datanator_rest_api.util package

Submodules

datanator_rest_api.util.paginator module

class datanator_rest_api.util.paginator.Paginator(count, docs)

Bases: object

page(_from=0, size=10)

Calculate page information.

Parameters

• _from (int, optional) – Page starting from. Defaults to 0.

• size (int, optional) – page size. Defaults to 10.

Returns

page info

Return type

(list)

datanator_rest_api.util.taxon_distance module

class datanator_rest_api.util.taxon_distance.TaxonDist(debugging=False)

Bases: object

arrange_distance_objs(docs, target_species='homo sapiens', tax_field='taxon_name', org_format='tax_name')

Arrange the distance object returned into arrays.

Parameters

• docs (Iter) – Documents that need calculation of taxon_distance and rearranging.

• target_species (str or int, optional) – User input for target species.

• tax_field (str, optional) – Field containing taxon information in documents.

• org_format (str, optional) – format of species identifier (tax_id or tax_name). Defaults to ‘tax_id’.

Returns

List of documents that have the taxon_distance objects.

Return type

(list of Obj)

get_dist_object(doc, queried_species, distance_obj, target_species, org_format='tax_id', tax_field='species_name', obj_name='taxon_distance')

Return taxon_distance object for frontend.

Parameters

• doc (Obj) – documents that need to be processed.

• queried_species (deque) – already queried species.

• distance_obj (Obj) – distance objects containing already queried species.

• target_species (str or int) – target species.

• org_format (str, optional) – format of species identifier (tax_id or tax_name). Defaults to ‘tax_id’.

• tax_field (str, optional) – field containing taxon information in documents.

• obj_name (str, optional) – name of the object containing taxon distance information.

Returns

(tuple of list, Obj, Obj)

Module contents