owmeta.data_trans.wormatlas module¶
- class owmeta.data_trans.wormatlas.WormAtlasCellListDataSource(*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_field_delimiter¶
“CSV field delimiter”, a
DatatypeProperty
Default value: ‘,’
- csv_header¶
“Header column names”, a
DatatypeProperty
- CSV file name
- class owmeta.data_trans.wormatlas.WormAtlasCellListDataTranslation(*args, no_type_decl=False, **kwargs)[source]¶
Bases:
GenericTranslation
- defined_augment()[source]¶
This fuction must return False if
identifier_augment()
would raise anIdentifierMissingException
. 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_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)[source]¶
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)[source]¶
It’s intended that implementations of
BaseDataTranslator
will override this method to make customTranslations
according with how different arguments totranslate
are (or are not) distinguished.The actual properties of a
Translation
subclass must be assigned within thetranslate
method- Parameters
- sources
tuple
The sources that go into the translation. Sub-classes may choose to pass these to their superclass’ make_translation method or not.
- sources
- Returns
a
description
of
the
translation
- translate(data_source, neurons_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")¶