Add MEPRAM and Redlabra schemas/templates to assets, add amr genes json to conf, and improve metadata template formatting#889
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ESapenaVentura
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May 27, 2026
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ESapenaVentura
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Haven't checked the JSON files, some minor comments in the code 👍
| if not isinstance(values, list): | ||
| return values | ||
| return self._unique_enum_values( | ||
| [self._clean_enum_ontology_annotation(value) for value in values] |
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| [self._clean_enum_ontology_annotation(value) for value in values] | |
| [BuildSchema._clean_enum_ontology_annotation(value) for value in values] |
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| @staticmethod | ||
| def _clean_enum_ontology_annotation(value: any) -> any: | ||
| """Remove ontology annotations displayed between brackets from enum labels.""" |
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If possible, I would recommend following this format for code comments:
| [re.sub(r"\s*\[.*?\]", "", item).strip() for item in enums] | ||
| if database_definition: | ||
| required_values = { | ||
| property_id: self._format_template_required_value( |
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| property_id: self._format_template_required_value( | |
| property_id: BuildSchema._format_template_required_value( |
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This PR adds MEPRAM and RedLabRA schemas/templates to assets, adds the AMR genes JSON to conf, and improves metadata template formatting.
Changes
Y if ....Y->YESN->NOY if ...->YES if ...PR Checklist
black and flake8).CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).