owmeta.data_trans.connections module

class owmeta.data_trans.connections.ConnectomeCSVDataSource(*args, no_type_decl=False, **kwargs)

Bases: DSMixin, CSVDataSource

A CSV data source whose CSV file describes a neural connectome

Basically, this is just a marker type to indicate what’s described in the CSV – there’s no consistent schema

Parameters

commit_opCommitOp, optional

The operation to use for commiting the file changes. The default is COPY

class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci/bio")

class owmeta.data_trans.connections.NeuronConnectomeCSVTranslation(*args, no_type_decl=False, **kwargs)

Bases: GenericTranslation

class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci/bio")

class owmeta.data_trans.connections.NeuronConnectomeCSVTranslator(*args, no_type_decl=False, **kwargs)

Bases: DTMixin, CSVDataTranslator

Input type(s): ConnectomeCSVDataSource, DataWithEvidenceDataSource

Output type(s): DataWithEvidenceDataSource

output_type

alias of DataWithEvidenceDataSource

translation_type

alias of NeuronConnectomeCSVTranslation

make_translation(sources)

It’s intended that implementations of BaseDataTranslator will override this method to make custom Translations according with how different arguments to translate are (or are not) distinguished.

The actual properties of a Translation subclass must be assigned within the translate method

Parameters

sourcestuple

The sources that go into the translation. Sub-classes may choose to pass these to their superclass’ make_translation method or not.

Returns

a description of the translation

translate(data_source, neurons_source, muscles_source)

Notionally, this method takes one or more data sources, and translates them into some other data source that captures essentially the same information, but, possibly, in a different format. Additional sources can be passed in as well for auxiliary information which are not “translated” in their entirety into the output data source. Such auxiliarry data sources should be distinguished from the primary ones in the translation

Parameters

*args

Input data sources

**kwargs

Named input data sources

Returns

the output data source

class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci/bio")

class owmeta.data_trans.connections.NeuronConnectomeSynapseClassTranslation(*args, no_type_decl=False, **kwargs)

Bases: GenericTranslation

class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci/bio")

class owmeta.data_trans.connections.NeuronConnectomeSynapseClassTranslator(*args, no_type_decl=False, **kwargs)

Bases: DTMixin, CSVDataTranslator

Adds synapse classes to existing connections

output_type

alias of DataWithEvidenceDataSource

translation_type

alias of NeuronConnectomeSynapseClassTranslation

make_translation(sources)

It’s intended that implementations of BaseDataTranslator will override this method to make custom Translations according with how different arguments to translate are (or are not) distinguished.

The actual properties of a Translation subclass must be assigned within the translate method

Parameters

sourcestuple

The sources that go into the translation. Sub-classes may choose to pass these to their superclass’ make_translation method or not.

Returns

a description of the translation

translate(data_source, neurotransmitter_source)

Notionally, this method takes one or more data sources, and translates them into some other data source that captures essentially the same information, but, possibly, in a different format. Additional sources can be passed in as well for auxiliary information which are not “translated” in their entirety into the output data source. Such auxiliarry data sources should be distinguished from the primary ones in the translation

Parameters

*args

Input data sources

**kwargs

Named input data sources

Returns

the output data source

class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci/bio")