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fix errors
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@khaled196
khaled196 committed Nov 20, 2023
1 parent 6616fe8 commit ecfd321
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Showing 2 changed files with 74 additions and 57 deletions.
105 changes: 57 additions & 48 deletions scripts/beacon_import.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -297,15 +297,14 @@ def read_json_file(file_path):
logging.info(f"JSON decoding error: {e}")




def connect_arguments(parser):
connection_group = parser.add_argument_group("Connection to MongoDB")
connection_group.add_argument("-H", "--db-host", type=str, default="127.0.0.1", dest="database_host", help="Hostname/IP of the beacon database")
connection_group.add_argument("-P", "--db-port", type=int, default=27017, dest="database_port", help="Port of the beacon database")

advance_connection_group = parser.add_argument_group("Addvanced Connection to MongoDB")
advance_connection_group.add_argument("-A", "--db-auth-source", type=str, metavar="ADMIN", default="admin", dest="Database_auth_source", help="auth source for the beacon database")
advance_connection_group.add_argument('-a', '--advance-connection', action="store_true", dest="advance", default=False, help="Connect to beacon database with authentication")
advance_connection_group.add_argument("-A", "--db-auth-source", type=str, metavar="ADMIN", default="", dest="Database_auth_source", help="auth source for the beacon database")
advance_connection_group.add_argument("-U", "--db-user", type=str, default="", dest="database_user", help="Login user for the beacon database")
advance_connection_group.add_argument("-W", "--db-password", type=str, default="", dest="database_password", help="Login password for the beacon database")
advance_connection_group.add_argument("-N", "--db-name", type=str, default="", dest="database_name", help="Name of the beacon database")
Expand All @@ -324,14 +323,60 @@ def connect_arguments(parser):

def connect_to_mongodb(args):
# Connect to MongoDB database with authentication
if args.database_user and args.database_password and args.database_auth_source and args.collection:
if args.advance:
# check advanced input for connection
advanced_required_args = ['database_auth_source', 'database_user', 'database_password', 'database_name']
if any(getattr(args, arg) == "" for arg in advanced_required_args):
for arg in advanced_required_args:
if not getattr(args, arg):
print(f"Missing value -> {arg}. Use -h or --help for usage details.")
logging.info(f"Missing value -> {arg}")
parser.print_help()
sys.exit(1)
# Connect to MongoDB database with authentication
client = MongoClient(f"mongodb://{args.database_user}:{args.database_password}@{args.database_host}:{args.database_port}/{args.collection}?authSource={args.database_auth_source}")
else:
# Connect to MongoDB database without authentication
client = MongoClient(args.database_host, args.database_port)

return client


def clear_collections(db, args):
"""
Clears collections in the MongoDB database based on the provided arguments.
Parameters:
db (MongoClient): MongoDB client connected to the database.
args (Namespace): Parsed command-line arguments.
Returns:
bool: True if collections are cleared successfully, False otherwise.
"""
existing_names = db.list_collection_names()

if args.clear_all:
# Clear all collections
for name in existing_names:
try:
db[name].drop()
except Exception as e:
print(f'Warning: Failed to clear collection {name}. Error: {e}')
logging.info(f'Warning: Failed to clear collection {name}. Error: {e}')
return False
return True

elif args.clear_coll:
# Clear a specific collection
for name in existing_names:
if name == args.removed_col_name:
try:
db[name].drop()
except Exception as e:
print(f'Warning: Failed to clear collection {name}. Error: {e}')
logging.info(f'Warning: Failed to clear collection {name}. Error: {e}')
return False
return True

return False # No action specified

def MongoDBimporter():
parser = argparse.ArgumentParser(description="Input arguments")
Expand All @@ -357,61 +402,25 @@ def MongoDBimporter():
required_args = ['database', 'collection', 'database_host', 'database_port','input_json_file']
for arg in required_args:
if not getattr(args, arg):
print(f"Missing value -> {arg}. Use -h or --help for usage details.")
logging.info(f"Missing value -> {arg}")
parser.print_help()
sys.exit(1)

# check advanced input for connection
advanced_required_args = ['database_auth_source', 'database_user', 'database_password', 'database_name']
if any(getattr(args, arg) != "" for arg in advanced_required_args):
print(args.database_auth_source)
for arg in advanced_required_args:
if not getattr(args, arg):
print(f"Missing value -> {arg}. Use -h or --help for usage details.")
logging.info(f"Missing value -> {arg}")
parser.print_help()
sys.exit(1)


print(f"Missing value -> {arg}. Use -h or --help for usage details.")
logging.info(f"Missing value -> {arg}")
parser.print_help()
sys.exit(1)

# connect to beacon
client= connect_to_mongodb(args)
db = client[args.database]
collection = db[args.collection]

clear_collections(db, args)


# Clean all collections inside the database
if args.clear_all:
existing_names = db.list_collection_names()
for name in existing_names:
try:
db[name].drop()
except:
print(f'Warning: Failed to clear database user:{self.database_user} db:{self.database_name}')
logging.info(f'Warning: Failed to clear database user:{self.database_user} db:{self.database_name}')
return False
return True

# Clean specific collection inside the database
if args.clear_coll:
existing_names = db.list_collection_names()
for name in existing_names:
if name == args.removed_col_name:
try:
db[name].drop()
except:
print(f'Warning: Failed to clear database user:{self.database_user} db:{self.database_name}')
logging.info(f'Warning: Failed to clear database user:{self.database_user} db:{self.database_name}')
return False
return True

# connect to Galaxy instance
if args.galaxy:
# Check galaxy inputs to connect to Galaxy
galaxy_args = ['galaxy_url', 'galaxy_key']
if any(getattr(args, arg) != "" for arg in galaxy_args):
if any(getattr(args, arg) == "" for arg in galaxy_args):
for arg in galaxy_args:
if not getattr(args, arg):
print(f"Missing value -> {arg}. Use -h or --help for usage details.")
Expand Down
26 changes: 17 additions & 9 deletions scripts/beacon_search.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ def common_arguments(parser):
connection_group.add_argument("-P", "--db-port", type=int, default=27017, dest="database_port", help="port of the beacon database")

advance_connection_group = parser.add_argument_group("Addvanced Connection to MongoDB")
advance_connection_group.add_argument('-a', '--advance-connection', action="store_true", dest="advance", default=False, help="Connect to beacon database with authentication")
advance_connection_group.add_argument("-A", "--db-auth-source", type=str, metavar="ADMIN", default="", dest="database_auth_source", help="auth source for the beacon database")
advance_connection_group.add_argument("-U", "--db-user", type=str, default="", dest="database_user", help="login user for the beacon database")
advance_connection_group.add_argument("-W", "--db-password", type=str, default="", dest="database_password", help="login password for the beacon database")
Expand All @@ -22,17 +23,22 @@ def common_arguments(parser):

def connect_to_mongodb(args):
# Connect to MongoDB database with authentication
if args.database_user and args.database_password and args.database_auth_source and args.database_name:
client = MongoClient(f"mongodb://{args.database_user}:{args.database_password}@{args.database_host}:{args.database_port}/{args.database_name}?authSource={args.database_auth_source}")
if args.advance:
# check advanced input for connection
advanced_required_args = ['database_auth_source', 'database_user', 'database_password', 'database_name']
if any(getattr(args, arg) == "" for arg in advanced_required_args):
for arg in advanced_required_args:
if not getattr(args, arg):
print(f"Missing value -> {arg}. Use -h or --help for usage details.")
logging.info(f"Missing value -> {arg}")
parser.print_help()
sys.exit(1)
# Connect to MongoDB database with authentication
client = MongoClient(f"mongodb://{args.database_user}:{args.database_password}@{args.database_host}:{args.database_port}/{args.collection}?authSource={args.database_auth_source}")
else:
# Connect to MongoDB database without authentication
client = MongoClient(args.database_host, args.database_port)

db = client[args.database]
collection = db[args.collection]

return collection

return client

def beacon_query():

Expand Down Expand Up @@ -204,7 +210,9 @@ def beacon_query():
parser_sequence.print_help()
sys.exit(1)

collection = connect_to_mongodb(args)
client = connect_to_mongodb(args)
db = client[args.database]
collection = db[args.collection]
# Create a new dictionary with non-empty and non-default values
filtered_query = {key: value for key, value in query.items() if value}
for v in collection.find(filtered_query):
Expand Down

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