Reproducibility¶
Bio2BEL database models.
Bio2BEL adds hooks to the populate and drop_all methods in the bio2bel.AbstractManager class to track when they
are run and therefore create provenance information for a given analysis.
The most recent population action from a given module can be retrieved with the following code:
from bio2bel.models import Action, _make_session
from sqlalchemy import desc
session = _make_session()
action = session.query(Action).filter(Action.resource == 'kegg').order_by(Action.created.desc()).first()
-
class
bio2bel.models.Action(**kwargs)[source]¶ Represents an update, dropping, population, etc. to the database.
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
-
resource¶ The normalized name of the Bio2BEL package (e.g., hgnc, chebi, etc)
-
created¶ The date and time of upload
-
static
make_populate_failed(resource)[source]¶ Make a
populate_failedinstance ofAction.- Return type
-
classmethod
store_populate(resource, session=None)[source]¶ Store a “populate” event.
- Parameters
resource (
str) – The normalized name of the resource to store
Example: >>> from bio2bel.models import Action >>> Action.store_populate(‘hgnc’)
- Return type
-
classmethod
store_populate_failed(resource, session=None)[source]¶ Store a “populate failed” event.
- Parameters
resource (
str) – The normalized name of the resource to store
Example: >>> from bio2bel.models import Action >>> Action.store_populate_failed(‘hgnc’)
- Return type
-