BioContextAligner

class BioContextAligner(force_download=None)[source]

Aligner for BioContext.

Instantiate the aligner.

Attributes Summary

`curation_header`	Header to put on the curation table, corresponding to `get_curation_row()`
`key`	The key for the external registry

Methods Summary

`get_curation_row`(external_id, external_entry)	Prepare curation rows for unaligned BioContext registry entries.
`get_skip`()	Get entries for BioContext that should be skipped.
`getter`()	Get the BioContext context map.
`prepare_external`(external_id, external_entry)	Prepare BioContext data to be added to the BioContext for each BioPortal registry entry.

Attributes Documentation

curation_header: ClassVar[Sequence[str]] = ['uri_format', 'identifiers', 'purl']: Header to put on the curation table, corresponding to get_curation_row()

Methods Documentation

get_curation_row(external_id, external_entry)[source]

Prepare curation rows for unaligned BioContext registry entries.

Get entries for BioContext that should be skipped.

getter()

Get the BioContext context map.

Parameters: force_download (bool) – If true, forces download. If false and the file is already cached, resuses it.
Return type: Mapping[str, Mapping[str, Any]]
Returns: The biocontext data dictionary