lamindb.models.FeatureValue¶

class lamindb.models.FeatureValue(*args, **kwargs)¶

Bases: SQLRecord, TracksRun

Non-categorical features values.

Categorical feature values are stored in their respective registries: ULabel, CellType, etc.

Unlike for ULabel, in FeatureValue, values are grouped by features and not by an ontological hierarchy.

Simple fields¶

value: Any¶: The JSON-like value.

hash: str¶: Value hash.

is_locked: bool¶: Whether the record is locked for edits.

created_at: datetime¶: Time of creation of record.

Relational fields¶

branch: Branch¶: Whether record is on a branch or in another “special state”.

space: Space¶: The space in which the record lives.

created_by: User¶: Creator of record.

run: Run | None¶: Run that created record.

feature: Feature | None¶: The dimension metadata.

runs¶

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

artifacts¶

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

Class methods¶

classmethod get_or_create(feature, value)¶

classmethod filter(*queries, **expressions)¶

Query records.

Parameters:

queries – One or multiple Q objects.
expressions – Fields and values passed as Django query expressions.

Return type:

QuerySet

Returns:

A QuerySet.

See also

Guide: Query & search registries
Django documentation: Queries

Examples

>>> ln.ULabel(name="my label").save()
>>> ln.ULabel.filter(name__startswith="my").to_dataframe()

classmethod get(idlike=None, **expressions)¶

Get a single record.

Parameters:

idlike (int | str | None, default: None) – Either a uid stub, uid or an integer id.
expressions – Fields and values passed as Django query expressions.

Raises:

docs:lamindb.errors.DoesNotExist – In case no matching record is found.

Return type:

SQLRecord

See also

Guide: Query & search registries
Django documentation: Queries

Examples

ulabel = ln.ULabel.get("FvtpPJLJ")
ulabel = ln.ULabel.get(name="my-label")

classmethod to_dataframe(include=None, features=False, limit=100)¶

Convert to pd.DataFrame.

By default, shows all direct fields, except updated_at.

Use arguments include or feature to include other data.

Parameters:

include (str | list[str] | None, default: None) – Related fields to include as columns. Takes strings of form "ulabels__name", "cell_types__name", etc. or a list of such strings.
features (bool | list[str], default: False) – If a list of feature names, filters Feature down to these features. If True, prints all features with dtypes in the core schema module. If "queryset", infers the features used within the set of artifacts or records. Only available for Artifact and Record.
limit (int, default: 100) – Maximum number of rows to display from a Pandas DataFrame. Defaults to 100 to reduce database load.

Return type:

DataFrame

Examples

Include the name of the creator in the DataFrame:

>>> ln.ULabel.to_dataframe(include="created_by__name"])

Include display of features for Artifact:

>>> df = ln.Artifact.to_dataframe(features=True)
>>> ln.view(df)  # visualize with type annotations

Only include select features:

>>> df = ln.Artifact.to_dataframe(features=["cell_type_by_expert", "cell_type_by_model"])

classmethod search(string, *, field=None, limit=20, case_sensitive=False)¶

Search.

Parameters:

string (str) – The input string to match against the field ontology values.
field (str | DeferredAttribute | None, default: None) – The field or fields to search. Search all string fields by default.
limit (int | None, default: 20) – Maximum amount of top results to return.
case_sensitive (bool, default: False) – Whether the match is case sensitive.

Return type:

QuerySet

Returns:

A sorted DataFrame of search results with a score in column score. If return_queryset is True. QuerySet.

See also

filter() lookup()

Examples

>>> ulabels = ln.ULabel.from_values(["ULabel1", "ULabel2", "ULabel3"], field="name")
>>> ln.save(ulabels)
>>> ln.ULabel.search("ULabel2")

classmethod lookup(field=None, return_field=None)¶

Return an auto-complete object for a field.

Parameters:

field (str | DeferredAttribute | None, default: None) – The field to look up the values for. Defaults to first string field.
return_field (str | DeferredAttribute | None, default: None) – The field to return. If None, returns the whole record.
keep – When multiple records are found for a lookup, how to return the records. - "first": return the first record. - "last": return the last record. - False: return all records.

Return type:

NamedTuple

Returns:

A NamedTuple of lookup information of the field values with a dictionary converter.

See also

search()

Examples

>>> import bionty as bt
>>> bt.settings.organism = "human"
>>> bt.Gene.from_source(symbol="ADGB-DT").save()
>>> lookup = bt.Gene.lookup()
>>> lookup.adgb_dt
>>> lookup_dict = lookup.dict()
>>> lookup_dict['ADGB-DT']
>>> lookup_by_ensembl_id = bt.Gene.lookup(field="ensembl_gene_id")
>>> genes.ensg00000002745
>>> lookup_return_symbols = bt.Gene.lookup(field="ensembl_gene_id", return_field="symbol")

classmethod using(instance)¶

Use a non-default LaminDB instance.

Parameters:: instance (str | None) – An instance identifier of form “account_handle/instance_name”.
Return type:: QuerySet

Examples

>>> ln.ULabel.using("account_handle/instance_name").search("ULabel7", field="name")
            uid    score
name
ULabel7  g7Hk9b2v  100.0
ULabel5  t4Jm6s0q   75.0
ULabel6  r2Xw8p1z   75.0

Methods¶

restore()¶

Restore from trash onto the main branch.

Return type:: None

delete(permanent=None, **kwargs)¶

Delete record.

Parameters:: permanent (bool | None, default: None) – Whether to permanently delete the record (skips trash). If None, performs soft delete if the record is not already in the trash.
Return type:: None

Examples

For any SQLRecord object record, call:

>>> record.delete()

save(*args, **kwargs)¶

Save.

Always saves to the default database.

Return type:: TypeVar(T, bound= SQLRecord)