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authorFrederick Muriuki Muriithi2021-11-22 13:56:03 +0300
committerFrederick Muriuki Muriithi2021-11-22 13:56:03 +0300
commit575da0baf4468d27782c73b19995b3adb934ba70 (patch)
tree2d9630a22488365939ed95dc71fe3c04b0d427c8 /tests
parent55d698b1fb07afe74bf1dd570f9f495aefea1086 (diff)
downloadgenenetwork3-575da0baf4468d27782c73b19995b3adb934ba70.tar.gz
Add test to query builders
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add some tests for the query builders to ensure that the queries are built up correctly.
Diffstat (limited to 'tests')
-rw-r--r--tests/unit/db/test_correlation.py90
1 files changed, 90 insertions, 0 deletions
diff --git a/tests/unit/db/test_correlation.py b/tests/unit/db/test_correlation.py
new file mode 100644
index 0000000..866d28d
--- /dev/null
+++ b/tests/unit/db/test_correlation.py
@@ -0,0 +1,90 @@
+"""
+Tests for the gn3.db.correlations module
+"""
+
+from unittest import TestCase
+
+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
+
+ def test_build_query_sgo_lit_corr(self):
+ 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))
+
+ def test_build_query_tissue_corr(self):
+ 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))