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import numpy as np
import pytest
import os
from astropy import units as u
from astropy.table import Table
from astroquery.linelists.cdms.core import CDMS, parse_letternumber, build_lookup
from astroquery.utils.mocks import MockResponse
colname_set = set(['FREQ', 'ERR', 'LGINT', 'DR', 'ELO', 'GUP', 'TAG', 'QNFMT',
'Ju', 'Jl', "vu", "F1u", "F2u", "F3u", "vl", "Ku", "Kl",
"F1l", "F2l", "F3l", "name", "MOLWT", "Lab"])
def data_path(filename):
data_dir = os.path.join(os.path.dirname(__file__), 'data')
return os.path.join(data_dir, filename)
def mockreturn(*args, method='GET', data={}, url='', **kwargs):
if method == 'GET':
molecule = url.split('cdmstab')[1].split('.')[0]
with open(data_path(molecule+".data"), 'rb') as fh:
content = fh.read()
return MockResponse(content=content)
elif method == 'POST':
molecule = dict(data)['Molecules']
with open(data_path("post_response.html"), 'r') as fh:
content = fh.read().format(replace=molecule).encode()
return MockResponse(content=content)
@pytest.fixture
def patch_post(request):
mp = request.getfixturevalue("monkeypatch")
mp.setattr(CDMS, '_request', mockreturn)
return mp
def test_input_async():
response = CDMS.query_lines_async(min_frequency=100 * u.GHz,
max_frequency=1000 * u.GHz,
min_strength=-500,
molecule="028503 CO, v=0",
get_query_payload=True)
response = dict(response)
assert response['Molecules'] == "028503 CO, v=0"
np.testing.assert_almost_equal(response['MinNu'], 100.)
np.testing.assert_almost_equal(response['MaxNu'], 1000.)
def test_input_multi():
response = CDMS.query_lines_async(min_frequency=500 * u.GHz,
max_frequency=1000 * u.GHz,
min_strength=-500,
molecule=r"^H[2D]O(-\d\d|)\+$",
parse_name_locally=True,
get_query_payload=True)
response = dict(response)
assert response['Molecules'] == '018505 H2O+'
np.testing.assert_almost_equal(response['MinNu'], 500.)
np.testing.assert_almost_equal(response['MaxNu'], 1000.)
@pytest.mark.skip(reason="fails on i386")
def test_query(patch_post):
tbl = CDMS.query_lines(min_frequency=100 * u.GHz,
max_frequency=1000 * u.GHz,
min_strength=-500,
molecule='028503 CO, v=0'
)
assert isinstance(tbl, Table)
assert len(tbl) == 8
assert set(tbl.keys()) == colname_set
assert tbl['FREQ'][0] == 115271.2018
assert tbl['ERR'][0] == .0005
assert tbl['LGINT'][0] == -7.1425
assert tbl['GUP'][0] == 3
assert tbl['GUP'][7] == 17
def test_parseletternumber():
"""
Very Important:
Exactly two characters are available for each quantum number. Therefore, half
integer quanta are rounded up ! In addition, capital letters are used to
indicate quantum numbers larger than 99. E. g. A0 is 100, Z9 is 359. Small
types are used to signal corresponding negative quantum numbers.
"""
# examples from the docs
assert parse_letternumber("A0") == 100
assert parse_letternumber("Z9") == 359
# inferred?
assert parse_letternumber("z9") == -359
assert parse_letternumber("ZZ") == 3535
@pytest.mark.skip(reason="fails on i386")
def test_hc7s(patch_post):
"""
Test for a very complicated molecule
CDMS.query_lines_async(100*u.GHz, 100.755608*u.GHz, molecule='HC7S', parse_name_locally=True)
"""
tbl = CDMS.query_lines(100*u.GHz, 100.755608*u.GHz, molecule='117501 HC7S',)
assert isinstance(tbl, Table)
assert len(tbl) == 5
assert set(tbl.keys()) == colname_set
assert tbl['FREQ'][0] == 100694.065
assert tbl['ERR'][0] == 0.4909
assert tbl['LGINT'][0] == -3.9202
assert tbl['MOLWT'][0] == 117
assert tbl['GUP'][0] == 255
assert tbl['Ju'][0] == 126
assert tbl['Jl'][0] == 125
assert tbl['vu'][0] == 127
assert tbl['vl'][0] == 126
assert tbl['Ku'][0] == -1
assert tbl['Kl'][0] == 1
assert tbl['F1u'][0] == 127
assert tbl['F1l'][0] == 126
@pytest.mark.skip(reason="fails on i386")
def test_hc7n(patch_post):
"""
Regression test for 2409, specifically that GUP>1000 was not being
processed correctly b/c the first digit of GUP was being included in the
previous column (frequency)
CDMS.query_lines(200*u.GHz, 230.755608*u.GHz, molecule='HC7N',parse_name_locally=True)
"""
tbl = CDMS.query_lines(200*u.GHz, 230.755608*u.GHz, molecule='099501 HC7N, v=0')
assert isinstance(tbl, Table)
assert len(tbl) == 27
assert set(tbl.keys()) == colname_set
assert tbl['FREQ'][0] == 200693.406
assert tbl['ERR'][0] == 0.01
assert tbl['LGINT'][0] == -2.241
assert tbl['MOLWT'][0] == 99
assert tbl['GUP'][0] == 1071
assert tbl['Ju'][0] == 178
assert tbl['Jl'][0] == 177
assert tbl['vu'][0].mask
assert tbl['vl'][0].mask
assert tbl['Ku'][0].mask
assert tbl['Kl'][0].mask
assert tbl['F1u'][0].mask
assert tbl['F1l'][0].mask
assert tbl['Lab'][0]
def test_retrieve_species_table_local():
species_table = CDMS.get_species_table(use_cached=True)
assert len(species_table) == 1306
assert 'int' in species_table['tag'].dtype.name
assert 'int' in species_table['#lines'].dtype.name
assert 'float' in species_table['lg(Q(1000))'].dtype.name
def test_lut_multitable():
# Regression test for the different names used in the partition table and the other tables
lut = build_lookup()
assert lut.find('ethyl formate', 0)['ethyl formate'] == 74514
assert lut.find('C2H5OCHO', 0)['C2H5OCHO'] == 74514
assert lut.find('C2H4O', 0)['c-C2H4O'] == 44504
assert lut.find('Ethylene oxide', 0)['Ethylene oxide'] == 44504
def test_lut_literal():
# regression for 2901
lut = build_lookup()
hcop = lut.find('HCO+', 0)
assert len(hcop) >= 16
hcopv0 = lut.find('HCO+, v=0', 0)
assert len(hcopv0) == 1
assert hcopv0['HCO+, v=0'] == 29507
# two spacings exist in the tables
hcopv0 = lut.find('HCO+, v = 0', 0)
assert len(hcopv0) == 1
assert hcopv0['HCO+, v = 0'] == 29507
thirteenco = lut.find('13CO', 0)
assert len(thirteenco) == 1
assert thirteenco['13CO'] == 29501
thirteencostar = lut.find('13CO*', 0)
assert len(thirteencostar) >= 252
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