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_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_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)
