Remove writing sample id to summary files#81
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berndbohmeier merged 2 commits intomainfrom Mar 24, 2026
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JasonAHendry
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Mar 23, 2026
| # for backwards compatibility to be able to show old experiments where this column was not in the data | ||
| df = df.join(self.metadata.required_metadata, on="barcode") | ||
| if "sample_id" in df.columns: | ||
| # We used to safe it, but this is not a good idea as it might be outdated if the metadata file is changed |
| # We used to safe it, but this is not a good idea as it might be outdated if the metadata file is changed | ||
| df.drop(columns=["sample_id"], inplace=True) | ||
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| df = df.join(self.metadata.required_metadata, on="barcode") |
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I was briefly considering whether we want to do any validation here, e.g. with the validate= flag, but maybe not?
The barcodes in the metadata file we know will be unique from MetadataTableParser. Maybe if people just wanted to look at a few barcodes, they could delete lines from the metadata file. But if we validate we would prevent that.
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Afaik validate checks only uniqueness of keys, not completeness, so we can use validate here as the barcodes should be unique.
I will add it.
This was not a good idea, as people make mistakes in the sample ids and then fixing it just in the metadata file wasn't working.
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This was not a good idea, as people make mistakes in the sample ids and then fixing it just in the metadata file wasn't working.