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"""Test functionalities of I/O in JSON format."""
import json
from pathlib import Path
from typing import Any, Callable, Dict, Union
import pytest
from importlib_resources import files
from cobra import Model
from cobra import io as cio
@pytest.fixture(scope="module")
def json_schema_v1() -> Dict[str, Union[str, bool, Any]]:
"""Fixture for cobra JSON-schema."""
with files(cio).joinpath("schema_v1.json").open("r") as handle:
schema_v1 = json.load(handle)
return schema_v1
def test_validate_json(
cobra_data_directory: Path, json_schema_v1: Dict[str, Union[str, bool, Any]]
) -> None:
"""Validate file according to JSON-schema."""
jsonschema = pytest.importorskip("jsonschema")
with open(
cobra_data_directory.joinpath("mini.json"), "r", encoding="utf-8"
) as infile:
loaded = json.load(infile)
assert jsonschema.validate(loaded, json_schema_v1) is None
def test_load_json_model(
compare_models: Callable, cobra_data_directory: Path, mini_model: Model
) -> None:
"""Test the reading of JSON model."""
json_model = cio.load_json_model(cobra_data_directory / "mini.json")
assert compare_models(mini_model, json_model) is None
json_model = cio.load_json_model(str(cobra_data_directory / "mini.json"))
assert compare_models(mini_model, json_model) is None
with open(cobra_data_directory / "mini.json", "r") as json_handle:
json_model = cio.load_json_model(json_handle)
assert compare_models(mini_model, json_model) is None
def test_save_json_model(
tmp_path: Path,
mini_model: Model,
json_schema_v1: Dict[str, Union[str, bool, Any]],
) -> None:
"""Test the writing of JSON model."""
jsonschema = pytest.importorskip("jsonschema")
output_file = tmp_path.joinpath("mini.json")
cio.save_json_model(mini_model, output_file, pretty=True)
# validate against JSONSchema
with open(output_file, "r") as infile:
loaded = json.load(infile)
assert jsonschema.validate(loaded, json_schema_v1) is None
output_file.unlink()
cio.save_json_model(mini_model, str(output_file), pretty=True)
# validate against JSONSchema
with open(output_file, "r") as infile:
loaded = json.load(infile)
assert jsonschema.validate(loaded, json_schema_v1) is None
output_file.unlink()
with output_file.open("w+") as json_outfile:
cio.save_json_model(mini_model, json_outfile, pretty=True)
# validate against JSONSchema
json_outfile.seek(0, 0)
loaded = json.load(json_outfile)
assert jsonschema.validate(loaded, json_schema_v1) is None
def test_reaction_bounds_json(data_directory: Path, tmp_path: Path) -> None:
"""Test reading and writing of model with inf bounds in JSON."""
# Path to XML file with INF bounds
path_to_xml_inf_file = data_directory / "fbc_ex1.xml"
model_xml_inf = cio.read_sbml_model(path_to_xml_inf_file)
path_to_output = tmp_path.joinpath("fbc_ex1_json.json")
# Saving model with inf bounds in json form without error
cio.save_json_model(model_xml_inf, path_to_output)
# Path to JSON file with INF bounds
path_to_JSON_inf_file = data_directory.joinpath("JSON_with_inf_bounds.json")
model_json_inf = cio.load_json_model(path_to_JSON_inf_file)
assert model_json_inf.reactions[0].upper_bound == float("inf")
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