def parse_comment_string(comment, values=None):
metadata = None
errors = []
re_key = re.compile(r'^[a-zA-Z0-9_\-]+$')
re_value = re.compile(r'^[^\x00-\x20\x7F-\xFF"]+$')
if comment.startswith('@@'):
_, metastring, comment = comment.split('@@')
metadata = {}
for key, value in [x.split('=') for x in metastring.strip().split()]:
if values:
if not key in values.keys():
errors.append('Invalid metadata key "{0}"'.format(key))
elif not values[key](value):
errors.append('Invalid metadata value "{0}"'.format(value))
else:
if not re_key.match(key):
errors.append('Invalid metadata key "{0}"'.format(key))
if not re_value.match(value):
errors.append('Invalid metadata value "{0}"'.format(value))
if key in metadata.keys():
metadata[key].append(value)
else:
metadata[key] = [value]
return comment, metadata, errors
def parse_comment_string(comment, values=None):
metadata = None
errors = []
re_key = re.compile(r'^[a-zA-Z0-9_\-]+$')
re_value = re.compile(r'^[^\x00-\x20\x7F-\xFF"]+$')
if comment.startswith('@@'):
_, metastring, comment = comment.split('@@')
metadata = {}
for key, value in [x.split('=') for x in metastring.strip().split()]:
if values:
if not key in values.keys():
errors.append('Invalid metadata key "{0}"'.format(key))
elif not value in values[key]:
errors.append('Invalid metadata value "{0}"'.format(value))
else:
if not re_key.match(key):
errors.append('Invalid metadata key "{0}"'.format(key))
if not re_value.match(value):
errors.append('Invalid metadata value "{0}"'.format(value))
if key in metadata.keys():
metadata[key].append(value)
else:
metadata[key] = [value]
return comment, metadata, errors
def iter_csv(csv_file, delimiter=",", quotechar='"'):
with open(csv_file, 'rU') as f:
csv_reader = csv.reader(f, delimiter=delimiter, quotechar=quotechar)
for i, row in enumerate(csv_reader):
if i == 0:
headers = row
if 'identifier' not in headers:
sys.stderr.write('ERROR! Missing "identifier" column.\n')
sys.exit(1)
continue
dirty_metadata = dict((k,v) for k,v in zip(headers, row))
metadata = compile_metadata(dirty_metadata)
if len(metadata.keys()) <= 1:
continue
else:
yield metadata['identifier'], metadata
