def tnrs_lookup(name, TIMEOUT=10, CACHE=True):
"""
Look up "name" on the TNRS web service. If a most likely standard name can be identified,
returns that name. Returns False if no or ambiguous result.
"""
name = name.replace("'", "").lower()
if name in cache and CACHE:
return cache[name]
url = "http://tnrs.iplantc.org/tnrsm-svc/matchNames?retrieve=best&names=%s"
# lookup canonical plant names on TNRS web service
try:
response = urllib2.urlopen(url % name.replace(" ", "%20"), timeout=TIMEOUT).read()
# response_dict = eval(response, {}, {'true':True, 'false':False, 'null':None})
response_dict = json.loads(response)
sci_name = response_dict["items"][0]["nameScientific"]
if sci_name:
result = sci_name
else:
result = None
except Exception as e:
print e
result = False
# cache results and return
cache[name] = result
if CACHE:
caching.save_cache(cache, "tnrs")
return result
def itis_lookup(name, TIMEOUT=10, CACHE=True):
'''
Look up "name" on itis.gov. If a standard name can be identified, returns
that name. Returns False if no or ambiguous result.
If a name matches multiple species that are all members of the same genus,
itis_lookup will return "Genus sp1/sp2/sp3..."
'''
name = name.replace("'", '').lower()
if name in cache and CACHE:
return cache[name]
url = 'http://www.itis.gov/servlet/SingleRpt/SingleRpt'
values = {'search_topic': 'all',
'search_kingdom':'every',
'search_span':'containing',
'search_value': name.decode(),
'categories':'All',
'source':'html',
'search_credRating': 'All'}
data = urllib.urlencode(values)
req = urllib2.Request(url, data)
response = urllib2.urlopen(req, timeout=TIMEOUT)
html = response.read()
# parse results to pull out unique species
results = [s.tail for s in p(html)('td.body a')]
results = sum([re.findall('Species: [A-Z][a-z ]*', result) for result in results], [])
results = [s.split(':')[1].strip() for s in results]
if results:
genus = set()
all_species = []
result = None
for this_species in results:
genus.add(this_species.split()[0])
if len(genus) > 1:
result = False
break
all_species.append(' '.join(this_species.split()[1:]))
if not result is False:
result = list(genus)[0] + ' ' + '/'.join(sorted(list(set(all_species))))
cache[name] = result
else:
cache[name] = False
if CACHE: caching.save_cache(cache, 'itis')
return cache[name]
