Models¶

Module contents¶

Creates Model and Manager subclasses to represent and manage all the different parts of an analysis pipeline.

For an illustration of the app’s models, see the Overview.

Subpackages¶

Submodules¶

django_analyses.models.analysis module¶

Definition of the Analysis class.

class django_analyses.models.analysis.Analysis(*args, **kwargs)¶

Bases: django_extensions.db.models.TitleDescriptionModel, django_extensions.db.models.TimeStampedModel

A Model representing a single analysis in the database.

category¶: A Category instance associated with this analysis.

inputspecification_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

objects = <django_analyses.models.managers.analysis.AnalysisManager object>¶

outputspecification_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

version_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

django_analyses.models.analysis_version module¶

Definition of the AnalysisVersion class.

class django_analyses.models.analysis_version.AnalysisVersion(*args, **kwargs)¶

Bases: django_extensions.db.models.TitleDescriptionModel, django_extensions.db.models.TimeStampedModel

A Model representing a single analysis version in the database.

Each AnalysisVersion instance should be assigned an interface through the project’s ANALYSIS_INTERFACES setting (for more information see Interface Integration and Integration Customization).

analysis¶: The Analysis instance to which this analysis version belongs.

extract_results(results: Any) → dict¶

Extracts a results dictionary from an arbitrary results object in case the nested_results_attribute is not None.

Parameters:	results (Any) – Arbitrary results object
Returns:	Results dictionary
Return type:	dict

fixed_run_method_kwargs¶: Any “fixed” keyword arguments that should always be passed to the interface’s run method at execution.

get_interface() → object¶

Queries the project’s settings to locate the instance’s interface. For more information see Interface Integration.

Returns:	Interface class used to run this version of the analysis
Return type:	`object`
Raises:	`NotImplementedError` – No interface could be found for this analysis

get_interface_initialization_kwargs(**kwargs) → dict¶

Returns the parameters required at the interface’s class initialization.

Returns:	Initialization parameters as a keyword arguments dict
Return type:	dict

get_run_method_kwargs(**kwargs) → dict¶

Returns the parameters required when calling the interface’s run() method.

Returns:	`run()` method parameters as a keyword arguments dict
Return type:	dict

input_definitions¶

Returns the associated instance’s InputDefinition subclasses as defined in its input_specification.

Returns:	`InputDefinition` subclasses
Return type:	`QuerySet`

input_specification¶: The InputSpecification instance specifying the InputDefinition subclasses associated with this analysis version.

interface¶

Returns the associated interface for this instance.

Returns:	Analysis interface class
Return type:	type

max_parallel¶: Maximal number of parallel executions that may be run using Celery. This attribute is used in execute_node() to chunk an iterable of node inputs in case it is longer than this value. For more information see Celery’s Chunks documentation.

nested_results_attribute¶

Analysis interfaces are expected to return a dictionary of the results. In case this analysis version’s interface returns some object which conatins the desired dictionary, this field allows specifying the attribute or method that may be used to retrieve it.

Example

Nipype’s interfaces generally return some kind of InterfaceResults object with an outputs attribute that may be used to create a dictionary of the results by calling the get_traitsfree() method. In order to integrate smoothly with Nipype’s interfaces, we could simply specify nested_results_attribute=”outputs.get_traitsfree” when creating the appropriate analysis versions.

nested_results_parts¶

Splits the nested_results_attribute at “.” indices in case of a deeply nested attribute.

Returns:	Listed parts of nested result dictionary location
Return type:	list

node_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

objects = <django_analyses.models.managers.analysis_version.AnalysisVersionManager object>¶

output_definitions¶

Returns the associated instance’s OutputDefinition subclasses as defined in its output_specification.

Returns:	`OutputDefinition` subclasses
Return type:	`QuerySet`

output_specification¶: The OutputSpecification instance specifying the OutputDefinition subclasses associated with this analysis version.

run(**kwargs) → dict¶

Runs the interface safely by validating the input according to the instance’s input_specification and applying any special integration customizations (for more information see Integration Customization).

Returns:	Results dictionary
Return type:	dict

run_interface(**kwargs) → dict¶

Call the interface class’s run() method with the given keyword arguments.

Returns:	Dictionary of results
Return type:	dict

run_method_key¶: Custom run method name for the interface. Each analysis version is expected to have some class associated with it and used as an interface for running the analysis. This field determines the name of the method that will be called (default value is “run”).

run_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

update_input_with_defaults(configuration: dict) → dict¶

Updates a configuration specified as keyword arguments with the instance’s input_specification defaults.

Parameters:	configuration (dict) – Input configuration (excluding default values)
Returns:	Configuration updated with default values
Return type:	dict

django_analyses.models.category module¶

Definition of the Category class.

class django_analyses.models.category.Category(*args, **kwargs)¶

Bases: django_extensions.db.models.TitleDescriptionModel, django_extensions.db.models.TimeStampedModel

A Model representing a category of analyses in the databse.

analysis_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

objects = <django.db.models.manager.Manager object>¶

parent¶: If this is a nested category, this field holds the association with the parent.

subcategories¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

django_analyses.models.run module¶

Definition of the Run model.

class django_analyses.models.run.Run(*args, **kwargs)¶

Bases: django_extensions.db.models.TimeStampedModel

Model representing a single analysis version’s run in the database.

analysis_version¶: The AnalysisVersion that was run.

base_input_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

base_output_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

check_null_configuration() → bool¶

Checks whether this run’s configuration is equivalent to the input specification’s default settings.

Returns:	Whether this run has only default configuration settings
Return type:	bool

duration¶

Returns the time delta between this instance’s end_time and start_time. If end_time isn’t set yet returns time since start_time.

Returns:	Run duration
Return type:	datetime.timedelta

end_time¶: Run end time.

fix_input_value(inpt) → Any¶

Reverts changes that may have been made to a given input in order to return the “raw” input configuration of this run (i.e. the input as it was passed by the user).

Parameters:	inpt (`Input`) – An input of this run
Returns:	The “raw” input value
Return type:	Any

get_input(key: str) → Any¶

Returns a particular output created in this run according to its definition’s key field.

Parameters:	key (str) – The desired `Input`’s associated definition keyword
Returns:	Input value
Return type:	Any

get_input_configuration(include_non_configuration: bool = True, include_defaults: bool = True) → dict¶

Returns the input configuration of this run.

Parameters:	include_non_configuration (bool) – Whether to include inputs for which the associated definition’s `is_configuration` attribute is set to False, default is True include_defaults (bool) – Whether to include default input configuration values, default is True
Returns:	Input configuration
Return type:	dict

get_input_set() → model_utils.managers.InheritanceQuerySet¶

Returns the Input subclasses’ instances created for this execution of the analysis_version.

Returns:	This run’s inputs
Return type:	`InheritanceQuerySet`

get_output(key: str) → Any¶

Returns a particular output created in this run according to its definition’s key field.

Parameters:	key (str) – The desired `Output`’s associated definition keyword
Returns:	Output value
Return type:	Any

get_output_configuration() → dict¶

Returns the output configuration of this run.

Returns:	Output configuration
Return type:	dict

get_output_parser() → object¶

get_output_set() → model_utils.managers.InheritanceQuerySet¶

Returns the Output subclasses’ instances created on this execution of the analysis_version.

Returns:	This run’s outputs
Return type:	`InheritanceQuerySet`

get_raw_input_configuration() → dict¶

Returns the “raw” configuration of this run. As some inputs may have been transformed, this method is used to reverse these changes in case this run’s parameters are compared in the future to new input parameters.

Returns:	Raw input configuration as provided by the user
Return type:	dict

get_results_json() → dict¶

Returns a JSON serializable dictionary of the results.

Returns:	JSON serializable output dictionary
Return type:	dict

get_status_display(*, field=<django.db.models.fields.CharField: status>)¶

get_visualizer(provider: str = None) → callable¶

input_configuration¶

Returns a dictionary with the full input configuration of this run.

Returns:	Full input configuration
Return type:	dict

See also

get_input_configuration()

input_defaults¶

Returns the default configuration parameters according to this instance’s InputSpecification’s default_configuration property.

Returns:	This analysis version’s default input configuration
Return type:	dict

input_set¶

Returns the Input subclasses’ instances created for this run.

Returns:	This run’s inputs
Return type:	`QuerySet`

See also

get_input_set()

objects = <django_analyses.models.managers.run.RunManager object>¶

output_configuration¶

Returns a dictionary of the output configuration of this run.

Returns:	Output configuration
Return type:	dict

See also

get_output_configuration()

output_parser¶

output_set¶

Returns the Output subclasses’ instances created by this run.

Returns:	This run’s outputs
Return type:	`QuerySet`

See also

get_output_set()

parse_output()¶

path¶

Retruns the default Path for any artifacts created by this run.

Returns:	Run artifacts directory under MEDIA_ROOT.
Return type:	`pathlib.Path`

raw_input_configuration¶

Returns a dictionary of this run’s raw input configuration.

Returns:	This run’s raw input configuration
Return type:	dict

See also

get_raw_input_configuration()

start_time¶: Run start time.

status¶: The status of this run.

task_result¶: The TaskResult instance associated with this run.

task_result_id¶

traceback¶: Traceback saved in case of run failure.

user¶: The user who created this run.

visualize() → None¶