def set_simg(self, target, simg):
# simg will be empty string if not provided by the user
if simg:
try:
self.replace_by_arg(target,
self.params[target].format(simg))
except KeyError:
Display.error(
what='Singularity Image for Cluster {0} '.format(
self.__class__.__name__),
info=' [ Not Supported ]',
fill='-')
self.replace_by_arg(target, '')
else:
Display.error(what='Singularity Image for Cluster {0} '.format(
self.__class__.__name__),
info=' [ not provided ]',
fill='-')
self.replace_by_arg(target, '')
def __housekeeping(self):
Display.title(title='Setting Up Working Directory for {0}'.format(
self.__class__.__name__))
try:
workdir = os.path.abspath(self.args.workdir)
except Exception:
raise Exception(
'No default or user provided Working directory was provided...'
)
else:
if workdir == settings.HOME_DIRECTORY:
Display.warning(
what="Using tool's directory as working directory ",
info=' [ Warning ]')
confirmation = input("Type 'y/Y' to proceed? ")
if not confirmation in ['y', 'Y']:
Display.error(what='You chose not to proceed ',
info=' [ ABORTING ]')
os._exit(-1)
if workdir != settings.DEFAULT_WORKDIR:
os.chdir(workdir)
else:
if workdir != settings.DEFAULT_WORKDIR:
os.chdir(workdir)
Display.info(what='{0} '.format(workdir),
info=' [ Set as Working Dirrectory ]',
fill='-')
# Creating Directory for the benchmark
print('\n')
Display.title(title='Creating Benchmark Directory for {0}'.format(
self.__class__.__name__))
self.benchmark_directory = os.path.join(
os.getcwd(),
os.path.join(
self.args.name,
os.path.join(str(date.today()), self.__class__.__name__)))
if os.path.exists(self.benchmark_directory):
contents_here = os.listdir(self.benchmark_directory)
if contents_here:
Display.info(what='{0} '.format(self.benchmark_directory),
info=' [ Directory Not Empty ]',
fill='-')
confirmation = input(
"\nType 'o/O' to override, 'b/b' for backup contents and any other key to quit?\n"
.format(self.benchmark_directory))
if confirmation in ['o', 'O']:
# Remove every thing from the directory
Display.warning(what='Overriding {0} '.format(
self.benchmark_directory),
info=' [ Warning ]',
fill='-')
os.system('rm -rf {0}'.format(
os.path.join(self.benchmark_directory, '*')))
elif confirmation in ['b', 'B']:
Display.title(title='BACKING UP CONTENTS')
Display.info(what='{0} with suffix '.format(
os.path.join(self.benchmark_directory, '*')),
info=' [ "{0}" ]'.format(
settings.DEFAULT_FILE_BACKUP_SUFFIX),
fill='-')
# Storing current working directory to get back
cwd = os.getcwd()
os.chdir(self.benchmark_directory)
for content in sorted(contents_here, reverse=True):
os.rename(
content,
content + settings.DEFAULT_FILE_BACKUP_SUFFIX)
# going back to the working directory as it was
os.chdir(cwd)
else:
Display.error(what='You chose not to proceed ',
info=' [ ABORTING ]')
sys.exit()
else:
os.system('mkdir -p {0}'.format(self.benchmark_directory))