Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy.exceptions package

This module defines Galaxy’s custom exceptions.

A Galaxy exception is an exception that extends MessageException which defines an HTTP status code (represented by the status_code attribute) and a default error message.

New exceptions should be defined by adding an entry to error_codes.json in this directory to define a default error message and a Galaxy “error code”. A concrete Python class should be added in this file defining an HTTP status code (as status_code) and error code (error_code) object loaded dynamically from error_codes.json.

Reflecting Galaxy’s origins as a web application, these exceptions tend to be a bit web-oriented. However this module is a dependency of modules and tools that have nothing to do with the web - keep this in mind when defining exception names and messages.

exception galaxy.exceptions.MessageException(err_msg=None, type='info', **extra_error_info)

Bases: exceptions.Exception

Most generic Galaxy exception - indicates merely that some exceptional condition happened.

status_code = 400

err_code = ErrorCode[code=0,message=Unknown error occurred while processing request.]

__init__(err_msg=None, type='info', **extra_error_info)

exception galaxy.exceptions.ItemDeletionException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

exception galaxy.exceptions.ObjectInvalid

Bases: exceptions.Exception

Accessed object store ID is invalid

exception galaxy.exceptions.ActionInputError(err_msg, type='error')

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400008,message=Request contained invalid parameter, action could not be completed.]

__init__(err_msg, type='error')

exception galaxy.exceptions.DuplicatedSlugException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400006,message=Slug must be unique per user.]

exception galaxy.exceptions.DuplicatedIdentifierException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400011,message=Request contained a duplicated identifier that must be unique.]

exception galaxy.exceptions.ObjectAttributeInvalidException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400004,message=Attempted to create or update object with invalid attribute value.]

exception galaxy.exceptions.ObjectAttributeMissingException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400005,message=Attempted to create object without required attribute.]

exception galaxy.exceptions.MalformedId(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400009,message=The id of the resource is malformed.]

exception galaxy.exceptions.MalformedContents(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400013,message=The contents of the request are malformed.]

exception galaxy.exceptions.UnknownContentsType(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400010,message=The request contains unknown type of contents.]

exception galaxy.exceptions.RequestParameterMissingException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400007,message=Request is missing parameter required to complete desired action.]

exception galaxy.exceptions.ToolMetaParameterException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400012,message=Supplied incorrect or incompatible tool meta parameters.]

exception galaxy.exceptions.ToolMissingException(err_msg=None, type='info', tool_id=None, **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400014,message=Tool could not be found.]

__init__(err_msg=None, type='info', tool_id=None, **extra_error_info)

exception galaxy.exceptions.RequestParameterInvalidException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 400

err_code = ErrorCode[code=400008,message=Request contained invalid parameter, action could not be completed.]

exception galaxy.exceptions.AuthenticationFailed(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 401

err_code = ErrorCode[code=401001,message=Authentication failed, invalid credentials supplied.]

exception galaxy.exceptions.AuthenticationRequired(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 403

err_code = ErrorCode[code=403001,message=Authentication required for this request]

exception galaxy.exceptions.ItemAccessibilityException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 403

err_code = ErrorCode[code=403002,message=User cannot access specified item.]

exception galaxy.exceptions.ItemOwnershipException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 403

err_code = ErrorCode[code=403003,message=User does not own specified item.]

exception galaxy.exceptions.ConfigDoesNotAllowException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 403

err_code = ErrorCode[code=403004,message=The configuration of this Galaxy instance does not allow that operation]

exception galaxy.exceptions.InsufficientPermissionsException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 403

err_code = ErrorCode[code=403005,message=You don't have proper permissions to perform the requested operation]

exception galaxy.exceptions.AdminRequiredException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 403

err_code = ErrorCode[code=403006,message=Action requires admin account.]

exception galaxy.exceptions.ObjectNotFound(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

Accessed object was not found

status_code = 404

err_code = ErrorCode[code=404001,message=No such object found.]

exception galaxy.exceptions.DeprecatedMethod(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

Method (or a particular form/arg signature) has been removed and won’t be available later

status_code = 404

err_code = ErrorCode[code=404002,message=This API method or call signature has been deprecated and is no longer available]

exception galaxy.exceptions.Conflict(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 409

err_code = ErrorCode[code=409001,message=Database conflict prevented fulfilling the request.]

exception galaxy.exceptions.ConfigurationError

Bases: exceptions.Exception

status_code = 500

err_code = ErrorCode[code=500003,message=Error in a configuration file.]

exception galaxy.exceptions.InconsistentDatabase(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 500

err_code = ErrorCode[code=500002,message=Inconsistent database prevented fulfilling the request.]

exception galaxy.exceptions.InternalServerError(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 500

err_code = ErrorCode[code=500001,message=Internal server error.]

exception galaxy.exceptions.NotImplemented(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.MessageException

status_code = 501

err_code = ErrorCode[code=501001,message=Method is not implemented.]

exception galaxy.exceptions.ContainerCLIError(msg=None, stdout=None, stderr=None, returncode=None, command=None, subprocess_command=None, **kwargs)

Bases: exceptions.Exception

__init__(msg=None, stdout=None, stderr=None, returncode=None, command=None, subprocess_command=None, **kwargs)

exception galaxy.exceptions.ContainerNotFound(msg=None, container_id=None, **kwargs)

Bases: exceptions.Exception

__init__(msg=None, container_id=None, **kwargs)

exception galaxy.exceptions.ContainerImageNotFound(msg=None, image=None, **kwargs)

Bases: exceptions.Exception

__init__(msg=None, image=None, **kwargs)

exception galaxy.exceptions.ContainerRunError(msg=None, image=None, command=None, **kwargs)

Bases: exceptions.Exception

__init__(msg=None, image=None, command=None, **kwargs)

Submodules

galaxy.exceptions.error_codes module

Defines the ErrorCode class and instantiates concrete objects from JSON.

See the file error_codes.json for actual error code descriptions.

class galaxy.exceptions.error_codes.ErrorCode(code, default_error_message)

Bases: object

Small class allowing object representation for error descriptions loaded from JSON.

__init__(code, default_error_message)

Construct a ErrorCode from supplied integer and error message.