execution Package

execution Package

This package contains all modules related directly to the execution

basenoderun Module

class fastr.execution.basenoderun.BaseNodeRun

Bases: fastr.abc.updateable.Updateable, fastr.abc.serializable.Serializable

NODE_RUN_MAP = {'AdvancedFlowNode': <class 'fastr.execution.flownoderun.AdvancedFlowNodeRun'>, 'ConstantNode': <class 'fastr.execution.sourcenoderun.ConstantNodeRun'>, 'FlowNode': <class 'fastr.execution.flownoderun.FlowNodeRun'>, 'MacroNode': <class 'fastr.execution.macronoderun.MacroNodeRun'>, 'Node': <class 'fastr.execution.noderun.NodeRun'>, 'SinkNode': <class 'fastr.execution.sinknoderun.SinkNodeRun'>, 'SourceNode': <class 'fastr.execution.sourcenoderun.SourceNodeRun'>}

NODE_RUN_TYPES = {'AdvancedFlowNodeRun': <class 'fastr.execution.flownoderun.AdvancedFlowNodeRun'>, 'ConstantNodeRun': <class 'fastr.execution.sourcenoderun.ConstantNodeRun'>, 'FlowNodeRun': <class 'fastr.execution.flownoderun.FlowNodeRun'>, 'MacroNodeRun': <class 'fastr.execution.macronoderun.MacroNodeRun'>, 'NodeRun': <class 'fastr.execution.noderun.NodeRun'>, 'SinkNodeRun': <class 'fastr.execution.sinknoderun.SinkNodeRun'>, 'SourceNodeRun': <class 'fastr.execution.sourcenoderun.SourceNodeRun'>}

__abstractmethods__ = frozenset({'_update'})

classmethod __init_subclass__(**kwargs)

Register nodes in class for easly location

__module__ = 'fastr.execution.basenoderun'

environmentmodules Module

This module contains a class to interact with EnvironmentModules

class fastr.execution.environmentmodules.EnvironmentModules(protected=None)

Bases: object

This class can control the module environments in python. It can list, load and unload environmentmodules. These modules are then used if subprocess is called from python.

__dict__ = mappingproxy({'__module__': 'fastr.execution.environmentmodules', '__doc__': '\n This class can control the module environments in python. It can list, load\n and unload environmentmodules. These modules are then used if subprocess is\n called from python.\n ', '_module_settings_loaded': False, '_module_settings_warning': 'Cannot find Environment Modules home directory (environment variables not setup properly?)', '__init__': <function EnvironmentModules.__init__>, '__repr__': <function EnvironmentModules.__repr__>, 'sync': <function EnvironmentModules.sync>, '_sync_loaded': <function EnvironmentModules._sync_loaded>, '_sync_avail': <function EnvironmentModules._sync_avail>, '_module': <function EnvironmentModules._module>, 'totuple_modvalue': <staticmethod object>, 'tostring_modvalue': <staticmethod object>, '_run_commands_string': <function EnvironmentModules._run_commands_string>, 'loaded_modules': <property object>, 'avail_modules': <property object>, 'avail': <function EnvironmentModules.avail>, 'isloaded': <function EnvironmentModules.isloaded>, 'load': <function EnvironmentModules.load>, 'unload': <function EnvironmentModules.unload>, 'reload': <function EnvironmentModules.reload>, 'swap': <function EnvironmentModules.swap>, 'clear': <function EnvironmentModules.clear>, '__dict__': <attribute '__dict__' of 'EnvironmentModules' objects>, '__weakref__': <attribute '__weakref__' of 'EnvironmentModules' objects>})

__init__(protected=None)

Create the environmentmodules control object

Parameters

protected (list) – list of modules that should never be unloaded

Returns

newly created EnvironmentModules

__module__ = 'fastr.execution.environmentmodules'

__repr__()

Return repr(self).

__weakref__

list of weak references to the object (if defined)

avail(namestart=None)

Print available modules in same way as commandline version

Parameters

namestart – filter on modules that start with namestart

property avail_modules

List of avaible modules

clear()

Unload all modules (except the protected modules as they cannot be unloaded). This should result in a clean environment.

isloaded(module)

Check if a specific module is loaded

Parameters

module – module to check

Returns

flag indicating the module is loaded

load(module)

Load specified module

Parameters

module – module to load

property loaded_modules

List of currently loaded modules

reload(module)

Reload specified module

Parameters

module – module to reload

swap(module1, module2)

Swap one module for another one

Parameters

• module1 – module to unload

• module2 – module to load

sync()

Sync the object with the underlying environment. Re-checks the available and loaded modules

static tostring_modvalue(value)

Turn a representation of a module into a string representation

Parameters

value – module representation (either str or tuple)

Returns

string representation

static totuple_modvalue(value)

Turn a representation of a module into a tuple representation

Parameters

value – module representation (either str or tuple)

Returns

tuple representation (name, version, default)

unload(module)

Unload specified module

Parameters

module – module to unload

class fastr.execution.environmentmodules.ModuleSystem

Bases: enum.Enum

An enumeration.

__module__ = 'fastr.execution.environmentmodules'

envmod = 'enviromentmodules'

lmod = 'Lmod'

executionscript Module

The executionscript is the script that wraps around a tool executable. It takes a job, builds the command, executes the command (while profiling it) and collects the results.

fastr.execution.executionscript.execute_job(job)

Execute a Job and save the result to disk

Parameters

job – the job to execute

fastr.execution.executionscript.main(joblist=None)

This is the main code. Wrapped inside a function to avoid the variables being seen as globals and to shut up pylint. Also if the joblist argument is given it can run any given job, otherwise it takes the first command line argument.

flownoderun Module

class fastr.execution.flownoderun.FlowNodeRun(node, parent)

Bases: fastr.execution.noderun.NodeRun

A Flow NodeRun is a special subclass of Nodes in which the amount of samples can vary per Output. This allows non-default data flows.

__abstractmethods__ = frozenset({})

__module__ = 'fastr.execution.flownoderun'

property blocking

A FlowNodeRun is (for the moment) always considered blocking.

Returns

True

property dimnames

Names of the dimensions in the NodeRun output. These will be reflected in the SampleIdList of this NodeRun.

property outputsize

Size of the outputs in this NodeRun

set_result(job, failed_annotation)

Incorporate result of a job into the FlowNodeRun.

Parameters

job (Type) – job of which the result to store

class fastr.execution.flownoderun.AdvancedFlowNodeRun(node, parent)

Bases: fastr.execution.flownoderun.FlowNodeRun

__abstractmethods__ = frozenset({})

__module__ = 'fastr.execution.flownoderun'

execute()

Execute the node and create the jobs that need to run

Returns

list of jobs to run

Return type

list of Jobs

set_result(job, failed_annotation)

Incorporate result of a job into the FlowNodeRun.

Parameters

job (Type) – job of which the result to store

inputoutputrun Module

Classes for arranging the input and output for nodes.

Exported classes:

Input – An input for a node (holding datatype). Output – The output of a node (holding datatype and value). ConstantOutput – The output of a node (holding datatype and value).

Warning

Don’t mess with the Link, Input and Output internals from other places. There will be a huge chances of breaking the network functionality!

class fastr.execution.inputoutputrun.AdvancedFlowOutputRun(node_run, template)

Bases: fastr.execution.inputoutputrun.OutputRun

__abstractmethods__ = frozenset({})

__module__ = 'fastr.execution.inputoutputrun'

class fastr.execution.inputoutputrun.BaseInputRun(node_run, template)

Bases: fastr.core.samples.HasSamples, fastr.planning.inputoutput.BaseInput

Base class for all inputs runs.

__abstractmethods__ = frozenset({'__getitem__', '_update', 'dimensions', 'fullid', 'itersubinputs'})

__init__(node_run, template)

Instantiate a BaseInput

Parameters

• node – the parent node the input/output belongs to.

• description – the ParameterDescription describing the input/output.

Returns

the created BaseInput

Raises

• FastrTypeError – if description is not of class ParameterDescription

• FastrDataTypeNotAvailableError – if the DataType requested cannot be found in the fastr.types

__module__ = 'fastr.execution.inputoutputrun'

abstract itersubinputs()

Iterator over the SubInputs

Returns

iterator

example:

>>> for subinput in input_a.itersubinputs():
        print subinput

class fastr.execution.inputoutputrun.InputRun(node_run, template)

Bases: fastr.execution.inputoutputrun.BaseInputRun

Class representing an input of a node. Such an input will be connected to the output of another node or the output of an constant node to provide the input value.

__abstractmethods__ = frozenset({})

__getitem__(key)

Retrieve an item from this Input.

Parameters

key (str, SampleId or tuple) – the key of the requested item, can be a key str, sample index tuple or a SampleId

Returns

the return value depends on the requested key. If the key was an int the corresponding SubInput will be returned. If the key was a SampleId or sample index tuple, the corresponding SampleItem will be returned.

Return type

SampleItem or SubInput

Raises

• FastrTypeError – if key is not of a valid type

• FastrKeyError – if the key is not found

__getstate__()

Retrieve the state of the Input

Returns

the state of the object

Rtype dict

__init__(node_run, template)

Instantiate an input.

Parameters

template – the Input that the InputRun is based on

__module__ = 'fastr.execution.inputoutputrun'

__setstate__(state)

Set the state of the Input by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

__str__()

Get a string version for the Input

Returns

the string version

Return type

str

cardinality(key=None, job_data=None)

Cardinality for an Input is the sum the cardinalities of the SubInputs, unless defined otherwise.

Parameters

key (tuple of int or SampleId) – key for a specific sample, can be sample index or id

Returns

the cardinality

Return type

int, sympy.Symbol, or None

property datatype

The datatype of this Input

property dimensions

The size of the sample collections that can accessed via this Input.

property fullid

The full defining ID for the Input

get_sourced_nodes()

Get a list of all Nodes connected as sources to this Input

Returns

list of all connected Nodes

Return type

list

get_sourced_outputs()

Get a list of all Outputs connected as sources to this Input

Returns

tuple of all connected Outputs

Return type

tuple

index(value)

Find index of a SubInput

Parameters

value (SubInput) – the SubInput to find the index of

Returns

key

Return type

int, str

property input_group

The id of the InputGroup this Input belongs to.

insert(index)

Insert a new SubInput at index in the sources list

Parameters

key (int) – positive integer for position in _source list to insert to

Returns

newly inserted SubInput

Return type

SubInput

itersubinputs()

Iterate over the SubInputs in this Input.

Returns

iterator yielding SubInput

example:

>>> for subinput in input_a.itersubinputs():
        print subinput

remove(value)

Remove a SubInput from the SubInputs list.

Parameters

value (SubInput) – the SubInput to removed from this Input

property source

The mapping of SubInputs that are connected and have more than 0 elements.

class fastr.execution.inputoutputrun.MacroOutputRun(node_run, template)

Bases: fastr.execution.inputoutputrun.OutputRun

__abstractmethods__ = frozenset({})

__module__ = 'fastr.execution.inputoutputrun'

property dimensions

The dimensions has to be implemented by any subclass. It has to provide a tuple of Dimensions.

Returns

dimensions

Return type

tuple

class fastr.execution.inputoutputrun.NamedSubinputRun(parent)

Bases: fastr.execution.inputoutputrun.InputRun

A named subinput for cases where the value of an input is mapping.

__abstractmethods__ = frozenset({})

__getitem__(key)

Retrieve an item (a SubInput) from this NamedSubInput.

Parameters

key (int) – the key of the requested item

Return type

Union[SubInputRun, SampleItem]

Returns

The SubInput corresponding with the key will be returned.

Raises

• FastrTypeError – if key is not of a valid type

• FastrKeyError – if the key is not found

__init__(parent)

Instantiate an input.

Parameters

template – the Input that the InputRun is based on

__module__ = 'fastr.execution.inputoutputrun'

__str__()

Get a string version for the NamedSubInput

Returns

the string version

Return type

str

property fullid

The full defining ID for the NamedSubInputRun

property item_index

class fastr.execution.inputoutputrun.OutputRun(node_run, template)

Bases: fastr.planning.inputoutput.BaseOutput, fastr.core.samples.ContainsSamples

Class representing an output of a node. It holds the output values of the tool ran. Output fields can be connected to inputs of other nodes.

__abstractmethods__ = frozenset({})

__getitem__(key)

Retrieve an item from this Output. The returned value depends on what type of key used:

• Retrieving data using index tuple: [index_tuple]

• Retrieving data sample_id str: [SampleId]

• Retrieving a list of data using SampleId list: [sample_id1, …, sample_idN]

• Retrieving a SubOutput using an int or slice: [n] or [n:m]

Parameters

key (int, slice, SampleId or tuple) – the key of the requested item, can be a number, slice, sample index tuple or a SampleId

Returns

the return value depends on the requested key. If the key was an int or slice the corresponding SubOutput will be returned (and created if needed). If the key was a SampleId or sample index tuple, the corresponding SampleItem will be returned. If the key was a list of SampleId a tuple of SampleItem will be returned.

Return type

SubInput or SampleItem or list of SampleItem

Raises

• FastrTypeError – if key is not of a valid type

• FastrKeyError – if the parent Node has not been executed

__getstate__()

Retrieve the state of the Output

Returns

the state of the object

Rtype dict

__init__(node_run, template)

Instantiate an Output

Parameters

• node – the parent node the output belongs to.

• description – the ParameterDescription describing the output.

Returns

created Output

Raises

• FastrTypeError – if description is not of class ParameterDescription

• FastrDataTypeNotAvailableError – if the DataType requested cannot be found in the fastr.types

__module__ = 'fastr.execution.inputoutputrun'

__setitem__(key, value)

Store an item in the Output

Parameters

• key (tuple of int or SampleId) – key of the value to store

• value – the value to store

Returns

None

Raises

FastrTypeError – if key is not of correct type

__setstate__(state)

Set the state of the Output by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

__str__()

Get a string version for the Output

Returns

the string version

Return type

str

property automatic

Flag indicating that the Output is generated automatically without being specified on the command line

cardinality(key=None, job_data=None)

Cardinality of this Output, may depend on the inputs of the parent Node.

Parameters

key (tuple of int or SampleId) – key for a specific sample, can be sample index or id

Returns

the cardinality

Return type

int, sympy.Symbol, or None

Raises

• FastrCardinalityError – if cardinality references an invalid Input

• FastrTypeError – if the referenced cardinality values type cannot be case to int

• FastrValueError – if the referenced cardinality value cannot be case to int

property datatype

The datatype of this Output

property fullid

The full defining ID for the Output

iterconvergingindices(collapse_dims)

Iterate over all data, but collapse certain dimension to create lists of data.

Parameters

collapse_dims (iterable of int) – dimension to collapse

Returns

iterator SampleIndex (possibly containing slices)

property listeners

The list of Links connected to this Output.

property preferred_types

The list of preferred DataTypes for this Output.

property resulting_datatype

The DataType that will the results of this Output will have.

property samples

The SampleCollection of the samples in this Output. None if the NodeRun has not yet been executed. Otherwise a SampleCollection.

property valid

Check if the output is valid, i.e. has a valid cardinality

class fastr.execution.inputoutputrun.SourceOutputRun(node_run, template)

Bases: fastr.execution.inputoutputrun.OutputRun

Output for a SourceNodeRun, this type of Output determines the cardinality in a different way than a normal NodeRun.

__abstractmethods__ = frozenset({})

__getitem__(item)

Retrieve an item from this Output. The returned value depends on what type of key used:

• Retrieving data using index tuple: [index_tuple]

• Retrieving data sample_id str: [SampleId]

• Retrieving a list of data using SampleId list: [sample_id1, …, sample_idN]

• Retrieving a SubOutput using an int or slice: [n] or [n:m]

Parameters

key (int, slice, SampleId or tuple) – the key of the requested item, can be a number, slice, sample index tuple or a SampleId

Returns

the return value depends on the requested key. If the key was an int or slice the corresponding SubOutput will be returned (and created if needed). If the key was a SampleId or sample index tuple, the corresponding SampleItem will be returned. If the key was a list of SampleId a tuple of SampleItem will be returned.

Return type

SubInput or SampleItem or list of SampleItem

Raises

• FastrTypeError – if key is not of a valid type

• FastrKeyError – if the parent NodeRun has not been executed

__init__(node_run, template)

Instantiate a FlowOutput

Parameters

• node – the parent node the output belongs to.

• description – the ParameterDescription describing the output.

Returns

created FlowOutput

Raises

• FastrTypeError – if description is not of class ParameterDescription

• FastrDataTypeNotAvailableError – if the DataType requested cannot be found in the fastr.types

__module__ = 'fastr.execution.inputoutputrun'

__setitem__(key, value)

Store an item in the Output

Parameters

• key (tuple of int or SampleId) – key of the value to store

• value – the value to store

Returns

None

Raises

FastrTypeError – if key is not of correct type

cardinality(key=None, job_data=None)

Cardinality of this SourceOutput, may depend on the inputs of the parent NodeRun.

Parameters

key (tuple of int or SampleId) – key for a specific sample, can be sample index or id

Returns

the cardinality

Return type

int, sympy.Symbol, or None

property dimensions

The dimensions of this SourceOutputRun

property linearized

A linearized version of the sample data, this is lazily cached linearized version of the underlying SampleCollection.

property ndims

The number of dimensions in this SourceOutput

property size

The sample size of the SourceOutput

class fastr.execution.inputoutputrun.SubInputRun(input_)

Bases: fastr.execution.inputoutputrun.BaseInputRun

This class is used by Input to allow for multiple links to an Input. The SubInput class can hold only a single Link to a (Sub)Output, but behaves very similar to an Input otherwise.

__abstractmethods__ = frozenset({})

__getitem__(key)

Retrieve an item from this SubInput.

Parameters

key (int, SampleId or SampleIndex) – the key of the requested item, can be a number, sample index tuple or a SampleId

Returns

the return value depends on the requested key. If the key was an int the corresponding SubInput will be returned. If the key was a SampleId or sample index tuple, the corresponding SampleItem will be returned.

Return type

SampleItem or SubInput

Raises

FastrTypeError – if key is not of a valid type

Note

As a SubInput has only one SubInput, only requesting int key 0 or -1 is allowed, and it will return self

__getstate__()

Retrieve the state of the SubInput

Returns

the state of the object

Rtype dict

__init__(input_)

Instantiate an SubInput.

Parameters

input (Input) – the parent of this SubInput.

Returns

the created SubInput

__module__ = 'fastr.execution.inputoutputrun'

__setstate__(state)

Set the state of the SubInput by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

__str__()

Get a string version for the SubInput

Returns

the string version

Return type

str

cardinality(key=None, job_data=None)

Get the cardinality for this SubInput. The cardinality for a SubInputs is defined by the incoming link.

Parameters

key (SampleIndex or SampleId) – key for a specific sample, can be sample index or id

Returns

the cardinality

Return type

int, sympy.Symbol, or None

property description

The description object of this input/output

property dimensions

The sample size of the SubInput

property fullid

The full defining ID for the SubInput

get_sourced_nodes()

Get a list of all Nodes connected as sources to this SubInput

Returns

list of all connected Nodes

Return type

list

get_sourced_outputs()

Get a list of all Outputs connected as sources to this SubInput

Returns

list of all connected Outputs

Return type

list

property input_group

The id of the InputGroup this SubInputs parent belongs to.

property item_index

iteritems()

Iterate over the SampleItems that are in the SubInput.

Returns

iterator yielding SampleItem objects

itersubinputs()

Iterate over SubInputs (for a SubInput it will yield self and stop iterating after that)

Returns

iterator yielding SubInput

example:

>>> for subinput in input_a.itersubinputs():
        print subinput

property node

The Node to which this SubInputs parent belongs

property source

A list with the source Link. The list is to be compatible with Input

property source_output

The Output linked to this SubInput

class fastr.execution.inputoutputrun.SubOutputRun(output, index)

Bases: fastr.execution.inputoutputrun.OutputRun

The SubOutput is an Output that represents a slice of another Output.

__abstractmethods__ = frozenset({})

__getitem__(key)

Retrieve an item from this SubOutput. The returned value depends on what type of key used:

• Retrieving data using index tuple: [index_tuple]

• Retrieving data sample_id str: [SampleId]

• Retrieving a list of data using SampleId list: [sample_id1, …, sample_idN]

• Retrieving a SubOutput using an int or slice: [n] or [n:m]

Parameters

key (int, slice, SampleId or tuple) – the key of the requested item, can be a number, slice, sample index tuple or a SampleId

Returns

the return value depends on the requested key. If the key was an int or slice the corresponding SubOutput will be returned (and created if needed). If the key was a SampleId or sample index tuple, the corresponding SampleItem will be returned. If the key was a list of SampleId a tuple of SampleItem will be returned.

Return type

SubInput or SampleItem or list of SampleItem

Raises

FastrTypeError – if key is not of a valid type

__getstate__()

Retrieve the state of the SubOutput

Returns

the state of the object

Rtype dict

__init__(output, index)

Instantiate a SubOutput

Parameters

• output – the parent output the suboutput slices.

• index (int or slice) – the way to slice the parent output

Returns

created SubOutput

Raises

• FastrTypeError – if the output argument is not an instance of Output

• FastrTypeError – if the index argument is not an int or slice

__len__()

Return the length of the Output.

Note

In a SubOutput this is always 1.

__module__ = 'fastr.execution.inputoutputrun'

__setitem__(key, value)

A function blocking the assignment operator. Values cannot be assigned to a SubOutput.

Raises

FastrNotImplementedError – if called

__setstate__(state)

Set the state of the SubOutput by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

__str__()

Get a string version for the SubOutput

Returns

the string version

Return type

str

cardinality(key=None, job_data=None)

Cardinality of this SubOutput depends on the parent Output and self.index

Parameters

key (tuple of int or SampleId) – key for a specific sample, can be sample index or id

Returns

the cardinality

Return type

int, sympy.Symbol, or None

Raises

• FastrCardinalityError – if cardinality references an invalid Input

• FastrTypeError – if the referenced cardinality values type cannot be case to int

• FastrValueError – if the referenced cardinality value cannot be case to int

property datatype

The datatype of this SubOutput

property fullid

The full defining ID for the SubOutput

property indexrep

Simple representation of the index.

property listeners

The list of Links connected to this Output.

property node

The NodeRun to which this SubOutput belongs

property preferred_types

The list of preferred DataTypes for this SubOutput.

property resulting_datatype

The DataType that will the results of this SubOutput will have.

property samples

The SampleCollection for this SubOutput

job Module

This module contains the Job class and some related classes.

class fastr.execution.job.InlineJob(*args, **kwargs)

Bases: fastr.execution.job.Job

Job that does not actually need to run but is used for consistency in data processing and logging.

__init__(*args, **kwargs)

Create a job

Parameters

• node (fastr.planning.node.Node) – the node the job is based on

• sample_id – the id of the sample

• sample_index – the index of the sample

• input_arguments – the argument list

• output_arguments – the argument list

• hold_jobs – the jobs on which this jobs depend

• preferred_types – The list of preferred types to use

Returns

__module__ = 'fastr.execution.job'

collect_provenance()

Collect the provenance for this job

get_result()

Get the result of the job if it is available. Load the output file if found and check if the job matches the current object. If so, load and return the result.

Returns

Job after execution or None if not available

Return type

Job | None

class fastr.execution.job.Job(node, sample_id, sample_index, input_arguments, output_arguments, hold_jobs=None, preferred_types=None)

Bases: fastr.abc.serializable.Serializable

Class describing a job.

Arguments: tool_name - the name of the tool (str) tool_version - the version of the tool (Version) argument - the arguments used when calling the tool (list) tmpdir - temporary directory to use to store output data hold_jobs - list of jobs that need to finished before this job can run (list)

COMMAND_DUMP = '__fastr_command__.pickle.gz'

INFO_DUMP = '__fastr_extra_job_info__.json'

PROV_DUMP = '__fastr_prov__.json'

RESULT_DUMP = '__fastr_result__.pickle.gz'

STDERR_DUMP = '__fastr_stderr__.txt'

STDOUT_DUMP = '__fastr_stdout__.txt'

__getstate__()

Get the state of the job

Returns

job state

Return type

dict

__init__(node, sample_id, sample_index, input_arguments, output_arguments, hold_jobs=None, preferred_types=None)

Create a job

Parameters

• node (fastr.planning.node.Node) – the node the job is based on

• sample_id (SampleId) – the id of the sample

• sample_index (SampleIndex) – the index of the sample

• input_arguments (Dict[str, SampleIndex]) – the argument list

• output_arguments (Dict[str, Dict]) – the argument list

• hold_jobs (Optional[List[str]]) – the jobs on which this jobs depend

• preferred_types (Optional[List]) – The list of preferred types to use

Returns

__module__ = 'fastr.execution.job'

__repr__()

String representation of the Job

__setstate__(state)

Set the state of the job

Parameters

state (dict) –

static cast_to_type(value, datatypes)

Try to cast value to one of the given datatypes. Will try all the datatypes in order.

Parameters

datatypes (tuple) – Possible datatypes to cast to

Return type

DataType

Returns

casted value

clean()

collect_provenance()

Collect the provenance for this job.

property commandfile

The path of the command pickle

property commandurl

The url of the command pickle

create_payload()

Create the payload for this object based on all the input/output arguments

Returns

the payload

Return type

dict

ensure_tmp_dir()

execute()

Execute this job

Returns

The result of the execution

Return type

InterFaceResult

property extrainfofile

The path where the extra job info document is saved

property extrainfourl

The url where the extra job info document is saved

classmethod fill_output_argument(output_spec, cardinality, desired_type, requested, tmpurl)

This is an abstract class method. The method should take the argument_dict generated from calling self.get_argument_dict() and turn it into a list of commandline arguments that represent this Input/Output.

Parameters

• cardinality (int) – the cardinality for this output (can be non for automatic outputs)

• desired_type (DataType) – the desired datatype for this output

• requested (bool) – flag to indicate that the output is requested by Fastr

Returns

the values for this output

Return type

list

property fullid

The full id of the job

get_deferred(output_id, cardinality_nr, sample_id=None)

Get a deferred pointing to a specific output value in the Job

Parameters

• output_id (str) – the output to select from

• cardinality_nr (int) – the index of the cardinality

• sample_id (str) – the sample id to select (optional)

Returns

The deferred

get_output_datatype(output_id)

Get the datatype for a specific output

Parameters

output_id (str) – the id of the output to get the datatype for

Returns

the requested datatype

Return type

tuple

get_result()

Get the result of the job if it is available. Load the output file if found and check if the job matches the current object. If so, load and return the result.

Returns

Job after execution or None if not available

Return type

Job | None

classmethod get_value(value)

Get a value

Parameters

• value – the url of the value

• datatype – datatype of the value

Returns

the retrieved value

hash_inputs()

Create hashes for all input values and store them in the info store

hash_results()

Create hashes of all output values and store them in the info store

property id

The id of this job

property logfile

The path of the result pickle

property logurl

The url of the result pickle

property provfile

The path where the prov document is saved

property provurl

The url where the prov document is saved

property resources

The compute resources required for this job

property status

The status of the job

property stderrfile

The path where the stderr text is saved

property stderrurl

The url where the stderr text is saved

property stdoutfile

The path where the stdout text is saved

property stdouturl

The url where the stdout text is saved

property tmpurl

The URL of the tmpdir to use

property tool

classmethod translate_argument(value)

Translate an argument from a URL to an actual path.

Parameters

• value – value to translate

• datatype – the datatype of the value

Returns

the translated value

static translate_output_results(value, datatypes, mountpoint=None)

Translate the results for on Output

Parameters

• value – the results value for the output

• datatypes (tuple) – tuple of possible datatypes for the output

• preferred_type – the preferred datatype of the output

Returns

the update value for the result

translate_results(result)

Translate the results of an interface (using paths etc) to the proper form using URI’s instead.

Parameters

result (dict) – the result data of an interface

Returns

the translated result

Return type

dict

validate_results(payload)

Validate the results of the Job

Returns

flag indicating the results are complete and valid

write()

class fastr.execution.job.JobCleanupLevel

Bases: enum.Enum

The cleanup level for Jobs that are finished.

__module__ = 'fastr.execution.job'

all = 'all'

no_cleanup = 'no_cleanup'

non_failed = 'non_failed'

class fastr.execution.job.JobState(_, stage, error)

Bases: enum.Enum

The possible states a Job can be in. An overview of the states and the adviced transitions are depicted in the following figure:

__init__(_, stage, error)

Initialize self. See help(type(self)) for accurate signature.

__module__ = 'fastr.execution.job'

cancelled = ('cancelled', 'done', True)

created = ('created', 'idle', False)

property done

execution_done = ('execution_done', 'in_progress', False)

execution_failed = ('execution_failed', 'in_progress', True)

failed = ('failed', 'done', True)

finished = ('finished', 'done', False)

hold = ('hold', 'idle', False)

property idle

property in_progress

nonexistent = ('nonexistent', 'idle', False)

processing_callback = ('processing_callback', 'in_progress', False)

queued = ('queued', 'idle', False)

running = ('running', 'in_progress', False)

class fastr.execution.job.SinkJob(node, sample_id, sample_index, input_arguments, output_arguments, hold_jobs=None, substitutions=None, preferred_types=None)

Bases: fastr.execution.job.Job

Special SinkJob for the Sink

__init__(node, sample_id, sample_index, input_arguments, output_arguments, hold_jobs=None, substitutions=None, preferred_types=None)

Create a job

Parameters

• node (fastr.planning.node.Node) – the node the job is based on

• sample_id – the id of the sample

• sample_index – the index of the sample

• input_arguments – the argument list

• output_arguments – the argument list

• hold_jobs – the jobs on which this jobs depend

• preferred_types – The list of preferred types to use

Returns

__module__ = 'fastr.execution.job'

__repr__()

String representation for the SinkJob

create_payload()

Create the payload for this object based on all the input/output arguments

Returns

the payload

Return type

dict

get_result()

Get the result of the job if it is available. Load the output file if found and check if the job matches the current object. If so, load and return the result.

Returns

Job after execution

hash_inputs()

Create hashes for all input values and store them in the info store

property id

The id of this job

substitute(value, datatype=None)

Substitute the special fields that can be used in a SinkJob.

Parameters

• value (str) – the value to substitute fields in

• datatype (BaseDataType) – the datatype for the value

Returns

string with substitutions performed

Return type

str

property tmpurl

The URL of the tmpdir to use

validate_results(payload)

Validate the results of the SinkJob

Returns

flag indicating the results are complete and valid

class fastr.execution.job.SourceJob(node, sample_id, sample_index, input_arguments, output_arguments, hold_jobs=None, preferred_types=None)

Bases: fastr.execution.job.Job

Special SourceJob for the Source

__module__ = 'fastr.execution.job'

__repr__()

String representation for the SourceJob

collect_provenance()

Collect the provenance for this job

get_output_datatype(output_id)

Get the datatype for a specific output

Parameters

output_id (str) – the id of the output to get the datatype for

Returns

the requested datatype

Return type

BaseDataType

hash_inputs()

Create hashes for all input values and store them in the info store

validate_results(payload)

Validate the results of the Job

Returns

flag indicating the results are complete and valid

linkrun Module

The link module contain the Link class. This class represents the links in a network. These links lead from an output (BaseOutput) to an input (BaseInput) and indicate the desired data flow. Links are smart objects, in the sense that when you set their start or end point, they register themselves with the Input and Output. They do all the book keeping, so as long as you only set the source and target of the Link, the link should be valid.

Warning

Don’t mess with the Link, Input and Output internals from other places. There will be a huge chances of breaking the network functionality!

class fastr.execution.linkrun.LinkRun(link, parent=None)

Bases: fastr.abc.updateable.Updateable, fastr.abc.serializable.Serializable

Class for linking outputs (BaseOutput) to inputs (BaseInput)

Examples:

>>> import fastr
>>> network = fastr.Network()
>>> link1 = network.create_link( n1.ouputs['out1'], n2.inputs['in2'] )

link2 = Link()
link2.source = n1.ouputs['out1']
link2.target = n2.inputs['in2']

__abstractmethods__ = frozenset({})

__dataschemafile__ = 'Link.schema.json'

__eq__(other)

Test for equality between two Links

Parameters

other (LinkRun) – object to test against

Returns

True for equality, False otherwise

Return type

bool

__getitem__(index)

Get a an item for this Link. The item will be retrieved from the connected output, but a diverging or converging flow can change the number of samples/cardinality.

Parameters

index (SampleIndex) – index of the item to retrieve

Returns

the requested item

Return type

SampleItem

Raises

FastrIndexError – if the index length does not match the number dimensions in the source data (after collapsing/expanding)

__getstate__()

Retrieve the state of the Link

Returns

the state of the object

Rtype dict

__hash__ = None

__init__(link, parent=None)

Create a new Link in a Network.

Parameters

• link (Link) – the base link

• parent (Network or None) – the parent network, if None is given the fastr.current_network is assumed to be the parent

Returns

newly created LinkRun

Raises

• FastrValueError – if parent is not given and fastr.current_network is not set

• FastrValueError – if the source output is not in the same network as the Link

• FastrValueError – if the target input is not in the same network as the Link

__module__ = 'fastr.execution.linkrun'

__repr__()

Get a string representation for the Link

Returns

the string representation

Return type

str

__setstate__(state)

Set the state of the Link by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

Raises

FastrValueError – if the parent network and fastr.current_network are not set

cardinality(index=None)

Cardinality for a Link is given by source Output and the collapse/expand settings

Parameters

key (SampleIndex) – key for a specific sample (can be only a sample index!)

Returns

the cardinality

Return type

int, sympy.Symbol

Raises

FastrIndexError – if the index length does not match the number of dimension in the data

property collapse

The converging dimensions of this link. Collapsing changes some dimensions of sample lists into cardinality, reshaping the data.

Collapse can be set to a tuple or an int/str, in which case it will be automatically wrapped in a tuple. The int will be seen as indices of the dimensions to collapse. The str will be seen as the name of the dimensions over which to collapse.

Raises

FastrTypeError – if assigning a collapse value of a wrong type

property collapse_indexes

The converging dimensions of this link as integers. Dimension names are replaces with the corresponding int.

Collapsing changes some dimensions of sample lists into cardinality, reshaping the data

classmethod createobj(state, network=None)

Create object function for Link

Parameters

• cls – The class to create

• state – The state to use to create the Link

• network – the parent Network

Returns

newly created Link

destroy()

The destroy function of a link removes all default references to a link. This means the references in the network, input and output connected to this link. If there is no references in other places in the code, it will destroy the link (reference count dropping to zero).

This function is called when a source for an input is set to another value and the links becomes disconnected. This makes sure there is no dangling links.

property dimensions

The dimensions of the data delivered by the link. This can be different from the source dimensions because the link can make data collapse or expand.

property expand

Flag indicating that the link will expand the cardininality into a new sample dimension to be created.

property fullid

The full defining ID for the Input

property parent

The Network to which this Link belongs.

property size

The size of the data delivered by the link. This can be different from the source size because the link can make data collapse or expand.

property source

The source BaseOutput of the Link. Setting the source will automatically register the Link with the source BaseOutput. Updating source will also make sure the Link is unregistered with the previous source.

Raises

FastrTypeError – if assigning a non BaseOutput

property status

property target

The target BaseInput of the Link. Setting the target will automatically register the Link with the target BaseInput. Updating target will also make sure the Link is unregistered with the previous target.

Raises

FastrTypeError – if assigning a non BaseInput

macronoderun Module

class fastr.execution.macronoderun.MacroNodeRun(node, parent)

Bases: fastr.execution.noderun.NodeRun

MacroNodeRun encapsulates an entire network in a single node.

__abstractmethods__ = frozenset({})

__getstate__()

Retrieve the state of the MacroNodeRun

Returns

the state of the object

Rtype dict

__init__(node, parent)

Parameters

network (fastr.planning.network.Network) – network to create macronode for

__module__ = 'fastr.execution.macronoderun'

__setstate__(state)

Set the state of the NodeRun by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

execute()

Execute the node and create the jobs that need to run

Returns

list of jobs to run

Return type

list of Jobs

get_output_info(output)

property network_run

networkanalyzer Module

Module that defines the NetworkAnalyzer and holds the reference implementation.

class fastr.execution.networkanalyzer.DefaultNetworkAnalyzer

Bases: fastr.execution.networkanalyzer.NetworkAnalyzer

Default implementation of the NetworkAnalyzer.

__module__ = 'fastr.execution.networkanalyzer'

analyze_network(network, chunk)

Analyze a chunk of a Network. Simply process the Nodes in the chunk sequentially.

Parameters

• network – Network corresponding with the chunk

• chunk – The chunk of the network to analyze

class fastr.execution.networkanalyzer.NetworkAnalyzer

Bases: object

Base class for NetworkAnalyzers

__dict__ = mappingproxy({'__module__': 'fastr.execution.networkanalyzer', '__doc__': '\n Base class for NetworkAnalyzers\n ', 'analyze_network': <function NetworkAnalyzer.analyze_network>, '__dict__': <attribute '__dict__' of 'NetworkAnalyzer' objects>, '__weakref__': <attribute '__weakref__' of 'NetworkAnalyzer' objects>})

__module__ = 'fastr.execution.networkanalyzer'

__weakref__

list of weak references to the object (if defined)

abstract analyze_network(network, chunk)

Analyze a chunk of a Network.

Parameters

• network – Network corresponding with the chunk

• chunk – The chunk of the network to analyze

networkchunker Module

This module contains the NetworkChunker class and its default implementation the DefaultNetworkChunker

class fastr.execution.networkchunker.DefaultNetworkChunker

Bases: fastr.execution.networkchunker.NetworkChunker

The default implementation of the NetworkChunker. It tries to create as large as possible chunks so the execution blocks as little as possible.

__init__()

Initialize self. See help(type(self)) for accurate signature.

__module__ = 'fastr.execution.networkchunker'

chunck_network(network)

Create a list of Network chunks that can be pre-analyzed completely. Each chunk needs to be executed before the next can be analyzed and executed.

The returned chunks are (at the moment) in the format of a tuple (start, nodes) which are both tuples. The tuple contain the nodes where to start execution (should ready if previous chunks are done) and all nodes of the chunk respectively.

Parameters

network – Network to split into chunks

Returns

tuple containing chunks

class fastr.execution.networkchunker.NetworkChunker

Bases: object

The base class for NetworkChunkers. A Network chunker is a class that takes a Network and produces a list of chunks that can each be analyzed and executed in one go.

__dict__ = mappingproxy({'__module__': 'fastr.execution.networkchunker', '__doc__': '\n The base class for NetworkChunkers. A Network chunker is a class that takes\n a Network and produces a list of chunks that can each be analyzed and\n executed in one go.\n ', 'chunck_network': <function NetworkChunker.chunck_network>, '__dict__': <attribute '__dict__' of 'NetworkChunker' objects>, '__weakref__': <attribute '__weakref__' of 'NetworkChunker' objects>})

__module__ = 'fastr.execution.networkchunker'

__weakref__

list of weak references to the object (if defined)

abstract chunck_network(network)

Create a list of Network chunks that can be pre-analyzed completely. Each chunk needs to be executed before the next can be analyzed and executed.

Parameters

network – Network to split into chunks

Returns

list containing chunks

networkrun Module

Network module containing Network facilitators and analysers.

class fastr.execution.networkrun.NetworkRun(network)

Bases: fastr.abc.serializable.Serializable

The Network class represents a workflow. This includes all Nodes (including ConstantNodes, SourceNodes and Sinks) and Links.

NETWORK_DUMP_FILE_NAME = '__fastr_network__.json'

SINK_DUMP_FILE_NAME = '__sink_data__.json'

SOURCE_DUMP_FILE_NAME = '__source_data__.pickle.gz'

__bool__()

A network run is True if it finish running successfully and False otherwise

__eq__(other)

Compare two Networks and see if they are equal.

Parameters

other (Network) –

Returns

flag indicating that the Networks are the same

Return type

bool

__getitem__(item)

Get an item by its fullid. The fullid can point to a link, node, input, output or even subinput/suboutput.

Parameters

item (str,unicode) – fullid of the item to retrieve

Returns

the requested item

__getstate__()

Retrieve the state of the Network

Returns

the state of the object

Rtype dict

__hash__ = None

__init__(network)

Create a new, empty Network

Parameters

name (str) – name of the Network

Returns

newly created Network

Raises

OSError – if the tmp mount in the config is not a writable directory

__module__ = 'fastr.execution.networkrun'

__ne__(other)

Tests for non-equality, this is the negated version __eq__

__repr__()

Return repr(self).

__setstate__(state)

Set the state of the Network by the given state. This completely overwrites the old state!

Parameters

state (dict) – The state to populate the object with

Returns

None

abort(signal_code=None, current_frame=None)

check_id(id_)

Check if an id for an object is valid and unused in the Network. The method will always returns True if it does not raise an exception.

Parameters

id (str) – the id to check

Returns

True

Raises

• FastrValueError – if the id is not correctly formatted

• FastrValueError – if the id is already in use

property constantlist

execute(sourcedata, sinkdata, execution_plugin=None, tmpdir=None, cluster_queue=None, timestamp=None)

Execute the Network with the given data. This will analyze the Network, create jobs and send them to the execution backend of the system.

Parameters

• sourcedata (dict) – dictionary containing all data for the sources

• sinkdata (dict) – dictionary containing directives for the sinks

• execution_plugin (str) – the execution plugin to use (None will use the config value)

Raises

• FastrKeyError – if a source has not corresponding key in sourcedata

• FastrKeyError – if a sink has not corresponding key in sinkdata

execution_finished()

property fullid

The fullid of the Network

generate_jobs()

property global_id

The global id of the Network, this is different for networks used in macronodes, as they still have parents.

property id

The id of the Network. This is a read only property.

job_finished(job)

Call-back handler for when a job is finished. Will collect the results and handle blocking jobs. This function is automatically called when the execution plugin finished a job.

Parameters

job (Job) – the job that finished

property long_id

property network

property nodegroups

Give an overview of the nodegroups in the network

register_signals()

Register handles to handle SIGINT and SIGTERM handlers to gracefully shut down the execution :return:

set_data(sourcedata, sinkdata)

property sinklist

property sourcelist

unregister_signals()

Unregister the signal handlers (set to default). Sending these signals twice will result that the second time the default handler is used.

noderun Module

A module to maintain a run of a network node.

class fastr.execution.noderun.NodeRun(node, parent)

Bases: fastr.execution.basenoderun.BaseNodeRun

The class encapsulating a node in the network. The node is responsible for setting and checking inputs and outputs based on the description provided by a tool instance.

__abstractmethods__ = frozenset({})

__dataschemafile__ = 'NodeRun.schema.json'

__eq__(other)

Compare two Node instances with each other. This function ignores the parent and update status, but tests rest of the dict for equality. equality

Parameters

other (NodeRun) – the other instances to compare to

Returns

True if equal, False otherwise

__getstate__()

Retrieve the state of the NodeRun

Returns

the state of the object

Rtype dict

__hash__ = None

__init__(node, parent)

Instantiate a node.

Parameters

• node (Tool) – The node to base the noderun on

• parent (Network) – the parent network of the node

Returns

the newly created NodeRun

__module__ = 'fastr.execution.noderun'

__repr__()

Get a string representation for the NodeRun

Returns

the string representation

Return type

str

__setstate__(state)

Set the state of the NodeRun by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

__str__()

Get a string version for the NodeRun

Returns

the string version

Return type

str

property blocking

Indicate that the results of this NodeRun cannot be determined without first executing the NodeRun, causing a blockage in the creation of jobs. A blocking Nodes causes the Chunk borders.

create_job(sample_id, sample_index, job_data, job_dependencies, **kwargs)

Create a job based on the sample id, job data and job dependencies.

Parameters

• sample_id (SampleId) – the id of the corresponding sample

• sample_index (SampleIndex) – the index of the corresponding sample

• job_data (dict) – dictionary containing all input data for the job

• job_dependencies – other jobs that need to finish before this job can run

Returns

the created job

Return type

Job

classmethod createobj(state, network=None)

Create object function for generic objects

Parameters

• cls – The class to create

• state – The state to use to create the Link

• network – the parent Network

Returns

newly created Link

property dimnames

Names of the dimensions in the NodeRun output. These will be reflected in the SampleIdList of this NodeRun.

execute()

Execute the node and create the jobs that need to run

Returns

list of jobs to run

Return type

list of Jobs

find_source_index(target_index, target, source)

property fullid

The full defining ID for the NodeRun inside the network

get_sourced_nodes()

A list of all Nodes connected as sources to this NodeRun

Returns

list of all nodes that are connected to an input of this node

property global_id

The global defining ID for the Node from the main network (goes out of macro nodes to root network)

property id

The id of the NodeRun

property input_groups

A list of input groups for this NodeRun. An input group is InputGroup

object filled according to the NodeRun

property listeners

All the listeners requesting output of this node, this means the listeners of all Outputs and SubOutputs

property merge_dimensions

property name

Name of the Tool the NodeRun was based on. In case a Toolless NodeRun was used the class name is given.

property outputsize

Size of the outputs in this NodeRun

property parent

The parent network of this node.

property resources

Number of cores required for the execution of this NodeRun

set_result(job, failed_annotation)

Incorporate result of a job into the NodeRun.

Parameters

• job (Type) – job of which the result to store

• failed_annotation – A set of annotations, None if no errors else containing a tuple describing the errors

property status

property tool

update_input_groups()

Update all input groups in this node

sinknoderun Module

class fastr.execution.sinknoderun.SinkNodeRun(node, parent)

Bases: fastr.execution.noderun.NodeRun

Class which handles where the output goes. This can be any kind of file, e.g. image files, textfiles, config files, etc.

__abstractmethods__ = frozenset({})

__dataschemafile__ = 'SinkNodeRun.schema.json'

__getstate__()

Retrieve the state of the NodeRun

Returns

the state of the object

Rtype dict

__init__(node, parent)

Instantiation of the SinkNodeRun.

Parameters

• node (fastr.planning.node.Node) – The Node that this Run is based on.

• parent (NetworkRun) – The NetworkRun that this NodeRun belongs to

Returns

newly created sink node run

__module__ = 'fastr.execution.sinknoderun'

__setstate__(state)

Set the state of the NodeRun by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

create_job(sample_id, sample_index, job_data, job_dependencies, **kwargs)

Create a job for a sink based on the sample id, job data and job dependencies.

Parameters

• sample_id (SampleId) – the id of the corresponding sample

• job_data (dict) – dictionary containing all input data for the job

• job_dependencies – other jobs that need to finish before this job can run

Returns

the created job

Return type

Job

property datatype

The datatype of the data this sink can store.

execute()

Execute the sink node and create the jobs that need to run

Returns

list of jobs to run

Return type

list of Jobs

property input

The default input of the sink NodeRun

set_data(data)

Set the targets of this sink node.

Parameters

data (dict or list of urls) – the targets rules for where to write the data

The target rules can include a few fields that can be filled out:

field	description
sample_id	the sample id of the sample written in string form
cardinality	the cardinality of the sample written
ext	the extension of the datatype of the written data, including the .
extension	the extension of the datatype of the written data, excluding the .
network	the id of the network the sink is part of
node	the id of the node of the sink
timestamp	the iso formatted datetime the network execution started
uuid	the uuid of the network run (generated using uuid.uuid1)

An example of a valid target could be:

>>> target = 'vfs://output_mnt/some/path/image_{sample_id}_{cardinality}{ext}'

Note

The {ext} and {extension} are very similar but are both offered. In many cases having a name.{extension} will feel like the correct way to do it. However, if you have DataTypes with and without extension that can both exported by the same sink, this would cause either name.ext or name. to be generated. In this particular case name{ext} can help as it will create either name.ext or name.

Note

If a datatype has multiple extensions (e.g. .tiff and .tif) the first extension defined in the extension tuple of the datatype will be used.

set_result(job, failed_annotation)

Incorporate result of a sink job into the Network.

Parameters

• job (Type) – job of which the result to store

• failed_annotation (set) – A set of annotations, None if no errors else containing a tuple describing the errors

sourcenoderun Module

class fastr.execution.sourcenoderun.SourceNodeRun(node, parent)

Bases: fastr.execution.flownoderun.FlowNodeRun

Class providing a connection to data resources. This can be any kind of file, stream, database, etc from which data can be received.

__abstractmethods__ = frozenset({})

__dataschemafile__ = 'SourceNodeRun.schema.json'

__eq__(other)

Compare two Node instances with each other. This function ignores the parent and update status, but tests rest of the dict for equality. equality

Parameters

other (NodeRun) – the other instances to compare to

Returns

True if equal, False otherwise

__getstate__()

Retrieve the state of the SourceNodeRun

Returns

the state of the object

Rtype dict

__hash__ = None

__init__(node, parent)

Instantiation of the SourceNodeRun.

Parameters

• node (fastr.planning.node.Node) – The Node that this Run is based on.

• parent (NetworkRun) – The NetworkRun that this NodeRun belongs to

Returns

newly created sink node run

__module__ = 'fastr.execution.sourcenoderun'

__setstate__(state)

Set the state of the SourceNodeRun by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

create_job(sample_id, sample_index, job_data, job_dependencies, **kwargs)

Create a job based on the sample id, job data and job dependencies.

Parameters

• sample_id (SampleId) – the id of the corresponding sample

• sample_index (SampleIndex) – the index of the corresponding sample

• job_data (dict) – dictionary containing all input data for the job

• job_dependencies – other jobs that need to finish before this job can run

Returns

the created job

Return type

Job

property datatype

The datatype of the data this source supplies.

property dimnames

Names of the dimensions in the SourceNodeRun output. These will be reflected in the SampleIdLists.

execute()

Execute the source node and create the jobs that need to run

Returns

list of jobs to run

Return type

list of Jobs

property output

Shorthand for self.outputs['output']

property outputsize

The size of output of this SourceNodeRun

set_data(data, ids=None)

Set the data of this source node.

Parameters

• data (dict, OrderedDict or list of urls) – the data to use

• ids – if data is a list, a list of accompanying ids

property sourcegroup

property valid

This does nothing. It only overloads the valid method of NodeRun(). The original is intended to check if the inputs are connected to some output. Since this class does not implement inputs, it is skipped.

class fastr.execution.sourcenoderun.ConstantNodeRun(node, parent)

Bases: fastr.execution.sourcenoderun.SourceNodeRun

Class encapsulating one output for which a value can be set. For example used to set a scalar value to the input of a node.

__abstractmethods__ = frozenset({})

__dataschemafile__ = 'ConstantNodeRun.schema.json'

__getstate__()

Retrieve the state of the ConstantNodeRun

Returns

the state of the object

Rtype dict

__init__(node, parent)

Instantiation of the ConstantNodeRun.

Parameters

• datatype – The datatype of the output.

• data – the prefilled data to use.

• id – The url pattern.

This class should never be instantiated directly (unless you know what you are doing). Instead create a constant using the network class like shown in the usage example below.

usage example:

>>> import fastr
>>> network = fastr.Network()
>>> source = network.create_source(datatype=types['ITKImageFile'], id_='sourceN')

or alternatively create a constant node by assigning data to an item in an InputDict:

>>> node_a.inputs['in'] = ['some', 'data']

which automatically creates and links a ConstantNodeRun to the specified Input

__module__ = 'fastr.execution.sourcenoderun'

__setstate__(state)

Set the state of the ConstantNodeRun by the given state.

Parameters

state (dict) – The state to populate the object with

Returns

None

property data

The data stored in this constant node

execute()

Execute the constant node and create the jobs that need to run

Returns

list of jobs to run

Return type

list of Jobs

set_data(data=None, ids=None)

Set the data of this constant node in the correct way. This is mainly for compatibility with the parent class SourceNodeRun

Parameters

• data (dict or list of urls) – the data to use

• ids – if data is a list, a list of accompanying ids