def __connect(self, username, password, caller):
payload = (
'<?xml version="1.0"?>\n'
'<xf>\n'
f' <request caller="{caller}">\n'
f' <statement command="connect" username="******" password="******"/>\n'
' </request>\n'
'</xf>')
session = Session()
response = session.post(self._url, payload)
debug(response.text)
root = XML(response.content)
if next(root.getiterator('status')).text == 'OK':
return session, next(root.getiterator('sessionid')).text
raise Exception(
next(root.getiterator('message')).text.split(';', 1)[0])
def extractNamespaces2(doc):
"""Extract xmlns:prefix="namespace" pairs from the root element of the
XML document and return a dictionary. The default namespace (xmlns="ns")
is also extracted and saved under the null ('') prefix.
"""
ns = {}
tree = XML(doc)
for elt in tree.getiterator():
for key, ns in elt.attrib.items():
if key.startswith('xmlns'):
if key.find(':') > 0:
junk, prefix = key.split(':')
else:
prefix = '_default'
ns[prefix] = ns
return ns
def __call__(self, session, response):
debug(response.text)
root = XML(response.content)
res = xml_dict(next(root.getiterator('reactions')),
['sup', 'sub', 'i', 'b'])['reaction']
response.data = data = []
if isinstance(res, list):
for x in res:
try:
data.append(self.__parser(x))
except (KeyError, StopIteration, ValueError) as e:
print(e)
else:
try:
data.append(self.__parser(res))
except (KeyError, StopIteration, ValueError) as e:
print(e)
def search(self,
query,
context=None,
dbname='RX',
no_coresult=False,
worker=False,
single_step=False,
without_trash=True,
**kwargs):
options = []
if no_coresult:
options.append('NO_CORESULT')
if worker:
options.append('WORKER')
if isinstance(query, MoleculeContainer):
query = self.__mol2query(query, kwargs)
if context == 'R':
options.extend(self.__options(kwargs))
else:
if context is None:
context = 'S'
elif context != 'S':
raise ValueError('Invalid context')
if single_step:
raise ValueError(
'single step applicable for reactions only')
if without_trash:
without_trash = False
elif isinstance(query, ReactionContainer):
context = 'R'
query = self.__rxn2query(query, kwargs)
elif not isinstance(query, str):
raise ValueError('Invalid query')
elif context not in ('S', 'R'):
raise ValueError('Invalid context value')
elif context == 'S':
if without_trash:
without_trash = False
if single_step:
raise ValueError('single step applicable for reactions only')
payload = (
'<?xml version="1.0" encoding="UTF-8"?>\n'
'<xf>\n'
f' <request caller="{self._caller}" sessionid="{self._sessionid}">\n'
' <statement command="select"/>\n'
' <select_list><select_item/></select_list>\n'
f' <from_clause dbname="{dbname}" context="{context}"/>\n'
f' <where_clause>{query}{single_step and " and RXD.STP=1" or ""}</where_clause>\n'
' <order_by_clause></order_by_clause>\n'
f' <options>{",".join(options)}</options>\n'
' </request>\n'
'</xf>')
response = self._session.post(self._url, payload)
debug(response.text)
root = XML(response.content)
resultname = next(root.getiterator('resultname')).text
resultsize = int(next(root.getiterator('resultsize')).text)
if resultsize:
return (Structure if context == 'S' else Reaction)(self,
resultname,
resultsize,
single_step,
without_trash)
