lmpy.data_wrangling.common.accepted_name_wrangler

Module containing a data wrangler base class for resolving taxon names.

Module Contents

Classes

_AcceptedNameWrangler

Constructor for the base accepted name wrangler.

Functions

_resolve_gbif_synonym_match(match_response[, wait_time])

Resolve names using GBIF's taxonomic name resolution service.

resolve_names_gbif(names[, wait_time])

Resolve names using GBIF's taxonomic name resolution service.
class lmpy.data_wrangling.common.accepted_name_wrangler._AcceptedNameWrangler(name_map=None, name_resolver=None, out_map_filename=None, map_write_interval=100, out_map_format='json')[source]

Bases: lmpy.data_wrangling.base._DataWrangler

Constructor for the base accepted name wrangler.

Parameters

  • name_map (dict or str or None) – An existing name mapping.

  • name_resolver (Method or None) – If provided, this should be a function that takes a list of names as input and returns a dictionary of name mappings. If omitted, resolving of new names will be skipped.

  • out_map_filename (str) – A file location to write the updated name map.

  • map_write_interval (int) – Update the name map output file after each set of this many iterations.

  • out_map_format (str) – The format to write the names map (csv or json).

__del__()[source]

Destructor method, sync map to disk if needed.

Raises

Exception – Raised if writing name map fails.

_load_name_map(name_map)[source]

Attempt to load names from the name_map provided.

Parameters

name_map (dict or str) – A mapping dictionary or a filename with names.

Raises

FileNotFoundError – on missing name_map file

resolve_names(names)[source]

Attempts to resolve a list of names.

Parameters

names (list or str) – A list of names to resolve.

Returns

A dictionary of input name keys and resolved name values.

Return type

dict

write_map_to_file(filename, output_format, mode='wt')[source]

Write the name map to a file so it can be reused.

Parameters

  • filename (str) – A file location where the map should be written.

  • output_format (str) – The format to write the map, either ‘csv’ or ‘json’.

  • mode (str) – How the file should be opened.

Raises

  • OSError – on failure to write to filename.

  • IOError – on failure to write to filename.

lmpy.data_wrangling.common.accepted_name_wrangler._resolve_gbif_synonym_match(match_response, wait_time=1)[source]

Resolve names using GBIF’s taxonomic name resolution service.

Parameters

  • match_response (urllib.Response) – A response from a GBIF species match query.

  • wait_time (number) – A number of seconds to before request to avoid server ire.

Returns

An accepted canonical name for the GBIF acceptedUsageKey.

Return type

namestr

lmpy.data_wrangling.common.accepted_name_wrangler.resolve_names_gbif(names, wait_time=1)[source]

Resolve names using GBIF’s taxonomic name resolution service.

Parameters

  • names (list of str) – A list of name strings to resolve.

  • wait_time (number) – A number of seconds to wait after each request to avoid server ire.

Returns

Input names are keys and resolved name or None are values.

Return type

dict