Possible (ugly) fix for Windows path length errors

[bandrewfox]

Due to the file/path name length limit in Windows, the getFirehouseData does not work for many downloads. This is a known issue in the documentation of RTCGAToolbox.

So, I grabbed the code and made an ugly fix which I haven't tested too much... but maybe someone else can take it from here? Also, it requires installing 7-zip. I have only tested this using the rnaseqv2 files and nothing else... But it does work nicely for me.

In getFirehouseData.R, after line 234, replace the "untar" and "rename" commands with this:

    if (length(fileList) == 1 & nchar(fileList) > 200) {
      ## in windows, need to use 7zip for long filenames (I don't know if 200 is the right limit - needs some testing to be sure!!)
      # should also somehow check if this is a windows platform and if 7zip is installed

      # clear out any previous tmp dirs
      unlink(c("tmp1", "tmp3"), recursive = T)

      system(paste("C:/Progra~1/7-Zip/7z e -otmp1", tcgafile))
      tmp2.long.tar = paste("tmp1/", list.files("tmp1", pattern="*.tar"), sep="")
      write(paste("renaming file", tmp2.long.tar, sep=""), stderr() )
      file.copy(from=tmp2.long.tar,to="tmp1/tmp2.tar")

      system("C:/Progra~1/7-Zip/7z e -otmp3 tmp1/tmp2.tar")
      tmp3.long.txt = paste("tmp3/", list.files("tmp3", pattern = searchName), sep="")
      if (length(tmp3.long.txt) != 1) {
        stop("Can't find output file")
      }
      file.rename(from=tmp3.long.txt,to=destfile)
      unlink(c("tmp1", "tmp3"), recursive = T)

    } else {
      untar(tcgafile,files=fileList)
      file.rename(from=fileList,to=destfile)
    }

[lwaldron]

Was reminded of this by someone in my lab having the problem... Mehmet, are you going to apply this fix?

[mksamur]

This is a good question with different components. :) I don't like the idea
of using external tools but I also don't like the problem. I think I'll
integrate this but I will also control it with a parameter. By default it
will be OFF even on Windows machine and users then can turn it on if they
force it.

On Thu, Jan 28, 2016 at 5:26 AM, Levi Waldron notifications@github.com
wrote:

Was reminded of this by someone in my lab having the problem... Mehmet,
are you going to apply this fix?

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