MediatorLocalAccessionMixin

class MediatorLocalAccessionMixin(database, acs_refrep='tid', acs_sub_nodes=False, acs_filter_method=None, acs_filter_value=None, **kwargs)[source]

Mixin class for local mediator that handle accession data.

Mixin class constructor for MediatorLocalAccessionMixin

Parameters

  • database (pmaf.database._metakit.DatabaseAccessionMetabase) – Instance of DatabaseBase and DatabaseAccessionMixin

  • acs_refrep (str) – Taxonomy lookup level. Can be either “tid” for tids or “rid” for rids

  • acs_sub_nodes (bool) – Whether mediator should include subs

  • acs_filter_method (Optional[str]) – Method to filter accession numbers. Can be “random” and “first”

  • acs_filter_value (Optional[str]) – Complementary value for the acs_filter_method.

  • kwargs (Any) – Compatibility

Attributes

ACS_FILTER_METHODS

client

Current active client that mediator mediates.

configs

All current configs.

state

State of the mediator(client)

Methods

get_accession_by_identifier(docker, factor, …)

Get accession data that matches identifiers in docker within local database client.

get_identifier_by_accession(docker, factor, …)

Get local database identifiers that match target accession numbers in docker within local database client.

reconfig(name, value)

Set config name to value

verify_factor(factor)

Verify/validate compatibility of the current mediator and factor