[CZID-8857] Add ConsensusGenomes to seed script #122
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j-x-han
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j-x-han
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Nov 17, 2023
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| # For each file, find the entity associated with it | ||
| # and update the file_id for that entity. | ||
| files = session.query(File).all() | ||
| for file in files: | ||
| if file.entity_id: | ||
| entity_field_name = file.entity_field_name | ||
| entity = session.query(Entity).filter(Entity.id == file.entity_id).first() | ||
| if entity: | ||
| entity_name = entity.type | ||
| session.execute( | ||
| sa.text( | ||
| f"""UPDATE {entity_name} SET {entity_field_name}_id = file.id | ||
| FROM file WHERE {entity_name}.entity_id = file.entity_id""", | ||
| ) | ||
| ) |
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Definitely open to suggestions on how to improve this 😓
robertaboukhalil
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Nov 17, 2023
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| # For each file, find the entity associated with it | ||
| # and update the file_id for that entity. | ||
| files = session.query(File).all() | ||
| for file in files: | ||
| if file.entity_id: | ||
| entity_field_name = file.entity_field_name | ||
| entity = session.query(Entity).filter(Entity.id == file.entity_id).first() | ||
| if entity: | ||
| entity_name = entity.type | ||
| session.execute( | ||
| sa.text( | ||
| f"""UPDATE {entity_name} SET {entity_field_name}_id = file.id | ||
| FROM file WHERE {entity_name}.entity_id = file.entity_id""", | ||
| ) | ||
| ) |
| @@ -80,11 +80,11 @@ async def load_{{ related_field.related_class.snake_name }}_rows( | |||
| dataloader = info.context["sqlalchemy_loader"] | |||
| mapper = inspect(db.{{ cls.name }}) | |||
| {%- if related_field.multivalued %} | |||
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Can you explain this change? Just curious how it still works for plural entities like this one 😅 🪄
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This just pulls the related_field's name as it's defined in the schema; so for the example you linked, the class is Sample and the related_field we're looking at is sequencing_reads!
I'm making the assumption here that since the field is multivalued, the name defined in the schema is plural.
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Ticket: CZID-8857
typesto use the proper field name when getting the relationship from the mappersqlalchemy.exc.IntegrityError: (psycopg.errors.NotNullViolation) null value in column "file_id" of relation "reference_genome" violates not-null constraintFileFactory.update_file_idsso all file columns are populatedExample of querying CG data generated from
seed.py: