コード例 #1
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 def test_ignores_unused_column_changes_in_compare_row(self):
     releaseDiff.added_data = self.added_data
     self.oldRow['pyhgvs_Protein'] = "NP_009225.1:p.?"
     self.newRow['HGVS_Protein'] = "NM_000059:p.His1085Arg"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     self.assertIsNone(change_type)
コード例 #2
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 def test_builds_diff_with_adjusted_column_names_to_match_db(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.oldRow['pyhgvs_Protein'] = "NP_009225.1:p.?"
     self.newRow['pyhgvs_Protein'] = "NM_000059:p.His1085Arg"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json[variant]
     self.assertIs(diff[0]['field'], 'HGVS_Protein')
コード例 #3
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 def test_properly_classifies_variants_with_removed_columns_of_empty_data(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.oldRow["Functional_analysis_result_LOVD"] = "-"
     self.newRow['Source'] += ",ENIGMA"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json[variant]
     self.assertEqual(len(diff), 1)
     self.assertIs(change_type, "added_information")
コード例 #4
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 def test_catches_reordered_source_urls(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     self.oldRow["Source_URL"] = "http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000075538, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000144133, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000109288"
     self.newRow["Source_URL"] = "http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000144133, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000075538, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000109288"
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json
     self.assertEqual(diff, {})
     self.assertIsNone(change_type)
コード例 #5
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    def test_ignore_added_or_removed_white_space(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json

        self.oldRow['Synonyms'] = '-2498del2'
        self.newRow['Synonyms'] = '-2498 del2'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #6
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    def test_ignore_date_format_changes(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json

        self.oldRow['Date_last_evaluated_ENIGMA'] = '1 / 12 / 2015'
        self.newRow['Date_last_evaluated_ENIGMA'] = '2015 - 01 - 12'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #7
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    def test_ignore_white_spaces(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json

        self.oldRow['BIC_Nomenclature'] = 'IVS7-680del2'
        self.newRow['BIC_Nomenclature'] = 'IVS 7-680del2'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #8
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    def test_ignores_max_allele_frequency_field(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)

        self.newRow["Max_Allele_Frequency"] = "-"

        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #9
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 def test_catches_new_column_changes_in_compare_row(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.oldRow['pyhgvs_Protein'] = "NP_009225.1:p.?"
     self.newRow['pyhgvs_Protein'] = "NM_000059:p.His1085Arg"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json[variant]
     self.assertEqual(change_type, "changed_information")
     self.assertIs(diff[0]['removed'], 'NP_009225.1:p.?')
     self.assertIs(diff[0]['added'], 'NM_000059:p.His1085Arg')
コード例 #10
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 def test_catches_pathogenicity_changes(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.oldRow['Pathogenicity_all'] = "Pathogenic,not_provided (ClinVar); Class 5 (BIC)"
     self.oldRow['Pathogenicity_expert'] = "Not Yet Classified"
     self.newRow['Pathogenicity_all'] = "Pathogenic(ENIGMA); Pathogenic,not_provided (ClinVar); Class 5 (BIC)"
     self.newRow['Pathogenicity_expert'] = "Pathogenic"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json[variant]
     self.assertEqual(len(diff), 2)
     self.assertIs(change_type, "changed_classification")
コード例 #11
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 def test_catches_pathogenicity_changes(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.oldRow['Pathogenicity_all'] = "Pathogenic,not_provided (ClinVar); Class 5 (BIC)"
     self.oldRow['Pathogenicity_expert'] = "Not Yet Classified"
     self.newRow['Pathogenicity_all'] = "Pathogenic(ENIGMA); Pathogenic,not_provided (ClinVar); Class 5 (BIC)"
     self.newRow['Pathogenicity_expert'] = "Pathogenic"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
     diff = releaseDiff.diff_json[variant]
     self.assertEqual(len(diff), 2)
     self.assertIs(change_type, "changed_classification")
コード例 #12
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 def test_change_type_ignores_reorders(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.oldRow['Pathogenicity_all'] = "Pathogenic(ENIGMA); not_provided,Pathogenic (ClinVar); Class 5 (BIC)"
     self.oldRow['Pathogenicity_expert'] = "Pathogenic"
     self.newRow['Pathogenicity_all'] = "Pathogenic(ENIGMA); Pathogenic,not_provided (ClinVar); Class 5 (BIC)"
     self.newRow['Pathogenicity_expert'] = "Pathogenic"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
     diff = releaseDiff.diff_json
     self.assertEqual(len(diff), 0)
     self.assertIsNone(change_type)
コード例 #13
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    def test_properly_ignores_exac_minus_tcga_rounding_changes_for_generic_allele_frequency(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_Frequency'] = '9.419e-06 (ExAC minus TCGA)'
        self.newRow['Allele_Frequency'] = '9.42e-06 (ExAC minus TCGA)'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #14
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    def test_ignored_exac_minus_tcga_instead_of_exac(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_Frequency'] = '9.42e-06 (ExAC)'
        self.newRow['Allele_Frequency'] = '9.42e-06 (ExAC minus TCGA)'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #15
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 def test_catches_reordered_source_urls(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     self.oldRow[
         "Source_URL"] = "http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000075538, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000144133, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000109288"
     self.newRow[
         "Source_URL"] = "http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000144133, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000075538, http://www.ncbi.nlm.nih.gov/clinvar/?term=SCV000109288"
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json
     self.assertEqual(diff, {})
     self.assertIsNone(change_type)
コード例 #16
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 def test_handles_null_data_in_new_columns_in_v2_data_correctly(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.updated_fieldnames = self.fieldnames + ['Genetic_origin_LOVD', 'RNA_LOVD', 'Submitters_LOVD']
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)
     self.newRow["Genetic_origin_LOVD"] = ""
     self.newRow["RNA_LOVD"] = None
     self.newRow["Submitters_LOVD"] = "-"
     change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
     diff = releaseDiff.diff_json
     self.assertEqual(diff, {})
     self.assertIsNone(change_type)
コード例 #17
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    def test_ignored_exac_minus_tcga_instead_of_exac(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_Frequency'] = '9.42e-06 (ExAC)'
        self.newRow['Allele_Frequency'] = '9.42e-06 (ExAC minus TCGA)'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #18
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    def test_ignores_rounding_for_exac_af_fields(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_frequency_FIN_ExAC'] = '9.4181237657'
        self.newRow['Allele_frequency_FIN_ExAC'] = '9.42'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #19
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 def test_handles_new_data_in_new_columns_in_v2_data_correctly(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.updated_fieldnames = self.fieldnames + ['Genetic_origin_LOVD', 'RNA_LOVD', 'Submitters_LOVD']
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)
     self.newRow["Genetic_origin_LOVD"] = "lorem ipsum"
     self.newRow["RNA_LOVD"] = "lorem ipsum"
     self.newRow["Submitters_LOVD"] = "lorem ipsum"
     change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
     diff = releaseDiff.diff_json
     self.assertEqual(change_type, "added_information")
     self.assertTrue(len(diff[variant]) == 3)
コード例 #20
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    def test_ignores_rounding_for_exac_af_fields(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_frequency_FIN_ExAC'] = '9.4181237657'
        self.newRow['Allele_frequency_FIN_ExAC'] = '9.42'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #21
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    def test_catches_changed_numeric_values_after_normalization(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)

        self.oldRow['Allele_frequency_ExAC'] = '9.841e-06'
        self.newRow['Allele_frequency_ExAC'] = '9.841e-07'

        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        self.assertEqual(len(diff), 1)
        self.assertIs(change_type, "changed_information")
コード例 #22
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 def test_change_type_ignores_reorders(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.oldRow['Pathogenicity_all'] = "Pathogenic(ENIGMA); not_provided,Pathogenic (ClinVar); Class 5 (BIC)"
     self.oldRow['Pathogenicity_expert'] = "Pathogenic"
     self.newRow['Pathogenicity_all'] = "Pathogenic(ENIGMA); Pathogenic,not_provided (ClinVar); Class 5 (BIC)"
     self.newRow['Pathogenicity_expert'] = "Pathogenic"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json
     self.assertEqual(len(diff), 0)
     self.assertIsNone(change_type)
コード例 #23
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    def test_ignores_change_from_none_to_empty_string(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)

        self.oldRow["Submitter_ClinVar"] = "Quest_Diagnostics_Nichols_Institute_San_Juan_Capistrano"
        self.newRow["Submitter_ClinVar"] = ",Quest_Diagnostics_Nichols_Institute_San_Juan_Capistrano"

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #24
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    def test_properly_ignores_exac_minus_tcga_rounding_changes_for_generic_allele_frequency(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_Frequency'] = '9.419e-06 (ExAC minus TCGA)'
        self.newRow['Allele_Frequency'] = '9.42e-06 (ExAC minus TCGA)'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #25
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    def test_ignores_change_from_none_to_empty_string(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)

        self.oldRow["Submitter_ClinVar"] = "Quest_Diagnostics_Nichols_Institute_San_Juan_Capistrano"
        self.newRow["Submitter_ClinVar"] = ",Quest_Diagnostics_Nichols_Institute_San_Juan_Capistrano"

        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #26
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    def test_ignores_polyphen_fields(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)

        self.newRow["Polyphen_Score"] = "0.283"
        self.newRow["Polyphen_Prediction"] = "probably_damaging"

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #27
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 def test_handles_null_data_in_new_columns_in_v2_data_correctly(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.updated_fieldnames = self.fieldnames + ['Genetic_origin_LOVD', 'RNA_LOVD', 'Submitters_LOVD']
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)
     self.newRow["Genetic_origin_LOVD"] = ""
     self.newRow["RNA_LOVD"] = None
     self.newRow["Submitters_LOVD"] = "-"
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json
     self.assertEqual(diff, {})
     self.assertIsNone(change_type)
コード例 #28
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    def test_ignores_polyphen_fields(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)

        self.newRow["Polyphen_Score"] = "0.283"
        self.newRow["Polyphen_Prediction"] = "probably_damaging"

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #29
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 def test_handles_new_data_in_new_columns_in_v2_data_correctly(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     self.updated_fieldnames = self.fieldnames + ['Genetic_origin_LOVD', 'RNA_LOVD', 'Submitters_LOVD']
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)
     self.newRow["Genetic_origin_LOVD"] = "lorem ipsum"
     self.newRow["RNA_LOVD"] = "lorem ipsum"
     self.newRow["Submitters_LOVD"] = "lorem ipsum"
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json
     self.assertEqual(change_type, "added_information")
     self.assertTrue(len(diff[variant]) == 3)
コード例 #30
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    def test_catches_changed_numeric_values_after_normalization(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)

        self.oldRow['Allele_frequency_ExAC'] = '9.841e-06'
        self.newRow['Allele_frequency_ExAC'] = '9.841e-07'

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(len(diff), 1)
        self.assertIs(change_type, "changed_information")
コード例 #31
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 def test_add_gs_to_genomic_coordinate(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     self.oldRow['pyhgvs_Genomic_Coordinate_38'] = "chr17:43049067:C>T"
     self.newRow['pyhgvs_Genomic_Coordinate_38'] = "chr17:g.43049067:C>T"
     self.oldRow['pyhgvs_Genomic_Coordinate_37'] = "chr17:43049067:C>T"
     self.newRow['pyhgvs_Genomic_Coordinate_37'] = "chr17:g.43049067:C>T"
     self.oldRow['pyhgvs_Genomic_Coordinate_36'] = "chr17:43049067:C>T"
     self.newRow['pyhgvs_Genomic_Coordinate_36'] = "chr17:g.43049067:C>T"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     self.oldRow = releaseDiff.addGsIfNecessary(self.oldRow)
     self.oldRow = releaseDiff.addGsIfNecessary(self.newRow)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     self.assertIsNone(change_type)
コード例 #32
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 def test_add_gs_to_genomic_coordinate(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     self.oldRow['pyhgvs_Genomic_Coordinate_38'] = "chr17:43049067:C>T"
     self.newRow['pyhgvs_Genomic_Coordinate_38'] = "chr17:g.43049067:C>T"
     self.oldRow['pyhgvs_Genomic_Coordinate_37'] = "chr17:43049067:C>T"
     self.newRow['pyhgvs_Genomic_Coordinate_37'] = "chr17:g.43049067:C>T"
     self.oldRow['pyhgvs_Genomic_Coordinate_36'] = "chr17:43049067:C>T"
     self.newRow['pyhgvs_Genomic_Coordinate_36'] = "chr17:g.43049067:C>T"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     self.oldRow = releaseDiff.addGsIfNecessary(self.oldRow)
     self.oldRow = releaseDiff.addGsIfNecessary(self.newRow)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     self.assertIsNone(change_type)
コード例 #33
0
 def test_handle_repeat_data_correctly(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     self.oldRow["Pathogenicity_all"] = "Pathogenic,Pathogenic,not_provided"
     self.newRow["Pathogenicity_all"] = "Pathogenic,not_provided"
     self.oldRow["Clinical_Significance_ClinVar"] = "Pathogenic,Pathogenic,not_provided"
     self.newRow["Clinical_Significance_ClinVar"] = "Pathogenic,not_provided"
     self.oldRow["Submitter_ClinVar"] = "PreventionGenetics"
     self.newRow["Submitter_ClinVar"] = "PreventionGenetics,PreventionGenetics"
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json
     self.assertEqual(diff, {})
     self.assertIsNone(change_type)
コード例 #34
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 def test_handle_repeat_data_correctly(self):
     releaseDiff.added_data = self.added_data
     releaseDiff.diff = self.diff
     releaseDiff.diff_json = self.diff_json
     variant = 'chr17:g.43049067:C>T'
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     self.oldRow["Pathogenicity_all"] = "Pathogenic,Pathogenic,not_provided"
     self.newRow["Pathogenicity_all"] = "Pathogenic,not_provided"
     self.oldRow["Clinical_Significance_ClinVar"] = "Pathogenic,Pathogenic,not_provided"
     self.newRow["Clinical_Significance_ClinVar"] = "Pathogenic,not_provided"
     self.oldRow["Submitter_ClinVar"] = "PreventionGenetics"
     self.newRow["Submitter_ClinVar"] = "PreventionGenetics,PreventionGenetics"
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     diff = releaseDiff.diff_json
     self.assertEqual(diff, {})
     self.assertIsNone(change_type)
コード例 #35
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    def test_displays_integers_as_integers_not_floats(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        self.oldRow['Allele_count_AFR'] = '-'
        self.newRow['Allele_count_AFR'] = '567'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(len(diff), 1)
        self.assertEqual(v_diff['field'], 'Allele_count_AFR')
        self.assertEqual(v_diff['added'], '567')
        self.assertEqual(v_diff['removed'], '-')
コード例 #36
0
    def test_displays_integers_as_integers_not_floats(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        self.oldRow['Allele_count_AFR'] = '-'
        self.newRow['Allele_count_AFR'] = '567'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(len(diff), 1)
        self.assertEqual(v_diff['field'], 'Allele_count_AFR')
        self.assertEqual(v_diff['added'], '567')
        self.assertEqual(v_diff['removed'], '-')
コード例 #37
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    def test_properly_handles_field_name_changes_same_data(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.updated_fieldnames = self.fieldnames + ['Minor_allele_frequency_percent_ESP']
        self.fieldnames = self.fieldnames + ['Minor_allele_frequency_ESP']

        self.oldRow['Minor_allele_frequency_ESP'] = '2.5'
        self.newRow['Minor_allele_frequency_percent_ESP'] = '2.5'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #38
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    def test_properly_handles_field_name_changes_same_data(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.updated_fieldnames = self.fieldnames + ['Minor_allele_frequency_percent_ESP']
        self.fieldnames = self.fieldnames + ['Minor_allele_frequency_ESP']

        self.oldRow['Minor_allele_frequency_ESP'] = '2.5'
        self.newRow['Minor_allele_frequency_percent_ESP'] = '2.5'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #39
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    def test_different_values_for_exac_af_fields(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_frequency_FIN_ExAC'] = '9.4181237657'
        self.newRow['Allele_frequency_FIN_ExAC'] = '9.41'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(len(diff), 1)
        self.assertEqual(v_diff['field'], 'Allele_frequency_FIN_ExAC')
        self.assertEqual(v_diff['added'], '9.41')
        self.assertEqual(v_diff['removed'], '9.42')
        self.assertEqual(change_type, "changed_information")
コード例 #40
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    def test_catches_value_change_for_exac_allele_frequency(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_Frequency'] = '9.42e-06 (ExAC)'
        self.newRow['Allele_Frequency'] = '9.99e-06 (ExAC minus TCGA)'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(len(diff), 1)
        self.assertEqual(v_diff['field'], 'Allele_Frequency')
        self.assertEqual(v_diff['added'], '9.99e-06 (ExAC minus TCGA)')
        self.assertEqual(v_diff['removed'], '9.42e-06 (ExAC minus TCGA)')
        self.assertEqual(change_type, "changed_information")
コード例 #41
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    def test_different_values_for_exac_af_fields(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_frequency_FIN_ExAC'] = '9.4181237657'
        self.newRow['Allele_frequency_FIN_ExAC'] = '9.41'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(len(diff), 1)
        self.assertEqual(v_diff['field'], 'Allele_frequency_FIN_ExAC')
        self.assertEqual(v_diff['added'], '9.41')
        self.assertEqual(v_diff['removed'], '9.42')
        self.assertEqual(change_type, "changed_information")
コード例 #42
0
    def test_catches_value_change_for_exac_allele_frequency(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.oldRow['Allele_Frequency'] = '9.42e-06 (ExAC)'
        self.newRow['Allele_Frequency'] = '9.99e-06 (ExAC minus TCGA)'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(len(diff), 1)
        self.assertEqual(v_diff['field'], 'Allele_Frequency')
        self.assertEqual(v_diff['added'], '9.99e-06 (ExAC minus TCGA)')
        self.assertEqual(v_diff['removed'], '9.42e-06 (ExAC minus TCGA)')
        self.assertEqual(change_type, "changed_information")
コード例 #43
0
    def test_ignores_cosmetic_changes_in_diff(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)

        self.oldRow[
            "Submitter_ClinVar"] = "The_Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),c/o_University_of_Cambridge"
        self.newRow[
            "Submitter_ClinVar"] = "Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),_c/o_University_of_Cambridge"

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)

        self.oldRow[
            "Submitter_ClinVar"] = "Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),_c/o_University_of_Cambridge"
        self.newRow[
            "Submitter_ClinVar"] = "The_Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),c/o_University_of_Cambridge"

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)

        self.newRow['EAS_Allele_frequency_1000_Genomes'] = '0.0'
        self.newRow['Allele_frequency_ExAC'] = '9.841e-06'

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)

        self.oldRow['EAS_Allele_frequency_1000_Genomes'] = '0.0'
        self.oldRow['Allele_frequency_ExAC'] = '9.841e-06'
        self.newRow['EAS_Allele_frequency_1000_Genomes'] = '0'
        self.newRow['Allele_frequency_ExAC'] = '9.841E-06'

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #44
0
    def test_handles_fields_with_commas_in_parentheses_correctly(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        self.updated_fieldnames = self.fieldnames + ['Genetic_origin_LOVD', 'RNA_LOVD', 'Submitters_LOVD']
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)

        self.newRow["Submitters_LOVD"] = "Ans M.W. van den Ouweland (Rotterdam,NL), Genevieve Michils (Leuven,BE), Rien Blok (Maastricht NL)"

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(len(diff), 1)
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(v_diff['field'], 'Submitters_LOVD')
        self.assertEqual(len(v_diff['added']), 3)
        self.assertIn("Ans M.W. van den Ouweland (Rotterdam,NL)", v_diff['added'])
        self.assertIn("Genevieve Michils (Leuven,BE)", v_diff['added'])
        self.assertIn("Rien Blok (Maastricht NL)", v_diff['added'])
コード例 #45
0
    def test_handles_fields_with_commas_in_parentheses_correctly(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        self.updated_fieldnames = self.fieldnames + ['Genetic_origin_LOVD', 'RNA_LOVD', 'Submitters_LOVD']
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)

        self.newRow["Submitters_LOVD"] = "Ans M.W. van den Ouweland (Rotterdam,NL), Genevieve Michils (Leuven,BE), Rien Blok (Maastricht NL)"

        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        self.assertEqual(len(diff), 1)
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(v_diff['field'], 'Submitters_LOVD')
        self.assertEqual(len(v_diff['added']), 3)
        self.assertIn("Ans M.W. van den Ouweland (Rotterdam,NL)", v_diff['added'])
        self.assertIn("Genevieve Michils (Leuven,BE)", v_diff['added'])
        self.assertIn("Rien Blok (Maastricht NL)", v_diff['added'])
コード例 #46
0
    def test_properly_handles_field_name_changes_added_data(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.updated_fieldnames = self.fieldnames + ['Minor_allele_frequency_percent_ESP']
        self.fieldnames = self.fieldnames + ['Minor_allele_frequency_ESP']

        self.oldRow['Minor_allele_frequency_ESP'] = '-'
        self.newRow['Minor_allele_frequency_percent_ESP'] = '2.5'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(len(diff), 1)
        self.assertEqual(v_diff['field'], 'Minor_allele_frequency_percent_ESP')
        self.assertEqual(v_diff['added'], '2.5')
        self.assertEqual(v_diff['removed'], '-')
        self.assertEqual(change_type, "added_information")
コード例 #47
0
    def test_properly_handles_field_name_changes_added_data(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'

        self.updated_fieldnames = self.fieldnames + ['Minor_allele_frequency_percent_ESP']
        self.fieldnames = self.fieldnames + ['Minor_allele_frequency_ESP']

        self.oldRow['Minor_allele_frequency_ESP'] = '-'
        self.newRow['Minor_allele_frequency_percent_ESP'] = '2.5'

        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.updated_fieldnames)
        change_type = v1v2.compareRow(self.oldRow, self.newRow, False)
        diff = releaseDiff.diff_json
        v_diff = diff['chr17:g.43049067:C>T'][0]
        self.assertEqual(len(diff), 1)
        self.assertEqual(v_diff['field'], 'Minor_allele_frequency_percent_ESP')
        self.assertEqual(v_diff['added'], '2.5')
        self.assertEqual(v_diff['removed'], '-')
        self.assertEqual(change_type, "added_information")
コード例 #48
0
    def test_ignores_cosmetic_changes_in_diff(self):
        releaseDiff.added_data = self.added_data
        releaseDiff.diff = self.diff
        releaseDiff.diff_json = self.diff_json
        variant = 'chr17:g.43049067:C>T'
        v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)

        self.oldRow["Submitter_ClinVar"] = "The_Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),c/o_University_of_Cambridge"
        self.newRow["Submitter_ClinVar"] = "Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),_c/o_University_of_Cambridge"

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)

        self.oldRow["Submitter_ClinVar"] = "Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),_c/o_University_of_Cambridge"
        self.newRow["Submitter_ClinVar"] = "The_Consortium_of_Investigators_of_Modifiers_of_BRCA1/2_(CIMBA),c/o_University_of_Cambridge"

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)

        self.newRow['EAS_Allele_frequency_1000_Genomes'] = '0.0'
        self.newRow['Allele_frequency_ExAC'] = '9.841e-06'

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)

        self.oldRow['EAS_Allele_frequency_1000_Genomes'] = '0.0'
        self.oldRow['Allele_frequency_ExAC'] = '9.841e-06'
        self.newRow['EAS_Allele_frequency_1000_Genomes'] = '0'
        self.newRow['Allele_frequency_ExAC'] = '9.841E-06'

        change_type = v1v2.compareRow(self.oldRow, self.newRow)
        diff = releaseDiff.diff_json
        self.assertEqual(diff, {})
        self.assertIsNone(change_type)
コード例 #49
0
 def test_compare_row_added_data(self):
     releaseDiff.added_data = self.added_data
     self.newRow['Source'] += ",ENIGMA"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     self.assertEqual(change_type, "added_information")
コード例 #50
0
 def test_compare_row_equal_rows(self):
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     self.assertIsNone(change_type)
コード例 #51
0
 def test_compare_row_added_data(self):
     releaseDiff.added_data = self.added_data
     self.newRow['Source'] += ",ENIGMA"
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     self.assertEqual(change_type, "added_information")
コード例 #52
0
 def test_compare_row_equal_rows(self):
     v1v2 = releaseDiff.v1ToV2(self.fieldnames, self.fieldnames)
     change_type = v1v2.compareRow(self.oldRow, self.newRow)
     self.assertIsNone(change_type)