def test_derive_adduct_from_name_parametrized(metadata,
remove_adduct_from_name,
expected_adduct, expected_name,
removed_adduct):
set_matchms_logger_level("INFO")
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
with LogCapture() as log:
spectrum = derive_adduct_from_name(
spectrum_in, remove_adduct_from_name=remove_adduct_from_name)
assert spectrum.get(
"adduct") == expected_adduct, "Expected different adduct."
assert spectrum.get(
"compound_name") == expected_name, "Expected different cleaned name."
expected_log = []
if spectrum.get("compound_name") != spectrum_in.get("compound_name"):
expected_log.append(
('matchms', 'INFO',
f'Removed adduct {removed_adduct} from compound name.'))
if spectrum.get("adduct") != spectrum_in.get("adduct"):
expected_log.append(('matchms', 'INFO',
f'Added adduct {expected_adduct} to metadata.'))
log.check(*expected_log)
reset_matchms_logger()
def test_add_fingerprint_no_smiles_no_inchi():
"""Test if fingerprint it generated correctly."""
set_matchms_logger_level("INFO")
spectrum_in = SpectrumBuilder().with_metadata({"compound_name": "test name"}).build()
with LogCapture() as log:
spectrum = add_fingerprint(spectrum_in)
assert spectrum.get("fingerprint", None) is None, "Expected None."
log.check(
("matchms", "INFO", "No fingerprint was added (name: test name).")
)
reset_matchms_logger()
def test_add_precursor_mz_only_pepmass_present(caplog):
"""Test if precursor_mz is correctly derived if only pepmass is present."""
set_matchms_logger_level("INFO")
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"pepmass": (444.0, 10)}
spectrum_in = SpectrumBuilder().with_metadata(
metadata).with_mz(mz).with_intensities(intensities).build()
spectrum = add_precursor_mz(spectrum_in)
assert spectrum.get("precursor_mz") == 444.0, "Expected different precursor_mz."
assert "Added precursor_mz entry based on field 'pepmass'" in caplog.text, \
"Expected different log message"
reset_matchms_logger()
def test_require_precursor_below_mz_max_50():
"""Set max_mz to 50."""
set_matchms_logger_level("INFO")
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = SpectrumBuilder().with_mz(mz).with_intensities(
intensities).build()
spectrum_in.set("precursor_mz", 60.)
with LogCapture() as log:
spectrum = require_precursor_below_mz(spectrum_in, max_mz=50)
assert spectrum is None, "Expected spectrum to be None."
log.check(('matchms', 'INFO',
'Spectrum with precursor_mz 60.0 (>50) was set to None.'))
reset_matchms_logger()
def test_derive_smiles_from_inchi():
"""Test if conversion to smiles works when only inchi is given.
"""
pytest.importorskip("rdkit")
set_matchms_logger_level("INFO")
spectrum_in = SpectrumBuilder().with_metadata({
"inchi": '"InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2"',
"smiles": ""
}).build()
with LogCapture() as log:
spectrum = derive_smiles_from_inchi(spectrum_in)
assert spectrum.get("smiles") == "C1CCCCC1", "Expected different smiles"
log.check(('matchms', 'INFO',
'Added smiles C1CCCCC1 to metadata (was converted from InChI)'))
reset_matchms_logger()
def test_require_precursor_mz_fail_when_mz_too_small(precursor_mz):
"""Test if spectrum is None when precursor_mz <= minimum_accepted_mz"""
set_matchms_logger_level("INFO")
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = SpectrumBuilder().with_mz(mz).with_intensities(
intensities).build()
spectrum_in.set("precursor_mz", precursor_mz)
with LogCapture() as log:
spectrum = require_precursor_mz(spectrum_in)
assert spectrum is None, "Expected spectrum to be None."
log.check(
('matchms', 'INFO', 'Spectrum without precursor_mz was set to None.'))
reset_matchms_logger()
def test_reduce_to_number_of_peaks_set_to_none():
"""Test is spectrum is set to None if not enough peaks."""
set_matchms_logger_level("INFO")
mz = numpy.array([10, 20], dtype="float")
intensities = numpy.array([0.5, 1], dtype="float")
spectrum_in = SpectrumBuilder().with_mz(mz).with_intensities(
intensities).with_metadata({
"parent_mass": 50
}).build()
with LogCapture() as log:
spectrum = reduce_to_number_of_peaks(spectrum_in, n_required=5)
assert spectrum is None, "Expected spectrum to be set to None."
log.check(
('matchms', 'INFO', "Spectrum with 2 (<5) peaks was set to None."))
reset_matchms_logger()
def test_set_and_reset_matchms_logger_level(caplog):
"""Test logging functionality."""
logger = logging.getLogger("matchms")
assert logger.getEffectiveLevel() == 30, "Expected different logging level"
set_matchms_logger_level("INFO")
logger.debug("debug test")
logger.info("info test")
assert logger.name == "matchms", "Expected different logger name"
assert logger.getEffectiveLevel() == 20, "Expected different logging level"
assert "debug test" not in caplog.text, "Debug log should not be shown."
assert "info test" in caplog.text, "Info log should have been shown."
reset_matchms_logger()
assert logger.getEffectiveLevel() == 30, "Expected different logging level"
reset_matchms_logger()
def test_derive_inchikey_from_inchi():
"""Test if conversion from inchi and inchikey works."""
pytest.importorskip("rdkit")
set_matchms_logger_level("INFO")
spectrum_in = SpectrumBuilder().with_metadata({
"inchi": '"InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2"',
"inchikey": 'n/a'
}).build()
with LogCapture() as log:
spectrum = derive_inchikey_from_inchi(spectrum_in)
assert spectrum.get(
"inchikey")[:14] == 'XDTMQSROBMDMFD', "Expected different inchikey"
log.check((
'matchms', 'INFO',
'Added InChIKey XDTMQSROBMDMFD-UHFFFAOYSA-N to metadata (was converted from inchi)'
))
reset_matchms_logger()
def test_add_logging_to_file_only_file(tmp_path, capsys):
"""Test writing logs to file."""
reset_matchms_logger()
set_matchms_logger_level("INFO")
filename = os.path.join(tmp_path, "test.log")
add_logging_to_file(filename, remove_stream_handlers=True)
logger = logging.getLogger("matchms")
logger.info("test message no.1")
# Test streamed logs
not_expected_log_entry = "test message no.1"
assert len(logger.handlers) == 1, "Expected only one Handler"
assert not_expected_log_entry not in capsys.readouterr(
).out, "Did not expect log message"
# Test log file
expected_log_entry = "INFO:matchms:test_logging:test message no.1"
assert os.path.isfile(filename), "Log file not found."
with open(filename, "r", encoding="utf-8") as file:
logs = file.read()
assert expected_log_entry in logs, "Expected different log file content"
reset_matchms_logger()
def test_add_logging_to_file(tmp_path, caplog, capsys):
"""Test writing logs to file."""
reset_matchms_logger()
set_matchms_logger_level("INFO")
filename = os.path.join(tmp_path, "test.log")
add_logging_to_file(filename)
logger = logging.getLogger("matchms")
logger.info("test message no.1")
expected_log_entry = "test message no.1"
# Test streamed logs
assert expected_log_entry in caplog.text, "Expected different log message."
assert expected_log_entry in capsys.readouterr().out, \
"Expected different log message in output (stdout/stderr)."
# Test log file
expected_log_entry = "INFO:matchms:test_logging:test message no.1"
assert len(logger.handlers) == 2, "Expected two Handler"
assert os.path.isfile(filename), "Log file not found."
with open(filename, "r", encoding="utf-8") as file:
logs = file.read()
assert expected_log_entry in logs, "Expected different log file content"
reset_matchms_logger()