def test_get_sorted_compounds_with_ri_and_pmz(requireMocking, compound_list):
from cis import compounds
conf = list(
filter(lambda x: x['target_type'] == 'CONFIRMED', compound_list))
without = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(conf[0]['method']),
'version': urllib.parse.quote('fixed'),
'tgt_type': 'confirmed' # only type with identified name, ATM
},
'queryStringParameters': {}
},
{})
assert without['statusCode'] == 200
filtered = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(conf[0]['method']),
'version': urllib.parse.quote('fixed'),
'tgt_type': 'confirmed' # only type with identified name, ATM
},
'queryStringParameters': {
'rivalue': conf[0]['ri'],
'pmzvalue': conf[0]['mass']
}
},
{})
assert filtered['statusCode'] == 200
assert json.loads(without['body']) != json.loads(filtered['body'])
def test_query_silly1(requireMocking, libraries_with_confirmed):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_confirmed[0]['library']),
'tgt_type':
urllib.parse.quote('CONFIRMED'),
'version':
urllib.parse.quote('fixed')
},
'queryStringParameters': {
'limit': 50,
'offset': 0,
'order_by': 'name',
'identified': 'true',
'name': 'unknown',
'direction': 'asc'
}
}, {})
assert response['statusCode'] in [200, 404]
splashes = json.loads(response['body'])
assert len(splashes) >= 0
def test_query_silly2(requireMocking, libraries_with_confirmed):
from cis import compounds
# querying unidentified compounds with name, which should NOT happen
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_confirmed[0]['library']),
'tgt_type':
urllib.parse.quote('CONFIRMED'),
'version':
urllib.parse.quote('fixed')
},
'queryStringParameters': {
'limit': 50,
'offset': 0,
'order_by': 'name',
'identified': 'false', # this is the default
'name': 'test',
'direction': 'asc'
}
},
{})
assert response['statusCode'] == 404
def test_get_sorted_compounds_with_range(requireMocking, compound_list):
from cis import compounds
conf = list(
filter(lambda x: x['target_type'] == 'UNCONFIRMED', compound_list))
splashes = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(conf[0]['method']),
'version': urllib.parse.quote('fixed'),
'tgt_type': urllib.parse.quote('unconfirmed')
},
'queryStringParameters': {
'limit': 10,
'order_by': 'pmz',
'pmzvalue': float(compound_list[0]['mass']) + 0.004,
'pmzaccuracy': 0.01
}
}, {})
assert splashes['statusCode'] == 200
comps_obj = json.loads(splashes['body'])
assert len(comps_obj) > 0
assert comps_obj[0]['precursor_mass'] >= float(
compound_list[0]['mass']) - 0.05
assert comps_obj[-1]['precursor_mass'] <= float(
compound_list[0]['mass']) + 0.05
def test_get_sorted_compounds_defaults(requireMocking,
libraries_with_different_tgt_types):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_different_tgt_types[1]),
'version':
'fixed',
'tgt_type':
'unconfirmed'
},
'queryStringParameters': {
'limit': 150,
'offset': 0,
'order_by': 'ri',
'direction': 'asc'
}
}, {})
assert response['statusCode'] == 200
compounds = json.loads(response['body'])
assert len(compounds) > 0
def test_query_bug2(requireMocking, libraries_with_unconfirmed):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_unconfirmed[0]['library']),
'version':
urllib.parse.quote('fixed'),
'tgt_type':
urllib.parse.quote('UNCONFIRMED')
},
'queryStringParameters': {
'limit': 150,
'offset': 0,
'order_by': 'name',
'identified': 'false',
'direction': 'asc'
}
}, {})
assert response['statusCode'] == 200
splashes = json.loads(response['body'])
assert len(splashes) > 0
ids = list(map(lambda x: x['id'], splashes))
assert len(ids) == len(set(ids))
def test_get_sorted_compounds_names_any_identified_confirmed(
requireMocking, libraries_with_confirmed):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_confirmed[0]['library'])
},
'queryStringParameters': {
'order_by': 'name',
'direction': 'desc'
}
}, {})
if response['statusCode'] == 404:
pytest.skip(
'It is possible that we do not have confirmed compounds in the db')
else:
assert response['statusCode'] == 200
result = json.loads(response['body'])
names = list(map(lambda x: x['preferred_name'], result))
assert any([n.lower().startswith('unknown') for n in names])
def test_get_sorted_compounds_ranges_gibberish(requireMocking, libraries_list,
compound_list):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(libraries_list[0]),
'version': urllib.parse.quote('fixed')
},
'queryStringParameters': {
'pmzvalue': 'boom'
}
}, {})
assert response['statusCode'] == 400
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(libraries_list[0]),
'version': urllib.parse.quote('fixed')
},
'queryStringParameters': {
'rivalue': 'blah - blah'
}
}, {})
assert response['statusCode'] == 400
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(libraries_list[0]),
'version': urllib.parse.quote('fixed')
},
'queryStringParameters': {
'rivalue': float(compound_list[0]['ri']),
'riaccuracy': 'hacked'
}
}, {})
assert response['statusCode'] == 400
def test_get_sorted_compounds_no_library(requireMocking):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {},
'queryStringParameters': {}
}, {})
assert response['statusCode'] == 400
assert json.loads(
response['body'])['error'] == 'you need to provide a "library" name'
def test_get_sorted_compounds_second_page(requireMocking,
libraries_with_confirmed):
from cis import compounds
first = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_confirmed[0]['library']),
'version':
urllib.parse.quote('fixed')
},
'queryStringParameters': {
'limit': 10,
'offset': 0
}
}, {})
assert first['statusCode'] == 200
second = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_confirmed[0]['library']),
'version':
urllib.parse.quote('fixed')
},
'queryStringParameters': {
'limit': 10,
'offset': 10
}
}, {})
assert second['statusCode'] == 200
assert json.loads(first['body']) != json.loads(second['body'])
def test_get_sorted_compounds_filtered_version(requireMocking, libraries_list):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': libraries_list[0],
'version': '1'
},
'queryStringParameters': {}
}, {})
assert response['statusCode'] in [200, 404]
splashes = json.loads(response['body'])
assert len(splashes) >= 0
def test_get_sorted_compounds_invalid_identified_names(requireMocking,
libraries_list):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(libraries_list[0]),
'version': urllib.parse.quote('fixed')
},
'queryStringParameters': {
'identified': 'blah'
}
}, {})
assert response['statusCode'] == http.HTTPStatus.INTERNAL_SERVER_ERROR
assert json.loads(response['body'])['error'] == [
"Invalid value for queryString 'identified'. Please use 'true' or 'false'."
]
def test_get_sorted_compounds_name_filtered_default_order(
requireMocking, compound_list):
from cis import compounds
splashes = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(compound_list[0]['method']),
'version': urllib.parse.quote(compound_list[0]['version'])
},
'queryStringParameters': {
'limit': 150,
'name': compound_list[0]['name'][3:7]
}
}, {})
assert splashes['statusCode'] == 200
comps_obj = json.loads(splashes['body'])
assert len(comps_obj) >= 1
def test_get_sorted_compounds_name_filtered(requireMocking, compound_list):
from cis import compounds
splashes = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(compound_list[0]['method']),
'version': urllib.parse.quote('fixed'),
'tgt_type': compound_list[0]['target_type']
},
'queryStringParameters': {
'limit': 30,
'order_by': 'pmz',
'name': compound_list[0]['name']
}
}, {})
assert splashes['statusCode'] == 200
comps_obj = json.loads(splashes['body'])
assert len(comps_obj) >= 1
def test_get_sorted_compounds_filtered_adduct_only(requireMocking,
comps_with_adducts):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(comps_with_adducts[0]['method']),
'version': urllib.parse.quote('fixed'),
'tgt_type': comps_with_adducts[0]['target_type']
},
'queryStringParameters': {
'adduct': '[M-H]-'
}
}, {})
assert response['statusCode'] == 200
splashes = json.loads(response['body'])
assert len(splashes) >= 1
def test_get_sorted_compounds_queryString_none(
requireMocking, libraries_with_different_tgt_types):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_different_tgt_types[-1]),
'version':
urllib.parse.quote('fixed'),
'tgt_type':
'unconfirmed'
},
'queryStringParameters': None
}, {})
assert response['statusCode'] == 200
compounds = json.loads(response['body'])
assert len(compounds) > 0
def test_get_sorted_compounds_big_page(requireMocking,
libraries_with_confirmed):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_confirmed[0]['library']),
'version':
urllib.parse.quote('fixed')
},
'queryStringParameters': {
'limit': 100
}
}, {})
assert response['statusCode'] == 200
compounds = json.loads(response['body'])
assert len(compounds) > 10
def test_get_sorted_compounds_names_identified_confirmed(
requireMocking, libraries_with_confirmed):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(
'5m splash one | orbitrap | beh c18 | negative')
},
'queryStringParameters': {
'identified': 'true'
}
}, {})
assert response['statusCode'] == 200
result = json.loads(response['body'])
for c in result:
assert len(c['associated_names']) > 0 or c['preferred_name'] != ''
def test_get_sorted_compounds_hidden(requireMocking, libs_with_hidden_comps):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(libs_with_hidden_comps[-1]),
'version': 'fixed',
'tgt_type': 'unconfirmed'
},
'queryStringParameters': {
'hidden': 'x' # whatever value, value not used.
}
},
{})
assert response['statusCode'] == 200
compounds = json.loads(response['body'], use_decimal=True)
assert all([x['hidden'] for x in compounds])
def test_get_sorted_compounds_filtered_lowercase_adduct_only(
requireMocking, libraries_list):
from cis import compounds
[print(i, x) for i, x in enumerate(libraries_list)]
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library': urllib.parse.quote(libraries_list[5]),
'version': urllib.parse.quote('fixed'),
'tgt_type': 'ISTD'
},
'queryStringParameters': {
'adduct': urllib.parse.quote('[m-h]-')
}
}, {})
assert response['statusCode'] in [200, 404]
splashes = json.loads(response['body'])
assert len(splashes) >= 0
def test_get_sorted_compounds_by_type(requireMocking,
libraries_with_confirmed):
from cis import compounds
response = compounds.get_sorted_compounds(
{
'pathParameters': {
'library':
urllib.parse.quote(libraries_with_confirmed[0]['library']),
'tgt_type':
urllib.parse.quote('confirmed'),
'version':
urllib.parse.quote(urllib.parse.quote('fixed'))
},
'queryStringParameters': {
'limit': 150,
'order_by': 'splash'
}
}, {})
compounds = json.loads(response['body'])
tgt_type = compounds[0]['target_type']
assert tgt_type == 'CONFIRMED'