def get_issues(self, issues, limit=300):
result = []
keys = ','.join(issues)
request = 'project=%s AND key in (%s)' % (self.settings.project, keys)
LOGGER.debug(request)
response = self.proxy.getIssuesFromJqlSearch(self.get_token(), request, Types.intType(limit))
for item in response:
issue = JiraIssue()
issue.parse_raw(item)
result.append(issue)
return result
def updateGrid(index, src, dst, proto, data, date, notes, sess_str=SESS_K, sheetId=SHEETID):
wsdl.insertRow(sess_str, sheetId, 6, 1)
return wsdl.setCellValues(sess_str, sheetId, (
Types.structType({'text': '%s' % index, 'col': 0, 'sheetId': SHEETID, 'row': 6}),
Types.structType({'text': '%s' % src, 'col': 1, 'sheetId': SHEETID, 'row': 6}),
Types.structType({'text': '%s' % dst, 'col': 2, 'sheetId': SHEETID, 'row': 6}),
Types.structType({'text': '%s' % data, 'col': 3, 'sheetId': SHEETID, 'row': 6}),
Types.structType({'text': '%s' % proto, 'col': 4, 'sheetId': SHEETID, 'row': 6}),
Types.structType({'text': '%s' % date, 'col': 5, 'sheetId': SHEETID, 'row': 6}),
Types.structType({'text': '%s' % notes, 'col': 6, 'sheetId': SHEETID, 'row': 6}),
))
def store_outdated_issues():
env = jira_rpc_init(LOGGER)
client = env['client']
auth = env['auth']
project_name = env['project_name']
request = '''Sprint in openSprints() AND project = {project}
AND type in (Story, Bug, Improvement) AND status in (Defined,Undefined,"In Progress")
AND "Estimation Date" <= endOfDay()'''.format(project=project_name)
LOGGER.info('Queuing JIRA for outdated issues...')
response = client.getIssuesFromJqlSearch(auth, request, Types.intType(20))
LOGGER.info('Response contains {count} issues'.format(count=len(response)))
LOGGER.info('Removing all outdated issues from database...')
OutdatedJiraIssue.objects.all().delete()
LOGGER.info('Starting to import issues to database...')
for issue in JiraUtil.__raw_data_to_issues_list__(response):
message = '\tIssue {key} is being saved in database'.format(key=issue.key)
LOGGER.info(message)
outdated_jira_issue = JiraUtil.get_filled_in_outdated_jira_issue_obj(issue)
outdated_jira_issue.save()
from SOAPpy import SOAPProxy
from SOAPpy import Types
import urllib2
import socket
# CONSTANTS
_url = 'http://api.google.com/search/beta2'
_namespace = 'urn:GoogleSearch'
# need to marshall into SOAP types
SOAP_FALSE = Types.booleanType(0)
SOAP_TRUE = Types.booleanType(1)
# Google search options
_license_key = 'Cu7YX75QFHLS3WD/7/4CO+GsI/jC69eb'
_query = ""
_start = 0
_maxResults = 10
_filter = SOAP_FALSE
_restrict = ''
_safeSearch = SOAP_FALSE
_lang_restrict = ''
def googleSearch(title):
'''
It is the function of the application that make the request at google WS using
getting the first url of response.
@param title: the title of the article to serach for
@return: the first url
# get the new namespace
if namespace is None:
new_ns = None
else:
new_ns = self.getNS(namespace, data)
# return response payload
return data, new_ns
username = "******"
password = "******"
url = "http://%s:%[email protected]:8080/FisboxWs/services/Fiskal" % (username, password)
namespace = "http://server.fiskal.llarik.sk/"
proxy = SOAPProxy(url, namespace=namespace, transport = AuthenticatedTransport(username, password))
proxy.config.strictNamespaces = 1
proxy.config.debug = 1
input = Types.stringType(name = (namespace, "message"), data = "Python")
print(proxy.connect(input))
print(proxy.getServerVersion())
print(proxy.getModuleVersion())
print(proxy.getModuleSerialNumber())
print(proxy.getModuleDate())
print(proxy.getModuleInfo())
input = Types.decimalType(name = (namespace, "fmId"), data = 100)
print(proxy.getParagonCopy(input))
def main2():
#go database
dbs = MySQLdb.connect(host='mysql.ebi.ac.uk',user='******',passwd='amigo',db='go_latest',port=4085)
cur = dbs.cursor()
#reactome
rwsdl = "http://www.reactome.org:8080/caBIOWebApp/services/caBIOService?wsdl"
rserv = WSDL.Proxy(rwsdl)
#kegg
kegg_url = "http://rest.kegg.jp"
conn = Connection(kegg_url)
#uniprot taxonomy
url = 'http://www.uniprot.org/taxonomy/'
print '---'
annotationArray = []
with open('annotations.dump','rb') as f:
ar = pickle.load(f)
for idx,element in enumerate(ar):
print idx
modelAnnotations = Counter()
for index in element:
for annotation in element[index]:
try:
bioArray = []
tAnnotation = annotation.replace('%3A',':')
tAnnotation = re.search(':([^:]+:[^:]+$)',tAnnotation).group(1)
if 'GO' in annotation:
cur.execute("SELECT * FROM term WHERE acc='{0}'".format(tAnnotation))
for row in cur.fetchall():
bioArray.append([row[1],row[3]])
modelAnnotations.update([row[1]])
elif 'reactome' in annotation:
tAnnotation2 = re.search('_([^_]+$)',tAnnotation).group(1)
try:
query = rserv.queryById(Types.longType(long(tAnnotation)))
except:
continue
bioArray.append([query['name'],tAnnotation])
modelAnnotations.update([query['name']])
elif 'kegg' in annotation:
if 'pathway' in tAnnotation:
tAnnotation2 = 'map' + re.search('[^0-9]+([0-9]+$)',tAnnotation).group(1)
reply = conn.request_get('find/pathway/{0}'.format(tAnnotation2), headers={'Accept':'text/json'})
if reply['body'] != '\n':
bioArray.append([reply['body'].split('\t')[1].strip(),tAnnotation])
modelAnnotations.update([reply['body'].split('\t')[1].strip()])
else:
print annotation
elif 'uniprot' in annotation:
identifier = annotation.split(':')[-1]
url = 'http://www.uniprot.org/uniprot/{0}.tab'.format(identifier)
params = {}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
proteinName = page.split('\n')[1].split('\t')[3]
modelAnnotations.update([proteinName])
elif 'interpro' in annotation:
identifier = annotation.split(':')[-1]
url = 'http://www.ebi.ac.uk/interpro/entry/{0}'.format(identifier)
params = {}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
pointer = page.index('h2 class="strapline"')
extract = page[pointer:pointer+100]
extract = extract[extract.index('>')+1:extract.index('<')]
modelAnnotations.update([extract])
#elif 'taxonomy' in annotation:
#uniprot stuff for taxonomy
# pass
'''
url = 'http://www.uniprot.org/taxonomy/'
params = {
'from':'ACC',
'to':'P_REFSEQ_AC',
'format':'tab',
'query':'P13368 P20806 Q9UM73 P97793 Q17192'
}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
contact = "" # Please set your email address here to help us debug in case of problems.
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
'''
else:
print '--',annotation,'GO' in tAnnotation
except:
continue
print modelAnnotations
annotationArray.append(modelAnnotations)
with open('parsedAnnotations.dump','wb') as f:
pickle.dump(annotationArray,f)
except ImportError:
#Edit Tom De Smedt, 2004
#For now, just use the legacy SOAP.py, no warning.
#warn( "SOAPpy not imported. Trying legacy SOAP.py.",
# DeprecationWarning )
try:
import SOAP
except ImportError:
raise RuntimeError( "Unable to find SOAPpy or SOAP. Can't continue.\n" )
#
# Constants that differ between the modules
#
if SOAPpy:
false = Types.booleanType(0)
true = Types.booleanType(1)
structType = Types.structType
faultType = Types.faultType
else:
false = SOAP.booleanType(0)
true = SOAP.booleanType(1)
structType = SOAP.structType
faultType = SOAP.faultType
#
# Get a SOAP Proxy object in the correct way for the module we're using
#
def getProxy( url, namespace, http_proxy ):
if SOAPpy:
return SOAPProxy( url,
# using sipXconfig SOAP from Python - example
# submitted by Joey Korkames<*****@*****.**>
sipx_host = 'sipxserver.example.com'
from SOAPpy import WSDL
from SOAPpy import URLopener
from SOAPpy import Types
# need to marshall into SOAP types
SOAP_FALSE = Types.booleanType(0)
SOAP_TRUE = Types.booleanType(1)
#I've manually disabled HTTP auth in my sipxconfig installation (to debug other issues), so the auth here may not actually work in a stock sipx environment....
sipx_auth = URLopener.URLopener(username='******',passwd='scrubscrub')
sipx_namespace = 'urn:ConfigService'
sipx_user_wsdl = 'http://' + sipx_host + '/sipxconfig/services/UserService?wsdl'
sipx_user = WSDL.Proxy(sipx_auth.open(sipx_user_wsdl), namespace=sipx_namespace)
sipx_phone_wsdl = 'http://' + sipx_host + '/sipxconfig/services/PhoneService?wsdl'
sipx_phone = WSDL.Proxy(sipx_auth.open(sipx_phone_wsdl), namespace=sipx_namespace)
#prints SOAP traffic to STDOUT
#sipx_user.soapproxy.config.dumpSOAPOut = 1
#sipx_user.soapproxy.config.dumpSOAPIn = 1
#sipx_phone.soapproxy.config.dumpSOAPOut = 1
#sipx_phone.soapproxy.config.dumpSOAPIn = 1
client = WSDL.Proxy(wsdlfile) job = dict() job['id'] = 1; job['name'] = 'job name'; job['task'] = []; task = dict() task['name'] = 'python_task_name'; task['progress'] = dict(); task['progress']['status'] = 'Stopped'; task['progress']['data'] = dict(); task['progress']['data']['start'] = 'python start data'; task['progress']['data']['end'] = 'python end data'; job['task'].append(task) print "\n" try: ret = client.create_job(username, job) if(ret == 1): print "Successfully created job \n" else: print ret + "\n" ret_list = client.get_jobs(username) print Types.simplify(ret_list) except Exception as e: print e
def __call__(self, *args, **keywords):
args = map(_type_conversion, self.__type_mask, args)
results = getattr(self.__target, self.__name)(*args, **keywords)
return Types.simplify(results)
def get_backlog_defects_count(self):
request = BACKLOG_DEFECTS_QUERY
response = self.proxy.getIssuesFromJqlSearch(self.get_token(), request, Types.intType(1000))
return len(response)
#
#############################################################################
from SOAPpy import SOAPProxy
from SOAPpy import Types
url = 'http://localhost:8180/mondrian/xmla'
n= 'urn:schemas-microsoft-com:xml-analysis'
server = SOAPProxy(url,n)
# if you want to see the SOAP message exchanged
# uncomment the two following lines
server.config.dumpSOAPOut = 1
#server.config.dumpSOAPIn = 1
server.namespace='ns1'
server.Discover(RequestType=Types.untypedType('MDSCHEMA_CUBES'))
###
### Genera la peticion
# <?xml version="1.0" encoding="UTF-8"?>
# <SOAP-ENV:Envelope SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/" xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/" xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/">
# <SOAP-ENV:Body>
# <ns1:Discover xmlns:ns1="ns1" SOAP-ENC:root="1">
# <RequestType>MDSCHEMA_CUBES</RequestType>
# </ns1:Discover>
# </SOAP-ENV:Body>
# </SOAP-ENV:Envelope>
def getResponsePrimitive(self):
return Types.simplify(self.getResponse())
#############################################################################
from SOAPpy import SOAPProxy
from SOAPpy import Types
url = 'http://localhost:8180/mondrian/xmla'
n= 'urn:schemas-microsoft-com:xml-analysis'
server = SOAPProxy(url,n)
# if you want to see the SOAP message exchanged
# uncomment the two following lines
server.config.dumpSOAPOut = 1
#server.config.dumpSOAPIn = 1
server.namespace='ns1'
server.Discover({'ns1:RequestType':Types.untypedType('MDSCHEMA_CUBES')})
###
### Genera la peticion
# <?xml version="1.0" encoding="UTF-8"?>
# <SOAP-ENV:Envelope SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/" xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/" xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/">
# <SOAP-ENV:Body>
# <ns1:Discover xmlns:ns1="ns1" SOAP-ENC:root="1">
# <v1>
# <ns1:RequestType>MDSCHEMA_CUBES</ns1:RequestType>
# </v1>
# </ns1:Discover>
# </SOAP-ENV:Body>
# </SOAP-ENV:Envelope>
except ImportError:
#Edit Tom De Smedt, 2004
#For now, just use the legacy SOAP.py, no warning.
#warn( "SOAPpy not imported. Trying legacy SOAP.py.",
# DeprecationWarning )
try:
import SOAP
except ImportError:
raise RuntimeError("Unable to find SOAPpy or SOAP. Can't continue.\n")
#
# Constants that differ between the modules
#
if SOAPpy:
false = Types.booleanType(0)
true = Types.booleanType(1)
structType = Types.structType
faultType = Types.faultType
else:
false = SOAP.booleanType(0)
true = SOAP.booleanType(1)
structType = SOAP.structType
faultType = SOAP.faultType
#
# Get a SOAP Proxy object in the correct way for the module we're using
#
def getProxy(url, namespace, http_proxy):
if SOAPpy:
def request(self):
client = self.__env['client']
auth = self.__env['auth']
LOGGER.info('JIRA Advanced Search request: {request}'.format(request=self.__request))
self.__response = client.getIssuesFromJqlSearch(auth, self.__request, Types.intType(self.__limit))
def main2():
#go database
dbs = MySQLdb.connect(host='mysql.ebi.ac.uk',
user='******',
passwd='amigo',
db='go_latest',
port=4085)
cur = dbs.cursor()
#reactome
rwsdl = "http://www.reactome.org:8080/caBIOWebApp/services/caBIOService?wsdl"
rserv = WSDL.Proxy(rwsdl)
#kegg
kegg_url = "http://rest.kegg.jp"
#conn = Connection(kegg_url)
#uniprot taxonomy
url = 'http://www.uniprot.org/taxonomy/'
print '---'
annotationArray = []
with open('annotations.dump', 'rb') as f:
ar = pickle.load(f)
for idx, element in enumerate(ar):
print idx
modelAnnotations = Counter()
for index in element:
for annotation in element[index]:
try:
bioArray = []
tAnnotation = annotation.replace('%3A', ':')
tAnnotation = re.search(':([^:]+:[^:]+$)',
tAnnotation).group(1)
if 'GO' in annotation:
cur.execute(
"SELECT * FROM term WHERE acc='{0}'".format(
tAnnotation))
for row in cur.fetchall():
bioArray.append([row[1], row[3]])
modelAnnotations.update([row[1]])
elif 'reactome' in annotation:
tAnnotation2 = re.search('_([^_]+$)',
tAnnotation).group(1)
try:
query = rserv.queryById(
Types.longType(long(tAnnotation)))
except:
continue
bioArray.append([query['name'], tAnnotation])
modelAnnotations.update([query['name']])
'''
elif 'kegg' in annotation:
if 'pathway' in tAnnotation:
tAnnotation2 = 'map' + re.search('[^0-9]+([0-9]+$)',tAnnotation).group(1)
reply = conn.request_get('find/pathway/{0}'.format(tAnnotation2), headers={'Accept':'text/json'})
if reply['body'] != '\n':
bioArray.append([reply['body'].split('\t')[1].strip(),tAnnotation])
modelAnnotations.update([reply['body'].split('\t')[1].strip()])
else:
print annotation
'''
elif 'uniprot' in annotation:
identifier = annotation.split(':')[-1]
url = 'http://www.uniprot.org/uniprot/{0}.tab'.format(
identifier)
params = {}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
proteinName = page.split('\n')[1].split('\t')[3]
modelAnnotations.update([proteinName])
elif 'interpro' in annotation:
identifier = annotation.split(':')[-1]
url = 'http://www.ebi.ac.uk/interpro/entry/{0}'.format(
identifier)
params = {}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
pointer = page.index('h2 class="strapline"')
extract = page[pointer:pointer + 100]
extract = extract[extract.index('>') +
1:extract.index('<')]
modelAnnotations.update([extract])
#elif 'taxonomy' in annotation:
#uniprot stuff for taxonomy
# pass
'''
url = 'http://www.uniprot.org/taxonomy/'
params = {
'from':'ACC',
'to':'P_REFSEQ_AC',
'format':'tab',
'query':'P13368 P20806 Q9UM73 P97793 Q17192'
}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
contact = "" # Please set your email address here to help us debug in case of problems.
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
'''
else:
print '--', annotation, 'GO' in tAnnotation
except:
continue
print modelAnnotations
annotationArray.append(modelAnnotations)
with open('parsedAnnotations.dump', 'wb') as f:
pickle.dump(annotationArray, f)
def __call__(self,*args,**keywords): args = map(_type_conversion,self.__type_mask,args) results = getattr(self.__target,self.__name)(*args,**keywords) return Types.simplify(results)
from SOAPpy import SOAPProxy from SOAPpy import Types namespace = "http://server.fiskal.llarik.sk/" url = "http://10.17.0.6:8080/FisboxWs/services/Fiskal" input = Types.stringType(name=(namespace, "message"), data="Python") proxy = SOAPProxy(url, namespace=namespace) proxy.config.debug = 1 proxy.connect(input)
from SOAPpy import SOAPProxy
from SOAPpy import Types
url = 'http://localhost:8180/mondrian/xmla'
n= 'urn:schemas-microsoft-com:xml-analysis'
server = SOAPProxy(url,n)
# if you want to see the SOAP message exchanged
# uncomment the two following lines
server.config.dumpSOAPOut = 1
#server.config.dumpSOAPIn = 1
cmd = {'Statement': Types.untypedType('SELECT [Measures].MEMBERS ON COLUMNS FROM [Sales]')}
prts={
'PropertyList': {
'DataSourceInfo':Types.untypedType('Provider=Mondrian;DataSource=MondrianFoodMart;'),
'Catalog':Types.untypedType('FoodMart'),
'Format':Types.untypedType('Multidimensional'),
'AxisFormat':Types.untypedType('ClusterFormat')
}
}
#server.Execute(Command=cmd, Properties=prts)
#server._callWithBody({'Excecute':{'Command':cmd, 'Properties':prts}})
restr={
'ns1:RestrictionList': {
def getResponsePrimitive(self):
return Types.simplify(self.getResponse())