def test_diff_json_handles_hgvs_protein_non_changes_correctly(self):
field = "HGVS_Protein"
prev = "NM_000059:p.His1085Arg"
new = "NM_000059:p.His1085Arg"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'HGVS_Protein')
self.assertEqual(diff['field_type'], 'individual')
self.assertIsNone(diff['added'])
self.assertIsNone(diff['removed'])
def test_diff_json_handles_list_changes_correctly(self):
field = "Source"
prev = "BIC,ClinVar,ENIGMA"
new = "ClinVar"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'Source')
self.assertEqual(diff['field_type'], 'list')
self.assertIsNone(diff['added'])
self.assertEqual(diff['removed'], ['BIC', 'ENIGMA'])
def test_diff_json_handles_individual_changes_data_added_from_nothing_correctly(self):
field = "HGVS_Protein"
prev = "-"
new = "NM_000059:p.His1085Arg"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'HGVS_Protein')
self.assertEqual(diff['field_type'], 'individual')
self.assertEqual(diff['added'], 'NM_000059:p.His1085Arg')
self.assertEqual(diff['removed'], '-')
def test_diff_json_handles_list_changes_correctly_changed_order(self):
field = "Source_URL"
prev = "http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000075545, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000187590, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000144137"
new = "http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000187590, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000075545, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000144137"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'Source_URL')
self.assertEqual(diff['field_type'], 'list')
self.assertIsNone(diff['added'])
self.assertIsNone(diff['removed'])
def test_diff_json_handles_hgvs_protein_non_changes_correctly(self):
field = "HGVS_Protein"
prev = "NM_000059:p.His1085Arg"
new = "NM_000059:p.His1085Arg"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'HGVS_Protein')
self.assertEqual(diff['field_type'], 'individual')
self.assertIsNone(diff['added'])
self.assertIsNone(diff['removed'])
def test_diff_json_handles_no_changes_correctly(self):
field = "Pathogenicity_all"
prev = "Uncertain_significance,Likely_benign (BIC); Pending (ClinVar)"
new = "Uncertain_significance,Likely_benign (BIC); Pending (ClinVar)"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'Pathogenicity_all')
self.assertEqual(diff['field_type'], 'list')
self.assertIsNone(diff['added'])
self.assertIsNone(diff['removed'])
def test_diff_json_handles_individual_changes_data_added_from_nothing_correctly(self):
field = "HGVS_Protein"
prev = "-"
new = "NM_000059:p.His1085Arg"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'HGVS_Protein')
self.assertEqual(diff['field_type'], 'individual')
self.assertEqual(diff['added'], 'NM_000059:p.His1085Arg')
self.assertEqual(diff['removed'], '-')
def test_diff_json_handles_list_changes_correctly_changed_order(self):
field = "Source_URL"
prev = "http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000075545, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000187590, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000144137"
new = "http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000187590, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000075545, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000144137"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'Source_URL')
self.assertEqual(diff['field_type'], 'list')
self.assertIsNone(diff['added'])
self.assertIsNone(diff['removed'])
def test_diff_json_handles_list_changes_correctly(self):
field = "Source"
prev = "BIC,ClinVar,ENIGMA"
new = "ClinVar"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'Source')
self.assertEqual(diff['field_type'], 'list')
self.assertIsNone(diff['added'])
self.assertEqual(diff['removed'], ['BIC', 'ENIGMA'])
def test_diff_json_handles_no_changes_correctly(self):
field = "Pathogenicity_all"
prev = "Uncertain_significance,Likely_benign (BIC); Pending (ClinVar)"
new = "Uncertain_significance,Likely_benign (BIC); Pending (ClinVar)"
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'Pathogenicity_all')
self.assertEqual(diff['field_type'], 'list')
self.assertIsNone(diff['added'])
self.assertIsNone(diff['removed'])
def test_diff_json_handles_list_data_added_from_nothing_correctly(self):
field = "Submitter_ClinVar"
prev = "-"
new = ("c/o_University_of_Cambridge,The_Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),"
"Ambry_Genetics,Breast_Cancer_Information_Core_(BIC)_(BRCA2),Invitae")
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'Submitter_ClinVar')
self.assertEqual(diff['field_type'], 'list')
self.assertIn('c/o_University_of_Cambridge', diff['added'])
self.assertIn('The_Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA)', diff['added'])
self.assertIn('Ambry_Genetics', diff['added'])
self.assertIn('Breast_Cancer_Information_Core_(BIC)_(BRCA2)', diff['added'])
self.assertIn('Invitae', diff['added'])
self.assertEqual(diff['removed'], ['-'])
def test_diff_json_handles_list_data_added_from_nothing_correctly(self):
field = "Submitter_ClinVar"
prev = "-"
new = ("c/o_University_of_Cambridge,The_Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),"
"Ambry_Genetics,Breast_Cancer_Information_Core_(BIC)_(BRCA2),Invitae")
diff = releaseDiff.determineDiffForJSON(field, prev, new)
self.assertEqual(diff['field'], 'Submitter_ClinVar')
self.assertEqual(diff['field_type'], 'list')
self.assertIn('c/o_University_of_Cambridge', diff['added'])
self.assertIn('The_Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA)', diff['added'])
self.assertIn('Ambry_Genetics', diff['added'])
self.assertIn('Breast_Cancer_Information_Core_(BIC)_(BRCA2)', diff['added'])
self.assertIn('Invitae', diff['added'])
self.assertEqual(diff['removed'], ['-'])
