def test_use_different_scheme(self):
lines = [
"%s%s %s" % (
MafHeader.HeaderLineStartSymbol,
MafHeader.VersionKey,
GdcV1_0_0_ProtectedScheme.version(),
),
"%s%s %s" % (
MafHeader.HeaderLineStartSymbol,
MafHeader.AnnotationSpecKey,
GdcV1_0_0_ProtectedScheme.annotation_spec(),
),
"\t".join(GdcV1_0_0_BasicScheme().column_names()),
]
reader = MafReader(lines=lines, scheme=None)
self.assertIsNone(next(reader, None))
self.assertEqual(len(reader.validation_errors), 1)
self.assertListEqual(
[e.tpe for e in reader.validation_errors],
[MafValidationErrorType.SCHEME_MISMATCHING_NUMBER_OF_COLUMN_NAMES],
)
self.assertEqual(reader.header().scheme().version(),
GdcV1_0_0_BasicScheme.version())
self.assertEqual(reader.scheme().version(),
GdcV1_0_0_ProtectedScheme().version())
self.assertEqual(
reader.scheme().annotation_spec(),
GdcV1_0_0_ProtectedScheme.annotation_spec(),
)
self.assertEqual(
reader.header().scheme().annotation_spec(),
GdcV1_0_0_ProtectedScheme.annotation_spec(),
)
def test_use_scheme_from_header_basic(self):
version = "%s%s %s" % (
MafHeader.HeaderLineStartSymbol,
MafHeader.VersionKey,
GdcV1_0_0_BasicScheme.version(),
)
lines = [version, "\t".join(GdcV1_0_0_BasicScheme().column_names())]
reader = MafReader(lines=lines, scheme=None)
self.assertIsNone(next(reader, None))
self.assertEqual(len(reader.validation_errors), 0)
self.assertEqual(reader.header().scheme().version(),
GdcV1_0_0_BasicScheme().version())
def test_use_default_scheme(self):
lines = [
TestMafReader.AnnotationSpec,
"\t".join(GdcV1_0_0_BasicScheme().column_names()),
]
reader = MafReader(lines=lines, scheme=None)
self.assertIsNone(next(reader, None))
self.assertEqual(len(reader.validation_errors), 2)
self.assertListEqual(
[e.tpe for e in reader.validation_errors],
[
MafValidationErrorType.HEADER_MISSING_VERSION,
MafValidationErrorType.HEADER_UNSUPPORTED_ANNOTATION_SPEC,
],
)
self.assertIsNone(reader.header().scheme())
self.assertEqual(
reader.scheme().version(),
NoRestrictionsScheme(column_names=list()).version(),
)