.copy(gmapSamflagsLoc, gstructSamflagsLoc)
   }
 }
 
 .getSVNProj <- function(projectSVNURL, extractDir) {

   ##grab from svn
   tmpDir <- file.path(tempdir(), basename(extractDir))
   dir.create(tmpDir, recursive=TRUE)
   command <- paste("svn co",
                    projectSVNURL,
                    tmpDir)
   if (!system(command) == 0) {
     stop("Could not check out project from SVN")
   }

 
   return(tmpDir)
 }
 
 ##assumes in the correct dir

 .bootstrapSVNCheckout <- function(bootstrap.script) {
   if (!system(paste0("./", bootstrap.script)) == 0) {

     stop("unable to bootstrap")
   }

 }
 

 .configureSrc <- function(program, samtoolsPath = NULL) {

   ##--with-gmapdb=${GMAPDB} --prefix=${PREFIX}
   ##configure. Set
   ##run a "make dist" to build a tarball
   command <- "./configure --disable-fulldist"

   if (!is.null(samtoolsPath)) {
       command <- paste0(command, " --with-samtools-lib=", samtoolsPath)
   }
   if (program == "gstruct") {
       command <- paste(command, "--disable-binaries")
   }

   if (!system(command) == 0) {
     stop("unable to configure")
   }
 
   ##gstruct SVN repo doesn't have config.site (this code needs to work
   ##today)
   if (program == "gstruct") {
     if (!file.exists("config.site")) {
       system("touch config.site")
     }
   }

 }
 
 .makeDist <- function() {

     system("make && make dist") ## possibly more robust than direct "make dist"

 }
 
 .extractDistTarballIntoSrcDirectory <- function(extractDir) {

   ##extract tarball into 'src' directory of package

   distTarball <- dir(pattern="*\\.tar\\.gz$", full.names=TRUE)

   if (length(distTarball) > 1) {
     stop("Found more than one tarball in directory. ",
          "Not sure which is the distribution. Aborting.")
   }

   distTarball <- tools::file_path_as_absolute(distTarball)
   if (file.exists(extractDir)) {
     unlink(extractDir, recursive=TRUE)

   }

   dir.create(extractDir, recursive=TRUE)
 
   distName <- sub("\\..*", "", basename(distTarball))

   command <- paste("tar xvf", distTarball,
                    "-C",
                    extractDir,
                    distName)
   if (!system(command) == 0) {
     stop("Could not extract source from distribution into specified directory.")
   }
 
   ##move contents of untarred dir up one level
   ##TODO: How (or can) you do this w/ a tar command?
   whereTarExtracted <- file.path(extractDir, distName)
   command <- paste("mv",
                    paste0(whereTarExtracted, "/*"),
                    extractDir)
   if (!system(command) == 0) {
     stop("Could not move extracted directory down one level")
   }
   unlink(whereTarExtracted, recursive=TRUE)
 }