owmeta.data_trans.wormbase module¶
- class owmeta.data_trans.wormbase.CellWormBaseCSVTranslator(*args, no_type_decl=False, **kwargs)[source]¶
Bases:
DTMixin
,CSVDataTranslator
Input type(s):
WormBaseCSVDataSource
Output type(s):
DataWithEvidenceDataSource
- input_type¶
alias of
WormBaseCSVDataSource
- output_type¶
alias of
DataWithEvidenceDataSource
- 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)[source]¶
Bases:
DSMixin
,CSVDataSource
- CSV file name
DatatypeProperty
Attribute:
csv_file_name
- Header column names
DatatypeProperty
Attribute:
csv_header
- CSV field delimiter
DatatypeProperty
Attribute:
csv_field_delimiter
Default value: ,
- File name
DatatypeProperty
Attribute:
file_name
- Torrent file name
DatatypeProperty
Attribute:
torrent_file_name
- MD5 hash
DatatypeProperty
Attribute:
md5
- SHA-256 hash
DatatypeProperty
Attribute:
sha256
- SHA-512 hash
DatatypeProperty
Attribute:
sha512
- Input source
ObjectProperty
Attribute:
source
The data source that was translated into this one
- Transformation
ObjectProperty
Attribute:
transformation
Information about the transformation process that created this object
- Translation
ObjectProperty
Attribute:
translation
Information about the translation process that created this object
- Description
DatatypeProperty
Attribute:
description
Free-text describing the data source
- Parameters
- commit_op
CommitOp
,optional
The operation to use for commiting the file changes. The default is
COPY
- commit_op
- class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci/bio")¶
- csv_header¶
“Header column names”, a
DatatypeProperty
- CSV file name
- class owmeta.data_trans.wormbase.WormbaseIonChannelCSVDataSource(*args, no_type_decl=False, **kwargs)[source]¶
Bases:
DSMixin
,CSVDataSource
- CSV file name
DatatypeProperty
Attribute:
csv_file_name
- Header column names
DatatypeProperty
Attribute:
csv_header
- CSV field delimiter
DatatypeProperty
Attribute:
csv_field_delimiter
Default value: ,
- File name
DatatypeProperty
Attribute:
file_name
- Torrent file name
DatatypeProperty
Attribute:
torrent_file_name
- MD5 hash
DatatypeProperty
Attribute:
md5
- SHA-256 hash
DatatypeProperty
Attribute:
sha256
- SHA-512 hash
DatatypeProperty
Attribute:
sha512
- Input source
ObjectProperty
Attribute:
source
The data source that was translated into this one
- Transformation
ObjectProperty
Attribute:
transformation
Information about the transformation process that created this object
- Translation
ObjectProperty
Attribute:
translation
Information about the translation process that created this object
- Description
DatatypeProperty
Attribute:
description
Free-text describing the data source
- Parameters
- commit_op
CommitOp
,optional
The operation to use for commiting the file changes. The default is
COPY
- commit_op
- class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci/bio")¶
- csv_header¶
“Header column names”, a
DatatypeProperty
- CSV file name
- class owmeta.data_trans.wormbase.WormbaseIonChannelCSVTranslator(*args, no_type_decl=False, **kwargs)[source]¶
Bases:
DTMixin
,CSVDataTranslator
Input type(s):
WormbaseIonChannelCSVDataSource
Output type(s):
DataWithEvidenceDataSource
- input_type¶
alias of
WormbaseIonChannelCSVDataSource
- output_type¶
alias of
DataWithEvidenceDataSource
- translate(data_source)[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)[source]¶
Bases:
DSMixin
,CSVDataSource
- initial_cell_column
DatatypeProperty
Attribute:
initial_cell_column
The index of the first column with a cell name
- cell_type
DatatypeProperty
Attribute:
cell_type
The type of cell to be produced
- CSV file name
DatatypeProperty
Attribute:
csv_file_name
- Header column names
DatatypeProperty
Attribute:
csv_header
- CSV field delimiter
DatatypeProperty
Attribute:
csv_field_delimiter
Default value: ,
- File name
DatatypeProperty
Attribute:
file_name
- Torrent file name
DatatypeProperty
Attribute:
torrent_file_name
- MD5 hash
DatatypeProperty
Attribute:
md5
- SHA-256 hash
DatatypeProperty
Attribute:
sha256
- SHA-512 hash
DatatypeProperty
Attribute:
sha512
- Input source
ObjectProperty
Attribute:
source
The data source that was translated into this one
- Transformation
ObjectProperty
Attribute:
transformation
Information about the transformation process that created this object
- Translation
ObjectProperty
Attribute:
translation
Information about the translation process that created this object
- Description
DatatypeProperty
Attribute:
description
Free-text describing the data source
- Parameters
- commit_op
CommitOp
,optional
The operation to use for commiting the file changes. The default is
COPY
- commit_op
- 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
- initial_cell_column
- class owmeta.data_trans.wormbase.WormbaseTextMatchCSVTranslator(*args, no_type_decl=False, **kwargs)[source]¶
Bases:
DTMixin
,CSVDataTranslator
Input type(s):
WormbaseTextMatchCSVDataSource
Output type(s):
DataWithEvidenceDataSource
- input_type¶
alias of
WormbaseTextMatchCSVDataSource
- output_type¶
alias of
DataWithEvidenceDataSource
- translate(data_source)[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")¶