From 1f353050aef2d4869e35d61bf68bc8b342ebad92 Mon Sep 17 00:00:00 2001
From: Dakota Howard <58985143+dthoward96@users.noreply.github.com>
Date: Fri, 5 Apr 2024 17:26:55 -0400
Subject: [PATCH] Bug fix process.py

Bug fix for upload log. When only one database was submitted it, it would convert the database name into a list and error out.
---
 process.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/process.py b/process.py
index 9ac66c9..23d3585 100644
--- a/process.py
+++ b/process.py
@@ -79,7 +79,7 @@ def get_required_colnames(database, organism):
 # Check the config file
 def get_config(config_file, database):
 	# Determine which portal is the database belongs to
-	submission_portals = ["NCBI" if x in ["BIOSAMPLE", "SRA", "GENBANK"] else "GISAID" for x in database]
+	submission_portals = ["NCBI" if x in ["BIOSAMPLE", "SRA", "GENBANK"] else "GISAID" if x in ["GISAID"] else "Unknown" for x in database]
 	# Read in config file
 	with open(config_file, "r") as f:
 		config_dict = yaml.load(f, Loader=yaml.BaseLoader) # Load yaml as str only
@@ -362,7 +362,7 @@ def update_submission_status(submission_dir, submission_name, organism, test):
 			print("Error: Config file for "+submission_name+" does not exist at "+config_file, file=sys.stderr)
 			sys.exit(1)
 		else:
-			config_dict = get_config(config_file=config_file, database=database_name)
+			config_dict = get_config(config_file=config_file, database=database)
 		# IF GISAID in a list of submitting databases, check if CLI is downloaded and store in the correct directory
 		gisaid_cli = os.path.join(submission_dir, "gisaid_cli", organism.lower()+"CLI", organism.lower()+"CLI") if "GISAID" in database_name else None
 		# Check if the gisaid_cli exists