owmeta.data_trans.wormatlas module

class owmeta.data_trans.wormatlas.WormAtlasCellListDataSource(*args, no_type_decl=False, **kwargs)

Bases: DSMixin, CSVDataSource

CSV file nameDatatypeProperty

Attribute: csv_file_name

Header column namesDatatypeProperty

Attribute: csv_header

CSV field delimiterDatatypeProperty

Attribute: csv_field_delimiter

Default value: ,

File nameDatatypeProperty

Attribute: file_name

Torrent file nameDatatypeProperty

Attribute: torrent_file_name

MD5 hashDatatypeProperty

Attribute: md5

SHA-256 hashDatatypeProperty

Attribute: sha256

SHA-512 hashDatatypeProperty

Attribute: sha512

Input sourceObjectProperty

Attribute: source

The data source that was translated into this one

TransformationObjectProperty

Attribute: transformation

Information about the transformation process that created this object

TranslationObjectProperty

Attribute: translation

Information about the translation process that created this object

DescriptionDatatypeProperty

Attribute: description

Free-text describing the data source

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")

csv_field_delimiter

“CSV field delimiter”, a DatatypeProperty

Default value: ‘,’

csv_header

“Header column names”, a DatatypeProperty

class owmeta.data_trans.wormatlas.WormAtlasCellListDataTranslation(*args, no_type_decl=False, **kwargs)

Bases: GenericTranslation

defined_augment()

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()

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

class owmeta.data_trans.wormatlas.WormAtlasCellListDataTranslator(*args, no_type_decl=False, **kwargs)

Bases: DTMixin, CSVDataTranslator

Input type(s): WormAtlasCellListDataSource, DataWithEvidenceDataSource

Output type(s): DataWithEvidenceDataSource

output_type

alias of DataWithEvidenceDataSource

translation_type

alias of WormAtlasCellListDataTranslation

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)

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")