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Bug fix process.py #51

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merged 1 commit into from
Apr 5, 2024
Merged

Bug fix process.py #51

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4 changes: 2 additions & 2 deletions process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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