lamindb.Transform#

class lamindb.Transform(name: str, short_name: Optional[str] = None, version: Optional[str] = None, type: Optional[TransformType] = None, reference: Optional[str] = None, reference_type: Optional[str] = None, is_new_version_of: Optional[Transform] = None)#

Bases: Registry, HasParents

Transforms of files & datasets.

Pipelines, notebooks, app uploads.

A pipeline is versioned software that transforms data. This can be anything from typical workflow tools (Nextflow, Snakemake, Prefect, Apache Airflow, etc.) to simple (versioned) scripts.

Parameters:

  • name – str A name or title.

  • short_name – Optional[str] = None A short name or abbreviation.

  • version – Optional[str] = None A version.

  • type – Optional[TransformType] = None Either 'notebook', 'pipeline' or 'app'. If None, defaults to 'notebook' within an IPython environment and to 'pipeline' outside of it.

  • reference – Optional[str] = None A reference like a URL.

  • is_new_version_of – Optional[Transform] = None An old version of the transform.

See also

lamindb.track()

Track global Transform & Run for a notebook or pipeline.

Run

Executions of the transform.

Notes

For more info, see tutorial: Data flow.

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

Transform name or title, a pipeline name, notebook title, etc..

short_name CharField

A short name (optional).

version CharField

Version (default None).

Use this to label different versions of a transform.

Consider using semantic versioning with Python versioning.

type CharField

Transform type.

Defaults to "notebook" if run from ipython and to "pipeline" if run from python.

If run from the UI, it defaults to app.

latest_report ForeignKey

Latest run report.

source_file ForeignKey

Source of the transform if stored as file within LaminDB.

reference CharField

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

reference_type CharField

Type of reference, e.g., github link.

initial_version ForeignKey

Initial version of the transform, a Transform record.

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.

parents ManyToManyField

Parent transforms (predecessors) in data flow.

These are auto-populated whenever a transform loads a file as run input.

Methods

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