def clear(self):
if self.hmmcmd_temp_dir is not None and pisdir(self.hmmcmd_temp_dir):
try:
shutil.rmtree(self.hmmcmd_temp_dir)
except OSError as err:
print(
f"Warning: OS error while removing {self.hmmcmd_temp_dir}",
file=sys.stderr)
print(f"OS error: {err}", file=sys.stderr)
if self.phmmer_temp_dir is not None and pisdir(self.phmmer_temp_dir):
try:
shutil.rmtree(self.phmmer_temp_dir)
except OSError as err:
print(
f"Warning: OS error while removing {self.phmmer_temp_dir}",
file=sys.stderr)
print(f"OS error: {err}", file=sys.stderr)
# Shutdown server, If a temp local server was set up
if (self.setup_type == SETUP_TYPE_EGGNOG or self.setup_type
== SETUP_TYPE_CUSTOM) and self.scantype == SCANTYPE_MEM:
for dbpath, port, master_pid, workers_pids in self.servers:
shutdown_server_by_pid(master_pid, workers_pids)
self.servers = []
return
def clear(self):
if self.outdir is not None and pisdir(self.outdir):
try:
shutil.rmtree(self.outdir)
except OSError as err:
print(f"Warning: OS error while removing {self.outdir}",
file=sys_stderr)
print(f"OS error: {err}", file=sys_stderr)
return
def run(self):
directory = pjoin(self._args.directory)
if pexists(directory) and not pisdir(directory):
error('{} is not directory'.format(directory))
return -1
if not pexists(self._args.file) and pisdir(self._args.file):
error('{} is not file'.format(self._args.file))
return -1
if not pexists(directory):
makedirs(directory)
if self._args.as_qpkg:
self.extract_qpkg(self._args.file, directory)
elif self._args.as_image:
self.extract_image(self._args.file, directory)
elif self._args.file.endswith('.img'):
self.extract_image(self._args.file, directory)
elif self._args.file.endswith('.qpkg'):
self.extract_qpkg(self._args.file, directory)
else:
error('Unknown file suffix. Speicify --qpkg or --image')
return -1
return 0
def run(self):
directory = pjoin(self._args.directory)
if pexists(directory) and not pisdir(directory):
error('{} is not directory'.format(directory))
return -1
if not pexists(self._args.file) and pisdir(self._args.file):
error('{} is not file'.format(self._args.file))
return -1
if not pexists(directory):
makedirs(directory)
if self._args.as_qpkg:
self.extract_qpkg(self._args.file, directory)
elif self._args.as_image:
self.extract_image(self._args.file, directory)
elif self._args.file.endswith('.img'):
self.extract_image(self._args.file, directory)
elif self._args.file.endswith('.qpkg'):
self.extract_qpkg(self._args.file, directory)
else:
error('Unknown file suffix. Speicify --qpkg or --image')
return -1
return 0