Mercurial > repos > jpayne > snp_pipeline
view snp-fuse.py @ 33:b6bc9158666c
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author | jpayne |
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date | Thu, 01 Feb 2018 17:46:04 -0500 (2018-02-01) |
parents | eefdd97a6749 |
children |
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#! /usr/bin/env python3 from fuse import FUSE, FuseOSError, Operations, LoggingMixIn from multiprocessing import Process import argparse import logging import os, os.path, sys import subprocess import tarfile class ArchiveDir(LoggingMixIn, Operations): "FUSE object to open a tar.bz file and expose it as a read-only directory" def __init__(self, archive): self.archive = archive self.openfiles = {} def readdir(self, path, fh): for symbol in ['.','..']: yield symbol for name in self.archive.getnames(): yield name # def statfs(self, fh): # return dict(f_bavail=0, # f_bfree=0, # f_blocks=0, # f_bsize=0, # f_favail=0, # f_ffree=0, # f_files=0, # f_flag=0, # f_frsize=0, # f_namemax=0) def getattr(self, path, fh=None): name = os.path.basename(path) info = self.archive.getmember(name) return dict(st_atime=info.mtime, st_ctime=info.mtime, st_gid=info.gid, st_mode=info.mode, st_nlink=2, st_size=info.size, st_mtime=info.mtime) def open(self, path, flags): name = os.path.basename(path) self.openfiles[name] = self.archive.extractfile(name) def release(self, path, fh): name = os.path.basename(path) self.openfiles[name].close() del self.openfiles[name] def read(self, path, length, offset, fh): name = os.path.basename(path) fh = self.openfiles[name] fh.seek(offset) return fh.read(length=length) def start_fs(arch, mount_point): FUSE(ArchiveDir(arch), mount_point, nothreads=True, foreground=False, rdonly=True, volname="snp-fuse") #does this block? def main(archive, mount_point, command): with tarfile.open(archive, 'r:bz2') as arch: #t = Process(target=start_fs, args=(arch, mount_point), daemon=True) #t.start() start_fs(arch, mount_point) subprocess.check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr) #t.terminate() #t.join() if __name__ == '__main__': # create the default logger used by the logging mixin logger = logging.getLogger('fuse.log-mixin') logger.setLevel(logging.DEBUG) # create console handler with a higher log level ch = logging.StreamHandler() ch.setLevel(logging.DEBUG) # add the handlers to the logger logger.addHandler(ch) parser = argparse.ArgumentParser(description="mount a bzip2 archive for reading") parser.add_argument('archive') parser.add_argument('mount_point') parser.add_argument('command') args = parser.parse_args() main(**vars(args))