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"""Test functionalities of I/O in JSON format."""
import json
from importlib.resources import files
from pathlib import Path
from typing import Any, Callable, Dict, Union
import pytest
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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