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# SPDX-License-Identifier: Apache-2.0
"""
CWL file formats utilities.
For more information, please visit https://www.commonwl.org/user_guide/16-file-formats/
"""
from typing import Optional, Union
from rdflib import OWL, RDFS, Graph, URIRef
from schema_salad.exceptions import ValidationException
from schema_salad.utils import aslist, json_dumps
from cwl_utils.types import CWLObjectType
def formatSubclassOf(
fmt: str, cls: str, ontology: Optional[Graph], visited: set[str]
) -> bool:
"""Determine if `fmt` is a subclass of `cls`."""
if URIRef(fmt) == URIRef(cls):
return True
if ontology is None:
return False
if fmt in visited:
return False
visited.add(fmt)
uriRefFmt = URIRef(fmt)
for _s, _p, o in ontology.triples((uriRefFmt, RDFS.subClassOf, None)):
# Find parent classes of `fmt` and search upward
if formatSubclassOf(o, cls, ontology, visited):
return True
for _s, _p, o in ontology.triples((uriRefFmt, OWL.equivalentClass, None)):
# Find equivalent classes of `fmt` and search horizontally
if formatSubclassOf(o, cls, ontology, visited):
return True
for s, _p, _o in ontology.triples((None, OWL.equivalentClass, uriRefFmt)):
# Find equivalent classes of `fmt` and search horizontally
if formatSubclassOf(s, cls, ontology, visited):
return True
return False
def check_format(
actual_file: Union[CWLObjectType, list[CWLObjectType]],
input_formats: Union[list[str], str],
ontology: Optional[Graph],
) -> None:
"""Confirm that the format present is valid for the allowed formats."""
for afile in aslist(actual_file):
if not afile:
continue
if "format" not in afile:
raise ValidationException(
f"File has no 'format' defined: {json_dumps(afile, indent=4)}"
)
for inpf in aslist(input_formats):
if afile["format"] == inpf or formatSubclassOf(
afile["format"], inpf, ontology, set()
):
return
raise ValidationException(
f"File has an incompatible format: {json_dumps(afile, indent=4)}"
)
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