def get_command_line():
from xia2.Handlers.CommandLine import CommandLine
CommandLine.print_command_line()
if not CommandLine.get_xinfo():
# write an xinfo file then
xinfo = os.path.join(os.getcwd(), "automatic.xinfo")
argv = CommandLine.get_argv()
if not CommandLine.get_directory():
directories = []
for arg in argv:
if os.path.isdir(arg):
directories.append(os.path.abspath(arg))
if not directories and not CommandLine.get_hdf5_master_files():
raise Sorry(
"No image directory found in command line arguments. "
"Run xia2 without any options for command line help."
)
else:
directories = CommandLine.get_directory()
directories = [os.path.abspath(d) for d in directories]
from xia2.Applications.xia2setup import write_xinfo
check_hdf5_master_files(CommandLine.get_hdf5_master_files())
if CommandLine.get_template() or CommandLine.get_hdf5_master_files():
write_xinfo(
xinfo,
directories,
template=CommandLine.get_template(),
hdf5_master_files=CommandLine.get_hdf5_master_files(),
)
else:
write_xinfo(xinfo, directories)
CommandLine.set_xinfo(xinfo)
return CommandLine
def run():
streams_off()
# test to see if sys.argv[-2] + path is a valid path - to work around
# spaced command lines
argv = CommandLine.get_argv()
if not CommandLine.get_directory():
directories = []
for arg in argv:
if os.path.isdir(arg):
directories.append(os.path.abspath(arg))
if not directories:
raise RuntimeError('directory not found in arguments')
else:
directories = [CommandLine.get_directory()]
directories = [os.path.abspath(d) for d in directories]
# perhaps move to a new directory...
settings = PhilIndex.get_python_object().xia2.settings
crystal = settings.crystal
with open(os.path.join(os.getcwd(), 'automatic.xinfo'), 'w') as fout:
start = os.path.abspath(os.getcwd())
directory = os.path.join(os.getcwd(), crystal, 'setup')
try:
os.makedirs(directory)
except OSError as e:
if not 'File exists' in str(e):
raise e
os.chdir(directory)
rummage(directories)
print_sweeps(fout)