diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/computations/test_partial_correlations.py | 16 | ||||
| -rw-r--r-- | tests/unit/db/test_correlation.py | 96 |
2 files changed, 105 insertions, 7 deletions
diff --git a/tests/unit/computations/test_partial_correlations.py b/tests/unit/computations/test_partial_correlations.py index 3e1b6e1..3690ca4 100644 --- a/tests/unit/computations/test_partial_correlations.py +++ b/tests/unit/computations/test_partial_correlations.py @@ -193,7 +193,7 @@ class TestPartialCorrelations(TestCase): Given: - the name of a primary trait - - the value of a primary trait + - a sequence of values for the primary trait - a sequence of names of control traits - a sequence of values of control traits When: @@ -204,12 +204,14 @@ class TestPartialCorrelations(TestCase): decimal places are considered """ for primn, primv, contn, contv, expected in ( - ("pt", 12.98395, ("ct0", "ct1", "ct2"), - (0.1234, 2.3456, 3.4567), tuple()), - ("pt", 12.98395, ("ct0", "ct1", "ct2"), - (12.98354, 2.3456, 3.4567), ("pt", "ct0")), - ("pt", 12.98395, ("ct0", "ct1", "ct2", "ct3"), - (0.1234, 2.3456, 0.1233, 4.5678), ("ct0", "ct2")) + ("pt", (12.98395,), ("ct0", "ct1", "ct2"), + ((0.1234, 2.3456, 3.4567),), tuple()), + ("pt", (12.98395, 2.3456, 3.4567), ("ct0", "ct1", "ct2"), + ((12.98354, 2.3456, 3.4567), (64.2334, 6.3256, 64.2364), + (4.2374, 67.2345, 7.48234)), ("pt", "ct0")), + ("pt", (12.98395, 75.52382), ("ct0", "ct1", "ct2", "ct3"), + ((0.1234, 2.3456), (0.3621, 6543.572), (0.1234, 2.3456), + (0.1233, 4.5678)), ("ct0", "ct2")) ): with self.subTest( primary_name=primn, primary_value=primv, diff --git a/tests/unit/db/test_correlation.py b/tests/unit/db/test_correlation.py new file mode 100644 index 0000000..3f940b2 --- /dev/null +++ b/tests/unit/db/test_correlation.py @@ -0,0 +1,96 @@ +""" +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): + """ + 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)) + + 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)) |