def _validate_experiment_library(entry_md, experiment_md, rna_seq_md, library): sample = rna_seq_md.get_run_by_file_acc(library).sample valid_samples = get_challenge_samples(entry_md.challenge_id) if sample not in valid_samples: raise LrgaspException( f"library '{library}' sample '{sample}' is not valid for challenge '{entry_md.challenge_id}'," " expected one of {}".format(iter_to_str(valid_samples)))
def validate_samples(entry_md): "validate that all samples are covered (requires all experiments" entry_samples = get_entry_samples(entry_md) challenge_samples = get_challenge_samples(entry_md.challenge_id) if entry_samples != challenge_samples: raise LrgaspException( "{} must have all of the samples '{}', only '{}' were found". format(challenge_desc(entry_md.challenge_id), iter_to_str(challenge_samples), iter_to_str(entry_samples)))
def validate_challenge_samples(entry_md): """validate that all samples for entry category challenge are covered; non-freestyle only (requires all experiments loaded)""" entry_samples = set(entry_md.samples) entry_category_samples = get_entry_category_samples(entry_md) challenge_samples = get_challenge_samples(entry_md.challenge_id) required_samples = entry_category_samples & challenge_samples if entry_samples != required_samples: raise LrgaspException( f"entry must use all of the available samples for {challenge_desc(entry_md.challenge_id)}," f" need '{iter_to_str(challenge_samples)}', only '{iter_to_str(entry_samples)}' were found" )
def _validate_sample_compat(rna_seq_md, experiment_md, run_type): valid_samples = get_challenge_samples(experiment_md.challenge_id) if run_type.sample not in valid_samples: raise LrgaspException( f"sample '{run_type.sample}' is not valid for challenge '{experiment_md.challenge_id}'," " expected one of {}".format(iter_to_str(valid_samples)))
def _validate_experiment_library(entry, experiment, rna_seq_md, library): sample = rna_seq_md.get_run_by_file_acc(library).sample valid_samples = get_challenge_samples(entry.challenge_id) if sample not in valid_samples: raise LrgaspException(f"library {library} sample {sample} is not valid for challenge {entry.challenge_id}," " expected one of {}".format(set_to_str(valid_samples)))