def is_time_valid(time):
try:
return match(r"([0-1][0-9]|[2][0-3]):[0-5][0-9]:[0-5][0-9]",
time).group(0)
except:
raise ArgumentTypeError("Invalid format for time provided")
def is_positive_integer(supposed_positive):
value = int(supposed_positive)
if value <= 0:
raise ArgumentTypeError('{0} is not an positive integer'.format(value))
return value
def __call__(self, string):
"""Parse `string` and return `self.key_value_class()` instance.
The best of `self.separators` is determined (first found, longest).
Back slash escaped characters aren't considered as separators
(or parts thereof). Literal back slash characters have to be escaped
as well (r'\\').
"""
class Escaped(str):
"""Represents an escaped character."""
def tokenize(string):
"""Tokenize `string`. There are only two token types - strings
and escaped characters:
tokenize(r'foo\=bar\\baz')
=> ['foo', Escaped('='), 'bar', Escaped('\\'), 'baz']
"""
tokens = ['']
characters = iter(string)
for char in characters:
if char == '\\':
char = next(characters, '')
if char not in self.special_characters:
tokens[-1] += '\\' + char
else:
tokens.extend([Escaped(char), ''])
else:
tokens[-1] += char
return tokens
tokens = tokenize(string)
# Sorting by length ensures that the longest one will be
# chosen as it will overwrite any shorter ones starting
# at the same position in the `found` dictionary.
separators = sorted(self.separators, key=len)
for i, token in enumerate(tokens):
if isinstance(token, Escaped):
continue
found = {}
for sep in separators:
pos = token.find(sep)
if pos != -1:
found[pos] = sep
if found:
# Starting first, longest separator found.
sep = found[min(found.keys())]
key, value = token.split(sep, 1)
# Any preceding tokens are part of the key.
key = ''.join(tokens[:i]) + key
# Any following tokens are part of the value.
value += ''.join(tokens[i + 1:])
break
else:
raise ArgumentTypeError(
u'"%s" is not a valid value' % string)
return self.key_value_class(
key=key, value=value, sep=sep, orig=string)
def check_is_directory(value):
if value is None or not os.path.isdir(value):
raise ArgumentTypeError("%s is not a directory!" % value)
return value
def date_arg(s):
try:
return datetime.strptime(s, "%Y-%m-%d")
except ValueError as e:
raise ArgumentTypeError(e) from e
def print_html_report(covdata: CovData, output_file, options):
css_data = CssRenderer.render(options)
medium_threshold = options.html_medium_threshold
high_threshold = options.html_high_threshold
show_decision = options.show_decision
data = {}
root_info = RootInfo(options)
data["info"] = root_info
data["SHOW_DECISION"] = show_decision
data["COVERAGE_MED"] = medium_threshold
data["COVERAGE_HIGH"] = high_threshold
self_contained = options.html_self_contained
if self_contained is None:
self_contained = not options.html_details
if output_file == "-":
if not self_contained:
raise ArgumentTypeError(
"Only self contained reports can be printed to STDOUT"
)
elif options.html_details:
raise ArgumentTypeError("Detailed reports can not be printed to STDOUT")
if output_file.endswith(os.sep):
output_file += (
"coverage_details.html" if options.html_details else "coverage.html"
)
formatter = get_formatter(options)
css_data += formatter.get_css()
if self_contained:
data["css"] = css_data
else:
css_output = os.path.splitext(output_file)[0] + ".css"
with open_text_for_writing(css_output) as f:
f.write(css_data)
if options.relative_anchors:
css_link = os.path.basename(css_output)
else:
css_link = css_output
data["css_link"] = css_link
root_info.set_coverage(covdata)
# Generate the coverage output (on a per-package basis)
# source_dirs = set()
files = []
dirs = []
filtered_fname = ""
keys = sort_coverage(
covdata,
show_branch=False,
by_num_uncovered=options.sort_uncovered,
by_percent_uncovered=options.sort_percent,
)
cdata_fname = {}
cdata_sourcefile = {}
for f in keys:
filtered_fname = options.root_filter.sub("", f)
files.append(filtered_fname)
dirs.append(os.path.dirname(filtered_fname) + os.sep)
cdata_fname[f] = filtered_fname
if options.html_details:
cdata_sourcefile[f] = _make_short_sourcename(output_file, filtered_fname)
else:
cdata_sourcefile[f] = None
# Define the common root directory, which may differ from options.root
# when source files share a common prefix.
root_directory = ""
if len(files) > 1:
commondir = commonpath(files)
if commondir != "":
root_directory = commondir
else:
dir_, _file = os.path.split(filtered_fname)
if dir_ != "":
root_directory = dir_ + os.sep
root_info.set_directory(root_directory)
for f in keys:
root_info.add_file(covdata[f], cdata_sourcefile[f], cdata_fname[f])
if options.html_details:
(output_prefix, output_suffix) = os.path.splitext(os.path.abspath(output_file))
if output_suffix == "":
output_suffix = ".html"
functions_fname = f"{output_prefix}.functions{output_suffix}"
data["FUNCTIONS_FNAME"] = os.path.basename(functions_fname)
html_string = templates().get_template("root_page.html").render(**data)
with open_text_for_writing(
output_file, encoding=options.html_encoding, errors="xmlcharrefreplace"
) as fh:
fh.write(html_string + "\n")
# Return, if no details are requested
if not options.html_details:
return
#
# Generate an HTML file for every source file
#
error_occurred = False
all_functions = dict()
for f in keys:
cdata = covdata[f]
data["filename"] = cdata_fname[f]
# Only use demangled names (containing a brace)
data["function_list"] = []
for name in sorted(cdata.functions.keys()):
fcdata = cdata.functions[name]
fdata = dict()
fdata["name"] = name
fdata["filename"] = cdata_fname[f]
fdata["html_filename"] = os.path.basename(cdata_sourcefile[f])
fdata["line"] = fcdata.lineno
fdata["count"] = fcdata.count
data["function_list"].append(fdata)
all_functions[(fdata["name"], fdata["filename"])] = fdata
def coverage_class(percent: Optional[float]) -> str:
return coverage_to_class(percent, medium_threshold, high_threshold)
data["functions"] = dict_from_stat(cdata.function_coverage(), coverage_class)
data["branches"] = dict_from_stat(cdata.branch_coverage(), coverage_class)
data["decisions"] = dict_from_stat(cdata.decision_coverage(), coverage_class)
data["lines"] = dict_from_stat(cdata.line_coverage(), coverage_class)
data["source_lines"] = []
currdir = os.getcwd()
os.chdir(options.root_dir)
max_line_from_cdata = max(cdata.lines.keys(), default=0)
try:
with io.open(
data["filename"],
"r",
encoding=options.source_encoding,
errors="replace",
) as source_file:
lines = formatter.highlighter_for_file(data["filename"])(
source_file.read()
)
for ctr, line in enumerate(lines, 1):
data["source_lines"].append(
source_row(ctr, line, cdata.lines.get(ctr))
)
if ctr < max_line_from_cdata:
logger.warning(
f"File {data['filename']} has {ctr} line(s) but coverage data has {max_line_from_cdata} line(s)."
)
except IOError as e:
logger.warning(f'File {data["filename"]} not found: {repr(e)}')
for ctr in range(1, max_line_from_cdata):
data["source_lines"].append(
source_row(
ctr,
"!!! File not found !!!" if ctr == 1 else "",
cdata.lines.get(ctr),
)
)
error_occurred = True
os.chdir(currdir)
html_string = templates().get_template("source_page.html").render(**data)
with open_text_for_writing(
cdata_sourcefile[f],
encoding=options.html_encoding,
errors="xmlcharrefreplace",
) as fh:
fh.write(html_string + "\n")
data["all_functions"] = [all_functions[k] for k in sorted(all_functions)]
html_string = templates().get_template("functions_page.html").render(**data)
with open_text_for_writing(
functions_fname, encoding=options.html_encoding, errors="xmlcharrefreplace"
) as fh:
fh.write(html_string + "\n")
return error_occurred
def is_valid_key(text_key):
"""Check if it's a valid familiar key."""
if len(text_key) != 44:
raise ArgumentTypeError("Invalid familiar key length. It must be 44.")
return text_key
def restricted_float(x): #avoid nonsense values for the threshold
x = float(x)
if x < 0.0 or x > 1.0:
raise ArgumentTypeError("%r not in range [0.0, 1.0]" % (x, ))
return x
def hash_type(string: str) -> str:
# check hash's length, prefix, lowcase.
if not is_valid_hash(string):
raise ArgumentTypeError(f"Invalid transaction hash '{string}'")
return string
def statut_type(s):
if s not in STATUS_MAPPING:
tous_statuts = ", ".join(f"'{s}'" for s in STATUS_MAPPING)
raise ArgumentTypeError(f"statut '{s}' inconnu (doit être un de {tous_statuts}")
return STATUS_MAPPING[s]
def positive_int(x): #avoid nonsense negative parameter values
x = int(x)
if x < 0:
raise ArgumentTypeError("%r is not a positive int" % (x, ))
return x
def check_positive_number_or_equal_to_negative_one(value):
if value:
value = int(value)
if value == 0 or value < -1:
raise ArgumentTypeError("{} is not valid.".format(value))
return value
def check_positive_number(value):
if value:
value = int(value)
if value <= 0:
raise ArgumentTypeError("{} should be a positive number.")
return value
def check_no_spaces(value):
"""checks for spaces in string"""
if ' ' in value:
raise ArgumentTypeError("{} should not have whitespace(s).")
return value
def _validate_format(self, value):
if value not in self._formats:
raise ArgumentTypeError(f'Incorrect format of export {value}')
return value
def check_subnet(value):
if value[-3:] != '/21':
raise ArgumentTypeError(value +
' is not a valid subnet mask. Use x.x.x.x/21')
return value
def directory(path):
if not os.path.isdir(path):
raise ArgumentTypeError("'{}' does not exist.".format(path))
return path
def percentage(n):
p = int(n)
if not p > 0 and p < 100:
raise ArgumentTypeError("Percent param must be 1-99")
return p
def valid_quarter(raw):
result = int(raw)
if not 1 <= result <= 4:
raise ArgumentTypeError('Quarter should be 1-4')
return result
def boolean(x):
if x in [True, False]:
return x
raise ArgumentTypeError("Argument must be a boolean")
def regexp_type(regexp):
try:
re.compile(regexp)
return regexp
except re.error as e:
raise ArgumentTypeError(e)
def main(args):
data_io.show_header()
# Understand input data format
if os.path.isdir(args.input_fname):
tiff_input = True
if args.dataset_name == "": args.dataset_name = "data"
elif args.input_fname.split('.')[-1] in ("hdf5", "h5"):
tiff_input = False
if args.dataset_name == "": raise ArgumentTypeError("dataset-name required for hdf5")
else:
raise ArgumentTypeError("input file type not recognized. must be tiff folder or hdf5 file")
input_fname = args.input_fname
# set up output file name / path / chunks parameter
if args.output_fpath == "":
args.output_fpath = os.path.split(args.input_fname)[0]
args.output_fname = args.output_fname.split('.')[0] + ".hdf5"
output_fname = os.path.join(args.output_fpath, args.output_fname)
if type(args.chunk_param) in (int, float):
chunk_size = args.chunk_param/1e3 # convert to GB
chunk_shape = None
elif type(args.chunk_param) == tuple:
chunk_shape = args.chunk_param
chunk_size = None
else:
chunk_shape = None
chunk_size = None
chunked_slice_size = args.chunked_slice_size
# print("Type chunk_param" + str(type(args.chunk_param)))
# print("Type chunked_slice_size" + str(type(args.chunked_slice_size)))
# print("Overwrite OK is %s"%args.overwrite_OK)
# print("Stats only is %s"%args.stats_only)
# print("Delete is %s"%args.delete)
# sys.exit()
# Define DataFile instances - quit here if stats_only requested
r_dfile = data_io.DataFile(input_fname, tiff = tiff_input, \
data_tag = args.dataset_name, \
VERBOSITY = args.verbosity)
print("Input data stats:")
r_dfile.show_stats()
if args.stats_only:
sys.exit()
w_shape = r_dfile.d_shape # future implementation must allow resampling dataset
w_dtype = r_dfile.d_type # future implementation must allow changing dtype (with renormalization)
w_dfile = data_io.DataFile(output_fname, tiff = False, \
data_tag = args.dataset_name, \
VERBOSITY = args.verbosity, \
d_shape = w_shape, d_type = w_dtype, \
chunk_shape = chunk_shape, \
chunk_size = chunk_size, \
chunked_slice_size = chunked_slice_size)
print("\nChunking scheme estimated as: %s"%str(w_dfile.chunk_shape))
input("\nHDF5 file will be saved to the following location.\n%s\nPress any key to continue."%output_fname)
w_dfile.create_new(overwrite = args.overwrite_OK)
t0 = time.time()
slice_start = 0
print("\n")
pbar = tqdm(total = r_dfile.d_shape[0])
while slice_start < r_dfile.d_shape[0]:
dd, s = r_dfile.read_chunk(axis = 0, slice_start = slice_start, \
max_GB = mem_thres, \
chunk_shape = w_dfile.chunk_shape)
w_dfile.write_chunk(dd, axis = 0, s = s)
slice_start = s.stop
pbar.update(s.stop - s.start)
pbar.close()
total_time = (time.time() - t0)/60.0 # minutes
print("\nTotal time: %.2f minutes"%(total_time))
if args.delete:
input("Delete old file? Press any key")
if tiff_input:
rmtree(input_fname)
else:
os.remove(input_fname)
def arg_type_directory(string):
if not isdir(string):
raise ArgumentTypeError(string + " is not directory")
return string
def validateIP(ip):
try:
if socket.inet_aton(ip):
return ip
except socket.error:
raise ArgumentTypeError('{}[x] Invalid ip provided{}'.format(FR, S))
def __valid_dir_path(file_path: str) -> str:
'''Verifies that specified file path exists.'''
file_path = path.abspath(file_path)
if not path.isdir(file_path):
raise ArgumentTypeError('{} does not exist.'.format(file_path))
return file_path
def __init__(self, regex, path_context=None):
if not regex:
raise ArgumentTypeError("filter cannot be empty")
super(NonEmptyFilterOption, self).__init__(regex, path_context)
def upload_limit(x):
limit = int(x)
if limit < 0:
raise ArgumentTypeError("invalid value: {}, must be positive".format(limit))
return limit
def _validate_path(value):
if not exists(value):
raise ArgumentTypeError(f'Incorrect path {value}')
return value
def readable_file_arg(filename):
try:
open(filename, 'rb')
except IOError as ex:
raise ArgumentTypeError('%s: %s' % (filename, ex.args[1]))
return filename
def is_date_valid(date):
try:
return match(r"[0-9]{4}-[0-9]{1,2}-[0-9]{1,2}", date).group(0)
except:
raise ArgumentTypeError("Invalid format for date provided")