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!lamin init --storage ./run-tests --name run-tests --schema bionty import lamindb as ln import bionty as bt import pandas as pd mondo_diseases = [ "Alzheimer's disease", "Parkinson's disease", "Breast cancer", "Colorectal cancer", "Asthma", "Diabetes mellitus type 2", "Hypertension", "Multiple sclerosis", "Osteoporosis", "Cystic fibrosis", "Huntington's disease", "Leukemia", "Lung cancer", "Prostate cancer", "Rheumatoid arthritis", "Sickle cell anemia", "Thalassemia", "Schizophrenia", "Bipolar disorder", "Liver cirrhosis", "Chronic obstructive pulmonary disease", "Pancreatic cancer", "Psoriasis", "Amyotrophic lateral sclerosis", "Epilepsy" ] fake_diseases = [f"FakeDisease_{i}" for i in range(1, 26)] df = pd.DataFrame({ "Disease": mondo_diseases + fake_diseases, }) curator = ln.Curator.from_df(df, categoricals={"Disease": bt.Disease.name}, verbosity="hint") curator.validate()
I expected this to also print the successfully validated terms.
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The text was updated successfully, but these errors were encountered:
In such cases
# inspect from public (bionty only) if hasattr(registry, "public"): verbosity = settings.verbosity try: settings.verbosity = "error" public_records = registry.from_values( non_validated, field=field, **kwargs_current, ) values_validated += [getattr(r, field.field.name) for r in public_records] finally: settings.verbosity = verbosity validated_hint_print = validated_hint_print or f".add_validated_from('{key}')" n_validated = len(values_validated) if n_validated > 0: _log_mapping_info() logger.warning( f"found {colors.yellow(n_validated)} validated terms: " f"{colors.yellow(', '.join(values_validated[:10]) + ', ...' if len(values_validated) > 10 else ', '.join(values_validated))}\n → save terms via " f"{colors.yellow(validated_hint_print)}" )
n_validated is apparently always 0. Hmm
n_validated
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I expected this to also print the successfully validated terms.
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The text was updated successfully, but these errors were encountered: