"""Test functionalities of I/O in JSON format."""
import json
from os.path import join
from typing import Any, Dict, Union
import pytest
from importlib_resources import open_text
from cobra import Model
from cobra import io as cio
from cobra.test.test_io.conftest import compare_models
@pytest.fixture(scope="module")
[docs]def json_schema_v1() -> Dict[str, Union[str, bool, Any]]:
"""Fixture for cobra JSON-schema."""
with open_text(cio, "schema_v1.json") as handle:
schema_v1 = json.load(handle)
return schema_v1
[docs]def test_validate_json(
data_directory: str, json_schema_v1: Dict[str, Union[str, bool, Any]]
) -> None:
"""Validate file according to JSON-schema."""
jsonschema = pytest.importorskip("jsonschema")
with open(join(data_directory, "mini.json"), "r", encoding="utf-8") as infile:
loaded = json.load(infile)
assert jsonschema.validate(loaded, json_schema_v1) is None
[docs]def test_load_json_model(data_directory: str, mini_model: Model) -> None:
"""Test the reading of JSON model."""
json_model = cio.load_json_model(join(data_directory, "mini.json"))
assert compare_models(mini_model, json_model) is None
[docs]def test_save_json_model(
tmpdir: str,
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 = tmpdir.join("mini.json")
cio.save_json_model(mini_model, output_file.strpath, pretty=True)
# validate against JSONSchema
with open(str(output_file), "r") as infile:
loaded = json.load(infile)
assert jsonschema.validate(loaded, json_schema_v1) is None
[docs]def test_reaction_bounds_json(data_directory: str, tmp_path: str) -> None:
"""Test reading and writing of model with inf bounds in JSON."""
# Path to XML file with INF bounds
path_to_xml_inf_file = join(data_directory, "fbc_ex1.xml")
model_xml_inf = cio.read_sbml_model(path_to_xml_inf_file)
path_to_output = join(str(tmp_path), "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 = join(data_directory, "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")