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


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


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.

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



alias of PyOpenWorm.data_trans.data_with_evidence_ds.DataWithEvidenceDataSource


alias of WormAtlasCellListDataTranslation


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.