def test_silva_taxidmap_format_validate_negative_nonnumeric_values(self):
filepath = self.get_data_path('silva_taxamap.tsv')
badtax = pd.read_csv(filepath, sep='\t', index_col=0, header=0)
# turn the taxids to a non-numeric column
badtax['taxid'] = 'peanuts'
junkpath = os.path.join(self.temp_dir.name, 'junk.tsv')
badtax.to_csv(junkpath, sep='\t', header=True)
format = SILVATaxidMapFormat(junkpath, mode='r')
with self.assertRaisesRegex(ValidationError, 'non-numeric value'):
format.validate()
def test_silva_taxidmap_format_validate_negative_invalid_taxonomy(self):
filepath = self.get_data_path('silva_taxamap.tsv')
badtax = pd.read_csv(filepath, sep='\t', index_col=0, header=0)
# replace the taxonomy with non-semicolon-delimited strings
badtax['path'] = 'foobar'
junkpath = os.path.join(self.temp_dir.name, 'junk.tsv')
badtax.to_csv(junkpath, sep='\t', header=True)
format = SILVATaxidMapFormat(junkpath, mode='r')
with self.assertRaisesRegex(ValidationError,
'not in SILVA taxonomy format'):
format.validate()
def test_silva_taxidmap_format_validate_negative_bad_header(self):
filepath = self.get_data_path('silva_taxa.tsv')
format = SILVATaxidMapFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError,
'Header line does not match SILVA format'):
format.validate()
def test_silva_taxidmap_format_validate_positive_version132(self):
filepath = self.get_data_path('silva_taxamap_v132.tsv')
format = SILVATaxidMapFormat(filepath, mode='r')
# These should both just succeed
format.validate('min')
format.validate('max')
def test_silva_taxidmap_format_validate_negative_empty_file(self):
filepath = self.get_data_path('empty_with_header.tsv')
format = SILVATaxidMapFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError,
'must be at least one.*record'):
format.validate()
def test_silva_taxidmap_format_validate_negative_row_count(self):
filepath = self.get_data_path('trash_taxamap.tsv')
format = SILVATaxidMapFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'Expected.*6 fields'):
format.validate()