def getAvailableDatabases(self, username, password):
print "retrieving available databases for user", username
rootUrl = "3dm.bio-prodict.nl"
service = "/jwebapp/mcsis-miner-web/webservice/SOAP/"
wsdl = "https://" + rootUrl + service + "?wsdl"
security = Security()
token = UsernameToken(username, password)
security.tokens.append(token)
proxies = utopia.queryProxyString(wsdl)
proxyDict = {}
gc = None
if proxies != "DIRECT":
proxyDict["https"] = proxies.split()[1]
gc = client.Client(
wsdl,
plugins=[MyPlugin()],
location="https://3dm.bio-prodict.nl/jwebapp/mcsis-miner-web/webservice/SOAP/",
proxy=proxyDict,
)
else:
gc = client.Client(
wsdl,
plugins=[MyPlugin()],
location="https://3dm.bio-prodict.nl/jwebapp/mcsis-miner-web/webservice/SOAP/",
)
gc.set_options(wsse=security)
gs = gc.service
databases = gs.getAvailableDatabases()
# print databases
return databases["databases"]
def getMentions(self, domain, text, pubmedId):
tmp = tempfile.gettempdir()
codecs.open(tmp + os.sep + "documentText.txt", "w", "utf-8").write(text)
text = codecs.open(tmp + os.sep + "documentText.txt", "r", "utf-8").read()
username = self.get_config("username")
password = self.get_config("password")
if self.validUsernameAndPassword(username, password):
rootUrl = "3dm.bio-prodict.nl"
service = "/jwebapp/mcsis-miner-web/webservice/SOAP/"
wsdl = "https://" + rootUrl + service + "?wsdl"
self.proteinJs = self.proteinJs.replace("#USERNAME#", urllib2.quote(self.get_config("username")))
self.proteinJs = self.proteinJs.replace("#PASSWORD#", urllib2.quote(self.get_config("password")))
self.mutationJs = self.mutationJs.replace("#USERNAME#", urllib2.quote(self.get_config("username")))
self.mutationJs = self.mutationJs.replace("#PASSWORD#", urllib2.quote(self.get_config("password")))
self.residueJs = self.residueJs.replace("#USERNAME#", urllib2.quote(self.get_config("username")))
self.residueJs = self.residueJs.replace("#PASSWORD#", urllib2.quote(self.get_config("password")))
security = Security()
token = UsernameToken(username, password)
security.tokens.append(token)
proxies = utopia.queryProxyString(wsdl)
proxyDict = {}
gc = None
if proxies != "DIRECT":
proxyDict["https"] = proxies.split()[1]
gc = client.Client(
wsdl,
plugins=[MyPlugin()],
location="https://3dm.bio-prodict.nl/jwebapp/mcsis-miner-web/webservice/SOAP/",
proxy=proxyDict,
)
else:
gc = client.Client(
wsdl,
plugins=[MyPlugin()],
location="https://3dm.bio-prodict.nl/jwebapp/mcsis-miner-web/webservice/SOAP/",
)
gc.set_options(wsse=security)
gs = gc.service
if domain == "hgvs_public":
mentions = gs.annotateHGVS(text, pubmedId)
else:
mentions = gs.annotate(domain, text, pubmedId)
print "retrieved " + str(len(mentions))
return mentions
else:
print "No credentials specified"
