fastr Package¶
fastr
Package¶
Initialize self. See help(type(self)) for accurate signature.
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fastr.__init__.
__dir__
() → list¶ default dir() implementation
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fastr.__init__.
__format__
()¶ default object formatter
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fastr.__init__.
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
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fastr.__init__.
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
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fastr.__init__.
__reduce__
()¶ helper for pickle
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fastr.__init__.
__reduce_ex__
()¶ helper for pickle
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fastr.__init__.
__sizeof__
() → int¶ size of object in memory, in bytes
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fastr.__init__.
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
exceptions
Module¶
This module contains all Fastr-related Exceptions
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exception
fastr.exceptions.
FastrAttributeError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
,AttributeError
AttributeError in the fastr system
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrCannotChangeAttributeError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
Attempting to change an attribute of an object that can be set only once.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrCardinalityError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
The description of the cardinality is not valid.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrCollectorError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
Cannot collect the results from a Job because of an error
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrDataTypeFileNotReadable
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
Could not read the datatype file.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrDataTypeMismatchError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
When using a DataType as the key for the DataTypeManager, the DataTypeManager found another DataType with the same name already in the DataTypeManager. The means fastr has two version of the same DataType in the system, which should never happen!
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrDataTypeNotAvailableError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
The DataType requested is not found by the fastr system. Typically this means that no matching DataType is found in the DataTypeManager.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrDataTypeNotInstantiableError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
The base classes for DataTypes cannot be instantiated and should always be sub-classed.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrDataTypeValueError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
This value in fastr did not pass the validation specificied for its DataType, typically means that the data is missing or corrupt.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrError
(*args, **kwargs)[source]¶ Bases:
Exception
This is the base class for all fastr related exceptions. Catching this class of exceptions should ensure a proper execution of fastr.
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__init__
(*args, **kwargs)[source]¶ Constructor for all exceptions. Saves the caller object fullid (if found) and the file, function and line number where the object was created.
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__module__
= 'fastr.exceptions'¶
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__weakref__
¶ list of weak references to the object (if defined)
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exception
fastr.exceptions.
FastrErrorInSubprocess
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrExecutionError
Encountered an error in the subprocess started by the execution script
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrExecutableNotFoundError
(executable=None, *args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrExecutionError
The executable could not be found!
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__init__
(executable=None, *args, **kwargs)[source]¶ Constructor for all exceptions. Saves the caller object fullid (if found) and the file, function and line number where the object was created.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrExecutionError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
Base class for all fastr execution related errors
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrFileNotFound
(filepath, message=None)[source]¶ Bases:
fastr.exceptions.FastrError
Could not find an expected file
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__init__
(filepath, message=None)[source]¶ Constructor for all exceptions. Saves the caller object fullid (if found) and the file, function and line number where the object was created.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrIOError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
,OSError
IOError in the fastr system
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__module__
= 'fastr.exceptions'¶
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__weakref__
¶ list of weak references to the object (if defined)
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exception
fastr.exceptions.
FastrImportError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
,ImportError
ImportError in the fastr system
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__module__
= 'fastr.exceptions'¶
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__weakref__
¶ list of weak references to the object (if defined)
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exception
fastr.exceptions.
FastrIndexError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
,IndexError
IndexError in the fastr system
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrIndexNonexistent
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrIndexError
This is an IndexError for samples requested from a sparse data array. The sample is not there but is probably not there because of sparseness rather than being a missing sample (e.g. out of bounds).
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrKeyError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
,KeyError
KeyError in the fastr system
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrLockNotAcquired
(directory, message=None)[source]¶ Bases:
fastr.exceptions.FastrError
Could not lock a directory
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__init__
(directory, message=None)[source]¶ Constructor for all exceptions. Saves the caller object fullid (if found) and the file, function and line number where the object was created.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrLookupError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
Could not find specified object in the fastr environment.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrMountUnknownError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrKeyError
Trying to access an undefined mount
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrNetworkMismatchError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
Two interacting objects belong to different fastr network.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrNetworkUnknownError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrKeyError
Reference to a Tool that is not recognised by the fastr system. This typically means the specific id/version combination of the requested tool has not been loaded by the ToolManager.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrNoValidTargetError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrKeyError
Cannot find a valid target for the tool
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrNodeAreadyPreparedError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrStateError
A attempt is made at preparing a NodeRun for the second time. This is not allowed as it would wipe the current execution data and cause data-loss.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrNodeNotPreparedError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrStateError
When trying to access executation data of a NodeRun, the NodeRun must be prepare. The NodeRun has not been prepared by the execution, so the data is not available!
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrNodeNotValidError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrStateError
A NodeRun is not in a valid state where it should be, typically an invalid NodeRun is passed to the executor causing trouble.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrNotExecutableError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrExecutionError
The command invoked by subprocess is not executable on the system
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrNotImplementedError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
,NotImplementedError
This function/method has not been implemented on purpose (e.g. should be overwritten in a sub-class)
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrOSError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
,OSError
OSError in the fastr system
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__module__
= 'fastr.exceptions'¶
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__weakref__
¶ list of weak references to the object (if defined)
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exception
fastr.exceptions.
FastrObjectUnknownError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrKeyError
Reference to a Tool that is not recognised by the fastr system. This typically means the specific id/version combination of the requested tool has not been loaded by the ToolManager.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrOptionalModuleNotAvailableError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrNotImplementedError
A optional modules for Fastr is needed for this function, but is not available on the current python installation.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrOutputValidationError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrExecutionError
An output of a Job does not pass validation
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrParentMismatchError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
Two interactive objects have different parent where they should be the same
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrPluginCapabilityNotImplemented
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrNotImplementedError
A plugin did not implement a capability that it advertised.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrPluginNotAvailable
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrKeyError
Indicates that a requested Plugin was not found on the system.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrPluginNotLoaded
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrStateError
The plugin was not successfully loaded. This means the plugin class cannot be instantiated.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrResultFileNotFound
(filepath, message=None)[source]¶ Bases:
fastr.exceptions.FastrFileNotFound
,fastr.exceptions.FastrExecutionError
Could not found the result file of job that finished. This means the executionscript process was killed during interruption. Generally this means a scheduler killed it because of resource shortage.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrScriptNotFoundError
(interpreter=None, script=None, paths=None, *args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrExecutionError
Script could not be found
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__init__
(interpreter=None, script=None, paths=None, *args, **kwargs)[source]¶ Constructor for all exceptions. Saves the caller object fullid (if found) and the file, function and line number where the object was created.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrSerializationError
(message, serializer, original_exception=None)[source]¶ Bases:
fastr.exceptions.FastrError
The serialization encountered a serious problem
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__init__
(message, serializer, original_exception=None)[source]¶ Constructor for all exceptions. Saves the caller object fullid (if found) and the file, function and line number where the object was created.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrSerializationIgnoreDefaultError
(message, serializer, original_exception=None)[source]¶ Bases:
fastr.exceptions.FastrSerializationError
The value and default are both None, so the value should not be serialized.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrSerializationInvalidDataError
(message, serializer, original_exception=None)[source]¶ Bases:
fastr.exceptions.FastrSerializationError
Encountered data to serialize that is invalid given the serialization schema.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrSerializationMethodError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrKeyError
The desired serialization method does not exist.
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__module__
= 'fastr.exceptions'¶
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Bases:
fastr.exceptions.FastrKeyError
Could not find the Sink data for the desire sink.
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exception
fastr.exceptions.
FastrSizeInvalidError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
The given size cannot be valid.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrSizeMismatchError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
The size of two object in fastr is not matching where it should.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrSizeUnknownError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
The size of object is not (yet) known and only a theoretical estimate is available at the moment.
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__module__
= 'fastr.exceptions'¶
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Bases:
fastr.exceptions.FastrKeyError
Could not find the Source data for the desire source.
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exception
fastr.exceptions.
FastrStateError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
An object is in an invalid/unexpected state.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrSubprocessNotFinished
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrExecutionError
Encountered an error before the subprocess call by the execution script was properly finished.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrToolNotAvailableError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
- The tool used is not available on the current platform (OS and architecture
- combination) and cannot be used.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrToolTargetNotFound
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
Could not determine the location of the tools target binary/script. The tool cannot be used.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrToolUnknownError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrKeyError
Reference to a Tool that is not recognised by the fastr system. This typically means the specific id/version combination of the requested tool has not been loaded by the ToolManager.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrToolVersionError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
Version mismatch, usually the installed tool version and version requested by the network mismatch.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrTypeError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
,TypeError
TypeError in the fastr system
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrUnknownURLSchemeError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrKeyError
Fastr encountered a data URL with a scheme that was not recognised by the IOPlugin manager.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrValueError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrError
,ValueError
ValueError in the fastr system
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrVersionInvalidError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrValueError
The string representation of the version is malformatted.
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__module__
= 'fastr.exceptions'¶
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exception
fastr.exceptions.
FastrVersionMismatchError
(*args, **kwargs)[source]¶ Bases:
fastr.exceptions.FastrValueError
There is a mismatch between different parts of the Fastr environment and integrity is compromised.
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__module__
= 'fastr.exceptions'¶
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fastr.exceptions.
get_message
(exception)[source]¶ Extract the message from an exception is a safe manner
Parameters: exception (BaseException) – exception to extract from Returns: message string Return type: str
version
Module¶
This module keeps track of the version of the currently used Fastr framework. It can check its version from mercurial or a saved file
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fastr.version.
get_base_version
()[source]¶ Get the version from the top-level version file
Return type: Optional
[str
]Returns: the version Rtype str:
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fastr.version.
get_hg_info
()[source]¶ Read information about the current mercurial branch and revision
Return type: Tuple
[Optional
[str
],Optional
[str
]]Returns: tuple containing head revision and branch
Subpackages¶
- api Package
- core Package
- data Package
- datatypes Package
- execution Package
- helpers Package
- planning Package
- plugins Package
- resources Package
resources
Package- Subpackages
- datatypes Package
datatypes
PackageAnalyzeImageFile
ModuleBoolean
ModuleDirectory
ModuleFilePrefix
ModuleFloat
ModuleITKImageFile
ModuleInt
ModuleJsonFile
ModuleMetaImageFile
ModuleNiftiImageFile
ModuleNiftiImageFileCompressed
ModuleNiftiImageFileUncompressed
ModuleNrrdImageFile
ModuleNumber
ModuleProvNFile
ModuleString
ModuleTifImageFile
ModuleTxtFile
ModuleUnsignedInt
Module
- tools Package
- datatypes Package
- test Package
- utils Package
- web Package