owmeta.data_trans.wormbase module

class owmeta.data_trans.wormbase.CellWormBaseCSVTranslator(*args, no_type_decl=False, **kwargs)

Bases: DTMixin, CSVDataTranslator

Input type(s): WormBaseCSVDataSource

Output type(s): DataWithEvidenceDataSource

input_type

alias of WormBaseCSVDataSource

output_type

alias of DataWithEvidenceDataSource

translate(data_source)

Translate wormbase CSV dump into Cells, Neurons, and Muscles

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

class owmeta.data_trans.wormbase.WormBaseCSVDataSource(*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_header

“Header column names”, a DatatypeProperty

class owmeta.data_trans.wormbase.WormbaseIonChannelCSVDataSource(*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_header

“Header column names”, a DatatypeProperty

class owmeta.data_trans.wormbase.WormbaseIonChannelCSVTranslator(*args, no_type_decl=False, **kwargs)

Bases: DTMixin, CSVDataTranslator

Input type(s): WormbaseIonChannelCSVDataSource

Output type(s): DataWithEvidenceDataSource

input_type

alias of WormbaseIonChannelCSVDataSource

output_type

alias of DataWithEvidenceDataSource

translate(data_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.wormbase.WormbaseTextMatchCSVDataSource(*args, no_type_decl=False, **kwargs)

Bases: DSMixin, CSVDataSource

initial_cell_columnDatatypeProperty

Attribute: initial_cell_column

The index of the first column with a cell name

cell_typeDatatypeProperty

Attribute: cell_type

The type of cell to be produced

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

cell_type

“cell_type”, a DatatypeProperty: The type of cell to be produced

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

initial_cell_column

“initial_cell_column”, a DatatypeProperty: The index of the first column with a cell name

class owmeta.data_trans.wormbase.WormbaseTextMatchCSVTranslator(*args, no_type_decl=False, **kwargs)

Bases: DTMixin, CSVDataTranslator

Input type(s): WormbaseTextMatchCSVDataSource

Output type(s): DataWithEvidenceDataSource

input_type

alias of WormbaseTextMatchCSVDataSource

output_type

alias of DataWithEvidenceDataSource

translate(data_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")