def getacceptednamesfromtsn(tsn, **kwargs):
'''
Get accepted names from tsn
:param tsn: taxonomic serial number (TSN) (character or numeric)
Usage::
# TSN accepted - good name
pytaxize.getacceptednamesfromtsn('208527')
# TSN not accepted - input TSN is old name
pytaxize.getacceptednamesfromtsn('504239')
'''
out = Refactor(itis_base + 'getAcceptedNamesFromTSN',
payload={
'tsn': tsn
},
request='get').xml(**kwargs)
temp = out.getchildren()
if (temp[0].getchildren()[1].values()[0] == 'true'):
dat = temp[0].getchildren()[0].text
else:
nodes = temp[0].getchildren()[1].getchildren()
dat = _parse_nodes(nodes)
dat.pop('author')
dat['submittedTsn'] = temp[0].getchildren()[0].text
return dat
def searchforanymatch(x, **kwargs):
'''
Search for any match
Usage::
pytaxize.searchforanymatch(x=202385)
pytaxize.searchforanymatch(x="dolphin")
'''
out = Refactor(itis_base + 'searchForAnyMatch',
payload={
'srchKey': x
},
request='get').xml(**kwargs)
# if isinstance(x, basestring):
tmp = out.getchildren()[0].getchildren()
output = []
for v in tmp:
tmp = v.getchildren()
for w in tmp:
output.append(
dict(
zip([gettag(e) for e in w.iter()],
[e.text for e in w.iter()])))
return output
def searchforanymatchpaged(x, pagesize, pagenum, ascend, **kwargs):
'''
Search for any matched page for descending (logical)
Usage::
pytaxize.searchforanymatchpaged(x=202385, pagesize=100, pagenum=1, ascend=False)
pytaxize.searchforanymatchpaged("Zy", pagesize=100, pagenum=1, ascend=False)
'''
args = {
'srchKey': x,
'pageSize': pagesize,
'pageNum': pagenum,
'ascend': ascend
}
out = Refactor(itis_base + 'searchForAnyMatchPaged',
payload=args,
request='get').xml(**kwargs)
tmp = out.getchildren()[0].getchildren()
output = []
for v in tmp:
tmp = v.getchildren()
for w in tmp:
output.append(
dict(
zip([gettag(e) for e in w.iter()],
[e.text for e in w.iter()])))
return output
def getjurisdictionvalues(**kwargs):
'''
Get possible jurisdiction values
Usage:
pytaxize.getjurisdictionvalues()
'''
out= Refactor(itis_base + 'getJurisdictionValues', payload={}, request='get').xml(**kwargs)
vals = [ x.text for x in out.getchildren()[0].getchildren() ]
return pd.DataFrame(vals, columns = ['jurisdictionValues'])
def getanymatchcount(x, **kwargs):
'''
Get any match count.
:param x: text or taxonomic serial number (TSN) (character or numeric)
:param **kwargs: optional additional curl options (debugging tools mostly)
Usage:
pytaxize.getanymatchcount(x=202385)
pytaxize.getanymatchcount(x="dolphin")
'''
out = Refactor(itis_base + 'getAnyMatchCount', payload={'srchKey': x}, request='get').xml(**kwargs)
return int(out.getchildren()[0].text)
def getjurisdictionvalues(**kwargs):
'''
Get possible jurisdiction values
Usage::
pytaxize.getjurisdictionvalues()
'''
out = Refactor(itis_base + 'getJurisdictionValues',
payload={},
request='get').xml(**kwargs)
vals = [x.text for x in out.getchildren()[0].getchildren()]
return pd.DataFrame(vals, columns=['jurisdictionValues'])
def gettsnfromlsid(lsid, **kwargs):
'''
Gets the TSN corresponding to the LSID, or an empty result if there is no match.
Usage:
pytaxize.gettsnfromlsid(lsid="urn:lsid:itis.gov:itis_tsn:28726")
pytaxize.gettsnfromlsid("urn:lsid:itis.gov:itis_tsn:0")
'''
out= Refactor(itis_base + 'getTSNFromLSID', payload={'lsid': lsid}, request='get').xml(**kwargs)
tt = out.getchildren()[0].text
if tt is None:
tt = "no match"
else:
pass
return tt
def searchforanymatch(x, **kwargs):
'''
Search for any match
pytaxize.searchforanymatch(x=202385)
pytaxize.searchforanymatch(x="dolphin")
'''
out= Refactor(itis_base + 'searchForAnyMatch', payload={'srchKey':x}, request='get').xml(**kwargs)
# if isinstance(x, basestring):
tmp = out.getchildren()[0].getchildren()
output = []
for v in tmp:
tmp = v.getchildren()
for w in tmp:
output.append(dict(zip([gettag(e) for e in w.iter()], [e.text for e in w.iter()])))
return output
def searchforanymatchpaged(x, pagesize, pagenum, ascend, **kwargs):
'''
Search for any matched page for descending (logical)
Usage:
pytaxize.searchforanymatchpaged(x=202385, pagesize=100, pagenum=1, ascend=False)
pytaxize.searchforanymatchpaged("Zy", pagesize=100, pagenum=1, ascend=False)
'''
args = {'srchKey':x, 'pageSize':pagesize, 'pageNum':pagenum, 'ascend':ascend}
out= Refactor(itis_base + 'searchForAnyMatchPaged', payload=args, request='get').xml(**kwargs)
tmp = out.getchildren()[0].getchildren()
output = []
for v in tmp:
tmp = v.getchildren()
for w in tmp:
output.append(dict(zip([gettag(e) for e in w.iter()], [e.text for e in w.iter()])))
return output
def getanymatchcount(x, **kwargs):
'''
Get any match count.
:param x: text or taxonomic serial number (TSN) (character or numeric)
:param **kwargs: Curl options passed on to `requests.get`
Usage::
pytaxize.getanymatchcount(x=202385)
pytaxize.getanymatchcount(x="dolphin")
'''
out = Refactor(itis_base + 'getAnyMatchCount',
payload={
'srchKey': x
},
request='get').xml(**kwargs)
return int(out.getchildren()[0].text)
def getlsidfromtsn(tsn, **kwargs):
'''
Gets the unique LSID for the TSN, or an empty result if there is no match.
Usage:
# valid TSN
pytaxize.getlsidfromtsn(155166)
# invalid TSN, returns nothing
pytaxize.getlsidfromtsn(0)
'''
out = _itisGET("getLSIDFromTSN", {'tsn': tsn}, **kwargs)
out= Refactor(itis_base + 'getLSIDFromTSN', payload={'tsn':tsn}, request='get').xml(**kwargs)
tt = out.getchildren()[0].text
if tt is None:
tt = "no match"
else:
pass
return tt
def gettsnfromlsid(lsid, **kwargs):
'''
Gets the TSN corresponding to the LSID, or an empty result if there is no match.
Usage::
pytaxize.gettsnfromlsid(lsid="urn:lsid:itis.gov:itis_tsn:28726")
pytaxize.gettsnfromlsid("urn:lsid:itis.gov:itis_tsn:0")
'''
out = Refactor(itis_base + 'getTSNFromLSID',
payload={
'lsid': lsid
},
request='get').xml(**kwargs)
tt = out.getchildren()[0].text
if tt is None:
tt = "no match"
else:
pass
return tt
def getacceptednamesfromtsn(tsn, **kwargs):
'''
Get accepted names from tsn
:param tsn: taxonomic serial number (TSN) (character or numeric)
Usage:
# TSN accepted - good name
pytaxize.getacceptednamesfromtsn('208527')
# TSN not accepted - input TSN is old name
pytaxize.getacceptednamesfromtsn('504239')
'''
out = Refactor(itis_base + 'getAcceptedNamesFromTSN', payload={'tsn': tsn}, request='get').xml(**kwargs)
temp = out.getchildren()
if(temp[0].getchildren()[1].values()[0] == 'true'):
dat = temp[0].getchildren()[0].text
else:
nodes = temp[0].getchildren()[1].getchildren()
dat = _parse_nodes(nodes)
dat.pop('author')
dat['submittedTsn'] = temp[0].getchildren()[0].text
return dat
def getlsidfromtsn(tsn, **kwargs):
'''
Gets the unique LSID for the TSN, or an empty result if there is no match.
Usage::
# valid TSN
pytaxize.getlsidfromtsn(155166)
# invalid TSN, returns nothing
pytaxize.getlsidfromtsn(0)
'''
out = _itisGET("getLSIDFromTSN", {'tsn': tsn}, **kwargs)
out = Refactor(itis_base + 'getLSIDFromTSN',
payload={
'tsn': tsn
},
request='get').xml(**kwargs)
tt = out.getchildren()[0].text
if tt is None:
tt = "no match"
else:
pass
return tt
