:py:mod:`biotaphy.client.ot_service_wrapper.open_tree`
======================================================

.. py:module:: biotaphy.client.ot_service_wrapper.open_tree

.. autoapi-nested-parse::

   Module for Open Tree of Life client.



Module Contents
---------------

Classes
~~~~~~~

.. autoapisummary::

   biotaphy.client.ot_service_wrapper.open_tree.LABEL_FORMAT



Functions
~~~~~~~~~

.. autoapisummary::

   biotaphy.client.ot_service_wrapper.open_tree.induced_subtree
   biotaphy.client.ot_service_wrapper.open_tree.resolve_names_otol
   biotaphy.client.ot_service_wrapper.open_tree.sanitize_name



Attributes
~~~~~~~~~~

.. autoapisummary::

   biotaphy.client.ot_service_wrapper.open_tree.INDUCED_SUBTREE_BASE_URL
   biotaphy.client.ot_service_wrapper.open_tree.MAX_NAMES_PER_REQUEST
   biotaphy.client.ot_service_wrapper.open_tree.OTT_TAXON_INFO_URL
   biotaphy.client.ot_service_wrapper.open_tree.PRODUCTION_SERVER


.. py:data:: INDUCED_SUBTREE_BASE_URL
   

   

.. py:class:: LABEL_FORMAT

   Represents the label format constants used when calling induced subtree.

   .. py:attribute:: ID
      :annotation: = id

      

   .. py:attribute:: NAME
      :annotation: = name

      

   .. py:attribute:: NAME_AND_ID
      :annotation: = name_and_id

      


.. py:data:: MAX_NAMES_PER_REQUEST
   :annotation: = 250

   

.. py:data:: OTT_TAXON_INFO_URL
   

   

.. py:data:: PRODUCTION_SERVER
   :annotation: = https://api.opentreeoflife.org/v3

   

.. py:function:: induced_subtree(ott_ids, label_format=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.

   :param ott_ids: A list of Open Tree IDs.  These will be converted to
                   integers in the request.
   :type ott_ids: list
   :param label_format: The label string format to use when creating the
                        tree on the server. (see: LABEL_FORMAT)
   :type label_format: str

   :returns: A dictionary of the subtree response after JSON processing.
   :rtype: dict


.. py:function:: resolve_names_otol(names_list)

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

   :param names_list: A list of taxon names to get
                      information for.
   :type names_list: :obj:`list` of :obj:`str`

   :returns:

             A dictionary where keys are the searched taxon names and the values are
                 dictionaries of values from Open Tree.
   :rtype: dict


.. py:function:: sanitize_name(name)

   Quick and dirty sanitization of a name string.

   :param name: A name string to sanitize.
   :type name: str

   :returns: A sanitized search name.
   :rtype: str