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"""
Tests for the gn3.db.correlations module
"""
from unittest import TestCase
import pytest
from gn3.db.correlations import (
build_query_sgo_lit_corr,
build_query_tissue_corr)
class TestCorrelation(TestCase):
"""Test cases for correlation data fetching functions"""
maxDiff = None
@pytest.mark.unit_test
def test_build_query_sgo_lit_corr(self):
"""
Test that the literature correlation query is built correctly.
"""
self.assertEqual(
build_query_sgo_lit_corr(
"Probeset",
"temp_table_xy45i7wd",
"T1.value, T2.value, T3.value",
(("LEFT JOIN ProbesetData AS T1 "
"ON T1.Id = ProbesetXRef.DataId "
"AND T1.StrainId=%(T1_sample_id)s"),
(
"LEFT JOIN ProbesetData AS T2 "
"ON T2.Id = ProbesetXRef.DataId "
"AND T2.StrainId=%(T2_sample_id)s"),
(
"LEFT JOIN ProbesetData AS T3 "
"ON T3.Id = ProbesetXRef.DataId "
"AND T3.StrainId=%(T3_sample_id)s"))),
(("SELECT Probeset.Name, temp_table_xy45i7wd.value, "
"T1.value, T2.value, T3.value "
"FROM (Probeset, ProbesetXRef, ProbesetFreeze) "
"LEFT JOIN temp_table_xy45i7wd ON temp_table_xy45i7wd.GeneId2=ProbeSet.GeneId "
"LEFT JOIN ProbesetData AS T1 "
"ON T1.Id = ProbesetXRef.DataId "
"AND T1.StrainId=%(T1_sample_id)s "
"LEFT JOIN ProbesetData AS T2 "
"ON T2.Id = ProbesetXRef.DataId "
"AND T2.StrainId=%(T2_sample_id)s "
"LEFT JOIN ProbesetData AS T3 "
"ON T3.Id = ProbesetXRef.DataId "
"AND T3.StrainId=%(T3_sample_id)s "
"WHERE ProbeSet.GeneId IS NOT NULL "
"AND temp_table_xy45i7wd.value IS NOT NULL "
"AND ProbesetXRef.ProbesetFreezeId = ProbesetFreeze.Id "
"AND ProbesetFreeze.Name = %(db_name)s "
"AND Probeset.Id = ProbesetXRef.ProbesetId "
"ORDER BY Probeset.Id"),
2))
@pytest.mark.unit_test
def test_build_query_tissue_corr(self):
"""
Test that the tissue correlation query is built correctly.
"""
self.assertEqual(
build_query_tissue_corr(
"Probeset",
"temp_table_xy45i7wd",
"T1.value, T2.value, T3.value",
(("LEFT JOIN ProbesetData AS T1 "
"ON T1.Id = ProbesetXRef.DataId "
"AND T1.StrainId=%(T1_sample_id)s"),
(
"LEFT JOIN ProbesetData AS T2 "
"ON T2.Id = ProbesetXRef.DataId "
"AND T2.StrainId=%(T2_sample_id)s"),
(
"LEFT JOIN ProbesetData AS T3 "
"ON T3.Id = ProbesetXRef.DataId "
"AND T3.StrainId=%(T3_sample_id)s"))),
(("SELECT Probeset.Name, temp_table_xy45i7wd.Correlation, "
"temp_table_xy45i7wd.PValue, "
"T1.value, T2.value, T3.value "
"FROM (Probeset, ProbesetXRef, ProbesetFreeze) "
"LEFT JOIN temp_table_xy45i7wd ON temp_table_xy45i7wd.Symbol=ProbeSet.Symbol "
"LEFT JOIN ProbesetData AS T1 "
"ON T1.Id = ProbesetXRef.DataId "
"AND T1.StrainId=%(T1_sample_id)s "
"LEFT JOIN ProbesetData AS T2 "
"ON T2.Id = ProbesetXRef.DataId "
"AND T2.StrainId=%(T2_sample_id)s "
"LEFT JOIN ProbesetData AS T3 "
"ON T3.Id = ProbesetXRef.DataId "
"AND T3.StrainId=%(T3_sample_id)s "
"WHERE ProbeSet.Symbol IS NOT NULL "
"AND temp_table_xy45i7wd.Correlation IS NOT NULL "
"AND ProbesetXRef.ProbesetFreezeId = ProbesetFreeze.Id "
"AND ProbesetFreeze.Name = %(db_name)s "
"AND Probeset.Id = ProbesetXRef.ProbesetId "
"ORDER BY Probeset.Id"),
3))
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