def test_parse_q2_data_file_does_not_exist(self):
resource_file = self.create_tempfile(suffix='.qza')
resource_filename = resource_file.name
resource_file.close()
with self.assertRaisesRegex(ConfigurationError,
r"does not exist"):
_parse_q2_data(resource_filename, SampleData[AlphaDiversity],
view_type=pd.Series)
def test_parse_q2_data_wrong_semantic_type(self):
resource_filename = self.create_tempfile(suffix='.qza').name
test_series = pd.Series({'feature1': 'k__1', 'feature2': 'k__2'},
name='Taxon')
test_series.index.name = 'Feature ID'
imported_artifact = Artifact.import_data(
# the distincion here is that this is not alpha diversity
"FeatureData[Taxonomy]", test_series
)
imported_artifact.save(resource_filename)
with self.assertRaisesRegex(ConfigurationError,
r"Expected (.*) "
r"'SampleData\[AlphaDiversity\]'. "
r"Received 'FeatureData\[Taxonomy\]'."):
_parse_q2_data(resource_filename, SampleData[AlphaDiversity],
view_type=pd.Series)
def test_parse_q2_data(self):
resource_filename = self.create_tempfile(suffix='.qza').name
test_series = pd.Series({'sample1': 7.15, 'sample2': 9.04},
name='chao1')
imported_artifact = Artifact.import_data(
"SampleData[AlphaDiversity]", test_series
)
imported_artifact.save(resource_filename)
loaded_artifact = _parse_q2_data(resource_filename,
SampleData[AlphaDiversity],
view_type=pd.Series)
assert_series_equal(test_series, loaded_artifact)