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)))