def test_reordered_pathogenicity_all_data(self): prev = "Pathogenic(ENIGMA); not_provided,Pathogenic (ClinVar); Class 5 (BIC)" new = "Pathogenic(ENIGMA); Pathogenic,not_provided (ClinVar); Class 5 (BIC)" prevTwo = "Uncertain_significance,Likely_benign (ClinVar); Pending (BIC)" newTwo = "Likely_benign,Uncertain_significance (ClinVar); Pending (BIC)" added, removed = releaseDiff.determineDiffForPathogenicityAll(prev, new) addedTwo, removedTwo = releaseDiff.determineDiffForPathogenicityAll(prevTwo, newTwo) self.assertIsNone(added) self.assertIsNone(removed) self.assertIsNone(addedTwo) self.assertIsNone(addedTwo)
def test_pathogenicity_all_diff_no_change(self): prev = "Uncertain_significance,Likely_benign (BIC); Pending (ClinVar)" new = "Uncertain_significance,Likely_benign (BIC); Pending (ClinVar)" (added, removed) = releaseDiff.determineDiffForPathogenicityAll(prev, new) self.assertIsNone(added) self.assertIsNone(removed)
def test_same_pathogenicity_all_data_single_source(self): prev = "Uncertain_significance,Likely_benign (ClinVar)" new = "Likely_benign,Uncertain_significance (ClinVar)" added, removed = releaseDiff.determineDiffForPathogenicityAll( prev, new) self.assertIsNone(added) self.assertIsNone(removed)
def test_different_pathogenicity_all_data(self): prev = "Uncertain_significance,Likely_benign (ClinVar); Pending (BIC)" new = "Likely_benign (ClinVar); Pending (BIC)" added, removed = releaseDiff.determineDiffForPathogenicityAll( prev, new) self.assertIsNone(added) self.assertIn('Uncertain_significance (ClinVar)', removed)
def test_swapped_pathogenicity_all_data(self): prev = "Uncertain_significance,Likely_benign (ClinVar); Pending (BIC)" new = "Uncertain_significance,Likely_benign (BIC); Pending (ClinVar)" added, removed = releaseDiff.determineDiffForPathogenicityAll(prev, new) self.assertIn('Uncertain_significance,Likely_benign (BIC)', added) self.assertIn('Pending (ClinVar)', added) self.assertIn('Pending (BIC)', removed) self.assertIn('Uncertain_significance,Likely_benign (ClinVar)', removed)
def test_same_pathogenicity_all_data_single_source(self): prev = "Uncertain_significance,Likely_benign (ClinVar)" new = "Likely_benign,Uncertain_significance (ClinVar)" added, removed = releaseDiff.determineDiffForPathogenicityAll(prev, new) self.assertIsNone(added) self.assertIsNone(removed)