Index

Symbols

--config vserver-local-files command line option vserver-local-import command line option vserver-local-shell command line option vserver-local-start command line option --debug vserver-local-start command line option --drop-all vserver-local-import command line option --environment vserver-local-files command line option vserver-local-import command line option vserver-local-new command line option vserver-local-shell command line option vserver-local-start command line option --ip vserver-local-start command line option --name vserver-local-files command line option vserver-local-import command line option vserver-local-new command line option vserver-local-shell command line option vserver-local-start command line option --port vserver-local-start command line option --system vserver-local-files command line option vserver-local-import command line option vserver-local-new command line option vserver-local-shell command line option vserver-local-start command line option

--user vserver-local-files command line option vserver-local-import command line option vserver-local-new command line option vserver-local-shell command line option vserver-local-start command line option -c vserver-local-files command line option vserver-local-import command line option vserver-local-shell command line option vserver-local-start command line option -e vserver-local-files command line option vserver-local-import command line option vserver-local-new command line option vserver-local-shell command line option vserver-local-start command line option -n vserver-local-files command line option vserver-local-import command line option vserver-local-new command line option vserver-local-shell command line option vserver-local-start command line option -p vserver-local-start command line option

_

_AnsiColorStreamHandler (class in vantage6.common.colors) _get_color() (_AnsiColorStreamHandler class method) (_WinColorStreamHandler class method)

_WinColorStreamHandler (class in vantage6.common.colors)

A

add() (RuleCollection method) add_col_to_table() (Database method) add_missing_columns() (Database method) AlgorithmClient (class in vantage6.client.algorithm_client) AlgorithmClient.Collaboration (class in vantage6.client.algorithm_client) AlgorithmClient.Node (class in vantage6.client.algorithm_client) AlgorithmClient.Organization (class in vantage6.client.algorithm_client) AlgorithmClient.Result (class in vantage6.client.algorithm_client) AlgorithmClient.Task (class in vantage6.client.algorithm_client) AlgorithmClient.VPN (class in vantage6.client.algorithm_client) AlgorithmPort (class in vantage6.server.model.algorithm_port) AppContext (class in vantage6.common.context) appender() (PermissionManager method)

assign_rule_to_container() (PermissionManager method) assign_rule_to_fixed_role() (PermissionManager static method) assign_rule_to_node() (PermissionManager method) assign_rule_to_root() (PermissionManager method) Authenticatable (class in vantage6.server.model.authenticatable) authenticate() (ClientBase method) (ContainerClient method) (UserClient method) AuthenticationException auto_wrapper() (in module vantage6.tools.wrapper) available_configurations() (AppContext class method) (NodeContext class method) (ServerContext class method) available_environments (ConfigurationManager property)

B

base64s_to_bytes() (in module vantage6.common) base_path (ClientBase property)

bytes_to_base64s() (in module vantage6.common) bytes_to_str() (CryptorBase static method)

C

can() (User method) change_my_password() (UserClient.Util method) check_config_name_allowed() (in module vantage6.cli.utils) check_config_writeable() (in module vantage6.common) check_if_docker_daemon_is_running() (in module vantage6.cli.utils) check_key() (Node method) check_password() (User method) check_user_rules() (PermissionManager static method) clear_data() (Database method) clear_session() (DatabaseSessionManager static method) ClickLogger (class in vantage6.common) Client (in module vantage6.client) ClientBase (class in vantage6.client) ClientBase.SubClient (class in vantage6.client) ClientMockProtocol (class in vantage6.tools.mock_client) close() (Database method) Collaboration (class in vantage6.server.model.collaboration) COLLABORATION (Scope attribute) CollaborationSchema (class in vantage6.server.resource.common._schema) CollaborationSchema.Meta (class in vantage6.server.resource.common._schema) CollaborationSchemaSimple (class in vantage6.server.resource.common._schema) CollaborationSchemaSimple.Meta (class in vantage6.server.resource.common._schema) collection() (PermissionManager method) ColorStreamHandler (in module vantage6.common.colors) complete (Result attribute) config_exists() (AppContext class method) (NodeContext class method) (ServerContext class method)

config_file (AppContext property) config_file_name (AppContext property) Configuration (class in vantage6.common.configuration_manager) configuration_wizard() (in module vantage6.cli.configuration_wizard) ConfigurationManager (class in vantage6.common.configuration_manager) configure_api() (ServerApp method) configure_flask() (ServerApp method) configure_jwt() (ServerApp method) configure_logger() (AppContext static method) connect() (Database method) ContainerClient (class in vantage6.client) CREATE (Operation attribute) create() (AlgorithmClient.Task method) (UserClient.Collaboration method) (UserClient.Node method) (UserClient.Organization method) (UserClient.Role method) (UserClient.Task method) (UserClient.User method) create_new_rsa_key() (RSACryptor static method) create_new_task() (ClientMockProtocol method) (ContainerClient method) create_public_key_bytes() (RSACryptor static method) create_qr_uri() (in module vantage6.server.resource.common.auth_helper) CryptorBase (class in vantage6.common.encryption) CSVWrapper (class in vantage6.tools.wrapper) CsvWrapper (in module vantage6.tools.wrapper)

D

Database (class in vantage6.server.model.base) databases (NodeContext property) DatabaseSessionManager (class in vantage6.server.model.base) debug() (ClickLogger static method) (in module vantage6.common) decrypt_str_to_bytes() (CryptorBase method) (RSACryptor method) DefaultSocketNamespace (class in vantage6.server.websockets) DELETE (Operation attribute) delete() (ModelBase method) (UserClient.Node method) (UserClient.Role method) (UserClient.Task method) DeserializationException

dispatch_rpc() (in module vantage6.tools.dispatch_rpc) docker_container_name (NodeContext property) (ServerContext property) docker_network_name (NodeContext property) docker_squid_volume_name (NodeContext property) docker_ssh_volume_name (NodeContext property) docker_temporary_volume_name() (NodeContext method) docker_volume_name (NodeContext property) docker_vpn_volume_name (NodeContext property) docker_wrapper() (in module vantage6.tools.wrapper) DockerWrapper (in module vantage6.tools.wrapper) drop_all() (Database method) DummyCryptor (class in vantage6.common.encryption) dump() (ServicesResources method)

E

echo() (in module vantage6.common) EDIT (Operation attribute) emit() (_WinColorStreamHandler method) encrypt_bytes_to_str() (CryptorBase method) (RSACryptor method) environment (AppContext property)

environments (ConfigurationManager property) error() (ClickLogger static method) (in module vantage6.common) (in module vantage6.tools.util) ExcelWrapper (class in vantage6.tools.wrapper) exists() (Node class method) (User class method)

F

FILE_ vserver-local-import command line option find_by_name() (Collaboration class method) find_config_file() (AppContext class method) format() (_AnsiColorStreamHandler method) from_external_config_file() (AppContext class method) (NodeContext class method) (ServerContext class method)

from_file() (ConfigurationManager class method) (NodeConfigurationManager class method) (ServerConfigurationManager class method) (TestingConfigurationManager class method) from_task() (UserClient.Result method)

G

generate_path_to() (ClientBase method) generate_private_key() (UserClient.Util method) get() (AlgorithmClient.Collaboration method) (AlgorithmClient.Node method) (AlgorithmClient.Organization method) (AlgorithmClient.Result method) (AlgorithmClient.Task method) (ConfigurationManager method) (ModelBase class method) (UserClient.Collaboration method) (UserClient.Node method) (UserClient.Organization method) (UserClient.Result method) (UserClient.Role method) (UserClient.Rule method) (UserClient.Task method) (UserClient.User method) get_addresses() (AlgorithmClient.VPN method) get_algorithm_address_by_label() (ContainerClient method) get_algorithm_addresses() (ContainerClient method) get_and_update_authenticatable_info() (in module vantage6.server.resource) get_by_() (Rule class method) get_by_api_key() (Node class method) get_by_email() (User class method) get_by_name() (Organization class method) (Role class method)

get_by_username() (User class method) get_child_addresses() (AlgorithmClient.VPN method) get_data_file() (AppContext method) get_database_config() (in module vantage6.common) get_database_uri() (NodeContext method) (ServerContext method) get_default_roles() (in module vantage6.server.default_roles) get_node_from_organization() (Collaboration method) get_nodes_from_organizations() (Collaboration method) get_non_existing_columns() (Database method) get_online_nodes() (Node class method) get_organization_ids() (Collaboration method) get_organizations_in_my_collaboration() (ClientMockProtocol method) (ContainerClient method) get_parent_address() (AlgorithmClient.VPN method) get_result_ids() (Organization method) get_results() (ClientBase method) (ClientMockProtocol method) (ContainerClient method) get_server_health() (UserClient.Util method) get_server_version() (UserClient.Util method) get_session() (DatabaseSessionManager static method) get_task() (ClientMockProtocol method) get_task_ids() (Collaboration method) GLOBAL (Scope attribute)

H

has_application (ConfigurationManager property) has_environments (ConfigurationManager property) has_task_failed() (in module vantage6.common.task_status) has_task_finished() (in module vantage6.common.task_status) hash() (Authenticatable static method)

HATEOASModelSchema (class in vantage6.server.resource.common._schema) headers (ClientBase property) help() (ModelBase class method) host (ClientBase property) (ServerInfo attribute)

I

id_ (WhoAmI attribute) in_flask_request() (DatabaseSessionManager static method) info() (ClickLogger static method) (in module vantage6.common) (in module vantage6.tools.util) INST_CONFIG_MANAGER (AppContext attribute) (NodeContext attribute) (ServerContext attribute)

instance_folders() (AppContext static method) is_blocked() (User method) is_column_missing() (Database static method) is_empty (ConfigurationManager property) is_included() (ServicesResources static method) is_ip_address() (in module vantage6.common) is_local_address() (in module vantage6.cli.rabbitmq) is_valid (Configuration property)

J

jsonable() (in module vantage6.server.db)

K

kill() (UserClient.Task method)

kill_tasks() (UserClient.Node method)

L

list() (AlgorithmClient.Organization method) (UserClient.Collaboration method) (UserClient.Node method) (UserClient.Organization method) (UserClient.Result method) (UserClient.Role method) (UserClient.Rule method) (UserClient.Task method) (UserClient.User method) load() (ConfigurationManager method) load_data() (CSVWrapper static method) (ExcelWrapper static method) (MultiDBWrapper static method) (OMOPWrapper static method) (ParquetWrapper static method) (SparqlDockerWrapper static method) (SQLWrapper static method) (WrapperBase static method)

load_input() (in module vantage6.tools.wrapper) load_resources() (ServerApp method) load_rules_from_resources() (PermissionManager method) log_file (AppContext property) log_file_name() (AppContext method) logger_name() (in module vantage6.common) LogLevel (class in vantage6.client.utils)

M

MailService (class in vantage6.server.mail_service) Member (in module vantage6.server.model.member) meta_dump() (HATEOASModelSchema method) model (CollaborationSchema.Meta attribute) (NodeConfigSchema.Meta attribute) (NodeSchema.Meta attribute) (NodeSchemaSimple.Meta attribute) (OrganizationSchema.Meta attribute) (PortSchema.Meta attribute) (ResultNodeSchema.Meta attribute) (ResultPortSchema.Meta attribute) (ResultSchema.Meta attribute) (RoleSchema.Meta attribute) (RuleSchema.Meta attribute) (TaskResultSchema.Meta attribute) (TaskSchema.Meta attribute) (UserSchema.Meta attribute) ModelBase (class in vantage6.server.model.base) module vantage6.cli.configuration_manager vantage6.cli.configuration_wizard vantage6.cli.context vantage6.cli.rabbitmq vantage6.cli.utils vantage6.client vantage6.client.algorithm_client vantage6.client.exceptions vantage6.client.utils vantage6.common vantage6.common.colors vantage6.common.configuration_manager vantage6.common.context vantage6.common.encryption vantage6.common.exceptions vantage6.common.task_status vantage6.server vantage6.server.db vantage6.server.exceptions vantage6.server.model.base vantage6.server.model.member vantage6.server.model.permission vantage6.server.model.role_rule_association vantage6.server.resource vantage6.server.resource.common._schema vantage6.server.resource.common.auth_helper vantage6.tools.dispatch_rpc vantage6.tools.mock_client vantage6.tools.util vantage6.tools.wrapper

multidb_wrapper() (in module vantage6.tools.wrapper) MultiDBWrapper (class in vantage6.tools.wrapper)

N

name (ClientBase property) (WhoAmI attribute) name_exists() (Collaboration class method) new_session() (DatabaseSessionManager static method) next_run_id() (Task class method) Node (class in vantage6.server.model.node) node (Result property) node_configuration_questionaire() (in module vantage6.cli.configuration_wizard) NodeConfigSchema (class in vantage6.server.resource.common._schema)

NodeConfigSchema.Meta (class in vantage6.server.resource.common._schema) NodeConfiguration (class in vantage6.cli.configuration_manager) NodeConfigurationManager (class in vantage6.cli.configuration_manager) NodeContext (class in vantage6.cli.context) NodeSchema (class in vantage6.server.resource.common._schema) NodeSchema.Meta (class in vantage6.server.resource.common._schema) NodeSchemaSimple (class in vantage6.server.resource.common._schema) NodeSchemaSimple.Meta (class in vantage6.server.resource.common._schema) notify_user_blocked() (in module vantage6.server.resource.common.auth_helper)

O

obtain_auth() (ServicesResources static method) obtain_auth_organization() (ServicesResources class method) obtain_organization_id() (ServicesResources static method) OMOPWrapper (class in vantage6.tools.wrapper) on_algorithm_status_change() (DefaultSocketNamespace method) on_connect() (DefaultSocketNamespace method) on_disconnect() (DefaultSocketNamespace method) on_error() (DefaultSocketNamespace method) on_message() (DefaultSocketNamespace method) on_node_info_update() (DefaultSocketNamespace method)

on_ping() (DefaultSocketNamespace method) only_for() (in module vantage6.server.resource) Operation (class in vantage6.server.model.rule) Organization (class in vantage6.server.model.organization) ORGANIZATION (Scope attribute) organization_id (WhoAmI attribute) organization_name (WhoAmI attribute) OrganizationSchema (class in vantage6.server.resource.common._schema) OrganizationSchema.Meta (class in vantage6.server.resource.common._schema) OWN (Scope attribute)

P

parquet_wrapper() (in module vantage6.tools.wrapper) ParquetWrapper (class in vantage6.tools.wrapper) parse_datetime() (in module vantage6.server.resource) path (ClientBase property) (ServerInfo attribute) Permission (in module vantage6.server.model.permission) PermissionManager (class in vantage6.server.permission) port (ClientBase property) (ServerInfo attribute)

PortSchema (class in vantage6.server.resource.common._schema) PortSchema.Meta (class in vantage6.server.resource.common._schema) post_task() (ClientBase method) (ContainerClient method) print_qr_code() (in module vantage6.client.utils) public_key (Organization attribute) public_key_bytes (RSACryptor property) public_key_str (RSACryptor property) put() (ConfigurationManager method)

R

refresh_token() (ClientBase method) (ContainerClient method) register_rule() (PermissionManager method) request() (AlgorithmClient method) (ClientBase method) reset_my_password() (UserClient.Util method) reset_two_factor_auth() (UserClient.Util method) response() (ServicesResources method) Result (class in vantage6.server.model.result) ResultNodeSchema (class in vantage6.server.resource.common._schema) ResultNodeSchema.Meta (class in vantage6.server.resource.common._schema) ResultPortSchema (class in vantage6.server.resource.common._schema) ResultPortSchema.Meta (class in vantage6.server.resource.common._schema) results_for_node() (Task method)

ResultSchema (class in vantage6.server.resource.common._schema) ResultSchema.Meta (class in vantage6.server.resource.common._schema) ResultTaskIncludedSchema (class in vantage6.server.resource.common._schema) Role (class in vantage6.server.model.role) role_rule_association (in module vantage6.server.model.role_rule_association) RoleSchema (class in vantage6.server.resource.common._schema) RoleSchema.Meta (class in vantage6.server.resource.common._schema) RSACryptor (class in vantage6.common.encryption) Rule (class in vantage6.server.model.rule) rule_exists_in_db() (PermissionManager static method) RuleCollection (class in vantage6.server.permission) RuleSchema (class in vantage6.server.resource.common._schema) RuleSchema.Meta (class in vantage6.server.resource.common._schema) run_dev_server() (in module vantage6.server) run_server() (in module vantage6.server)

S

save() (ConfigurationManager method) (ModelBase method) Scope (class in vantage6.server.model.rule) select_configuration_questionaire() (in module vantage6.cli.configuration_wizard) send_email() (MailService method) server_configuration_questionaire() (in module vantage6.cli.configuration_wizard) ServerApp (class in vantage6.server) ServerConfiguration (class in vantage6.cli.configuration_manager) ServerConfigurationManager (class in vantage6.cli.configuration_manager) ServerContext (class in vantage6.cli.context) ServerInfo (class in vantage6.client) ServicesResources (class in vantage6.server.resource) set_folders() (AppContext method)

set_my_password() (UserClient.Util method) set_password() (User method) set_two_factor_auth() (UserClient.Util method) setup_encryption() (ClientBase method) setup_logging() (AppContext method) setup_socket_connection() (ServerApp method) show_qr_code_image() (in module vantage6.client.utils) Singleton (class in vantage6.common) sparql_wrapper() (in module vantage6.tools.wrapper) SparqlDockerWrapper (class in vantage6.tools.wrapper) split_rabbitmq_uri() (in module vantage6.cli.rabbitmq) SQLWrapper (class in vantage6.tools.wrapper) start() (ServerApp method) str_to_bytes() (CryptorBase static method)

T

Task (class in vantage6.server.model.task) TaskIncludedSchema (class in vantage6.server.resource.common._schema) TaskResultSchema (class in vantage6.server.resource.common._schema) TaskResultSchema.Meta (class in vantage6.server.resource.common._schema) TaskSchema (class in vantage6.server.resource.common._schema) TaskSchema.Meta (class in vantage6.server.resource.common._schema)

TaskStatus (class in vantage6.common.task_status) TestConfiguration (class in vantage6.cli.configuration_manager) TestingConfigurationManager (class in vantage6.cli.configuration_manager) token (ClientBase property) type_ (WhoAmI attribute) type_data_folder() (AppContext static method) (NodeContext static method)

U

update() (UserClient.Node method) (UserClient.Organization method) (UserClient.Role method) (UserClient.User method) User (class in vantage6.server.model.user) user_login() (in module vantage6.server.resource.common.auth_helper) UserClient (class in vantage6.client) UserClient.Collaboration (class in vantage6.client) UserClient.Node (class in vantage6.client) UserClient.Organization (class in vantage6.client)

UserClient.Result (class in vantage6.client) UserClient.Role (class in vantage6.client) UserClient.Rule (class in vantage6.client) UserClient.Task (class in vantage6.client) UserClient.User (class in vantage6.client) UserClient.Util (class in vantage6.client) username_exists() (User class method) UserPermission (in module vantage6.server.model.permission) UserSchema (class in vantage6.server.resource.common._schema) UserSchema.Meta (class in vantage6.server.resource.common._schema)

V

vantage6.cli.configuration_manager module vantage6.cli.configuration_wizard module vantage6.cli.context module vantage6.cli.rabbitmq module vantage6.cli.utils module vantage6.client module vantage6.client.algorithm_client module vantage6.client.exceptions module vantage6.client.utils module vantage6.common module vantage6.common.colors module vantage6.common.configuration_manager module vantage6.common.context module vantage6.common.encryption module vantage6.common.exceptions module vantage6.common.task_status module vantage6.server module vantage6.server.db module vantage6.server.exceptions module vantage6.server.model.base module vantage6.server.model.member module vantage6.server.model.permission module vantage6.server.model.role_rule_association module vantage6.server.resource module vantage6.server.resource.common._schema module vantage6.server.resource.common.auth_helper module vantage6.tools.dispatch_rpc module vantage6.tools.mock_client module

vantage6.tools.util module vantage6.tools.wrapper module verify_public_key() (RSACryptor method) VIEW (Operation attribute) VPNConfigException VPNPortalAuthException vserver-local-files command line option --config --environment --name --system --user -c -e -n vserver-local-import command line option --config --drop-all --environment --name --system --user -c -e -n FILE_ vserver-local-new command line option --environment --name --system --user -e -n vserver-local-shell command line option --config --environment --name --system --user -c -e -n vserver-local-start command line option --config --debug --environment --ip --name --port --system --user -c -e -n -p

W

wait_for_results() (UserClient method) warn() (ClickLogger static method) (in module vantage6.tools.util) warning() (in module vantage6.common)

WhoAmI (class in vantage6.common) wrap_algorithm() (WrapperBase method) WrapperBase (class in vantage6.tools.wrapper) write_output() (in module vantage6.tools.wrapper)