def add_taxon(tsn):
#http://www.itis.gov/ITISWebService/services/ITISService/getScientificNameFromTSN?tsn=531894
taxon = Taxon(tsn=tsn)
sci_name_xml = _get_itis('getScientificNameFromTSN', {'tsn': tsn})
sci_name = None
for i in range(1,5):
this_name = sci_name_xml.xpath("//ns:return/ax:unitName%d" % i, namespaces=itis_namespaces)[0].text
if this_name:
sci_name = this_name
taxon.name = sci_name
rank_name_xml = _get_itis('getTaxonomicRankNameFromTSN', {'tsn': tsn})
rank_name = rank_name_xml.xpath("//ns:return/ax:rankName", namespaces=itis_namespaces)[0].text
taxon.rank = Taxon.ITIS_RANKS[rank_name]
supertaxon_xml = _get_itis('getParentTSNFromTSN', {'tsn': tsn})
supertaxon_tsn = supertaxon_xml.xpath("//ns:return/ax:parentTsn", namespaces=itis_namespaces)[0]
supertaxon_tsn = int(supertaxon_tsn.text)
q = Taxon.objects.filter(tsn=supertaxon_tsn)
if q.exists():
taxon.supertaxon = q[0]
common_names_xml = _get_itis('getCommonNamesFromTSN', {'tsn': tsn})
common_names_elements = common_names_xml.xpath("//ns:return/ax:commonNames", namespaces=itis_namespaces)
common_names = []
for name in common_names_elements:
name = objectify.fromstring(etree.tostring(name))
nil_key = '{%s}nil' % itis_namespaces['xsi']
if nil_key in name.attrib:
if name.attrib[nil_key] == 'true':
continue
if not len(name):
continue
if name.language != "English":
continue
common_names.append(unicode(name.commonName))
taxon.common_names = ", ".join(common_names)
return taxon
def itis_search(request):
xml_doc = _get_itis('searchForAnyMatch', request.GET)
match_elements = xml_doc.xpath("//ns:return/ax:anyMatchList", namespaces=itis_namespaces)
results = []
for e in match_elements:
# TODO better way to transmute an etree element into a objectified
# element
o = objectify.fromstring(etree.tostring(e))
if not len(o): # no matches were returned
break
try:
taxon = Taxon.objects.get(tsn=o.tsn)
except:
taxon = Taxon()
taxon.tsn = o.tsn
taxon.name = o.sciName
taxon.itis_rank = itis_get_rank(o.tsn)
taxon.rank = Taxon.ITIS_RANKS[taxon.itis_rank]
# skip taxa above Order
if taxon.rank > 2:
continue
common_names = []
for name in o.commonNameList.commonNames:
if len(name):
if name.language == 'English':
common_names.append(unicode(name.commonName))
taxon.common_names = ', '.join(common_names)
results.append(taxon)
# render an HTML fragment that can be inserted into the taxon_import page
return HttpResponse(
render_to_string('taxons/itis_search_results.html', {
'results': results,
'MEDIA_URL': settings.MEDIA_URL,
}),
mimetype="text/plain",
)
