/
ubio.py
executable file
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/
ubio.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Client that access uBio.'''
from base64 import b64decode
from urllib2 import urlopen, quote
from xml.etree.ElementTree import parse
from keycode import keycode_string
class uBio:
'''Integration with uBio.'''
def __init__(self):
self.baseurl = 'http://www.ubio.org/webservices/service.php?function='
self.key = keycode_string
print 'Started uBio.'
def call(self, url):
'''Standard function to call, parse, and return the results.'''
root = parse(urlopen(url)).getroot()
return root
def build_url(self, parameters, key=True):
'''Build url from a list of parameters, function name must be first.'''
if key:
parameters.append('keyCode=%s' % self.key)
parstring = '&'.join(parameters)
url = self.baseurl + parstring
return url
def xmltodic(self, elements):
'''Convert elements extracted from xml to a python dictionary.'''
if not elements:
return []
b64tags = ['nameString', 'fullNameString', 'nameStringLink',
'fullNameStringLink']
converted = []
for value in elements:
item = {}
for field in value:
if field.tag in b64tags:
item[field.tag] = b64decode(field.text)
else:
item[field.tag] = field.text
converted.append(item)
return converted
def compile(self, scientific, vernacular):
'''Compile list of taxa to be shown.
Uses the taxon name as key to store the different versions.
Layout:
{
'Clypeaster subdepressus': {
'vernacular': [{
'languageCode': 'xxx', 'nameStringLink': 'Schefflera
actinophylla', 'nameString': 'octopus tree',
'packageName': 'Apiales', 'packageID': '648',
'languageName': 'unspecified', 'fullNameStringLink':
'Schefflera actinophylla (Endl.) H. A. T. Harms',
'namebankIDLink': '475857', 'namebankID': '4755217'
},],
'scientific': [{
'fullNameString': 'Sepia octopus Molina, 1789',
'rankID': '24', 'nameString': 'Sepia octopus',
'packageName': 'Cephalopoda', 'packageID': '22',
'rankName': 'species', 'basionymUnit': '0',
'namebankID': '640849'
},]
}
}
'''
final = {}
# Prepare.
if scientific:
for entry in scientific:
final[entry['nameString']] = {'scientific': [], 'vernacular': []}
if vernacular:
for entry in vernacular:
final[entry['nameStringLink']] = {'scientific': [], 'vernacular': []}
# Populate scientific.
if scientific:
for entry in scientific:
final[entry['nameString']]['scientific'].append(entry)
# Populate vernacular.
if vernacular:
for entry in vernacular:
final[entry['nameStringLink']]['vernacular'].append(entry)
# Convert to list.
final_list = []
for k, v in final.iteritems():
final_list.append({
'name': k,
'vernacular': v['vernacular'],
'scientific': v['scientific'],
})
final_list.sort()
return final_list
def search_name(self, query):
'''Search for a name.
namebank_search:
This function will return NameBankIDs that match given search terms
ex: http://www.ubio.org/webservices/service.php?function=namebank_search&searchName=Octopus&sci=1&vern=1&keyCode=
searchName - search term to search by nameString
searchAuth - search term to search by authorship
searchYear - search term to search by year
order - (nameString or languageCode) by default the results will be ordered by nameString
sci - (0 or 1) to include scientific name results
vern - (0 or 1) to include vernacular (common name) results
keyCode - your personal uBio keycode. If you don't have one, obtain one here
Standard 'value' from xml scientificNames:
<value>
<namebankID>2842955</namebankID>
<nameString>QXN0cmFjYW50aGEgb2N0b3B1cw==</nameString>
<fullNameString>QXN0cmFjYW50aGEgb2N0b3B1cw==</fullNameString>
<packageID>663</packageID>
<packageName>Rosales</packageName>
<basionymUnit>722509</basionymUnit>
<rankID>24</rankID>
<rankName>species</rankName>
</value>
Standard 'value from xml vernacularNames:
<value>
<namebankID>4637287</namebankID>
<nameString>QW5nZWwgb2N0b3B1cw==</nameString>
<languageCode>eng</languageCode>
<languageName>English</languageName>
<packageID>22</packageID>
<packageName>Cephalopoda</packageName>
<namebankIDLink>514143</namebankIDLink>
<nameStringLink>VmVsb2RvbmEgdG9nYXRhIHRvZ2F0YQ==</nameStringLink>
<fullNameStringLink>VmVsb2RvbmEgdG9nYXRhIHRvZ2F0YSBDaHVuLCAxOTE1</fullNameStringLink>
</value>
'''
# Encode query (eg, replace ' ' by '%20').
quoted = quote(query)
parameters = [
'namebank_search', # function
'searchName=%s' % quoted, # search name
'sci=1', # scientific names
'vern=1', # vernacular names
]
url = self.build_url(parameters)
results = self.call(url)
# Parse raw xml values.
sci_names = results.findall('scientificNames/value')
vern_names = results.findall('vernacularNames/value')
# Convert to python list of dictionaries.
scientific_names = self.xmltodic(sci_names)
vernacular_names = self.xmltodic(vern_names)
final = self.compile(scientific_names, vernacular_names)
return final