Share artifacts in immunohub

!lamin load covim/immunohub

import lamindb as ln
import lnschema_covim as cv

# track the current notebook
# run ln.track() alone to generate the tracking id
ln.track()

Query artifacts from local instance:

local_instance = "anonymous/testdata"

artifacts = (
    ln.Artifact.using(local_instance)
    .filter(created_by__handle="anonymous", suffix=".h5ad")
    .all()
)
artifacts.df()

artifact = artifacts.first()
artifact.describe()

artifact.biosamples.df()

Transfer artifact to remote instance immunohub:

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# clean up the previously ingested record in case a run fails
cv.Biosample.filter(created_by__handle="anonymous").delete()

cv.transfer_artifact_to_immunohub(artifact)

Artifact record with metadata is now on the remote instance, but the linked file stays local:

artifact.describe()

artifact.path

Share notebook

Share your notebook report in the immunohub instance by running:

ln.finish()

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# clean up CI run
cv.Biosample.filter(created_by__handle="anonymous").delete()
artifact.delete(permanent=True, storage=False)
ln.Storage.get(artifact.storage.uid).delete()
transform = ln.context.transform
run = transform.runs.all().one()
feature_set = ln.FeatureSet.filter(run=run).one()
if feature_set.artifacts.count() == 0:
    feature_set.delete()
else:
    feature_set.run = None
    feature_set.save()
run.delete()
transform.delete()