def getSMILES(self, id):
'''
Retreive cid given a smiles input
'''
uri = 'http://' + _base +\
'/rest/pug/compound/smiles/%s/cids/TXT' % (id,)
txt = urlopen(uri).read().rstrip()
self.cid = txt
def DataFromURI (uri, archive_directory=None):
"""Retrieve the contents of the uri as raw data.
If the uri does not include a scheme (e.g., C{http:}), it is
assumed to be a file path on the local system."""
from pyxb.utils.six.moves.urllib.request import urlopen
stream = None
exc = None
# Only something that has a colon is a non-file URI. Some things
# that have a colon are a file URI (sans schema). Prefer urllib2,
# but allow urllib (which apparently works better on Windows).
if 0 <= uri.find(':'):
try:
stream = urlopen(uri)
except Exception as e:
exc = e
if (stream is None) and six.PY2:
import urllib
try:
stream = urllib.urlopen(uri)
exc = None
except:
# Prefer urllib exception
pass
if stream is None:
# No go as URI; give file a chance
try:
stream = open(uri, 'rb')
exc = None
except Exception as e:
if exc is None:
exc = e
if exc is not None:
_log.error('open %s', uri, exc_info=exc)
raise exc
try:
# Protect this in case whatever stream is doesn't have an fp
# attribute.
if isinstance(stream, six.file) or isinstance(stream.fp, six.file):
archive_directory = None
except:
pass
xmld = stream.read()
if archive_directory:
base_name = os.path.basename(os.path.normpath(urlparse.urlparse(uri)[2]))
counter = 1
dest_file = os.path.join(archive_directory, base_name)
while os.path.isfile(dest_file):
dest_file = os.path.join(archive_directory, '%s.%d' % (base_name, counter))
counter += 1
try:
OpenOrCreate(dest_file).write(xmld)
except OSError as e:
_log.warning('Unable to save %s in %s: %s', uri, dest_file, e)
return xmld
def synonym(self, label):
'''
Retreives the best PubChem id using a registered synonym
CAS # is an example of a synonym that works well.
'''
uri = _base + 'pug/compound/name/%s/xrefs/RegistryID/XML' % (label,)
xml = urlopen(uri).read()
xml = xml.replace('xmlns=' + _pug_rest, '')
order = pug_rest.CreateFromDOM(domutils.StringToDOM(xml))
o = order.Information[0].CID[0]
self.cid = str(o)
def pubchem_xrefs(self, id):
'''
Retrieves the external references, given a PubChem
identifier
'''
uri = _base + 'pug/compound/cid/%s/xrefs/SBURL/xml' % (id, )
xml = urlopen(uri).read()
xml = xml.replace('xmlns=' + _pug_rest, '')
order = pug_rest.CreateFromDOM(domutils.StringToDOM(xml))
o = order.Information[0]
urls = o.SBURL
self.urls = urls
def pubchem_xrefs(self, id):
'''
Retrieves the external references, given a PubChem
identifier
'''
uri = _base + 'pug/compound/cid/%s/xrefs/SBURL/xml' % (id,)
xml = urlopen(uri).read()
xml = xml.replace('xmlns=' + _pug_rest, '')
order = pug_rest.CreateFromDOM(domutils.StringToDOM(xml))
o = order.Information[0]
urls = o.SBURL
self.urls = urls
def getCAS(self, id):
'''
Retrieves the CAS from PubChem Identifier.
'''
uri = _base + 'pug_view/data/compound/%s/XML' % (id, )
xml = urlopen(uri).read()
xml_soup = BeautifulSoup(xml, "lxml")
self.xml = xml_soup
value = None
iupac = None
for x in xml_soup.find_all('name'):
name = x.get_text()
if name == "CAS" and value is None:
value = x.find_next_sibling('stringvalue').get_text()
if name == 'IUPAC Name' and iupac is None:
iupac = x.find_next_sibling('stringvalue').get_text()
self.cas = value
self.iupac = iupac
def getCAS(self, id):
'''
Retrieves the CAS from PubChem Identifier.
'''
uri = _base + 'pug_view/data/compound/%s/XML' % (id,)
xml = urlopen(uri).read()
xml_soup = BeautifulSoup(xml, "lxml")
self.xml = xml_soup
value = None
iupac = None
for x in xml_soup.find_all('name'):
name = x.get_text()
if name == "CAS" and value is None:
value = x.find_next_sibling('stringvalue').get_text()
if name == 'IUPAC Name' and iupac is None:
iupac = x.find_next_sibling('stringvalue').get_text()
self.cas = value
self.iupac = iupac
import collections
import sys
# Get the next seven days forecast for two locations
zip = [ 85711, 55108 ]
if 1 < len(sys.argv):
zip = sys.argv[1:]
begin = xsd.dateTime.today()
end = xsd.dateTime(begin + datetime.timedelta(7))
# Create the REST URI for this query
uri = 'http://www.weather.gov/forecasts/xml/sample_products/browser_interface/ndfdXMLclient.php?zipCodeList=%s&product=time-series&begin=%s&end=%s&maxt=maxt&mint=mint' % ("+".join([ str(_zc) for _zc in zip ]), begin.xsdLiteral(), end.xsdLiteral())
print(uri)
# Retrieve the data
xmld = urlopen(uri).read()
open('forecast.xml', 'wb').write(xmld)
#print xmld
# Convert it to DWML object
r = DWML.CreateFromDocument(xmld)
product = r.head.product
print('%s %s' % (product.title, product.category))
source = r.head.source
print(", ".join(source.production_center.content()))
data = r.data
if isinstance(data, collections.MutableSequence):
data = data.pop(0)
print(data)
import sys
# Get the next seven days forecast for two locations
zip = [85711, 55108]
if 1 < len(sys.argv):
zip = sys.argv[1:]
begin = xsd.dateTime.today()
end = xsd.dateTime(begin + datetime.timedelta(7))
# Create the REST URI for this query
uri = 'http://www.weather.gov/forecasts/xml/sample_products/browser_interface/ndfdXMLclient.php?zipCodeList=%s&product=time-series&begin=%s&end=%s&maxt=maxt&mint=mint' % (
"+".join([str(_zc) for _zc in zip]), begin.xsdLiteral(), end.xsdLiteral())
print(uri)
# Retrieve the data
xmld = urlopen(uri).read()
open('forecast.xml', 'wb').write(xmld)
#print xmld
# Convert it to DWML object
r = DWML.CreateFromDocument(xmld)
product = r.head.product
print('%s %s' % (product.title, product.category))
source = r.head.source
print(", ".join(source.production_center.content()))
data = r.data
if isinstance(data, collections.MutableSequence):
data = data.pop(0)
print(data)
spec_ns = spec.namespaceContext().targetNamespace()
binding = spec_ns.createExpandedName('ndfdXMLBinding').binding()
operation = binding.operationMap()['NDFDgen']
soap_op = operation.wildcardElements()[0]
soap_action = soap_op.soapAction
service = spec_ns.createExpandedName('ndfdXML').service()
soap_addr = service.port[0].wildcardElements()[0]
endpoint = soap_addr.location
# Execute the request
uri = urllib_request.Request(endpoint, soap_message, {
'SOAPAction': soap_action,
'Content-Type': 'text/xml'
})
rxml = urllib_request.urlopen(uri).read()
#rxml = open('rawresp.xml').read()
# Save the raw SOAP-wrapped response
open('rawresp.xml', 'w').write(rxml)
# The NDFD interface is "interesting" in that the response message for
# the SOAP interface is encoded as a text string, rather than being
# provided as XML directly. The noise below extracts it.
rdom = domutils.StringToDOM(rxml)
resp = soapenv.CreateFromDOM(rdom)
v = resp.Body.wildcardElements()[0]
rxml = v.childNodes[0].childNodes[0].value
# Save the extracted response
open('resp.xml', 'w').write(rxml)
#rxml = open('resp.xml').read()
import weather
zip = 55113
if 1 < len(sys.argv):
zip = int(sys.argv[1])
# Create an envelope, and give it a body that is the request for the
# service we want.
env = soapenv.Envelope(soapenv.Body(weather.GetCityForecastByZIP(ZIP=str(zip))))
open('request.xml', 'w').write(env.toxml("utf-8"))
# Invoke the service
uri = urllib_request.Request('http://wsf.cdyne.com/WeatherWS/Weather.asmx',
env.toxml("utf-8"),
{ 'SOAPAction' : "http://ws.cdyne.com/WeatherWS/GetCityForecastByZIP", 'Content-Type': 'text/xml' } )
rxml = urllib_request.urlopen(uri).read()
open('response.xml', 'w').write(rxml)
# Convert the response to a SOAP envelope, then extract the actual
# response from the wildcard elements of the body. Note that because
# the weather namespace was registered, PyXB already created the
# binding for the response.
soap_resp = soapenv.CreateFromDocument(rxml)
resp = soap_resp.Body.wildcardElements()[0]
fc_return = resp.GetCityForecastByZIPResult
if fc_return.Success:
print('Got response for %s, %s:' % (fc_return.City, fc_return.State))
for fc in fc_return.ForecastResult.Forecast:
when = time.strftime('%A, %B %d %Y', fc.Date.timetuple())
outlook = fc.Desciption # typos in WSDL left unchanged
from __future__ import print_function
import dict
from pyxb.utils.six.moves.urllib.request import urlopen
import pyxb.utils.domutils as domutils
from xml.dom import minidom
# Get the list of dictionaries available from the service.
port_uri = 'http://services.aonaware.com/DictService/DictService.asmx'
uri = port_uri + '/DictionaryList'
dle_xml = urlopen(uri).read()
dle_dom = domutils.StringToDOM(dle_xml)
dle = dict.ArrayOfDictionary.createFromDOM(dle_dom)
op_path = '/DictionaryInfo'
for d in dle.Dictionary:
# Create a REST-style query to retrieve the information about this dictionary.
uri = '%s%s?dictId=%s' % (port_uri, op_path, d.Id)
resp = urlopen(uri).read()
# The response is a simple type derived from string, so we can
# just extract and print it.
di_resp = dict.CreateFromDOM(domutils.StringToDOM(resp))
# Do the "encode" garbage because one of these dictionaries has a
# non-ASCII character
print("%s (%s)\n%s\n" % (d.Name.encode('utf-8'), d.Id.encode('utf-8'),
di_resp.encode('utf-8')))
from __future__ import print_function
import dict
from pyxb.utils.six.moves.urllib.request import urlopen
import pyxb.utils.domutils as domutils
from xml.dom import minidom
# Get the list of dictionaries available from the service.
port_uri = 'http://services.aonaware.com/DictService/DictService.asmx'
uri = port_uri + '/DictionaryList'
dle_xml = urlopen(uri).read()
dle_dom = domutils.StringToDOM(dle_xml)
dle = dict.ArrayOfDictionary.createFromDOM(dle_dom)
op_path = '/DictionaryInfo'
for d in dle.Dictionary:
# Create a REST-style query to retrieve the information about this dictionary.
uri = '%s%s?dictId=%s' % (port_uri, op_path, d.Id)
resp = urlopen(uri).read()
# The response is a simple type derived from string, so we can
# just extract and print it.
di_resp = dict.CreateFromDOM(domutils.StringToDOM(resp))
# Do the "encode" garbage because one of these dictionaries has a
# non-ASCII character
print("%s (%s)\n%s\n" % (d.Name.encode('utf-8'), d.Id.encode('utf-8'), di_resp.encode('utf-8')))
from __future__ import print_function
import dict
from pyxb.utils.six.moves.urllib.request import urlopen
import sys
from pyxb.utils import domutils
word = 'xml'
if 1 < len(sys.argv):
word = sys.argv[1]
# Create a REST-style query to retrieve the information about this dictionary.
uri = 'http://services.aonaware.com/DictService/DictService.asmx/Define?word=%s' % (
word, )
rxml = urlopen(uri).read()
resp = dict.CreateFromDOM(domutils.StringToDOM(rxml))
print('Definitions of %s:' % (resp.Word, ))
for definition in resp.Definitions.Definition:
print('From %s (%s):' %
(definition.Dictionary.Name, definition.Dictionary.Id))
print(definition.WordDefinition)
print()
from __future__ import print_function
import dict
from pyxb.utils.six.moves.urllib.request import urlopen
import sys
from pyxb.utils import domutils
word = 'xml'
if 1 < len(sys.argv):
word = sys.argv[1]
# Create a REST-style query to retrieve the information about this dictionary.
uri = 'http://services.aonaware.com/DictService/DictService.asmx/Define?word=%s' % (word,)
rxml = urlopen(uri).read()
resp = dict.CreateFromDOM(domutils.StringToDOM(rxml))
print('Definitions of %s:' % (resp.Word,))
for definition in resp.Definitions.Definition:
print('From %s (%s):' % (definition.Dictionary.Name, definition.Dictionary.Id))
print(definition.WordDefinition)
print()