lamindb.Transform

class lamindb.Transform(name: str, key: str | None = None, version: str | None = None, type: lnschema_core.types.TransformType | None = None, is_new_version_of: lnschema_core.models.Transform | None = None)

Bases: Registry, HasParents, IsVersioned

Transformations of artifacts & collections.

A transform can refer to a script, a notebook, or a pipeline. If you execute a transform, you generate a run of a transform (Run). A run has input and output data.

A pipeline is typically created with a workflow tool (Nextflow, Snakemake, Prefect, Flyte, MetaFlow, redun, Airflow, …) and stored in a versioned repository.

Transforms are versioned so that a given transform maps 1:1 to a specific version of code. If you switch on sync_git_repo, any script-like transform is synced its hashed state in a git repository.

Parameters:

• name – str A name or title.

• key – str | None = None A short name or path-like semantic key.

• version – str | None = None A version.

• type – TransformType | None = "pipeline" Either 'notebook', 'pipeline' or 'script'.

• is_new_version_of – Transform | None = None An old version of the transform.

See also

lamindb.track()

Globally track a script, notebook or pipeline run.

Run

Executions of scripts, notebooks or pipelines.

Notes

• Track notebooks & scripts

• Data lineage

• Redun

• Nextflow

• Snakemake

Examples

Create a transform for a pipeline:

>>> transform = ln.Transform(name="Cell Ranger", version="7.2.0", type="pipeline")
>>> transform.save()

Create a transform from a notebook:

>>> ln.track()

View parents of a transform:

>>> transform.view_parents()

Fields

id AutoField

Internal id, valid only in one DB instance.

uid CharField

Universal id.

name CharField

A name or title. For instance, a pipeline name, notebook title, etc.

key CharField

A key for concise reference & versioning (optional).

version CharField

Version (default None).

Defines version of a family of records characterized by the same stem_uid.

Consider using semantic versioning with Python versioning.

description CharField

A description (optional).

type CharField

Transform type (default "pipeline").

latest_report ForeignKey

Latest run report.

source_code ForeignKey

Source of the transform if stored as artifact within LaminDB.

reference CharField

Reference for the transform, e.g., a URL.

reference_type CharField

Type of reference, e.g., ‘url’ or ‘doi’.

created_at DateTimeField

Time of creation of record.

updated_at DateTimeField

Time of last update to record.

created_by ForeignKey

Creator of record, a User.

ulabels ManyToManyField

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.

parents ManyToManyField

Parent transforms (predecessors) in data flow.

These are auto-populated whenever a transform loads an artifact or collection as run input.

Methods

delete()

Return type:

None

get_type_display(*, field=<django.db.models.fields.CharField: type>)