def get_full_hierarchy_from_tsn(tsn, as_dataframe=True, include_children=True,
**kwargs):
"""
Returns a list of items from the ITIS getFullHierarchyFromTSN function.
The resulting pandas dataframe or list of dictionaries contains
the tsn, as well as common name
Parameters
----------
tsn : int
The ITIS taxonomic serial number to query
as_dataframe : bool
if True return pandas dataframe, if False return list of dictionaries
include_children : bool
flag to optionally return the child taxonomies of the given taxon
Returns
-------
pandas dataframe or list of dictionaries with common names and tsns
"""
results = _get_xml(ITIS_BASE_URL + 'getFullHierarchyFromTSN',
payload={'tsn': tsn})
hierarchy = results.xpath('//ax21:hierarchyList', namespaces=NS21)
if as_dataframe and pd:
df = xml_utils.element_to_df(hierarchy)
if not include_children:
df = df[df.parentTsn!=str(tsn)]
return df
else:
d = xml_utils.element_to_list(hierarchy)
if not include_children:
d = [r for r in d if r['parentTsn'] != str(tsn)]
return d
def search_by_scientific_name(scientific_name, as_dataframe=True, **kwargs):
"""
Returns a list of items from the ITIS searchByCommonName function.
The resulting pandas dataframe or list of dictionaries contains
the tsn, as well as common name
Parameters
----------
scientific_name : str
The string to match on
as_dataframe : bool
if True return pandas dataframe, if False return list of dictionaries
Returns
-------
pandas dataframe or list of dictionaries with scientific_names and tsns
"""
results = _get_xml(ITIS_BASE_URL + 'searchByScientificName',
payload={'srchKey': scientific_name})
scientific_names = results.xpath('//ax21:scientificNames', namespaces=NS21)
if as_dataframe and pd:
return xml_utils.element_to_df(scientific_names)
else:
return xml_utils.element_to_list(scientific_names)
def get_full_record_from_tsn(tsn, as_dataframe=False, **kwargs):
"""
Returns a list of items from the ITIS getFullHierarchyFromTSN function.
The resulting pandas dataframe or list of dictionaries contains
the tsn, as well as common name
Parameters
----------
tsn : int
The ITIS taxonomic serial number to query
as_dataframe : bool
if True return pandas dataframe, if False return list of dictionaries
Returns
-------
pandas dataframe or list of dictionaries with common names and tsns
"""
results = _get_xml(ITIS_BASE_URL + 'getFullRecordFromTSN',
payload={'tsn': tsn}).getchildren()[0]
if as_dataframe:
dfs = collections.OrderedDict()
for child in results.getchildren():
df = xml_utils.element_to_df([child]).dropna()
dfs[xml_utils._parse_tag(child.tag)] = df
return dfs
else:
return xml_utils.node_to_dict(results, add_fgdc=False)
def get_common_names_tsn(tsn, as_dataframe=True, **kwargs):
"""
Returns a list of items from the ITIS getFullHierarchyFromTSN function.
The resulting pandas dataframe or list of dictionaries contains
the tsn, as well as common name
Parameters
----------
tsn : int
The ITIS taxonomic serial number to query
as_dataframe : bool
if True return pandas dataframe, if False return list of dictionaries
Returns
-------
pandas dataframe or list of dictionaries with common names and tsns
"""
results = _get_xml(ITIS_BASE_URL + 'getCommonNamesFromTSN',
payload={'tsn': tsn})
commmon_names = results.xpath('//ax21:commonNames', namespaces=NS21)
if as_dataframe and pd:
return xml_utils.element_to_df(commmon_names)
else:
return xml_utils.element_to_list(commmon_names)
def get_rank_names(as_dataframe=True, **kwargs):
"""
Provides a list of all the unique rank names contained in the database and
their kingdom and rank ID values.
Parameters
----------
as_dataframe : bool
if True return pandas dataframe, if False return list of dictionaries
kwargs
Returns
-------
"""
results = _get_xml(ITIS_BASE_URL + "getRankNames", payload={})
rank_names = results.xpath("//ax23:rankNames", namespaces=NS23)
if as_dataframe and pd:
return xml_utils.element_to_df(rank_names)
else:
return xml_utils.element_to_list(rank_names)
def get_currency_from_tsn(tsn, as_dataframe=True, **kwargs):
"""
Returns a list of items from the ITIS getFullHierarchyFromTSN function.
The resulting pandas dataframe or list of dictionaries contains
the tsn, as well as common name
Parameters
----------
tsn : int
The ITIS taxonomic serial number to query
as_dataframe : bool
if True return pandas dataframe, if False return list of dictionaries
Returns
-------
pandas dataframe or list of dictionaries with common names and tsns
"""
results = _get_xml(ITIS_BASE_URL + "getCurrencyFromTSN",
payload={"tsn": tsn})
if as_dataframe and pd:
return xml_utils.element_to_df(results)
else:
return xml_utils.element_to_list(results)
