From b6fadcc7e8de9d7041f2bb00dcd1ada518a1932c Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 7 Sep 2022 11:47:26 +0300
Subject: Inject database connection to mrna_assay_tissue_data class

* wqflask/base/mrna_assay_tissue_data.py: Imports: Delete
database_connection, escape, and database_connector.
(MrnaAssayTissueData): Inject conn.  Re-format queries.  Rework 'if
... else' logic.  Re-work how results are assigned to
'self.data[symbol]' - remove dot-notation.
(MrnaAssayTissueData.get_symbol_values_pairs): Move box-comments to
doc-string.  Rework how results are assigned to 'symbol_values_dict' -
remove dot-notation.
* wqflask/tests/unit/base/test_mrna_assay_tissue_data.py
(test_mrna_assay_tissue_data_initialisation): New test.
* wqflask/wqflask/correlation/correlation_functions.py: Import
database_connection.
(get_trait_symbol_and_tissue_values): Inject conn object.
---
 .../tests/unit/base/test_mrna_assay_tissue_data.py | 51 ++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 wqflask/tests/unit/base/test_mrna_assay_tissue_data.py

(limited to 'wqflask/tests/unit/base')

diff --git a/wqflask/tests/unit/base/test_mrna_assay_tissue_data.py b/wqflask/tests/unit/base/test_mrna_assay_tissue_data.py
new file mode 100644
index 00000000..7a21124a
--- /dev/null
+++ b/wqflask/tests/unit/base/test_mrna_assay_tissue_data.py
@@ -0,0 +1,51 @@
+import pytest
+from 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)
-- 
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