Aligner

class Aligner(force_download: bool | None = None)[source]

Bases: object

A class for aligning new registries.

Instantiate the aligner.

Attributes Summary

`alt_key_match`	Set this if there's another part of the data besides the ID that should be matched
`alt_keys_match`
`getter_kwargs`	Keyword arguments to pass to the getter function on call
`include_new`	Should new entries be included automatically? Only set this true for aligners of very high confidence (e.g., OBO Foundry but not BioPortal)
`internal_registry`	Get the internal registry.
`normalize_invmap`
`skip_deprecated`	Set to true if you don't want to align to deprecated resources
`subkey`

Methods Summary

`align`([dry, show, force_download])	Align and output the curation sheet.
`cli`()	Construct a CLI for the aligner.
`get_curation_row`(external_id, external_entry)	Get a sequence of items that will be ech row in the curation table.
`get_curation_table`(**kwargs)	Get the curation table as a string, built by `tabulate`.
`get_skip`()	Get the mapping prefixes that should be skipped to their reasons (strings).
`prepare_external`(external_id, external_entry)	Prepare a dictionary to be added to the bioregistry for each external registry entry.
`print_curation_table`(**kwargs)	Print the curation table.
`write_curation_table`()	Write the curation table to a TSV.
`write_registry`()	Write the internal registry.

Attributes Documentation

alt_key_match: ClassVar[str | None] = None: Set this if there’s another part of the data besides the ID that should be matched

alt_keys_match: ClassVar[str | None] = None

getter_kwargs: ClassVar[Mapping[str, Any] | None] = None: Keyword arguments to pass to the getter function on call

include_new: ClassVar[bool] = False: Should new entries be included automatically? Only set this true for aligners of very high confidence (e.g., OBO Foundry but not BioPortal)

internal_registry: Get the internal registry.

normalize_invmap: ClassVar[bool] = False

skip_deprecated: ClassVar[bool] = False: Set to true if you don’t want to align to deprecated resources

subkey: ClassVar[str] = 'prefix'

Methods Documentation

classmethod align(dry: bool = False, show: bool = False, force_download: bool | None = None) → None[source]

Align and output the curation sheet.

Parameters:

dry – If true, don’t write changes to the registry
show – If true, print a curation table
force_download – Force re-download of the data

classmethod cli()[source]: Construct a CLI for the aligner.

get_curation_row(external_id, external_entry) → Sequence[str][source]

Get a sequence of items that will be ech row in the curation table.

Parameters:

external_id – The external registry identifier
external_entry – The external registry data

Returns:

A sequence of cells to add to the curation table.

Raises:

TypeError – If an invalid value is encountered

The default implementation of this function iterates over all of the keys in the class variable curation_header and looks inside each record for those in order.

Note

You don’t need to pass the external ID. this will automatically be the first element.

get_curation_table(**kwargs) → str | None[source]: Get the curation table as a string, built by tabulate.

get_skip() → Mapping[str, str][source]: Get the mapping prefixes that should be skipped to their reasons (strings).

prepare_external(external_id: str, external_entry: Dict[str, Any]) → Dict[str, Any][source]

Prepare a dictionary to be added to the bioregistry for each external registry entry.

The default implementation returns external_entry unchanged. If you need more than that, override this method.

Parameters:

external_id – The external registry identifier
external_entry – The external registry data

Returns:

The dictionary to be added to the bioregistry for the aligned entry

print_curation_table(**kwargs) → None[source]: Print the curation table.

write_curation_table() → None[source]: Write the curation table to a TSV.

write_registry() → None[source]: Write the internal registry.