upload database module updated #295
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Looks good @luissian ! Thanks! But i think you've removed some functionaligy with the LogSum, this is an addition to the "usual" log where we include warnigns and stuff. This other log generates a json summary of warnings and errors found for each sample. Did you found any error there and that's why you removed it? I think @Shettland can help here, maybe i'm missing something |
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I decided not to use because I need to write in the log a "Warning" that if something is missing. But according to summary log philosophy warnings messages are showed in terminal if no log file is indicated when running the tool. |
| @@ -153,34 +178,38 @@ def get_iskylims_fields_sample(self): | |||
| # the field name for the sample | |||
| sample_fields[property] = values["field_name"] | |||
| except KeyError as e: | |||
| self.logsum.add_warning(entry=f"Error mapping ontology {e}") | |||
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this warning should be added to log sum right?
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why not? If it's an error, why is log.info? And why not add it in the json summary so you can easyly check for sample errors?
| else: | ||
| # for the ones that do not have ontology label in the sample field | ||
| # and have an empty value: sample_fields[key] = "" | ||
| logtxt = f"No ontology found for {values.get('field_name')}" | ||
| self.logsum.add_warning(entry=logtxt) |
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don't know if this is the same as above, but one or the two should be added to the json summary
Configuration was changed to have parameters defined for upload_module under upload_module.
Change on code to apply this and fixing errors when upload data to iSkyLIMS.