v1.4.0 (#142)

mutants/orig_metadata.csv

@@ -0,0 +1,2 @@
+covv_virus_name
+sample1

src/tools.py

@@ -41,6 +41,16 @@ def decrypt_passwords(config_dict: dict[str, Any], submission_portals: set[str],
 			if not encrypted_string.endswith("="):
 				print("Passwords field does not appear to be encrypted. Use SeqSender command 'load_credentials' to encrypt your credentials before submission.", file=sys.stderr)
 			raise(InvalidToken)
+<<<<<<< HEAD
+		if parent_db == "GISAID":
+			encrypted_string = config_dict["Submission"]["GISAID"]["Client-Id"]
+			try:
+				decrypted_string = Fernet(key).decrypt(encrypted_string)
+				config_dict["Submission"]["GISAID"]["Client-Id"] = decrypted_string
+			except InvalidToken:
+				raise(InvalidToken)
+=======
+>>>>>>> gisaid_removed
 	return config_dict
 
 def encrypt_passwords(config_file: str, databases: list[str], encryption_key: Optional[str]) -> None:
@@ -57,6 +67,13 @@ def encrypt_passwords(config_file: str, databases: list[str], encryption_key: Op
 		password = getpass(f"Enter password for {parent_db} account: ")
 		if parent_db == "NCBI":
 			ncbi_handler.ncbi_login(config_dict["NCBI"], crash_on_error = True)
+<<<<<<< HEAD
+		elif parent_db == "GISAID":
+			client_id = getpass(f"Enter client_id for GISAID account: ")
+			encrypted_client_id = encrypter.encrypt(client_id.encode())
+			config_dict["GISAID"]["Client-Id"] = encrypted_client_id
+=======
+>>>>>>> gisaid_removed
 		encrypted_password = encrypter.encrypt(password.encode())
 		config_dict[parent_db]["Password"] = encrypted_password
 	file_handler.save_yaml(config_dict = config_dict, yaml_path = config_file)
@@ -100,17 +117,55 @@ def get_submission_schema_config_name(submission_portals: set[str]) -> str:
 	submission_schema_file_name += "schema.py"
 	return submission_schema_file_name
 
+<<<<<<< HEAD
+def validate_submission_position(config_dict: dict[str, Any]):
+	genbank_position = get_submission_position(config_dict=config_dict, database="GENBANK")
+	gisaid_position = get_submission_position(config_dict=config_dict, database="GISAID")
+	if (gisaid_position is None and genbank_position is not None) or (gisaid_position is not None and genbank_position is None) or (isinstance(gisaid_position, int) and isinstance(genbank_position, int) and gisaid_position == genbank_position):
+		print(f"Error: Config file is incorrect. Submission position for GISAID '{gisaid_position}' and GenBank '{genbank_position}' must both be either left empty, or set to '1' and '2' based on submission preference.", file=sys.stderr)
+		sys.exit(1)
+
+=======
+>>>>>>> gisaid_removed
 def get_submission_type(test: bool) -> str:
 	if test:
 		return "TEST"
 	else:
 		return "PRODUCTION"
 
+<<<<<<< HEAD
+def get_submission_position(config_dict: dict[str, Any], database: str) -> Optional[int]:
+	if database in ["BIOSAMPLE", "SRA", "GENBANK"]:
+		parent_database = "NCBI"
+	elif database == "GISAID":
+		parent_database = "GISAID"
+	else:
+		print(f"Error: database {database} is not a valid selection.", file=sys.stderr)
+		sys.exit(1)
+	if "Submission" in config_dict:
+		config_dict = config_dict["Submission"]
+	if parent_database in config_dict:
+		config_dict = config_dict[parent_database]
+	if "Submission_Position" in config_dict and isinstance(config_dict["Submission_Position"], int):
+		return config_dict["Submission_Position"]
+	else:
+		return None
+
+def password_encryption_config_schema_updates(schema: dict[str, Any], submission_portals: set[str]) -> dict[str, Any]:
+	if "NCBI" in submission_portals:
+		schema["Submission"]["schema"]["NCBI"]["schema"]["Password"]["required"] = False
+	if "GISAID" in submission_portals:
+		schema["Submission"]["schema"]["GISAID"]["schema"]["Password"]["required"] = False
+		schema["Submission"]["schema"]["GISAID"]["schema"]["Client-Id"]["required"] = False
+	return schema
+
+=======
 def password_encryption_config_schema_updates(schema: dict[str, Any], submission_portals: set[str]) -> dict[str, Any]:
 	if "NCBI" in submission_portals:
 		schema["Submission"]["schema"]["NCBI"]["schema"]["Password"]["required"] = False
 	return schema
 
+>>>>>>> gisaid_removed
 def database_specific_config_schema_updates(schema: dict[str, Any], database: list[str]) -> dict[str, Any]:
 	# Update seqsender base schema to include needed checks
 	if "BIOSAMPLE" in database: