Now json_summary custom log filename includes module called #278
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| @@ -307,7 +308,7 @@ def read_metadata_file(self): | |||
| log_text = f"Invalid date format in sample {str(key)}" | |||
| self.logsum.add_error(sample_id, log_text) | |||
| stderr.print(f"[red]{log_text}") | |||
| row[key] = None | |||
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Does the validation process checks for date format? If so this is ok as we'll get that information in the validation process, but if not, maybe we need to keep the "None" so we don't have a validated date field it it is not a date?
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It does not check date format, but the functionality of this "continue" is to not include this field in the final json. I don't think it makes much sense to include it as "None" instead of just removing it
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Ok, so then if it is required it won't validate. In any case make sure this information is not lost and is kept in the json-log so when we ask the hospital for modifications the problem is clear
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Hmmm to save the exact field in json logs i'd need a small change, I'll update it
Appart from a small fix in read_lab_metadata (Now when an invalid date is met is doesn't crash, just continues), now the output json file with the custom log from json_summary.py includes the name of the module called (e.g. if its generated from a read-lab-metadata call, the output name will be
DATE_read_lab_metadata_log_summary.json