Dthoward96 bugfix (#45)

* Update report.py

Bug fix to allow for other submit folders in FTP of ncbi

* Update process.py

bug fix for capitalization of folder name

process.py

@@ -308,7 +308,7 @@ def update_submission_status(submission_dir, submission_name, organism, test):
 	if test == True:
 		submission_type = "Test"
 	else:
-		submission_type = "production"
+		submission_type = "Production"
 	# Check if given organism exist in the log
 	df_partial = df.loc[(df["Organism"] == organism) & (df["Submission_Name"] == submission_name) & (df["Submission_Directory"] == submission_dir) & (df["Submission_Type"] == submission_type)]
 	if df_partial.shape[0] == 0:

report.py

@@ -40,7 +40,16 @@ def get_ncbi_process_report(database, submission_name, submission_files_dir, con
 		FTP_HOST = process.get_main_config()["PORTAL_NAMES"]["NCBI"]["FTP_HOST"]
 		ftp = ftplib.FTP(FTP_HOST)
 		ftp.login(user=config_dict["Username"], passwd=config_dict["Password"])
-		# CD to to test or production folder
+		# Check if submit folder exists
+		if "submit" in ftp.nlst():
+			ftp.cwd("submit")
+			# If submit folder exists check if Production/Test folder exists
+			if submission_type not in ftp.nlst():
+				print("Error: Cannot find submission folder on NCBI FTP site.", file=sys.stderr)
+				sys.exit(1)
+		else:
+			print("Error: Cannot find submission folder on NCBI FTP site.", file=sys.stderr)
+			sys.exit(1)
 		ftp.cwd(submission_type)
 		# Check if submission name exists
 		if ncbi_submission_name not in ftp.nlst():