def test_ErrorOutputDirNotExists(tmpdir):
'''Test the class ErrorOutputDirNotExists (error when a directory doesn't exist)'''
tmpdir = tmpdir.strpath
# Test instantiation
test_error = NCBImetaErrors.ErrorOutputDirNotExists(tmpdir)
# Test str representation (error message)
error_output = str(test_error)
error_expect = ("\n\nOutput directory does not exist." + "\n" +
"User entered: " + tmpdir)
assert error_output == error_expect
#--- Print the retrieved config file parameters ---#
print("\n" + "NCBImeta was run with the following options: " + "\n" + "\t" +
"Config File: " + str(config_path) + "\n" + "\t" + "Output Directory: " +
str(CONFIG_OUTPUT_DIR) + "\n" + "\t" + "Email: " + str(CONFIG_EMAIL) +
"\n" + "\t" + "API Key: " + "\t\t" + str(CONFIG_API_KEY) + "\n" + "\t" +
"User Database: " + str(CONFIG_DATABASE) + "\n" + "\t" + "Tables: " +
str(CONFIG_TABLES) + "\n" + "\t" + "Search Terms: ",
flush=True)
for table_search_term in CONFIG_SEARCH_TERMS:
print("\t\t" + str(table_search_term), flush=True)
print("\n", flush=True)
# Check if output dir exists
if not os.path.exists(CONFIG_OUTPUT_DIR):
raise NCBImetaErrors.ErrorOutputDirNotExists(CONFIG_OUTPUT_DIR)
# Flat mode checking
if flat_mode:
print(
"Flat mode was requested, organizational directories will not be used.",
flush=True)
DB_DIR = os.path.join(CONFIG_OUTPUT_DIR, "")
LOG_PATH = CONFIG_OUTPUT_DIR
# Or Create accessory directory (ex. log, data, database, etc.)
elif not flat_mode:
print(
"Flat mode was not requested, organization directories will be used.",
flush=True)
NCBImetaUtilities.check_accessory_dir(CONFIG_OUTPUT_DIR)
output_dir = args['outputDir']
#-----------------------------------------------------------------------#
# Argument Checking #
#-----------------------------------------------------------------------#
# Check if database exists
if os.path.exists(db_name):
conn = sqlite3.connect(db_name)
print('\nOpening database: ' + db_name, flush=True)
else:
raise NCBImetaErrors.ErrorDBNotExists(db_name)
# Check if output dir exists
if not os.path.exists(output_dir):
raise NCBImetaErrors.ErrorOutputDirNotExists(output_dir)
# no errors were raised, safe to connect to db
cur = conn.cursor()
#-----------------------------------------------------------------------#
# Process Database #
#-----------------------------------------------------------------------#
# Get a list of tables
cur.execute("SELECT name FROM sqlite_master WHERE type='table';")
table_list = cur.fetchall()
# Iterate through each table
for table in table_list:
# Skip sqlite_sequence default table
