PyOpenWorm.data_trans.wormatlas module

class PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataSource(**kwargs)[source]

Bases: PyOpenWorm.data_trans.csv_ds.CSVDataSource

CSV file name : DatatypeProperty
Attribute: csv_file_name
Header column names : DatatypeProperty
Attribute: csv_header
CSV field delimiter : DatatypeProperty
Attribute: csv_field_delimiter
File name : DatatypeProperty
Attribute: file_name
Description : DatatypeProperty

Attribute: description

Free-text describing the data source

Input source : ObjectProperty

Attribute: source

The data source that was translated into this one

Translation : ObjectProperty

Attribute: translation

Information about the translation process that created this object

class PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataTranslation(**kwargs)[source]

Bases: PyOpenWorm.datasource.GenericTranslation

defined_augment()[source]

This fuction must return False if identifier_augment() would raise an IdentifierMissingException. Override it when defining a non-standard identifier for subclasses of DataObjects.

identifier_augment()[source]

Override this method to define an identifier in lieu of one explicity set.

One must also override defined_augment() to return True whenever this method could return a valid identifier. IdentifierMissingException should be raised if an identifier cannot be generated by this method.

Raises:
IdentifierMissingException
class PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataTranslator[source]

Bases: PyOpenWorm.data_trans.csv_ds.CSVDataTranslator

Input type(s): PyOpenWorm.data_trans.wormatlas.WormAtlasCellListDataSource, PyOpenWorm.data_trans.data_with_evidence_ds.DataWithEvidenceDataSource

Output type(s): PyOpenWorm.data_trans.data_with_evidence_ds.DataWithEvidenceDataSource

URI: http://openworm.org/entities/translators/WormAtlasCellListDataTranslator

output_type

alias of PyOpenWorm.data_trans.data_with_evidence_ds.DataWithEvidenceDataSource

translation_type

alias of WormAtlasCellListDataTranslation

make_translation(sources)[source]

It’s intended that implementations of DataTranslator 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 defined within the ‘translate’ method

translate(data_source, neurons_source)[source]

Notionally, this method takes a data source, which is translated into some other data source. There doesn’t necessarily need to be an input data source.