Test bionty

import lamindb_setup as ln_setup
from subprocess import getoutput
import pandas as pd

Pass bionty to init:

ln_setup.init(storage="mydata2", schema="bionty")

Check whether sources are written:

from lnschema_bionty import PublicSource

sources_df = pd.DataFrame(PublicSource.objects.all().values())
sources_df.head()

from bionty_base import settings as bionty_base_settings

assert sources_df.shape[0] > 0
assert bionty_base_settings.lamindb_sources.exists()

Test what happens if we accidentally re-init the instance:

output = getoutput("lamin init --storage mydata2 --schema bionty")
print(output)

Now, let’s remove/corrupt the instance settings file so that the init is actually triggered:

ln_setup.settings.instance._get_settings_file().unlink()
output = getoutput("lamin init --storage mydata2 --schema bionty")
print(output)

Check that everything is still in place:

sources_df = pd.DataFrame(PublicSource.objects.all().values())
sources_df.head()

!lamin delete --force mydata2