Source code for test_json

"""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

[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")