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"