def result_file_validate(experiment, result_file):
desc = "experiment.result_files"
check_from_defs(desc, result_file_fields, result_file)
if result_file.ftype is ResultFileType.expression_matrix:
result_file_expression_validate(desc, experiment, result_file)
else:
result_file_model_validate(desc, experiment, result_file)
def experiment_validate(experiment):
desc = "experiment"
check_from_defs(desc, experiment_fields, experiment)
libraries_validate(experiment)
if len(get_extra_libraries(experiment)) > 0:
extra_libraries_validate(experiment)
experssion_units_validate(experiment)
def entry_validate(entry):
desc = "entry"
check_from_defs(desc, entry_fields, entry)
try:
validate_symbolic_ident(entry.entry_id)
except LrgaspException as ex:
raise LrgaspException(f"invalid {desc}.{fld_entry_id.name}") from ex
for contact in entry.contacts:
entry_contact_validate(contact)
def _validate_extra_libraries(experiment_md):
if experiment_md.data_category not in (DataCategory.long_short,
DataCategory.freestyle):
raise LrgaspException(
"experiment extra_libraries may only be specified for 'long_short' or 'freestyle' experiments"
)
dups = find_dups([el.acc for el in experiment_md.extra_libraries])
if len(dups) > 0:
raise LrgaspException(
f"duplicate accession in extra libraries: {dups}")
for ilib in range(len(experiment_md.extra_libraries)):
check_from_defs(f"experiment_md.extra_libraries[{ilib}]",
extra_libraries_fields,
experiment_md.extra_libraries[ilib])
def experiment_validate(experiment):
desc = "experiment"
check_from_defs(desc, experiment_fields, experiment)
if experiment.experiment_type is ExperimentType.expression:
if fld_model_experiment_id.name not in experiment:
raise LrgaspException(f"{desc} must specify experiment.{fld_model_experiment_id.name} for {experiment.experiment_type} experiments")
else:
if fld_model_experiment_id.name in experiment:
raise LrgaspException(f"{desc} must not specify experiment.{fld_model_experiment_id.name} for {experiment.experiment_type} experiments")
for data_file in experiment.data_files:
data_file_validate(data_file)
for result_file in experiment.result_files:
result_file_validate(experiment, result_file)
def entry_validate(entry):
desc = "entry"
check_from_defs(desc, entry_fields, entry)
try:
validate_symbolic_ident(entry.entry_id)
except LrgaspException as ex:
raise LrgaspException(f"invalid {desc} {fld_entry_id.name}") from ex
challenge_id = validate_entry_ident(entry.entry_id)
if entry.challenge_id != challenge_id:
raise LrgaspException(
f"invalid {desc} {fld_entry_id.name} entry_id {entry.entry-id} prefix does not match challenge_id {entry.challenge_id}"
)
for contact in entry.contacts:
entry_contact_validate(contact)
def load(entry_json):
"""load and validate entry metadata"""
try:
with gopen(entry_json) as fh:
entry_md = json.load(fh, object_pairs_hook=ObjDict)
except (json.decoder.JSONDecodeError, UnicodeDecodeError) as ex:
raise LrgaspException(
f"parse of entry metadata (JSON) failed: {entry_json}") from ex
try:
check_from_defs("entry", entry_fields, entry_md)
# add non-serialized fields after field check
entry_md.experiments = None
entry_md.entry_dir = None
entry_md.entry_json = entry_json
entry_validate(entry_md)
except LrgaspException as ex:
raise LrgaspException(
f"validation of entry metadata failed: {entry_json}") from ex
return entry_md
def _validate_software(experiment_md):
for isoft in range(len(experiment_md.software)):
check_from_defs(f"experiment_md.software[{isoft}]",
experiment_software_fields,
experiment_md.software[isoft])
def entry_contact_validate(contact):
desc = "entry.contacts"
check_from_defs(desc, entry_contact_fields, contact)
def data_file_validate(data_file):
desc = "experiment.data_files"
check_from_defs(desc, data_file_fields, data_file)
if (fld_acc.name not in data_file) and (fld_url not in data_file):
raise LrgaspException(f"{desc} must specify at least one of {fld_acc.name} or {fld_url.name}")
def extra_library_validate(extra_library):
desc = "experiment.extra_libraries"
check_from_defs(desc, extra_library_fields, extra_library)
def extra_library_validate(extra_libraries, ilib):
desc = f"experiment_md.extra_libraries[{ilib}]"
check_from_defs(desc, extra_libraries_fields, extra_libraries[ilib])
def entry_contact_validate(contact):
check_from_defs("entry.contacts", entry_contact_fields, contact)
