2 files changed, 13 insertions, 11 deletions
diff --git a/uploader/expression_data/dbinsert.py b/uploader/expression_data/dbinsert.py
index 32ca359..7040698 100644
--- a/uploader/expression_data/dbinsert.py
+++ b/uploader/expression_data/dbinsert.py
@@ -7,16 +7,17 @@ from datetime import datetime
 
 from redis import Redis
 from MySQLdb.cursors import DictCursor
+from gn_libs.mysqldb import database_connection
 from flask import (
     flash, request, url_for, Blueprint, redirect, render_template,
     current_app as app)
 
 from uploader import jobs
 from uploader.authorisation import require_login
+from uploader.db_utils import with_db_connection
 from uploader.population.models import populations_by_species
 from uploader.species.models import all_species, species_by_id
 from uploader.platforms.models import platform_by_species_and_id
-from uploader.db_utils import with_db_connection, database_connection
 
 dbinsertbp = Blueprint("dbinsert", __name__)
 
@@ -93,7 +94,7 @@ def select_platform():
         job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
         if job:
             filename = job["filename"]
-            filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
+            filepath = f"{app.config['UPLOADS_DIRECTORY']}/{filename}"
             if os.path.exists(filepath):
                 default_species = 1
                 gchips = genechips()
@@ -366,7 +367,7 @@ def insert_data():
         assert form.get("datasetid"), "dataset"
 
         filename = form["filename"]
-        filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
+        filepath = f"{app.config['UPLOADS_DIRECTORY']}/{filename}"
         redisurl = app.config["REDIS_URL"]
         if os.path.exists(filepath):
             with Redis.from_url(redisurl, decode_responses=True) as rconn:
@@ -376,7 +377,7 @@ def insert_data():
                         form["species"], form["genechipid"], form["datasetid"],
                         app.config["SQL_URI"], redisurl,
                         app.config["JOBS_TTL_SECONDS"]),
-                    redisurl, f"{app.config['UPLOAD_FOLDER']}/job_errors")
+                    redisurl, f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
 
             return redirect(url_for("dbinsert.insert_status", job_id=job["jobid"]))
         return render_error(f"File '{filename}' no longer exists.")
diff --git a/uploader/expression_data/views.py b/uploader/expression_data/views.py
index bbe6538..0e9b072 100644
--- a/uploader/expression_data/views.py
+++ b/uploader/expression_data/views.py
@@ -8,9 +8,9 @@ from zipfile import ZipFile, is_zipfile
 import jsonpickle
 from redis import Redis
 from werkzeug.utils import secure_filename
+from gn_libs.mysqldb import database_connection
 from flask import (flash,
                    request,
-                   url_for,
                    redirect,
                    Blueprint,
                    current_app as app)
@@ -18,11 +18,12 @@ from flask import (flash,
 from quality_control.errors import InvalidValue, DuplicateHeading
 
 from uploader import jobs
+from uploader.flask_extensions import url_for
 from uploader.datautils import order_by_family
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
+from uploader.db_utils import with_db_connection
 from uploader.species.models import all_species, species_by_id
-from uploader.db_utils import with_db_connection, database_connection
 from uploader.population.models import (populations_by_species,
                                         population_by_species_and_id)
 
@@ -161,7 +162,7 @@ def upload_file(species_id: int, population_id: int):
                                    species=species,
                                    population=population)
 
-        upload_dir = app.config["UPLOAD_FOLDER"]
+        upload_dir = app.config["UPLOADS_DIRECTORY"]
         request_errors = errors(request)
         if request_errors:
             for error in request_errors:
@@ -224,7 +225,7 @@ def parse_file(species_id: int, population_id: int):
         _errors = True
 
     if filename:
-        filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename)
+        filepath = os.path.join(app.config["UPLOADS_DIRECTORY"], filename)
         if not os.path.exists(filepath):
             flash("Selected file does not exist (any longer)", "alert-danger")
             _errors = True
@@ -240,7 +241,7 @@ def parse_file(species_id: int, population_id: int):
                 species_id, filepath, filetype,# type: ignore[arg-type]
                 app.config["JOBS_TTL_SECONDS"]),
             redisurl,
-            f"{app.config['UPLOAD_FOLDER']}/job_errors")
+            f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
 
     return redirect(url_for("species.populations.expression-data.parse_status",
                             species_id=species_id,
@@ -262,7 +263,7 @@ def parse_status(species_id: int, population_id: int, job_id: str):
             return render_template("no_such_job.html", job_id=job_id), 400
 
     error_filename = jobs.error_filename(
-        job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
+        job_id, f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
     if os.path.exists(error_filename):
         stat = os.stat(error_filename)
         if stat.st_size > 0:
@@ -344,7 +345,7 @@ def fail(species_id: int, population_id: int, job_id: str):
 
     if job:
         error_filename = jobs.error_filename(
-            job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
+            job_id, f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
         if os.path.exists(error_filename):
             stat = os.stat(error_filename)
             if stat.st_size > 0: