From 4c9470646627a7b8d454d87984016cfa6c53059c Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 25 Sep 2024 12:11:12 -0500
Subject: Provide missing database connection.

---
 uploader/expression_data/dbinsert.py | 63 ++++++++++++++++++------------------
 1 file changed, 32 insertions(+), 31 deletions(-)

(limited to 'uploader')

diff --git a/uploader/expression_data/dbinsert.py b/uploader/expression_data/dbinsert.py
index e746944..32ca359 100644
--- a/uploader/expression_data/dbinsert.py
+++ b/uploader/expression_data/dbinsert.py
@@ -319,37 +319,38 @@ def selected_keys(original: dict, keys: tuple) -> dict:
 @require_login
 def final_confirmation():
     "Preview the data before triggering entry into the database"
-    form = request.form
-    try:
-        assert form.get("filename"), "filename"
-        assert form.get("filetype"), "filetype"
-        assert form.get("species"), "species"
-        assert form.get("genechipid"), "platform"
-        assert form.get("studyid"), "study"
-        assert form.get("datasetid"), "dataset"
-
-        speciesid = form["species"]
-        genechipid = form["genechipid"]
-        studyid = form["studyid"]
-        datasetid=form["datasetid"]
-        return render_template(
-            "final_confirmation.html", filename=form["filename"],
-            filetype=form["filetype"], totallines=form["totallines"],
-            species=speciesid, genechipid=genechipid, studyid=studyid,
-            datasetid=datasetid, the_species=selected_keys(
-                with_db_connection(lambda conn: species_by_id(conn, speciesid)),
-                ("SpeciesName", "Name", "MenuName")),
-            platform=selected_keys(
-                platform_by_species_and_id(speciesid, genechipid),
-                ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")),
-            study=selected_keys(
-                study_by_id(studyid), ("Name", "FullName", "ShortName")),
-            dataset=selected_keys(
-                dataset_by_id(datasetid),
-                ("AvgMethodName", "Name", "Name2", "FullName", "ShortName",
-                 "DataScale")))
-    except AssertionError as aserr:
-        return render_error(f"Missing data: {aserr.args[0]}")
+    with database_connection(app.config["SQL_URI"]) as conn:
+        form = request.form
+        try:
+            assert form.get("filename"), "filename"
+            assert form.get("filetype"), "filetype"
+            assert form.get("species"), "species"
+            assert form.get("genechipid"), "platform"
+            assert form.get("studyid"), "study"
+            assert form.get("datasetid"), "dataset"
+
+            speciesid = form["species"]
+            genechipid = form["genechipid"]
+            studyid = form["studyid"]
+            datasetid=form["datasetid"]
+            return render_template(
+                "final_confirmation.html", filename=form["filename"],
+                filetype=form["filetype"], totallines=form["totallines"],
+                species=speciesid, genechipid=genechipid, studyid=studyid,
+                datasetid=datasetid, the_species=selected_keys(
+                    with_db_connection(lambda conn: species_by_id(conn, speciesid)),
+                    ("SpeciesName", "Name", "MenuName")),
+                platform=selected_keys(
+                    platform_by_species_and_id(conn, speciesid, genechipid),
+                    ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")),
+                study=selected_keys(
+                    study_by_id(studyid), ("Name", "FullName", "ShortName")),
+                dataset=selected_keys(
+                    dataset_by_id(datasetid),
+                    ("AvgMethodName", "Name", "Name2", "FullName", "ShortName",
+                     "DataScale")))
+        except AssertionError as aserr:
+            return render_error(f"Missing data: {aserr.args[0]}")
 
 @dbinsertbp.route("/insert-data", methods=["POST"])
 @require_login
-- 
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