MediatorLocalTaxonomyMixin

class MediatorLocalTaxonomyMixin(database, tax_rank_tolerance=None, tax_corr_method='lineage', tax_fuzzy_cutoff=95, tax_fuzzy_mode=False, tax_format=None, tax_refrep='tid', **kwargs)[source]

Mixin class for local mediator that handle taxonomy data.

Mixin class constructor for MediatorLocalTaxonomyMixin

Parameters

  • database (pmaf.database._metakit.DatabaseTaxonomyMetabase) – Instance of DatabaseBase and DatabaseTaxonomyMixin

  • tax_rank_tolerance (Optional[str]) – Rank tolerance level when match is not found

  • tax_corr_method (str) – Taxonomy correlation method. Can one of CORRELATION_METHODS - The “lineage” refer to lineage based correlation approach - The “complement” is used when missing taxonomy (from Family to Domain) must be complemented - The “taxon” refer to individual and cumulative taxon matching approach

  • tax_fuzzy_cutoff (int) – Cutoff value when fuzzy matching is enabled

  • tax_fuzzy_mode (bool) – If True enable fuzzy matching

  • tax_format (Optional[str]) – If not None then taxonomy formatting is enabled. # TODO: Elaborate on this

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

  • kwargs (Any) – Compatibility

Attributes

CORRELATION_METHODS

Available methods for taxonomy correlations

client

Current active client that mediator mediates.

configs

All current configs.

state

State of the mediator(client)

Methods

get_identifier_by_taxonomy(docker, factor, …)

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

get_taxonomy_by_identifier(docker, factor, …)

Get taxonomy data that matches identifiers 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