def test_reader_hnmr(hnmr_ethanol_file):
with open(hnmr_ethanol_file.resolve(), 'r') as fileobj:
jcamp_dict = jcamp._reader(fileobj)
xy_minmax_checker(jcamp_dict)
assert 'Ethanol' in jcamp_dict.get('title')
assert jcamp_dict.get('data type') == "LINK"
children = jcamp_dict.get('children')
assert len(children) == jcamp_dict.get('blocks')
atoms = children[0]
assert 'atomlist' in atoms
assert atoms.get('block_id') == 1
assignments = children[1]
assert assignments.get('block_id') == 2
assert assignments.get('data type') == "NMR PEAK ASSIGNMENTS"
assert assignments.get('data class') == "ASSIGNMENTS"
peaks = children[2]
assert peaks.get('block_id') == 3
assert peaks.get('data type') == "NMR SPECTRUM"
assert peaks.get('data class') == "PEAK TABLE"
assert peaks.get(jcamp._DATA_XY_TYPE_KEY) == '(XY..XY)'
xydata = children[3]
assert xydata.get('block_id') == 4
assert xydata.get('data type') == "NMR SPECTRUM"
assert xydata.get('data class') == "XYDATA"
assert xydata.get(jcamp._DATA_XY_TYPE_KEY) == '(X++(Y..Y))'
def test_reader_raman(raman_tannic_acid_file):
with open(raman_tannic_acid_file.resolve(), 'r') as fileobj:
jcamp_dict = jcamp._reader(fileobj)
xy_minmax_checker(jcamp_dict)
assert jcamp_dict.get('title') == "tannic acid"
assert jcamp_dict.get('data type') == "RAMAN SPECTRUM"
assert jcamp_dict.get(jcamp._DATA_XY_TYPE_KEY) == '(XY..XY)'
def test_reader_neutron(neutron_emodine_file):
with open(neutron_emodine_file.resolve(), 'r') as fileobj:
jcamp_dict = jcamp._reader(fileobj)
xy_minmax_checker(jcamp_dict)
assert jcamp_dict.get('title') == "Emodine, C15H10O4"
assert jcamp_dict.get('data type') == "INELASTIC NEUTRON SCATTERING"
assert jcamp_dict.get(jcamp._DATA_XY_TYPE_KEY) == '(X++(Y..Y))'
def test_reader_infrared_multiline(infrared_multiline_file):
with open(infrared_multiline_file.resolve(), 'r') as fileobj:
jcamp_dict = jcamp._reader(fileobj)
xy_minmax_checker(jcamp_dict)
assert jcamp_dict.get('title') == "multiline datasets test"
assert jcamp_dict.get('data type') == "INFRARED SPECTRUM"
assert jcamp_dict.get(jcamp._DATA_XY_TYPE_KEY) == '(X++(Y..Y))'
def test_reader_infrared_compressed(infrared_ethanol_compressed_file):
with open(infrared_ethanol_compressed_file.resolve(), 'r') as fileobj:
jcamp_dict = jcamp._reader(fileobj)
xy_minmax_checker(jcamp_dict)
assert jcamp_dict.get('title') == "$$ Begin of the data block"
assert jcamp_dict.get('data type') == "INFRARED SPECTRUM"
assert jcamp_dict.get(jcamp._DATA_XY_TYPE_KEY) == '(X++(Y..Y))'
def test_reader_uvvis(uvvis_toluene_file):
with open(uvvis_toluene_file.resolve(), 'r') as fileobj:
jcamp_dict = jcamp._reader(fileobj)
xy_minmax_checker(jcamp_dict)
assert jcamp_dict.get('title') == "Toluene"
assert jcamp_dict.get('data type') == "UV/VIS SPECTRUM"
assert jcamp_dict.get('molform') == "C7H8"
assert jcamp_dict.get(jcamp._DATA_XY_TYPE_KEY) == '(XY..XY)'
def test_reader_mass(mass_ethanol_file):
with open(mass_ethanol_file.resolve(), 'r') as fileobj:
jcamp_dict = jcamp._reader(fileobj)
xy_minmax_checker(jcamp_dict)
assert jcamp_dict.get('title') == "ethanol"
assert jcamp_dict.get('data type') == "MASS SPECTRUM"
assert jcamp_dict.get('data class') == "PEAK TABLE"
assert jcamp_dict.get(jcamp._DATA_XY_TYPE_KEY) == '(XY..XY)'
def test_reader_infrared(infrared_ethanol_file):
with open(infrared_ethanol_file.resolve(), 'r') as fileobj:
jcamp_dict = jcamp._reader(fileobj)
xy_minmax_checker(jcamp_dict)
assert jcamp_dict.get('title') == "ETHANOL"
assert jcamp_dict.get('data type') == "INFRARED SPECTRUM"
assert jcamp_dict.get('molform') == "C2 H6 O"
assert jcamp_dict.get(jcamp._DATA_XY_TYPE_KEY) == '(X++(Y..Y))'
def test_reader_exception_bad_datatype(tmp_path, infrared_ethanol_file):
# Create a "bad type" tmp file
jcamp_dir = tmp_path / "jcamp"
jcamp_dir.mkdir()
bad_file = jcamp_dir / "bad_data_type.jdx"
# Read input file lines and modify XYDATA file to "bad type"
with open(infrared_ethanol_file.resolve(), 'r') as fileobj:
lines = fileobj.readlines()
for i, line in enumerate(lines):
if line.startswith("##XYDATA"):
lines[i] = "##XYDATA=BAD_DATA_TYPE\n"
# Read modified lines to the "bad type" tmp file
with open(bad_file.resolve(), 'w') as fileobj:
fileobj.writelines(lines)
# Read in "bad file" for test
with open(bad_file.resolve(), 'r') as fileobj:
with pytest.raises(jcamp.UnsupportedDataTypeConfigException):
jcamp._reader(fileobj)
def test_reader_infrared_compound(infrared_compound_file):
with open(infrared_compound_file.resolve(), 'r') as fileobj:
jcamp_dict = jcamp._reader(fileobj)
xy_minmax_checker(jcamp_dict)
assert jcamp_dict.get('title') == ""
assert jcamp_dict.get('data type') == "LINK"
children = jcamp_dict.get('children')
assert len(children) == jcamp_dict.get('blocks')
for child in children:
assert child.get('data type') == "INFRARED SPECTRUM"
assert child.get(jcamp._DATA_XY_TYPE_KEY) == '(XY..XY)'