biotaphy.client.ot_service_wrapper package

Submodules

biotaphy.client.ot_service_wrapper.open_tree module

Module for Open Tree of Life client.

class biotaphy.client.ot_service_wrapper.open_tree.LABEL_FORMAT

Bases: object

Represents the label format constants used when calling induced subtree.

ID = 'id'

NAME = 'name'

NAME_AND_ID = 'name_and_id'

biotaphy.client.ot_service_wrapper.open_tree.induced_subtree(ott_ids, label_format='name')

Retrieves a Newick tree containing the nodes represented by the ids.

Calls the Open Tree ‘induced_subtree’ service to retrieve a tree, in Newick format, containing the nodes represented by the provided Open Tree IDs.

Parameters

• ott_ids (list) – A list of Open Tree IDs. These will be converted to integers in the request.

• label_format (str) – The label string format to use when creating the tree on the server. (see: LABEL_FORMAT)

Returns

A dictionary of the subtree response after JSON processing.

Return type

dict

biotaphy.client.ot_service_wrapper.open_tree.resolve_names_otol(names_list)

Get information from the OTL taxon match service for a list of names.

Parameters

names_list (list of str) – A list of taxon names to get information for.

Returns

A dictionary where keys are the searched taxon names and the values are

dictionaries of values from Open Tree.

Return type

dict

biotaphy.client.ot_service_wrapper.open_tree.sanitize_name(name)

Quick and dirty sanitization of a name string.

Parameters

name (str) – A name string to sanitize.

Returns

A sanitized search name.

Return type

str

Module contents

Open Tree service wrapper module __init__.