def test_save_as_json_with_minimal_json(tmp_path):
filename = tmp_path / "test.json"
spectrum1 = Spectrum(mz=numpy.array([100, 200, 300], dtype="float"),
intensities=numpy.array([10, 10, 500], dtype="float"),
metadata={"test_field": "test1"})
save_as_json([spectrum1], filename)
with open(filename) as f:
spectrum_imports = json.load(f)
expected = [{"test_field": "test1", "peaks_json": [[100.0, 10.0], [200.0, 10.0], [300.0, 500.0]]}]
assert spectrum_imports == expected, "Saved Spectrum not identical to expected JSON Document"
def test_load_from_json_zero_peaks(tmp_path):
spectrum1 = SpectrumBuilder().with_metadata(
{"test_field": "test1"}).build()
filename = tmp_path / "test.json"
save_as_json([spectrum1], filename)
# test if file exists
assert os.path.isfile(filename)
# Test if content of json file is correct
spectrum_imports = load_from_json(filename)
assert len(spectrum_imports) == 0, "Spectrum without peaks should be skipped"
def test_load_from_json_zero_peaks(tmp_path):
spectrum1 = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"test_field": "test1"})
filename = tmp_path / "test.json"
save_as_json([spectrum1], filename)
# test if file exists
assert os.path.isfile(filename)
# Test if content of json file is correct
spectrum_imports = load_from_json(filename)
assert len(spectrum_imports) == 0, "Spectrum without peaks should be skipped"
def test_save_as_json_with_minimal_json(tmp_path):
filename = tmp_path / "test.json"
mz = numpy.array([100, 200, 300], dtype="float")
intensities = numpy.array([10, 10, 500], dtype="float")
builder = SpectrumBuilder().with_mz(mz).with_intensities(intensities)
spectrum1 = builder.with_metadata({"test_field": "test1"},
metadata_harmonization=False).build()
save_as_json([spectrum1], filename)
with open(filename, encoding="utf-8") as f:
spectrum_imports = json.load(f)
expected = [{"test_field": "test1", "peaks_json": [
[100.0, 10.0], [200.0, 10.0], [300.0, 500.0]]}]
assert spectrum_imports == expected, "Saved Spectrum not identical to expected JSON Document"
def test_save_and_load_json_single_spectrum(tmp_path):
"""Test saving spectrum to .json file"""
spectrum = Spectrum(mz=numpy.array([100, 200, 300], dtype="float"),
intensities=numpy.array([10, 10, 500], dtype="float"),
metadata={"charge": -1,
"inchi": '"InChI=1S/C6H12"',
"precursor_mz": 222.2,
"test_field": "test"})
# Write to test file
filename = os.path.join(tmp_path, "test.json")
save_as_json(spectrum, filename)
# test if file exists
assert os.path.isfile(filename)
# Test if content of json file is correct
spectrum_import = load_from_json(filename)[0]
assert spectrum_import == spectrum, "Original and saved+loaded spectrum not identical"
def test_save_and_load_json_spectrum_list(tmp_path):
"""Test saving spectrum list to .json file"""
spectrum1 = Spectrum(mz=numpy.array([100, 200, 300], dtype="float"),
intensities=numpy.array([10, 10, 500], dtype="float"),
metadata={"test_field": "test1"})
spectrum2 = Spectrum(mz=numpy.array([100, 200, 300], dtype="float"),
intensities=numpy.array([10, 10, 500], dtype="float"),
metadata={"test_field": "test2"})
# Write to test file
filename = os.path.join(tmp_path, "test.json")
save_as_json([spectrum1, spectrum2], filename)
# test if file exists
assert os.path.isfile(filename)
# Test if content of json file is correct
spectrum_imports = load_from_json(filename)
assert spectrum_imports[0] == spectrum1, "Original and saved+loaded spectrum not identical"
assert spectrum_imports[1] == spectrum2, "Original and saved+loaded spectrum not identical"
def test_save_and_load_json_spectrum_list(metadata_harmonization, tmp_path):
"""Test saving spectrum list to .json file"""
mz = numpy.array([100, 200, 300], dtype="float")
intensities = numpy.array([10, 10, 500], dtype="float")
builder = SpectrumBuilder().with_mz(mz).with_intensities(intensities)
spectrum1 = builder.with_metadata({"test_field": "test1"},
metadata_harmonization=metadata_harmonization).build()
spectrum2 = builder.with_metadata({"test_field": "test2"},
metadata_harmonization=metadata_harmonization).build()
# Write to test file
filename = os.path.join(tmp_path, "test.json")
save_as_json([spectrum1, spectrum2], filename)
# test if file exists
assert os.path.isfile(filename)
# Test if content of json file is correct
spectrum_imports = load_from_json(filename, metadata_harmonization=metadata_harmonization)
assert spectrum_imports[0] == spectrum1, "Original and saved+loaded spectrum not identical"
assert spectrum_imports[1] == spectrum2, "Original and saved+loaded spectrum not identical"