def test_get_text_hexdigest_invalid():
"""raises TypeError when invalid data provided"""
with pytest.raises(TypeError):
get_text_hexdigest(None)
with pytest.raises(TypeError):
get_text_hexdigest([])
def test_md5sum_text():
"""md5 sum for text data should be computed"""
data = u"åbcde"
s = get_text_hexdigest(data)
assert s
data = "abcde"
s = get_text_hexdigest(data)
assert s
def read(self, identifier):
"""reads data corresponding to identifier"""
if isinstance(identifier, DataStoreMember) and identifier.parent is self:
identifier = identifier.name
source = self.open(identifier)
data = source.read()
if self._md5:
self._checksums[identifier] = get_text_hexdigest(data)
source.close()
return data
def test_md5sum_text():
"""md5 sum for text data should be computed"""
data = "åbcde"
s = get_text_hexdigest(data)
assert s
data = "abcde"
s = get_text_hexdigest(data)
assert s
# loading contents from files with diff line-endings and check
hex_path = [
("96eb2c2632bae19eb65ea9224aaafdad", "sample-lf.fasta"),
("e7e219f66be15d8afc7cdb85303305a7", "sample-crlf.fasta"),
]
for h, p in hex_path:
p = TEST_ROOTDIR / p
data = p.read_bytes()
print(p, repr(data))
got = get_text_hexdigest(data)
assert got == h, (p, repr(data))
def write(self, identifier, data):
relative_id = self.get_relative_identifier(identifier)
absolute_id = self.get_absolute_identifier(relative_id, from_relative=True)
if self._md5:
self._checksums[absolute_id] = get_text_hexdigest(data)
with atomic_write(str(relative_id), in_zip=self.source) as out:
out.write(data)
member = DataStoreMember(relative_id, self)
if relative_id not in self and relative_id.endswith(self.suffix):
self._members.append(member)
return member
def test_read_from_written():
"""create files with different line endings dynamically"""
text = "abcdeENDedfguENDyhbnd"
with TemporaryDirectory(dir=TEST_ROOTDIR) as dirname:
for ex, lf in (
("f06597f8a983dfc93744192b505a8af9", "\n"),
("39db5cc2f7749f02e0c712a3ece12ffc", "\r\n"),
):
p = Path(dirname) / "test.txt"
data = text.replace("END", lf)
p.write_bytes(data.encode("utf-8"))
expect = get_text_hexdigest(data)
assert expect == ex, (expect, ex)
got = get_file_hexdigest(p)
assert got == expect, f"FAILED: {repr(lf)}, {(ex, got)}"
def write(self, identifier, data):
super().write(identifier, data)
id_suffix = identifier.split(".")[-1]
if id_suffix not in (self.suffix, "log"):
raise ValueError(
f"identifier does not end with required suffix {self.suffix}"
)
relative_id = self.get_relative_identifier(identifier)
absolute_id = self.get_absolute_identifier(relative_id, from_relative=True)
if self._md5:
self._checksums[absolute_id] = get_text_hexdigest(data)
with atomic_write(str(absolute_id), in_zip=False) as out:
out.write(data)
member = DataStoreMember(relative_id, self)
if relative_id not in self and relative_id.endswith(self.suffix):
self._members.append(member)
return member
def read(self, identifier):
data = self.open(identifier)
if self._md5 and isinstance(data, str):
self._checksums[identifier] = get_text_hexdigest(data)
return data
