forked from MIRRI/mirri_utils
51 lines
1.9 KiB
Python
51 lines
1.9 KiB
Python
from mirri import rgetattr
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def validate_strain(strain, version='20200601'):
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if version == '20200601':
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return _validate_strain_v20200601(strain)
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raise NotImplementedError('Only v20200601 is implemented')
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def _validate_strain_v20200601(strain):
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mandatory_attrs = [{'label': 'Accession Number', 'attr': 'id.strain_id'},
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{'label': 'Nagoya protocol', 'attr': 'nagoya_protocol'},
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{'label': 'Restriction on use', 'attr': 'restriction_on_use'},
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{'label': 'Risk group', 'attr': 'risk_group'},
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{'label': 'Organism type', 'attr': 'taxonomy.organism_type'},
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{'label': 'Taxon name', 'attr': 'taxonomy.long_name'},
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{'label': 'Recommended temperature to growth', 'attr': 'growth.recommended_temp'},
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{'label': 'Recommended media', 'attr': 'growth.recommended_media'},
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{'label': 'Form of supply', 'attr': 'form_of_supply'},
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{'label': 'Country', 'attr': 'collect.location.country'}]
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errors = []
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for mandatory in mandatory_attrs:
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value = rgetattr(strain, mandatory['attr'])
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if value is None:
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errors.append(f"{mandatory['label']} is mandatory field")
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if not is_valid_nagoya(strain):
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errors.append('Not compliant wih nagoya protocol requirements')
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return errors
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def is_valid_nagoya(strain):
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# nagoya_requirements
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_date = strain.collect.date
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if _date is None:
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_date = strain.isolation.date
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if _date is None:
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_date = strain.deposit.date
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if _date is None:
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_date = strain.catalog_inclusion_date
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# print(_date)
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year = None if _date is None else _date._year
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if year is not None and year >= 2014 and strain.collect.location.country is None:
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return False
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return True
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