def test_record_validation_error(self):
scheme = TestMafWriter.TestScheme()
fd, path = tempfile.mkstemp()
# Create the header
header_lines = (MafHeader.scheme_header_lines(scheme) +
["#key1 value1", "#key2 value2"] +
["str1\tNone\tstr2"])
header = MafHeader.from_lines(
lines=header_lines,
validation_stringency=ValidationStringency.Silent)
# Create the record
values = ["string2", "error", "string1"]
record_line = MafRecord.ColumnSeparator.join(values)
record = MafRecord.from_line(
line=record_line,
scheme=scheme,
line_number=1,
validation_stringency=ValidationStringency.Silent,
)
# Write the header, and the record twice
with captured_output() as (stdout, stderr):
writer = MafWriter.from_path(
header=header,
validation_stringency=ValidationStringency.Lenient,
path=path,
)
writer += record
writer.write(record)
writer.close()
stdout = stdout.getvalue().rstrip('\r\n').split("\n")
stderr = stderr.getvalue().rstrip('\r\n').split("\n")
self.assertListEqual(stdout, [''])
# The errors that should be written stderr
errors = [
"HEADER_UNSUPPORTED_VERSION",
"HEADER_UNSUPPORTED_ANNOTATION_SPEC",
"RECORD_COLUMN_WITH_NO_VALUE",
"RECORD_COLUMN_WITH_NO_VALUE",
]
self.assertListEqualAndIn(errors, stderr)
# The second column should be None
err_record_line = record_line.replace("error", "None")
self.assertListEqual(read_lines(path),
header_lines + [err_record_line, err_record_line])
def add_records(self):
scheme = TestMafWriter.TestScheme()
fd, path = tempfile.mkstemp()
header_lines = MafHeader.scheme_header_lines(scheme) + [
"#key1 value1",
"#key2 value2",
]
header = MafHeader.from_lines(lines=header_lines)
writer = MafWriter.from_path(header=header, path=path)
values = ["string2", "3.14", "string1"]
record_line = MafRecord.ColumnSeparator.join(values)
record = MafRecord.from_line(line=record_line,
scheme=scheme,
line_number=1)
writer += record
writer.write(record)
writer.close()
self.assertListEqual(read_lines(path),
header_lines + [record_line, record_line])
def test_with_sorting(self):
scheme = TestMafWriter.TestCoordinateScheme()
fd, path = tempfile.mkstemp()
# Create the header
header_lines = (MafHeader.scheme_header_lines(scheme) +
["#key1 value1", "#key2 value2"] + [
"%s%s %s" % (
MafHeader.HeaderLineStartSymbol,
MafHeader.SortOrderKey,
Coordinate().name(),
)
] + ["\t".join(scheme.column_names())])
header = MafHeader.from_lines(
lines=header_lines,
validation_stringency=ValidationStringency.Silent)
# Write the header, and the record twice
writer = MafWriter.from_path(
header=header,
validation_stringency=ValidationStringency.Lenient,
path=path,
assume_sorted=False,
)
writer += TestMafWriter.DummyRecord("chr1", 2, 2)
writer += TestMafWriter.DummyRecord("chr1", 3, 3)
writer += TestMafWriter.DummyRecord("chr1", 4, 4)
writer.close()
reader = MafReader.reader_from(path=path, scheme=scheme)
header = reader.header()
records = [rec for rec in reader]
reader.close()
self.assertEqual(header.sort_order().name(), Coordinate.name())
self.assertListEqual([r["Start_Position"].value for r in records],
[2, 3, 4])
self.assertListEqual([r["End_Position"].value for r in records],
[2, 3, 4])
def test_scheme_header_lines(self):
scheme = TestMafHeader.Scheme
self.assertListEqual(
MafHeader.scheme_header_lines(scheme),
[TestMafHeader.__version_line, TestMafHeader.__annotation_line],
)
