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import pytest
from gn2.base.mrna_assay_tissue_data import MrnaAssayTissueData
@pytest.mark.parametrize(
('gene_symbols', 'expected_query', 'sql_fetch_all_results'),
(
(None,
(("SELECT t.Symbol, t.GeneId, t.DataId, "
"t.Chr, t.Mb, t.description, "
"t.Probe_Target_Description "
"FROM (SELECT Symbol, "
"max(Mean) AS maxmean "
"FROM TissueProbeSetXRef WHERE "
"TissueProbeSetFreezeId=1 AND "
"Symbol != '' AND Symbol IS NOT "
"Null GROUP BY Symbol) "
"AS x INNER JOIN TissueProbeSetXRef "
"AS t ON t.Symbol = x.Symbol "
"AND t.Mean = x.maxmean"),),
(("symbol", "gene_id",
"data_id", "chr", "mb",
"description",
"probe_target_description"),)),
(["k1", "k2", "k3"],
("SELECT t.Symbol, t.GeneId, t.DataId, "
"t.Chr, t.Mb, t.description, "
"t.Probe_Target_Description FROM (SELECT Symbol, "
"max(Mean) AS maxmean "
"FROM TissueProbeSetXRef WHERE "
"TissueProbeSetFreezeId=1 AND "
"Symbol IN (%s, %s, %s) "
"GROUP BY Symbol) AS x INNER JOIN "
"TissueProbeSetXRef AS "
"t ON t.Symbol = x.Symbol "
"AND t.Mean = x.maxmean",
("k1", "k2", "k3")),
(("k1", "203",
"112", "xy", "20.11",
"Sample Description",
"Sample Probe Target Description"),)),
),
)
def test_mrna_assay_tissue_data_initialisation(mocker, gene_symbols,
expected_query,
sql_fetch_all_results):
mock_conn = mocker.MagicMock()
with mock_conn.cursor() as cursor:
cursor.fetchall.return_value = sql_fetch_all_results
MrnaAssayTissueData(conn=mock_conn, gene_symbols=gene_symbols)
cursor.execute.assert_called_with(*expected_query)
def test_get_trait_symbol_and_tissue_values(mocker):
"""Test for getting trait symbol and tissue_values"""
mock_conn = mocker.MagicMock()
with mock_conn.cursor() as cursor:
cursor.fetchall.side_effect = [
(("k1", "203",
"112", "xy", "20.11",
"Sample Description",
"Sample Probe Target Description"),),
(("k1", "v1"),
("k2", "v2"),
("k3", "v3")),
]
_m = MrnaAssayTissueData(conn=mock_conn,
gene_symbols=["k1", "k2", "k3"])
assert _m.get_symbol_values_pairs() == {
"k1": ["v1"],
"k2": ["v2"],
"k3": ["v3"],
}
cursor.execute.assert_called_with(
"SELECT TissueProbeSetXRef.Symbol, "
"TissueProbeSetData.value FROM "
"TissueProbeSetXRef, TissueProbeSetData "
"WHERE TissueProbeSetData.Id IN (%s) "
"AND TissueProbeSetXRef.DataId = "
"TissueProbeSetData.Id",
('112',))
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