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hanarshanars
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diff cleanup
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‎seqr/views/apis/data_manager_api_tests.py‎

Lines changed: 19 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -624,29 +624,21 @@ def test_luigi_proxy(self, mock_hostname):
624624
'message_data_type': 'Expression Outlier',
625625
'header': ['sampleID', 'project', 'geneID', 'tissue', 'detail', 'pValue', 'padjust', 'zScore'],
626626
'optional_headers': ['detail'],
627-
'loaded_data_row': ['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000240361', 'muscle', 'detail1',
628-
0.01, 0.001, -3.1],
629-
'no_existing_data': ['NA19678', '1kg project nåme with uniçøde', 'ENSG00000233750', 'muscle', 'detail1',
630-
0.064, '0.0000057', 7.8],
627+
'loaded_data_row': ['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000240361', 'muscle', 'detail1', 0.01, 0.001, -3.1],
628+
'no_existing_data': ['NA19678', '1kg project nåme with uniçøde', 'ENSG00000233750', 'muscle', 'detail1', 0.064, '0.0000057', 7.8],
631629
'duplicated_indiv_id_data': [
632-
['NA20870', 'Test Reprocessed Project', 'ENSG00000233750', 'muscle', 'detail1', 0.064, '0.0000057',
633-
7.8],
634-
['NA20870', '1kg project nåme with uniçøde', 'ENSG00000240361', 'fibroblasts', 'detail2', 0.01, 0.13,
635-
-3.1],
630+
['NA20870', 'Test Reprocessed Project', 'ENSG00000233750', 'muscle', 'detail1', 0.064, '0.0000057', 7.8],
631+
['NA20870', '1kg project nåme with uniçøde', 'ENSG00000240361', 'fibroblasts', 'detail2', 0.01, 0.13, -3.1],
636632
],
637633
'write_data': {
638634
'{"gene_id": "ENSG00000233750", "p_value": "0.064", "p_adjust": "0.0000057", "z_score": "7.8"}\n',
639635
'{"gene_id": "ENSG00000240361", "p_value": "0.01", "p_adjust": "0.13", "z_score": "-3.1"}\n'
640636
},
641637
'new_data': [
642-
['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000240361', 'muscle', 'detail1', 0.01, 0.13,
643-
-3.1],
644-
['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000240361', 'muscle', 'detail2', 0.01, 0.13,
645-
-3.1],
646-
['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000233750', 'muscle', 'detail1', 0.064,
647-
'0.0000057', 7.8],
648-
['NA19675_D3', 'Test Reprocessed Project', 'ENSG00000233750', 'muscle', 'detail1', 0.064, '0.0000057',
649-
7.8],
638+
['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000240361', 'muscle', 'detail1', 0.01, 0.13, -3.1],
639+
['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000240361', 'muscle', 'detail2', 0.01, 0.13, -3.1],
640+
['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000233750', 'muscle', 'detail1', 0.064, '0.0000057', 7.8],
641+
['NA19675_D3', 'Test Reprocessed Project', 'ENSG00000233750', 'muscle', 'detail1', 0.064, '0.0000057', 7.8],
650642
['NA20888', 'Test Reprocessed Project', 'ENSG00000240361', 'muscle', '', 0.04, 0.112, 1.9],
651643
],
652644
'skipped_samples': 'NA19675_D3 (Test Reprocessed Project)',
@@ -662,10 +654,8 @@ def test_luigi_proxy(self, mock_hostname):
662654
'message_data_type': 'Expression',
663655
'header': ['sample_id', 'project', 'gene_id', 'individual_id', 'tissue', 'TPM'],
664656
'optional_headers': ['individual_id'],
665-
'loaded_data_row': ['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000135953', 'NA19675_D3',
666-
'muscle', 1.34],
667-
'no_existing_data': ['NA19678', '1kg project nåme with uniçøde', 'ENSG00000233750', 'NA19678', 'muscle',
668-
0.064],
657+
'loaded_data_row': ['NA19675_D2', '1kg project nåme with uniçøde', 'ENSG00000135953', 'NA19675_D3', 'muscle', 1.34],
658+
'no_existing_data': ['NA19678', '1kg project nåme with uniçøde', 'ENSG00000233750', 'NA19678', 'muscle', 0.064],
669659
'duplicated_indiv_id_data': [
670660
['NA20870', 'Test Reprocessed Project', 'ENSG00000240361', 'NA20870', 'muscle', 7.8],
671661
['NA20870', '1kg project nåme with uniçøde', 'ENSG00000233750', 'NA20870', 'fibroblasts', 0.0],
@@ -695,20 +685,14 @@ def test_luigi_proxy(self, mock_hostname):
695685
'model_cls': RnaSeqSpliceOutlier,
696686
'data_type': 'S',
697687
'message_data_type': 'Splice Outlier',
698-
'header': ['sampleID', 'projectName', 'geneID', 'chrom', 'start', 'end', 'strand', 'type', 'pValue',
699-
'pAdjust',
700-
'deltaIntronJaccardIndex', 'counts', 'meanCounts', 'totalCounts', 'meanTotalCounts', 'tissue',
701-
'rareDiseaseSamplesWithThisJunction',
688+
'header': ['sampleID', 'projectName', 'geneID', 'chrom', 'start', 'end', 'strand', 'type', 'pValue', 'pAdjust',
689+
'deltaIntronJaccardIndex', 'counts', 'meanCounts', 'totalCounts', 'meanTotalCounts', 'tissue', 'rareDiseaseSamplesWithThisJunction',
702690
'rareDiseaseSamplesTotal'],
703691
'optional_headers': [],
704-
'loaded_data_row': ['NA19675_1', '1kg project nåme with uniçøde', 'ENSG00000240361', 'chr7', 132885746,
705-
132886973, '*',
706-
'psi5', 1.08E-56, 3.08E-56, 12.34, 1297, 197, 129, 1297, 'fibroblasts', 0.53953638, 1,
707-
20],
708-
'no_existing_data': ['NA19678', '1kg project nåme with uniçøde', 'ENSG00000240361', 'chr7', 132885746,
709-
132886973, '*',
710-
'psi5', 1.08E-56, 3.08E-56, 12.34, 1297, 197, 129, 1297, 'fibroblasts', 0.53953638, 1,
711-
20],
692+
'loaded_data_row': ['NA19675_1', '1kg project nåme with uniçøde', 'ENSG00000240361', 'chr7', 132885746, 132886973, '*',
693+
'psi5', 1.08E-56, 3.08E-56, 12.34, 1297, 197, 129, 1297, 'fibroblasts', 0.53953638, 1, 20],
694+
'no_existing_data': ['NA19678', '1kg project nåme with uniçøde', 'ENSG00000240361', 'chr7', 132885746, 132886973, '*',
695+
'psi5', 1.08E-56, 3.08E-56, 12.34, 1297, 197, 129, 1297, 'fibroblasts', 0.53953638, 1, 20],
712696
'duplicated_indiv_id_data': [
713697
['NA20870', 'Test Reprocessed Project', 'ENSG00000233750', 'chr2', 167258096, 167258349, '*',
714698
'psi3', 1.56E-25, 6.33, 0.45, 143, 143, 143, 143, 'fibroblasts', 1, 20],
@@ -725,14 +709,12 @@ def test_luigi_proxy(self, mock_hostname):
725709
' "delta_intron_jaccard_index": "0.45", "counts": "143",'
726710
' "mean_counts": "143", "total_counts": "143", "mean_total_counts": "143",'
727711
' "rare_disease_samples_with_this_junction": "1", "rare_disease_samples_total": "20", "gene_id": "ENSG00000135953"}\n',
728-
},
712+
},
729713
'new_data': [
730714
# existing sample NA19675_1
731-
['NA19675_1', '1kg project nåme with uniçøde', 'ENSG00000233750;ENSG00000240361', 'chr2', 167254166,
732-
167258349, '*', 'psi3',
715+
['NA19675_1', '1kg project nåme with uniçøde', 'ENSG00000233750;ENSG00000240361', 'chr2', 167254166, 167258349, '*', 'psi3',
733716
1.56E-25, -4.9, -0.46, 166, 16.6, 1660, 1.66, 'fibroblasts', 1, 20],
734-
['NA19675_1', '1kg project nåme with uniçøde', 'ENSG00000240361', 'chr7', 132885746, 132975168, '*',
735-
'psi5',
717+
['NA19675_1', '1kg project nåme with uniçøde', 'ENSG00000240361', 'chr7', 132885746, 132975168, '*', 'psi5',
736718
1.08E-56, -6.53, -0.85, 231, 0.231, 2313, 231.3, 'fibroblasts', 1, 20],
737719
# no matched individual NA19675_D3
738720
['NA19675_D3', '1kg project nåme with uniçøde', 'ENSG00000233750', 'chr2', 167258096, 167258349, '*',

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