def test_guess_type():
log = logging.getLogger('test_guess_type')
log.debug('Testing function for guess the type of a file')
f = File(name=f"{os.getenv('DATADIR')}/test.txt")
assert f.guess_type() == "TXT"
def test_guess_type_default():
log = logging.getLogger('test_guess_type_default')
log.debug('Testing function to check when a default '
'type is assigned when the extension is'
'not recognised')
new_fname = f"{os.getenv('DATADIR')}/test.2020.pippo"
f = File(name=new_fname)
assert f.guess_type() == "MISC"
def test_guess_type1(rand_file):
log = logging.getLogger('test_guess_type1')
log.debug('Testing function for guess the type of a complex filename')
new_fname = f"{os.getenv('DATADIR')}/test_arch.2020.txt"
# change the basename to something more complex
os.rename(f"{os.getenv('DATADIR')}/test_arch.txt", new_fname)
f = File(name=new_fname)
# delete test type
os.remove(new_fname)
assert f.guess_type() == "TXT"
def print_changelog(self, ifile):
"""
Function that adds an entry to the CHANGELOG report
file
Parameters
----------
ifile : str
path to CHANGELOG file that will be updated.
Returns
-------
None
"""
now_str = self.dtime.strftime('%Y-%m-%d')
now_str1 = self.dtime.strftime('%Y%m%d')
lines_to_add = now_str + "\n\n"
for state, value in self.__dict__.items():
size = 0
if type(value) is set:
size = len(value)
elif type(value) is dict:
size = len(value.keys())
if size == 0: continue
types = []
for p in value:
# create File object to get its type
fObj = File(name=p)
types.append(fObj.guess_type())
# remove duplicates from list
types = list(set(types))
types = [s.lower() for s in types]
# get the changelog_details dir from config
dirname = CONFIG.get('ctree', 'chlog_details_dir')
lines_to_add += "Modification to: {0}\n\n".format(",".join(types))
lines_to_add += "Details can be found in\n" \
"{0}/changelog_details_{1}_{2}\n\n".format(dirname,
now_str1, state)
with open(ifile, 'r+') as f:
content = f.read()
f.seek(0, 0)
f.write(lines_to_add.rstrip('\r\n') + '\n\n' + content)
# Class to connect with Reseqtrack DB
db = DB(pwd=pwd, dbname=dbname)
# list with paths to be loaded
files = []
if args.file:
logger.info('File provided using -f, --file option')
if args.type is not None:
logger.debug('Type provided using -t, --type option')
f = File(name=args.file, type=args.type)
else:
logger.debug('No file type provided using -t, --type option')
logger.debug('File type will be guessed from its file extension')
f = File(name=args.file, settingsf=args.settings)
ftype = f.guess_type()
f.type = ftype
files.append(f)
elif args.list_file:
logger.info('File with paths provided using -l, --list_file option')
for path in args.list_file:
path = path.rstrip("\n")
cols = re.split(' +', path)
if len(cols) > 1:
raise Exception(f"Path provided {path} is not correct. "
f"Check format")
if args.type is not None:
logger.debug('Type provided using -t, --type option')
