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Improve robustness of the conversion from spreadsheet to JSON #153

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Improve robustness of the conversion from spreadsheet to JSON #153

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9 changes: 5 additions & 4 deletions eva_sub_cli/executables/xlsx2json.py
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Original file line number Diff line number Diff line change
Expand Up @@ -225,8 +225,9 @@ def serialize(value):
return str(value)

def get_sample_data_with_split_analysis_alias(self, data, analysis_alias, sample_name_in_vcf):
analysis_alias_list = data[analysis_alias].split(',')
sample_in_vcf_val = data[sample_name_in_vcf]
analysis_alias_val = data.get(analysis_alias)
analysis_alias_list = analysis_alias_val.split(',') if analysis_alias_val else []
sample_in_vcf_val = data.get(sample_name_in_vcf)
return {analysis_alias: analysis_alias_list, sample_name_in_vcf: sample_in_vcf_val}

def get_sample_json_data(self):
Expand All @@ -245,8 +246,8 @@ def get_sample_json_data(self):
sample_data.update(bioSampleAccession=json_value[bio_sample_acc])
sample_json[json_key].append(sample_data)
else:
json_value.pop(analysis_alias)
json_value.pop(sample_name_in_vcf)
json_value.pop(analysis_alias, None)
json_value.pop(sample_name_in_vcf, None)

biosample_obj = self.get_biosample_object(json_value)
sample_data.update(bioSampleObject=biosample_obj)
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