lamindb.Storage¶

class lamindb.Storage(root: str, type: str, region: str | None)¶

Bases: Record, TracksRun, TracksUpdates

Storage locations.

A storage location is either a directory/folder (local or in the cloud) or an entire S3/GCP bucket.

A LaminDB instance can manage and link multiple storage locations. But any storage location is managed by at most one LaminDB instance.

See also

storage: Default storage.
StorageSettings: Storage settings.

Examples

Configure the default storage location upon initiation of a LaminDB instance:

lamin init --storage ./mydata # or "s3://my-bucket" or "gs://my-bucket"

View the default storage location:

>>> ln.settings.storage
PosixPath('/home/runner/work/lamindb/lamindb/docs/guide/mydata')

Dynamically change the default storage:

>>> ln.settings.storage = "./storage_2" # or a cloud bucket

Attributes¶

property path: UPath¶

Bucket or folder path.

Cloud storage bucket:

>>> ln.Storage("s3://my-bucket").save()

Directory/folder in cloud storage:

>>> ln.Storage("s3://my-bucket/my-directory").save()

Local directory/folder:

>>> ln.Storage("./my-directory").save()

Simple fields¶

uid: str¶: Universal id, valid across DB instances.

root: str¶: Root path of storage. n s3 path. local path, etc. (required).

description: str | None¶: A description of what the storage location is used for (optional).

type: str¶: Can be “local” vs. “s3” vs. “gs”.

region: str | None¶: Cloud storage region, if applicable.

instance_uid: str | None¶: Instance that manages this storage location.

created_at: datetime¶: Time of creation of record.

updated_at: datetime¶: Time of last update to record.

Relational fields¶

created_by: User¶: Creator of record.

run: Run | None¶: Last run that created or updated the record.

artifacts: Artifact¶: Artifacts contained in this storage location.

Class methods¶

classmethod df(include=None, join='inner', limit=100)¶

Convert to pd.DataFrame.

By default, shows all direct fields, except updated_at.

Use parameter include to include other fields.

Parameters:

include (str | list[str] | None, default: None) – Related fields to include as columns. Takes strings of form "labels__name", "cell_types__name", etc. or a list of such strings.
join (str, default: 'inner') – The join parameter of pandas.
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

>>> labels = [ln.ULabel(name="Label {i}") for i in range(3)]
>>> ln.save(labels)
>>> ln.ULabel.filter().df(include=["created_by__name"])

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").df()

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.

Return type:

Record

Returns:

A record.

Raises:

lamindb.core.exceptions.DoesNotExist – In case no matching record is found.

See also

Guide: Query & search registries
Django documentation: Queries

Examples

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

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.

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 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 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¶

async adelete(using=None, keep_parents=False)¶

async arefresh_from_db(using=None, fields=None, from_queryset=None)¶

async asave(*args, force_insert=False, force_update=False, using=None, update_fields=None)¶

clean()¶: Hook for doing any extra model-wide validation after clean() has been called on every field by self.clean_fields. Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field defined by NON_FIELD_ERRORS.

clean_fields(exclude=None)¶: Clean all fields and raise a ValidationError containing a dict of all validation errors if any occur.

date_error_message(lookup_type, field_name, unique_for)¶

delete()¶

Delete.

Return type:: None

get_constraints()¶

get_deferred_fields()¶: Return a set containing names of deferred fields for this instance.

prepare_database_save(field)¶

refresh_from_db(using=None, fields=None, from_queryset=None)¶

Reload field values from the database.

By default, the reloading happens from the database this instance was loaded from, or by the read router if this instance wasn’t loaded from any database. The using parameter will override the default.

Fields can be used to specify which fields to reload. The fields should be an iterable of field attnames. If fields is None, then all non-deferred fields are reloaded.

When accessing deferred fields of an instance, the deferred loading of the field will call this method.

save(*args, **kwargs)¶

Save.

Always saves to the default database.

Return type:: Record

save_base(raw=False, force_insert=False, force_update=False, using=None, update_fields=None)¶

Handle the parts of saving which should be done only once per save, yet need to be done in raw saves, too. This includes some sanity checks and signal sending.

The ‘raw’ argument is telling save_base not to save any parent models and not to do any changes to the values before save. This is used by fixture loading.

serializable_value(field_name)¶

Return the value of the field name for this instance. If the field is a foreign key, return the id value instead of the object. If there’s no Field object with this name on the model, return the model attribute’s value.

Used to serialize a field’s value (in the serializer, or form output, for example). Normally, you would just access the attribute directly and not use this method.

unique_error_message(model_class, unique_check)¶

validate_constraints(exclude=None)¶

validate_unique(exclude=None)¶: Check unique constraints on the model and raise ValidationError if any failed.