#USING SANDVOX EXTRACTOR ARCHIVE#
#USING SANDVOX EXTRACTOR ZIP#

***Success rate in parentheses are for microsatellite loci and the CHD gene (DNA sexing) on polyacrylamide gels***Agarose gels and/or specing your DNA samples DO NOT give you an accurate idea of your DNA quality based on tests that we completed in 2006*** I modified protocols using the Qiagen DNeasy® Tissue Kit (animal tissue protocol) for the following tissue types: Protocol for isolation of total DNA from animal tissues, pp. Qiagen DNeasy® Tissue Kit - Animal Tissue Protocol Modification As new protocols are developed, they will be posted on the web site. phenol chloroform) and have found that nothing comes close to Qiagen for DNA quantity and quality especially when using small amounts of sample. I have tested numerous DNA extraction kits and old methods (e.g. A comparison of sample types varying in invasiveness for use in DNA sex determination in an endangered population of Greater Sage-Grouse (Centrocercus urophasianus). The tarfile class has not been similarly sanitized, so the above answer still apllies.Most of the following DNA extraction protocols are the web appendix for Bush, K.L., Vinsky, M.D., Aldridge, C.L., and Paszkowski, C.A. On Windows, illegal characters ( :,, |, ', ?, and *) replaced by underscore (_).

And all '.' components in a member filename will be removed, e.g. Note: If a member filename is an absolute path, a drive/UNC sharepoint and leading (back)slashes will be stripped, e.g.: ///foo/bar becomes foo/bar on Unix, and C:ooar becomes fooar on Windows.

#USING SANDVOX EXTRACTOR ZIP#

Print >stderr, finfo.name, 'is blocked: Symlink to', finfo.linknameĪr.extractall(path='./sandbox', members=safemembers(ar))Įdit: Starting with python 2.7.4, this is a non-issue for ZIP archives: The method zipfile.extract() prohibits the creation of files outside the sandbox: Print >stderr, finfo.name, 'is blocked: Hard link to', finfo.linknameĮlif finfo.islnk() and badlink(finfo,base): Print >stderr, finfo.name, 'is blocked (illegal path)'Įlif finfo.issym() and badlink(finfo,base): Tip = resolved(joinpath(base, dirname(info.name))) # Links are interpreted relative to the directory containing the link Return not resolved(joinpath(base,path)).startswith(base) # joinpath will ignore base if path is absolute

Resolved = lambda x: realpath(abspath(x)) import tarfileįrom os.path import abspath, realpath, dirname, join as joinpath I'm curious to hear if anyone can sneak any stray files or links past it. It prohibits not only the extraction of files to locations outside the sandbox (which is what was requested), but also the creation of links inside the sandbox that point to locations outside the sandbox. Since you ask for code, here's a bit that explicates the algorithm. Fortunately extractall() accepts a generator, so this is easy to do. The easiest way to do so is to wait until the previous files have been extracted and use os.path.realpath(). points to sandbox, so the path sandbox/subdir/foo/./.bashrc should be disallowed. Even a symlink that points within the sandbox can be dangerous: The symlink sandbox/subdir/foo ->. That's the aforementioned caveat: abspath will be misled if your sandbox already contains a symlink that points to a directory. This is important if you are worried about a proverbial 'malicious user' that would intentionally bypass your security, rather than an application that simply installs itself in system libraries.

#USING SANDVOX EXTRACTOR ARCHIVE#

If you normalize a path from your zipfile with abspath and it does not contain the current directory as a prefix, it's pointing outside it.īut you also need to check the value of any symlink extracted from your archive (both tarfiles and unix zipfiles can store symlinks).

To figure out where a path really points to, use os.path.abspath() (but note the caveat about symlinks as path components). Note: Starting with python 2.7.4, this is a non-issue for ZIP archives.

Using sandvox extractor