Merge branch 'master' of https://github.com/Clinical-Genomics/NIPTool …

…into report_view

tests/fixtures/not_a_valid_fluffy.csv

@@ -1,4 +1,4 @@
-SampleID,SampleType,SequencingDate,Flowcell,SampleProject,Index1,Index2,Library_nM,QCFlag,Zscore_13,Zscore_18,Zscore_21,Zscore_X,chr13_Ratio,chr18_Ratio,chr21_Ratio,chrX_Ratio,Chr1_Ratio,Chr2_Ratio,Chr3_Ratio,Chr4_Ratio,Chr5_Ratio,Chr6_Ratio,Chr7_Ratio,Chr8_Ratio,Chr9_Ratio,Chr10_Ratio,Chr11_Ratio,Chr12_Ratio,Chr14_Ratio,Chr15_Ratio,Chr16_Ratio,Chr17_Ratio,Chr19_Ratio,Chr20_Ratio,Chr22_Ratio,chrY_Ratio,MappedReads,Chr1,Chr2,Chr3,Chr4,Chr5,Chr6,Chr7,Chr8,Chr9,Chr10,Chr11,Chr12,Chr13,Chr14,Chr15,Chr16,Chr17,Chr18,Chr19,Chr20,Chr21,Chr22,ChrX,ChrY,Median_13,Median_18,Median_21,Median_X,Median_Y,Stdev_13,Stdev_18,Stdev_21,Stdev_X,Stdev_Y,FF_Formatted,FFY,FFX,DuplicationRate,GC_Dropout,AT_Dropout,Bin2BinVariance,UnfilteredCNVcalls,CNVSegment
- ,2020-03-10,,,,201862,CAGGTTCC,CGAACACC,,,1.56645731780181,5.7935003491953,-0.034484656889219,-22.4484387749091,1.00392976488,1.0145378044,0.999592517988,0.895534547566,0.00010705927715,29208118,1.2E-05,33.401583,0.995645196832,0.993212778561,0.962823087616,1.06202342547,0.99049923318,1.00919569724,1.03740345147,0.98228215486,0.980352236205,0.990497684064,0.961517632949,1.01303209758,0.986809900603,0.995026518647,0.996175293127,1.03451169241,1.04821216494,0.95282466333,1.04782507766,2029934,1858430,1420819,1157784,1259965,1230164,1245957,1088639,967314,1175662,1072024,1072024,626410,735444,748838,876563,935427,569534,745983,662560,297366,486441,1010813,3127,0.994623404680424,1.01950547134618,1.00710552415657,0.840822847230173,0.000112249820909,0.014076824975767,0.009517510060085,0.006751174544696,0.029800076293786,6.53186791196846E-05,9.804,0.0,10.44,0.1005291748,0.024194141925153,47,Found
-,2020-03-10,,,,201862,TTACCTGG,ACGATTGC,,,1.38366647361139,5.81331308777849,3.70734623274885,-35.5689808856014,1.00345380527,1.01458753978,1.01449670237,0.834596652286,0.000183798072485,19619357,0.000187,33.815994,0.990601777174,0.995167604367,0.962072961919,1.05777118464,0.993385479259,1.01240316831,1.03903325686,0.991366632222,0.983488534995,0.993293317385,0.95505612457,1.01314923931,0.973499284889,0.991858047435,0.988736547703,1.03613747718,1.05346928988,0.947528223568,1.03829176495,1354513,1243481,947437,772255,840547,827926,833468,730865,648361,787219,716799,716799,419651,486482,500012,580410,626225,378761,503768,442069,201359,324729,645131,3606,0.994623404680424,1.01950547134618,1.00710552415657,0.840822847230173,0.000112249820909,0.014076824975767,0.009517510060085,0.006751174544696,0.029800076293786,6.53186791196846E-05,10.56,4.6048225214,17.59,0.103652428568,0.023080843735203,42,Found
-2020-07455-02,2020-03-10,,,,201862,CTATCATT,GACCACCT,,,1.19771475047014,5.9936781609917,0.172213067367254,-27.3372140187147,1.00296961522,1.01504030531,1.00041582109,0.872828803296,0.000101746653098,30035386,9.7E-05,34.339258,0.994369406522,0.994050565447,0.963985487377,1.06586994,0.991903746769,1.01417054338,1.04011435706,0.989841130219,0.987191423231,0.990561923283,0.952624100278,1.01511372968,0.975874349841,0.997388670577,0.996128439123,1.04577514591,1.06297625217,0.947324666538,1.04127965945,2011620,1827738,1395600,1133559,1235029,1212946,1232408,1076087,965009,1163613,1060576,1060576,617068,723824,745525,876814,949260,556232,772443,660420,298174,492289,980817,3056,0.994623404680424,1.01950547134618,1.00710552415657,0.840822847230173,0.000112249820909,0.014076824975767,0.009517510060085,0.006751174544696,0.029800076293786,6.53186791196846E-05,10.87,0.0,12.81,0.100858034586,0.026603482197962,40,HEJ
+SampleID, Library_nM, MappedReads
+,,"3kg"
+"",hej,hej
+,[],"nan"

tests/parse/test_parse_batch.py

@@ -21,7 +21,8 @@ def test_parse_batch_file_with_missing_data(invalid_csv):
 
     # THEN assert results is a list and it has length 3
     assert isinstance(results, list)
-    assert len(results)==3
+    for sample in results:
+        assert sample == {}
 
 
 def test_parse_batch_file_with_missing_file():