Use extracted functions and fix bugs

1 files changed, 10 insertions, 4 deletions

diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 881c913..a878ff5 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -11,8 +11,10 @@ from flask import (
     flash, request, url_for, Blueprint, redirect, render_template,
     current_app as app)
 
+from qc_app.db_utils import with_db_connection, database_connection
+from qc_app.db import species, species_by_id, populations_by_species
+
 from . import jobs
-from .db_utils import with_db_connection, database_connection
 
 dbinsertbp = Blueprint("dbinsert", __name__)
 
@@ -91,7 +93,8 @@ def tissues() -> tuple:
 def select_platform():
     "Select the platform (GeneChipId) used for the data."
     job_id = request.form["job_id"]
-    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+    with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn,
+          database_connection(app.config["SQL_URI"]) as conn):
         job = jobs.job(rconn, job_id)
         if job:
             filename = job["filename"]
@@ -102,7 +105,7 @@ def select_platform():
                 return render_template(
                     "select_platform.html", filename=filename,
                     filetype=job["filetype"], totallines=int(job["currentline"]),
-                    default_species=default_species, species=species(),
+                    default_species=default_species, species=species(conn),
                     genechips=gchips[default_species],
                     genechips_data=json.dumps(gchips))
             return render_error(f"File '{filename}' no longer exists.")
@@ -124,7 +127,10 @@ def select_study():
 
         the_studies = studies_by_species_and_platform(speciesid, genechipid)
         the_groups = reduce(
-            organise_groups_by_family, groups_by_species(speciesid), {})
+            organise_groups_by_family,
+            with_db_connection(
+                lambda conn: populations_by_species(conn, speciesid)),
+            {})
         return render_template(
             "select_study.html", filename=form["filename"],
             filetype=form["filetype"], totallines=form["totallines"],