def test_error_duplicates_in_nt_col(self):
df = pd.DataFrame({
constants.nt_variant_col: ["c.100A>G", "c.100A>G"],
constants.pro_variant_col: ["p.G4L", "p.G4L"],
})
with self.assertRaises(ValueError):
validators.validate_mavedb_compliance(df, df_type=None)
def test_error_primary_column_as_pro_contains_null(self):
df = pd.DataFrame({
constants.nt_variant_col: [None, None],
constants.pro_variant_col: ["p.G4L", None],
})
with self.assertRaises(ValueError):
validators.validate_mavedb_compliance(df, df_type=None)
def test_error_neither_column_defines_variants(self):
df = pd.DataFrame({
constants.nt_variant_col: [None, None],
constants.pro_variant_col: [None, None],
})
with self.assertRaises(ValueError):
validators.validate_mavedb_compliance(df, df_type=None)
def test_keyerror_missing_score_column_df_type_is_scores(self):
df = pd.DataFrame({
constants.pro_variant_col: [None, "pG4L"],
constants.nt_variant_col: ["c.100A>G", "c.101A>G"],
})
with self.assertRaises(KeyError):
validators.validate_mavedb_compliance(df,
df_type=constants.score_type)
def test_pass_coding_(self):
df = pd.DataFrame({
constants.nt_variant_col: ["c.100A>G", "c.101A>G"],
constants.pro_variant_col: ["p.G4L", "p.G5L"],
})
validators.validate_mavedb_compliance(df, df_type=None)
df = pd.DataFrame({
constants.nt_variant_col: ["n.100A>G", "n.101A>G"],
constants.pro_variant_col: [None, None],
})
validators.validate_mavedb_compliance(df, df_type=None)
def test_allows_duplicates_in_pro_col(self):
df = pd.DataFrame({
constants.nt_variant_col: [None, None],
constants.pro_variant_col: ["p.G4L", "p.G4L"],
})
validators.validate_mavedb_compliance(df, df_type=None) # passes
def test_error_missing_nt_pro_columns(self):
df = pd.DataFrame({"A": ["c.100A>G", "c.101A>G"], "B": [None, None]})
with self.assertRaises(ValueError):
validators.validate_mavedb_compliance(df, df_type=None)