laminlabs / lamindb

A data framework for biology.
https://docs.lamin.ai
Apache License 2.0
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🐛 `print_types=True` seems to lead to weird output on main branch, it's OK in the release #2100

Open falexwolf opened 1 month ago

falexwolf commented 1 month ago

It's OK In prod (e.g. here https://docs.lamin.ai/scrna#populate-metadata-registries-based-on-an-artifact)

image

I just saw it in a notebook from @sunnyosun

sunnyosun commented 1 month ago
Artifact(uid='kOUejI4cVj3rHcOG0000', is_latest=True, description='mock AnnData', suffix='.h5ad', type='dataset', size=20336, hash='8z6kAdTVBaDIDuA6aivzNg', n_observations=3, _hash_type='md5', _accessor='AnnData', visibility=1, _key_is_virtual=True, created_at=2024-10-22 19:44:26 UTC)
  Provenance
    .storage: Storage = 's3://lamin-us-west-2/6uvjeXbzpPH2'
    .transform: Transform = 'Curate datasets'
    .run: Run = '2024-10-22 19:37:01 UTC'
    .created_by: User = 'sunnyosun'
  Labels
    .cell_types: CellType
  Simple fields
    .uid: CharField
    .name: CharField
    .ontology_id: CharField
    .abbr: CharField
    .synonyms: TextField
    .description: TextField
    .created_at: DateTimeField
    .updated_at: DateTimeField
  Relational fields
    .created_by: User
    .run: Run
    .source: bionty.Source
    .parents: bionty.CellType
    .artifacts: Artifact
  Bionty fields
    .children: bionty.CellType = 'astrocyte', 'cerebral cortex pyramidal neuron', 'oligodendrocyte'
    .experimental_factors: ExperimentalFactor
  Simple fields
    .uid: CharField
    .name: CharField
    .ontology_id: CharField
    .abbr: CharField
    .synonyms: TextField
    .description: TextField
    .molecule: TextField
    .instrument: TextField
    .measurement: TextField
    .created_at: DateTimeField
    .updated_at: DateTimeField
  Relational fields
    .created_by: User
    .run: Run
    .source: bionty.Source
    .parents: bionty.ExperimentalFactor
    .artifacts: Artifact
  Bionty fields
    .children: bionty.ExperimentalFactor = 'single-cell RNA sequencing'
    .ulabels: ULabel
  Simple fields
    .uid: CharField
    .name: CharField
    .description: TextField
    .reference: CharField
    .reference_type: CharField
    .created_at: DateTimeField
    .updated_at: DateTimeField
  Relational fields
    .created_by: User
    .run: Run
    .parents: ULabel
    .transforms: Transform
    .children: ULabel
    .artifacts: Artifact
    .collections: Collection = 'D0001', 'D0002', 'D0003'
  Features
    'assay_ontology_id': cat[bionty.ExperimentalFactor] = 'single-cell RNA sequencing'
    'cell_type': cat[bionty.CellType] = 'astrocyte', 'cerebral cortex pyramidal neuron', 'oligodendrocyte'
    'donor': cat[ULabel] = 'D0001', 'D0002', 'D0003'
  Feature sets
    'var' = 'CD4', 'TCF7', 'CD8A', 'CD3E', 'PDCD1'
    'obs' = 'cell_type', 'assay_ontology_id', 'donor'