def test_update_rdf_using_dicts_in_place(unet2d_nuclei_broad_latest):
from bioimageio.spec.commands import update_rdf
source = unet2d_nuclei_broad_latest
update = dict(name="updated",
outputs=[{
"name": "updated",
"halo": ["KEEP", "DROP", 0, 9, 9]
}])
update_rdf(source, update, output=source)
actual = source
assert actual["name"] == "updated"
assert actual["outputs"][0]["name"] == "updated"
assert actual["outputs"][0]["halo"] == [0, 0, 9, 9]
def update_rdf(
source: str = typer.Argument(
..., help="relative file path or URI to RDF source"),
update: str = typer.Argument(
..., help="relative file path or URI to (partial) RDF as update"),
output: Path = typer.Argument(..., help="Path to save the updated RDF to"),
validate: bool = typer.Option(
True, help="Whether or not to validate the updated RDF"),
):
"""Update a given RDF with a (partial) RDF-like update"""
try:
commands.update_rdf(source, update, output, validate)
ret_code = 0
except Exception as e:
print(f"update-rdf failed with {e}")
ret_code = 1
sys.exit(ret_code)
def test_update_rdf_using_paths(unet2d_nuclei_broad_base_path, tmp_path):
from bioimageio.spec.commands import update_rdf
in_path = unet2d_nuclei_broad_base_path / "rdf.yaml"
assert in_path.exists()
update_path = tmp_path / "update.yaml"
yaml.dump(
dict(name="updated",
outputs=[{
"name": "updated",
"halo": ["KEEP", "DROP", 0, 9, 9]
}]), update_path)
out_path = tmp_path / "output.yaml"
update_rdf(in_path, update_path, out_path)
actual = yaml.load(out_path)
assert actual["name"] == "updated"
assert actual["outputs"][0]["name"] == "updated"
assert actual["outputs"][0]["halo"] == [0, 0, 9, 9]
def test_update_rdf_using_rd(unet2d_nuclei_broad_latest):
from bioimageio.spec.commands import update_rdf
source = load_raw_resource_description(unet2d_nuclei_broad_latest)
update = dict(name="updated",
outputs=[{
"name": "updated",
"halo": ["KEEP", "DROP", 0, 9, 9]
}])
actual = update_rdf(source, update)
assert isinstance(actual, raw_nodes.Model)
assert actual.name == "updated"
assert actual.outputs[0].name == "updated"
assert actual.outputs[0].halo == [0, 0, 9, 9]