def _itisterms(endpt, args={}, **kwargs):
'''
Get itis term
Usage::
pytaxize._itisterms("buya")
'''
out = Refactor(itis_base + endpt, payload=args,
request='get').xml(**kwargs)
nodes = out.xpath("//ax21:itisTerms", namespaces=ns21)
nodes2 = [x.getchildren() for x in nodes]
allnodes = [[_get_text_single(y) for y in x] for x in nodes2]
output = []
for x in allnodes:
kyz = [y.keys()[0] for y in x]
notuniq = set([v for v in kyz if kyz.count(v) > 1])
if len(notuniq) > 0:
for z in notuniq:
tt = ','.join([m.values()[0] for m in x if m.keys()[0] == z])
toadd = {z: tt}
uu = [v for v in x if v.keys()[0] not in z]
uu.append(toadd)
output.append(uu)
else:
output.append(x)
df = pd.DataFrame([{k: v
for d in R for k, v in d.items()} for R in output])
return df[[x.keys()[0] for x in allnodes[0]]]
def func(x, y, checklist):
url = "https://www.catalogueoflife.org/col/webservice"
if checklist is None:
pass
else:
checklist = str(checklist)
if checklist in ["2012", "2011", "2010"]:
url = re.sub("col", "annual-checklist/" + checklist, url)
else:
url = "https://www.catalogueoflife.org/annual-checklist/year/webservice"
url = re.sub("year", checklist, url)
payload = {
"name": x,
"id": y,
"format": format,
"response": "full",
"start": start,
}
payload = {k: v for k, v in payload.items() if v is not None}
tt = Refactor(url, payload, request="get").xml()
childtaxa = tt.xpath("//child_taxa//taxon")
if len(childtaxa) == 0:
sys.exit("Please enter a valid search name")
outlist = []
for i in range(len(childtaxa)):
tt_ = childtaxa[i].getchildren()
outlist.append(
dict(zip(["id", "name", "rank"], [x.text for x in tt_[:3]])))
return outlist
def func(x, y):
url = "http://www.catalogueoflife.org/col/webservice"
if (checklist.__class__.__name__ == 'NoneType'):
pass
else:
if (checklist in ['2012', '2011', '2010']):
url = re.sub("col", "annual-checklist/" + checklist, url)
else:
url = "http://www.catalogueoflife.org/annual-checklist/year/webservice"
url = re.sub("year", checklist, url)
payload = {
'name': x,
'id': y,
'format': format,
'response': "full",
'start': start
}
tt = Refactor(url, payload, request='get').xml()
childtaxa = tt.xpath('//child_taxa//taxon')
if len(childtaxa) == 0:
sys.exit('Please enter a valid search name')
outlist = []
for i in range(len(childtaxa)):
tt_ = childtaxa[i].getchildren()
outlist.append(
dict(zip(['id', 'name', 'rank'], [x.text for x in tt_[:3]])))
return outlist
def _itisterms(endpt, args={}, **kwargs):
'''
Get itis terms
Usage:
pytaxize._itisterms(x="buya")
'''
out = Refactor(itis_base + endpt, payload=args, request='get').xml(**kwargs)
nodes = out.xpath("//ax21:itisTerms", namespaces=ns21)
nodes2 = [x.getchildren() for x in nodes]
allnodes = [[_get_text_single(y) for y in x] for x in nodes2]
output = []
for x in allnodes:
kyz = [y.keys()[0] for y in x]
notuniq = set([v for v in kyz if kyz.count(v) > 1])
if len(notuniq) > 0:
for z in notuniq:
tt = ','.join([ m.values()[0] for m in x if m.keys()[0] == z ])
toadd = { z: tt }
uu = [ v for v in x if v.keys()[0] not in z ]
uu.append(toadd)
output.append(uu)
else:
output.append(x)
df = pd.concat([pd.DataFrame([y.values()[0] for y in x]).transpose() for x in output])
df.columns = [x.keys()[0] for x in allnodes[0]]
return df
def func(x, y):
url = "http://www.catalogueoflife.org/col/webservice"
if(checklist.__class__.__name__ == 'NoneType'):
pass
else:
if(checklist in ['2012','2011','2010']):
url = re.sub("col", "annual-checklist/" + checklist, url)
else:
url = "http://www.catalogueoflife.org/annual-checklist/year/webservice"
url = re.sub("year", checklist, url)
payload = {'name': x, 'id': y, 'start': start}
tt = Refactor(url, payload, request='get').xml()
stuff = tt.xpath('//result')
outlist = []
for i in range(len(stuff)):
tt_ = stuff[i]
each = {}
for g in range(len(tt_)):
for e in tt_[g].iter():
each.update({e.tag: e.text})
outlist.append(each)
# values = [x.text for x in tt_[:4]]
# tags = [x.tag for x in tt_[:4]]
# mydict = dict(zip(tags, values))
df = pd.DataFrame(outlist)
# tt_ = stuff[0].getchildren()
# res = [x.text for x in tt_[:4]]
return df
def searchcol(x):
payload = {'name':x, 'format':format, 'response':"full", 'start':start}
tt = Refactor(url, payload, request='get').xml()
childtaxa = tt.xpath('//child_taxa//taxon')
outlist = []
for i in range(len(childtaxa)):
tt_ = childtaxa[i].getchildren()
outlist.append([x.text for x in tt_[:3]])
df = pd.DataFrame(outlist, columns=['id','name','rank'])
return df
def searchbycommonnameendswith(x, **kwargs):
'''
Search for tsn by common name ending with
Usage:
pytaxize.searchbycommonnameendswith("snake")
'''
out= Refactor(itis_base + 'searchByCommonNameEndsWith', payload={'srchKey':x}, request='get').xml(**kwargs)
matches = ["commonName","language","tsn"]
tmp = out.xpath('//ax21:commonNames', namespaces=ns21)
return _itisdf(tmp[0], ns21, matches, _tolower(matches))
def getgeographicvalues(**kwargs):
'''
Get all possible geographic values
:param **kwargs: Curl options passed on to \code{\link[httr]{GET}}
Usage
pytaxize.getgeographicvalues()
'''
out = Refactor(itis_base + 'getGeographicValues', payload={}, request='get').xml(**kwargs)
ns = {'ax21':'http://metadata.itis_service.itis.usgs.gov/xsd'}
nodes = out.xpath("//ax21:geographicValues", namespaces=ns)
gv = [x.text for x in nodes]
return pd.DataFrame(gv, columns=['geographicvalues'])
def getcredibilityratings(**kwargs):
'''
Get possible credibility ratings
:param **kwargs: Curl options passed on to \code{\link[httr]{GET}}
Usage:
pytaxize.getcredibilityratings()
'''
out = Refactor(itis_base + 'getCredibilityRatings', payload={}, request='get').xml(**kwargs)
nodes = out.xpath("//ax23:credibilityValues", namespaces=ns23)
credibilityValues = [x.text for x in nodes]
df = pd.DataFrame(credibilityValues, columns=['credibilityValues'])
return df
def ncbi(self, x, **kwargs):
if x is None:
return []
key = os.environ.get("ENTREZ_KEY")
if key is None:
raise Exception("ENTREZ_KEY is not defined")
query = {"db": "taxonomy", "ID": x, "api_key": key}
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
res = Refactor(url, query, "get").xml(**kwargs)
z = res.xpath("//TaxaSet/Taxon/OtherNames/GenbankCommonName")
return [w.text for w in z]
def searchbycommonname(x, **kwargs):
'''
Search for tsn by common name
Usage:
pytaxize.searchbycommonname(x="american bullfrog")
pytaxize.searchbycommonname("ferret-badger")
pytaxize.searchbycommonname("polar bear")
'''
out= Refactor(itis_base + 'searchByCommonName', payload={'srchKey':x}, request='get').xml(**kwargs)
matches = ["commonName","language","tsn"]
tmp = out.xpath('//ax21:commonNames', namespaces=ns21)
return _itisdf(tmp[0], ns21, matches, _tolower(matches))
def getcredibilityratings(**kwargs):
'''
Get possible credibility ratings
:param **kwargs: Curl options passed on to `requests.get`
Usage::
pytaxize.getcredibilityratings()
'''
out = Refactor(itis_base + 'getCredibilityRatings', payload={}, request='get').xml(**kwargs)
nodes = out.xpath("//ax23:credibilityValues", namespaces=ns23)
return [x.text for x in nodes]
def getlastchangedate(**kwargs):
'''
Provides the date the ITIS database was last updated.
Usage:
pytaxize.getlastchangedate()
'''
out= Refactor(itis_base + 'getLastChangeDate', payload={}, request='get').xml(**kwargs)
ns = {'ax23':"http://metadata.itis_service.itis.usgs.gov/xsd"}
nodes = out.xpath("//ax23:updateDate", namespaces=ns)
bb = nodes[0].text
dt = time.strptime(bb.split()[0], "%Y-%m-%d")
return dt
def itis_ping(**kwargs):
'''
Ping the ITIS API
Usage:
>>> import pytaxize
>>> pytaxize.itis_ping()
u'<ns:getDescriptionResponse xmlns:ns="http://itis_service.itis.usgs.gov"><ns:return xmlns:ax21="http://data.itis_service.itis.usgs.gov/xsd" xmlns:ax26="http://itis_service.itis.usgs.gov/xsd" xmlns:ax23="http://metadata.itis_service.itis.usgs.gov/xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ax26:SvcDescription"><ax26:description>This is the ITIS Web Service, providing access to the data behind www.itis.gov. The database contains 641,468 scientific names (486,232 of them valid/accepted) and 118,145 common names.</ax26:description></ns:return></ns:getDescriptionResponse>'
'''
tt = Refactor(itis_base + 'getDescription', payload={}, request='get').xml(**kwargs)
ns = {'ax26':'http://itis_service.itis.usgs.gov/xsd'}
nodes = tt.xpath('//ax26:description', namespaces=ns)
text = [x.text for x in nodes][0]
return text
def getgeographicvalues(**kwargs):
'''
Get all possible geographic values
:param **kwargs: Curl options passed on to `requests.get`
Usage::
pytaxize.getgeographicvalues()
'''
out = Refactor(itis_base + 'getGeographicValues', payload={}, request='get').xml(**kwargs)
ns = {'ax21':'http://metadata.itis_service.itis.usgs.gov/xsd'}
nodes = out.xpath("//ax21:geographicValues", namespaces=ns)
return [x.text for x in nodes]
def itis_ping(**kwargs):
'''
Ping the ITIS API
Usage::
import pytaxize
pytaxize.itis_ping()
'''
tt = Refactor(itis_base + 'getDescription', payload={}, request='get').xml(**kwargs)
ns = {'ax26':'http://itis_service.itis.usgs.gov/xsd'}
nodes = tt.xpath('//ax26:description', namespaces=ns)
text = [x.text for x in nodes][0]
return text
def searchcol(x):
payload = {
'name': x,
'format': format,
'response': "full",
'start': start
}
tt = Refactor(url, payload, request='get').xml()
childtaxa = tt.xpath('//child_taxa//taxon')
outlist = []
for i in range(len(childtaxa)):
tt_ = childtaxa[i].getchildren()
outlist.append([x.text for x in tt_[:3]])
df = pd.DataFrame(outlist, columns=['id', 'name', 'rank'])
return df
def getlastchangedate(**kwargs):
'''
Provides the date the ITIS database was last updated.
Usage::
pytaxize.getlastchangedate()
'''
out = Refactor(itis_base + 'getLastChangeDate', payload={},
request='get').xml(**kwargs)
ns = {'ax23': "http://metadata.itis_service.itis.usgs.gov/xsd"}
nodes = out.xpath("//ax23:updateDate", namespaces=ns)
bb = nodes[0].text
dt = time.strptime(bb.split()[0], "%Y-%m-%d")
return dt
def getcredibilityratings(**kwargs):
'''
Get possible credibility ratings
:param **kwargs: Curl options passed on to `requests.get`
Usage::
pytaxize.getcredibilityratings()
'''
out = Refactor(itis_base + 'getCredibilityRatings',
payload={},
request='get').xml(**kwargs)
nodes = out.xpath("//ax23:credibilityValues", namespaces=ns23)
return [x.text for x in nodes]
def itis_ping(**kwargs):
'''
Ping the ITIS API
Usage::
import pytaxize
pytaxize.itis_ping()
'''
tt = Refactor(itis_base + 'getDescription', payload={},
request='get').xml(**kwargs)
ns = {'ax26': 'http://itis_service.itis.usgs.gov/xsd'}
nodes = tt.xpath('//ax26:description', namespaces=ns)
text = [x.text for x in nodes][0]
return text
def searchbycommonnameendswith(x, **kwargs):
'''
Search for tsn by common name ending with
Usage::
pytaxize.searchbycommonnameendswith("snake")
'''
out = Refactor(itis_base + 'searchByCommonNameEndsWith',
payload={
'srchKey': x
},
request='get').xml(**kwargs)
matches = ["commonName", "language", "tsn"]
tmp = out.xpath('//ax21:commonNames', namespaces=ns21)
return _itisdf(tmp[0], ns21, matches, _tolower(matches))
def getgeographicvalues(**kwargs):
'''
Get all possible geographic values
:param **kwargs: Curl options passed on to `requests.get`
Usage::
pytaxize.getgeographicvalues()
'''
out = Refactor(itis_base + 'getGeographicValues',
payload={},
request='get').xml(**kwargs)
ns = {'ax21': 'http://metadata.itis_service.itis.usgs.gov/xsd'}
nodes = out.xpath("//ax21:geographicValues", namespaces=ns)
return [x.text for x in nodes]
def searchbycommonname(x, **kwargs):
'''
Search for tsn by common name
Usage::
pytaxize.searchbycommonname(x="american bullfrog")
pytaxize.searchbycommonname("ferret-badger")
pytaxize.searchbycommonname("polar bear")
'''
out = Refactor(itis_base + 'searchByCommonName',
payload={
'srchKey': x
},
request='get').xml(**kwargs)
matches = ["commonName", "language", "tsn"]
tmp = out.xpath('//ax21:commonNames', namespaces=ns21)
return _itisdf(tmp[0], ns21, matches, _tolower(matches))
def ubio_search(searchName = None, searchAuth = None, searchYear = None,
order = None, sci = None, vern = None, keyCode = None):
'''
ubio_search returns NameBankIDs that match search terms
:param searchName: (string) - term to search within name string
:param searchAuth: (string) - term to search within name authorship
:param searchYear: (string) - term to search within name year
:param order: (string) - (name or namebankID) field by which the results will
be sorted (default is namebankID)
:param sci: (int) - (sci, vern, or all) type of results to be returned
(default is all)
:param vern: (int) - (limit 1000) maximum number of results to be returned
(default is 1000)
:param keyCode: Your uBio API key; loads from .Rprofile. If you don't have
one, obtain one at http://www.ubio.org/index.php?pagename=form.
:param callopts: Parameters passed on to httr::GET call.
Usage
# A basic example
>>> import pytaxize
>>>
>>> pytaxize.ubio_search(searchName = 'elephant', sci = 1, vern = 0)
>>> pytaxize.ubio_search(searchName = 'Astragalus aduncus', sci = 1, vern = 0)
'''
url = "http://www.ubio.org/webservices/service.php"
ubioApiKey = "b052625da5f330e334471f8efe725c07bf4630a6"
payload = {'function': 'namebank_search', 'searchName': searchName,
'searchAuth': searchAuth, 'searchYear': searchYear, 'order': order,
'sci': sci, 'vern': vern, 'keyCode': ubioApiKey}
tt = Refactor(url, payload, request='get').xml()
nodes = tt.xpath('//value')
if (len(nodes) == 0):
sys.exit('Please enter a valid searchName')
outlist = []
for i in range(len(nodes)):
tt_ = nodes[i].getchildren()
outlist.append([x.text for x in tt_[:8]])
df = pd.DataFrame(outlist, columns=['namebankID','nameString','fullNameString','packageID','packageName','basionymunit','rankID','rankName'])
return df
def func(x, y):
url = "https://www.catalogueoflife.org/col/webservice"
if checklist is None:
pass
else:
if checklist in ["2012", "2011", "2010"]:
url = re.sub("col", "annual-checklist/" + checklist, url)
else:
url = "https://www.catalogueoflife.org/annual-checklist/year/webservice"
url = re.sub("year", checklist, url)
payload = {"name": x, "id": y, "start": start}
tt = Refactor(url, payload, request="get").xml()
stuff = tt.xpath("//result")
outlist = []
for i in range(len(stuff)):
tt_ = stuff[i]
each = {}
for g in range(len(tt_)):
for e in tt_[g].iter():
each.update({e.tag: e.text})
outlist.append(each)
return outlist
def func(x, y):
url = "http://www.catalogueoflife.org/col/webservice"
if(checklist.__class__.__name__ == 'NoneType'):
pass
else:
if(checklist in ['2012','2011','2010']):
url = re.sub("col", "annual-checklist/" + checklist, url)
else:
url = "http://www.catalogueoflife.org/annual-checklist/year/webservice"
url = re.sub("year", checklist, url)
payload = {'name':x, 'id':y, 'format':format, 'response':"full", 'start':start}
tt = Refactor(url, payload, request='get').xml()
childtaxa = tt.xpath('//child_taxa//taxon')
if len(childtaxa) == 0:
sys.exit('Please enter a valid search name')
outlist = []
for i in range(len(childtaxa)):
tt_ = childtaxa[i].getchildren()
outlist.append([x.text for x in tt_[:3]])
df = pd.DataFrame(outlist, columns=['id','name','rank'])
return df
def func(x, y):
url = "http://www.catalogueoflife.org/col/webservice"
if (checklist.__class__.__name__ == 'NoneType'):
pass
else:
if (checklist in ['2012', '2011', '2010']):
url = re.sub("col", "annual-checklist/" + checklist, url)
else:
url = "http://www.catalogueoflife.org/annual-checklist/year/webservice"
url = re.sub("year", checklist, url)
payload = {'name': x, 'id': y, 'start': start}
tt = Refactor(url, payload, request='get').xml()
stuff = tt.xpath('//result')
outlist = []
for i in range(len(stuff)):
tt_ = stuff[i]
each = {}
for g in range(len(tt_)):
for e in tt_[g].iter():
each.update({e.tag: e.text})
outlist.append(each)
return outlist
